Multiple sequence alignment - TraesCS7A01G399500

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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 TraesCS7A01G399500 chr7A 100.000 2796 0 0 1 2796 579483627 579480832 0.000000e+00 5164.0
1 TraesCS7A01G399500 chr7A 96.676 1805 58 2 992 2796 1550069 1548267 0.000000e+00 3000.0
2 TraesCS7A01G399500 chr7A 96.929 1270 37 2 983 2251 481749999 481748731 0.000000e+00 2128.0
3 TraesCS7A01G399500 chr7A 97.147 1262 31 3 1535 2796 578431337 578430081 0.000000e+00 2126.0
4 TraesCS7A01G399500 chr7A 99.415 171 1 0 568 738 481750162 481749992 7.520000e-81 311.0
5 TraesCS7A01G399500 chr7A 96.341 164 6 0 736 899 220993160 220993323 1.280000e-68 270.0
6 TraesCS7A01G399500 chr7A 97.561 82 2 0 488 569 481750435 481750354 1.040000e-29 141.0
7 TraesCS7A01G399500 chr5A 96.916 1816 53 3 983 2796 572301297 572303111 0.000000e+00 3040.0
8 TraesCS7A01G399500 chr5A 91.600 250 12 3 1 241 544897931 544898180 1.240000e-88 337.0
9 TraesCS7A01G399500 chr5A 91.165 249 13 3 1 240 384013613 384013861 2.080000e-86 329.0
10 TraesCS7A01G399500 chr5A 94.836 213 7 4 278 490 544898423 544898631 2.080000e-86 329.0
11 TraesCS7A01G399500 chr5A 100.000 171 0 0 568 738 572301134 572301304 1.620000e-82 316.0
12 TraesCS7A01G399500 chr5A 93.491 169 11 0 731 899 384014083 384014251 4.620000e-63 252.0
13 TraesCS7A01G399500 chr5A 98.765 81 1 0 658 738 5809498 5809418 8.070000e-31 145.0
14 TraesCS7A01G399500 chr5A 98.765 81 1 0 658 738 501869158 501869238 8.070000e-31 145.0
15 TraesCS7A01G399500 chr5A 97.561 82 2 0 488 569 572300783 572300864 1.040000e-29 141.0
16 TraesCS7A01G399500 chr1A 96.187 1836 47 3 983 2796 470996020 470997854 0.000000e+00 2981.0
17 TraesCS7A01G399500 chr1A 97.429 1400 34 2 983 2381 497975904 497977302 0.000000e+00 2385.0
18 TraesCS7A01G399500 chr1A 97.143 1400 37 3 983 2381 443854161 443855558 0.000000e+00 2361.0
19 TraesCS7A01G399500 chr1A 98.830 171 2 0 568 738 470995857 470996027 3.500000e-79 305.0
20 TraesCS7A01G399500 chr1A 100.000 88 0 0 568 655 50647952 50647865 2.230000e-36 163.0
21 TraesCS7A01G399500 chr1A 97.561 82 2 0 488 569 470995506 470995587 1.040000e-29 141.0
22 TraesCS7A01G399500 chr1A 100.000 64 0 0 658 721 50647730 50647667 4.890000e-23 119.0
23 TraesCS7A01G399500 chr1A 96.667 60 2 0 240 299 50647834 50647775 1.770000e-17 100.0
24 TraesCS7A01G399500 chr3A 95.207 1836 43 6 983 2796 157725635 157723823 0.000000e+00 2861.0
25 TraesCS7A01G399500 chr3A 99.415 171 1 0 568 738 157725798 157725628 7.520000e-81 311.0
26 TraesCS7A01G399500 chr3A 95.556 45 2 0 942 986 615143513 615143469 3.860000e-09 73.1
27 TraesCS7A01G399500 chr3A 100.000 33 0 0 537 569 157725992 157725960 8.360000e-06 62.1
28 TraesCS7A01G399500 chr2A 97.857 1400 27 3 983 2381 655909046 655907649 0.000000e+00 2416.0
29 TraesCS7A01G399500 chr2A 94.649 299 16 0 1 299 259576707 259577005 5.450000e-127 464.0
30 TraesCS7A01G399500 chr2A 100.000 171 0 0 568 738 774012000 774011830 1.620000e-82 316.0
31 TraesCS7A01G399500 chr2A 91.324 219 7 7 278 489 259577089 259577302 3.520000e-74 289.0
