Multiple sequence alignment - TraesCS2A01G192100

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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 TraesCS2A01G192100 chr2A 100.000 9710 0 0 1 9710 159206040 159196331 0.000000e+00 17932.0
1 TraesCS2A01G192100 chr7A 99.180 3658 27 2 2685 6339 20033585 20029928 0.000000e+00 6586.0
2 TraesCS2A01G192100 chr7A 99.124 3652 31 1 2689 6339 12899282 12895631 0.000000e+00 6565.0
3 TraesCS2A01G192100 chr7B 99.179 3655 28 2 2686 6339 507839961 507843614 0.000000e+00 6582.0
4 TraesCS2A01G192100 chr7B 99.070 3656 34 0 2684 6339 544117800 544121455 0.000000e+00 6564.0
5 TraesCS2A01G192100 chr7B 93.417 319 18 3 1801 2117 435675635 435675952 4.110000e-128 470.0
6 TraesCS2A01G192100 chr7B 78.443 668 105 24 1 640 725727795 725727139 5.460000e-107 399.0
7 TraesCS2A01G192100 chr7B 97.531 162 4 0 6333 6494 436757608 436757447 2.670000e-70 278.0
8 TraesCS2A01G192100 chr7B 97.516 161 4 0 6333 6493 91793203 91793043 9.610000e-70 276.0
9 TraesCS2A01G192100 chr7B 86.047 86 10 2 1184 1268 437673059 437672975 3.730000e-14 91.6
10 TraesCS2A01G192100 chr3A 99.179 3655 29 1 2686 6339 364139592 364135938 0.000000e+00 6582.0
11 TraesCS2A01G192100 chr3A 83.220 441 54 16 1 433 367796150 367796578 4.250000e-103 387.0
12 TraesCS2A01G192100 chr3A 87.879 264 26 4 8801 9059 505842976 505842714 1.230000e-78 305.0
13 TraesCS2A01G192100 chr3A 95.930 172 6 1 6333 6503 610374812 610374983 2.670000e-70 278.0
14 TraesCS2A01G192100 chr3A 80.247 81 14 2 1188 1267 439277850 439277929 1.050000e-04 60.2
15 TraesCS2A01G192100 chr5B 99.152 3656 30 1 2685 6339 533756864 533760519 0.000000e+00 6578.0
16 TraesCS2A01G192100 chr5B 78.225 969 115 48 8764 9678 45709873 45708947 5.160000e-147 532.0
17 TraesCS2A01G192100 chr5B 92.835 321 20 3 1801 2118 283986387 283986067 6.870000e-126 462.0
18 TraesCS2A01G192100 chr5B 96.933 163 3 2 6333 6493 673310912 673311074 1.240000e-68 272.0
19 TraesCS2A01G192100 chr5B 76.436 505 99 12 9159 9646 517571762 517572263 1.250000e-63 255.0
20 TraesCS2A01G192100 chr5B 87.059 170 18 3 8760 8926 97515690 97515522 1.290000e-43 189.0
21 TraesCS2A01G192100 chr5B 87.786 131 10 3 9044 9174 580680964 580680840 2.180000e-31 148.0
22 TraesCS2A01G192100 chr5B 88.506 87 10 0 9087 9173 441056056 441056142 1.330000e-18 106.0
23 TraesCS2A01G192100 chr1B 99.312 3636 25 0 2704 6339 62440305 62443940 0.000000e+00 6577.0
24 TraesCS2A01G192100 chr1B 78.485 581 89 21 9044 9601 520083075 520083642 2.010000e-91 348.0
25 TraesCS2A01G192100 chr1B 96.407 167 4 2 6333 6498 44507288 44507123 3.450000e-69 274.0
26 TraesCS2A01G192100 chr1B 96.933 163 4 1 6333 6494 481286200 481286038 1.240000e-68 272.0
27 TraesCS2A01G192100 chr1B 96.914 162 4 1 6333 6493 42291613 42291774 4.470000e-68 270.0
28 TraesCS2A01G192100 chr1B 96.914 162 4 1 6333 6493 656506337 656506498 4.470000e-68 270.0
29 TraesCS2A01G192100 chr1B 94.737 171 7 2 6333 6501 427964330 427964160 2.080000e-66 265.0
30 TraesCS2A01G192100 chr1B 83.618 293 32 10 8787 9069 62715623 62715909 2.690000e-65 261.0
31 TraesCS2A01G192100 chr1B 78.348 351 33 18 8867 9174 580625854 580625504 4.630000e-43 187.0
32 TraesCS2A01G192100 chr1B 81.991 211 26 10 8865 9067 520082850 520083056 1.680000e-37 169.0
33 TraesCS2A01G192100 chr4B 99.125 3657 31 1 2684 6339 72899452 72895796 0.000000e+00 6575.0
34 TraesCS2A01G192100 chr4B 89.251 307 27 4 8770 9072 441682896 441682592 7.120000e-101 379.0
35 TraesCS2A01G192100 chr4B 96.894 161 4 1 6333 6492 211651274 211651434 1.610000e-67 268.0
36 TraesCS2A01G192100 chr3B 99.070 3657 31 2 2686 6339 762470693 762467037 0.000000e+00 6562.0
37 TraesCS2A01G192100 chr3B 93.103 319 19 3 1801 2117 245527544 245527861 1.910000e-126 464.0
38 TraesCS2A01G192100 chr3B 89.369 301 28 3 8770 9067 728078517 728078816 9.210000e-100 375.0
39 TraesCS2A01G192100 chr3B 75.243 925 137 48 8799 9651 717047124 717048028 1.200000e-93 355.0
40 TraesCS2A01G192100 chr3B 85.938 128 15 2 9047 9174 20564338 20564214 6.120000e-27 134.0
41 TraesCS2A01G192100 chr2D 91.961 3197 180 43 6493 9658 141996321 141999471 0.000000e+00 4409.0
42 TraesCS2A01G192100 chr2D 89.482 1217 79 22 124 1314 141994206 141995399 0.000000e+00 1493.0
43 TraesCS2A01G192100 chr2D 94.293 368 17 2 2316 2682 141995958 141996322 2.370000e-155 560.0
44 TraesCS2A01G192100 chr2D 77.720 965 135 42 8772 9666 17468885 17467931 1.450000e-142 518.0
45 TraesCS2A01G192100 chr2D 76.981 934 130 44 8785 9651 46206088 46207003 1.150000e-123 455.0
46 TraesCS2A01G192100 chr2D 82.535 355 18 8 1433 1787 141995448 141995758 1.240000e-68 272.0
47 TraesCS2A01G192100 chr2D 91.228 171 9 2 2117 2287 141995793 141995957 2.730000e-55 228.0
48 TraesCS2A01G192100 chr2B 89.342 2158 144 40 6617 8760 198758190 198756105 0.000000e+00 2632.0
49 TraesCS2A01G192100 chr2B 91.274 573 24 9 2120 2685 198759288 198758735 0.000000e+00 758.0
50 TraesCS2A01G192100 chr2B 90.706 538 33 8 6496 7032 198758736 198758215 0.000000e+00 701.0
51 TraesCS2A01G192100 chr2B 86.239 654 41 21 644 1281 198760517 198759897 0.000000e+00 664.0
52 TraesCS2A01G192100 chr2B 92.515 334 18 5 1784 2115 373485280 373485608 1.140000e-128 472.0
53 TraesCS2A01G192100 chr2B 79.843 635 88 26 23 626 302083623 302082998 2.510000e-115 427.0
54 TraesCS2A01G192100 chr2B 80.577 520 76 17 87 595 755645106 755645611 2.560000e-100 377.0
55 TraesCS2A01G192100 chr2B 90.210 286 16 5 1429 1710 198759836 198759559 7.170000e-96 363.0
56 TraesCS2A01G192100 chr2B 96.226 53 2 0 1708 1760 198759398 198759346 4.830000e-13 87.9
57 TraesCS2A01G192100 chr2B 100.000 43 0 0 1337 1379 198759896 198759854 8.080000e-11 80.5
58 TraesCS2A01G192100 chr5D 85.054 649 65 14 9044 9661 503182934 503183581 4.950000e-177 632.0
59 TraesCS2A01G192100 chr5D 77.674 645 87 29 9043 9650 82481759 82482383 3.360000e-89 340.0
60 TraesCS2A01G192100 chr5D 80.134 448 79 8 9211 9656 371291321 371291760 9.400000e-85 326.0
61 TraesCS2A01G192100 chr5D 77.156 429 43 32 8787 9174 34446636 34447050 2.140000e-46 198.0
62 TraesCS2A01G192100 chr5D 87.059 170 18 3 8760 8926 92173095 92172927 1.290000e-43 189.0
63 TraesCS2A01G192100 chr5D 86.076 158 21 1 8771 8927 110870113 110869956 1.680000e-37 169.0
64 TraesCS2A01G192100 chr5D 84.524 168 24 2 9489 9656 60553950 60554115 2.170000e-36 165.0
65 TraesCS2A01G192100 chr5D 88.506 87 10 0 9087 9173 371291161 371291247 1.330000e-18 106.0
66 TraesCS2A01G192100 chr5D 88.462 78 9 0 7642 7719 308354524 308354447 2.890000e-15 95.3
67 TraesCS2A01G192100 chr7D 79.051 864 118 36 8799 9615 23088500 23089347 1.440000e-147 534.0
68 TraesCS2A01G192100 chr7D 81.176 595 75 19 9074 9642 634595442 634596025 2.490000e-120 444.0
69 TraesCS2A01G192100 chr7D 82.292 480 68 14 9236 9707 496362061 496361591 5.460000e-107 399.0
