Multiple sequence alignment - TraesCS3A01G253900

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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 TraesCS3A01G253900 chr3A 100.000 4919 0 0 1 4919 475284500 475279582 0.000000e+00 9084.0
1 TraesCS3A01G253900 chr3A 100.000 1746 0 0 5090 6835 475279411 475277666 0.000000e+00 3225.0
2 TraesCS3A01G253900 chr3A 94.895 666 16 7 4071 4723 749166720 749166060 0.000000e+00 1026.0
3 TraesCS3A01G253900 chr3A 90.458 262 23 2 3183 3442 706868065 706867804 1.830000e-90 344.0
4 TraesCS3A01G253900 chr3A 100.000 28 0 0 6269 6296 529183640 529183667 1.200000e-02 52.8
5 TraesCS3A01G253900 chr3B 95.254 3203 97 19 705 3883 457576713 457573542 0.000000e+00 5022.0
6 TraesCS3A01G253900 chr3B 93.598 1640 45 17 5095 6701 457572838 457571226 0.000000e+00 2392.0
7 TraesCS3A01G253900 chr3B 92.920 452 29 2 1 451 457631597 457631148 0.000000e+00 654.0
8 TraesCS3A01G253900 chr3B 89.170 277 10 7 439 706 457577035 457576770 1.840000e-85 327.0
9 TraesCS3A01G253900 chr3B 94.783 115 6 0 3072 3186 521797757 521797871 5.450000e-41 180.0
10 TraesCS3A01G253900 chr3B 95.588 68 3 0 6768 6835 457570883 457570816 7.250000e-20 110.0
11 TraesCS3A01G253900 chr3D 94.172 2385 95 20 705 3087 356592672 356590330 0.000000e+00 3594.0
12 TraesCS3A01G253900 chr3D 92.494 1159 58 13 5090 6235 356589539 356588397 0.000000e+00 1631.0
13 TraesCS3A01G253900 chr3D 89.902 713 51 8 1 706 356593424 356592726 0.000000e+00 898.0
14 TraesCS3A01G253900 chr3D 88.023 693 41 15 4067 4721 522550766 522551454 0.000000e+00 782.0
15 TraesCS3A01G253900 chr3D 90.674 579 49 3 3493 4067 356590331 356589754 0.000000e+00 765.0
16 TraesCS3A01G253900 chr3D 91.546 485 33 4 6227 6704 356579702 356579219 0.000000e+00 662.0
17 TraesCS3A01G253900 chr3D 87.209 258 28 4 4467 4723 590127742 590127489 8.670000e-74 289.0
18 TraesCS3A01G253900 chr3D 89.100 211 22 1 4068 4277 590127491 590127701 1.890000e-65 261.0
19 TraesCS3A01G253900 chr3D 90.000 200 18 2 4530 4729 522550957 522550760 2.450000e-64 257.0
20 TraesCS3A01G253900 chr3D 95.070 142 7 0 4068 4209 590128177 590128036 2.480000e-54 224.0
21 TraesCS3A01G253900 chr3D 85.854 205 10 4 4068 4272 266414380 266414565 4.180000e-47 200.0
22 TraesCS3A01G253900 chr3D 95.763 118 4 1 6718 6835 356579178 356579062 9.050000e-44 189.0
23 TraesCS3A01G253900 chr3D 100.000 68 0 0 4722 4789 107462702 107462635 7.200000e-25 126.0
24 TraesCS3A01G253900 chr3D 97.222 72 2 0 4722 4793 441134504 441134575 9.310000e-24 122.0
25 TraesCS3A01G253900 chr3D 95.946 74 3 0 4716 4789 431631817 431631890 3.350000e-23 121.0
26 TraesCS3A01G253900 chr3D 86.239 109 15 0 200 308 23667502 23667610 1.200000e-22 119.0
27 TraesCS3A01G253900 chr3D 84.821 112 15 2 201 311 35711420 35711530 2.020000e-20 111.0
28 TraesCS3A01G253900 chr3D 100.000 32 0 0 4036 4067 123309585 123309554 7.400000e-05 60.2
29 TraesCS3A01G253900 chr3D 100.000 32 0 0 4036 4067 172830734 172830765 7.400000e-05 60.2
30 TraesCS3A01G253900 chr1A 98.636 660 6 3 4064 4721 244989526 244990184 0.000000e+00 1166.0
31 TraesCS3A01G253900 chr1A 95.884 656 14 5 4067 4721 588675591 588674948 0.000000e+00 1050.0
32 TraesCS3A01G253900 chr1A 94.895 666 18 5 4068 4721 427716454 427715793 0.000000e+00 1027.0
33 TraesCS3A01G253900 chr1A 94.665 656 11 6 4067 4721 16408325 16407693 0.000000e+00 996.0
34 TraesCS3A01G253900 chr1A 88.889 684 24 9 4068 4721 192012436 192013097 0.000000e+00 795.0
35 TraesCS3A01G253900 chr1A 88.596 684 30 10 4068 4721 567981694 567982359 0.000000e+00 787.0
36 TraesCS3A01G253900 chr1A 88.502 661 18 10 4067 4723 480600914 480601520 0.000000e+00 747.0
37 TraesCS3A01G253900 chr1A 93.538 325 15 6 4400 4721 501020187 501020508 4.800000e-131 479.0
38 TraesCS3A01G253900 chr1A 93.231 325 20 2 4064 4387 501019815 501020138 1.720000e-130 477.0
39 TraesCS3A01G253900 chr1A 88.889 225 22 3 4063 4286 541467770 541467548 2.430000e-69 274.0
40 TraesCS3A01G253900 chr1A 96.296 108 3 1 3083 3189 459273228 459273335 7.050000e-40 176.0
41 TraesCS3A01G253900 chr1A 90.476 105 10 0 200 304 352174092 352174196 9.240000e-29 139.0
42 TraesCS3A01G253900 chr2A 98.779 655 7 1 4067 4721 358945211 358944558 0.000000e+00 1164.0
43 TraesCS3A01G253900 chr2A 96.289 485 13 5 4240 4722 51694428 51693947 0.000000e+00 791.0
44 TraesCS3A01G253900 chr2A 96.082 485 15 4 4240 4722 51755482 51755000 0.000000e+00 787.0
45 TraesCS3A01G253900 chr7A 97.859 654 13 1 4069 4721 490273864 490274517 0.000000e+00 1129.0
46 TraesCS3A01G253900 chr7A 91.343 670 17 13 4067 4721 285665380 285664737 0.000000e+00 878.0
47 TraesCS3A01G253900 chr7A 85.496 131 17 2 1814 1943 712494357 712494228 1.200000e-27 135.0
48 TraesCS3A01G253900 chr4A 97.252 655 14 4 4068 4721 636325861 636326512 0.000000e+00 1107.0
49 TraesCS3A01G253900 chr4A 91.643 706 24 7 4032 4724 64140006 64139323 0.000000e+00 944.0
50 TraesCS3A01G253900 chr4A 95.167 600 14 5 4137 4723 628154085 628154682 0.000000e+00 933.0
51 TraesCS3A01G253900 chr4A 92.273 660 29 7 4067 4721 488031977 488032619 0.000000e+00 917.0
52 TraesCS3A01G253900 chr4A 90.038 261 24 2 3184 3442 165816284 165816544 3.050000e-88 337.0
53 TraesCS3A01G253900 chr5A 95.231 671 16 4 4068 4724 348188814 348189482 0.000000e+00 1048.0
54 TraesCS3A01G253900 chr5A 94.075 692 24 6 4042 4721 480097442 480096756 0.000000e+00 1035.0
