Multiple sequence alignment - TraesCS2D01G242200

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BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G242200 chr2D 100.000 4399 0 0 4667 9065 268896224 268900622 0.000000e+00 8124.0
1 TraesCS2D01G242200 chr2D 100.000 4351 0 0 1 4351 268891558 268895908 0.000000e+00 8035.0
2 TraesCS2D01G242200 chr2D 86.010 629 74 8 197 815 38261590 38262214 0.000000e+00 662.0
3 TraesCS2D01G242200 chr2D 77.948 653 103 21 5693 6322 236122191 236122825 4.000000e-98 370.0
4 TraesCS2D01G242200 chr2D 81.124 445 71 7 5261 5699 373889657 373889220 2.420000e-90 344.0
5 TraesCS2D01G242200 chr2D 77.112 651 111 22 5693 6322 601958598 601959231 8.720000e-90 342.0
6 TraesCS2D01G242200 chr2D 96.482 199 7 0 1 199 589533521 589533719 6.790000e-86 329.0
7 TraesCS2D01G242200 chr2D 78.611 547 79 18 5693 6217 373889193 373888663 2.440000e-85 327.0
8 TraesCS2D01G242200 chr2D 76.336 655 104 31 5693 6313 153796527 153797164 4.110000e-78 303.0
9 TraesCS2D01G242200 chr2D 73.933 867 161 45 5468 6312 233386781 233387604 1.150000e-73 289.0
10 TraesCS2D01G242200 chr2D 95.882 170 7 0 2737 2906 512768303 512768134 8.970000e-70 276.0
11 TraesCS2D01G242200 chr2D 75.000 480 103 14 5230 5699 272823300 272822828 1.190000e-48 206.0
12 TraesCS2D01G242200 chr2D 75.730 445 88 11 5267 5700 601958136 601958571 1.190000e-48 206.0
13 TraesCS2D01G242200 chr2D 92.647 68 5 0 3853 3920 589522343 589522276 2.080000e-16 99.0
14 TraesCS2D01G242200 chr2D 96.000 50 1 1 8688 8736 130436905 130436856 7.540000e-11 80.5
15 TraesCS2D01G242200 chr2D 93.182 44 3 0 9022 9065 31329489 31329532 2.110000e-06 65.8
16 TraesCS2D01G242200 chr2B 93.015 3436 138 29 5610 9003 308723553 308726928 0.000000e+00 4922.0
17 TraesCS2D01G242200 chr2B 97.270 1868 36 5 838 2697 308714413 308716273 0.000000e+00 3153.0
18 TraesCS2D01G242200 chr2B 95.339 1223 39 5 2678 3887 308719629 308720846 0.000000e+00 1927.0
19 TraesCS2D01G242200 chr2B 96.919 422 10 3 3922 4341 308720960 308721380 0.000000e+00 704.0
20 TraesCS2D01G242200 chr2B 90.929 463 30 6 4748 5204 308721742 308722198 6.020000e-171 612.0
21 TraesCS2D01G242200 chr2B 91.789 341 22 2 5282 5619 308722382 308722719 3.830000e-128 470.0
22 TraesCS2D01G242200 chr2B 95.882 170 7 0 2737 2906 602995416 602995247 8.970000e-70 276.0
23 TraesCS2D01G242200 chr2B 84.982 273 31 6 5433 5699 443786906 443786638 1.500000e-67 268.0
24 TraesCS2D01G242200 chr2B 87.692 65 8 0 8664 8728 716127256 716127320 9.760000e-10 76.8
25 TraesCS2D01G242200 chr2A 98.745 2231 19 6 837 3062 317955239 317953013 0.000000e+00 3956.0
26 TraesCS2D01G242200 chr2A 96.121 2346 55 10 4667 7008 317943972 317941659 0.000000e+00 3795.0
27 TraesCS2D01G242200 chr2A 96.304 1975 56 7 7050 9021 317941659 317939699 0.000000e+00 3227.0
28 TraesCS2D01G242200 chr2A 98.203 1280 21 2 3051 4330 317945700 317944423 0.000000e+00 2235.0
29 TraesCS2D01G242200 chr2A 75.472 954 154 46 5342 6271 552479778 552478881 8.530000e-105 392.0
30 TraesCS2D01G242200 chr2A 77.103 642 104 20 5693 6312 27991461 27992081 1.890000e-86 331.0
31 TraesCS2D01G242200 chr2A 73.341 859 166 45 5468 6312 286423778 286424587 9.030000e-65 259.0
32 TraesCS2D01G242200 chr2A 75.100 502 104 13 5211 5700 333713622 333713130 1.980000e-51 215.0
33 TraesCS2D01G242200 chr2A 75.058 429 85 15 5284 5700 503028240 503028658 7.230000e-41 180.0
34 TraesCS2D01G242200 chr2A 91.358 81 4 3 4667 4747 353473831 353473908 3.460000e-19 108.0
35 TraesCS2D01G242200 chr2A 92.754 69 5 0 3852 3920 57166862 57166930 5.790000e-17 100.0
36 TraesCS2D01G242200 chr2A 89.024 82 8 1 4667 4748 655038210 655038130 5.790000e-17 100.0
37 TraesCS2D01G242200 chr2A 93.023 43 3 0 9023 9065 440688774 440688732 7.600000e-06 63.9
38 TraesCS2D01G242200 chr1D 89.189 629 56 6 197 815 491945350 491944724 0.000000e+00 774.0
39 TraesCS2D01G242200 chr1D 77.607 652 107 19 5693 6322 2267421 2266787 8.650000e-95 359.0
40 TraesCS2D01G242200 chr1D 95.980 199 8 0 1 199 5530816 5531014 3.160000e-84 324.0
41 TraesCS2D01G242200 chr1D 95.980 199 8 0 1 199 454773200 454773398 3.160000e-84 324.0
42 TraesCS2D01G242200 chr1D 95.980 199 8 0 1 199 482075976 482076174 3.160000e-84 324.0
43 TraesCS2D01G242200 chr1D 76.551 661 104 28 5693 6322 163674376 163673736 1.900000e-81 315.0
44 TraesCS2D01G242200 chr1D 90.123 81 5 3 4667 4747 62167975 62168052 1.610000e-17 102.0
45 TraesCS2D01G242200 chr1D 88.889 81 8 1 4667 4747 478405257 478405336 2.080000e-16 99.0
46 TraesCS2D01G242200 chr1D 88.608 79 5 4 4670 4747 143953741 143953666 9.690000e-15 93.5
47 TraesCS2D01G242200 chr1D 92.857 56 2 1 4692 4747 197525121 197525174 7.540000e-11 80.5
48 TraesCS2D01G242200 chr1D 87.692 65 7 1 4667 4731 212500571 212500508 3.510000e-09 75.0
49 TraesCS2D01G242200 chr1D 100.000 38 0 0 8529 8566 254448790 254448753 4.540000e-08 71.3
50 TraesCS2D01G242200 chr1D 88.679 53 5 1 4667 4719 212496149 212496098 7.600000e-06 63.9
51 TraesCS2D01G242200 chr1D 100.000 31 0 0 4701 4731 204632908 204632878 3.540000e-04 58.4
52 TraesCS2D01G242200 chr1D 84.746 59 7 2 4667 4725 400392342 400392398 3.540000e-04 58.4
53 TraesCS2D01G242200 chr1D 100.000 29 0 0 4323 4351 143951673 143951645 5.000000e-03 54.7