70 TraesCS2A01G192100 chr7D 78.758 499 85 15 9163 9650 464085507 464085019 2.040000e-81 315.0
71 TraesCS2A01G192100 chr7D 77.301 489 96 8 9159 9635 147576547 147577032 3.450000e-69 274.0
72 TraesCS2A01G192100 chr7D 76.190 546 103 19 9172 9696 437205063 437205602 7.480000e-66 263.0
73 TraesCS2A01G192100 chr7D 75.466 322 50 18 9149 9448 561885843 561886157 7.910000e-26 130.0
74 TraesCS2A01G192100 chr7D 86.885 61 8 0 7653 7713 244149079 244149139 1.750000e-07 69.4
75 TraesCS2A01G192100 chr4D 81.184 659 85 23 1 627 308815215 308815866 2.440000e-135 494.0
76 TraesCS2A01G192100 chr4D 83.537 164 25 1 8768 8929 344120034 344120197 1.690000e-32 152.0
77 TraesCS2A01G192100 chr4D 83.333 162 25 1 8770 8929 82143581 82143742 2.180000e-31 148.0
78 TraesCS2A01G192100 chr6A 80.988 668 85 27 3 638 531376582 531375925 8.760000e-135 492.0
79 TraesCS2A01G192100 chr6A 96.894 161 4 1 6333 6492 383533581 383533421 1.610000e-67 268.0
80 TraesCS2A01G192100 chr6A 95.783 166 6 1 6333 6497 315475346 315475181 5.780000e-67 267.0
81 TraesCS2A01G192100 chr6A 80.571 175 33 1 9469 9643 521883279 521883106 6.120000e-27 134.0
82 TraesCS2A01G192100 chr6A 77.778 144 29 3 1127 1267 26815953 26815810 1.740000e-12 86.1
83 TraesCS2A01G192100 chr6A 100.000 32 0 0 1237 1268 504394512 504394481 1.050000e-04 60.2
84 TraesCS2A01G192100 chr4A 86.486 444 50 6 9213 9655 106898768 106899202 6.820000e-131 479.0
85 TraesCS2A01G192100 chr4A 93.396 318 18 2 1801 2117 110087943 110088258 1.480000e-127 468.0
86 TraesCS2A01G192100 chr4A 93.103 319 18 3 1801 2117 110087414 110087730 1.910000e-126 464.0
87 TraesCS2A01G192100 chr4A 86.449 428 34 9 8770 9174 106898202 106898628 1.920000e-121 448.0
88 TraesCS2A01G192100 chr4A 81.711 339 38 13 8853 9174 675958594 675958263 2.690000e-65 261.0
89 TraesCS2A01G192100 chr5A 93.103 319 20 2 1801 2117 228892574 228892256 5.310000e-127 466.0
90 TraesCS2A01G192100 chr5A 93.103 319 20 2 1801 2117 374886159 374885841 5.310000e-127 466.0
91 TraesCS2A01G192100 chr5A 93.125 320 17 5 1801 2117 40613909 40613592 1.910000e-126 464.0
92 TraesCS2A01G192100 chr5A 79.161 763 88 43 8922 9627 275969920 275970668 6.870000e-126 462.0
93 TraesCS2A01G192100 chr5A 80.233 602 81 20 4 572 472280954 472280358 1.510000e-112 418.0
94 TraesCS2A01G192100 chr5A 98.148 162 2 1 6333 6493 692268860 692269021 2.060000e-71 281.0
95 TraesCS2A01G192100 chr5A 97.516 161 4 0 6333 6493 575275497 575275657 9.610000e-70 276.0
96 TraesCS2A01G192100 chr5A 97.516 161 3 1 6333 6492 524317459 524317619 3.450000e-69 274.0
97 TraesCS2A01G192100 chr5A 93.151 73 5 0 9155 9227 627012987 627012915 3.710000e-19 108.0
98 TraesCS2A01G192100 chr6D 80.125 639 96 24 1 629 41546249 41545632 1.920000e-121 448.0
99 TraesCS2A01G192100 chr6D 83.745 486 58 9 9175 9656 114169497 114169029 3.220000e-119 440.0
100 TraesCS2A01G192100 chr6D 86.391 169 18 4 8764 8929 131683517 131683683 7.750000e-41 180.0
101 TraesCS2A01G192100 chr6D 85.455 165 20 3 8768 8929 248516130 248515967 1.680000e-37 169.0
102 TraesCS2A01G192100 chr6D 85.906 149 18 3 8784 8929 276117675 276117527 1.310000e-33 156.0
103 TraesCS2A01G192100 chr6D 83.750 160 24 2 8768 8925 457479799 457479958 6.070000e-32 150.0
104 TraesCS2A01G192100 chr6D 83.030 165 18 7 8768 8926 455835816 455835976 3.660000e-29 141.0
105 TraesCS2A01G192100 chr6D 100.000 32 0 0 1237 1268 363455147 363455116 1.050000e-04 60.2
106 TraesCS2A01G192100 chr1A 79.242 660 99 21 1 628 266179165 266178512 9.010000e-115 425.0
107 TraesCS2A01G192100 chr1A 82.353 187 24 7 8772 8951 575131448 575131264 4.700000e-33 154.0
108 TraesCS2A01G192100 chr6B 79.607 662 73 33 1 623 140455250 140455888 1.510000e-112 418.0
109 TraesCS2A01G192100 chr6B 86.611 239 27 3 8789 9023 591257495 591257258 9.670000e-65 259.0
110 TraesCS2A01G192100 chr6B 78.472 144 28 3 1127 1267 46531652 46531509 3.730000e-14 91.6
111 TraesCS2A01G192100 chr3D 89.844 256 21 4 8800 9051 4502608 4502862 3.380000e-84 324.0
112 TraesCS2A01G192100 chr3D 85.864 191 25 1 9465 9655 264120464 264120276 1.650000e-47 202.0
113 TraesCS2A01G192100 chr3D 82.716 81 12 2 1188 1267 325993889 325993810 4.870000e-08 71.3
114 TraesCS2A01G192100 chr3D 100.000 29 0 0 601 629 394193642 394193670 5.000000e-03 54.7
115 TraesCS2A01G192100 chrUn 76.895 541 101 17 9044 9580 303981184 303980664 1.600000e-72 285.0
116 TraesCS2A01G192100 chrUn 96.914 162 4 1 6333 6493 321168283 321168444 4.470000e-68 270.0
117 TraesCS2A01G192100 chrUn 95.322 171 7 1 6333 6502 463818192 463818362 4.470000e-68 270.0
118 TraesCS2A01G192100 chrUn 96.894 161 4 1 6333 6492 63227353 63227193 1.610000e-67 268.0
119 TraesCS2A01G192100 chrUn 96.296 162 5 1 6333 6493 87135768 87135929 2.080000e-66 265.0
120 TraesCS2A01G192100 chrUn 96.296 162 5 1 6333 6493 87263479 87263640 2.080000e-66 265.0
121 TraesCS2A01G192100 chrUn 93.785 177 9 2 6333 6507 222070968 222071144 2.080000e-66 265.0
122 TraesCS2A01G192100 chrUn 93.785 177 9 2 6333 6507 311113368 311113544 2.080000e-66 265.0
123 TraesCS2A01G192100 chrUn 93.785 177 9 2 6333 6507 311308631 311308807 2.080000e-66 265.0
124 TraesCS2A01G192100 chrUn 96.273 161 5 1 6333 6492 271452794 271452954 7.480000e-66 263.0
125 TraesCS2A01G192100 chrUn 84.681 235 25 8 8801 9027 303981477 303981246 3.530000e-54 224.0
126 TraesCS2A01G192100 chrUn 83.600 250 30 8 8786 9027 356554239 356554485 3.530000e-54 224.0
127 TraesCS2A01G192100 chrUn 77.946 331 66 5 9254 9583 2671495 2671171 5.950000e-47 200.0
128 TraesCS2A01G192100 chrUn 85.496 131 14 5 9044 9171 356554547 356554675 2.200000e-26 132.0
129 TraesCS2A01G192100 chr1D 88.199 161 14 2 8867 9022 429602506 429602346 4.630000e-43 187.0
130 TraesCS2A01G192100 chr1D 77.990 209 38 8 9467 9671 35858525 35858729 3.680000e-24 124.0
131 TraesCS2A01G192100 chr1D 82.456 114 20 0 9211 9324 215721344 215721231 6.210000e-17 100.0


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 TraesCS2A01G192100 chr2A 159196331 159206040 9709 True 17932.0 17932 100.000000 1 9710 1 chr2A.!!$R1 9709
1 TraesCS2A01G192100 chr7A 20029928 20033585 3657 True 6586.0 6586 99.180000 2685 6339 1 chr7A.!!$R2 3654
2 TraesCS2A01G192100 chr7A 12895631 12899282 3651 True 6565.0 6565 99.124000 2689 6339 1 chr7A.!!$R1 3650
3 TraesCS2A01G192100 chr7B 507839961 507843614 3653 False 6582.0 6582 99.179000 2686 6339 1 chr7B.!!$F2 3653
4 TraesCS2A01G192100 chr7B 544117800 544121455 3655 False 6564.0 6564 99.070000 2684 6339 1 chr7B.!!$F3 3655
5 TraesCS2A01G192100 chr7B 725727139 725727795 656 True 399.0 399 78.443000 1 640 1 chr7B.!!$R4 639
6 TraesCS2A01G192100 chr3A 364135938 364139592 3654 True 6582.0 6582 99.179000 2686 6339 1 chr3A.!!$R1 3653
7 TraesCS2A01G192100 chr5B 533756864 533760519 3655 False 6578.0 6578 99.152000 2685 6339 1 chr5B.!!$F3 3654
8 TraesCS2A01G192100 chr5B 45708947 45709873 926 True 532.0 532 78.225000 8764 9678 1 chr5B.!!$R1 914