55 TraesCS3A01G253900 chr5A 94.903 667 19 6 4068 4721 706067793 706068457 0.000000e+00 1029.0
56 TraesCS3A01G253900 chr5A 93.413 668 26 7 4069 4723 178602143 178602805 0.000000e+00 974.0
57 TraesCS3A01G253900 chr5A 93.465 658 25 5 4064 4718 419679001 419679643 0.000000e+00 961.0
58 TraesCS3A01G253900 chr5A 91.994 662 37 12 4067 4724 698130683 698130034 0.000000e+00 915.0
59 TraesCS3A01G253900 chr5A 92.066 668 17 7 4071 4727 675628950 675628308 0.000000e+00 907.0
60 TraesCS3A01G253900 chr6A 93.853 667 25 8 4068 4721 555438180 555437517 0.000000e+00 990.0
61 TraesCS3A01G253900 chr6A 93.835 665 26 9 4067 4721 68792907 68792248 0.000000e+00 987.0
62 TraesCS3A01G253900 chr6A 92.730 674 13 9 4064 4722 554107150 554107802 0.000000e+00 941.0
63 TraesCS3A01G253900 chr6A 91.947 683 26 5 4067 4721 562592319 562593000 0.000000e+00 929.0
64 TraesCS3A01G253900 chr6A 90.029 682 20 8 4068 4721 108949435 108950096 0.000000e+00 839.0
65 TraesCS3A01G253900 chr6A 89.416 274 26 3 3180 3450 613738801 613738528 6.560000e-90 342.0
66 TraesCS3A01G253900 chr6A 96.330 109 2 2 3083 3189 538097835 538097727 1.960000e-40 178.0
67 TraesCS3A01G253900 chr6A 98.529 68 1 0 4722 4789 557970115 557970048 3.350000e-23 121.0
68 TraesCS3A01G253900 chr4D 86.760 574 39 13 4182 4721 81172903 81172333 7.580000e-169 604.0
69 TraesCS3A01G253900 chr4D 93.458 321 17 3 4068 4387 102162796 102162479 2.230000e-129 473.0
70 TraesCS3A01G253900 chr4D 90.798 326 22 5 4400 4724 102162425 102162107 4.900000e-116 429.0
71 TraesCS3A01G253900 chr4D 91.753 194 15 1 4528 4721 102162604 102162796 1.130000e-67 268.0
72 TraesCS3A01G253900 chr4D 90.426 188 17 1 4068 4254 81172333 81172520 5.290000e-61 246.0
73 TraesCS3A01G253900 chr4D 89.286 196 18 3 4067 4260 102162109 102162303 6.850000e-60 243.0
74 TraesCS3A01G253900 chr4D 96.330 109 2 2 3083 3189 119822903 119822795 1.960000e-40 178.0
75 TraesCS3A01G253900 chr4D 81.657 169 21 4 4561 4721 296701075 296700909 1.550000e-26 132.0
76 TraesCS3A01G253900 chr4D 98.551 69 1 0 4722 4790 479997645 479997577 9.310000e-24 122.0
77 TraesCS3A01G253900 chr4D 92.683 82 6 0 4064 4145 304220248 304220329 1.200000e-22 119.0
78 TraesCS3A01G253900 chr4D 95.946 74 2 1 4722 4794 371926831 371926904 1.200000e-22 119.0
79 TraesCS3A01G253900 chr4D 95.946 74 2 1 4722 4795 478671869 478671941 1.200000e-22 119.0
80 TraesCS3A01G253900 chr4D 93.590 78 5 0 4644 4721 304220329 304220252 4.330000e-22 117.0
81 TraesCS3A01G253900 chr4D 97.101 69 2 0 4722 4790 489228361 489228429 4.330000e-22 117.0
82 TraesCS3A01G253900 chr4D 92.683 41 2 1 4028 4068 236940224 236940185 2.660000e-04 58.4
83 TraesCS3A01G253900 chr4D 97.059 34 1 0 4034 4067 258922359 258922326 2.660000e-04 58.4
84 TraesCS3A01G253900 chr4D 100.000 30 0 0 4041 4070 505353885 505353914 1.000000e-03 56.5
85 TraesCS3A01G253900 chr4D 94.118 34 2 0 4035 4068 6572212 6572245 1.200000e-02 52.8
86 TraesCS3A01G253900 chr2B 90.038 261 24 2 3184 3442 673002426 673002686 3.050000e-88 337.0
87 TraesCS3A01G253900 chr2B 93.827 81 4 1 4710 4790 309475468 309475389 3.350000e-23 121.0
88 TraesCS3A01G253900 chr2B 84.127 63 8 2 4005 4067 142399938 142399998 7.400000e-05 60.2
89 TraesCS3A01G253900 chr2B 100.000 29 0 0 6268 6296 34392450 34392422 3.000000e-03 54.7
90 TraesCS3A01G253900 chrUn 89.219 269 27 2 3179 3445 92971136 92970868 1.100000e-87 335.0
91 TraesCS3A01G253900 chrUn 98.551 69 1 0 4722 4790 378270585 378270653 9.310000e-24 122.0
92 TraesCS3A01G253900 chrUn 98.551 69 1 0 4722 4790 447954329 447954261 9.310000e-24 122.0
93 TraesCS3A01G253900 chrUn 97.101 69 2 0 4722 4790 104668825 104668893 4.330000e-22 117.0
94 TraesCS3A01G253900 chrUn 97.101 69 2 0 4722 4790 197752412 197752480 4.330000e-22 117.0
95 TraesCS3A01G253900 chrUn 97.101 69 2 0 4722 4790 320620136 320620068 4.330000e-22 117.0
96 TraesCS3A01G253900 chrUn 95.833 72 2 1 4722 4793 31861277 31861207 1.560000e-21 115.0
97 TraesCS3A01G253900 chrUn 97.101 69 1 1 4722 4789 84435448 84435380 1.560000e-21 115.0
98 TraesCS3A01G253900 chrUn 94.366 71 4 0 4722 4792 110002972 110002902 7.250000e-20 110.0
99 TraesCS3A01G253900 chrUn 95.588 68 3 0 4722 4789 222975787 222975854 7.250000e-20 110.0
100 TraesCS3A01G253900 chrUn 100.000 32 0 0 4037 4068 153386154 153386185 7.400000e-05 60.2
101 TraesCS3A01G253900 chrUn 96.970 33 1 0 4035 4067 48610506 48610474 1.000000e-03 56.5
102 TraesCS3A01G253900 chrUn 100.000 29 0 0 4041 4069 93374734 93374762 3.000000e-03 54.7
103 TraesCS3A01G253900 chrUn 100.000 29 0 0 6268 6296 201682649 201682621 3.000000e-03 54.7
104 TraesCS3A01G253900 chrUn 100.000 28 0 0 4040 4067 382894045 382894072 1.200000e-02 52.8
105 TraesCS3A01G253900 chr2D 89.474 266 26 2 3179 3442 647763095 647763360 1.100000e-87 335.0
106 TraesCS3A01G253900 chr2D 88.930 271 26 4 3183 3449 630180074 630179804 1.420000e-86 331.0
107 TraesCS3A01G253900 chr2D 98.529 68 1 0 4722 4789 592288583 592288516 3.350000e-23 121.0
108 TraesCS3A01G253900 chr2D 82.609 69 5 6 4003 4068 85926030 85925966 3.000000e-03 54.7
109 TraesCS3A01G253900 chr5B 88.930 271 28 2 3175 3443 273258518 273258248 3.950000e-87 333.0
110 TraesCS3A01G253900 chr6D 89.313 262 17 6 4469 4730 55069188 55068938 1.110000e-82 318.0
111 TraesCS3A01G253900 chr6D 89.686 223 20 3 4065 4286 55068943 55069163 1.450000e-71 281.0
