Multiple sequence alignment - TraesCS3B01G056900

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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 TraesCS3B01G056900 chr3B 100.000 4843 0 0 1 4843 29755016 29759858 0.000000e+00 8944.0
1 TraesCS3B01G056900 chr3B 98.842 691 6 2 4155 4843 795997566 795996876 0.000000e+00 1230.0
2 TraesCS3B01G056900 chr3B 84.565 1069 118 32 1180 2220 512170267 512169218 0.000000e+00 1016.0
3 TraesCS3B01G056900 chr3B 97.015 603 17 1 1619 2220 29748084 29748686 0.000000e+00 1013.0
4 TraesCS3B01G056900 chr3B 86.339 732 53 20 2830 3522 29728142 29728865 0.000000e+00 754.0
5 TraesCS3B01G056900 chr3B 89.535 344 31 5 3109 3450 30469355 30469695 9.630000e-117 431.0
6 TraesCS3B01G056900 chr3B 98.690 229 2 1 410 638 66467818 66468045 5.840000e-109 405.0
7 TraesCS3B01G056900 chr3B 81.215 543 53 27 2844 3368 29848617 29849128 4.540000e-105 392.0
8 TraesCS3B01G056900 chr3B 85.583 326 45 2 2283 2607 27510870 27511194 1.670000e-89 340.0
9 TraesCS3B01G056900 chr3B 85.329 334 43 3 2280 2607 29614186 29614519 1.670000e-89 340.0
10 TraesCS3B01G056900 chr3B 88.889 171 19 0 3352 3522 29849214 29849384 1.370000e-50 211.0
11 TraesCS3B01G056900 chr3B 83.673 147 21 2 2617 2763 29614625 29614768 8.460000e-28 135.0
12 TraesCS3B01G056900 chr3A 96.582 1580 51 3 721 2298 26444638 26446216 0.000000e+00 2615.0
13 TraesCS3B01G056900 chr3A 98.983 688 6 1 4157 4843 25272283 25271596 0.000000e+00 1230.0
14 TraesCS3B01G056900 chr3A 98.429 700 9 2 4145 4843 690200036 690200734 0.000000e+00 1230.0
15 TraesCS3B01G056900 chr3A 95.352 667 28 3 1557 2221 504312283 504312948 0.000000e+00 1057.0
16 TraesCS3B01G056900 chr3A 96.265 589 13 3 2615 3201 26446587 26447168 0.000000e+00 957.0
17 TraesCS3B01G056900 chr3A 93.548 589 16 9 2615 3201 26411026 26411594 0.000000e+00 857.0
18 TraesCS3B01G056900 chr3A 86.733 603 50 12 2943 3522 26416620 26417215 1.140000e-180 643.0
19 TraesCS3B01G056900 chr3A 96.732 306 8 2 2329 2634 26446218 26446521 4.320000e-140 508.0
20 TraesCS3B01G056900 chr3A 92.857 336 17 3 3194 3522 26412762 26413097 9.430000e-132 481.0
21 TraesCS3B01G056900 chr3A 95.113 266 13 0 3257 3522 26448281 26448546 2.080000e-113 420.0
22 TraesCS3B01G056900 chr3A 88.253 332 37 2 2277 2607 26410593 26410923 3.510000e-106 396.0
23 TraesCS3B01G056900 chr3A 91.597 238 5 6 1 238 26444412 26444634 1.010000e-81 315.0
24 TraesCS3B01G056900 chr3A 94.944 178 9 0 238 415 279554485 279554662 3.690000e-71 279.0
25 TraesCS3B01G056900 chr3A 87.079 178 23 0 238 415 20553647 20553824 8.220000e-48 202.0
26 TraesCS3B01G056900 chr3A 89.231 130 13 1 3520 3648 594498129 594498000 1.390000e-35 161.0
27 TraesCS3B01G056900 chr3A 97.802 91 2 0 626 716 108372734 108372824 1.800000e-34 158.0
28 TraesCS3B01G056900 chr3A 86.014 143 14 5 3511 3648 131351963 131352104 1.090000e-31 148.0
29 TraesCS3B01G056900 chr3A 93.878 98 5 1 626 723 727293688 727293784 3.910000e-31 147.0
30 TraesCS3B01G056900 chr3A 86.301 73 8 2 2219 2291 443725434 443725364 1.450000e-10 78.7
31 TraesCS3B01G056900 chr5A 95.847 1517 60 3 708 2221 46756402 46757918 0.000000e+00 2449.0
32 TraesCS3B01G056900 chr5A 99.552 223 0 1 412 634 675426094 675426315 5.840000e-109 405.0
33 TraesCS3B01G056900 chr5A 96.218 238 9 0 1 238 46756170 46756407 1.630000e-104 390.0
34 TraesCS3B01G056900 chr5A 97.674 86 2 0 629 714 644903669 644903584 1.090000e-31 148.0
35 TraesCS3B01G056900 chr2B 89.740 1540 116 23 708 2220 580472388 580473912 0.000000e+00 1930.0
36 TraesCS3B01G056900 chr2B 87.631 1334 118 27 916 2220 446020843 446022158 0.000000e+00 1506.0
37 TraesCS3B01G056900 chr2B 98.844 692 6 2 4154 4843 712073653 712072962 0.000000e+00 1232.0
38 TraesCS3B01G056900 chr2B 87.060 1051 116 12 930 1974 206395337 206394301 0.000000e+00 1170.0
39 TraesCS3B01G056900 chr2B 99.550 222 1 0 412 633 551636659 551636438 5.840000e-109 405.0
40 TraesCS3B01G056900 chr2B 97.468 237 3 2 399 634 40498873 40498639 7.550000e-108 401.0
41 TraesCS3B01G056900 chr2B 98.253 229 4 0 411 639 52914479 52914251 7.550000e-108 401.0
42 TraesCS3B01G056900 chr2B 89.960 249 14 2 1 238 580472145 580472393 1.310000e-80 311.0
43 TraesCS3B01G056900 chr2B 88.281 128 14 1 3522 3648 184955327 184955200 8.400000e-33 152.0
44 TraesCS3B01G056900 chr2B 88.189 127 14 1 3523 3648 444844267 444844141 3.020000e-32 150.0
45 TraesCS3B01G056900 chr6B 99.128 688 5 1 4157 4843 146152111 146152798 0.000000e+00 1236.0
46 TraesCS3B01G056900 chr6B 85.824 783 82 20 1180 1938 714388219 714388996 0.000000e+00 804.0
47 TraesCS3B01G056900 chr6B 91.154 260 18 3 3733 3987 458016182 458015923 9.980000e-92 348.0
48 TraesCS3B01G056900 chr6B 86.695 233 25 5 3522 3750 458016431 458016201 2.240000e-63 254.0
49 TraesCS3B01G056900 chr6B 90.055 181 14 3 237 415 244954725 244954547 1.050000e-56 231.0
50 TraesCS3B01G056900 chr6B 89.888 178 16 1 238 415 11435466 11435641 1.360000e-55 228.0
51 TraesCS3B01G056900 chr6B 89.209 139 13 2 4018 4156 458015927 458015791 6.440000e-39 172.0
52 TraesCS3B01G056900 chr7B 98.984 689 6 1 4156 4843 625934495 625935183 0.000000e+00 1232.0
53 TraesCS3B01G056900 chr7B 86.269 1056 120 18 930 1974 688945846 688946887 0.000000e+00 1123.0
54 TraesCS3B01G056900 chr7B 99.552 223 1 0 412 634 411546102 411545880 1.620000e-109 407.0
55 TraesCS3B01G056900 chr7B 97.778 90 2 0 629 718 588373429 588373518 6.490000e-34 156.0
56 TraesCS3B01G056900 chr7B 97.753 89 2 0 629 717 603479518 603479606 2.330000e-33 154.0
57 TraesCS3B01G056900 chr4A 98.844 692 5 3 4154 4843 712924618 712925308 0.000000e+00 1230.0
58 TraesCS3B01G056900 chr4A 88.827 179 19 1 238 415 440189205 440189383 8.160000e-53 219.0
59 TraesCS3B01G056900 chr4A 81.048 248 38 5 3896 4135 740116496 740116250 6.400000e-44 189.0
60 TraesCS3B01G056900 chr4A 86.364 132 17 1 3519 3649 735399701 735399832 5.050000e-30 143.0
61 TraesCS3B01G056900 chrUn 98.841 690 7 1 4155 4843 211249960 211250649 0.000000e+00 1229.0
62 TraesCS3B01G056900 chrUn 95.604 91 3 1 622 712 31198935 31199024 1.400000e-30 145.0
63 TraesCS3B01G056900 chrUn 97.590 83 2 0 629 711 31477170 31477252 5.050000e-30 143.0
64 TraesCS3B01G056900 chrUn 96.512 86 3 0 629 714 36486386 36486471 5.050000e-30 143.0
65 TraesCS3B01G056900 chrUn 97.590 83 2 0 629 711 40943366 40943284 5.050000e-30 143.0
66 TraesCS3B01G056900 chrUn 95.402 87 4 0 629 715 358211136 358211222 6.540000e-29 139.0
67 TraesCS3B01G056900 chr7A 98.153 704 11 2 4141 4843 16382519 16383221 0.000000e+00 1227.0
68 TraesCS3B01G056900 chr7A 97.368 228 6 0 412 639 621353443 621353216 5.880000e-104 388.0
69 TraesCS3B01G056900 chr7A 93.506 154 10 0 262 415 706490243 706490090 3.770000e-56 230.0
70 TraesCS3B01G056900 chr7A 89.474 171 18 0 245 415 357695232 357695062 2.940000e-52 217.0
71 TraesCS3B01G056900 chr7A 74.497 596 102 35 761 1341 686463588 686463028 3.800000e-51 213.0
72 TraesCS3B01G056900 chr7A 92.661 109 8 0 603 711 664784115 664784223 1.800000e-34 158.0
73 TraesCS3B01G056900 chr7A 86.861 137 15 3 3513 3648 715248356 715248222 3.020000e-32 150.0
74 TraesCS3B01G056900 chr7A 94.792 96 4 1 626 720 694032855 694032760 1.090000e-31 148.0
75 TraesCS3B01G056900 chr2A 93.501 754 48 1 1468 2220 478343812 478344565 0.000000e+00 1120.0
76 TraesCS3B01G056900 chr2A 93.134 670 38 7 1557 2220 678385579 678384912 0.000000e+00 976.0