32 TraesCS7A01G399500 chr2A 98.438 128 2 0 363 490 259675756 259675883 2.800000e-55 226.0
33 TraesCS7A01G399500 chr2A 96.341 82 2 1 488 569 774012350 774012270 1.750000e-27 134.0
34 TraesCS7A01G399500 chr4B 93.469 1424 72 14 838 2253 113838132 113839542 0.000000e+00 2095.0
35 TraesCS7A01G399500 chr4B 95.266 169 8 0 731 899 644594378 644594546 4.590000e-68 268.0
36 TraesCS7A01G399500 chr4B 92.899 169 6 1 731 899 368725584 368725746 1.000000e-59 241.0
37 TraesCS7A01G399500 chr4B 93.671 158 10 0 742 899 200932576 200932733 1.290000e-58 237.0
38 TraesCS7A01G399500 chr4B 97.727 88 2 0 568 655 647882819 647882732 4.820000e-33 152.0
39 TraesCS7A01G399500 chr4B 96.591 88 3 0 568 655 288477090 288477003 2.240000e-31 147.0
40 TraesCS7A01G399500 chr4B 95.455 88 4 0 568 655 15098012 15097925 1.040000e-29 141.0
41 TraesCS7A01G399500 chr4B 96.667 60 2 0 240 299 288476855 288476796 1.770000e-17 100.0
42 TraesCS7A01G399500 chr3B 93.329 1424 81 11 838 2253 648363480 648362063 0.000000e+00 2091.0
43 TraesCS7A01G399500 chr6B 92.697 1424 81 15 838 2253 180278785 180277377 0.000000e+00 2032.0
44 TraesCS7A01G399500 chr6B 96.571 175 6 0 731 905 238444904 238444730 9.800000e-75 291.0
45 TraesCS7A01G399500 chr6B 96.324 136 5 0 69 204 152492348 152492483 1.010000e-54 224.0
46 TraesCS7A01G399500 chr2B 92.783 1344 62 10 914 2253 242205345 242206657 0.000000e+00 1912.0
47 TraesCS7A01G399500 chr2B 92.571 175 13 0 731 905 124027135 124026961 4.620000e-63 252.0
48 TraesCS7A01G399500 chr2B 98.305 59 1 0 241 299 250952798 250952740 1.370000e-18 104.0
49 TraesCS7A01G399500 chr2B 95.833 48 2 0 939 986 539865556 539865603 8.300000e-11 78.7
50 TraesCS7A01G399500 chr6D 96.990 299 9 0 1 299 446392752 446392454 1.160000e-138 503.0
51 TraesCS7A01G399500 chr6D 96.244 213 4 4 278 490 446392370 446392162 2.060000e-91 346.0
52 TraesCS7A01G399500 chr6D 96.000 75 3 0 69 143 75486271 75486345 3.780000e-24 122.0
53 TraesCS7A01G399500 chr6D 95.000 60 3 0 240 299 46527227 46527168 8.240000e-16 95.3
54 TraesCS7A01G399500 chr6D 95.000 60 3 0 240 299 452662268 452662327 8.240000e-16 95.3
55 TraesCS7A01G399500 chr6D 90.909 55 2 3 805 859 202663135 202663186 1.390000e-08 71.3
56 TraesCS7A01G399500 chr6D 90.909 55 2 3 805 859 202663207 202663258 1.390000e-08 71.3
57 TraesCS7A01G399500 chr6D 93.182 44 3 0 305 348 446392227 446392184 6.460000e-07 65.8
58 TraesCS7A01G399500 chr5D 96.990 299 9 0 1 299 384519965 384519667 1.160000e-138 503.0
59 TraesCS7A01G399500 chr5D 95.652 299 13 0 1 299 313521310 313521012 5.420000e-132 481.0
60 TraesCS7A01G399500 chr5D 96.714 213 3 4 278 490 384519583 384519375 4.430000e-93 351.0
61 TraesCS7A01G399500 chr5D 96.698 212 3 4 278 489 313520928 313520721 1.590000e-92 350.0
62 TraesCS7A01G399500 chr5D 95.652 161 7 0 745 905 29809769 29809609 2.760000e-65 259.0
63 TraesCS7A01G399500 chr5D 93.529 170 11 0 736 905 20273180 20273011 1.290000e-63 254.0
64 TraesCS7A01G399500 chr5D 94.304 158 9 0 742 899 401772539 401772696 2.780000e-60 243.0
65 TraesCS7A01G399500 chr5D 90.857 175 16 0 731 905 16496424 16496250 4.660000e-58 235.0