9 TraesCS2A01G192100 chr5B 517571762 517572263 501 False 255.0 255 76.436000 9159 9646 1 chr5B.!!$F2 487
10 TraesCS2A01G192100 chr1B 62440305 62443940 3635 False 6577.0 6577 99.312000 2704 6339 1 chr1B.!!$F2 3635
11 TraesCS2A01G192100 chr1B 520082850 520083642 792 False 258.5 348 80.238000 8865 9601 2 chr1B.!!$F5 736
12 TraesCS2A01G192100 chr4B 72895796 72899452 3656 True 6575.0 6575 99.125000 2684 6339 1 chr4B.!!$R1 3655
13 TraesCS2A01G192100 chr3B 762467037 762470693 3656 True 6562.0 6562 99.070000 2686 6339 1 chr3B.!!$R2 3653
14 TraesCS2A01G192100 chr3B 717047124 717048028 904 False 355.0 355 75.243000 8799 9651 1 chr3B.!!$F2 852
15 TraesCS2A01G192100 chr2D 141994206 141999471 5265 False 1392.4 4409 89.899800 124 9658 5 chr2D.!!$F2 9534
16 TraesCS2A01G192100 chr2D 17467931 17468885 954 True 518.0 518 77.720000 8772 9666 1 chr2D.!!$R1 894
17 TraesCS2A01G192100 chr2D 46206088 46207003 915 False 455.0 455 76.981000 8785 9651 1 chr2D.!!$F1 866
18 TraesCS2A01G192100 chr2B 198756105 198760517 4412 True 755.2 2632 91.999571 644 8760 7 chr2B.!!$R2 8116
19 TraesCS2A01G192100 chr2B 302082998 302083623 625 True 427.0 427 79.843000 23 626 1 chr2B.!!$R1 603
20 TraesCS2A01G192100 chr2B 755645106 755645611 505 False 377.0 377 80.577000 87 595 1 chr2B.!!$F2 508
21 TraesCS2A01G192100 chr5D 503182934 503183581 647 False 632.0 632 85.054000 9044 9661 1 chr5D.!!$F4 617
22 TraesCS2A01G192100 chr5D 82481759 82482383 624 False 340.0 340 77.674000 9043 9650 1 chr5D.!!$F3 607
23 TraesCS2A01G192100 chr5D 371291161 371291760 599 False 216.0 326 84.320000 9087 9656 2 chr5D.!!$F5 569
24 TraesCS2A01G192100 chr7D 23088500 23089347 847 False 534.0 534 79.051000 8799 9615 1 chr7D.!!$F1 816
25 TraesCS2A01G192100 chr7D 634595442 634596025 583 False 444.0 444 81.176000 9074 9642 1 chr7D.!!$F6 568
26 TraesCS2A01G192100 chr7D 437205063 437205602 539 False 263.0 263 76.190000 9172 9696 1 chr7D.!!$F4 524
27 TraesCS2A01G192100 chr4D 308815215 308815866 651 False 494.0 494 81.184000 1 627 1 chr4D.!!$F2 626
28 TraesCS2A01G192100 chr6A 531375925 531376582 657 True 492.0 492 80.988000 3 638 1 chr6A.!!$R6 635
29 TraesCS2A01G192100 chr4A 110087414 110088258 844 False 466.0 468 93.249500 1801 2117 2 chr4A.!!$F2 316
30 TraesCS2A01G192100 chr4A 106898202 106899202 1000 False 463.5 479 86.467500 8770 9655 2 chr4A.!!$F1 885
31 TraesCS2A01G192100 chr5A 275969920 275970668 748 False 462.0 462 79.161000 8922 9627 1 chr5A.!!$F1 705
32 TraesCS2A01G192100 chr5A 472280358 472280954 596 True 418.0 418 80.233000 4 572 1 chr5A.!!$R4 568
33 TraesCS2A01G192100 chr6D 41545632 41546249 617 True 448.0 448 80.125000 1 629 1 chr6D.!!$R1 628
34 TraesCS2A01G192100 chr1A 266178512 266179165 653 True 425.0 425 79.242000 1 628 1 chr1A.!!$R1 627
35 TraesCS2A01G192100 chr6B 140455250 140455888 638 False 418.0 418 79.607000 1 623 1 chr6B.!!$F1 622
36 TraesCS2A01G192100 chrUn 303980664 303981477 813 True 254.5 285 80.788000 8801 9580 2 chrUn.!!$R3 779

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
599 708 0.804364 TGAGCTATGTTGCTTTGCGG 59.196 50.000 0.00 0.0 44.17 5.69 F
1990 2832 0.034896 AGCTTTTGTCACCGGATCGT 59.965 50.000 9.46 0.0 0.00 3.73 F
2626 3476 0.550914 TTGGGTTGCAGTTGGAGAGT 59.449 50.000 0.00 0.0 0.00 3.24 F
3937 4790 0.396435 TTGCCTTGGACAGACGACAT 59.604 50.000 0.00 0.0 0.00 3.06 F
4775 5628 2.662596 GTGATGACTGCCCCGACA 59.337 61.111 0.00 0.0 0.00 4.35 F
6340 7193 0.034477 CGGAGCCATGGTAGGGTTTT 60.034 55.000 14.67 0.0 40.02 2.43 F
6368 7221 0.109597 AACGGACGTAACCTAGCGTG 60.110 55.000 0.00 0.0 41.70 5.34 F
6429 7282 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.0 0.00 2.15 F
8040 9327 0.737715 GTAGGCTGGCTCGACAACTG 60.738 60.000 7.13 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2840 0.250901 GGAGGCAGGTGCTTGAAGAA 60.251 55.000 0.00 0.00 41.70 2.52 R
3460 4313 1.427368 AGTATTGTTGGTGGGCTCCAA 59.573 47.619 9.77 9.77 44.03 3.53 R
4549 5402 2.033602 TCGTCTGTCCCGAGCTCA 59.966 61.111 15.40 0.00 0.00 4.26 R
5940 6793 2.519002 GCATGTTTTGCGTCGTCATA 57.481 45.000 0.00 0.00 42.54 2.15 R
6383 7236 0.033503 CGGTTCCCCCAAAGCCTATT 60.034 55.000 0.00 0.00 0.00 1.73 R
8075 9363 0.034896 GAAGTTCCTTCCACCGAGCA 59.965 55.000 0.00 0.00 34.71 4.26 R
8250 9538 0.604578 CGTCAGGGTAGGTTTTCCGA 59.395 55.000 0.00 0.00 46.35 4.55 R
8387 9676 0.109412 AGGACACTACGTACGCAAGC 60.109 55.000 16.72 0.00 45.62 4.01 R
9417 11074 1.006043 TCCCAGAGATCGAGACCAAGT 59.994 52.381 0.00 0.00 0.00 3.16 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
96 98 8.770438 TTGCCATGGTGAATTACTTAAATTTC 57.230 30.769 14.67 0.00 37.93 2.17
383 447 6.983890 AGTGTAAACTTTATGGCAACTTTTGG 59.016 34.615 0.00 0.00 37.61 3.28
439 536 8.528643 TGGAATCTAGTTTTAAAGATCTCGTCA 58.471 33.333 0.00 0.00 31.20 4.35
560 669 9.643693 ATGTCATCTGTTTTGATATGGAAAAAC 57.356 29.630 9.50 9.50 43.43 2.43
577 686 6.884295 TGGAAAAACGGATGATAATGAAGACT 59.116 34.615 0.00 0.00 0.00 3.24
599 708 0.804364 TGAGCTATGTTGCTTTGCGG 59.196 50.000 0.00 0.00 44.17 5.69
631 740 9.088512 GTGTGACACTTATCATTTAGGTAAGAG 57.911 37.037 8.76 0.00 31.55 2.85
670 779 1.154727 GCGGACTTTGCGTAACGTG 60.155 57.895 0.00 0.00 32.35 4.49
688 798 1.535462 GTGATCCACCAAAGTCCAACG 59.465 52.381 0.00 0.00 0.00 4.10
875 1003 4.626081 CGCCGATCCACCCATCCC 62.626 72.222 0.00 0.00 0.00 3.85
876 1004 4.271016 GCCGATCCACCCATCCCC 62.271 72.222 0.00 0.00 0.00 4.81
877 1005 3.570212 CCGATCCACCCATCCCCC 61.570 72.222 0.00 0.00 0.00 5.40
907 1039 1.469251 CCCCTCAAAACCCCACCAT 59.531 57.895 0.00 0.00 0.00 3.55
962 1094 2.047179 GCACTCGTCCTTCACCCC 60.047 66.667 0.00 0.00 0.00 4.95
964 1096 2.995574 ACTCGTCCTTCACCCCCG 60.996 66.667 0.00 0.00 0.00 5.73
1003 1141 0.834261 TCACCTGACCCACGGAATGA 60.834 55.000 0.00 0.00 0.00 2.57
1288 1429 3.047718 TACGTCTTCGCTCGCTGGG 62.048 63.158 0.00 0.00 41.18 4.45
1314 1455 3.244044 GCCTTCAGTCTCAAACTCTCAGT 60.244 47.826 0.00 0.00 35.45 3.41
1315 1456 4.021894 GCCTTCAGTCTCAAACTCTCAGTA 60.022 45.833 0.00 0.00 35.45 2.74
1316 1457 5.337169 GCCTTCAGTCTCAAACTCTCAGTAT 60.337 44.000 0.00 0.00 35.45 2.12
1317 1458 6.696411 CCTTCAGTCTCAAACTCTCAGTATT 58.304 40.000 0.00 0.00 35.45 1.89
1318 1459 6.811170 CCTTCAGTCTCAAACTCTCAGTATTC 59.189 42.308 0.00 0.00 35.45 1.75
1319 1460 5.944013 TCAGTCTCAAACTCTCAGTATTCG 58.056 41.667 0.00 0.00 35.45 3.34
1320 1461 4.560819 CAGTCTCAAACTCTCAGTATTCGC 59.439 45.833 0.00 0.00 35.45 4.70
1321 1462 4.218635 AGTCTCAAACTCTCAGTATTCGCA 59.781 41.667 0.00 0.00 30.02 5.10
1322 1463 4.923871 GTCTCAAACTCTCAGTATTCGCAA 59.076 41.667 0.00 0.00 0.00 4.85
1323 1464 4.923871 TCTCAAACTCTCAGTATTCGCAAC 59.076 41.667 0.00 0.00 0.00 4.17
1324 1465 4.627058 TCAAACTCTCAGTATTCGCAACA 58.373 39.130 0.00 0.00 0.00 3.33
1325 1466 5.053811 TCAAACTCTCAGTATTCGCAACAA 58.946 37.500 0.00 0.00 0.00 2.83