77 TraesCS3B01G056900 chr2A 74.554 617 110 34 752 1355 503604920 503605502 4.880000e-55 226.0
78 TraesCS3B01G056900 chr2A 90.654 107 8 2 606 711 771527277 771527172 1.820000e-29 141.0
79 TraesCS3B01G056900 chr4D 91.310 748 62 2 738 1483 405228560 405229306 0.000000e+00 1018.0
80 TraesCS3B01G056900 chr4D 89.956 229 22 1 11 238 405228019 405228247 1.320000e-75 294.0
81 TraesCS3B01G056900 chr4D 93.548 93 6 0 629 721 463708516 463708424 6.540000e-29 139.0
82 TraesCS3B01G056900 chr6A 92.868 687 40 8 1541 2220 350693353 350694037 0.000000e+00 989.0
83 TraesCS3B01G056900 chr6A 78.861 790 127 22 711 1480 342198254 342197485 9.360000e-137 497.0
84 TraesCS3B01G056900 chr6A 78.707 789 130 20 711 1480 342239864 342239095 4.360000e-135 492.0
85 TraesCS3B01G056900 chr6A 90.749 227 20 1 13 238 342240088 342239862 7.880000e-78 302.0
86 TraesCS3B01G056900 chr6A 89.083 229 24 1 11 238 342198480 342198252 2.850000e-72 283.0
87 TraesCS3B01G056900 chr6A 98.851 87 1 0 629 715 530251176 530251262 6.490000e-34 156.0
88 TraesCS3B01G056900 chr6A 96.703 91 2 1 629 719 21571498 21571409 3.020000e-32 150.0
89 TraesCS3B01G056900 chr6A 97.701 87 2 0 629 715 562065505 562065419 3.020000e-32 150.0
90 TraesCS3B01G056900 chr6A 95.556 90 3 1 629 718 30734785 30734873 5.050000e-30 143.0
91 TraesCS3B01G056900 chr7D 93.711 636 33 7 3526 4156 53915342 53914709 0.000000e+00 946.0
92 TraesCS3B01G056900 chr7D 81.582 771 96 25 738 1480 235125525 235126277 3.230000e-166 595.0
93 TraesCS3B01G056900 chr7D 96.639 238 8 0 1 238 235124965 235125202 3.510000e-106 396.0
94 TraesCS3B01G056900 chr7D 83.541 401 58 4 3762 4156 22081141 22081539 7.660000e-98 368.0
95 TraesCS3B01G056900 chr7D 84.234 222 32 3 3768 3987 38891281 38891061 3.800000e-51 213.0
96 TraesCS3B01G056900 chr4B 85.714 798 92 12 1180 1957 540390869 540390074 0.000000e+00 822.0
97 TraesCS3B01G056900 chr4B 99.107 224 2 0 408 631 647306406 647306629 2.100000e-108 403.0
98 TraesCS3B01G056900 chr4B 74.611 579 97 35 778 1341 324743248 324742705 4.910000e-50 209.0
99 TraesCS3B01G056900 chr1A 88.226 654 52 10 827 1477 488060803 488061434 0.000000e+00 758.0
100 TraesCS3B01G056900 chr1A 96.104 154 5 1 11 163 488022469 488022622 2.890000e-62 250.0
101 TraesCS3B01G056900 chr1A 73.884 605 108 35 752 1341 35672890 35673459 3.820000e-46 196.0
102 TraesCS3B01G056900 chr1A 97.647 85 2 0 629 713 47896704 47896620 3.910000e-31 147.0
103 TraesCS3B01G056900 chr1A 98.780 82 1 0 629 710 553880870 553880951 3.910000e-31 147.0
104 TraesCS3B01G056900 chr1A 100.000 31 0 0 800 830 488022698 488022728 1.880000e-04 58.4
105 TraesCS3B01G056900 chr6D 82.797 622 89 14 3521 4136 28759636 28759027 1.530000e-149 540.0
106 TraesCS3B01G056900 chr6D 82.407 324 46 6 3807 4121 43950550 43950871 6.180000e-69 272.0
107 TraesCS3B01G056900 chr6D 86.957 184 18 2 237 415 201748077 201748259 8.220000e-48 202.0
108 TraesCS3B01G056900 chr6D 85.075 201 23 7 3524 3721 43950340 43950536 1.060000e-46 198.0
109 TraesCS3B01G056900 chr6D 95.604 91 2 2 629 719 99228539 99228451 1.400000e-30 145.0
110 TraesCS3B01G056900 chr6D 88.793 116 12 1 3813 3928 25812871 25812985 1.820000e-29 141.0
111 TraesCS3B01G056900 chr1B 79.695 655 100 16 3523 4156 487312431 487311789 4.450000e-120 442.0
112 TraesCS3B01G056900 chr1B 98.276 232 4 0 407 638 561755678 561755447 1.620000e-109 407.0
113 TraesCS3B01G056900 chr1B 89.444 180 16 3 238 415 174407686 174407508 1.750000e-54 224.0
114 TraesCS3B01G056900 chr1B 73.039 612 109 33 752 1341 180558491 180559068 1.080000e-36 165.0
115 TraesCS3B01G056900 chr1B 94.624 93 5 0 621 713 309119909 309120001 1.400000e-30 145.0
116 TraesCS3B01G056900 chr1B 88.889 63 7 0 2219 2281 355589256 355589318 1.450000e-10 78.7
117 TraesCS3B01G056900 chr3D 90.000 330 18 4 3046 3374 18790452 18790767 3.490000e-111 412.0
118 TraesCS3B01G056900 chr3D 86.707 331 44 0 2283 2613 17526142 17525812 7.660000e-98 368.0
119 TraesCS3B01G056900 chr3D 81.145 297 38 11 3091 3374 18726315 18726606 6.310000e-54 222.0
120 TraesCS3B01G056900 chr3D 89.404 151 15 1 2615 2764 17525715 17525565 6.400000e-44 189.0
121 TraesCS3B01G056900 chr3D 95.745 94 2 2 621 714 613709819 613709728 3.020000e-32 150.0
122 TraesCS3B01G056900 chr3D 96.591 88 3 0 629 716 609900521 609900608 3.910000e-31 147.0
123 TraesCS3B01G056900 chr3D 81.507 146 24 2 2617 2762 17653625 17653483 3.060000e-22 117.0
124 TraesCS3B01G056900 chr3D 94.872 39 2 0 1 39 498493430 498493468 1.460000e-05 62.1
125 TraesCS3B01G056900 chr5B 96.739 92 2 1 629 719 657275326 657275235 8.400000e-33 152.0
126 TraesCS3B01G056900 chr1D 88.136 118 13 1 602 718 26147363 26147246 6.540000e-29 139.0


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 TraesCS3B01G056900 chr3B 29755016 29759858 4842 False 8944.00 8944 100.000000 1 4843 1 chr3B.!!$F4 4842
1 TraesCS3B01G056900 chr3B 795996876 795997566 690 True 1230.00 1230 98.842000 4155 4843 1 chr3B.!!$R2 688
2 TraesCS3B01G056900 chr3B 512169218 512170267 1049 True 1016.00 1016 84.565000 1180 2220 1 chr3B.!!$R1 1040
3 TraesCS3B01G056900 chr3B 29748084 29748686 602 False 1013.00 1013 97.015000 1619 2220 1 chr3B.!!$F3 601
4 TraesCS3B01G056900 chr3B 29728142 29728865 723 False 754.00 754 86.339000 2830 3522 1 chr3B.!!$F2 692
5 TraesCS3B01G056900 chr3B 29848617 29849384 767 False 301.50 392 85.052000 2844 3522 2 chr3B.!!$F8 678
6 TraesCS3B01G056900 chr3B 29614186 29614768 582 False 237.50 340 84.501000 2280 2763 2 chr3B.!!$F7 483
7 TraesCS3B01G056900 chr3A 25271596 25272283 687 True 1230.00 1230 98.983000 4157 4843 1 chr3A.!!$R1 686
8 TraesCS3B01G056900 chr3A 690200036 690200734 698 False 1230.00 1230 98.429000 4145 4843 1 chr3A.!!$F6 698
9 TraesCS3B01G056900 chr3A 504312283 504312948 665 False 1057.00 1057 95.352000 1557 2221 1 chr3A.!!$F5 664
10 TraesCS3B01G056900 chr3A 26444412 26448546 4134 False 963.00 2615 95.257800 1 3522 5 chr3A.!!$F9 3521
11 TraesCS3B01G056900 chr3A 26410593 26417215 6622 False 594.25 857 90.347750 2277 3522 4 chr3A.!!$F8 1245
12 TraesCS3B01G056900 chr5A 46756170 46757918 1748 False 1419.50 2449 96.032500 1 2221 2 chr5A.!!$F2 2220
13 TraesCS3B01G056900 chr2B 446020843 446022158 1315 False 1506.00 1506 87.631000 916 2220 1 chr2B.!!$F1 1304
14 TraesCS3B01G056900 chr2B 712072962 712073653 691 True 1232.00 1232 98.844000 4154 4843 1 chr2B.!!$R7 689
15 TraesCS3B01G056900 chr2B 206394301 206395337 1036 True 1170.00 1170 87.060000 930 1974 1 chr2B.!!$R4 1044
16 TraesCS3B01G056900 chr2B 580472145 580473912 1767 False 1120.50 1930 89.850000 1 2220 2 chr2B.!!$F2 2219
17 TraesCS3B01G056900 chr6B 146152111 146152798 687 False 1236.00 1236 99.128000 4157 4843 1 chr6B.!!$F2 686
18 TraesCS3B01G056900 chr6B 714388219 714388996 777 False 804.00 804 85.824000 1180 1938 1 chr6B.!!$F3 758
19 TraesCS3B01G056900 chr6B 458015791 458016431 640 True 258.00 348 89.019333 3522 4156 3 chr6B.!!$R2 634
20 TraesCS3B01G056900 chr7B 625934495 625935183 688 False 1232.00 1232 98.984000 4156 4843 1 chr7B.!!$F3 687
21 TraesCS3B01G056900 chr7B 688945846 688946887 1041 False 1123.00 1123 86.269000 930 1974 1 chr7B.!!$F4 1044
22 TraesCS3B01G056900 chr4A 712924618 712925308 690 False 1230.00 1230 98.844000 4154 4843 1 chr4A.!!$F2 689
23 TraesCS3B01G056900 chrUn 211249960 211250649 689 False 1229.00 1229 98.841000 4155 4843 1 chrUn.!!$F4 688