66 TraesCS7A01G399500 chr5D 96.000 75 3 0 69 143 541771512 541771586 3.780000e-24 122.0
67 TraesCS7A01G399500 chr5D 94.667 75 4 0 69 143 30980431 30980357 1.760000e-22 117.0
68 TraesCS7A01G399500 chr5D 98.305 59 1 0 241 299 30980207 30980149 1.370000e-18 104.0
69 TraesCS7A01G399500 chr5D 93.023 43 3 0 306 348 313520784 313520742 2.330000e-06 63.9
70 TraesCS7A01G399500 chr5D 93.023 43 3 0 306 348 384519439 384519397 2.330000e-06 63.9
71 TraesCS7A01G399500 chr5D 92.857 42 3 0 305 346 313520737 313520696 8.360000e-06 62.1
72 TraesCS7A01G399500 chr1D 96.990 299 9 0 1 299 463802085 463801787 1.160000e-138 503.0
73 TraesCS7A01G399500 chr1D 95.283 212 6 4 278 489 463801703 463801496 1.600000e-87 333.0
74 TraesCS7A01G399500 chr1D 95.858 169 7 0 731 899 417105723 417105891 9.870000e-70 274.0
75 TraesCS7A01G399500 chr1D 95.000 60 3 0 240 299 336737266 336737207 8.240000e-16 95.3
76 TraesCS7A01G399500 chr1D 92.857 42 1 1 317 356 463801548 463801507 3.010000e-05 60.2
77 TraesCS7A01G399500 chr3D 96.656 299 10 0 1 299 416544843 416545141 5.380000e-137 497.0
78 TraesCS7A01G399500 chr3D 93.789 161 10 0 745 905 229434370 229434210 2.780000e-60 243.0
79 TraesCS7A01G399500 chr3D 82.540 126 20 2 834 958 571760509 571760385 2.940000e-20 110.0
80 TraesCS7A01G399500 chr3D 95.000 60 3 0 240 299 57607214 57607273 8.240000e-16 95.3
81 TraesCS7A01G399500 chr3D 81.443 97 6 9 731 823 330477451 330477363 5.000000e-08 69.4
82 TraesCS7A01G399500 chr5B 98.830 171 2 0 568 738 133701689 133701859 3.500000e-79 305.0
83 TraesCS7A01G399500 chr5B 87.302 252 10 3 69 299 399756476 399756726 4.590000e-68 268.0
84 TraesCS7A01G399500 chr5B 93.064 173 12 0 69 241 189704393 189704565 1.290000e-63 254.0
85 TraesCS7A01G399500 chr5B 95.588 136 6 0 69 204 352729607 352729472 4.690000e-53 219.0
86 TraesCS7A01G399500 chr5B 97.727 88 2 0 568 655 639286477 639286564 4.820000e-33 152.0
87 TraesCS7A01G399500 chr5B 96.591 88 3 0 568 655 345108300 345108387 2.240000e-31 147.0
88 TraesCS7A01G399500 chr5B 97.561 82 2 0 488 569 71846099 71846180 1.040000e-29 141.0
89 TraesCS7A01G399500 chr5B 100.000 75 0 0 658 732 62386881 62386807 3.760000e-29 139.0
90 TraesCS7A01G399500 chr5B 96.341 82 3 0 488 569 133701338 133701419 4.860000e-28 135.0
91 TraesCS7A01G399500 chr5B 100.000 66 0 0 673 738 71846459 71846524 3.780000e-24 122.0
92 TraesCS7A01G399500 chr5B 96.667 60 2 0 240 299 62386985 62386926 1.770000e-17 100.0
93 TraesCS7A01G399500 chr4A 98.830 171 2 0 568 738 361391489 361391659 3.500000e-79 305.0
94 TraesCS7A01G399500 chr4A 98.701 154 2 0 568 721 369764817 369764664 9.870000e-70 274.0
95 TraesCS7A01G399500 chr4A 100.000 88 0 0 568 655 52482364 52482277 2.230000e-36 163.0
96 TraesCS7A01G399500 chr4A 100.000 88 0 0 568 655 326304093 326304006 2.230000e-36 163.0
97 TraesCS7A01G399500 chr4A 100.000 88 0 0 568 655 523832383 523832470 2.230000e-36 163.0
98 TraesCS7A01G399500 chr4A 98.864 88 1 0 568 655 525186747 525186660 1.040000e-34 158.0
99 TraesCS7A01G399500 chr4A 100.000 81 0 0 658 738 52482142 52482062 1.730000e-32 150.0