54 TraesCS2D01G242200 chr1D 100.000 28 0 0 4692 4719 12248487 12248514 1.600000e-02 52.8
55 TraesCS2D01G242200 chr5D 88.854 628 60 5 197 815 477840512 477841138 0.000000e+00 763.0
56 TraesCS2D01G242200 chr5D 88.384 594 56 7 233 816 6509324 6508734 0.000000e+00 702.0
57 TraesCS2D01G242200 chr5D 77.557 655 102 25 5693 6322 187946502 187947136 4.030000e-93 353.0
58 TraesCS2D01G242200 chr5D 77.287 634 104 23 5693 6303 236420139 236419523 4.050000e-88 337.0
59 TraesCS2D01G242200 chr5D 76.805 651 114 22 5693 6322 492350032 492350666 1.890000e-86 331.0
60 TraesCS2D01G242200 chr5D 96.482 199 7 0 1 199 164647789 164647591 6.790000e-86 329.0
61 TraesCS2D01G242200 chr5D 96.571 175 6 0 2736 2910 299073583 299073409 3.200000e-74 291.0
62 TraesCS2D01G242200 chr5D 74.021 485 92 21 5225 5700 256467610 256468069 5.630000e-37 167.0
63 TraesCS2D01G242200 chr5D 85.000 100 10 2 8642 8737 35546867 35546769 7.490000e-16 97.1
64 TraesCS2D01G242200 chr5D 88.608 79 6 2 4667 4745 164607424 164607499 9.690000e-15 93.5
65 TraesCS2D01G242200 chr5D 85.333 75 11 0 8664 8738 451159129 451159203 2.710000e-10 78.7
66 TraesCS2D01G242200 chr5D 95.556 45 2 0 9021 9065 327846633 327846589 1.260000e-08 73.1
67 TraesCS2D01G242200 chr5D 100.000 38 0 0 8529 8566 6261152 6261189 4.540000e-08 71.3
68 TraesCS2D01G242200 chr5D 100.000 38 0 0 8529 8566 503305623 503305586 4.540000e-08 71.3
69 TraesCS2D01G242200 chr5D 97.368 38 1 0 8529 8566 6163159 6163196 2.110000e-06 65.8
70 TraesCS2D01G242200 chr5D 100.000 31 0 0 4317 4347 256466932 256466962 3.540000e-04 58.4
71 TraesCS2D01G242200 chr6D 88.651 608 57 7 199 796 126623516 126622911 0.000000e+00 730.0
72 TraesCS2D01G242200 chr6D 87.380 626 63 11 197 813 387407404 387408022 0.000000e+00 704.0
73 TraesCS2D01G242200 chr6D 87.581 620 62 6 197 806 412198288 412197674 0.000000e+00 704.0
74 TraesCS2D01G242200 chr6D 76.911 654 108 23 5693 6322 160469698 160469064 1.890000e-86 331.0
75 TraesCS2D01G242200 chr6D 95.980 199 8 0 1 199 4652897 4652699 3.160000e-84 324.0
76 TraesCS2D01G242200 chr6D 95.980 199 8 0 1 199 38871856 38871658 3.160000e-84 324.0
77 TraesCS2D01G242200 chr6D 76.599 641 109 20 5693 6310 6331681 6332303 1.900000e-81 315.0
78 TraesCS2D01G242200 chr6D 75.573 655 112 24 5693 6313 4393730 4394370 6.930000e-71 279.0
79 TraesCS2D01G242200 chr6D 87.654 81 7 2 4667 4747 174380613 174380536 3.490000e-14 91.6
80 TraesCS2D01G242200 chr6D 87.654 81 7 2 4667 4747 448078982 448079059 3.490000e-14 91.6
81 TraesCS2D01G242200 chr6D 86.420 81 7 4 4667 4747 229421151 229421075 1.620000e-12 86.1
82 TraesCS2D01G242200 chr6D 92.982 57 2 2 4695 4751 335991279 335991333 2.100000e-11 82.4
83 TraesCS2D01G242200 chr6D 94.340 53 1 1 4695 4747 402837571 402837521 7.540000e-11 80.5
84 TraesCS2D01G242200 chr4D 87.034 617 67 8 197 803 414228821 414228208 0.000000e+00 684.0
85 TraesCS2D01G242200 chr4D 77.182 653 114 13 5693 6322 37433468 37434108 1.870000e-91 348.0
86 TraesCS2D01G242200 chr4D 77.335 653 107 20 5693 6322 335332805 335332171 1.870000e-91 348.0
87 TraesCS2D01G242200 chr4D 77.217 654 106 22 5693 6322 95788538 95789172 8.720000e-90 342.0
88 TraesCS2D01G242200 chr4D 75.794 661 109 28 5693 6322 9331025 9331665 4.140000e-73 287.0
89 TraesCS2D01G242200 chr4D 77.637 474 79 12 5693 6146 220357164 220357630 6.980000e-66 263.0
90 TraesCS2D01G242200 chr4D 75.800 500 103 13 5211 5700 220356646 220357137 4.230000e-58 237.0
91 TraesCS2D01G242200 chr4D 73.824 489 108 15 5223 5700 423867698 423867219 9.350000e-40 176.0
92 TraesCS2D01G242200 chr4D 88.889 81 6 2 4667 4747 344812541 344812618 7.490000e-16 97.1
93 TraesCS2D01G242200 chr4D 88.750 80 6 3 4667 4746 140903837 140903761 2.690000e-15 95.3
94 TraesCS2D01G242200 chr4D 87.654 81 9 1 4667 4747 350493429 350493508 9.690000e-15 93.5
95 TraesCS2D01G242200 chr4D 87.654 81 7 2 4667 4747 37432398 37432475 3.490000e-14 91.6
96 TraesCS2D01G242200 chr4D 86.585 82 9 2 4667 4747 297307792 297307712 1.250000e-13 89.8
97 TraesCS2D01G242200 chr4D 100.000 38 0 0 8529 8566 206977610 206977647 4.540000e-08 71.3
98 TraesCS2D01G242200 chr4D 100.000 38 0 0 8529 8566 348382843 348382880 4.540000e-08 71.3
99 TraesCS2D01G242200 chr4D 100.000 36 0 0 8531 8566 19882177 19882142 5.870000e-07 67.6
100 TraesCS2D01G242200 chr4D 100.000 34 0 0 5546 5579 234412163 234412196 7.600000e-06 63.9
101 TraesCS2D01G242200 chr3A 86.371 631 69 11 197 815 17107301 17106676 0.000000e+00 673.0
102 TraesCS2D01G242200 chr3A 74.303 502 108 15 5210 5700 353181512 353181021 9.290000e-45 193.0
103 TraesCS2D01G242200 chr3A 74.111 506 97 24 5210 5696 269659627 269659137 2.600000e-40 178.0
104 TraesCS2D01G242200 chr3A 95.238 63 3 0 3858 3920 429325421 429325483 5.790000e-17 100.0
105 TraesCS2D01G242200 chr3A 88.889 81 6 2 4667 4747 35166235 35166158 7.490000e-16 97.1
106 TraesCS2D01G242200 chr3A 88.889 81 6 2 4667 4747 212121117 212121040 7.490000e-16 97.1
107 TraesCS2D01G242200 chr3A 82.609 69 8 2 8820 8888 112410495 112410431 3.540000e-04 58.4
108 TraesCS2D01G242200 chr3B 80.634 599 85 21 5693 6277 345006225 345005644 1.400000e-117 435.0
109 TraesCS2D01G242200 chr3B 75.190 395 79 15 5211 5591 346619133 346618744 1.570000e-37 169.0