112 TraesCS3A01G253900 chr6D 91.875 160 7 6 4055 4209 55069590 55069432 1.150000e-52 219.0
113 TraesCS3A01G253900 chr6D 96.262 107 3 1 3084 3189 320698233 320698127 2.530000e-39 174.0
114 TraesCS3A01G253900 chr6D 95.413 109 3 2 3083 3189 392273230 392273122 9.110000e-39 172.0
115 TraesCS3A01G253900 chr6D 98.551 69 1 0 4722 4790 78083146 78083078 9.310000e-24 122.0
116 TraesCS3A01G253900 chr6D 98.551 69 0 1 4722 4789 120657593 120657661 3.350000e-23 121.0
117 TraesCS3A01G253900 chr6D 98.529 68 1 0 4722 4789 387886007 387886074 3.350000e-23 121.0
118 TraesCS3A01G253900 chr6D 95.890 73 2 1 4722 4794 309072571 309072500 4.330000e-22 117.0
119 TraesCS3A01G253900 chr6D 100.000 28 0 0 4041 4068 81394188 81394215 1.200000e-02 52.8
120 TraesCS3A01G253900 chr6D 100.000 28 0 0 4041 4068 120657662 120657635 1.200000e-02 52.8
121 TraesCS3A01G253900 chr6D 100.000 28 0 0 4040 4067 132853787 132853814 1.200000e-02 52.8
122 TraesCS3A01G253900 chr5D 86.275 255 22 3 4468 4722 330830044 330829803 1.460000e-66 265.0
123 TraesCS3A01G253900 chr5D 91.566 166 12 2 4067 4231 386656004 386655840 1.920000e-55 228.0
124 TraesCS3A01G253900 chr5D 85.135 222 23 3 4065 4286 330829801 330830012 1.150000e-52 219.0
125 TraesCS3A01G253900 chr5D 92.517 147 10 1 4580 4726 298965094 298964949 6.950000e-50 209.0
126 TraesCS3A01G253900 chr5D 92.199 141 11 0 4068 4208 298965615 298965475 4.180000e-47 200.0
127 TraesCS3A01G253900 chr5D 87.791 172 18 3 4561 4732 386655844 386656012 1.500000e-46 198.0
128 TraesCS3A01G253900 chr5D 92.063 126 10 0 4067 4192 330830448 330830323 1.960000e-40 178.0
129 TraesCS3A01G253900 chr5D 87.255 102 13 0 193 294 367671685 367671584 4.330000e-22 117.0
130 TraesCS3A01G253900 chr5D 100.000 34 0 0 4035 4068 538567676 538567709 5.720000e-06 63.9
131 TraesCS3A01G253900 chr5D 100.000 33 0 0 4036 4068 199520642 199520610 2.060000e-05 62.1
132 TraesCS3A01G253900 chr5D 100.000 31 0 0 4038 4068 408541210 408541240 2.660000e-04 58.4
133 TraesCS3A01G253900 chr1D 91.071 168 14 1 4561 4728 459409597 459409431 6.900000e-55 226.0
134 TraesCS3A01G253900 chr1D 88.439 173 20 0 4059 4231 459410224 459410052 6.950000e-50 209.0
135 TraesCS3A01G253900 chr1D 90.062 161 15 1 4561 4721 459410056 459410215 2.500000e-49 207.0
136 TraesCS3A01G253900 chr1D 89.024 164 17 1 4068 4231 18046271 18046109 1.160000e-47 202.0
137 TraesCS3A01G253900 chr1D 90.210 143 14 0 4579 4721 58441778 58441920 3.250000e-43 187.0
138 TraesCS3A01G253900 chr1D 87.117 163 19 2 4561 4723 18046113 18046273 4.210000e-42 183.0
139 TraesCS3A01G253900 chr1D 97.222 72 2 0 4722 4793 35756935 35756864 9.310000e-24 122.0
140 TraesCS3A01G253900 chr1D 98.551 69 1 0 4722 4790 440050375 440050443 9.310000e-24 122.0
141 TraesCS3A01G253900 chr1D 97.222 72 1 1 4722 4793 47644810 47644740 3.350000e-23 121.0
142 TraesCS3A01G253900 chr1D 95.946 74 3 0 4722 4795 455143436 455143509 3.350000e-23 121.0
143 TraesCS3A01G253900 chr1D 95.890 73 3 0 4722 4794 295954283 295954211 1.200000e-22 119.0
144 TraesCS3A01G253900 chr1D 89.655 87 8 1 4716 4802 22428282 22428367 7.250000e-20 110.0
145 TraesCS3A01G253900 chr1D 87.209 86 9 2 4644 4728 22953810 22953894 5.640000e-16 97.1
146 TraesCS3A01G253900 chr1D 87.179 78 9 1 4068 4145 22953886 22953810 3.400000e-13 87.9
147 TraesCS3A01G253900 chr1D 100.000 32 0 0 4036 4067 473933021 473932990 7.400000e-05 60.2
148 TraesCS3A01G253900 chr1D 100.000 29 0 0 4039 4067 5423589 5423617 3.000000e-03 54.7
149 TraesCS3A01G253900 chr1D 100.000 29 0 0 4039 4067 411567630 411567658 3.000000e-03 54.7
150 TraesCS3A01G253900 chr1D 100.000 29 0 0 4040 4068 415628104 415628076 3.000000e-03 54.7
151 TraesCS3A01G253900 chr7D 94.595 111 4 2 3081 3189 74596199 74596089 3.280000e-38 171.0
152 TraesCS3A01G253900 chr1B 89.147 129 12 2 3063 3189 518807865 518807993 7.100000e-35 159.0
153 TraesCS3A01G253900 chr1B 94.872 78 3 1 4722 4798 357919633 357919556 3.350000e-23 121.0
154 TraesCS3A01G253900 chr1B 97.143 35 1 0 4035 4069 15035111 15035077 7.400000e-05 60.2
155 TraesCS3A01G253900 chr1B 94.737 38 0 2 4031 4067 418228734 418228698 2.660000e-04 58.4
156 TraesCS3A01G253900 chr7B 87.500 112 13 1 201 311 648156497 648156386 2.000000e-25 128.0
157 TraesCS3A01G253900 chr7B 84.483 116 16 2 195 308 740536610 740536725 5.600000e-21 113.0
158 TraesCS3A01G253900 chr7B 89.535 86 9 0 1858 1943 713595252 713595167 7.250000e-20 110.0
159 TraesCS3A01G253900 chr6B 96.000 75 3 0 4716 4790 717901548 717901622 9.310000e-24 122.0
160 TraesCS3A01G253900 chr6B 86.364 110 15 0 201 310 301572373 301572482 3.350000e-23 121.0
161 TraesCS3A01G253900 chr4B 97.183 71 0 1 4722 4790 34029115 34029045 1.200000e-22 119.0
162 TraesCS3A01G253900 chr4B 97.143 35 1 0 4036 4070 604005477 604005443 7.400000e-05 60.2


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 TraesCS3A01G253900 chr3A 475277666 475284500 6834 True 6154.50 9084 100.0000 1 6835 2 chr3A.!!$R3 6834
1 TraesCS3A01G253900 chr3A 749166060 749166720 660 True 1026.00 1026 94.8950 4071 4723 1 chr3A.!!$R2 652
2 TraesCS3A01G253900 chr3B 457570816 457577035 6219 True 1962.75 5022 93.4025 439 6835 4 chr3B.!!$R2 6396
3 TraesCS3A01G253900 chr3D 356588397 356593424 5027 True 1722.00 3594 91.8105 1 6235 4 chr3D.!!$R5 6234
4 TraesCS3A01G253900 chr3D 522550766 522551454 688 False 782.00 782 88.0230 4067 4721 1 chr3D.!!$F7 654