24 TraesCS3B01G056900 chr7A 16382519 16383221 702 False 1227.00 1227 98.153000 4141 4843 1 chr7A.!!$F1 702
25 TraesCS3B01G056900 chr7A 686463028 686463588 560 True 213.00 213 74.497000 761 1341 1 chr7A.!!$R3 580
26 TraesCS3B01G056900 chr2A 478343812 478344565 753 False 1120.00 1120 93.501000 1468 2220 1 chr2A.!!$F1 752
27 TraesCS3B01G056900 chr2A 678384912 678385579 667 True 976.00 976 93.134000 1557 2220 1 chr2A.!!$R1 663
28 TraesCS3B01G056900 chr2A 503604920 503605502 582 False 226.00 226 74.554000 752 1355 1 chr2A.!!$F2 603
29 TraesCS3B01G056900 chr4D 405228019 405229306 1287 False 656.00 1018 90.633000 11 1483 2 chr4D.!!$F1 1472
30 TraesCS3B01G056900 chr6A 350693353 350694037 684 False 989.00 989 92.868000 1541 2220 1 chr6A.!!$F2 679
31 TraesCS3B01G056900 chr6A 342239095 342240088 993 True 397.00 492 84.728000 13 1480 2 chr6A.!!$R4 1467
32 TraesCS3B01G056900 chr6A 342197485 342198480 995 True 390.00 497 83.972000 11 1480 2 chr6A.!!$R3 1469
33 TraesCS3B01G056900 chr7D 53914709 53915342 633 True 946.00 946 93.711000 3526 4156 1 chr7D.!!$R2 630
34 TraesCS3B01G056900 chr7D 235124965 235126277 1312 False 495.50 595 89.110500 1 1480 2 chr7D.!!$F2 1479
35 TraesCS3B01G056900 chr4B 540390074 540390869 795 True 822.00 822 85.714000 1180 1957 1 chr4B.!!$R2 777
36 TraesCS3B01G056900 chr4B 324742705 324743248 543 True 209.00 209 74.611000 778 1341 1 chr4B.!!$R1 563
37 TraesCS3B01G056900 chr1A 488060803 488061434 631 False 758.00 758 88.226000 827 1477 1 chr1A.!!$F2 650
38 TraesCS3B01G056900 chr6D 28759027 28759636 609 True 540.00 540 82.797000 3521 4136 1 chr6D.!!$R1 615
39 TraesCS3B01G056900 chr6D 43950340 43950871 531 False 235.00 272 83.741000 3524 4121 2 chr6D.!!$F3 597
40 TraesCS3B01G056900 chr1B 487311789 487312431 642 True 442.00 442 79.695000 3523 4156 1 chr1B.!!$R2 633
41 TraesCS3B01G056900 chr3D 17525565 17526142 577 True 278.50 368 88.055500 2283 2764 2 chr3D.!!$R3 481

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
248 261 0.101759 GATGCGTTAGGCTGGTCGTA 59.898 55.0 0.00 0.0 44.05 3.43 F
709 722 0.331616 ACTCCCCATTACAACCAGCC 59.668 55.0 0.00 0.0 0.00 4.85 F
2020 2415 0.037882 CTGGTCTGCGCATATCCGAT 60.038 55.0 12.24 0.0 0.00 4.18 F
2520 2921 0.318107 CAAGCTTCCAACAGTTGCCG 60.318 55.0 7.88 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2415 1.270094 CCACTCAGCCGTGTAACTCAA 60.270 52.381 0.0 0.0 33.07 3.02 R
2327 2722 1.569548 AGATCTTCCCACCTCCTCGTA 59.430 52.381 0.0 0.0 0.00 3.43 R
3710 9932 0.034756 CACCAGGGTTGTGTCGATCA 59.965 55.000 0.0 0.0 0.00 2.92 R
4010 10287 1.091771 AAGAGCCGTGCATCCAATCG 61.092 55.000 0.0 0.0 0.00 3.34 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
164 177 1.067974 GCAATGATGGCTGCATGCTTA 59.932 47.619 20.33 0.00 42.39 3.09
205 218 3.099141 CAAGTCCCCATTTAATGCTGGT 58.901 45.455 0.00 0.00 0.00 4.00
212 225 4.142182 CCCCATTTAATGCTGGTTGTACTG 60.142 45.833 0.00 0.00 0.00 2.74
238 251 1.650912 GCATGGGCTGATGCGTTAG 59.349 57.895 6.33 0.00 39.47 2.34
239 252 1.789078 GCATGGGCTGATGCGTTAGG 61.789 60.000 6.33 0.00 39.47 2.69
240 253 1.526917 ATGGGCTGATGCGTTAGGC 60.527 57.895 15.10 15.10 40.82 3.93
241 254 1.987807 ATGGGCTGATGCGTTAGGCT 61.988 55.000 21.29 2.51 44.05 4.58
242 255 2.182842 GGGCTGATGCGTTAGGCTG 61.183 63.158 21.29 0.00 44.05 4.85
243 256 2.182842 GGCTGATGCGTTAGGCTGG 61.183 63.158 16.00 0.00 44.05 4.85
244 257 1.450312 GCTGATGCGTTAGGCTGGT 60.450 57.895 0.00 0.00 44.05 4.00
245 258 1.432270 GCTGATGCGTTAGGCTGGTC 61.432 60.000 0.00 0.00 44.05 4.02
246 259 1.148157 CTGATGCGTTAGGCTGGTCG 61.148 60.000 0.00 0.00 44.05 4.79
247 260 1.153628 GATGCGTTAGGCTGGTCGT 60.154 57.895 0.00 0.00 44.05 4.34
248 261 0.101759 GATGCGTTAGGCTGGTCGTA 59.898 55.000 0.00 0.00 44.05 3.43
249 262 0.533491 ATGCGTTAGGCTGGTCGTAA 59.467 50.000 0.00 0.00 44.05 3.18
250 263 0.533491 TGCGTTAGGCTGGTCGTAAT 59.467 50.000 0.00 0.00 44.05 1.89
251 264 0.928229 GCGTTAGGCTGGTCGTAATG 59.072 55.000 0.00 0.00 39.11 1.90
252 265 1.567504 CGTTAGGCTGGTCGTAATGG 58.432 55.000 0.00 0.00 31.67 3.16
253 266 1.134907 CGTTAGGCTGGTCGTAATGGT 60.135 52.381 0.00 0.00 31.67 3.55
254 267 2.099592 CGTTAGGCTGGTCGTAATGGTA 59.900 50.000 0.00 0.00 31.67 3.25
255 268 3.714391 GTTAGGCTGGTCGTAATGGTAG 58.286 50.000 0.00 0.00 0.00 3.18
256 269 1.861982 AGGCTGGTCGTAATGGTAGT 58.138 50.000 0.00 0.00 0.00 2.73
257 270 3.022557 AGGCTGGTCGTAATGGTAGTA 57.977 47.619 0.00 0.00 0.00 1.82
258 271 3.573695 AGGCTGGTCGTAATGGTAGTAT 58.426 45.455 0.00 0.00 0.00 2.12
259 272 3.573110 AGGCTGGTCGTAATGGTAGTATC 59.427 47.826 0.00 0.00 0.00 2.24
260 273 3.319972 GGCTGGTCGTAATGGTAGTATCA 59.680 47.826 0.00 0.00 0.00 2.15
261 274 4.021368 GGCTGGTCGTAATGGTAGTATCAT 60.021 45.833 0.00 0.00 0.00 2.45
262 275 5.184479 GGCTGGTCGTAATGGTAGTATCATA 59.816 44.000 0.00 0.00 0.00 2.15
263 276 6.323266 GCTGGTCGTAATGGTAGTATCATAG 58.677 44.000 0.00 0.00 0.00 2.23
264 277 6.072064 GCTGGTCGTAATGGTAGTATCATAGT 60.072 42.308 0.00 0.00 0.00 2.12
265 278 7.523380 GCTGGTCGTAATGGTAGTATCATAGTT 60.523 40.741 0.00 0.00 0.00 2.24
266 279 8.922931 TGGTCGTAATGGTAGTATCATAGTTA 57.077 34.615 0.00 0.00 0.00 2.24
267 280 9.006839 TGGTCGTAATGGTAGTATCATAGTTAG 57.993 37.037 0.00 0.00 0.00 2.34
268 281 9.007901 GGTCGTAATGGTAGTATCATAGTTAGT 57.992 37.037 0.00 0.00 0.00 2.24
276 289 9.528489 TGGTAGTATCATAGTTAGTATCATGCA 57.472 33.333 0.00 0.00 0.00 3.96
279 292 8.939201 AGTATCATAGTTAGTATCATGCATGC 57.061 34.615 22.25 11.82 0.00 4.06
280 293 7.984050 AGTATCATAGTTAGTATCATGCATGCC 59.016 37.037 22.25 11.72 0.00 4.40
281 294 6.112927 TCATAGTTAGTATCATGCATGCCA 57.887 37.500 22.25 8.84 0.00 4.92
282 295 6.532826 TCATAGTTAGTATCATGCATGCCAA 58.467 36.000 22.25 5.34 0.00 4.52
283 296 6.427853 TCATAGTTAGTATCATGCATGCCAAC 59.572 38.462 22.25 17.59 0.00 3.77
284 297 4.785301 AGTTAGTATCATGCATGCCAACT 58.215 39.130 22.25 22.78 0.00 3.16
285 298 5.928976 AGTTAGTATCATGCATGCCAACTA 58.071 37.500 22.25 21.88 0.00 2.24
286 299 5.994054 AGTTAGTATCATGCATGCCAACTAG 59.006 40.000 22.25 0.00 0.00 2.57
287 300 3.748083 AGTATCATGCATGCCAACTAGG 58.252 45.455 22.25 0.00 41.84 3.02
301 314 5.002464 CCAACTAGGCAATTTTGATGAGG 57.998 43.478 0.00 0.00 0.00 3.86
302 315 4.463891 CCAACTAGGCAATTTTGATGAGGT 59.536 41.667 0.00 0.00 0.00 3.85
303 316 5.404946 CAACTAGGCAATTTTGATGAGGTG 58.595 41.667 0.00 0.00 0.00 4.00
304 317 4.666512 ACTAGGCAATTTTGATGAGGTGT 58.333 39.130 0.00 0.00 0.00 4.16
305 318 4.702131 ACTAGGCAATTTTGATGAGGTGTC 59.298 41.667 0.00 0.00 0.00 3.67
306 319 3.499338 AGGCAATTTTGATGAGGTGTCA 58.501 40.909 0.00 0.00 37.02 3.58
307 320 4.091549 AGGCAATTTTGATGAGGTGTCAT 58.908 39.130 0.00 0.00 46.75 3.06
308 321 5.263599 AGGCAATTTTGATGAGGTGTCATA 58.736 37.500 0.00 0.00 43.92 2.15
309 322 5.716228 AGGCAATTTTGATGAGGTGTCATAA 59.284 36.000 0.00 0.00 43.92 1.90
310 323 5.807011 GGCAATTTTGATGAGGTGTCATAAC 59.193 40.000 0.00 0.00 43.92 1.89
311 324 6.389091 GCAATTTTGATGAGGTGTCATAACA 58.611 36.000 0.00 0.00 43.92 2.41
312 325 7.037438 GCAATTTTGATGAGGTGTCATAACAT 58.963 34.615 0.00 0.00 43.92 2.71
313 326 7.546667 GCAATTTTGATGAGGTGTCATAACATT 59.453 33.333 0.00 0.00 43.92 2.71
319 332 9.460019 TTGATGAGGTGTCATAACATTAAATGA 57.540 29.630 0.00 0.00 43.92 2.57
320 333 9.460019 TGATGAGGTGTCATAACATTAAATGAA 57.540 29.630 0.00 0.00 43.92 2.57
321 334 9.941664 GATGAGGTGTCATAACATTAAATGAAG 57.058 33.333 0.00 0.00 43.92 3.02
322 335 9.685276 ATGAGGTGTCATAACATTAAATGAAGA 57.315 29.630 0.00 0.00 41.96 2.87