100 TraesCS7A01G399500 chr4A 100.000 81 0 0 658 738 326303871 326303791 1.730000e-32 150.0
101 TraesCS7A01G399500 chr4A 97.561 82 2 0 488 569 369765168 369765087 1.040000e-29 141.0
102 TraesCS7A01G399500 chr4A 96.341 82 3 0 488 569 361391138 361391219 4.860000e-28 135.0
103 TraesCS7A01G399500 chr4A 98.305 59 1 0 241 299 29810915 29810973 1.370000e-18 104.0
104 TraesCS7A01G399500 chr2D 94.675 169 9 0 731 899 397123514 397123682 2.140000e-66 263.0
105 TraesCS7A01G399500 chr2D 75.294 255 46 16 737 986 645241526 645241284 3.810000e-19 106.0
106 TraesCS7A01G399500 chr2D 95.833 48 2 0 939 986 397123681 397123728 8.300000e-11 78.7
107 TraesCS7A01G399500 chr7B 94.083 169 10 0 731 899 725302899 725303067 9.940000e-65 257.0
108 TraesCS7A01G399500 chr7B 96.324 136 5 0 69 204 692732929 692733064 1.010000e-54 224.0
109 TraesCS7A01G399500 chrUn 96.610 118 4 0 69 186 35789771 35789888 2.200000e-46 196.0
110 TraesCS7A01G399500 chr4D 95.960 99 4 0 807 905 222630232 222630134 8.010000e-36 161.0
111 TraesCS7A01G399500 chr4D 95.000 60 3 0 240 299 222630044 222629985 8.240000e-16 95.3
112 TraesCS7A01G399500 chr4D 95.000 60 3 0 240 299 236680816 236680757 8.240000e-16 95.3
113 TraesCS7A01G399500 chr4D 92.857 56 1 3 805 860 225341338 225341286 8.300000e-11 78.7
114 TraesCS7A01G399500 chr4D 92.727 55 1 2 805 859 410838942 410838993 2.990000e-10 76.8
115 TraesCS7A01G399500 chr4D 90.909 55 2 3 805 859 196903952 196904003 1.390000e-08 71.3
116 TraesCS7A01G399500 chr4D 97.500 40 1 0 731 770 222630267 222630228 5.000000e-08 69.4
117 TraesCS7A01G399500 chr4D 96.970 33 1 0 805 837 152469199 152469167 3.890000e-04 56.5
118 TraesCS7A01G399500 chr1B 97.727 88 2 0 568 655 681885251 681885338 4.820000e-33 152.0
119 TraesCS7A01G399500 chr1B 96.591 88 3 0 568 655 516774391 516774478 2.240000e-31 147.0
120 TraesCS7A01G399500 chr6A 96.000 75 3 0 69 143 445419483 445419557 3.780000e-24 122.0
121 TraesCS7A01G399500 chr6A 96.610 59 2 0 241 299 202729607 202729549 6.370000e-17 99.0
122 TraesCS7A01G399500 chr6A 96.610 59 2 0 241 299 445419707 445419765 6.370000e-17 99.0
123 TraesCS7A01G399500 chr7D 90.000 80 6 2 731 810 17944549 17944472 4.930000e-18 102.0


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 TraesCS7A01G399500 chr7A 579480832 579483627 2795 True 5164.000000 5164 100.000000 1 2796 1 chr7A.!!$R3 2795
1 TraesCS7A01G399500 chr7A 1548267 1550069 1802 True 3000.000000 3000 96.676000 992 2796 1 chr7A.!!$R1 1804
2 TraesCS7A01G399500 chr7A 578430081 578431337 1256 True 2126.000000 2126 97.147000 1535 2796 1 chr7A.!!$R2 1261
3 TraesCS7A01G399500 chr7A 481748731 481750435 1704 True 860.000000 2128 97.968333 488 2251 3 chr7A.!!$R4 1763
4 TraesCS7A01G399500 chr5A 572300783 572303111 2328 False 1165.666667 3040 98.159000 488 2796 3 chr5A.!!$F4 2308
5 TraesCS7A01G399500 chr5A 544897931 544898631 700 False 333.000000 337 93.218000 1 490 2 chr5A.!!$F3 489
6 TraesCS7A01G399500 chr5A 384013613 384014251 638 False 290.500000 329 92.328000 1 899 2 chr5A.!!$F2 898
7 TraesCS7A01G399500 chr1A 497975904 497977302 1398 False 2385.000000 2385 97.429000 983 2381 1 chr1A.!!$F2 1398