5 TraesCS3A01G253900 chr3D 356579062 356579702 640 True 425.50 662 93.6545 6227 6835 2 chr3D.!!$R4 608
6 TraesCS3A01G253900 chr3D 590127489 590128177 688 True 256.50 289 91.1395 4068 4723 2 chr3D.!!$R6 655
7 TraesCS3A01G253900 chr1A 244989526 244990184 658 False 1166.00 1166 98.6360 4064 4721 1 chr1A.!!$F2 657
8 TraesCS3A01G253900 chr1A 588674948 588675591 643 True 1050.00 1050 95.8840 4067 4721 1 chr1A.!!$R4 654
9 TraesCS3A01G253900 chr1A 427715793 427716454 661 True 1027.00 1027 94.8950 4068 4721 1 chr1A.!!$R2 653
10 TraesCS3A01G253900 chr1A 16407693 16408325 632 True 996.00 996 94.6650 4067 4721 1 chr1A.!!$R1 654
11 TraesCS3A01G253900 chr1A 192012436 192013097 661 False 795.00 795 88.8890 4068 4721 1 chr1A.!!$F1 653
12 TraesCS3A01G253900 chr1A 567981694 567982359 665 False 787.00 787 88.5960 4068 4721 1 chr1A.!!$F6 653
13 TraesCS3A01G253900 chr1A 480600914 480601520 606 False 747.00 747 88.5020 4067 4723 1 chr1A.!!$F5 656
14 TraesCS3A01G253900 chr1A 501019815 501020508 693 False 478.00 479 93.3845 4064 4721 2 chr1A.!!$F7 657
15 TraesCS3A01G253900 chr2A 358944558 358945211 653 True 1164.00 1164 98.7790 4067 4721 1 chr2A.!!$R3 654
16 TraesCS3A01G253900 chr7A 490273864 490274517 653 False 1129.00 1129 97.8590 4069 4721 1 chr7A.!!$F1 652
17 TraesCS3A01G253900 chr7A 285664737 285665380 643 True 878.00 878 91.3430 4067 4721 1 chr7A.!!$R1 654
18 TraesCS3A01G253900 chr4A 636325861 636326512 651 False 1107.00 1107 97.2520 4068 4721 1 chr4A.!!$F4 653
19 TraesCS3A01G253900 chr4A 64139323 64140006 683 True 944.00 944 91.6430 4032 4724 1 chr4A.!!$R1 692
20 TraesCS3A01G253900 chr4A 628154085 628154682 597 False 933.00 933 95.1670 4137 4723 1 chr4A.!!$F3 586
21 TraesCS3A01G253900 chr4A 488031977 488032619 642 False 917.00 917 92.2730 4067 4721 1 chr4A.!!$F2 654
22 TraesCS3A01G253900 chr5A 348188814 348189482 668 False 1048.00 1048 95.2310 4068 4724 1 chr5A.!!$F2 656
23 TraesCS3A01G253900 chr5A 480096756 480097442 686 True 1035.00 1035 94.0750 4042 4721 1 chr5A.!!$R1 679
24 TraesCS3A01G253900 chr5A 706067793 706068457 664 False 1029.00 1029 94.9030 4068 4721 1 chr5A.!!$F4 653
25 TraesCS3A01G253900 chr5A 178602143 178602805 662 False 974.00 974 93.4130 4069 4723 1 chr5A.!!$F1 654
26 TraesCS3A01G253900 chr5A 419679001 419679643 642 False 961.00 961 93.4650 4064 4718 1 chr5A.!!$F3 654
27 TraesCS3A01G253900 chr5A 698130034 698130683 649 True 915.00 915 91.9940 4067 4724 1 chr5A.!!$R3 657
28 TraesCS3A01G253900 chr5A 675628308 675628950 642 True 907.00 907 92.0660 4071 4727 1 chr5A.!!$R2 656
29 TraesCS3A01G253900 chr6A 555437517 555438180 663 True 990.00 990 93.8530 4068 4721 1 chr6A.!!$R3 653
30 TraesCS3A01G253900 chr6A 68792248 68792907 659 True 987.00 987 93.8350 4067 4721 1 chr6A.!!$R1 654
31 TraesCS3A01G253900 chr6A 554107150 554107802 652 False 941.00 941 92.7300 4064 4722 1 chr6A.!!$F2 658
32 TraesCS3A01G253900 chr6A 562592319 562593000 681 False 929.00 929 91.9470 4067 4721 1 chr6A.!!$F3 654
33 TraesCS3A01G253900 chr6A 108949435 108950096 661 False 839.00 839 90.0290 4068 4721 1 chr6A.!!$F1 653
34 TraesCS3A01G253900 chr4D 81172333 81172903 570 True 604.00 604 86.7600 4182 4721 1 chr4D.!!$R1 539
35 TraesCS3A01G253900 chr4D 102162107 102162796 689 True 451.00 473 92.1280 4068 4724 2 chr4D.!!$R8 656
36 TraesCS3A01G253900 chr4D 102162109 102162796 687 False 255.50 268 90.5195 4067 4721 2 chr4D.!!$F8 654
37 TraesCS3A01G253900 chr6D 55068938 55069590 652 True 268.50 318 90.5940 4055 4730 2 chr6D.!!$R6 675
38 TraesCS3A01G253900 chr5D 330829803 330830448 645 True 221.50 265 89.1690 4067 4722 2 chr5D.!!$R5 655
39 TraesCS3A01G253900 chr5D 298964949 298965615 666 True 204.50 209 92.3580 4068 4726 2 chr5D.!!$R4 658
40 TraesCS3A01G253900 chr1D 459409431 459410224 793 True 217.50 226 89.7550 4059 4728 2 chr1D.!!$R8 669

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
760 833 0.183492 TACATACTAGGCCCGTCCGT 59.817 55.000 0.00 0.73 40.77 4.69 F
1566 1663 0.035056 ATGCAGTACTTGGGCACTCC 60.035 55.000 8.40 0.00 40.83 3.85 F
1758 1856 0.242825 CTTCGCTTACCTCGGACACA 59.757 55.000 0.00 0.00 0.00 3.72 F
3049 3148 0.614134 AGGTCGTGGAACTACTCCCC 60.614 60.000 0.00 0.00 44.69 4.81 F
3620 3722 1.378646 ATCGCTGGTCCTCGACAGA 60.379 57.895 8.58 0.00 37.55 3.41 F
3652 3754 3.058160 GCTGAAGTGGCGCCATGT 61.058 61.111 35.23 23.84 0.00 3.21 F
4793 5500 1.273838 TGGGACAGAGGGAGTAGCAAT 60.274 52.381 0.00 0.00 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1789 3.058224 AGTGCAGGAAACAATTCGCTTAC 60.058 43.478 0.0 0.0 36.36 2.34 R
3422 3522 3.649843 TGTACTCCCTCCGTTCCATAAT 58.350 45.455 0.0 0.0 0.00 1.28 R
3657 3759 0.783850 ACATGGGGCTACAAAGGGTT 59.216 50.000 0.0 0.0 0.00 4.11 R
4772 5479 0.339859 TGCTACTCCCTCTGTCCCAT 59.660 55.000 0.0 0.0 0.00 4.00 R
4776 5483 3.895232 TTGATTGCTACTCCCTCTGTC 57.105 47.619 0.0 0.0 0.00 3.51 R
4837 5544 3.953612 TGCATCCAAGAATATCCAACCAC 59.046 43.478 0.0 0.0 0.00 4.16 R
6711 7632 0.322816 CAAGGTGTGGGTCATCAGGG 60.323 60.000 0.0 0.0 0.00 4.45 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
166 168 5.188434 TGCTAGCATTATTATGGGCATCTC 58.812 41.667 14.93 0.00 32.15 2.75
197 199 7.642669 CATCATCTACCGTCATGCTTAAAAAT 58.357 34.615 0.00 0.00 0.00 1.82
272 274 9.444600 AACGTATTTTAGTGTTGAATACATCCT 57.555 29.630 0.00 0.00 39.39 3.24
285 287 5.122239 TGAATACATCCTTTTGAGCGACAAG 59.878 40.000 0.00 0.00 39.77 3.16