110 TraesCS2D01G242200 chr7D 80.034 596 91 18 5693 6277 460284845 460284267 5.060000e-112 416.0
111 TraesCS2D01G242200 chr7D 75.857 642 112 21 5693 6313 440575792 440575173 4.140000e-73 287.0
112 TraesCS2D01G242200 chr7D 75.720 486 104 10 5223 5700 484418698 484419177 1.970000e-56 231.0
113 TraesCS2D01G242200 chr7D 87.356 87 8 2 4667 4753 631086625 631086708 7.490000e-16 97.1
114 TraesCS2D01G242200 chr7D 100.000 37 0 0 8529 8565 29136985 29137021 1.630000e-07 69.4
115 TraesCS2D01G242200 chr4B 79.933 598 91 18 5693 6277 295674823 295675404 6.550000e-111 412.0
116 TraesCS2D01G242200 chr4B 96.482 199 7 0 1 199 191657768 191657966 6.790000e-86 329.0
117 TraesCS2D01G242200 chr4B 76.606 654 110 22 5693 6322 192122363 192121729 4.080000e-83 320.0
118 TraesCS2D01G242200 chr4B 96.774 62 2 0 3859 3920 644785330 644785269 4.480000e-18 104.0
119 TraesCS2D01G242200 chr4B 97.059 34 1 0 5546 5579 270825325 270825358 3.540000e-04 58.4
120 TraesCS2D01G242200 chr3D 77.761 652 106 19 5693 6322 37542096 37542730 1.860000e-96 364.0
121 TraesCS2D01G242200 chr3D 77.103 642 107 19 5693 6312 37528227 37528850 1.460000e-87 335.0
122 TraesCS2D01G242200 chr3D 96.482 199 7 0 1 199 474845671 474845869 6.790000e-86 329.0
123 TraesCS2D01G242200 chr3D 94.915 177 9 0 2738 2914 467283489 467283665 2.490000e-70 278.0
124 TraesCS2D01G242200 chr3D 73.930 514 101 26 5210 5700 263807194 263807697 9.350000e-40 176.0
125 TraesCS2D01G242200 chr3D 72.837 497 107 23 5211 5696 541603429 541603908 2.640000e-30 145.0
126 TraesCS2D01G242200 chr3D 100.000 38 0 0 8529 8566 596658568 596658531 4.540000e-08 71.3
127 TraesCS2D01G242200 chr5B 77.642 653 105 21 5693 6322 180032826 180032192 8.650000e-95 359.0
128 TraesCS2D01G242200 chr5B 94.886 176 9 0 2736 2911 573003544 573003719 8.970000e-70 276.0
129 TraesCS2D01G242200 chr5B 73.913 644 115 29 5693 6304 618170891 618170269 9.220000e-50 209.0
130 TraesCS2D01G242200 chr5B 94.286 70 3 1 4667 4736 665975979 665975911 1.240000e-18 106.0
131 TraesCS2D01G242200 chr5B 95.238 63 3 0 3858 3920 62940322 62940384 5.790000e-17 100.0
132 TraesCS2D01G242200 chr5B 90.541 74 5 2 4667 4739 545802714 545802786 7.490000e-16 97.1
133 TraesCS2D01G242200 chr7B 76.971 647 110 25 5692 6317 13864543 13863915 5.250000e-87 333.0
134 TraesCS2D01G242200 chr7B 76.577 444 73 17 5895 6313 66392491 66392054 1.980000e-51 215.0
135 TraesCS2D01G242200 chr7B 87.778 90 7 4 4667 4755 291578283 291578197 1.610000e-17 102.0
136 TraesCS2D01G242200 chr7B 80.952 84 15 1 8771 8854 70521782 70521864 2.110000e-06 65.8
137 TraesCS2D01G242200 chr1A 76.827 643 114 14 5693 6312 169593361 169593991 6.790000e-86 329.0
138 TraesCS2D01G242200 chr1A 75.190 657 111 22 5693 6313 563846401 563847041 6.980000e-66 263.0
139 TraesCS2D01G242200 chr1A 74.695 656 116 24 5693 6313 448882799 448882159 7.030000e-61 246.0
140 TraesCS2D01G242200 chr1A 100.000 29 0 0 4323 4351 145379505 145379533 5.000000e-03 54.7
141 TraesCS2D01G242200 chr6A 75.951 657 106 24 5693 6313 64590934 64591574 3.200000e-74 291.0
142 TraesCS2D01G242200 chr6A 74.351 655 120 16 5693 6313 557974827 557975467 1.520000e-57 235.0
143 TraesCS2D01G242200 chr6A 89.157 83 6 2 4667 4749 30442111 30442190 5.790000e-17 100.0
144 TraesCS2D01G242200 chr6A 89.474 76 6 2 3845 3918 55552651 55552576 2.690000e-15 95.3
145 TraesCS2D01G242200 chr6A 89.655 58 6 0 8776 8833 38769389 38769446 3.510000e-09 75.0
146 TraesCS2D01G242200 chr6A 95.349 43 2 0 9023 9065 227560612 227560654 1.630000e-07 69.4
147 TraesCS2D01G242200 chr6A 93.333 45 2 1 9021 9065 464900929 464900886 2.110000e-06 65.8
148 TraesCS2D01G242200 chr4A 94.444 180 9 1 2732 2911 80843707 80843885 8.970000e-70 276.0
149 TraesCS2D01G242200 chr4A 75.142 527 95 16 5820 6322 320843201 320842687 1.980000e-51 215.0
150 TraesCS2D01G242200 chr4A 78.512 363 51 11 5361 5699 429242547 429242188 7.130000e-51 213.0
151 TraesCS2D01G242200 chr4A 80.864 162 22 9 6309 6464 3330249 3330407 1.600000e-22 119.0
152 TraesCS2D01G242200 chr7A 95.376 173 6 1 2738 2910 503442319 503442489 3.220000e-69 274.0
153 TraesCS2D01G242200 chr7A 75.342 657 110 22 5693 6313 567532288 567532928 1.500000e-67 268.0
154 TraesCS2D01G242200 chr5A 74.886 657 113 26 5693 6313 222595671 222596311 1.510000e-62 252.0
155 TraesCS2D01G242200 chr5A 75.983 483 104 8 5225 5700 282590978 282591455 1.180000e-58 239.0
156 TraesCS2D01G242200 chr5A 78.689 305 47 13 5871 6165 657049981 657049685 4.320000e-43 187.0
157 TraesCS2D01G242200 chr5A 92.958 71 3 2 4667 4736 657051566 657051497 1.610000e-17 102.0
158 TraesCS2D01G242200 chr6B 80.603 232 43 2 6082 6313 408130939 408130710 2.600000e-40 178.0
159 TraesCS2D01G242200 chr6B 95.238 63 3 0 3858 3920 474189202 474189264 5.790000e-17 100.0
160 TraesCS2D01G242200 chr6B 95.238 63 3 0 3858 3920 512256534 512256596 5.790000e-17 100.0
161 TraesCS2D01G242200 chr6B 80.189 106 17 2 8783 8887 15882160 15882058 9.760000e-10 76.8
162 TraesCS2D01G242200 chr6B 100.000 38 0 0 8529 8566 18746312 18746349 4.540000e-08 71.3
163 TraesCS2D01G242200 chr6B 100.000 38 0 0 8529 8566 202431825 202431788 4.540000e-08 71.3
164 TraesCS2D01G242200 chr6B 100.000 38 0 0 8529 8566 621339008 621339045 4.540000e-08 71.3