323 336 9.513906 TGAGGTGTCATAACATTAAATGAAGAA 57.486 29.630 0.00 0.00 37.81 2.52
334 347 8.250143 ACATTAAATGAAGAAAAAGAGGGTGT 57.750 30.769 0.00 0.00 0.00 4.16
335 348 9.362151 ACATTAAATGAAGAAAAAGAGGGTGTA 57.638 29.630 0.00 0.00 0.00 2.90
336 349 9.846248 CATTAAATGAAGAAAAAGAGGGTGTAG 57.154 33.333 0.00 0.00 0.00 2.74
337 350 8.990163 TTAAATGAAGAAAAAGAGGGTGTAGT 57.010 30.769 0.00 0.00 0.00 2.73
340 353 8.794335 AATGAAGAAAAAGAGGGTGTAGTATC 57.206 34.615 0.00 0.00 0.00 2.24
341 354 7.311092 TGAAGAAAAAGAGGGTGTAGTATCA 57.689 36.000 0.00 0.00 0.00 2.15
342 355 7.918076 TGAAGAAAAAGAGGGTGTAGTATCAT 58.082 34.615 0.00 0.00 0.00 2.45
343 356 9.042450 TGAAGAAAAAGAGGGTGTAGTATCATA 57.958 33.333 0.00 0.00 0.00 2.15
351 364 9.726438 AAGAGGGTGTAGTATCATATTAAATGC 57.274 33.333 0.00 0.00 0.00 3.56
352 365 9.105844 AGAGGGTGTAGTATCATATTAAATGCT 57.894 33.333 0.00 0.00 0.00 3.79
371 384 6.851222 ATGCTATACTACTTTGTGTCATGC 57.149 37.500 0.00 0.00 0.00 4.06
372 385 5.729510 TGCTATACTACTTTGTGTCATGCA 58.270 37.500 0.00 0.00 0.00 3.96
373 386 6.348498 TGCTATACTACTTTGTGTCATGCAT 58.652 36.000 0.00 0.00 0.00 3.96
374 387 6.258507 TGCTATACTACTTTGTGTCATGCATG 59.741 38.462 21.07 21.07 0.00 4.06
375 388 6.293081 GCTATACTACTTTGTGTCATGCATGG 60.293 42.308 25.97 10.76 0.00 3.66
376 389 2.489329 ACTACTTTGTGTCATGCATGGC 59.511 45.455 24.40 24.40 0.00 4.40
377 390 1.330234 ACTTTGTGTCATGCATGGCA 58.670 45.000 29.45 29.45 44.86 4.92
378 391 1.687660 ACTTTGTGTCATGCATGGCAA 59.312 42.857 34.01 25.74 44.94 4.52
379 392 2.300723 ACTTTGTGTCATGCATGGCAAT 59.699 40.909 34.01 15.19 44.94 3.56
380 393 3.510753 ACTTTGTGTCATGCATGGCAATA 59.489 39.130 34.01 22.99 44.94 1.90
381 394 4.021280 ACTTTGTGTCATGCATGGCAATAA 60.021 37.500 34.01 26.82 44.94 1.40
382 395 4.532314 TTGTGTCATGCATGGCAATAAA 57.468 36.364 34.01 24.20 44.94 1.40
383 396 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
384 397 5.848833 TGTGTCATGCATGGCAATAAATA 57.151 34.783 34.01 14.13 44.94 1.40
385 398 5.834169 TGTGTCATGCATGGCAATAAATAG 58.166 37.500 34.01 0.35 44.94 1.73
386 399 5.593502 TGTGTCATGCATGGCAATAAATAGA 59.406 36.000 34.01 6.92 44.94 1.98
387 400 6.147581 GTGTCATGCATGGCAATAAATAGAG 58.852 40.000 34.01 0.00 44.94 2.43
388 401 5.829391 TGTCATGCATGGCAATAAATAGAGT 59.171 36.000 30.82 0.00 43.62 3.24
389 402 6.997476 TGTCATGCATGGCAATAAATAGAGTA 59.003 34.615 30.82 3.13 43.62 2.59
390 403 7.041167 TGTCATGCATGGCAATAAATAGAGTAC 60.041 37.037 30.82 13.36 43.62 2.73
391 404 7.173907 GTCATGCATGGCAATAAATAGAGTACT 59.826 37.037 26.04 0.00 43.62 2.73
392 405 8.374743 TCATGCATGGCAATAAATAGAGTACTA 58.625 33.333 25.97 0.00 43.62 1.82
393 406 7.962964 TGCATGGCAATAAATAGAGTACTAC 57.037 36.000 0.00 0.00 34.76 2.73
394 407 7.505258 TGCATGGCAATAAATAGAGTACTACA 58.495 34.615 0.00 0.00 34.76 2.74
395 408 8.156820 TGCATGGCAATAAATAGAGTACTACAT 58.843 33.333 0.00 0.00 34.76 2.29
396 409 8.446273 GCATGGCAATAAATAGAGTACTACATG 58.554 37.037 0.00 0.00 34.30 3.21
397 410 9.710900 CATGGCAATAAATAGAGTACTACATGA 57.289 33.333 0.00 0.00 33.32 3.07
418 431 9.775539 ACATGATACTAACATATGATACTCCCT 57.224 33.333 10.38 0.00 0.00 4.20
420 433 8.824756 TGATACTAACATATGATACTCCCTCC 57.175 38.462 10.38 0.00 0.00 4.30
421 434 7.556635 TGATACTAACATATGATACTCCCTCCG 59.443 40.741 10.38 0.00 0.00 4.63
422 435 5.642165 ACTAACATATGATACTCCCTCCGT 58.358 41.667 10.38 0.00 0.00 4.69
423 436 5.711036 ACTAACATATGATACTCCCTCCGTC 59.289 44.000 10.38 0.00 0.00 4.79
424 437 3.432378 ACATATGATACTCCCTCCGTCC 58.568 50.000 10.38 0.00 0.00 4.79
425 438 2.195741 TATGATACTCCCTCCGTCCG 57.804 55.000 0.00 0.00 0.00 4.79
426 439 0.539901 ATGATACTCCCTCCGTCCGG 60.540 60.000 0.00 0.00 0.00 5.14
427 440 1.902432 GATACTCCCTCCGTCCGGG 60.902 68.421 0.00 0.00 43.38 5.73
428 441 2.637383 GATACTCCCTCCGTCCGGGT 62.637 65.000 0.00 0.00 42.56 5.28
429 442 2.923634 ATACTCCCTCCGTCCGGGTG 62.924 65.000 0.00 0.00 42.56 4.61
431 444 3.650298 CTCCCTCCGTCCGGGTGTA 62.650 68.421 0.00 0.00 42.56 2.90
432 445 2.443390 CCCTCCGTCCGGGTGTAT 60.443 66.667 0.00 0.00 36.91 2.29
433 446 1.152694 CCCTCCGTCCGGGTGTATA 60.153 63.158 0.00 0.00 36.91 1.47
434 447 0.756442 CCCTCCGTCCGGGTGTATAA 60.756 60.000 0.00 0.00 36.91 0.98
435 448 0.672342 CCTCCGTCCGGGTGTATAAG 59.328 60.000 0.00 0.00 37.00 1.73
436 449 1.396653 CTCCGTCCGGGTGTATAAGT 58.603 55.000 0.00 0.00 37.00 2.24
437 450 1.336125 CTCCGTCCGGGTGTATAAGTC 59.664 57.143 0.00 0.00 37.00 3.01
438 451 1.105457 CCGTCCGGGTGTATAAGTCA 58.895 55.000 0.00 0.00 0.00 3.41
439 452 1.684983 CCGTCCGGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 0.00 3.06
440 453 2.101917 CCGTCCGGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 0.00 2.57
441 454 3.378339 CGTCCGGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
442 455 3.378339 GTCCGGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
443 456 2.132762 CCGGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
444 457 1.784856 CGGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
445 458 2.797087 CGGGTGTATAAGTCATTCGCGT 60.797 50.000 5.77 0.00 0.00 6.01
446 459 3.548616 CGGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
447 460 3.979495 GGGTGTATAAGTCATTCGCGTAG 59.021 47.826 5.77 0.00 0.00 3.51
448 461 4.498682 GGGTGTATAAGTCATTCGCGTAGT 60.499 45.833 5.77 0.00 0.00 2.73
449 462 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
450 463 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
451 464 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
452 465 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
453 466 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
454 467 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
455 468 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
456 469 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
457 470 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
458 471 3.630769 TCATTCGCGTAGTTCTAGGTCAT 59.369 43.478 5.77 0.00 0.00 3.06
459 472 3.687572 TTCGCGTAGTTCTAGGTCATC 57.312 47.619 5.77 0.00 0.00 2.92
460 473 1.596260 TCGCGTAGTTCTAGGTCATCG 59.404 52.381 5.77 0.00 0.00 3.84
461 474 1.596260 CGCGTAGTTCTAGGTCATCGA 59.404 52.381 0.00 0.00 0.00 3.59
462 475 2.223611 CGCGTAGTTCTAGGTCATCGAT 59.776 50.000 0.00 0.00 0.00 3.59
463 476 3.303857 CGCGTAGTTCTAGGTCATCGATT 60.304 47.826 0.00 0.00 0.00 3.34
464 477 4.608951 GCGTAGTTCTAGGTCATCGATTT 58.391 43.478 0.00 0.00 0.00 2.17
465 478 4.441415 GCGTAGTTCTAGGTCATCGATTTG 59.559 45.833 0.00 0.00 0.00 2.32
466 479 5.732528 GCGTAGTTCTAGGTCATCGATTTGA 60.733 44.000 0.00 0.00 0.00 2.69
467 480 5.910166 CGTAGTTCTAGGTCATCGATTTGAG 59.090 44.000 0.00 0.00 0.00 3.02
468 481 5.269505 AGTTCTAGGTCATCGATTTGAGG 57.730 43.478 0.00 0.00 0.00 3.86
469 482 4.956700 AGTTCTAGGTCATCGATTTGAGGA 59.043 41.667 0.00 0.00 34.44 3.71
470 483 5.422331 AGTTCTAGGTCATCGATTTGAGGAA 59.578 40.000 0.00 0.00 39.46 3.36
471 484 6.098982 AGTTCTAGGTCATCGATTTGAGGAAT 59.901 38.462 0.00 0.00 39.46 3.01
472 485 6.485830 TCTAGGTCATCGATTTGAGGAATT 57.514 37.500 0.00 0.00 39.46 2.17
473 486 7.597288 TCTAGGTCATCGATTTGAGGAATTA 57.403 36.000 0.00 0.00 39.46 1.40
474 487 8.018537 TCTAGGTCATCGATTTGAGGAATTAA 57.981 34.615 0.00 0.00 39.46 1.40
475 488 8.482943 TCTAGGTCATCGATTTGAGGAATTAAA 58.517 33.333 0.00 0.00 39.46 1.52
476 489 9.277783 CTAGGTCATCGATTTGAGGAATTAAAT 57.722 33.333 0.00 0.00 39.46 1.40