291 293 5.607119 TCCTTTTGAGCGACAAGTAATTC 57.393 39.130 0.00 0.00 39.77 2.17
293 295 4.394795 CTTTTGAGCGACAAGTAATTCCG 58.605 43.478 0.00 0.00 39.77 4.30
301 303 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
323 325 4.843220 GAATACCTTCCATGGCATTCTG 57.157 45.455 6.96 0.00 37.07 3.02
368 370 0.454196 ATCGCATTTACCCCAAACGC 59.546 50.000 0.00 0.00 32.03 4.84
371 373 1.536943 GCATTTACCCCAAACGCCCA 61.537 55.000 0.00 0.00 29.04 5.36
374 376 0.537828 TTTACCCCAAACGCCCAGTC 60.538 55.000 0.00 0.00 0.00 3.51
403 405 6.677781 TGCTACAAATAACACCAGAATAGC 57.322 37.500 0.00 0.00 34.46 2.97
404 406 6.176896 TGCTACAAATAACACCAGAATAGCA 58.823 36.000 0.00 0.00 39.98 3.49
436 438 2.605366 GACTGCGAGCTTAATCCTTGAC 59.395 50.000 0.00 0.00 0.00 3.18
483 485 6.038603 TCCTATATGCAATTGCTTCAACAGAC 59.961 38.462 29.37 0.00 42.66 3.51
495 497 1.012086 CAACAGACCAGCGATCCATG 58.988 55.000 0.00 0.00 0.00 3.66
504 506 1.135721 CAGCGATCCATGACTCTGTCA 59.864 52.381 2.77 2.77 46.90 3.58
506 508 2.159128 AGCGATCCATGACTCTGTCAAG 60.159 50.000 4.46 0.50 45.96 3.02
507 509 2.417924 GCGATCCATGACTCTGTCAAGT 60.418 50.000 4.46 0.00 45.96 3.16
508 510 3.185330 CGATCCATGACTCTGTCAAGTG 58.815 50.000 4.46 0.15 45.96 3.16
509 511 3.367806 CGATCCATGACTCTGTCAAGTGT 60.368 47.826 4.46 0.00 45.96 3.55
510 512 3.667497 TCCATGACTCTGTCAAGTGTC 57.333 47.619 4.46 0.00 45.96 3.67
738 811 1.526575 CCGTGAAATTGCAGCCCAGT 61.527 55.000 0.00 0.00 0.00 4.00
760 833 0.183492 TACATACTAGGCCCGTCCGT 59.817 55.000 0.00 0.73 40.77 4.69
761 834 0.183492 ACATACTAGGCCCGTCCGTA 59.817 55.000 0.00 0.00 40.77 4.02
764 837 0.748005 TACTAGGCCCGTCCGTACAC 60.748 60.000 0.00 0.00 40.77 2.90
769 842 2.510691 CCCGTCCGTACACATGCC 60.511 66.667 0.00 0.00 0.00 4.40
779 852 3.124636 CCGTACACATGCCTGTTCTTTAC 59.875 47.826 0.00 0.00 31.62 2.01
784 857 5.971763 ACACATGCCTGTTCTTTACAAAAA 58.028 33.333 0.00 0.00 36.02 1.94
890 964 2.049156 TTCTCGTGCGGCAGTCTG 60.049 61.111 1.18 0.00 0.00 3.51
891 965 2.561037 TTCTCGTGCGGCAGTCTGA 61.561 57.895 1.18 0.00 0.00 3.27
892 966 2.749110 TTCTCGTGCGGCAGTCTGAC 62.749 60.000 1.18 0.00 0.00 3.51
1227 1311 8.665685 AGCGATTAGGTGAGTTTTAATTAGTTG 58.334 33.333 0.00 0.00 0.00 3.16
1233 1317 7.228590 AGGTGAGTTTTAATTAGTTGCTGGTA 58.771 34.615 0.00 0.00 0.00 3.25
1246 1330 5.411781 AGTTGCTGGTAGAAGTCTTAATCG 58.588 41.667 0.00 0.00 0.00 3.34
1375 1470 9.939802 AATACGAGTACCTCTTAAATTTTCACT 57.060 29.630 0.00 0.00 0.00 3.41
1424 1519 4.179926 TGCTCCATATACTTCTGCGATC 57.820 45.455 0.00 0.00 0.00 3.69
1476 1571 5.001232 TGAATTGTCTGGTTTAGCAGTACC 58.999 41.667 8.61 0.00 34.93 3.34
1483 1578 2.299582 TGGTTTAGCAGTACCAGCGTAA 59.700 45.455 2.63 0.00 39.44 3.18
1490 1585 1.917955 CAGTACCAGCGTAATGACACG 59.082 52.381 0.00 0.00 41.94 4.49
1566 1663 0.035056 ATGCAGTACTTGGGCACTCC 60.035 55.000 8.40 0.00 40.83 3.85
1758 1856 0.242825 CTTCGCTTACCTCGGACACA 59.757 55.000 0.00 0.00 0.00 3.72
1779 1877 4.715297 ACACCGGTCTTAGAAGATACCAAT 59.285 41.667 2.59 0.00 37.39 3.16
1894 1992 3.724374 TCTCAAACGTTAAGTGTGGAGG 58.276 45.455 0.00 0.00 38.62 4.30
2066 2164 9.611284 TTCTGTGATAATTCAGAAATTTGTTCG 57.389 29.630 0.00 0.00 44.29 3.95
2166 2264 6.349860 GGGAAATCAGTTATGTTGGTTACCAC 60.350 42.308 2.39 0.00 30.78 4.16
2188 2286 9.905713 ACCACTTAACACAATCATATATCTGTT 57.094 29.630 0.00 0.00 0.00 3.16
2280 2378 3.668447 CTTTACATCTGATCATCCCCCG 58.332 50.000 0.00 0.00 0.00 5.73
2281 2379 2.694616 TACATCTGATCATCCCCCGA 57.305 50.000 0.00 0.00 0.00 5.14
2302 2400 7.364200 CCCGAACACATTGTAACAATTTTCTA 58.636 34.615 0.00 0.00 0.00 2.10
2303 2401 7.863375 CCCGAACACATTGTAACAATTTTCTAA 59.137 33.333 0.00 0.00 0.00 2.10
2319 2417 9.981114 CAATTTTCTAACCCTTAAATGAACACT 57.019 29.630 0.00 0.00 0.00 3.55
2511 2609 4.320870 GAGTCGGGATTTTTGTCCTGTTA 58.679 43.478 2.00 0.00 43.76 2.41
2720 2818 4.992951 GGTAGGTCTTGTTGTACAATTCGT 59.007 41.667 12.26 5.50 37.48 3.85
2810 2908 7.827729 GGTAATGTGGTTCTTACTTTATCCTGT 59.172 37.037 0.00 0.00 0.00 4.00
2871 2969 2.403252 AGTGTGATCGGGTGGAAATC 57.597 50.000 0.00 0.00 0.00 2.17
2920 3018 2.131972 TCGTGGTGAACTCATGTTTCG 58.868 47.619 0.00 0.00 36.39 3.46
2924 3022 2.104111 TGGTGAACTCATGTTTCGGAGT 59.896 45.455 0.00 0.00 45.85 3.85
2992 3091 1.820519 TGTGGAGCCATTTGCAGAATC 59.179 47.619 0.00 0.00 44.83 2.52
3002 3101 5.346822 GCCATTTGCAGAATCTAAGTTGTTG 59.653 40.000 0.00 0.00 40.77 3.33
3003 3102 6.449698 CCATTTGCAGAATCTAAGTTGTTGT 58.550 36.000 0.00 0.00 0.00 3.32
3004 3103 6.925165 CCATTTGCAGAATCTAAGTTGTTGTT 59.075 34.615 0.00 0.00 0.00 2.83
3049 3148 0.614134 AGGTCGTGGAACTACTCCCC 60.614 60.000 0.00 0.00 44.69 4.81
3050 3149 1.509923 GTCGTGGAACTACTCCCCG 59.490 63.158 0.00 0.00 45.62 5.73
3192 3291 9.884814 ACTAAAACATGTCTATATACTCCCTCT 57.115 33.333 0.00 0.00 0.00 3.69
3210 3309 5.843969 TCCCTCTGTTCCATAATATAGTGCA 59.156 40.000 0.00 0.00 0.00 4.57
3522 3622 6.780198 TTACCCCTGCTTTCCTATCAATAT 57.220 37.500 0.00 0.00 0.00 1.28
3620 3722 1.378646 ATCGCTGGTCCTCGACAGA 60.379 57.895 8.58 0.00 37.55 3.41
3652 3754 3.058160 GCTGAAGTGGCGCCATGT 61.058 61.111 35.23 23.84 0.00 3.21
3657 3759 3.848301 AAGTGGCGCCATGTCTGCA 62.848 57.895 35.23 2.76 0.00 4.41
3723 3825 5.564259 GCACAAACATGAGAAATGAAGCTCT 60.564 40.000 0.00 0.00 32.44 4.09
3743 3845 7.902087 AGCTCTGATACTAGATTTTATGGGAC 58.098 38.462 0.00 0.00 0.00 4.46
3839 3941 7.201644 CCATATGAAAGGCATGACCGTATAATC 60.202 40.741 3.65 0.00 46.52 1.75