8 TraesCS7A01G399500 chr1A 443854161 443855558 1397 False 2361.000000 2361 97.143000 983 2381 1 chr1A.!!$F1 1398
9 TraesCS7A01G399500 chr1A 470995506 470997854 2348 False 1142.333333 2981 97.526000 488 2796 3 chr1A.!!$F3 2308
10 TraesCS7A01G399500 chr3A 157723823 157725992 2169 True 1078.033333 2861 98.207333 537 2796 3 chr3A.!!$R2 2259
11 TraesCS7A01G399500 chr2A 655907649 655909046 1397 True 2416.000000 2416 97.857000 983 2381 1 chr2A.!!$R1 1398
12 TraesCS7A01G399500 chr2A 259576707 259577302 595 False 376.500000 464 92.986500 1 489 2 chr2A.!!$F2 488
13 TraesCS7A01G399500 chr2A 774011830 774012350 520 True 225.000000 316 98.170500 488 738 2 chr2A.!!$R2 250
14 TraesCS7A01G399500 chr4B 113838132 113839542 1410 False 2095.000000 2095 93.469000 838 2253 1 chr4B.!!$F1 1415
15 TraesCS7A01G399500 chr3B 648362063 648363480 1417 True 2091.000000 2091 93.329000 838 2253 1 chr3B.!!$R1 1415
16 TraesCS7A01G399500 chr6B 180277377 180278785 1408 True 2032.000000 2032 92.697000 838 2253 1 chr6B.!!$R1 1415
17 TraesCS7A01G399500 chr2B 242205345 242206657 1312 False 1912.000000 1912 92.783000 914 2253 1 chr2B.!!$F1 1339
18 TraesCS7A01G399500 chr6D 446392162 446392752 590 True 304.933333 503 95.472000 1 490 3 chr6D.!!$R2 489
19 TraesCS7A01G399500 chr5D 384519375 384519965 590 True 305.966667 503 95.575667 1 490 3 chr5D.!!$R6 489
20 TraesCS7A01G399500 chr5D 313520696 313521310 614 True 239.250000 481 94.557500 1 489 4 chr5D.!!$R5 488
21 TraesCS7A01G399500 chr1D 463801496 463802085 589 True 298.733333 503 95.043333 1 489 3 chr1D.!!$R2 488
22 TraesCS7A01G399500 chr5B 133701338 133701859 521 False 220.000000 305 97.585500 488 738 2 chr5B.!!$F6 250
23 TraesCS7A01G399500 chr4A 361391138 361391659 521 False 220.000000 305 97.585500 488 738 2 chr4A.!!$F3 250
24 TraesCS7A01G399500 chr4A 369764664 369765168 504 True 207.500000 274 98.131000 488 721 2 chr4A.!!$R4 233

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
910 1464 0.112025 TGATGTTGGTGATGGGTGCA 59.888 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 3370 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.0 0.0 0.0 2.83 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
24 25 5.869649 AATTTGAAAGCCCACAACTAAGT 57.130 34.783 0.00 0.00 0.00 2.24
165 175 3.726607 TGATGTTGATGTTTTTGGTGCC 58.273 40.909 0.00 0.00 0.00 5.01
223 233 5.613329 AGTGATGTTGATGTTTTTGCCATT 58.387 33.333 0.00 0.00 0.00 3.16
527 810 2.366266 TGTTGTGGTAGGTAGTGTGGTC 59.634 50.000 0.00 0.00 0.00 4.02
529 812 1.202915 TGTGGTAGGTAGTGTGGTCGA 60.203 52.381 0.00 0.00 0.00 4.20
738 1292 7.039784 TGCTTGTTTCCTATTGCTTGTTTAGAT 60.040 33.333 0.00 0.00 0.00 1.98
739 1293 8.458843 GCTTGTTTCCTATTGCTTGTTTAGATA 58.541 33.333 0.00 0.00 0.00 1.98
742 1296 9.461312 TGTTTCCTATTGCTTGTTTAGATATGT 57.539 29.630 0.00 0.00 0.00 2.29
745 1299 9.679661 TTCCTATTGCTTGTTTAGATATGTTCA 57.320 29.630 0.00 0.00 0.00 3.18
746 1300 9.851686 TCCTATTGCTTGTTTAGATATGTTCAT 57.148 29.630 0.00 0.00 0.00 2.57
783 1337 6.374417 ACAATGTCCAGTCCTGTTTATAGT 57.626 37.500 0.00 0.00 0.00 2.12
899 1453 2.086869 GTGGTCACCTGATGATGTTGG 58.913 52.381 0.00 0.00 40.28 3.77