1326 1467 5.525745 TCAAACTCTCAGTATTCGCAACAAA 59.474 36.000 0.00 0.00 0.00 2.83
1327 1468 6.037720 TCAAACTCTCAGTATTCGCAACAAAA 59.962 34.615 0.00 0.00 0.00 2.44
1328 1469 6.371809 AACTCTCAGTATTCGCAACAAAAA 57.628 33.333 0.00 0.00 0.00 1.94
1377 1518 1.606737 GGAGCTCTTCAAAGTCGCTGT 60.607 52.381 14.64 0.00 35.31 4.40
1382 1523 4.158764 AGCTCTTCAAAGTCGCTGTAGTAT 59.841 41.667 7.96 0.00 34.44 2.12
1460 1601 1.325355 TCACCCGTTCGATCTATCCC 58.675 55.000 0.00 0.00 0.00 3.85
1515 1656 1.340697 GGGTTGATAAGGCCGAAACCT 60.341 52.381 20.20 0.00 43.91 3.50
1545 1686 4.854173 TCACTTGCAGGAGCCAATAAATA 58.146 39.130 1.40 0.00 41.13 1.40
1552 1693 4.397417 GCAGGAGCCAATAAATATAGCCTG 59.603 45.833 0.00 0.00 42.39 4.85
1605 1749 2.947754 GGCAATTTTGAAAGCCAACG 57.052 45.000 2.22 0.00 46.26 4.10
1611 1755 3.595709 TTTTGAAAGCCAACGTCGTAG 57.404 42.857 0.00 0.00 33.85 3.51
1613 1757 3.367992 TTGAAAGCCAACGTCGTAGTA 57.632 42.857 0.00 0.00 0.00 1.82
1614 1758 2.664916 TGAAAGCCAACGTCGTAGTAC 58.335 47.619 0.00 0.00 0.00 2.73
1615 1759 2.294233 TGAAAGCCAACGTCGTAGTACT 59.706 45.455 0.00 0.00 0.00 2.73
1616 1760 3.501828 TGAAAGCCAACGTCGTAGTACTA 59.498 43.478 0.00 0.00 0.00 1.82
1618 1762 2.426522 AGCCAACGTCGTAGTACTACA 58.573 47.619 28.03 15.12 35.87 2.74
1619 1763 2.417933 AGCCAACGTCGTAGTACTACAG 59.582 50.000 28.03 20.91 35.87 2.74
1620 1764 2.778659 CCAACGTCGTAGTACTACAGC 58.221 52.381 28.03 19.38 35.87 4.40
1621 1765 2.425283 CAACGTCGTAGTACTACAGCG 58.575 52.381 28.98 28.98 38.16 5.18
1622 1766 1.714794 ACGTCGTAGTACTACAGCGT 58.285 50.000 29.89 29.89 39.43 5.07
1623 1767 2.876091 ACGTCGTAGTACTACAGCGTA 58.124 47.619 32.17 14.04 41.02 4.42
1624 1768 2.854777 ACGTCGTAGTACTACAGCGTAG 59.145 50.000 32.17 20.03 41.02 3.51
1625 1769 2.854777 CGTCGTAGTACTACAGCGTAGT 59.145 50.000 28.03 19.93 35.87 2.73
1627 1771 4.499399 CGTCGTAGTACTACAGCGTAGTTA 59.501 45.833 28.03 9.94 35.87 2.24
1631 1775 6.359883 TCGTAGTACTACAGCGTAGTTATACG 59.640 42.308 29.20 29.20 44.85 3.06
1763 2076 8.983724 GTAATAAAATGCTAAGAGCTGGAGTAG 58.016 37.037 0.00 0.00 42.97 2.57
1775 2088 2.162408 GCTGGAGTAGGATGTTGTTTGC 59.838 50.000 0.00 0.00 0.00 3.68
1776 2089 2.416547 CTGGAGTAGGATGTTGTTTGCG 59.583 50.000 0.00 0.00 0.00 4.85
1777 2090 1.130561 GGAGTAGGATGTTGTTTGCGC 59.869 52.381 0.00 0.00 0.00 6.09
1787 2100 2.420372 TGTTGTTTGCGCTACTTTGTGA 59.580 40.909 9.73 0.00 0.00 3.58
1790 2103 2.680841 TGTTTGCGCTACTTTGTGACTT 59.319 40.909 9.73 0.00 0.00 3.01
1791 2104 3.242608 TGTTTGCGCTACTTTGTGACTTC 60.243 43.478 9.73 0.00 0.00 3.01
1792 2105 1.136690 TGCGCTACTTTGTGACTTCG 58.863 50.000 9.73 0.00 0.00 3.79
1793 2106 1.137513 GCGCTACTTTGTGACTTCGT 58.862 50.000 0.00 0.00 0.00 3.85
1794 2107 1.136611 GCGCTACTTTGTGACTTCGTG 60.137 52.381 0.00 0.00 0.00 4.35
1796 2109 2.153247 CGCTACTTTGTGACTTCGTGTC 59.847 50.000 4.78 4.78 45.54 3.67
1809 2122 0.901827 TCGTGTCACTGGGCATGTAT 59.098 50.000 0.65 0.00 0.00 2.29
1895 2737 1.354031 TCTTCCCAATGCAAGCTACCA 59.646 47.619 0.00 0.00 0.00 3.25
1964 2806 5.426689 TGCATCTCTACTTTCACTCCAAT 57.573 39.130 0.00 0.00 0.00 3.16
1987 2829 2.270352 TTCAGCTTTTGTCACCGGAT 57.730 45.000 9.46 0.00 0.00 4.18
1989 2831 0.443869 CAGCTTTTGTCACCGGATCG 59.556 55.000 9.46 0.00 0.00 3.69
1990 2832 0.034896 AGCTTTTGTCACCGGATCGT 59.965 50.000 9.46 0.00 0.00 3.73
2020 2862 2.360852 CAAGCACCTGCCTCCTGG 60.361 66.667 0.00 0.00 43.38 4.45
2037 2879 1.458588 GGAGAGGATCCCGCTTCCT 60.459 63.158 8.55 0.00 46.41 3.36
2055 2897 5.752472 GCTTCCTTATCCGAACCTACTTTAC 59.248 44.000 0.00 0.00 0.00 2.01
2069 2911 5.766670 ACCTACTTTACGTCATATCCGATCA 59.233 40.000 0.00 0.00 0.00 2.92
2117 2959 3.885297 GAGGTTATGCATTGTACATGCCT 59.115 43.478 20.37 15.58 43.94 4.75
2118 2960 5.047566 AGGTTATGCATTGTACATGCCTA 57.952 39.130 20.37 14.85 43.94 3.93
2129 2971 1.204146 ACATGCCTAGTCCGTTGGAT 58.796 50.000 0.00 0.00 32.73 3.41
2162 3004 9.396351 AGTACTCCTGGAATAGTATAGAGTAGT 57.604 37.037 0.00 0.00 31.25 2.73
2259 3108 4.214971 TGTTGCTCAAGAAGATCTGAAAGC 59.785 41.667 0.00 2.55 31.04 3.51
2291 3140 4.574674 TCACATCCTGCCTTGAATAAGT 57.425 40.909 0.00 0.00 31.80 2.24
2301 3150 3.552068 GCCTTGAATAAGTTGCGGTTGTT 60.552 43.478 0.00 0.00 31.80 2.83
2302 3151 3.980775 CCTTGAATAAGTTGCGGTTGTTG 59.019 43.478 0.00 0.00 31.80 3.33
2303 3152 4.499019 CCTTGAATAAGTTGCGGTTGTTGT 60.499 41.667 0.00 0.00 31.80 3.32
2491 3341 2.107750 CATCGATCGCCAGCCAGT 59.892 61.111 11.09 0.00 0.00 4.00
2492 3342 1.953138 CATCGATCGCCAGCCAGTC 60.953 63.158 11.09 0.00 0.00 3.51
2510 3360 3.760035 AGCTGCCTACCGACACCG 61.760 66.667 0.00 0.00 0.00 4.94
2524 3374 1.302431 CACCGTCCTGTGCAATCCA 60.302 57.895 0.00 0.00 0.00 3.41
2591 3441 2.512286 ACTGCCATGCCATCGTCG 60.512 61.111 0.00 0.00 0.00 5.12
2618 3468 2.765699 AGATTTTGTGTTGGGTTGCAGT 59.234 40.909 0.00 0.00 0.00 4.40
2626 3476 0.550914 TTGGGTTGCAGTTGGAGAGT 59.449 50.000 0.00 0.00 0.00 3.24
2627 3477 1.429930 TGGGTTGCAGTTGGAGAGTA 58.570 50.000 0.00 0.00 0.00 2.59
2628 3478 1.347707 TGGGTTGCAGTTGGAGAGTAG 59.652 52.381 0.00 0.00 0.00 2.57
2652 3502 2.656560 ATCGTGCACCAGTACTCTTC 57.343 50.000 12.15 0.00 0.00 2.87
2669 3519 0.908910 TTCTGGCTTTCGGGATGCTA 59.091 50.000 0.00 0.00 0.00 3.49
2680 3530 3.606687 TCGGGATGCTAGTTTTCCTTTC 58.393 45.455 7.42 0.00 0.00 2.62
2681 3531 3.263425 TCGGGATGCTAGTTTTCCTTTCT 59.737 43.478 7.42 0.00 0.00 2.52
2682 3532 3.375299 CGGGATGCTAGTTTTCCTTTCTG 59.625 47.826 7.42 0.00 0.00 3.02
3460 4313 1.533338 GGTCGCGTGATCGTCAAGTAT 60.533 52.381 5.77 0.00 39.49 2.12
3937 4790 0.396435 TTGCCTTGGACAGACGACAT 59.604 50.000 0.00 0.00 0.00 3.06
4775 5628 2.662596 GTGATGACTGCCCCGACA 59.337 61.111 0.00 0.00 0.00 4.35
5240 6093 9.823647 GACATTTGTATCCTTTATGAAGAGAGA 57.176 33.333 0.00 0.00 34.71 3.10
6339 7192 0.912487 TCGGAGCCATGGTAGGGTTT 60.912 55.000 14.67 0.00 40.02 3.27
6340 7193 0.034477 CGGAGCCATGGTAGGGTTTT 60.034 55.000 14.67 0.00 40.02 2.43
6341 7194 1.615919 CGGAGCCATGGTAGGGTTTTT 60.616 52.381 14.67 0.00 40.02 1.94
6342 7195 2.356330 CGGAGCCATGGTAGGGTTTTTA 60.356 50.000 14.67 0.00 40.02 1.52
6343 7196 3.288092 GGAGCCATGGTAGGGTTTTTAG 58.712 50.000 14.67 0.00 40.02 1.85
6344 7197 3.288092 GAGCCATGGTAGGGTTTTTAGG 58.712 50.000 14.67 0.00 40.02 2.69
6345 7198 1.754803 GCCATGGTAGGGTTTTTAGGC 59.245 52.381 14.67 0.00 0.00 3.93
6346 7199 2.021457 CCATGGTAGGGTTTTTAGGCG 58.979 52.381 2.57 0.00 0.00 5.52
6347 7200 2.021457 CATGGTAGGGTTTTTAGGCGG 58.979 52.381 0.00 0.00 0.00 6.13
6348 7201 1.360185 TGGTAGGGTTTTTAGGCGGA 58.640 50.000 0.00 0.00 0.00 5.54
6349 7202 1.704070 TGGTAGGGTTTTTAGGCGGAA 59.296 47.619 0.00 0.00 0.00 4.30
6350 7203 2.107901 TGGTAGGGTTTTTAGGCGGAAA 59.892 45.455 0.00 0.00 0.00 3.13
6351 7204 2.489329 GGTAGGGTTTTTAGGCGGAAAC 59.511 50.000 5.30 5.30 35.54 2.78
6365 7218 1.633561 GGAAACGGACGTAACCTAGC 58.366 55.000 0.00 0.00 0.00 3.42
6366 7219 1.262882 GAAACGGACGTAACCTAGCG 58.737 55.000 0.00 0.00 0.00 4.26