165 TraesCS2D01G242200 chrUn 86.420 81 9 2 4667 4747 67790234 67790156 4.510000e-13 87.9
166 TraesCS2D01G242200 chrUn 92.857 56 4 0 4692 4747 402808261 402808316 2.100000e-11 82.4
167 TraesCS2D01G242200 chrUn 95.556 45 2 0 9021 9065 136983770 136983814 1.260000e-08 73.1
168 TraesCS2D01G242200 chrUn 100.000 38 0 0 8529 8566 411196700 411196663 4.540000e-08 71.3


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 TraesCS2D01G242200 chr2D 268891558 268900622 9064 False 8079.500000 8124 100.000000 1 9065 2 chr2D.!!$F7 9064
1 TraesCS2D01G242200 chr2D 38261590 38262214 624 False 662.000000 662 86.010000 197 815 1 chr2D.!!$F2 618
2 TraesCS2D01G242200 chr2D 236122191 236122825 634 False 370.000000 370 77.948000 5693 6322 1 chr2D.!!$F5 629
3 TraesCS2D01G242200 chr2D 373888663 373889657 994 True 335.500000 344 79.867500 5261 6217 2 chr2D.!!$R5 956
4 TraesCS2D01G242200 chr2D 153796527 153797164 637 False 303.000000 303 76.336000 5693 6313 1 chr2D.!!$F3 620
5 TraesCS2D01G242200 chr2D 233386781 233387604 823 False 289.000000 289 73.933000 5468 6312 1 chr2D.!!$F4 844
6 TraesCS2D01G242200 chr2D 601958136 601959231 1095 False 274.000000 342 76.421000 5267 6322 2 chr2D.!!$F8 1055
7 TraesCS2D01G242200 chr2B 308714413 308726928 12515 False 1964.666667 4922 94.210167 838 9003 6 chr2B.!!$F2 8165
8 TraesCS2D01G242200 chr2A 317953013 317955239 2226 True 3956.000000 3956 98.745000 837 3062 1 chr2A.!!$R1 2225
9 TraesCS2D01G242200 chr2A 317939699 317945700 6001 True 3085.666667 3795 96.876000 3051 9021 3 chr2A.!!$R6 5970
10 TraesCS2D01G242200 chr2A 552478881 552479778 897 True 392.000000 392 75.472000 5342 6271 1 chr2A.!!$R4 929
11 TraesCS2D01G242200 chr2A 27991461 27992081 620 False 331.000000 331 77.103000 5693 6312 1 chr2A.!!$F1 619
12 TraesCS2D01G242200 chr2A 286423778 286424587 809 False 259.000000 259 73.341000 5468 6312 1 chr2A.!!$F3 844
13 TraesCS2D01G242200 chr1D 491944724 491945350 626 True 774.000000 774 89.189000 197 815 1 chr1D.!!$R7 618
14 TraesCS2D01G242200 chr1D 2266787 2267421 634 True 359.000000 359 77.607000 5693 6322 1 chr1D.!!$R1 629
15 TraesCS2D01G242200 chr1D 163673736 163674376 640 True 315.000000 315 76.551000 5693 6322 1 chr1D.!!$R2 629
16 TraesCS2D01G242200 chr5D 477840512 477841138 626 False 763.000000 763 88.854000 197 815 1 chr5D.!!$F6 618
17 TraesCS2D01G242200 chr5D 6508734 6509324 590 True 702.000000 702 88.384000 233 816 1 chr5D.!!$R1 583
18 TraesCS2D01G242200 chr5D 187946502 187947136 634 False 353.000000 353 77.557000 5693 6322 1 chr5D.!!$F4 629
19 TraesCS2D01G242200 chr5D 236419523 236420139 616 True 337.000000 337 77.287000 5693 6303 1 chr5D.!!$R4 610
20 TraesCS2D01G242200 chr5D 492350032 492350666 634 False 331.000000 331 76.805000 5693 6322 1 chr5D.!!$F7 629
21 TraesCS2D01G242200 chr6D 126622911 126623516 605 True 730.000000 730 88.651000 199 796 1 chr6D.!!$R3 597
22 TraesCS2D01G242200 chr6D 387407404 387408022 618 False 704.000000 704 87.380000 197 813 1 chr6D.!!$F4 616
23 TraesCS2D01G242200 chr6D 412197674 412198288 614 True 704.000000 704 87.581000 197 806 1 chr6D.!!$R8 609
24 TraesCS2D01G242200 chr6D 160469064 160469698 634 True 331.000000 331 76.911000 5693 6322 1 chr6D.!!$R4 629
25 TraesCS2D01G242200 chr6D 6331681 6332303 622 False 315.000000 315 76.599000 5693 6310 1 chr6D.!!$F2 617
26 TraesCS2D01G242200 chr6D 4393730 4394370 640 False 279.000000 279 75.573000 5693 6313 1 chr6D.!!$F1 620
27 TraesCS2D01G242200 chr4D 414228208 414228821 613 True 684.000000 684 87.034000 197 803 1 chr4D.!!$R5 606
28 TraesCS2D01G242200 chr4D 335332171 335332805 634 True 348.000000 348 77.335000 5693 6322 1 chr4D.!!$R4 629
29 TraesCS2D01G242200 chr4D 95788538 95789172 634 False 342.000000 342 77.217000 5693 6322 1 chr4D.!!$F2 629
30 TraesCS2D01G242200 chr4D 9331025 9331665 640 False 287.000000 287 75.794000 5693 6322 1 chr4D.!!$F1 629
31 TraesCS2D01G242200 chr4D 220356646 220357630 984 False 250.000000 263 76.718500 5211 6146 2 chr4D.!!$F9 935
32 TraesCS2D01G242200 chr4D 37432398 37434108 1710 False 219.800000 348 82.418000 4667 6322 2 chr4D.!!$F8 1655
33 TraesCS2D01G242200 chr3A 17106676 17107301 625 True 673.000000 673 86.371000 197 815 1 chr3A.!!$R1 618
34 TraesCS2D01G242200 chr3B 345005644 345006225 581 True 435.000000 435 80.634000 5693 6277 1 chr3B.!!$R1 584
35 TraesCS2D01G242200 chr7D 460284267 460284845 578 True 416.000000 416 80.034000 5693 6277 1 chr7D.!!$R2 584
36 TraesCS2D01G242200 chr7D 440575173 440575792 619 True 287.000000 287 75.857000 5693 6313 1 chr7D.!!$R1 620
37 TraesCS2D01G242200 chr4B 295674823 295675404 581 False 412.000000 412 79.933000 5693 6277 1 chr4B.!!$F3 584
38 TraesCS2D01G242200 chr4B 192121729 192122363 634 True 320.000000 320 76.606000 5693 6322 1 chr4B.!!$R1 629
39 TraesCS2D01G242200 chr3D 37542096 37542730 634 False 364.000000 364 77.761000 5693 6322 1 chr3D.!!$F2 629
40 TraesCS2D01G242200 chr3D 37528227 37528850 623 False 335.000000 335 77.103000 5693 6312 1 chr3D.!!$F1 619
41 TraesCS2D01G242200 chr5B 180032192 180032826 634 True 359.000000 359 77.642000 5693 6322 1 chr5B.!!$R1 629