3883 3985 7.125356 ACAAGGAGGGTATATACGAAAAGAACT 59.875 37.037 6.79 0.00 0.00 3.01
3921 4023 5.155905 GAGAGGGGGAAACAGGAGATATAA 58.844 45.833 0.00 0.00 0.00 0.98
3953 4055 8.686334 ACTGTATAAGGTTTATTGATTGCTTGG 58.314 33.333 0.00 0.00 0.00 3.61
3975 4077 5.045213 TGGTTACAATGGACATGATGGTAGT 60.045 40.000 0.00 0.00 0.00 2.73
3981 4085 4.487714 TGGACATGATGGTAGTCTTTCC 57.512 45.455 0.00 0.00 32.98 3.13
3988 4092 7.390027 ACATGATGGTAGTCTTTCCTATATGC 58.610 38.462 0.00 0.00 0.00 3.14
3991 4095 4.476297 TGGTAGTCTTTCCTATATGCGGA 58.524 43.478 0.00 0.00 0.00 5.54
4731 5438 9.434420 AATATGCACTTCTCTCAATATAAGAGC 57.566 33.333 9.27 3.95 40.11 4.09
4732 5439 5.284864 TGCACTTCTCTCAATATAAGAGCG 58.715 41.667 9.27 6.47 40.11 5.03
4733 5440 5.163509 TGCACTTCTCTCAATATAAGAGCGT 60.164 40.000 9.27 6.93 40.11 5.07
4734 5441 5.751028 GCACTTCTCTCAATATAAGAGCGTT 59.249 40.000 9.27 0.00 40.11 4.84
4735 5442 6.256757 GCACTTCTCTCAATATAAGAGCGTTT 59.743 38.462 9.27 0.00 40.11 3.60
4736 5443 7.201565 GCACTTCTCTCAATATAAGAGCGTTTT 60.202 37.037 9.27 0.00 40.11 2.43
4737 5444 8.660373 CACTTCTCTCAATATAAGAGCGTTTTT 58.340 33.333 9.27 0.00 40.11 1.94
4738 5445 8.660373 ACTTCTCTCAATATAAGAGCGTTTTTG 58.340 33.333 9.27 0.00 40.11 2.44
4739 5446 8.771920 TTCTCTCAATATAAGAGCGTTTTTGA 57.228 30.769 9.27 0.00 40.11 2.69
4740 5447 8.186178 TCTCTCAATATAAGAGCGTTTTTGAC 57.814 34.615 9.27 0.00 40.11 3.18
4741 5448 7.817478 TCTCTCAATATAAGAGCGTTTTTGACA 59.183 33.333 9.27 0.00 40.11 3.58
4742 5449 7.739295 TCTCAATATAAGAGCGTTTTTGACAC 58.261 34.615 1.23 0.00 33.15 3.67
4743 5450 7.602644 TCTCAATATAAGAGCGTTTTTGACACT 59.397 33.333 1.23 0.00 33.15 3.55
4744 5451 8.766000 TCAATATAAGAGCGTTTTTGACACTA 57.234 30.769 0.00 0.00 0.00 2.74
4745 5452 8.653338 TCAATATAAGAGCGTTTTTGACACTAC 58.347 33.333 0.00 0.00 0.00 2.73
4746 5453 8.440059 CAATATAAGAGCGTTTTTGACACTACA 58.560 33.333 0.00 0.00 0.00 2.74
4747 5454 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
4748 5455 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
4749 5456 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
4750 5457 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
4751 5458 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
4793 5500 1.273838 TGGGACAGAGGGAGTAGCAAT 60.274 52.381 0.00 0.00 0.00 3.56
4794 5501 1.414550 GGGACAGAGGGAGTAGCAATC 59.585 57.143 0.00 0.00 0.00 2.67
4795 5502 2.111384 GGACAGAGGGAGTAGCAATCA 58.889 52.381 0.00 0.00 0.00 2.57
4796 5503 2.501723 GGACAGAGGGAGTAGCAATCAA 59.498 50.000 0.00 0.00 0.00 2.57
4803 5510 6.994496 CAGAGGGAGTAGCAATCAATTAATCA 59.006 38.462 0.00 0.00 0.00 2.57
4858 5565 3.953612 TGTGGTTGGATATTCTTGGATGC 59.046 43.478 0.00 0.00 0.00 3.91
4915 5624 6.575162 AATAAAGTAGCAACTGAGTTTGGG 57.425 37.500 0.00 0.00 35.62 4.12
4916 5625 3.857157 AAGTAGCAACTGAGTTTGGGA 57.143 42.857 0.00 0.00 35.62 4.37
4917 5626 3.857157 AGTAGCAACTGAGTTTGGGAA 57.143 42.857 0.00 0.00 33.57 3.97
4918 5627 3.477530 AGTAGCAACTGAGTTTGGGAAC 58.522 45.455 0.00 0.00 33.57 3.62
5161 5874 8.015658 GTCCTGATATTTCCGTAAACAATATGC 58.984 37.037 0.00 0.00 0.00 3.14
5244 5957 3.376859 ACACGTCACACAACACATCATTT 59.623 39.130 0.00 0.00 0.00 2.32
5420 6140 1.943340 GCTTAGTAATGCCTGGCTGTC 59.057 52.381 21.03 7.81 0.00 3.51
5540 6263 4.811908 TGTTCATTCCAGCAAATCATGTG 58.188 39.130 0.00 0.00 0.00 3.21
5609 6332 3.782523 TCTTAGCATGTCTCATTTCCCCT 59.217 43.478 0.00 0.00 0.00 4.79
5842 6569 5.071519 ACATTCCAGATCCTTGACTCATAGG 59.928 44.000 0.00 0.00 0.00 2.57
5843 6570 2.968574 TCCAGATCCTTGACTCATAGGC 59.031 50.000 0.00 0.00 0.00 3.93
5844 6571 2.971330 CCAGATCCTTGACTCATAGGCT 59.029 50.000 0.00 0.00 0.00 4.58
5845 6572 3.006752 CCAGATCCTTGACTCATAGGCTC 59.993 52.174 0.00 0.00 0.00 4.70
5846 6573 3.640498 CAGATCCTTGACTCATAGGCTCA 59.360 47.826 0.00 0.00 30.78 4.26
5847 6574 4.283978 CAGATCCTTGACTCATAGGCTCAT 59.716 45.833 0.00 0.00 30.78 2.90
5848 6575 5.479724 CAGATCCTTGACTCATAGGCTCATA 59.520 44.000 0.00 0.00 30.78 2.15
5849 6576 5.716228 AGATCCTTGACTCATAGGCTCATAG 59.284 44.000 0.00 0.00 30.78 2.23
5874 6601 7.040478 AGCACAGCAATTAAAGTAGTCAATGAA 60.040 33.333 0.00 0.00 0.00 2.57
5988 6715 5.311265 TGATGAACTGCAGAGAAATTGTCT 58.689 37.500 23.35 0.00 40.25 3.41
6022 6749 7.865385 CGGTCTGGAATTGAATAAACTGAAAAA 59.135 33.333 0.00 0.00 0.00 1.94
6134 6861 8.739972 GGGTATCACAAGATCAACTAATTTTGT 58.260 33.333 0.00 0.00 35.12 2.83
6332 7065 6.010294 AGCATGACAATTTCTTCAAGTGAG 57.990 37.500 0.00 0.00 33.92 3.51
6335 7068 5.173774 TGACAATTTCTTCAAGTGAGCAC 57.826 39.130 0.00 0.00 33.92 4.40
6374 7107 5.957798 TCCTTGATTTGCTAGAAATTGCTG 58.042 37.500 0.00 0.00 0.00 4.41
6393 7128 3.550842 GCTGTGTTTCCGAAGAAATTGCT 60.551 43.478 0.00 0.00 43.67 3.91
6447 7204 2.267426 TCGCAAATGTCATGTCTACCG 58.733 47.619 0.00 0.00 0.00 4.02
6461 7218 1.612950 TCTACCGGTGAACGTTTGCTA 59.387 47.619 19.93 0.00 42.24 3.49
6481 7238 4.156739 GCTAGCTATTGCAGTCCTTGTTTT 59.843 41.667 7.70 0.00 42.74 2.43
6482 7239 4.773323 AGCTATTGCAGTCCTTGTTTTC 57.227 40.909 1.12 0.00 42.74 2.29
6492 7249 4.093998 CAGTCCTTGTTTTCTCATCATCGG 59.906 45.833 0.00 0.00 0.00 4.18
6512 7269 2.228822 GGTAAGCCAACACAATGGAGTG 59.771 50.000 0.00 0.00 43.54 3.51
6704 7625 5.066505 CACCTTCTATGTTTCCAGTTATGCC 59.933 44.000 0.00 0.00 0.00 4.40
6705 7626 4.580580 CCTTCTATGTTTCCAGTTATGCCC 59.419 45.833 0.00 0.00 0.00 5.36