478 491 9.799106 AGGTCATCGATTTGAGGAATTAAATAT 57.201 29.630 0.00 0.00 39.46 1.28
479 492 9.831737 GGTCATCGATTTGAGGAATTAAATATG 57.168 33.333 0.00 0.00 39.46 1.78
518 531 9.529325 TGAAAAGTATATCACTAGATTTCCACG 57.471 33.333 0.00 0.00 36.04 4.94
519 532 7.948278 AAAGTATATCACTAGATTTCCACGC 57.052 36.000 0.00 0.00 36.04 5.34
520 533 5.700846 AGTATATCACTAGATTTCCACGCG 58.299 41.667 3.53 3.53 34.98 6.01
521 534 2.225068 ATCACTAGATTTCCACGCGG 57.775 50.000 12.47 0.00 0.00 6.46
522 535 1.179152 TCACTAGATTTCCACGCGGA 58.821 50.000 12.47 0.00 40.60 5.54
523 536 1.754803 TCACTAGATTTCCACGCGGAT 59.245 47.619 12.47 0.00 42.41 4.18
524 537 1.860950 CACTAGATTTCCACGCGGATG 59.139 52.381 12.47 0.00 42.41 3.51
525 538 1.480954 ACTAGATTTCCACGCGGATGT 59.519 47.619 12.47 0.00 42.41 3.06
526 539 2.691526 ACTAGATTTCCACGCGGATGTA 59.308 45.455 12.47 0.00 42.41 2.29
527 540 2.225068 AGATTTCCACGCGGATGTAG 57.775 50.000 12.47 0.00 42.41 2.74
528 541 1.480954 AGATTTCCACGCGGATGTAGT 59.519 47.619 12.47 0.00 42.41 2.73
529 542 2.093658 AGATTTCCACGCGGATGTAGTT 60.094 45.455 12.47 0.00 42.41 2.24
530 543 2.172851 TTTCCACGCGGATGTAGTTT 57.827 45.000 12.47 0.00 42.41 2.66
531 544 1.717194 TTCCACGCGGATGTAGTTTC 58.283 50.000 12.47 0.00 42.41 2.78
532 545 0.892755 TCCACGCGGATGTAGTTTCT 59.107 50.000 12.47 0.00 35.91 2.52
533 546 2.093890 TCCACGCGGATGTAGTTTCTA 58.906 47.619 12.47 0.00 35.91 2.10
534 547 2.492881 TCCACGCGGATGTAGTTTCTAA 59.507 45.455 12.47 0.00 35.91 2.10
535 548 3.056678 TCCACGCGGATGTAGTTTCTAAA 60.057 43.478 12.47 0.00 35.91 1.85
536 549 3.869246 CCACGCGGATGTAGTTTCTAAAT 59.131 43.478 12.47 0.00 0.00 1.40
537 550 5.045215 CCACGCGGATGTAGTTTCTAAATA 58.955 41.667 12.47 0.00 0.00 1.40
538 551 5.694910 CCACGCGGATGTAGTTTCTAAATAT 59.305 40.000 12.47 0.00 0.00 1.28
539 552 6.864685 CCACGCGGATGTAGTTTCTAAATATA 59.135 38.462 12.47 0.00 0.00 0.86
540 553 7.544566 CCACGCGGATGTAGTTTCTAAATATAT 59.455 37.037 12.47 0.00 0.00 0.86
541 554 9.563898 CACGCGGATGTAGTTTCTAAATATATA 57.436 33.333 12.47 0.00 0.00 0.86
598 611 7.859875 AGTTAAATTATCGACCTAGAACTACGC 59.140 37.037 0.00 0.00 0.00 4.42
599 612 3.867055 TTATCGACCTAGAACTACGCG 57.133 47.619 3.53 3.53 0.00 6.01
600 613 1.945387 ATCGACCTAGAACTACGCGA 58.055 50.000 15.93 0.00 0.00 5.87
601 614 1.725641 TCGACCTAGAACTACGCGAA 58.274 50.000 15.93 0.00 0.00 4.70
602 615 2.283298 TCGACCTAGAACTACGCGAAT 58.717 47.619 15.93 0.00 0.00 3.34
603 616 2.031314 TCGACCTAGAACTACGCGAATG 59.969 50.000 15.93 4.47 0.00 2.67
604 617 2.031314 CGACCTAGAACTACGCGAATGA 59.969 50.000 15.93 0.00 0.00 2.57
605 618 3.361414 GACCTAGAACTACGCGAATGAC 58.639 50.000 15.93 0.66 0.00 3.06
606 619 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
607 620 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
608 621 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
609 622 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
610 623 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
611 624 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
612 625 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
613 626 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
614 627 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
615 628 2.456989 ACGCGAATGACTTATACACCG 58.543 47.619 15.93 0.00 0.00 4.94
616 629 1.784856 CGCGAATGACTTATACACCGG 59.215 52.381 0.00 0.00 0.00 5.28
617 630 2.132762 GCGAATGACTTATACACCGGG 58.867 52.381 6.32 0.00 0.00 5.73
618 631 2.223876 GCGAATGACTTATACACCGGGA 60.224 50.000 6.32 0.00 0.00 5.14
619 632 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
635 648 1.885233 GGGACGGAGGTAGTACTATGC 59.115 57.143 5.75 0.00 0.00 3.14
636 649 2.579873 GGACGGAGGTAGTACTATGCA 58.420 52.381 5.75 0.00 0.00 3.96
637 650 3.155501 GGACGGAGGTAGTACTATGCAT 58.844 50.000 5.75 3.79 0.00 3.96
638 651 3.573110 GGACGGAGGTAGTACTATGCATT 59.427 47.826 3.54 0.00 0.00 3.56
639 652 4.763793 GGACGGAGGTAGTACTATGCATTA 59.236 45.833 3.54 0.00 0.00 1.90
640 653 5.242393 GGACGGAGGTAGTACTATGCATTAA 59.758 44.000 3.54 0.00 0.00 1.40
641 654 6.239120 GGACGGAGGTAGTACTATGCATTAAA 60.239 42.308 3.54 0.00 0.00 1.52
642 655 6.746120 ACGGAGGTAGTACTATGCATTAAAG 58.254 40.000 3.54 0.00 0.00 1.85
643 656 6.548622 ACGGAGGTAGTACTATGCATTAAAGA 59.451 38.462 3.54 0.00 0.00 2.52
644 657 7.085116 CGGAGGTAGTACTATGCATTAAAGAG 58.915 42.308 3.54 0.00 0.00 2.85
645 658 7.379750 GGAGGTAGTACTATGCATTAAAGAGG 58.620 42.308 3.54 0.00 0.00 3.69
646 659 7.015389 GGAGGTAGTACTATGCATTAAAGAGGT 59.985 40.741 3.54 0.00 0.00 3.85
647 660 9.075678 GAGGTAGTACTATGCATTAAAGAGGTA 57.924 37.037 3.54 0.00 0.00 3.08
648 661 9.080097 AGGTAGTACTATGCATTAAAGAGGTAG 57.920 37.037 3.54 0.00 0.00 3.18
649 662 8.858094 GGTAGTACTATGCATTAAAGAGGTAGT 58.142 37.037 3.54 0.88 0.00 2.73
658 671 9.712305 ATGCATTAAAGAGGTAGTATCATACAC 57.288 33.333 0.00 0.00 0.00 2.90
659 672 8.924303 TGCATTAAAGAGGTAGTATCATACACT 58.076 33.333 0.00 0.00 0.00 3.55
695 708 9.355916 TGCATGATACTAGTATATGATACTCCC 57.644 37.037 22.89 9.00 0.00 4.30
696 709 8.798402 GCATGATACTAGTATATGATACTCCCC 58.202 40.741 22.89 8.64 0.00 4.81
697 710 9.868160 CATGATACTAGTATATGATACTCCCCA 57.132 37.037 15.42 5.35 0.00 4.96
705 718 8.147244 AGTATATGATACTCCCCATTACAACC 57.853 38.462 0.00 0.00 0.00 3.77
706 719 7.737607 AGTATATGATACTCCCCATTACAACCA 59.262 37.037 0.00 0.00 0.00 3.67
707 720 4.771114 TGATACTCCCCATTACAACCAG 57.229 45.455 0.00 0.00 0.00 4.00
708 721 3.118038 TGATACTCCCCATTACAACCAGC 60.118 47.826 0.00 0.00 0.00 4.85
709 722 0.331616 ACTCCCCATTACAACCAGCC 59.668 55.000 0.00 0.00 0.00 4.85
710 723 0.625849 CTCCCCATTACAACCAGCCT 59.374 55.000 0.00 0.00 0.00 4.58
711 724 1.005924 CTCCCCATTACAACCAGCCTT 59.994 52.381 0.00 0.00 0.00 4.35
712 725 2.241176 CTCCCCATTACAACCAGCCTTA 59.759 50.000 0.00 0.00 0.00 2.69
733 746 7.174946 GCCTTATATACACAGTTAATGGCATGT 59.825 37.037 0.00 0.00 35.94 3.21
784 1101 3.564027 GTGTATCGGGTGCTGCGC 61.564 66.667 0.00 0.00 0.00 6.09
835 1155 0.461163 CCGATCCCGTGTACATGCAA 60.461 55.000 9.72 0.00 0.00 4.08
996 1323 1.716826 CGGACGACAGCCTAGAGGTC 61.717 65.000 0.00 0.00 37.57 3.85
1341 1682 2.682136 TTCATCGTCCGGGAGCCA 60.682 61.111 0.00 0.00 0.00 4.75
1410 1764 6.215845 GTGTGCATACAGGAAAAGAACAAAT 58.784 36.000 8.93 0.00 37.52 2.32
1594 1950 5.859300 CCATATGCACCATGGTTCGATAGAT 60.859 44.000 16.84 1.86 38.73 1.98
1605 1961 1.377725 CGATAGATGCCATGCCCCC 60.378 63.158 0.00 0.00 39.76 5.40
1659 2015 3.624205 CGACAGTAAGAGAGGGGTAGGAA 60.624 52.174 0.00 0.00 0.00 3.36
1698 2058 2.483538 CGAGATGCATATGGGTGACACA 60.484 50.000 8.08 0.00 0.00 3.72
1715 2075 6.073222 GGTGACACAGTGATTTTATCGAGTTT 60.073 38.462 7.81 0.00 0.00 2.66
1771 2131 2.124942 GCTCCGGAGAGGCTTTGG 60.125 66.667 35.69 6.40 40.79 3.28
1920 2314 3.005539 AGTGCGCCACCCTCTCAT 61.006 61.111 4.18 0.00 34.49 2.90
2020 2415 0.037882 CTGGTCTGCGCATATCCGAT 60.038 55.000 12.24 0.00 0.00 4.18
2034 2429 0.892755 TCCGATTGAGTTACACGGCT 59.107 50.000 0.00 0.00 42.73 5.52
2046 2441 0.396435 ACACGGCTGAGTGGAATGAA 59.604 50.000 0.00 0.00 45.80 2.57
2228 2623 0.673985 TGTCCTCGTCACTCACAAGG 59.326 55.000 0.00 0.00 0.00 3.61
2327 2722 1.558756 CTGACCCATTCTGGCTCTCTT 59.441 52.381 0.00 0.00 35.79 2.85
2393 2788 5.286082 GTCGCTTGCCATAACAATAGTTTTG 59.714 40.000 0.00 0.00 39.15 2.44
2483 2884 2.165362 TTTGCGCGTGGTTGATCGAC 62.165 55.000 8.43 4.31 0.00 4.20
2490 2891 1.079405 TGGTTGATCGACGCCTTCC 60.079 57.895 7.01 0.00 0.00 3.46