900 1454 1.704628 TGGTCACCTGATGATGTTGGT 59.295 47.619 0.00 0.00 40.28 3.67
905 1459 3.008835 ACCTGATGATGTTGGTGATGG 57.991 47.619 0.00 0.00 0.00 3.51
906 1460 2.304092 CCTGATGATGTTGGTGATGGG 58.696 52.381 0.00 0.00 0.00 4.00
907 1461 2.357465 CCTGATGATGTTGGTGATGGGT 60.357 50.000 0.00 0.00 0.00 4.51
908 1462 2.686405 CTGATGATGTTGGTGATGGGTG 59.314 50.000 0.00 0.00 0.00 4.61
909 1463 1.406539 GATGATGTTGGTGATGGGTGC 59.593 52.381 0.00 0.00 0.00 5.01
910 1464 0.112025 TGATGTTGGTGATGGGTGCA 59.888 50.000 0.00 0.00 0.00 4.57
911 1465 0.527565 GATGTTGGTGATGGGTGCAC 59.472 55.000 8.80 8.80 35.56 4.57
912 1466 0.178967 ATGTTGGTGATGGGTGCACA 60.179 50.000 20.43 0.00 37.99 4.57
915 1469 0.112025 TTGGTGATGGGTGCACATGA 59.888 50.000 20.43 1.17 37.99 3.07
927 1481 3.057386 GGTGCACATGATGTTGATGTTGA 60.057 43.478 20.43 0.00 31.46 3.18
931 1485 4.678622 CACATGATGTTGATGTTGATGGG 58.321 43.478 0.00 0.00 31.46 4.00
932 1486 4.158949 CACATGATGTTGATGTTGATGGGT 59.841 41.667 0.00 0.00 31.46 4.51
933 1487 4.158949 ACATGATGTTGATGTTGATGGGTG 59.841 41.667 0.00 0.00 29.39 4.61
937 1491 1.612950 GTTGATGTTGATGGGTGCACA 59.387 47.619 20.43 0.00 0.00 4.57
943 1497 1.820519 GTTGATGGGTGCACATGATGT 59.179 47.619 20.43 0.00 0.00 3.06
948 1502 2.868899 TGGGTGCACATGATGTTGTTA 58.131 42.857 20.43 0.00 0.00 2.41
951 1505 5.012893 TGGGTGCACATGATGTTGTTATTA 58.987 37.500 20.43 0.00 0.00 0.98
960 1538 8.862074 CACATGATGTTGTTATTATTGTTGTGG 58.138 33.333 0.00 0.00 0.00 4.17
962 1540 9.421806 CATGATGTTGTTATTATTGTTGTGGTT 57.578 29.630 0.00 0.00 0.00 3.67
964 1542 9.900710 TGATGTTGTTATTATTGTTGTGGTTAC 57.099 29.630 0.00 0.00 0.00 2.50
965 1543 9.349145 GATGTTGTTATTATTGTTGTGGTTACC 57.651 33.333 0.00 0.00 0.00 2.85
967 1545 8.353684 TGTTGTTATTATTGTTGTGGTTACCTG 58.646 33.333 2.07 0.00 0.00 4.00
968 1546 8.569641 GTTGTTATTATTGTTGTGGTTACCTGA 58.430 33.333 2.07 0.00 0.00 3.86
970 1548 8.735315 TGTTATTATTGTTGTGGTTACCTGATG 58.265 33.333 2.07 0.00 0.00 3.07
971 1549 6.773976 ATTATTGTTGTGGTTACCTGATGG 57.226 37.500 2.07 0.00 39.83 3.51
1103 1709 7.828223 ACTCATTTCTTTATCATCACTCTGCTT 59.172 33.333 0.00 0.00 0.00 3.91
1180 1786 1.946081 TGACAAGTTTGCGAAGATGCA 59.054 42.857 0.00 0.00 44.61 3.96
1193 1799 4.881440 ATGCACGCGGGCCATGAT 62.881 61.111 33.29 15.38 0.00 2.45
1237 1843 2.434884 CGACAGCGGGCTTCACAT 60.435 61.111 0.00 0.00 0.00 3.21
1382 1988 0.816018 ACGCCATGTTCACCGTGAAA 60.816 50.000 15.52 7.00 38.22 2.69
1425 2031 1.403647 GCATGTACTACCAGCACGACA 60.404 52.381 0.00 0.00 0.00 4.35
1492 2098 2.073252 TCCTCTACCTGCACGATGAT 57.927 50.000 0.00 0.00 0.00 2.45
2199 2827 0.606604 GACTCAAACCCTAGCCACGA 59.393 55.000 0.00 0.00 0.00 4.35
2615 3244 1.472728 CGTAGCTACTCCCGGCAATTT 60.473 52.381 21.20 0.00 0.00 1.82
2741 3370 3.657398 AGGCATTCCATCACAGAATCA 57.343 42.857 0.00 0.00 31.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.461222 CAAATCATATTTTGCTAGGTCAGTCAA 58.539 33.333 0.00 0.00 30.51 3.18
117 127 7.158021 CAGGGCCTCAATAGTAGATAAGAAAG 58.842 42.308 0.95 0.00 0.00 2.62
165 175 8.442632 TCTTCTACTCATTCCATATTTTGCTG 57.557 34.615 0.00 0.00 0.00 4.41