42 TraesCS2D01G242200 chr5B 618170269 618170891 622 True 209.000000 209 73.913000 5693 6304 1 chr5B.!!$R2 611
43 TraesCS2D01G242200 chr7B 13863915 13864543 628 True 333.000000 333 76.971000 5692 6317 1 chr7B.!!$R1 625
44 TraesCS2D01G242200 chr1A 169593361 169593991 630 False 329.000000 329 76.827000 5693 6312 1 chr1A.!!$F2 619
45 TraesCS2D01G242200 chr1A 563846401 563847041 640 False 263.000000 263 75.190000 5693 6313 1 chr1A.!!$F3 620
46 TraesCS2D01G242200 chr1A 448882159 448882799 640 True 246.000000 246 74.695000 5693 6313 1 chr1A.!!$R1 620
47 TraesCS2D01G242200 chr6A 64590934 64591574 640 False 291.000000 291 75.951000 5693 6313 1 chr6A.!!$F3 620
48 TraesCS2D01G242200 chr6A 557974827 557975467 640 False 235.000000 235 74.351000 5693 6313 1 chr6A.!!$F5 620
49 TraesCS2D01G242200 chr4A 320842687 320843201 514 True 215.000000 215 75.142000 5820 6322 1 chr4A.!!$R1 502
50 TraesCS2D01G242200 chr7A 567532288 567532928 640 False 268.000000 268 75.342000 5693 6313 1 chr7A.!!$F2 620
51 TraesCS2D01G242200 chr5A 222595671 222596311 640 False 252.000000 252 74.886000 5693 6313 1 chr5A.!!$F1 620

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
191 192 0.179004 TGTCTTCCGCATTGGGTGTT 60.179 50.000 0.0 0.00 38.76 3.32 F
646 658 0.179084 GGGCGAATCTGGACGATTGA 60.179 55.000 0.0 0.00 42.31 2.57 F
782 800 1.478137 CCGATGGATTTCGACGTCTC 58.522 55.000 14.7 3.88 41.62 3.36 F
2827 6232 0.886563 ACAGCCTCTTGCAGAAATGC 59.113 50.000 0.0 0.00 44.83 3.56 F
3803 7222 2.159338 GCATGATGAACGAGTTTGGCAT 60.159 45.455 0.0 0.00 0.00 4.40 F
5140 8964 0.038166 GATGCCACCTCCTGGTTCAA 59.962 55.000 0.0 0.00 46.05 2.69 F
6579 11534 1.373435 CCAGTTCCCAGCCGTTACA 59.627 57.895 0.0 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2102 3.105937 GACGAAACAAGCAGGTCAAAAC 58.894 45.455 0.00 0.00 0.0 2.43 R
2827 6232 0.535335 TAGTACGCAGCCTTTCCCTG 59.465 55.000 0.00 0.00 0.0 4.45 R
2909 6325 8.565896 ACTAGCAAGTCAATGACATGATAAAA 57.434 30.769 20.94 0.71 33.1 1.52 R
4995 8688 4.537433 GCGGCGAGGCAGAGGATT 62.537 66.667 12.98 0.00 0.0 3.01 R
5510 9505 1.414181 CGATACATCTCAAGGGCCACT 59.586 52.381 6.18 0.00 0.0 4.00 R
6811 11788 1.340889 TGCAGGCAATTCAGTGAAACC 59.659 47.619 10.14 11.70 37.8 3.27 R
8402 13386 0.592637 CAATTCAGCACCGCACAAGA 59.407 50.000 0.00 0.00 0.0 3.02 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
17 18 2.348998 CAGAGGTCCTGTGTGGCC 59.651 66.667 7.90 0.00 38.10 5.36
18 19 2.122413 AGAGGTCCTGTGTGGCCA 60.122 61.111 0.00 0.00 35.39 5.36
19 20 2.032681 GAGGTCCTGTGTGGCCAC 59.967 66.667 29.67 29.67 42.19 5.01
20 21 3.553095 GAGGTCCTGTGTGGCCACC 62.553 68.421 32.62 23.09 41.09 4.61
32 33 2.436115 GCCACCGCCTCAAGTACC 60.436 66.667 0.00 0.00 0.00 3.34
33 34 3.065306 CCACCGCCTCAAGTACCA 58.935 61.111 0.00 0.00 0.00 3.25
34 35 1.375523 CCACCGCCTCAAGTACCAC 60.376 63.158 0.00 0.00 0.00 4.16
35 36 1.369692 CACCGCCTCAAGTACCACA 59.630 57.895 0.00 0.00 0.00 4.17
36 37 0.949105 CACCGCCTCAAGTACCACAC 60.949 60.000 0.00 0.00 0.00 3.82
37 38 1.119574 ACCGCCTCAAGTACCACACT 61.120 55.000 0.00 0.00 40.05 3.55
38 39 0.892755 CCGCCTCAAGTACCACACTA 59.107 55.000 0.00 0.00 36.04 2.74
39 40 1.403780 CCGCCTCAAGTACCACACTAC 60.404 57.143 0.00 0.00 36.04 2.73
40 41 1.271379 CGCCTCAAGTACCACACTACA 59.729 52.381 0.00 0.00 36.04 2.74
41 42 2.288579 CGCCTCAAGTACCACACTACAA 60.289 50.000 0.00 0.00 36.04 2.41
42 43 3.064931 GCCTCAAGTACCACACTACAAC 58.935 50.000 0.00 0.00 36.04 3.32
43 44 3.244112 GCCTCAAGTACCACACTACAACT 60.244 47.826 0.00 0.00 36.04 3.16
44 45 4.307432 CCTCAAGTACCACACTACAACTG 58.693 47.826 0.00 0.00 36.04 3.16
45 46 3.724374 TCAAGTACCACACTACAACTGC 58.276 45.455 0.00 0.00 36.04 4.40
46 47 2.806244 CAAGTACCACACTACAACTGCC 59.194 50.000 0.00 0.00 36.04 4.85
47 48 2.326428 AGTACCACACTACAACTGCCT 58.674 47.619 0.00 0.00 34.98 4.75
48 49 2.704065 AGTACCACACTACAACTGCCTT 59.296 45.455 0.00 0.00 34.98 4.35
49 50 2.729028 ACCACACTACAACTGCCTTT 57.271 45.000 0.00 0.00 0.00 3.11
50 51 2.297701 ACCACACTACAACTGCCTTTG 58.702 47.619 0.00 0.00 0.00 2.77
51 52 1.608590 CCACACTACAACTGCCTTTGG 59.391 52.381 0.01 0.00 0.00 3.28
61 62 3.361174 GCCTTTGGCGCCTTTGTA 58.639 55.556 29.70 2.88 39.62 2.41
62 63 1.080772 GCCTTTGGCGCCTTTGTAC 60.081 57.895 29.70 9.13 39.62 2.90
63 64 1.801309 GCCTTTGGCGCCTTTGTACA 61.801 55.000 29.70 1.01 39.62 2.90
64 65 0.887933 CCTTTGGCGCCTTTGTACAT 59.112 50.000 29.70 0.00 0.00 2.29
65 66 1.135402 CCTTTGGCGCCTTTGTACATC 60.135 52.381 29.70 0.00 0.00 3.06
66 67 0.885196 TTTGGCGCCTTTGTACATCC 59.115 50.000 29.70 0.00 0.00 3.51
67 68 0.963355 TTGGCGCCTTTGTACATCCC 60.963 55.000 29.70 0.00 0.00 3.85
68 69 2.119029 GGCGCCTTTGTACATCCCC 61.119 63.158 22.15 0.00 0.00 4.81
69 70 1.077716 GCGCCTTTGTACATCCCCT 60.078 57.895 0.00 0.00 0.00 4.79
70 71 0.179468 GCGCCTTTGTACATCCCCTA 59.821 55.000 0.00 0.00 0.00 3.53
71 72 1.949465 CGCCTTTGTACATCCCCTAC 58.051 55.000 0.00 0.00 0.00 3.18
72 73 1.474498 CGCCTTTGTACATCCCCTACC 60.474 57.143 0.00 0.00 0.00 3.18
73 74 1.562475 GCCTTTGTACATCCCCTACCA 59.438 52.381 0.00 0.00 0.00 3.25
74 75 2.025699 GCCTTTGTACATCCCCTACCAA 60.026 50.000 0.00 0.00 0.00 3.67
75 76 3.886123 CCTTTGTACATCCCCTACCAAG 58.114 50.000 0.00 0.00 0.00 3.61
76 77 3.279434 CTTTGTACATCCCCTACCAAGC 58.721 50.000 0.00 0.00 0.00 4.01