6367 7220 0.598065 AAACGGACGTAACCTAGCGT 59.402 50.000 0.00 0.00 44.50 5.07
6368 7221 0.109597 AACGGACGTAACCTAGCGTG 60.110 55.000 0.00 0.00 41.70 5.34
6369 7222 0.955428 ACGGACGTAACCTAGCGTGA 60.955 55.000 0.00 0.00 41.70 4.35
6370 7223 0.379669 CGGACGTAACCTAGCGTGAT 59.620 55.000 0.00 0.00 41.70 3.06
6371 7224 1.599071 CGGACGTAACCTAGCGTGATA 59.401 52.381 0.00 0.00 41.70 2.15
6372 7225 2.600792 CGGACGTAACCTAGCGTGATAC 60.601 54.545 0.00 0.00 41.70 2.24
6373 7226 2.287248 GGACGTAACCTAGCGTGATACC 60.287 54.545 0.00 0.00 41.70 2.73
6374 7227 2.355756 GACGTAACCTAGCGTGATACCA 59.644 50.000 0.00 0.00 41.70 3.25
6375 7228 2.954318 ACGTAACCTAGCGTGATACCAT 59.046 45.455 0.00 0.00 40.03 3.55
6376 7229 3.243301 ACGTAACCTAGCGTGATACCATG 60.243 47.826 0.00 0.00 40.03 3.66
6377 7230 3.243301 CGTAACCTAGCGTGATACCATGT 60.243 47.826 0.00 0.00 0.00 3.21
6378 7231 4.023792 CGTAACCTAGCGTGATACCATGTA 60.024 45.833 0.00 0.00 0.00 2.29
6379 7232 5.506151 CGTAACCTAGCGTGATACCATGTAA 60.506 44.000 0.00 0.00 0.00 2.41
6380 7233 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
6381 7234 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
6382 7235 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
6383 7236 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
6384 7237 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
6385 7238 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
6386 7239 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
6387 7240 6.216569 AGCGTGATACCATGTAAGACAATAG 58.783 40.000 0.00 0.00 0.00 1.73
6388 7241 5.405571 GCGTGATACCATGTAAGACAATAGG 59.594 44.000 0.00 0.00 0.00 2.57
6389 7242 5.405571 CGTGATACCATGTAAGACAATAGGC 59.594 44.000 0.00 0.00 0.00 3.93
6390 7243 6.525629 GTGATACCATGTAAGACAATAGGCT 58.474 40.000 0.00 0.00 0.00 4.58
6391 7244 6.992715 GTGATACCATGTAAGACAATAGGCTT 59.007 38.462 0.00 0.00 0.00 4.35
6392 7245 7.499232 GTGATACCATGTAAGACAATAGGCTTT 59.501 37.037 0.00 0.00 0.00 3.51
6393 7246 7.498900 TGATACCATGTAAGACAATAGGCTTTG 59.501 37.037 0.00 0.00 0.00 2.77
6394 7247 4.949856 ACCATGTAAGACAATAGGCTTTGG 59.050 41.667 0.00 0.00 0.00 3.28
6395 7248 4.339247 CCATGTAAGACAATAGGCTTTGGG 59.661 45.833 0.00 0.00 0.00 4.12
6396 7249 3.963129 TGTAAGACAATAGGCTTTGGGG 58.037 45.455 0.00 0.00 0.00 4.96
6397 7250 2.532250 AAGACAATAGGCTTTGGGGG 57.468 50.000 0.00 0.00 0.00 5.40
6398 7251 1.681229 AGACAATAGGCTTTGGGGGA 58.319 50.000 0.00 0.00 0.00 4.81
6399 7252 2.000048 AGACAATAGGCTTTGGGGGAA 59.000 47.619 0.00 0.00 0.00 3.97
6400 7253 2.100197 GACAATAGGCTTTGGGGGAAC 58.900 52.381 0.00 0.00 0.00 3.62
6412 7265 2.833957 GGGAACCGACACAACCCT 59.166 61.111 0.00 0.00 40.86 4.34
6413 7266 1.302271 GGGAACCGACACAACCCTC 60.302 63.158 0.00 0.00 40.86 4.30
6414 7267 1.752833 GGAACCGACACAACCCTCT 59.247 57.895 0.00 0.00 0.00 3.69
6415 7268 0.971386 GGAACCGACACAACCCTCTA 59.029 55.000 0.00 0.00 0.00 2.43
6416 7269 1.067071 GGAACCGACACAACCCTCTAG 60.067 57.143 0.00 0.00 0.00 2.43
6417 7270 0.974383 AACCGACACAACCCTCTAGG 59.026 55.000 0.00 0.00 43.78 3.02
6428 7281 3.074788 CCTCTAGGGGTGGCCTATC 57.925 63.158 3.32 0.00 0.00 2.08
6429 7282 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.00 0.00 2.15
6430 7283 1.203364 CCTCTAGGGGTGGCCTATCAT 60.203 57.143 3.32 0.00 0.00 2.45
6431 7284 2.044492 CCTCTAGGGGTGGCCTATCATA 59.956 54.545 3.32 0.00 0.00 2.15
6432 7285 3.310954 CCTCTAGGGGTGGCCTATCATAT 60.311 52.174 3.32 0.00 0.00 1.78
6433 7286 4.078571 CCTCTAGGGGTGGCCTATCATATA 60.079 50.000 3.32 0.00 0.00 0.86
6434 7287 5.401939 CCTCTAGGGGTGGCCTATCATATAT 60.402 48.000 3.32 0.00 0.00 0.86
6435 7288 6.183361 CCTCTAGGGGTGGCCTATCATATATA 60.183 46.154 3.32 0.00 0.00 0.86
6436 7289 7.436204 TCTAGGGGTGGCCTATCATATATAT 57.564 40.000 3.32 0.00 0.00 0.86
6437 7290 8.548403 TCTAGGGGTGGCCTATCATATATATA 57.452 38.462 3.32 0.00 0.00 0.86
6438 7291 9.152046 TCTAGGGGTGGCCTATCATATATATAT 57.848 37.037 3.32 0.00 0.00 0.86
6463 7316 9.918630 ATATAATGAGGTGGTATACAACGTTAC 57.081 33.333 7.03 0.00 43.31 2.50
6464 7317 5.664294 ATGAGGTGGTATACAACGTTACA 57.336 39.130 7.03 2.59 43.31 2.41
6465 7318 5.465532 TGAGGTGGTATACAACGTTACAA 57.534 39.130 7.03 0.00 43.31 2.41
6466 7319 6.040209 TGAGGTGGTATACAACGTTACAAT 57.960 37.500 7.03 0.00 43.31 2.71
6467 7320 7.167924 TGAGGTGGTATACAACGTTACAATA 57.832 36.000 7.03 0.00 43.31 1.90
6468 7321 7.784037 TGAGGTGGTATACAACGTTACAATAT 58.216 34.615 7.03 0.00 43.31 1.28
6469 7322 8.911965 TGAGGTGGTATACAACGTTACAATATA 58.088 33.333 7.03 0.00 43.31 0.86
6470 7323 9.185192 GAGGTGGTATACAACGTTACAATATAC 57.815 37.037 7.03 10.70 43.31 1.47
6471 7324 8.694540 AGGTGGTATACAACGTTACAATATACA 58.305 33.333 20.89 12.28 43.31 2.29
6472 7325 8.755018 GGTGGTATACAACGTTACAATATACAC 58.245 37.037 20.89 18.40 32.62 2.90
6473 7326 9.299963 GTGGTATACAACGTTACAATATACACA 57.700 33.333 20.89 16.35 32.62 3.72
6630 7484 2.614520 TCTTTTCGATGCGTGTTTTCCA 59.385 40.909 0.00 0.00 0.00 3.53
6781 7640 3.944015 CAGAAGTAATTCCAAGAGGGCTG 59.056 47.826 0.00 0.00 36.21 4.85
6852 7714 6.255453 TGCAACACTTCATTTTTACTTTCTGC 59.745 34.615 0.00 0.00 0.00 4.26
6856 7718 5.403466 CACTTCATTTTTACTTTCTGCTGGC 59.597 40.000 0.00 0.00 0.00 4.85
6905 7768 5.423886 GCTAGTTAGAGACCTTGCATTCTT 58.576 41.667 0.00 0.00 0.00 2.52
7098 8368 7.535997 AGCAGCGTGATCGTATTATATAAAGA 58.464 34.615 0.00 0.75 39.49 2.52
7301 8572 4.501400 GCTATTTGTTGCCAAAACTGGTCT 60.501 41.667 0.00 0.00 43.43 3.85
7326 8597 5.825593 AAGAATTCAGAACCAGGACACTA 57.174 39.130 8.44 0.00 0.00 2.74
7379 8651 5.469479 CCAGTGTTTGGTGCTATTTTTAGG 58.531 41.667 0.00 0.00 42.41 2.69
7412 8684 1.970917 GCGAAATGCTCAGTGGACGG 61.971 60.000 0.00 0.00 41.73 4.79
7440 8712 8.908786 AGAAACAGAAATTAGAACTCATCACA 57.091 30.769 0.00 0.00 0.00 3.58
7547 8823 2.902705 AAGTGCGTACCTCAACTCAA 57.097 45.000 0.00 0.00 0.00 3.02
7582 8858 3.825611 CAGGGGGCCAATTTCGCG 61.826 66.667 4.39 0.00 0.00 5.87
7754 9034 6.300354 CCAAATTTGGCCTATCTTAGTACG 57.700 41.667 23.81 0.00 42.21 3.67
7798 9085 9.606631 ACTGAAGATCCATTCTGTTTATCTTAC 57.393 33.333 0.00 0.00 37.91 2.34
7924 9211 1.840741 CTACTTCGCGAACATGACGAG 59.159 52.381 19.38 8.13 37.11 4.18
8035 9322 1.360911 GCTAGTAGGCTGGCTCGAC 59.639 63.158 7.13 0.87 44.51 4.20
8036 9323 1.384989 GCTAGTAGGCTGGCTCGACA 61.385 60.000 7.13 0.00 44.51 4.35
8037 9324 1.103803 CTAGTAGGCTGGCTCGACAA 58.896 55.000 7.13 0.00 0.00 3.18
8038 9325 0.815734 TAGTAGGCTGGCTCGACAAC 59.184 55.000 7.13 0.00 0.00 3.32
8039 9326 0.900647 AGTAGGCTGGCTCGACAACT 60.901 55.000 7.13 1.99 0.00 3.16
8040 9327 0.737715 GTAGGCTGGCTCGACAACTG 60.738 60.000 7.13 0.00 0.00 3.16
8049 9336 1.001268 GCTCGACAACTGACTGACTGA 60.001 52.381 0.00 0.00 0.00 3.41
8175 9463 2.746277 GCCGCGGTCAAGGACAAT 60.746 61.111 28.70 0.00 33.68 2.71
8238 9526 1.140312 ACCAGAGGCTCAAGGAAACA 58.860 50.000 26.52 0.00 0.00 2.83
8246 9534 1.815408 GCTCAAGGAAACAGTGGCTCA 60.815 52.381 0.00 0.00 0.00 4.26