223 233 5.860941 TGGCAAAAACAAGGACATTTCTA 57.139 34.783 0.00 0.00 0.00 2.10
288 405 5.248640 ACATATCTGCCCGATTTGGAATAG 58.751 41.667 7.90 0.00 42.00 1.73
299 416 6.818142 TGAACATATATGAACATATCTGCCCG 59.182 38.462 19.63 0.00 33.62 6.13
527 810 3.244009 ACCAACAGAGCATAGATCCATCG 60.244 47.826 0.00 0.00 0.00 3.84
529 812 4.904251 ACTACCAACAGAGCATAGATCCAT 59.096 41.667 0.00 0.00 0.00 3.41
746 1300 9.778741 GACTGGACATTGTTCCATATCTATAAA 57.221 33.333 7.97 0.00 44.97 1.40
747 1301 8.375506 GGACTGGACATTGTTCCATATCTATAA 58.624 37.037 7.97 0.00 44.97 0.98
748 1302 7.734865 AGGACTGGACATTGTTCCATATCTATA 59.265 37.037 7.75 0.00 44.97 1.31
749 1303 6.560304 AGGACTGGACATTGTTCCATATCTAT 59.440 38.462 7.75 2.53 44.97 1.98
750 1304 5.905331 AGGACTGGACATTGTTCCATATCTA 59.095 40.000 7.75 0.00 44.97 1.98
751 1305 4.723789 AGGACTGGACATTGTTCCATATCT 59.276 41.667 7.75 4.41 44.97 1.98
752 1306 4.818546 CAGGACTGGACATTGTTCCATATC 59.181 45.833 7.75 8.56 44.97 1.63
753 1307 4.228210 ACAGGACTGGACATTGTTCCATAT 59.772 41.667 7.75 1.71 44.97 1.78
754 1308 3.587061 ACAGGACTGGACATTGTTCCATA 59.413 43.478 7.75 0.00 44.97 2.74
755 1309 2.376518 ACAGGACTGGACATTGTTCCAT 59.623 45.455 7.75 1.19 44.97 3.41
756 1310 1.774254 ACAGGACTGGACATTGTTCCA 59.226 47.619 7.75 7.60 43.83 3.53
757 1311 2.568623 ACAGGACTGGACATTGTTCC 57.431 50.000 4.14 0.00 36.03 3.62
758 1312 6.879458 ACTATAAACAGGACTGGACATTGTTC 59.121 38.462 4.14 0.00 31.30 3.18
759 1313 6.779860 ACTATAAACAGGACTGGACATTGTT 58.220 36.000 4.14 0.00 33.73 2.83
760 1314 6.374417 ACTATAAACAGGACTGGACATTGT 57.626 37.500 4.14 0.00 34.19 2.71
761 1315 6.655003 ACAACTATAAACAGGACTGGACATTG 59.345 38.462 4.14 2.35 34.19 2.82
762 1316 6.655003 CACAACTATAAACAGGACTGGACATT 59.345 38.462 4.14 0.00 34.19 2.71
763 1317 6.173339 CACAACTATAAACAGGACTGGACAT 58.827 40.000 4.14 0.00 34.19 3.06
764 1318 5.071250 ACACAACTATAAACAGGACTGGACA 59.929 40.000 4.14 0.00 34.19 4.02
765 1319 5.548406 ACACAACTATAAACAGGACTGGAC 58.452 41.667 4.14 0.00 34.19 4.02
766 1320 5.279809 GGACACAACTATAAACAGGACTGGA 60.280 44.000 4.14 0.00 34.19 3.86
767 1321 4.935808 GGACACAACTATAAACAGGACTGG 59.064 45.833 4.14 0.00 34.19 4.00
768 1322 5.639506 CAGGACACAACTATAAACAGGACTG 59.360 44.000 0.00 0.00 0.00 3.51
783 1337 5.830991 ACCAAAAGCTATAAACAGGACACAA 59.169 36.000 0.00 0.00 0.00 3.33
867 1421 1.378646 TGACCACCAACGGCAACAA 60.379 52.632 0.00 0.00 0.00 2.83
868 1422 2.115911 GTGACCACCAACGGCAACA 61.116 57.895 0.00 0.00 0.00 3.33
899 1453 1.466856 ACATCATGTGCACCCATCAC 58.533 50.000 15.69 0.00 35.14 3.06
900 1454 1.819903 CAACATCATGTGCACCCATCA 59.180 47.619 15.69 0.00 0.00 3.07
901 1455 2.093890 TCAACATCATGTGCACCCATC 58.906 47.619 15.69 0.00 0.00 3.51
902 1456 2.219080 TCAACATCATGTGCACCCAT 57.781 45.000 15.69 0.00 0.00 4.00
903 1457 1.819903 CATCAACATCATGTGCACCCA 59.180 47.619 15.69 0.00 0.00 4.51
904 1458 1.820519 ACATCAACATCATGTGCACCC 59.179 47.619 15.69 0.00 33.04 4.61
905 1459 3.057386 TCAACATCAACATCATGTGCACC 60.057 43.478 15.69 0.00 34.59 5.01
906 1460 4.163458 TCAACATCAACATCATGTGCAC 57.837 40.909 10.75 10.75 34.59 4.57