77 78 1.959710 TGTACATCCCCTACCAAGCA 58.040 50.000 0.00 0.00 0.00 3.91
78 79 2.270858 TGTACATCCCCTACCAAGCAA 58.729 47.619 0.00 0.00 0.00 3.91
79 80 2.645297 TGTACATCCCCTACCAAGCAAA 59.355 45.455 0.00 0.00 0.00 3.68
80 81 3.268334 TGTACATCCCCTACCAAGCAAAT 59.732 43.478 0.00 0.00 0.00 2.32
81 82 2.738743 ACATCCCCTACCAAGCAAATG 58.261 47.619 0.00 0.00 0.00 2.32
82 83 2.034124 CATCCCCTACCAAGCAAATGG 58.966 52.381 2.02 2.02 46.38 3.16
83 84 0.334676 TCCCCTACCAAGCAAATGGG 59.665 55.000 7.93 0.00 45.18 4.00
84 85 1.329913 CCCCTACCAAGCAAATGGGC 61.330 60.000 7.93 0.00 45.18 5.36
85 86 0.614415 CCCTACCAAGCAAATGGGCA 60.614 55.000 7.93 0.00 45.18 5.36
86 87 0.819582 CCTACCAAGCAAATGGGCAG 59.180 55.000 7.93 4.74 45.18 4.85
87 88 1.549203 CTACCAAGCAAATGGGCAGT 58.451 50.000 7.93 0.00 45.18 4.40
88 89 1.895131 CTACCAAGCAAATGGGCAGTT 59.105 47.619 7.93 0.00 45.18 3.16
89 90 0.681175 ACCAAGCAAATGGGCAGTTC 59.319 50.000 7.93 0.00 45.18 3.01
90 91 0.971386 CCAAGCAAATGGGCAGTTCT 59.029 50.000 0.00 0.00 36.79 3.01
91 92 1.345415 CCAAGCAAATGGGCAGTTCTT 59.655 47.619 0.00 0.00 36.79 2.52
92 93 2.224354 CCAAGCAAATGGGCAGTTCTTT 60.224 45.455 0.00 0.00 36.79 2.52
93 94 3.062042 CAAGCAAATGGGCAGTTCTTTC 58.938 45.455 0.00 0.00 35.83 2.62
94 95 2.318908 AGCAAATGGGCAGTTCTTTCA 58.681 42.857 0.00 0.00 35.83 2.69
95 96 2.901839 AGCAAATGGGCAGTTCTTTCAT 59.098 40.909 0.00 0.00 35.83 2.57
96 97 3.325716 AGCAAATGGGCAGTTCTTTCATT 59.674 39.130 0.00 0.00 35.83 2.57
97 98 4.067192 GCAAATGGGCAGTTCTTTCATTT 58.933 39.130 0.00 0.00 38.20 2.32
98 99 4.152938 GCAAATGGGCAGTTCTTTCATTTC 59.847 41.667 0.00 0.00 36.33 2.17
99 100 4.541973 AATGGGCAGTTCTTTCATTTCC 57.458 40.909 0.00 0.00 0.00 3.13
100 101 2.956132 TGGGCAGTTCTTTCATTTCCA 58.044 42.857 0.00 0.00 0.00 3.53
101 102 3.303938 TGGGCAGTTCTTTCATTTCCAA 58.696 40.909 0.00 0.00 0.00 3.53
102 103 3.903090 TGGGCAGTTCTTTCATTTCCAAT 59.097 39.130 0.00 0.00 0.00 3.16
103 104 4.248058 GGGCAGTTCTTTCATTTCCAATG 58.752 43.478 0.00 0.00 0.00 2.82
104 105 3.681417 GGCAGTTCTTTCATTTCCAATGC 59.319 43.478 0.00 0.00 0.00 3.56
105 106 4.309099 GCAGTTCTTTCATTTCCAATGCA 58.691 39.130 0.00 0.00 0.00 3.96
106 107 4.933400 GCAGTTCTTTCATTTCCAATGCAT 59.067 37.500 0.00 0.00 0.00 3.96
107 108 5.163893 GCAGTTCTTTCATTTCCAATGCATG 60.164 40.000 0.00 0.00 0.00 4.06
108 109 4.933400 AGTTCTTTCATTTCCAATGCATGC 59.067 37.500 11.82 11.82 0.00 4.06
109 110 4.538746 TCTTTCATTTCCAATGCATGCA 57.461 36.364 25.04 25.04 0.00 3.96
110 111 4.500127 TCTTTCATTTCCAATGCATGCAG 58.500 39.130 26.69 13.25 0.00 4.41
111 112 3.965379 TTCATTTCCAATGCATGCAGT 57.035 38.095 26.69 21.79 0.00 4.40
112 113 3.513680 TCATTTCCAATGCATGCAGTC 57.486 42.857 26.69 0.00 0.00 3.51
113 114 2.159352 TCATTTCCAATGCATGCAGTCG 60.159 45.455 26.69 16.82 0.00 4.18
114 115 1.532523 TTTCCAATGCATGCAGTCGA 58.467 45.000 26.69 19.10 0.00 4.20
115 116 1.753930 TTCCAATGCATGCAGTCGAT 58.246 45.000 26.69 5.62 0.00 3.59
116 117 1.018910 TCCAATGCATGCAGTCGATG 58.981 50.000 26.69 17.46 0.00 3.84
135 136 3.985410 CTTCCAAGCATCCCAGGAA 57.015 52.632 0.00 0.00 37.79 3.36
136 137 2.220653 CTTCCAAGCATCCCAGGAAA 57.779 50.000 0.00 0.00 39.47 3.13
137 138 2.743553 CTTCCAAGCATCCCAGGAAAT 58.256 47.619 0.00 0.00 39.47 2.17
138 139 2.925966 TCCAAGCATCCCAGGAAATT 57.074 45.000 0.00 0.00 0.00 1.82
139 140 2.738743 TCCAAGCATCCCAGGAAATTC 58.261 47.619 0.00 0.00 0.00 2.17
140 141 2.312741 TCCAAGCATCCCAGGAAATTCT 59.687 45.455 0.00 0.00 0.00 2.40
141 142 2.692041 CCAAGCATCCCAGGAAATTCTC 59.308 50.000 0.00 0.00 0.00 2.87
142 143 3.626729 CCAAGCATCCCAGGAAATTCTCT 60.627 47.826 0.00 0.00 0.00 3.10
143 144 4.021916 CAAGCATCCCAGGAAATTCTCTT 58.978 43.478 0.00 0.00 0.00 2.85
144 145 3.629087 AGCATCCCAGGAAATTCTCTTG 58.371 45.455 0.00 0.00 0.00 3.02
145 146 2.100418 GCATCCCAGGAAATTCTCTTGC 59.900 50.000 0.00 0.00 29.74 4.01
146 147 3.629087 CATCCCAGGAAATTCTCTTGCT 58.371 45.455 0.00 0.00 29.74 3.91
147 148 3.077484 TCCCAGGAAATTCTCTTGCTG 57.923 47.619 0.00 0.00 42.58 4.41
148 149 1.475682 CCCAGGAAATTCTCTTGCTGC 59.524 52.381 0.00 0.00 41.85 5.25
149 150 2.165167 CCAGGAAATTCTCTTGCTGCA 58.835 47.619 0.00 0.00 41.85 4.41
150 151 2.758979 CCAGGAAATTCTCTTGCTGCAT 59.241 45.455 1.84 0.00 41.85 3.96
151 152 3.194968 CCAGGAAATTCTCTTGCTGCATT 59.805 43.478 1.84 0.00 41.85 3.56
152 153 4.421948 CAGGAAATTCTCTTGCTGCATTC 58.578 43.478 1.84 2.06 37.84 2.67
153 154 4.158025 CAGGAAATTCTCTTGCTGCATTCT 59.842 41.667 1.84 0.00 37.84 2.40
154 155 4.158025 AGGAAATTCTCTTGCTGCATTCTG 59.842 41.667 1.84 0.00 0.00 3.02
155 156 4.082354 GGAAATTCTCTTGCTGCATTCTGT 60.082 41.667 1.84 0.00 0.00 3.41
156 157 5.124457 GGAAATTCTCTTGCTGCATTCTGTA 59.876 40.000 1.84 0.00 0.00 2.74
157 158 5.557891 AATTCTCTTGCTGCATTCTGTAC 57.442 39.130 1.84 0.00 0.00 2.90
158 159 3.969287 TCTCTTGCTGCATTCTGTACT 57.031 42.857 1.84 0.00 0.00 2.73
159 160 5.405935 TTCTCTTGCTGCATTCTGTACTA 57.594 39.130 1.84 0.00 0.00 1.82
160 161 5.003692 TCTCTTGCTGCATTCTGTACTAG 57.996 43.478 1.84 0.00 0.00 2.57
161 162 4.118410 CTCTTGCTGCATTCTGTACTAGG 58.882 47.826 1.84 0.00 0.00 3.02
162 163 3.769300 TCTTGCTGCATTCTGTACTAGGA 59.231 43.478 1.84 0.00 0.00 2.94
163 164 4.406972 TCTTGCTGCATTCTGTACTAGGAT 59.593 41.667 1.84 0.00 0.00 3.24