8250 9538 3.152341 CAAGGAAACAGTGGCTCATCTT 58.848 45.455 0.00 0.00 0.00 2.40
8265 9553 3.178865 TCATCTTCGGAAAACCTACCCT 58.821 45.455 0.00 0.00 0.00 4.34
8301 9589 3.017314 GTCGATGTCTACGCCGCG 61.017 66.667 12.14 12.14 0.00 6.46
8387 9676 1.575244 ATGCATACGTGTAGCTGCTG 58.425 50.000 13.43 0.00 35.66 4.41
8414 9703 3.128242 CGTACGTAGTGTCCTGGAGAAAT 59.872 47.826 7.22 0.00 45.73 2.17
8432 9721 2.249413 ATCTGAGGCTGGGCGTTCTG 62.249 60.000 0.00 0.00 0.00 3.02
8559 9848 1.456705 GTGGGTGGTGCTGGGAAAA 60.457 57.895 0.00 0.00 0.00 2.29
8629 9918 1.668151 GAGGCGGCGAACAAGTTCT 60.668 57.895 12.98 0.00 37.44 3.01
8735 10024 2.357034 CGGGTCGTTGGTCAGGTG 60.357 66.667 0.00 0.00 0.00 4.00
8761 10050 2.037136 CCGCTGCTGCTGCTACTTT 61.037 57.895 25.43 0.00 40.48 2.66
8847 10157 4.843220 AGTGTCTTTTGCATCTCCAAAG 57.157 40.909 2.05 2.05 36.21 2.77
8851 10163 3.319122 GTCTTTTGCATCTCCAAAGGTGT 59.681 43.478 7.73 0.00 35.92 4.16
9097 10586 8.362639 TGAACTACACCGAAGATAAAACTACTT 58.637 33.333 0.00 0.00 0.00 2.24
9201 10741 2.590092 GGATCACCGTCAAGGGGG 59.410 66.667 0.00 0.00 45.91 5.40
9222 10776 1.038681 GGTCTCGTCCTCCTCCTTCC 61.039 65.000 0.00 0.00 0.00 3.46
9231 10860 2.044252 CCTCCTTCCCCTCGACGA 60.044 66.667 0.00 0.00 0.00 4.20
9240 10869 2.870161 CCTCGACGACGTGCTTCG 60.870 66.667 4.58 2.28 44.87 3.79
9267 10896 3.730761 CTTGCTCGGCCTGCACAC 61.731 66.667 17.99 0.00 40.40 3.82
9417 11074 2.184322 GAGCAACTCCGCATCCGA 59.816 61.111 0.00 0.00 36.29 4.55
9420 11077 1.741770 GCAACTCCGCATCCGACTT 60.742 57.895 0.00 0.00 36.29 3.01
9457 11114 1.718280 AGTTGAGGTCCTTCTTCGGT 58.282 50.000 0.00 0.00 0.00 4.69
9601 11264 1.840635 GGCCTCACATAGAAGAACCCT 59.159 52.381 0.00 0.00 0.00 4.34
9605 11268 3.195825 CCTCACATAGAAGAACCCTCGTT 59.804 47.826 0.00 0.00 33.88 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 6.201425 GCAAATTTTAGTGCATGTATCATGGG 59.799 38.462 10.96 0.00 40.58 4.00
412 509 9.367444 GACGAGATCTTTAAAACTAGATTCCAA 57.633 33.333 0.00 0.00 31.46 3.53
439 536 7.270047 TCCGTCTTCATTATTAAATCCGTCTT 58.730 34.615 0.00 0.00 0.00 3.01
550 658 8.836413 GTCTTCATTATCATCCGTTTTTCCATA 58.164 33.333 0.00 0.00 0.00 2.74
560 669 6.259608 AGCTCAAAAGTCTTCATTATCATCCG 59.740 38.462 0.00 0.00 0.00 4.18
577 686 3.307674 CGCAAAGCAACATAGCTCAAAA 58.692 40.909 0.00 0.00 45.89 2.44
599 708 2.131972 TGATAAGTGTCACACGTGTGC 58.868 47.619 37.70 31.18 45.25 4.57
637 746 7.794349 CGCAAAGTCCGCAAAAATAAATAAAAA 59.206 29.630 0.00 0.00 0.00 1.94
657 766 1.127951 GGTGGATCACGTTACGCAAAG 59.872 52.381 4.09 0.00 34.83 2.77
670 779 1.165270 CCGTTGGACTTTGGTGGATC 58.835 55.000 0.00 0.00 0.00 3.36
763 873 3.881104 GTGGTGGGGGTGAACGGT 61.881 66.667 0.00 0.00 0.00 4.83
829 957 1.216444 GGCGAGTGTGAGATGAGCA 59.784 57.895 0.00 0.00 0.00 4.26
881 1009 4.338710 TTTTGAGGGGGTCGCGGG 62.339 66.667 6.13 0.00 0.00 6.13
887 1015 2.785776 GGTGGGGTTTTGAGGGGGT 61.786 63.158 0.00 0.00 0.00 4.95
890 1018 0.614697 GGATGGTGGGGTTTTGAGGG 60.615 60.000 0.00 0.00 0.00 4.30
1054 1192 2.559840 CAGCAAGAACAGCAGCGG 59.440 61.111 0.00 0.00 0.00 5.52
1113 1254 2.188161 GTTGAACACGGCCGGGAAA 61.188 57.895 38.56 22.17 0.00 3.13
1288 1429 0.793250 GTTTGAGACTGAAGGCGCTC 59.207 55.000 7.64 0.00 0.00 5.03
1328 1469 7.770897 ACAGTACTGAGAGTTTGAGACATTTTT 59.229 33.333 29.30 0.00 0.00 1.94
1329 1470 7.275920 ACAGTACTGAGAGTTTGAGACATTTT 58.724 34.615 29.30 0.00 0.00 1.82
1330 1471 6.821388 ACAGTACTGAGAGTTTGAGACATTT 58.179 36.000 29.30 0.00 0.00 2.32
1331 1472 6.040955 TGACAGTACTGAGAGTTTGAGACATT 59.959 38.462 29.30 0.24 0.00 2.71
1332 1473 5.536538 TGACAGTACTGAGAGTTTGAGACAT 59.463 40.000 29.30 0.94 0.00 3.06
1333 1474 4.887655 TGACAGTACTGAGAGTTTGAGACA 59.112 41.667 29.30 0.39 0.00 3.41
1334 1475 5.440234 TGACAGTACTGAGAGTTTGAGAC 57.560 43.478 29.30 0.00 0.00 3.36
1335 1476 4.520874 CCTGACAGTACTGAGAGTTTGAGA 59.479 45.833 29.30 0.02 0.00 3.27
1421 1562 9.983804 CGGGTGAAAAGTAATAAGAAAAGTATC 57.016 33.333 0.00 0.00 0.00 2.24
1422 1563 9.511272 ACGGGTGAAAAGTAATAAGAAAAGTAT 57.489 29.630 0.00 0.00 0.00 2.12
1423 1564 8.907222 ACGGGTGAAAAGTAATAAGAAAAGTA 57.093 30.769 0.00 0.00 0.00 2.24
1424 1565 7.812690 ACGGGTGAAAAGTAATAAGAAAAGT 57.187 32.000 0.00 0.00 0.00 2.66
1425 1566 7.532884 CGAACGGGTGAAAAGTAATAAGAAAAG 59.467 37.037 0.00 0.00 0.00 2.27
1426 1567 7.226325 TCGAACGGGTGAAAAGTAATAAGAAAA 59.774 33.333 0.00 0.00 0.00 2.29
1427 1568 6.705381 TCGAACGGGTGAAAAGTAATAAGAAA 59.295 34.615 0.00 0.00 0.00 2.52
1428 1569 6.222389 TCGAACGGGTGAAAAGTAATAAGAA 58.778 36.000 0.00 0.00 0.00 2.52
1460 1601 2.383527 GCCGTGCAGAAGAACCGAG 61.384 63.158 0.00 0.00 0.00 4.63
1515 1656 1.003839 CCTGCAAGTGAAGGCGGTA 60.004 57.895 0.00 0.00 33.21 4.02
1545 1686 3.879295 CACATGGAACGAATTCAGGCTAT 59.121 43.478 6.22 0.00 36.46 2.97
1552 1693 2.030457 CCGCTACACATGGAACGAATTC 59.970 50.000 0.00 0.00 0.00 2.17
1605 1749 4.849111 AACTACGCTGTAGTACTACGAC 57.151 45.455 24.36 18.26 38.85 4.34
1621 1765 9.224058 CAGAACTCTTAGAAAGCGTATAACTAC 57.776 37.037 0.00 0.00 0.00 2.73
1622 1766 9.170734 TCAGAACTCTTAGAAAGCGTATAACTA 57.829 33.333 0.00 0.00 0.00 2.24
1623 1767 8.053026 TCAGAACTCTTAGAAAGCGTATAACT 57.947 34.615 0.00 0.00 0.00 2.24
1624 1768 8.684973 TTCAGAACTCTTAGAAAGCGTATAAC 57.315 34.615 0.00 0.00 0.00 1.89
1625 1769 7.974501 CCTTCAGAACTCTTAGAAAGCGTATAA 59.025 37.037 0.00 0.00 0.00 0.98
1627 1771 6.153000 TCCTTCAGAACTCTTAGAAAGCGTAT 59.847 38.462 0.00 0.00 0.00 3.06
1631 1775 6.031751 TCTCCTTCAGAACTCTTAGAAAGC 57.968 41.667 0.00 0.00 0.00 3.51
1636 1780 9.936759 ACTTTTATTCTCCTTCAGAACTCTTAG 57.063 33.333 0.00 0.00 44.28 2.18
1638 1782 9.061435 CAACTTTTATTCTCCTTCAGAACTCTT 57.939 33.333 0.00 0.00 44.28 2.85
1763 2076 2.979813 CAAAGTAGCGCAAACAACATCC 59.020 45.455 11.47 0.00 0.00 3.51
1775 2088 2.124903 ACACGAAGTCACAAAGTAGCG 58.875 47.619 0.00 0.00 41.61 4.26
1776 2089 3.772522 GACACGAAGTCACAAAGTAGC 57.227 47.619 7.67 0.00 46.77 3.58
1790 2103 0.901827 ATACATGCCCAGTGACACGA 59.098 50.000 0.00 0.00 0.00 4.35
1791 2104 2.595124 TATACATGCCCAGTGACACG 57.405 50.000 0.00 0.00 0.00 4.49
1792 2105 3.565482 CCATTATACATGCCCAGTGACAC 59.435 47.826 0.00 0.00 0.00 3.67
1793 2106 3.201930 ACCATTATACATGCCCAGTGACA 59.798 43.478 0.00 0.00 0.00 3.58
1794 2107 3.565482 CACCATTATACATGCCCAGTGAC 59.435 47.826 0.00 0.00 0.00 3.67
1796 2109 2.886523 CCACCATTATACATGCCCAGTG 59.113 50.000 0.00 0.00 0.00 3.66
1797 2110 2.752829 GCCACCATTATACATGCCCAGT 60.753 50.000 0.00 0.00 0.00 4.00
1798 2111 1.888512 GCCACCATTATACATGCCCAG 59.111 52.381 0.00 0.00 0.00 4.45
1876 2718 1.838112 TGGTAGCTTGCATTGGGAAG 58.162 50.000 0.00 0.00 44.50 3.46
1877 2719 2.530460 ATGGTAGCTTGCATTGGGAA 57.470 45.000 0.00 0.00 0.00 3.97
1878 2720 2.530460 AATGGTAGCTTGCATTGGGA 57.470 45.000 0.00 0.00 0.00 4.37
1964 2806 2.357637 CCGGTGACAAAAGCTGAAAAGA 59.642 45.455 0.00 0.00 0.00 2.52