907 1461 4.381079 CCATCAACATCAACATCATGTGCA 60.381 41.667 0.00 0.00 34.59 4.57
908 1462 4.109766 CCATCAACATCAACATCATGTGC 58.890 43.478 0.00 0.00 34.59 4.57
909 1463 4.158949 ACCCATCAACATCAACATCATGTG 59.841 41.667 0.00 0.00 34.59 3.21
910 1464 4.158949 CACCCATCAACATCAACATCATGT 59.841 41.667 0.00 0.00 35.94 3.21
911 1465 4.678622 CACCCATCAACATCAACATCATG 58.321 43.478 0.00 0.00 0.00 3.07
912 1466 3.131577 GCACCCATCAACATCAACATCAT 59.868 43.478 0.00 0.00 0.00 2.45
915 1469 2.231964 GTGCACCCATCAACATCAACAT 59.768 45.455 5.22 0.00 0.00 2.71
927 1481 1.927487 ACAACATCATGTGCACCCAT 58.073 45.000 15.69 0.00 30.82 4.00
931 1485 8.374728 CAACAATAATAACAACATCATGTGCAC 58.625 33.333 10.75 10.75 32.81 4.57
932 1486 8.087136 ACAACAATAATAACAACATCATGTGCA 58.913 29.630 0.00 0.00 32.81 4.57
933 1487 8.374728 CACAACAATAATAACAACATCATGTGC 58.625 33.333 0.00 0.00 32.81 4.57
943 1497 8.693120 TCAGGTAACCACAACAATAATAACAA 57.307 30.769 0.00 0.00 37.17 2.83
948 1502 5.656416 CCCATCAGGTAACCACAACAATAAT 59.344 40.000 0.00 0.00 37.17 1.28
951 1505 3.430453 CCCATCAGGTAACCACAACAAT 58.570 45.455 0.00 0.00 37.17 2.71
964 1542 2.517959 ACATCAACAACACCCATCAGG 58.482 47.619 0.00 0.00 43.78 3.86
965 1543 4.589216 AAACATCAACAACACCCATCAG 57.411 40.909 0.00 0.00 0.00 2.90
967 1545 4.942852 TGAAAACATCAACAACACCCATC 58.057 39.130 0.00 0.00 34.30 3.51
968 1546 4.648762 TCTGAAAACATCAACAACACCCAT 59.351 37.500 0.00 0.00 37.67 4.00
970 1548 4.338118 TCTCTGAAAACATCAACAACACCC 59.662 41.667 0.00 0.00 37.67 4.61
971 1549 5.499139 TCTCTGAAAACATCAACAACACC 57.501 39.130 0.00 0.00 37.67 4.16
973 1551 6.374053 TCACTTCTCTGAAAACATCAACAACA 59.626 34.615 0.00 0.00 37.67 3.33
974 1552 6.785191 TCACTTCTCTGAAAACATCAACAAC 58.215 36.000 0.00 0.00 37.67 3.32
975 1553 6.823182 TCTCACTTCTCTGAAAACATCAACAA 59.177 34.615 0.00 0.00 37.67 2.83
977 1555 6.851222 TCTCACTTCTCTGAAAACATCAAC 57.149 37.500 0.00 0.00 37.67 3.18
978 1556 6.429078 CCATCTCACTTCTCTGAAAACATCAA 59.571 38.462 0.00 0.00 37.67 2.57
979 1557 5.936372 CCATCTCACTTCTCTGAAAACATCA 59.064 40.000 0.00 0.00 36.38 3.07
980 1558 5.163774 GCCATCTCACTTCTCTGAAAACATC 60.164 44.000 0.00 0.00 0.00 3.06
981 1559 4.699257 GCCATCTCACTTCTCTGAAAACAT 59.301 41.667 0.00 0.00 0.00 2.71
983 1561 4.153835 CAGCCATCTCACTTCTCTGAAAAC 59.846 45.833 0.00 0.00 0.00 2.43
1103 1709 3.138884 TGTGGCAATCAAGCACTAGAA 57.861 42.857 0.00 0.00 35.83 2.10
1193 1799 0.823356 GCAGCTTCACTTTGTGGGGA 60.823 55.000 0.00 0.00 33.87 4.81
1237 1843 1.102154 CACCAACACTTTCCACAGCA 58.898 50.000 0.00 0.00 0.00 4.41
1382 1988 2.287547 GCACATGGTGTTGTCGAACATT 60.288 45.455 0.00 0.00 43.95 2.71
1425 2031 1.827969 AGAGAGCTTACTGGCATCGTT 59.172 47.619 0.00 0.00 34.17 3.85
1492 2098 5.645624 CAACAAAGTGTGAACATGGTGTTA 58.354 37.500 0.00 0.00 41.28 2.41
1714 2341 3.632080 TCGTCCGCCACCACCATT 61.632 61.111 0.00 0.00 0.00 3.16
1793 2420 3.157518 TGGTCCTGTCACCAAGCTA 57.842 52.632 0.00 0.00 43.88 3.32
2529 3158 6.436027 AGGGTCTACTTTGAGATAGACATGA 58.564 40.000 0.00 0.00 46.14 3.07
2676 3305 5.379732 TTTAGTGAAAATAACGGGCAAGG 57.620 39.130 0.00 0.00 0.00 3.61
2741 3370 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.