164 165 4.327982 TGCTGCATTCTGTACTAGGATC 57.672 45.455 0.00 0.00 0.00 3.36
165 166 3.070159 TGCTGCATTCTGTACTAGGATCC 59.930 47.826 2.48 2.48 0.00 3.36
166 167 3.070159 GCTGCATTCTGTACTAGGATCCA 59.930 47.826 15.82 0.00 0.00 3.41
167 168 4.443457 GCTGCATTCTGTACTAGGATCCAA 60.443 45.833 15.82 0.00 0.00 3.53
168 169 5.282055 TGCATTCTGTACTAGGATCCAAG 57.718 43.478 15.82 1.59 0.00 3.61
169 170 4.061596 GCATTCTGTACTAGGATCCAAGC 58.938 47.826 15.82 0.00 0.00 4.01
170 171 4.443457 GCATTCTGTACTAGGATCCAAGCA 60.443 45.833 15.82 4.55 0.00 3.91
171 172 5.295950 CATTCTGTACTAGGATCCAAGCAG 58.704 45.833 15.82 13.76 0.00 4.24
172 173 3.982516 TCTGTACTAGGATCCAAGCAGT 58.017 45.455 15.82 13.17 0.00 4.40
173 174 3.701542 TCTGTACTAGGATCCAAGCAGTG 59.298 47.826 15.82 0.00 0.00 3.66
174 175 3.441101 TGTACTAGGATCCAAGCAGTGT 58.559 45.455 15.82 4.26 0.00 3.55
175 176 3.447586 TGTACTAGGATCCAAGCAGTGTC 59.552 47.826 15.82 9.33 0.00 3.67
176 177 2.826488 ACTAGGATCCAAGCAGTGTCT 58.174 47.619 15.82 0.00 0.00 3.41
177 178 3.177228 ACTAGGATCCAAGCAGTGTCTT 58.823 45.455 15.82 0.00 0.00 3.01
178 179 2.777832 AGGATCCAAGCAGTGTCTTC 57.222 50.000 15.82 0.00 0.00 2.87
179 180 1.280421 AGGATCCAAGCAGTGTCTTCC 59.720 52.381 15.82 0.00 0.00 3.46
180 181 1.363744 GATCCAAGCAGTGTCTTCCG 58.636 55.000 0.00 0.00 0.00 4.30
181 182 0.674895 ATCCAAGCAGTGTCTTCCGC 60.675 55.000 0.00 0.00 0.00 5.54
182 183 1.597854 CCAAGCAGTGTCTTCCGCA 60.598 57.895 0.00 0.00 0.00 5.69
183 184 0.957395 CCAAGCAGTGTCTTCCGCAT 60.957 55.000 0.00 0.00 0.00 4.73
184 185 0.877071 CAAGCAGTGTCTTCCGCATT 59.123 50.000 0.00 0.00 0.00 3.56
185 186 0.877071 AAGCAGTGTCTTCCGCATTG 59.123 50.000 0.00 0.00 0.00 2.82
186 187 0.957395 AGCAGTGTCTTCCGCATTGG 60.957 55.000 0.00 0.00 40.09 3.16
187 188 1.926511 GCAGTGTCTTCCGCATTGGG 61.927 60.000 0.00 0.00 38.76 4.12
188 189 0.606401 CAGTGTCTTCCGCATTGGGT 60.606 55.000 0.00 0.00 38.76 4.51
189 190 0.606401 AGTGTCTTCCGCATTGGGTG 60.606 55.000 0.00 0.00 38.76 4.61
190 191 0.889186 GTGTCTTCCGCATTGGGTGT 60.889 55.000 0.00 0.00 38.76 4.16
191 192 0.179004 TGTCTTCCGCATTGGGTGTT 60.179 50.000 0.00 0.00 38.76 3.32
192 193 0.521735 GTCTTCCGCATTGGGTGTTC 59.478 55.000 0.00 0.00 38.76 3.18
193 194 0.953471 TCTTCCGCATTGGGTGTTCG 60.953 55.000 0.00 0.00 38.76 3.95
194 195 2.527547 CTTCCGCATTGGGTGTTCGC 62.528 60.000 0.00 0.00 38.76 4.70
195 196 3.361158 CCGCATTGGGTGTTCGCA 61.361 61.111 0.00 0.00 34.75 5.10
236 237 1.153086 GCCTTCCAGACGATGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
346 348 2.670148 GGTGTTCCTCGGCCTGGAT 61.670 63.158 14.02 0.00 33.09 3.41
527 530 2.671682 GTGGTGGAGAGGCTTCCC 59.328 66.667 11.55 6.29 36.35 3.97
528 531 1.920835 GTGGTGGAGAGGCTTCCCT 60.921 63.158 11.55 0.00 46.74 4.20
534 537 3.378399 GAGAGGCTTCCCTGGCGAC 62.378 68.421 0.00 0.00 43.12 5.19
545 548 1.536073 CCTGGCGACACCTTCTCTCA 61.536 60.000 0.00 0.00 40.22 3.27
557 560 1.476891 CTTCTCTCATTTCCGACGGGA 59.523 52.381 15.25 0.77 41.83 5.14
646 658 0.179084 GGGCGAATCTGGACGATTGA 60.179 55.000 0.00 0.00 42.31 2.57
668 681 3.181469 ACTTGACTTTTCGCCTGACAGTA 60.181 43.478 0.93 0.00 0.00 2.74
698 714 2.981350 GTTTTCCCCTTGCGCCGA 60.981 61.111 4.18 0.00 0.00 5.54
782 800 1.478137 CCGATGGATTTCGACGTCTC 58.522 55.000 14.70 3.88 41.62 3.36
819 838 2.637025 TTTTTCAGCGCCGAGTGC 59.363 55.556 2.29 1.74 39.59 4.40
1908 1934 6.210185 GGTGAGGGTTAAGTGTCTTCTACTTA 59.790 42.308 0.00 0.00 39.06 2.24
1946 1972 2.300433 GATGTAGGCATGGTCATTGCA 58.700 47.619 0.00 0.00 35.07 4.08
1957 1983 3.877559 TGGTCATTGCAGTGAAGGATAG 58.122 45.455 14.07 0.00 0.00 2.08
2827 6232 0.886563 ACAGCCTCTTGCAGAAATGC 59.113 50.000 0.00 0.00 44.83 3.56
3553 6972 5.453567 TGGTGACATATTATCTCGGTCAG 57.546 43.478 0.00 0.00 38.98 3.51
3558 6977 5.012046 TGACATATTATCTCGGTCAGCCATT 59.988 40.000 0.00 0.00 33.88 3.16
3803 7222 2.159338 GCATGATGAACGAGTTTGGCAT 60.159 45.455 0.00 0.00 0.00 4.40
3849 7268 5.904941 TGAACTGAAAATCTTGTTGCATGT 58.095 33.333 0.00 0.00 0.00 3.21
3872 7291 3.900966 ATTTGGTACTCCCTCCGTAAC 57.099 47.619 0.00 0.00 0.00 2.50
3887 7306 3.486841 TCCGTAACGAAATATAAGTGCGC 59.513 43.478 0.00 0.00 0.00 6.09
3928 7440 5.023452 TGATCTAAACACTCTCTGGCCTAA 58.977 41.667 3.32 0.00 0.00 2.69
4290 7804 8.098912 TCCACTAGTCTTAAAATGTAGGGTTTC 58.901 37.037 0.00 0.00 0.00 2.78
4771 8408 4.039357 CTCAGGTCCACGCGTCGT 62.039 66.667 9.86 0.00 42.36 4.34
4995 8688 4.355720 CTGCCTGCTTGCCTCCCA 62.356 66.667 0.00 0.00 0.00 4.37
5127 8951 2.048597 AGTTTCGACGCGATGCCA 60.049 55.556 15.93 0.00 35.23 4.92
5140 8964 0.038166 GATGCCACCTCCTGGTTCAA 59.962 55.000 0.00 0.00 46.05 2.69
5354 9325 4.201930 CGTCTATGGAGCGTTCTTTCTAGT 60.202 45.833 0.00 0.00 0.00 2.57
5510 9505 2.229792 CAGCAAGCCTTGAACTACCAA 58.770 47.619 9.04 0.00 0.00 3.67
6219 11171 4.074970 ACTTCGAAATCTTCAGCCATTGT 58.925 39.130 0.00 0.00 0.00 2.71
6476 11431 2.282391 ACACACGCCATGCACCAT 60.282 55.556 0.00 0.00 0.00 3.55
6579 11534 1.373435 CCAGTTCCCAGCCGTTACA 59.627 57.895 0.00 0.00 0.00 2.41
6594 11549 2.223735 CGTTACACCTGGCGTGATCTAT 60.224 50.000 0.00 0.00 46.20 1.98
6811 11788 8.519492 AGGATCAACATTTTGTTATGTTTTCG 57.481 30.769 0.00 0.00 44.18 3.46
6991 11968 9.665719 AACTGTTTGGACAATTACAATTTCTTT 57.334 25.926 0.00 0.00 34.85 2.52