1998 2840 0.250901 GGAGGCAGGTGCTTGAAGAA 60.251 55.000 0.00 0.00 41.70 2.52
2020 2862 1.705873 TAAGGAAGCGGGATCCTCTC 58.294 55.000 12.58 3.23 46.65 3.20
2037 2879 5.895636 TGACGTAAAGTAGGTTCGGATAA 57.104 39.130 0.00 0.00 0.00 1.75
2055 2897 3.798878 GCCATGTATGATCGGATATGACG 59.201 47.826 5.34 0.00 0.00 4.35
2069 2911 1.148949 TGCCTCGCATGCCATGTAT 59.851 52.632 13.15 0.00 31.71 2.29
2099 2941 5.063204 GGACTAGGCATGTACAATGCATAA 58.937 41.667 22.92 12.02 46.21 1.90
2117 2959 2.108168 CTTCCAGGATCCAACGGACTA 58.892 52.381 15.82 2.13 32.98 2.59
2118 2960 0.905357 CTTCCAGGATCCAACGGACT 59.095 55.000 15.82 0.00 32.98 3.85
2259 3108 3.431207 GGCAGGATGTGAAATGAAATGGG 60.431 47.826 0.00 0.00 39.31 4.00
2365 3214 1.748122 CTTGCTTCGGCCATGCTCT 60.748 57.895 2.24 0.00 40.91 4.09
2491 3341 2.646175 GGTGTCGGTAGGCAGCTGA 61.646 63.158 20.43 0.00 46.03 4.26
2492 3342 2.125512 GGTGTCGGTAGGCAGCTG 60.126 66.667 10.11 10.11 46.03 4.24
2510 3360 1.896220 TCTGTTGGATTGCACAGGAC 58.104 50.000 0.00 0.00 40.81 3.85
2591 3441 1.336795 CCCAACACAAAATCTTCCCGC 60.337 52.381 0.00 0.00 0.00 6.13
2652 3502 0.179000 ACTAGCATCCCGAAAGCCAG 59.821 55.000 0.00 0.00 0.00 4.85
2669 3519 6.650120 TGTCTTACAGTCAGAAAGGAAAACT 58.350 36.000 0.00 0.00 0.00 2.66
2680 3530 5.352569 CCAAAGCCTATTGTCTTACAGTCAG 59.647 44.000 0.00 0.00 0.00 3.51
2681 3531 5.245531 CCAAAGCCTATTGTCTTACAGTCA 58.754 41.667 0.00 0.00 0.00 3.41
2682 3532 4.636206 CCCAAAGCCTATTGTCTTACAGTC 59.364 45.833 0.00 0.00 0.00 3.51
3460 4313 1.427368 AGTATTGTTGGTGGGCTCCAA 59.573 47.619 9.77 9.77 44.03 3.53
4419 5272 3.603158 TTCAGCCTAAGCAACGTCATA 57.397 42.857 0.00 0.00 43.56 2.15
4549 5402 2.033602 TCGTCTGTCCCGAGCTCA 59.966 61.111 15.40 0.00 0.00 4.26
5940 6793 2.519002 GCATGTTTTGCGTCGTCATA 57.481 45.000 0.00 0.00 42.54 2.15
6339 7192 0.600557 TACGTCCGTTTCCGCCTAAA 59.399 50.000 0.00 0.00 0.00 1.85
6340 7193 0.600557 TTACGTCCGTTTCCGCCTAA 59.399 50.000 0.00 0.00 0.00 2.69
6341 7194 0.109319 GTTACGTCCGTTTCCGCCTA 60.109 55.000 0.00 0.00 0.00 3.93
6342 7195 1.373371 GTTACGTCCGTTTCCGCCT 60.373 57.895 0.00 0.00 0.00 5.52
6343 7196 2.382746 GGTTACGTCCGTTTCCGCC 61.383 63.158 0.00 0.00 0.00 6.13
6344 7197 0.109319 TAGGTTACGTCCGTTTCCGC 60.109 55.000 0.00 0.00 0.00 5.54
6345 7198 1.900237 CTAGGTTACGTCCGTTTCCG 58.100 55.000 0.00 0.00 0.00 4.30
6346 7199 1.633561 GCTAGGTTACGTCCGTTTCC 58.366 55.000 0.00 1.50 0.00 3.13
6347 7200 1.262882 CGCTAGGTTACGTCCGTTTC 58.737 55.000 0.00 0.00 0.00 2.78
6348 7201 0.598065 ACGCTAGGTTACGTCCGTTT 59.402 50.000 0.00 0.00 38.28 3.60
6349 7202 0.109597 CACGCTAGGTTACGTCCGTT 60.110 55.000 0.00 0.00 41.32 4.44
6350 7203 0.955428 TCACGCTAGGTTACGTCCGT 60.955 55.000 0.00 0.00 41.32 4.69
6351 7204 0.379669 ATCACGCTAGGTTACGTCCG 59.620 55.000 0.00 0.00 41.32 4.79
6352 7205 2.287248 GGTATCACGCTAGGTTACGTCC 60.287 54.545 0.00 0.00 41.32 4.79
6353 7206 2.355756 TGGTATCACGCTAGGTTACGTC 59.644 50.000 0.00 0.00 41.32 4.34
6354 7207 2.368439 TGGTATCACGCTAGGTTACGT 58.632 47.619 0.00 0.00 44.75 3.57
6355 7208 3.243301 ACATGGTATCACGCTAGGTTACG 60.243 47.826 0.00 0.00 0.00 3.18
6356 7209 4.317671 ACATGGTATCACGCTAGGTTAC 57.682 45.455 0.00 0.00 0.00 2.50
6357 7210 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
6358 7211 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
6359 7212 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
6360 7213 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
6361 7214 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
6362 7215 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
6363 7216 4.465632 TTGTCTTACATGGTATCACGCT 57.534 40.909 0.00 0.00 0.00 5.07
6364 7217 5.405571 CCTATTGTCTTACATGGTATCACGC 59.594 44.000 0.00 0.00 0.00 5.34
6365 7218 5.405571 GCCTATTGTCTTACATGGTATCACG 59.594 44.000 0.00 0.00 0.00 4.35
6366 7219 6.525629 AGCCTATTGTCTTACATGGTATCAC 58.474 40.000 0.00 0.00 0.00 3.06
6367 7220 6.747414 AGCCTATTGTCTTACATGGTATCA 57.253 37.500 0.00 0.00 0.00 2.15
6368 7221 7.041098 CCAAAGCCTATTGTCTTACATGGTATC 60.041 40.741 0.00 0.00 0.00 2.24
6369 7222 6.772716 CCAAAGCCTATTGTCTTACATGGTAT 59.227 38.462 0.00 0.00 0.00 2.73
6370 7223 6.119536 CCAAAGCCTATTGTCTTACATGGTA 58.880 40.000 0.00 0.00 0.00 3.25
6371 7224 4.949856 CCAAAGCCTATTGTCTTACATGGT 59.050 41.667 0.00 0.00 0.00 3.55
6372 7225 4.339247 CCCAAAGCCTATTGTCTTACATGG 59.661 45.833 0.00 0.00 0.00 3.66
6373 7226 4.339247 CCCCAAAGCCTATTGTCTTACATG 59.661 45.833 0.00 0.00 0.00 3.21
6374 7227 4.536765 CCCCAAAGCCTATTGTCTTACAT 58.463 43.478 0.00 0.00 0.00 2.29
6375 7228 3.308832 CCCCCAAAGCCTATTGTCTTACA 60.309 47.826 0.00 0.00 0.00 2.41
6376 7229 3.053917 TCCCCCAAAGCCTATTGTCTTAC 60.054 47.826 0.00 0.00 0.00 2.34
6377 7230 3.194620 TCCCCCAAAGCCTATTGTCTTA 58.805 45.455 0.00 0.00 0.00 2.10
6378 7231 2.000048 TCCCCCAAAGCCTATTGTCTT 59.000 47.619 0.00 0.00 0.00 3.01
6379 7232 1.681229 TCCCCCAAAGCCTATTGTCT 58.319 50.000 0.00 0.00 0.00 3.41
6380 7233 2.100197 GTTCCCCCAAAGCCTATTGTC 58.900 52.381 0.00 0.00 0.00 3.18
6381 7234 1.273041 GGTTCCCCCAAAGCCTATTGT 60.273 52.381 0.00 0.00 0.00 2.71
6382 7235 1.485124 GGTTCCCCCAAAGCCTATTG 58.515 55.000 0.00 0.00 0.00 1.90
6383 7236 0.033503 CGGTTCCCCCAAAGCCTATT 60.034 55.000 0.00 0.00 0.00 1.73
6384 7237 0.917333 TCGGTTCCCCCAAAGCCTAT 60.917 55.000 0.00 0.00 0.00 2.57
6385 7238 1.539372 TCGGTTCCCCCAAAGCCTA 60.539 57.895 0.00 0.00 0.00 3.93
6386 7239 2.856988 TCGGTTCCCCCAAAGCCT 60.857 61.111 0.00 0.00 0.00 4.58
6387 7240 2.675423 GTCGGTTCCCCCAAAGCC 60.675 66.667 0.00 0.00 0.00 4.35
6388 7241 2.114411 TGTCGGTTCCCCCAAAGC 59.886 61.111 0.00 0.00 0.00 3.51
6389 7242 0.466555 TTGTGTCGGTTCCCCCAAAG 60.467 55.000 0.00 0.00 0.00 2.77
6390 7243 0.752376 GTTGTGTCGGTTCCCCCAAA 60.752 55.000 0.00 0.00 0.00 3.28
6391 7244 1.152922 GTTGTGTCGGTTCCCCCAA 60.153 57.895 0.00 0.00 0.00 4.12
6392 7245 2.511900 GTTGTGTCGGTTCCCCCA 59.488 61.111 0.00 0.00 0.00 4.96
6393 7246 2.281970 GGTTGTGTCGGTTCCCCC 60.282 66.667 0.00 0.00 0.00 5.40
6394 7247 2.281970 GGGTTGTGTCGGTTCCCC 60.282 66.667 0.00 0.00 32.66 4.81
6395 7248 1.302271 GAGGGTTGTGTCGGTTCCC 60.302 63.158 0.00 0.00 38.50 3.97
6396 7249 0.971386 TAGAGGGTTGTGTCGGTTCC 59.029 55.000 0.00 0.00 0.00 3.62
6397 7250 1.067071 CCTAGAGGGTTGTGTCGGTTC 60.067 57.143 0.00 0.00 0.00 3.62
6398 7251 0.974383 CCTAGAGGGTTGTGTCGGTT 59.026 55.000 0.00 0.00 0.00 4.44
6399 7252 2.667348 CCTAGAGGGTTGTGTCGGT 58.333 57.895 0.00 0.00 0.00 4.69
6437 7290 9.918630 GTAACGTTGTATACCACCTCATTATAT 57.081 33.333 11.99 0.00 0.00 0.86
6438 7291 8.911965 TGTAACGTTGTATACCACCTCATTATA 58.088 33.333 11.99 0.00 0.00 0.98
6439 7292 7.784037 TGTAACGTTGTATACCACCTCATTAT 58.216 34.615 11.99 0.00 0.00 1.28
6440 7293 7.167924 TGTAACGTTGTATACCACCTCATTA 57.832 36.000 11.99 0.00 0.00 1.90
6441 7294 6.040209 TGTAACGTTGTATACCACCTCATT 57.960 37.500 11.99 0.00 0.00 2.57
6442 7295 5.664294 TGTAACGTTGTATACCACCTCAT 57.336 39.130 11.99 0.00 0.00 2.90