2520 2921 0.318107 CAAGCTTCCAACAGTTGCCG 60.318 55.000 7.88 0.00 0.00 5.69
2940 3526 7.975866 ATTATGTAAAGAAAGCTCAAATGCG 57.024 32.000 0.00 0.00 38.13 4.73
2962 3562 5.564651 GCGGAATCCTGAAACAGAAATTTCA 60.565 40.000 19.99 0.00 44.40 2.69
3086 3708 2.205074 CACCGCACCATCTCATTAGTC 58.795 52.381 0.00 0.00 0.00 2.59
3087 3709 1.831106 ACCGCACCATCTCATTAGTCA 59.169 47.619 0.00 0.00 0.00 3.41
3088 3710 2.236146 ACCGCACCATCTCATTAGTCAA 59.764 45.455 0.00 0.00 0.00 3.18
3089 3711 2.868583 CCGCACCATCTCATTAGTCAAG 59.131 50.000 0.00 0.00 0.00 3.02
3164 3786 1.063616 CATCGCTCAGCCAGTCAATTG 59.936 52.381 0.00 0.00 0.00 2.32
3604 9816 0.612744 CCCGATTTTGGGCCAATGTT 59.387 50.000 21.65 7.84 43.70 2.71
3613 9825 7.647715 CGATTTTGGGCCAATGTTTAGTATTAG 59.352 37.037 21.65 0.00 0.00 1.73
3649 9865 1.896220 TTTTCACAGCTAGCACAGGG 58.104 50.000 18.83 7.65 0.00 4.45
3710 9932 2.277404 GAGCCTCTCCCGAGTCCT 59.723 66.667 0.00 0.00 35.43 3.85
3963 10240 3.753272 GTGCTTTTGACTCTGCTGGATTA 59.247 43.478 0.00 0.00 0.00 1.75
4010 10287 4.085772 GCGTTTCGGTTTTGAGAACAATTC 60.086 41.667 0.00 0.00 35.85 2.17
4015 10292 5.448438 TCGGTTTTGAGAACAATTCGATTG 58.552 37.500 6.18 6.18 45.59 2.67
4056 10333 6.960542 TCCTCTCTTCTTCTATTACAAGGGTT 59.039 38.462 0.00 0.00 0.00 4.11
4066 10350 7.120923 TCTATTACAAGGGTTATGGTGACTC 57.879 40.000 0.00 0.00 0.00 3.36
4104 10390 1.202758 TCTGGCAGGTTTCGTCAACAT 60.203 47.619 15.73 0.00 37.07 2.71
4124 10410 5.367302 ACATGTTGCTTAATGCCAAGTTTT 58.633 33.333 0.00 0.00 42.00 2.43
4141 10428 5.291905 AGTTTTGGTAGTGTAGACTGCTT 57.708 39.130 8.00 0.00 35.29 3.91
4244 10532 3.584868 AACGGCGCGACTAAAGGCT 62.585 57.895 12.10 0.00 0.00 4.58
4648 10937 9.826574 TTAATGCATATAAAGTTCTACGTCCTT 57.173 29.630 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.865865 TTTCACTCGGACTTGCTGAC 58.134 50.000 0.00 0.00 0.00 3.51
164 177 3.164268 TGATTGGTAGCATGCAAAACCT 58.836 40.909 27.08 14.89 32.99 3.50
205 218 2.345876 CCATGCATGTCGTCAGTACAA 58.654 47.619 24.58 0.00 0.00 2.41
212 225 0.816825 ATCAGCCCATGCATGTCGTC 60.817 55.000 24.58 10.60 41.13 4.20
238 251 3.319972 TGATACTACCATTACGACCAGCC 59.680 47.826 0.00 0.00 0.00 4.85
239 252 4.579454 TGATACTACCATTACGACCAGC 57.421 45.455 0.00 0.00 0.00 4.85
240 253 7.450124 ACTATGATACTACCATTACGACCAG 57.550 40.000 0.00 0.00 0.00 4.00
241 254 7.828508 AACTATGATACTACCATTACGACCA 57.171 36.000 0.00 0.00 0.00 4.02
242 255 9.007901 ACTAACTATGATACTACCATTACGACC 57.992 37.037 0.00 0.00 0.00 4.79
250 263 9.528489 TGCATGATACTAACTATGATACTACCA 57.472 33.333 0.00 0.00 0.00 3.25
254 267 7.984050 GGCATGCATGATACTAACTATGATACT 59.016 37.037 30.64 0.00 0.00 2.12
255 268 7.765819 TGGCATGCATGATACTAACTATGATAC 59.234 37.037 30.64 5.71 0.00 2.24
256 269 7.850193 TGGCATGCATGATACTAACTATGATA 58.150 34.615 30.64 0.00 0.00 2.15
257 270 6.714278 TGGCATGCATGATACTAACTATGAT 58.286 36.000 30.64 0.00 0.00 2.45
258 271 6.112927 TGGCATGCATGATACTAACTATGA 57.887 37.500 30.64 0.00 0.00 2.15
259 272 6.429078 AGTTGGCATGCATGATACTAACTATG 59.571 38.462 30.64 0.23 0.00 2.23
260 273 6.537355 AGTTGGCATGCATGATACTAACTAT 58.463 36.000 30.64 8.95 0.00 2.12
261 274 5.928976 AGTTGGCATGCATGATACTAACTA 58.071 37.500 30.64 5.53 0.00 2.24
262 275 4.785301 AGTTGGCATGCATGATACTAACT 58.215 39.130 30.64 24.73 0.00 2.24
263 276 5.180117 CCTAGTTGGCATGCATGATACTAAC 59.820 44.000 30.64 23.11 0.00 2.34
264 277 5.308014 CCTAGTTGGCATGCATGATACTAA 58.692 41.667 30.64 13.55 0.00 2.24
265 278 4.898320 CCTAGTTGGCATGCATGATACTA 58.102 43.478 30.64 25.87 0.00 1.82
266 279 3.748083 CCTAGTTGGCATGCATGATACT 58.252 45.455 30.64 26.11 0.00 2.12
279 292 4.463891 ACCTCATCAAAATTGCCTAGTTGG 59.536 41.667 0.00 0.00 39.35 3.77
280 293 5.047802 ACACCTCATCAAAATTGCCTAGTTG 60.048 40.000 0.00 0.00 0.00 3.16
281 294 5.079643 ACACCTCATCAAAATTGCCTAGTT 58.920 37.500 0.00 0.00 0.00 2.24
282 295 4.666512 ACACCTCATCAAAATTGCCTAGT 58.333 39.130 0.00 0.00 0.00 2.57
283 296 4.701651 TGACACCTCATCAAAATTGCCTAG 59.298 41.667 0.00 0.00 0.00 3.02
284 297 4.661222 TGACACCTCATCAAAATTGCCTA 58.339 39.130 0.00 0.00 0.00 3.93
285 298 3.499338 TGACACCTCATCAAAATTGCCT 58.501 40.909 0.00 0.00 0.00 4.75
286 299 3.940209 TGACACCTCATCAAAATTGCC 57.060 42.857 0.00 0.00 0.00 4.52
287 300 6.389091 TGTTATGACACCTCATCAAAATTGC 58.611 36.000 0.00 0.00 38.21 3.56
288 301 8.991243 AATGTTATGACACCTCATCAAAATTG 57.009 30.769 0.00 0.00 38.91 2.32
293 306 9.460019 TCATTTAATGTTATGACACCTCATCAA 57.540 29.630 4.77 0.00 38.91 2.57
294 307 9.460019 TTCATTTAATGTTATGACACCTCATCA 57.540 29.630 4.77 0.00 38.91 3.07
295 308 9.941664 CTTCATTTAATGTTATGACACCTCATC 57.058 33.333 4.77 0.00 38.91 2.92
296 309 9.685276 TCTTCATTTAATGTTATGACACCTCAT 57.315 29.630 4.77 0.00 38.91 2.90
297 310 9.513906 TTCTTCATTTAATGTTATGACACCTCA 57.486 29.630 4.77 0.00 38.91 3.86
308 321 8.704668 ACACCCTCTTTTTCTTCATTTAATGTT 58.295 29.630 4.77 0.00 0.00 2.71
309 322 8.250143 ACACCCTCTTTTTCTTCATTTAATGT 57.750 30.769 4.77 0.00 0.00 2.71
310 323 9.846248 CTACACCCTCTTTTTCTTCATTTAATG 57.154 33.333 0.00 0.00 0.00 1.90
311 324 9.588096 ACTACACCCTCTTTTTCTTCATTTAAT 57.412 29.630 0.00 0.00 0.00 1.40
312 325 8.990163 ACTACACCCTCTTTTTCTTCATTTAA 57.010 30.769 0.00 0.00 0.00 1.52
314 327 9.232473 GATACTACACCCTCTTTTTCTTCATTT 57.768 33.333 0.00 0.00 0.00 2.32
315 328 8.383175 TGATACTACACCCTCTTTTTCTTCATT 58.617 33.333 0.00 0.00 0.00 2.57
316 329 7.918076 TGATACTACACCCTCTTTTTCTTCAT 58.082 34.615 0.00 0.00 0.00 2.57
317 330 7.311092 TGATACTACACCCTCTTTTTCTTCA 57.689 36.000 0.00 0.00 0.00 3.02
325 338 9.726438 GCATTTAATATGATACTACACCCTCTT 57.274 33.333 0.00 0.00 0.00 2.85
326 339 9.105844 AGCATTTAATATGATACTACACCCTCT 57.894 33.333 0.00 0.00 0.00 3.69
345 358 8.826710 GCATGACACAAAGTAGTATAGCATTTA 58.173 33.333 0.00 0.00 0.00 1.40
346 359 7.336679 TGCATGACACAAAGTAGTATAGCATTT 59.663 33.333 0.00 0.00 0.00 2.32
347 360 6.823182 TGCATGACACAAAGTAGTATAGCATT 59.177 34.615 0.00 0.00 0.00 3.56
348 361 6.348498 TGCATGACACAAAGTAGTATAGCAT 58.652 36.000 0.00 0.00 0.00 3.79
349 362 5.729510 TGCATGACACAAAGTAGTATAGCA 58.270 37.500 0.00 0.00 0.00 3.49
350 363 6.293081 CCATGCATGACACAAAGTAGTATAGC 60.293 42.308 28.31 0.00 0.00 2.97
351 364 6.293081 GCCATGCATGACACAAAGTAGTATAG 60.293 42.308 28.31 5.81 0.00 1.31
352 365 5.527214 GCCATGCATGACACAAAGTAGTATA 59.473 40.000 28.31 0.00 0.00 1.47
353 366 4.336433 GCCATGCATGACACAAAGTAGTAT 59.664 41.667 28.31 0.00 0.00 2.12
354 367 3.689161 GCCATGCATGACACAAAGTAGTA 59.311 43.478 28.31 0.00 0.00 1.82
355 368 2.489329 GCCATGCATGACACAAAGTAGT 59.511 45.455 28.31 0.00 0.00 2.73
356 369 2.488937 TGCCATGCATGACACAAAGTAG 59.511 45.455 28.31 8.01 31.71 2.57
357 370 2.512705 TGCCATGCATGACACAAAGTA 58.487 42.857 28.31 5.91 31.71 2.24
358 371 1.330234 TGCCATGCATGACACAAAGT 58.670 45.000 28.31 0.00 31.71 2.66
359 372 2.442212 TTGCCATGCATGACACAAAG 57.558 45.000 28.31 10.23 38.76 2.77
360 373 4.532314 TTATTGCCATGCATGACACAAA 57.468 36.364 28.31 15.45 38.76 2.83
361 374 4.532314 TTTATTGCCATGCATGACACAA 57.468 36.364 28.31 25.14 38.76 3.33
362 375 4.739587 ATTTATTGCCATGCATGACACA 57.260 36.364 28.31 18.81 38.76 3.72
363 376 6.075762 TCTATTTATTGCCATGCATGACAC 57.924 37.500 28.31 16.49 38.76 3.67
364 377 5.829391 ACTCTATTTATTGCCATGCATGACA 59.171 36.000 28.31 20.53 38.76 3.58
365 378 6.323203 ACTCTATTTATTGCCATGCATGAC 57.677 37.500 28.31 17.77 38.76 3.06