6706 7627 4.164843 TCTATGTTTCCAGTTATGCCCC 57.835 45.455 0.00 0.00 0.00 5.80
6707 7628 2.159179 ATGTTTCCAGTTATGCCCCC 57.841 50.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 3.945285 CAGCCTTCGGGTTATGTACAAAT 59.055 43.478 0.00 0.00 37.45 2.32
90 92 2.564721 GCTTTTGCAGCCTTCGGGT 61.565 57.895 0.00 0.00 43.65 5.28
151 153 4.738685 TGCAATGGAGATGCCCATAATAA 58.261 39.130 0.00 0.00 45.69 1.40
152 154 4.385478 TGCAATGGAGATGCCCATAATA 57.615 40.909 0.00 0.00 45.69 0.98
166 168 2.837498 TGACGGTAGATGATGCAATGG 58.163 47.619 0.00 0.00 0.00 3.16
205 207 4.802039 GCGACAACTAATTCCATACGAAGA 59.198 41.667 0.00 0.00 32.78 2.87
211 213 6.038161 CCATTTCAGCGACAACTAATTCCATA 59.962 38.462 0.00 0.00 0.00 2.74
212 214 5.163622 CCATTTCAGCGACAACTAATTCCAT 60.164 40.000 0.00 0.00 0.00 3.41
213 215 4.155826 CCATTTCAGCGACAACTAATTCCA 59.844 41.667 0.00 0.00 0.00 3.53
255 257 6.092122 CGCTCAAAAGGATGTATTCAACACTA 59.908 38.462 0.00 0.00 42.09 2.74
258 260 5.000591 TCGCTCAAAAGGATGTATTCAACA 58.999 37.500 0.00 0.00 43.86 3.33
262 264 5.122396 ACTTGTCGCTCAAAAGGATGTATTC 59.878 40.000 0.00 0.00 35.48 1.75
271 273 4.394795 CGGAATTACTTGTCGCTCAAAAG 58.605 43.478 0.00 0.00 35.48 2.27
272 274 3.187637 CCGGAATTACTTGTCGCTCAAAA 59.812 43.478 0.00 0.00 35.48 2.44
285 287 0.826062 TTCCCTCCGTCCGGAATTAC 59.174 55.000 5.23 0.00 44.66 1.89
291 293 1.047034 AAGGTATTCCCTCCGTCCGG 61.047 60.000 0.00 0.00 45.47 5.14
335 337 7.148507 GGGTAAATGCGATGATCATTAGAGAAG 60.149 40.741 10.14 0.00 34.09 2.85
355 357 0.537828 GACTGGGCGTTTGGGGTAAA 60.538 55.000 0.00 0.00 0.00 2.01
371 373 5.186198 GTGTTATTTGTAGCATCCAGGACT 58.814 41.667 0.00 0.00 0.00 3.85
374 376 4.269183 TGGTGTTATTTGTAGCATCCAGG 58.731 43.478 0.00 0.00 0.00 4.45
403 405 2.030213 GCTCGCAGTCTATTGCTTCTTG 59.970 50.000 0.00 0.00 41.90 3.02
404 406 2.093764 AGCTCGCAGTCTATTGCTTCTT 60.094 45.455 0.00 0.00 41.90 2.52
436 438 1.766143 GCTTTATGCCTCGCTCACGG 61.766 60.000 0.00 0.00 36.25 4.94
483 485 0.463204 ACAGAGTCATGGATCGCTGG 59.537 55.000 16.05 3.21 36.19 4.85
495 497 5.297547 TGGTTATTGACACTTGACAGAGTC 58.702 41.667 0.00 0.00 40.17 3.36
504 506 4.755123 CCTTCGTTCTGGTTATTGACACTT 59.245 41.667 0.00 0.00 0.00 3.16
506 508 3.120304 GCCTTCGTTCTGGTTATTGACAC 60.120 47.826 0.00 0.00 0.00 3.67
507 509 3.071479 GCCTTCGTTCTGGTTATTGACA 58.929 45.455 0.00 0.00 0.00 3.58
508 510 2.418976 GGCCTTCGTTCTGGTTATTGAC 59.581 50.000 0.00 0.00 0.00 3.18
509 511 2.617021 GGGCCTTCGTTCTGGTTATTGA 60.617 50.000 0.84 0.00 0.00 2.57
510 512 1.743394 GGGCCTTCGTTCTGGTTATTG 59.257 52.381 0.84 0.00 0.00 1.90
511 513 1.340697 GGGGCCTTCGTTCTGGTTATT 60.341 52.381 0.84 0.00 0.00 1.40
571 580 2.030451 GCAAAGGAAGAGCTTTCAGTGG 60.030 50.000 9.75 0.00 0.00 4.00
572 581 2.883386 AGCAAAGGAAGAGCTTTCAGTG 59.117 45.455 9.75 0.00 34.37 3.66
573 582 3.145286 GAGCAAAGGAAGAGCTTTCAGT 58.855 45.455 9.75 0.00 39.02 3.41
574 583 2.487372 GGAGCAAAGGAAGAGCTTTCAG 59.513 50.000 9.75 0.90 39.02 3.02
575 584 2.158623 TGGAGCAAAGGAAGAGCTTTCA 60.159 45.455 9.75 0.00 39.02 2.69
576 585 2.227626 GTGGAGCAAAGGAAGAGCTTTC 59.772 50.000 0.00 0.00 39.02 2.62
577 586 2.158549 AGTGGAGCAAAGGAAGAGCTTT 60.159 45.455 0.00 0.00 39.02 3.51
678 688 2.294233 CCCATTGTATTTCCATGAGCGG 59.706 50.000 0.00 0.00 0.00 5.52
738 811 2.034124 GGACGGGCCTAGTATGTACAA 58.966 52.381 0.84 0.00 0.00 2.41
760 833 6.701145 TTTTGTAAAGAACAGGCATGTGTA 57.299 33.333 4.03 0.00 40.39 2.90
761 834 5.590530 TTTTGTAAAGAACAGGCATGTGT 57.409 34.783 4.03 0.00 40.39 3.72
843 917 0.251787 GGGGCCCAGATGTCACTTTT 60.252 55.000 26.86 0.00 0.00 2.27
844 918 1.384191 GGGGCCCAGATGTCACTTT 59.616 57.895 26.86 0.00 0.00 2.66
845 919 2.971598 CGGGGCCCAGATGTCACTT 61.972 63.158 26.86 0.00 0.00 3.16
846 920 3.402681 CGGGGCCCAGATGTCACT 61.403 66.667 26.86 0.00 0.00 3.41
847 921 3.399181 TCGGGGCCCAGATGTCAC 61.399 66.667 26.86 1.48 0.00 3.67
890 964 2.280592 GGTGTGGTGGTGGTCGTC 60.281 66.667 0.00 0.00 0.00 4.20
891 965 2.199613 TTTGGTGTGGTGGTGGTCGT 62.200 55.000 0.00 0.00 0.00 4.34
892 966 1.452289 TTTGGTGTGGTGGTGGTCG 60.452 57.895 0.00 0.00 0.00 4.79
896 970 1.404851 GGTTTGTTTGGTGTGGTGGTG 60.405 52.381 0.00 0.00 0.00 4.17
1227 1311 3.124560 GGCGATTAAGACTTCTACCAGC 58.875 50.000 0.00 0.00 0.00 4.85
1233 1317 3.243771 CCATACGGGCGATTAAGACTTCT 60.244 47.826 0.00 0.00 0.00 2.85
1243 1327 2.494471 TCGAATTATCCATACGGGCGAT 59.506 45.455 0.00 0.00 36.21 4.58
1246 1330 4.083484 CCTTTTCGAATTATCCATACGGGC 60.083 45.833 0.00 0.00 36.21 6.13
1424 1519 5.840243 TTTTCATGTTCATAGCATCCAGG 57.160 39.130 0.00 0.00 0.00 4.45
1476 1571 0.672401 AACCCCGTGTCATTACGCTG 60.672 55.000 0.00 0.00 42.44 5.18
1483 1578 2.695666 CTGAGAGATAACCCCGTGTCAT 59.304 50.000 0.00 0.00 0.00 3.06
1490 1585 1.210478 TGCAAGCTGAGAGATAACCCC 59.790 52.381 0.00 0.00 0.00 4.95
1599 1697 9.646522 AAAGGGCTATGTGTATTCAATAAAGAT 57.353 29.630 0.00 0.00 0.00 2.40
1691 1789 3.058224 AGTGCAGGAAACAATTCGCTTAC 60.058 43.478 0.00 0.00 36.36 2.34
1743 1841 4.592426 GGTGTGTCCGAGGTAAGC 57.408 61.111 0.00 0.00 0.00 3.09
1758 1856 6.134754 ACTATTGGTATCTTCTAAGACCGGT 58.865 40.000 6.92 6.92 37.98 5.28
2066 2164 6.876257 ACTATCAGAGTTGTTGAGGATGAAAC 59.124 38.462 0.00 0.00 33.13 2.78
2280 2378 8.974408 GGGTTAGAAAATTGTTACAATGTGTTC 58.026 33.333 11.60 14.12 0.00 3.18
2281 2379 8.700973 AGGGTTAGAAAATTGTTACAATGTGTT 58.299 29.630 11.60 6.50 0.00 3.32
2302 2400 4.832266 TGCATCAGTGTTCATTTAAGGGTT 59.168 37.500 0.00 0.00 0.00 4.11