6443 7296 5.465532 TTGTAACGTTGTATACCACCTCA 57.534 39.130 11.99 0.00 0.00 3.86
6444 7297 9.185192 GTATATTGTAACGTTGTATACCACCTC 57.815 37.037 11.99 0.00 0.00 3.85
6445 7298 8.694540 TGTATATTGTAACGTTGTATACCACCT 58.305 33.333 11.99 0.00 30.78 4.00
6446 7299 8.755018 GTGTATATTGTAACGTTGTATACCACC 58.245 37.037 11.99 6.07 30.78 4.61
6447 7300 9.299963 TGTGTATATTGTAACGTTGTATACCAC 57.700 33.333 11.99 14.15 30.78 4.16
6469 7322 9.719355 TCAGTGTTAGATTGTATTTACATGTGT 57.281 29.630 9.11 0.00 35.89 3.72
6470 7323 9.973246 GTCAGTGTTAGATTGTATTTACATGTG 57.027 33.333 9.11 0.00 35.89 3.21
6471 7324 9.719355 TGTCAGTGTTAGATTGTATTTACATGT 57.281 29.630 2.69 2.69 35.89 3.21
6475 7328 9.988350 CCATTGTCAGTGTTAGATTGTATTTAC 57.012 33.333 0.00 0.00 0.00 2.01
6476 7329 9.173021 CCCATTGTCAGTGTTAGATTGTATTTA 57.827 33.333 0.00 0.00 0.00 1.40
6477 7330 7.888021 TCCCATTGTCAGTGTTAGATTGTATTT 59.112 33.333 0.00 0.00 0.00 1.40
6478 7331 7.402054 TCCCATTGTCAGTGTTAGATTGTATT 58.598 34.615 0.00 0.00 0.00 1.89
6479 7332 6.957631 TCCCATTGTCAGTGTTAGATTGTAT 58.042 36.000 0.00 0.00 0.00 2.29
6480 7333 6.367374 TCCCATTGTCAGTGTTAGATTGTA 57.633 37.500 0.00 0.00 0.00 2.41
6481 7334 5.241403 TCCCATTGTCAGTGTTAGATTGT 57.759 39.130 0.00 0.00 0.00 2.71
6482 7335 5.449588 GCATCCCATTGTCAGTGTTAGATTG 60.450 44.000 0.00 0.00 0.00 2.67
6483 7336 4.641989 GCATCCCATTGTCAGTGTTAGATT 59.358 41.667 0.00 0.00 0.00 2.40
6484 7337 4.080129 AGCATCCCATTGTCAGTGTTAGAT 60.080 41.667 0.00 0.00 0.00 1.98
6485 7338 3.264193 AGCATCCCATTGTCAGTGTTAGA 59.736 43.478 0.00 0.00 0.00 2.10
6486 7339 3.376234 CAGCATCCCATTGTCAGTGTTAG 59.624 47.826 0.00 0.00 0.00 2.34
6487 7340 3.008923 TCAGCATCCCATTGTCAGTGTTA 59.991 43.478 0.00 0.00 0.00 2.41
6488 7341 2.165167 CAGCATCCCATTGTCAGTGTT 58.835 47.619 0.00 0.00 0.00 3.32
6489 7342 1.352017 TCAGCATCCCATTGTCAGTGT 59.648 47.619 0.00 0.00 0.00 3.55
6490 7343 2.118313 TCAGCATCCCATTGTCAGTG 57.882 50.000 0.00 0.00 0.00 3.66
6491 7344 3.377253 AATCAGCATCCCATTGTCAGT 57.623 42.857 0.00 0.00 0.00 3.41
6494 7347 3.949754 TCTCAAATCAGCATCCCATTGTC 59.050 43.478 0.00 0.00 0.00 3.18
6577 7431 2.160417 GCCAAATTCTCTGGAACTGTCG 59.840 50.000 0.00 0.00 35.85 4.35
6630 7484 4.439968 GGAAAATTCCGACCTACGAATCT 58.560 43.478 0.00 0.00 45.77 2.40
6752 7611 8.049721 CCCTCTTGGAATTACTTCTGAGTTATT 58.950 37.037 0.00 0.00 37.71 1.40
6753 7612 7.569240 CCCTCTTGGAATTACTTCTGAGTTAT 58.431 38.462 0.00 0.00 34.96 1.89
6754 7613 6.576442 GCCCTCTTGGAATTACTTCTGAGTTA 60.576 42.308 0.00 0.00 34.96 2.24
6776 7635 0.595095 CTTGAGAAGCACAACAGCCC 59.405 55.000 0.00 0.00 34.23 5.19
6781 7640 4.354587 CCTTGTTTCTTGAGAAGCACAAC 58.645 43.478 9.39 0.00 43.27 3.32
6852 7714 1.933853 GTCACCTAATGCTAACGCCAG 59.066 52.381 0.00 0.00 34.43 4.85
6905 7768 8.337739 AGTGATCTAGGTCTTACTTAGGAAAGA 58.662 37.037 4.28 0.00 36.50 2.52
6988 8258 8.644374 ACACTTAAGACCAGCCAAATTATTTA 57.356 30.769 10.09 0.00 0.00 1.40
6994 8264 4.074970 CTGACACTTAAGACCAGCCAAAT 58.925 43.478 10.09 0.00 0.00 2.32
7001 8271 3.391296 AGCTTTCCTGACACTTAAGACCA 59.609 43.478 10.09 3.03 0.00 4.02
7098 8368 4.212636 GCCAATAATTAATGTACGGCGTCT 59.787 41.667 19.21 2.02 0.00 4.18
7301 8572 4.821805 GTGTCCTGGTTCTGAATTCTTTCA 59.178 41.667 7.05 0.00 39.54 2.69
7326 8597 3.960102 TGCCTCCAACATTTCTTGTTTCT 59.040 39.130 0.00 0.00 46.51 2.52
7373 8645 3.684788 CGCTTTTCTCAGCTAGCCTAAAA 59.315 43.478 12.13 11.62 37.68 1.52
7379 8651 3.678662 CATTTCGCTTTTCTCAGCTAGC 58.321 45.455 6.62 6.62 37.68 3.42
7412 8684 9.436957 TGATGAGTTCTAATTTCTGTTTCTACC 57.563 33.333 0.00 0.00 0.00 3.18
7547 8823 1.137872 CTGCGAGAAGTTGCTCCCTAT 59.862 52.381 0.00 0.00 33.65 2.57
7582 8858 2.125512 ATTGTCGAGCCGGCTGTC 60.126 61.111 38.41 23.11 30.55 3.51
7738 9018 4.789807 AGACTTCGTACTAAGATAGGCCA 58.210 43.478 13.63 0.00 0.00 5.36
7739 9019 5.771153 AAGACTTCGTACTAAGATAGGCC 57.229 43.478 13.63 0.00 0.00 5.19
7754 9034 7.649973 TCTTCAGTTCTGTGTACTAAGACTTC 58.350 38.462 0.00 0.00 0.00 3.01
7797 9084 1.768870 GCCACCTACATACATGGGAGT 59.231 52.381 0.00 0.00 32.49 3.85
7798 9085 1.768275 TGCCACCTACATACATGGGAG 59.232 52.381 0.00 0.00 32.49 4.30
7924 9211 2.121786 TGAACGCTACGACTTGTTCAC 58.878 47.619 11.78 0.00 44.01 3.18
8035 9322 6.649973 AGATCAATTCTTCAGTCAGTCAGTTG 59.350 38.462 0.00 0.00 0.00 3.16
8036 9323 6.649973 CAGATCAATTCTTCAGTCAGTCAGTT 59.350 38.462 0.00 0.00 29.93 3.16
8037 9324 6.164876 CAGATCAATTCTTCAGTCAGTCAGT 58.835 40.000 0.00 0.00 29.93 3.41
8038 9325 5.063691 GCAGATCAATTCTTCAGTCAGTCAG 59.936 44.000 0.00 0.00 29.93 3.51
8039 9326 4.934001 GCAGATCAATTCTTCAGTCAGTCA 59.066 41.667 0.00 0.00 29.93 3.41
8040 9327 4.934001 TGCAGATCAATTCTTCAGTCAGTC 59.066 41.667 0.00 0.00 29.93 3.51
8049 9336 2.676839 CACGCTCTGCAGATCAATTCTT 59.323 45.455 18.63 0.00 29.93 2.52
8075 9363 0.034896 GAAGTTCCTTCCACCGAGCA 59.965 55.000 0.00 0.00 34.71 4.26
8082 9370 2.305927 GTGGATCCAGAAGTTCCTTCCA 59.694 50.000 16.81 4.62 40.98 3.53
8175 9463 1.227943 GGTGACAGAGCAGCCAACA 60.228 57.895 0.00 0.00 0.00 3.33
8238 9526 2.427506 GTTTTCCGAAGATGAGCCACT 58.572 47.619 0.00 0.00 0.00 4.00
8246 9534 3.055312 GTCAGGGTAGGTTTTCCGAAGAT 60.055 47.826 0.00 0.00 46.35 2.40
8250 9538 0.604578 CGTCAGGGTAGGTTTTCCGA 59.395 55.000 0.00 0.00 46.35 4.55
8265 9553 3.672447 TAGGTGAACGCGGCGTCA 61.672 61.111 29.53 23.13 39.99 4.35
8387 9676 0.109412 AGGACACTACGTACGCAAGC 60.109 55.000 16.72 0.00 45.62 4.01
8414 9703 2.604686 AGAACGCCCAGCCTCAGA 60.605 61.111 0.00 0.00 0.00 3.27
8432 9721 2.811317 CGTCGAAGCCTGCAGACC 60.811 66.667 17.39 5.70 0.00 3.85
8629 9918 2.540515 GCCGACGATCTGATCAAAGAA 58.459 47.619 17.19 0.00 0.00 2.52
8761 10050 2.946329 GTCGGAGATGCTCTTACAGAGA 59.054 50.000 4.89 0.00 41.73 3.10
8782 10071 5.962433 ACATCTCCAAATTTGCATCTTCTG 58.038 37.500 12.92 5.87 0.00 3.02
8822 10112 5.186996 TGGAGATGCAAAAGACACTTTTC 57.813 39.130 6.52 3.99 0.00 2.29
8847 10157 5.542779 ACATCTTCTGTTAGAGTTGACACC 58.457 41.667 0.00 0.00 32.90 4.16
9029 10373 4.058817 AGTAGTAGTTGAGTTTGCTGTGC 58.941 43.478 0.00 0.00 0.00 4.57
9097 10586 1.895798 AGTTCAAGAGCTCCGATGACA 59.104 47.619 10.93 2.10 0.00 3.58
9201 10741 3.519930 GGAGGAGGACGAGACCGC 61.520 72.222 0.00 0.00 39.95 5.68
9205 10745 1.306970 GGGAAGGAGGAGGACGAGA 59.693 63.158 0.00 0.00 0.00 4.04
9222 10776 2.504244 GAAGCACGTCGTCGAGGG 60.504 66.667 18.29 8.96 40.62 4.30
9231 10860 1.609555 AGAGTTCTTCTCGAAGCACGT 59.390 47.619 1.81 0.00 46.86 4.49
9240 10869 1.355005 GCCGAGCAAGAGTTCTTCTC 58.645 55.000 0.00 2.36 43.05 2.87
9417 11074 1.006043 TCCCAGAGATCGAGACCAAGT 59.994 52.381 0.00 0.00 0.00 3.16
9420 11077 1.006043 ACTTCCCAGAGATCGAGACCA 59.994 52.381 0.00 0.00 0.00 4.02
9591 11253 1.605753 GGCAAAACGAGGGTTCTTCT 58.394 50.000 0.00 0.00 34.62 2.85
9601 11264 2.345991 CCTCGAGGGGCAAAACGA 59.654 61.111 24.62 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.