366 379 7.226441 AGTACTCTATTTATTGCCATGCATGA 58.774 34.615 28.31 8.76 38.76 3.07
367 380 7.444629 AGTACTCTATTTATTGCCATGCATG 57.555 36.000 20.19 20.19 38.76 4.06
368 381 8.156820 TGTAGTACTCTATTTATTGCCATGCAT 58.843 33.333 0.00 0.00 38.76 3.96
369 382 7.505258 TGTAGTACTCTATTTATTGCCATGCA 58.495 34.615 0.00 0.00 36.47 3.96
370 383 7.962964 TGTAGTACTCTATTTATTGCCATGC 57.037 36.000 0.00 0.00 0.00 4.06
371 384 9.710900 TCATGTAGTACTCTATTTATTGCCATG 57.289 33.333 0.00 0.00 0.00 3.66
392 405 9.775539 AGGGAGTATCATATGTTAGTATCATGT 57.224 33.333 1.90 0.00 36.25 3.21
394 407 9.427821 GGAGGGAGTATCATATGTTAGTATCAT 57.572 37.037 1.90 0.00 36.25 2.45
395 408 7.556635 CGGAGGGAGTATCATATGTTAGTATCA 59.443 40.741 1.90 0.00 36.25 2.15
396 409 7.556996 ACGGAGGGAGTATCATATGTTAGTATC 59.443 40.741 1.90 2.16 36.25 2.24
397 410 7.411808 ACGGAGGGAGTATCATATGTTAGTAT 58.588 38.462 1.90 0.00 36.25 2.12
398 411 6.787170 ACGGAGGGAGTATCATATGTTAGTA 58.213 40.000 1.90 0.00 36.25 1.82
399 412 5.642165 ACGGAGGGAGTATCATATGTTAGT 58.358 41.667 1.90 1.66 36.25 2.24
400 413 5.125739 GGACGGAGGGAGTATCATATGTTAG 59.874 48.000 1.90 0.00 36.25 2.34
401 414 5.014858 GGACGGAGGGAGTATCATATGTTA 58.985 45.833 1.90 0.00 36.25 2.41
402 415 3.833070 GGACGGAGGGAGTATCATATGTT 59.167 47.826 1.90 0.00 36.25 2.71
403 416 3.432378 GGACGGAGGGAGTATCATATGT 58.568 50.000 1.90 0.00 36.25 2.29
404 417 2.423892 CGGACGGAGGGAGTATCATATG 59.576 54.545 0.00 0.00 36.25 1.78
405 418 2.620886 CCGGACGGAGGGAGTATCATAT 60.621 54.545 4.40 0.00 34.77 1.78
406 419 1.271762 CCGGACGGAGGGAGTATCATA 60.272 57.143 4.40 0.00 34.77 2.15
407 420 0.539901 CCGGACGGAGGGAGTATCAT 60.540 60.000 4.40 0.00 34.77 2.45
408 421 1.152819 CCGGACGGAGGGAGTATCA 60.153 63.158 4.40 0.00 34.77 2.15
409 422 3.760917 CCGGACGGAGGGAGTATC 58.239 66.667 4.40 0.00 37.50 2.24
416 429 0.672342 CTTATACACCCGGACGGAGG 59.328 60.000 13.13 6.21 37.50 4.30
417 430 1.336125 GACTTATACACCCGGACGGAG 59.664 57.143 13.13 6.96 37.50 4.63
418 431 1.340893 TGACTTATACACCCGGACGGA 60.341 52.381 13.13 0.00 37.50 4.69
419 432 1.105457 TGACTTATACACCCGGACGG 58.895 55.000 0.73 3.25 37.81 4.79
420 433 3.378339 GAATGACTTATACACCCGGACG 58.622 50.000 0.73 0.00 0.00 4.79
421 434 3.378339 CGAATGACTTATACACCCGGAC 58.622 50.000 0.73 0.00 0.00 4.79
422 435 2.223876 GCGAATGACTTATACACCCGGA 60.224 50.000 0.73 0.00 0.00 5.14
423 436 2.132762 GCGAATGACTTATACACCCGG 58.867 52.381 0.00 0.00 0.00 5.73
424 437 1.784856 CGCGAATGACTTATACACCCG 59.215 52.381 0.00 0.00 0.00 5.28
425 438 2.817901 ACGCGAATGACTTATACACCC 58.182 47.619 15.93 0.00 0.00 4.61
426 439 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
427 440 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
428 441 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
429 442 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
430 443 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
431 444 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
432 445 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
433 446 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
434 447 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
435 448 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
436 449 3.011818 TGACCTAGAACTACGCGAATGA 58.988 45.455 15.93 0.00 0.00 2.57
437 450 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
438 451 3.303857 CGATGACCTAGAACTACGCGAAT 60.304 47.826 15.93 0.00 0.00 3.34
439 452 2.031314 CGATGACCTAGAACTACGCGAA 59.969 50.000 15.93 0.00 0.00 4.70
440 453 1.596260 CGATGACCTAGAACTACGCGA 59.404 52.381 15.93 0.00 0.00 5.87
441 454 1.596260 TCGATGACCTAGAACTACGCG 59.404 52.381 3.53 3.53 0.00 6.01
442 455 3.900388 ATCGATGACCTAGAACTACGC 57.100 47.619 0.00 0.00 0.00 4.42
443 456 5.817988 TCAAATCGATGACCTAGAACTACG 58.182 41.667 0.00 0.00 0.00 3.51
444 457 6.039493 TCCTCAAATCGATGACCTAGAACTAC 59.961 42.308 0.00 0.00 0.00 2.73
445 458 6.127101 TCCTCAAATCGATGACCTAGAACTA 58.873 40.000 0.00 0.00 0.00 2.24
446 459 4.956700 TCCTCAAATCGATGACCTAGAACT 59.043 41.667 0.00 0.00 0.00 3.01
447 460 5.263968 TCCTCAAATCGATGACCTAGAAC 57.736 43.478 0.00 0.00 0.00 3.01
448 461 5.932619 TTCCTCAAATCGATGACCTAGAA 57.067 39.130 0.00 0.00 0.00 2.10
449 462 6.485830 AATTCCTCAAATCGATGACCTAGA 57.514 37.500 0.00 0.00 0.00 2.43
450 463 8.662781 TTTAATTCCTCAAATCGATGACCTAG 57.337 34.615 0.00 0.00 0.00 3.02
452 465 9.799106 ATATTTAATTCCTCAAATCGATGACCT 57.201 29.630 0.00 0.00 0.00 3.85
453 466 9.831737 CATATTTAATTCCTCAAATCGATGACC 57.168 33.333 0.00 0.00 0.00 4.02
492 505 9.529325 CGTGGAAATCTAGTGATATACTTTTCA 57.471 33.333 0.00 0.00 40.89 2.69
493 506 8.488764 GCGTGGAAATCTAGTGATATACTTTTC 58.511 37.037 0.00 0.00 40.89 2.29
494 507 7.169308 CGCGTGGAAATCTAGTGATATACTTTT 59.831 37.037 0.00 0.00 40.89 2.27
495 508 6.641314 CGCGTGGAAATCTAGTGATATACTTT 59.359 38.462 0.00 0.00 40.89 2.66
496 509 6.150318 CGCGTGGAAATCTAGTGATATACTT 58.850 40.000 0.00 0.00 40.89 2.24
497 510 5.335740 CCGCGTGGAAATCTAGTGATATACT 60.336 44.000 10.20 0.00 39.66 2.12
498 511 4.857588 CCGCGTGGAAATCTAGTGATATAC 59.142 45.833 10.20 0.00 37.49 1.47
499 512 4.763279 TCCGCGTGGAAATCTAGTGATATA 59.237 41.667 17.09 0.00 42.85 0.86
500 513 3.572682 TCCGCGTGGAAATCTAGTGATAT 59.427 43.478 17.09 0.00 42.85 1.63
501 514 2.953648 TCCGCGTGGAAATCTAGTGATA 59.046 45.455 17.09 0.00 42.85 2.15
502 515 1.754803 TCCGCGTGGAAATCTAGTGAT 59.245 47.619 17.09 0.00 42.85 3.06
503 516 1.179152 TCCGCGTGGAAATCTAGTGA 58.821 50.000 17.09 0.00 42.85 3.41
504 517 3.733236 TCCGCGTGGAAATCTAGTG 57.267 52.632 17.09 0.00 42.85 2.74
514 527 2.572191 TAGAAACTACATCCGCGTGG 57.428 50.000 9.28 9.28 0.00 4.94
515 528 6.764877 ATATTTAGAAACTACATCCGCGTG 57.235 37.500 4.92 0.00 0.00 5.34
572 585 7.859875 GCGTAGTTCTAGGTCGATAATTTAACT 59.140 37.037 0.00 0.00 0.00 2.24
573 586 7.149224 CGCGTAGTTCTAGGTCGATAATTTAAC 60.149 40.741 0.00 0.00 0.00 2.01
574 587 6.852853 CGCGTAGTTCTAGGTCGATAATTTAA 59.147 38.462 0.00 0.00 0.00 1.52
575 588 6.202762 TCGCGTAGTTCTAGGTCGATAATTTA 59.797 38.462 5.77 0.00 0.00 1.40
576 589 5.008019 TCGCGTAGTTCTAGGTCGATAATTT 59.992 40.000 5.77 0.00 0.00 1.82
577 590 4.512944 TCGCGTAGTTCTAGGTCGATAATT 59.487 41.667 5.77 0.00 0.00 1.40
578 591 4.060900 TCGCGTAGTTCTAGGTCGATAAT 58.939 43.478 5.77 0.00 0.00 1.28
579 592 3.457234 TCGCGTAGTTCTAGGTCGATAA 58.543 45.455 5.77 0.00 0.00 1.75
580 593 3.097877 TCGCGTAGTTCTAGGTCGATA 57.902 47.619 5.77 0.00 0.00 2.92
581 594 1.945387 TCGCGTAGTTCTAGGTCGAT 58.055 50.000 5.77 0.00 0.00 3.59
582 595 1.725641 TTCGCGTAGTTCTAGGTCGA 58.274 50.000 5.77 11.56 0.00 4.20
583 596 2.031314 TCATTCGCGTAGTTCTAGGTCG 59.969 50.000 5.77 5.99 0.00 4.79
584 597 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
585 598 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
586 599 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
587 600 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
588 601 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
589 602 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
590 603 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
591 604 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
592 605 4.604976 GGTGTATAAGTCATTCGCGTAGT 58.395 43.478 5.77 0.00 0.00 2.73
593 606 3.662645 CGGTGTATAAGTCATTCGCGTAG 59.337 47.826 5.77 0.00 0.00 3.51
594 607 3.548616 CCGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
595 608 2.456989 CGGTGTATAAGTCATTCGCGT 58.543 47.619 5.77 0.00 0.00 6.01