2303 2401 4.218417 GTGCATCAGTGTTCATTTAAGGGT 59.782 41.667 0.00 0.00 0.00 4.34
2319 2417 4.940654 TCCAAGAACGAATTATGTGCATCA 59.059 37.500 0.00 0.00 0.00 3.07
2511 2609 6.151817 GCAAAGGTCTCCAGACTTTATCAATT 59.848 38.462 4.64 0.00 42.44 2.32
2810 2908 6.661805 GGGTAACTTCAGGATCCAAATAACAA 59.338 38.462 15.82 0.00 0.00 2.83
2929 3027 7.865385 GCAAAATACAAACTGGACTGATAAACA 59.135 33.333 0.00 0.00 0.00 2.83
2950 3048 8.666573 CCACATTATCATTAAGCAATTGCAAAA 58.333 29.630 30.89 23.14 45.16 2.44
3002 3101 5.492855 TGGGCCTACCATGTATGTATAAC 57.507 43.478 4.53 0.00 46.80 1.89
3356 3456 5.930837 TGACCAAGTTTGTGGAGAAAAAT 57.069 34.783 0.00 0.00 41.65 1.82
3422 3522 3.649843 TGTACTCCCTCCGTTCCATAAT 58.350 45.455 0.00 0.00 0.00 1.28
3657 3759 0.783850 ACATGGGGCTACAAAGGGTT 59.216 50.000 0.00 0.00 0.00 4.11
3690 3792 3.054878 CTCATGTTTGTGCAAGCTTTCC 58.945 45.455 0.00 0.00 0.00 3.13
3723 3825 9.613428 CAAGTTGTCCCATAAAATCTAGTATCA 57.387 33.333 0.00 0.00 0.00 2.15
3820 3922 5.036117 ACAGATTATACGGTCATGCCTTT 57.964 39.130 4.92 0.00 34.25 3.11
3839 3941 7.308589 CCTCCTTGTACCTTTTGTGATTAACAG 60.309 40.741 0.00 0.00 40.74 3.16
3883 3985 3.895656 CCCCTCTCCTTCGTATATCACAA 59.104 47.826 0.00 0.00 0.00 3.33
3894 3996 0.621082 CCTGTTTCCCCCTCTCCTTC 59.379 60.000 0.00 0.00 0.00 3.46
3921 4023 9.990868 AATCAATAAACCTTATACAGTCCCTTT 57.009 29.630 0.00 0.00 0.00 3.11
3953 4055 6.349300 AGACTACCATCATGTCCATTGTAAC 58.651 40.000 0.00 0.00 0.00 2.50
3975 4077 2.897969 GGAGGTCCGCATATAGGAAAGA 59.102 50.000 1.11 0.00 39.84 2.52
3991 4095 5.193728 TCTTAAATATTGCTTGGGAGGAGGT 59.806 40.000 0.00 0.00 0.00 3.85
4026 4130 6.768381 CAGAGGGAGTATTTGTTAGGGATTTC 59.232 42.308 0.00 0.00 0.00 2.17
4728 5435 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
4755 5462 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
4756 5463 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
4757 5464 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
4758 5465 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
4759 5466 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
4760 5467 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
4761 5468 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
4762 5469 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
4772 5479 0.339859 TGCTACTCCCTCTGTCCCAT 59.660 55.000 0.00 0.00 0.00 4.00
4776 5483 3.895232 TTGATTGCTACTCCCTCTGTC 57.105 47.619 0.00 0.00 0.00 3.51
4837 5544 3.953612 TGCATCCAAGAATATCCAACCAC 59.046 43.478 0.00 0.00 0.00 4.16
4879 5586 9.683069 GTTGCTACTTTATTATTTGCATGCTAT 57.317 29.630 20.33 14.38 0.00 2.97
4891 5598 7.455058 TCCCAAACTCAGTTGCTACTTTATTA 58.545 34.615 0.00 0.00 30.26 0.98
4894 5601 5.298989 TCCCAAACTCAGTTGCTACTTTA 57.701 39.130 0.00 0.00 30.26 1.85
5161 5874 8.463930 AACCATGTAATATATTGGGTTGTCAG 57.536 34.615 17.54 1.12 35.93 3.51
5201 5914 4.263905 TGTGCCTAAAATCCTCAACCAGAT 60.264 41.667 0.00 0.00 0.00 2.90
5420 6140 5.343249 GCAATCCTTTAATAACAGGCACAG 58.657 41.667 0.00 0.00 0.00 3.66
5540 6263 5.238006 AGAACGTCAGCTAAGATGTAGTC 57.762 43.478 0.00 0.00 36.78 2.59
5842 6569 5.240713 ACTTTAATTGCTGTGCTATGAGC 57.759 39.130 0.00 0.00 42.82 4.26
5843 6570 7.278646 TGACTACTTTAATTGCTGTGCTATGAG 59.721 37.037 0.00 0.00 0.00 2.90
5844 6571 7.102993 TGACTACTTTAATTGCTGTGCTATGA 58.897 34.615 0.00 0.00 0.00 2.15
5845 6572 7.307493 TGACTACTTTAATTGCTGTGCTATG 57.693 36.000 0.00 0.00 0.00 2.23
5846 6573 7.921786 TTGACTACTTTAATTGCTGTGCTAT 57.078 32.000 0.00 0.00 0.00 2.97
5847 6574 7.606073 TCATTGACTACTTTAATTGCTGTGCTA 59.394 33.333 0.00 0.00 0.00 3.49
5848 6575 6.430925 TCATTGACTACTTTAATTGCTGTGCT 59.569 34.615 0.00 0.00 0.00 4.40
5849 6576 6.611381 TCATTGACTACTTTAATTGCTGTGC 58.389 36.000 0.00 0.00 0.00 4.57
5874 6601 7.618019 TCAATTTACAGTGAGGAGGCTATAT 57.382 36.000 0.00 0.00 0.00 0.86
5988 6715 4.014569 TCAATTCCAGACCGACAAATCA 57.985 40.909 0.00 0.00 0.00 2.57
6022 6749 3.494332 AGCCAACAGATCAGCTCTTTTT 58.506 40.909 0.00 0.00 29.16 1.94
6025 6752 2.399916 GAGCCAACAGATCAGCTCTT 57.600 50.000 11.92 0.00 46.50 2.85
6039 6766 3.797039 CATCGAACATCCTAAAGAGCCA 58.203 45.455 0.00 0.00 0.00 4.75
6332 7065 4.855531 AGGATTTGTTGTAAAAGTCGTGC 58.144 39.130 0.00 0.00 0.00 5.34
6335 7068 8.574196 AAATCAAGGATTTGTTGTAAAAGTCG 57.426 30.769 3.56 0.00 40.24 4.18
6374 7107 4.473199 GGTAGCAATTTCTTCGGAAACAC 58.527 43.478 0.00 0.00 45.25 3.32
6393 7128 2.094078 CGAATAACGTTGTGGGAGGGTA 60.094 50.000 11.99 0.00 37.22 3.69
6447 7204 3.727970 GCAATAGCTAGCAAACGTTCACC 60.728 47.826 18.83 0.00 37.91 4.02
6461 7218 4.401925 AGAAAACAAGGACTGCAATAGCT 58.598 39.130 0.00 0.00 42.74 3.32
6481 7238 2.499693 TGTTGGCTTACCGATGATGAGA 59.500 45.455 0.00 0.00 39.70 3.27
6482 7239 2.609459 GTGTTGGCTTACCGATGATGAG 59.391 50.000 0.00 0.00 39.70 2.90
6492 7249 3.559238 CACTCCATTGTGTTGGCTTAC 57.441 47.619 0.00 0.00 36.66 2.34
6576 7333 3.127425 AGGGAAAAAGGACGTCAGAAG 57.873 47.619 18.91 0.00 0.00 2.85
6709 7630 2.677228 GTGTGGGTCATCAGGGGG 59.323 66.667 0.00 0.00 0.00 5.40
6710 7631 1.500783 AAGGTGTGGGTCATCAGGGG 61.501 60.000 0.00 0.00 0.00 4.79
6711 7632 0.322816 CAAGGTGTGGGTCATCAGGG 60.323 60.000 0.00 0.00 0.00 4.45
6714 7635 0.478072 AAGCAAGGTGTGGGTCATCA 59.522 50.000 0.00 0.00 0.00 3.07
6715 7636 2.084546 GTAAGCAAGGTGTGGGTCATC 58.915 52.381 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.