596 609 1.784856 CCGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
597 610 2.132762 CCCGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
598 611 3.378339 GTCCCGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
599 612 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
600 613 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
601 614 1.684983 CCGTCCCGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 42.73 3.06
602 615 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
603 616 3.953201 CCGTCCCGGTGTATAAGTC 57.047 57.895 0.00 0.00 42.73 3.01
614 627 2.149578 CATAGTACTACCTCCGTCCCG 58.850 57.143 4.31 0.00 0.00 5.14
615 628 1.885233 GCATAGTACTACCTCCGTCCC 59.115 57.143 4.31 0.00 0.00 4.46
616 629 2.579873 TGCATAGTACTACCTCCGTCC 58.420 52.381 4.31 0.00 0.00 4.79
617 630 4.850347 AATGCATAGTACTACCTCCGTC 57.150 45.455 4.31 0.00 0.00 4.79
618 631 6.548622 TCTTTAATGCATAGTACTACCTCCGT 59.451 38.462 4.31 0.00 0.00 4.69
619 632 6.978338 TCTTTAATGCATAGTACTACCTCCG 58.022 40.000 4.31 0.00 0.00 4.63
620 633 7.015389 ACCTCTTTAATGCATAGTACTACCTCC 59.985 40.741 4.31 0.00 0.00 4.30
621 634 7.953752 ACCTCTTTAATGCATAGTACTACCTC 58.046 38.462 4.31 0.00 0.00 3.85
622 635 7.916077 ACCTCTTTAATGCATAGTACTACCT 57.084 36.000 4.31 0.00 0.00 3.08
623 636 8.858094 ACTACCTCTTTAATGCATAGTACTACC 58.142 37.037 4.31 0.05 0.00 3.18
632 645 9.712305 GTGTATGATACTACCTCTTTAATGCAT 57.288 33.333 4.03 0.00 0.00 3.96
633 646 8.924303 AGTGTATGATACTACCTCTTTAATGCA 58.076 33.333 4.03 0.00 0.00 3.96
669 682 9.355916 GGGAGTATCATATACTAGTATCATGCA 57.644 37.037 18.68 1.71 36.25 3.96
670 683 8.798402 GGGGAGTATCATATACTAGTATCATGC 58.202 40.741 18.68 12.34 36.25 4.06
671 684 9.868160 TGGGGAGTATCATATACTAGTATCATG 57.132 37.037 18.68 17.93 36.25 3.07
679 692 9.263446 GGTTGTAATGGGGAGTATCATATACTA 57.737 37.037 0.00 0.00 36.25 1.82
680 693 7.737607 TGGTTGTAATGGGGAGTATCATATACT 59.262 37.037 0.00 0.00 36.25 2.12
681 694 7.913789 TGGTTGTAATGGGGAGTATCATATAC 58.086 38.462 0.00 0.00 36.25 1.47
682 695 7.311046 GCTGGTTGTAATGGGGAGTATCATATA 60.311 40.741 0.00 0.00 36.25 0.86
683 696 6.522459 GCTGGTTGTAATGGGGAGTATCATAT 60.522 42.308 0.00 0.00 36.25 1.78
684 697 5.221843 GCTGGTTGTAATGGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
685 698 4.446311 GCTGGTTGTAATGGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
686 699 3.118038 GCTGGTTGTAATGGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
687 700 3.477530 GCTGGTTGTAATGGGGAGTATC 58.522 50.000 0.00 0.00 0.00 2.24
688 701 2.174854 GGCTGGTTGTAATGGGGAGTAT 59.825 50.000 0.00 0.00 0.00 2.12
689 702 1.562475 GGCTGGTTGTAATGGGGAGTA 59.438 52.381 0.00 0.00 0.00 2.59
690 703 0.331616 GGCTGGTTGTAATGGGGAGT 59.668 55.000 0.00 0.00 0.00 3.85
691 704 0.625849 AGGCTGGTTGTAATGGGGAG 59.374 55.000 0.00 0.00 0.00 4.30
692 705 1.080638 AAGGCTGGTTGTAATGGGGA 58.919 50.000 0.00 0.00 0.00 4.81
693 706 2.818751 TAAGGCTGGTTGTAATGGGG 57.181 50.000 0.00 0.00 0.00 4.96
694 707 6.430000 GTGTATATAAGGCTGGTTGTAATGGG 59.570 42.308 0.00 0.00 0.00 4.00
695 708 6.995686 TGTGTATATAAGGCTGGTTGTAATGG 59.004 38.462 0.00 0.00 0.00 3.16
696 709 7.715249 ACTGTGTATATAAGGCTGGTTGTAATG 59.285 37.037 0.00 0.00 0.00 1.90
697 710 7.802117 ACTGTGTATATAAGGCTGGTTGTAAT 58.198 34.615 0.00 0.00 0.00 1.89
698 711 7.190335 ACTGTGTATATAAGGCTGGTTGTAA 57.810 36.000 0.00 0.00 0.00 2.41
699 712 6.801718 ACTGTGTATATAAGGCTGGTTGTA 57.198 37.500 0.00 0.00 0.00 2.41
700 713 5.693769 ACTGTGTATATAAGGCTGGTTGT 57.306 39.130 0.00 0.00 0.00 3.32
701 714 8.559536 CATTAACTGTGTATATAAGGCTGGTTG 58.440 37.037 0.00 0.00 0.00 3.77
702 715 7.719633 CCATTAACTGTGTATATAAGGCTGGTT 59.280 37.037 0.00 0.00 0.00 3.67
703 716 7.224297 CCATTAACTGTGTATATAAGGCTGGT 58.776 38.462 0.00 0.00 0.00 4.00
704 717 6.149474 GCCATTAACTGTGTATATAAGGCTGG 59.851 42.308 0.00 0.00 34.59 4.85
705 718 6.710295 TGCCATTAACTGTGTATATAAGGCTG 59.290 38.462 0.00 0.00 38.07 4.85
706 719 6.837312 TGCCATTAACTGTGTATATAAGGCT 58.163 36.000 0.00 0.00 38.07 4.58
707 720 7.174946 ACATGCCATTAACTGTGTATATAAGGC 59.825 37.037 0.00 0.00 37.75 4.35
708 721 8.506437 CACATGCCATTAACTGTGTATATAAGG 58.494 37.037 0.00 0.00 35.42 2.69
709 722 9.271828 TCACATGCCATTAACTGTGTATATAAG 57.728 33.333 0.00 0.00 39.89 1.73
710 723 9.271828 CTCACATGCCATTAACTGTGTATATAA 57.728 33.333 0.00 0.00 39.89 0.98
711 724 7.387673 GCTCACATGCCATTAACTGTGTATATA 59.612 37.037 0.00 0.00 39.89 0.86
712 725 6.205464 GCTCACATGCCATTAACTGTGTATAT 59.795 38.462 0.00 0.00 39.89 0.86
733 746 1.140852 CCATTGGATCGGTTAGGCTCA 59.859 52.381 0.00 0.00 0.00 4.26
784 1101 3.381949 GAGCCCTTAACTGCGTACATAG 58.618 50.000 0.00 0.00 0.00 2.23
835 1155 0.323629 TTTTCTTCCATCCTCGCGGT 59.676 50.000 6.13 0.00 0.00 5.68
996 1323 1.372748 GCTCATCCTCCTCATCGCG 60.373 63.158 0.00 0.00 0.00 5.87
1341 1682 2.884639 CCTTTGTTCCGATTGGTGACTT 59.115 45.455 0.00 0.00 36.30 3.01
1410 1764 9.176460 TCAAACATTGCAATGATCTAACTATGA 57.824 29.630 38.99 24.19 39.67 2.15
1698 2058 3.694566 GGCCCAAACTCGATAAAATCACT 59.305 43.478 0.00 0.00 0.00 3.41
1920 2314 3.521937 CCCCCACTTTGTAACATAGGAGA 59.478 47.826 0.00 0.00 0.00 3.71
2020 2415 1.270094 CCACTCAGCCGTGTAACTCAA 60.270 52.381 0.00 0.00 33.07 3.02
2034 2429 3.056821 ACTCGACGAATTCATTCCACTCA 60.057 43.478 6.22 0.00 33.28 3.41
2255 2650 6.207810 GGTGAACCATTATGTAACCAAGTTGA 59.792 38.462 3.87 0.00 35.64 3.18
2262 2657 6.257193 CGTCTTAGGTGAACCATTATGTAACC 59.743 42.308 1.62 0.00 38.89 2.85
2327 2722 1.569548 AGATCTTCCCACCTCCTCGTA 59.430 52.381 0.00 0.00 0.00 3.43
2393 2788 1.611519 ATAGAGCTCCGTAGACCTGC 58.388 55.000 10.93 0.00 0.00 4.85
2490 2891 2.083774 TGGAAGCTTGCAGTAATTCCG 58.916 47.619 17.55 0.00 41.92 4.30
2520 2921 4.738740 CGGAGGTGTTCAATATCGTTACTC 59.261 45.833 0.00 0.00 0.00 2.59
2962 3562 1.712056 ATGCAGCAATGCCATGGTAT 58.288 45.000 14.67 12.26 0.00 2.73
3086 3708 5.121811 CCATGGGATAAGTCTTGACTCTTG 58.878 45.833 2.85 0.87 0.00 3.02
3087 3709 4.164988 CCCATGGGATAAGTCTTGACTCTT 59.835 45.833 28.27 0.00 37.50 2.85
3088 3710 3.713764 CCCATGGGATAAGTCTTGACTCT 59.286 47.826 28.27 0.00 37.50 3.24
3089 3711 3.456277 ACCCATGGGATAAGTCTTGACTC 59.544 47.826 38.07 0.00 38.96 3.36
3132 3754 4.090498 GGCTGAGCGATGATTTTTCAAAAC 59.910 41.667 0.00 0.00 0.00 2.43
3164 3786 1.446966 GACAGCCAGAGTCCGAAGC 60.447 63.158 0.00 0.00 0.00 3.86
3604 9816 6.553857 TGGCCCAAAAGGAAACTAATACTAA 58.446 36.000 0.00 0.00 42.68 2.24
3613 9825 4.036262 GTGAAAAATGGCCCAAAAGGAAAC 59.964 41.667 0.00 0.00 38.24 2.78
3710 9932 0.034756 CACCAGGGTTGTGTCGATCA 59.965 55.000 0.00 0.00 0.00 2.92
4010 10287 1.091771 AAGAGCCGTGCATCCAATCG 61.092 55.000 0.00 0.00 0.00 3.34
4015 10292 2.109126 GGACAAGAGCCGTGCATCC 61.109 63.158 0.00 0.00 0.00 3.51
4056 10333 3.084039 ACCTAAACGTCGAGTCACCATA 58.916 45.455 0.00 0.00 0.00 2.74
4066 10350 3.172050 CAGATGAGTCACCTAAACGTCG 58.828 50.000 0.00 0.00 0.00 5.12
4124 10410 4.682778 AAACAAGCAGTCTACACTACCA 57.317 40.909 0.00 0.00 0.00 3.25
4127 10413 6.639686 CGTAGAAAAACAAGCAGTCTACACTA 59.360 38.462 9.18 0.00 40.35 2.74
4141 10428 3.805422 CACCAGTGTAGCGTAGAAAAACA 59.195 43.478 0.00 0.00 0.00 2.83
4195 10482 3.098555 GCAACCGCGACTAATGGG 58.901 61.111 8.23 0.00 0.00 4.00
4244 10532 1.474332 AACCGCGACTAAAGGGTGGA 61.474 55.000 8.23 0.00 35.36 4.02


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

AutoCloner maintained by Alex Coulton.