7010 11987 7.804843 TTCTTTCGAGTATTCTAGGTCTAGG 57.195 40.000 5.31 0.00 34.06 3.02
7020 11997 9.624037 AGTATTCTAGGTCTAGGAGAAGATAGA 57.376 37.037 5.31 0.00 32.94 1.98
7065 12046 4.173256 CACTTTTTCGGCAGTTTGTTTCT 58.827 39.130 0.00 0.00 0.00 2.52
7246 12227 6.238648 ACCTTATTGTTAGTTAGCTTGCTGT 58.761 36.000 5.26 0.00 0.00 4.40
7580 12562 6.328934 TCCAGGTATAGCTATCCAATTGTTCA 59.671 38.462 10.16 0.00 0.00 3.18
7588 12570 5.649831 AGCTATCCAATTGTTCAGACCTTTC 59.350 40.000 4.43 0.00 0.00 2.62
8402 13386 4.769688 TCCTGATGTTTGCTGACGATTAT 58.230 39.130 0.00 0.00 0.00 1.28
8405 13389 5.295292 CCTGATGTTTGCTGACGATTATCTT 59.705 40.000 0.00 0.00 0.00 2.40
8429 13413 1.200716 CGGTGCTGAATTGAAGTGCAT 59.799 47.619 0.00 0.00 36.04 3.96
8753 13737 3.926616 TCCGACTTCAAAGGAGATGTTC 58.073 45.455 0.00 0.00 0.00 3.18
8762 13746 3.347411 GGAGATGTTCCCGTCGAAG 57.653 57.895 0.00 0.00 40.37 3.79
8763 13747 0.179108 GGAGATGTTCCCGTCGAAGG 60.179 60.000 10.80 10.80 40.37 3.46
8764 13748 0.806492 GAGATGTTCCCGTCGAAGGC 60.806 60.000 12.40 0.00 0.00 4.35
8794 13778 1.336755 GGCGTTTGTGGTGACTTCATT 59.663 47.619 0.00 0.00 0.00 2.57
8800 13784 6.307155 CGTTTGTGGTGACTTCATTAATCTC 58.693 40.000 0.00 0.00 0.00 2.75
8812 13796 9.107177 GACTTCATTAATCTCAAGATGATGTGT 57.893 33.333 8.00 12.32 37.16 3.72
8818 13802 6.738832 AATCTCAAGATGATGTGTTGACTG 57.261 37.500 0.00 0.00 35.40 3.51
8870 13854 3.257873 TGTGTGCATTGGGTTCATAAAGG 59.742 43.478 0.00 0.00 0.00 3.11
8896 13880 4.405116 TGTATGTGCATACATCTGAGCA 57.595 40.909 17.95 0.00 46.11 4.26
8959 13945 1.930133 TGGGTCCCATCAGTGCCAT 60.930 57.895 6.47 0.00 0.00 4.40
9007 13995 1.916000 CGCACTTAACGCTGTACTACC 59.084 52.381 0.00 0.00 0.00 3.18
9008 13996 2.415090 CGCACTTAACGCTGTACTACCT 60.415 50.000 0.00 0.00 0.00 3.08
9009 13997 3.177487 GCACTTAACGCTGTACTACCTC 58.823 50.000 0.00 0.00 0.00 3.85
9010 13998 3.767278 CACTTAACGCTGTACTACCTCC 58.233 50.000 0.00 0.00 0.00 4.30
9011 13999 2.421424 ACTTAACGCTGTACTACCTCCG 59.579 50.000 0.00 0.00 0.00 4.63
9012 14000 2.113860 TAACGCTGTACTACCTCCGT 57.886 50.000 0.00 0.00 0.00 4.69
9013 14001 0.807496 AACGCTGTACTACCTCCGTC 59.193 55.000 0.00 0.00 0.00 4.79
9014 14002 1.028868 ACGCTGTACTACCTCCGTCC 61.029 60.000 0.00 0.00 0.00 4.79
9015 14003 0.747283 CGCTGTACTACCTCCGTCCT 60.747 60.000 0.00 0.00 0.00 3.85
9016 14004 1.472188 GCTGTACTACCTCCGTCCTT 58.528 55.000 0.00 0.00 0.00 3.36
9017 14005 2.648059 GCTGTACTACCTCCGTCCTTA 58.352 52.381 0.00 0.00 0.00 2.69
9018 14006 3.220940 GCTGTACTACCTCCGTCCTTAT 58.779 50.000 0.00 0.00 0.00 1.73
9019 14007 3.635836 GCTGTACTACCTCCGTCCTTATT 59.364 47.826 0.00 0.00 0.00 1.40
9020 14008 4.099113 GCTGTACTACCTCCGTCCTTATTT 59.901 45.833 0.00 0.00 0.00 1.40
9030 14018 5.221204 CCTCCGTCCTTATTTGTACTACCTC 60.221 48.000 0.00 0.00 0.00 3.85
9042 14030 4.406456 TGTACTACCTCCGTCCTTGTTTA 58.594 43.478 0.00 0.00 0.00 2.01
9043 14031 5.018809 TGTACTACCTCCGTCCTTGTTTAT 58.981 41.667 0.00 0.00 0.00 1.40
9044 14032 5.481473 TGTACTACCTCCGTCCTTGTTTATT 59.519 40.000 0.00 0.00 0.00 1.40
9045 14033 6.663093 TGTACTACCTCCGTCCTTGTTTATTA 59.337 38.462 0.00 0.00 0.00 0.98
9046 14034 6.218108 ACTACCTCCGTCCTTGTTTATTAG 57.782 41.667 0.00 0.00 0.00 1.73
9047 14035 5.718607 ACTACCTCCGTCCTTGTTTATTAGT 59.281 40.000 0.00 0.00 0.00 2.24
9048 14036 5.082251 ACCTCCGTCCTTGTTTATTAGTC 57.918 43.478 0.00 0.00 0.00 2.59
9049 14037 4.081254 ACCTCCGTCCTTGTTTATTAGTCC 60.081 45.833 0.00 0.00 0.00 3.85
9050 14038 4.439968 CTCCGTCCTTGTTTATTAGTCCC 58.560 47.826 0.00 0.00 0.00 4.46
9051 14039 4.098894 TCCGTCCTTGTTTATTAGTCCCT 58.901 43.478 0.00 0.00 0.00 4.20
9052 14040 4.533311 TCCGTCCTTGTTTATTAGTCCCTT 59.467 41.667 0.00 0.00 0.00 3.95
9053 14041 5.013391 TCCGTCCTTGTTTATTAGTCCCTTT 59.987 40.000 0.00 0.00 0.00 3.11
9054 14042 5.708697 CCGTCCTTGTTTATTAGTCCCTTTT 59.291 40.000 0.00 0.00 0.00 2.27
9055 14043 6.349033 CCGTCCTTGTTTATTAGTCCCTTTTG 60.349 42.308 0.00 0.00 0.00 2.44
9056 14044 6.206048 CGTCCTTGTTTATTAGTCCCTTTTGT 59.794 38.462 0.00 0.00 0.00 2.83
9057 14045 7.388500 CGTCCTTGTTTATTAGTCCCTTTTGTA 59.612 37.037 0.00 0.00 0.00 2.41
9058 14046 9.070179 GTCCTTGTTTATTAGTCCCTTTTGTAA 57.930 33.333 0.00 0.00 0.00 2.41
9059 14047 9.816787 TCCTTGTTTATTAGTCCCTTTTGTAAT 57.183 29.630 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.436115 GGTACTTGAGGCGGTGGC 60.436 66.667 0.00 0.00 38.90 5.01
16 17 1.375523 GTGGTACTTGAGGCGGTGG 60.376 63.158 0.00 0.00 0.00 4.61
17 18 0.949105 GTGTGGTACTTGAGGCGGTG 60.949 60.000 0.00 0.00 0.00 4.94
18 19 1.119574 AGTGTGGTACTTGAGGCGGT 61.120 55.000 0.00 0.00 35.67 5.68
19 20 0.892755 TAGTGTGGTACTTGAGGCGG 59.107 55.000 0.00 0.00 40.89 6.13
20 21 1.271379 TGTAGTGTGGTACTTGAGGCG 59.729 52.381 0.00 0.00 40.89 5.52
21 22 3.064931 GTTGTAGTGTGGTACTTGAGGC 58.935 50.000 0.00 0.00 40.89 4.70
22 23 4.307432 CAGTTGTAGTGTGGTACTTGAGG 58.693 47.826 0.00 0.00 40.89 3.86
23 24 3.741344 GCAGTTGTAGTGTGGTACTTGAG 59.259 47.826 0.00 0.00 40.89 3.02
24 25 3.493699 GGCAGTTGTAGTGTGGTACTTGA 60.494 47.826 0.00 0.00 40.89 3.02
25 26 2.806244 GGCAGTTGTAGTGTGGTACTTG 59.194 50.000 0.00 0.00 40.89 3.16
26 27 2.704065 AGGCAGTTGTAGTGTGGTACTT 59.296 45.455 0.00 0.00 40.89 2.24
27 28 2.326428 AGGCAGTTGTAGTGTGGTACT 58.674 47.619 0.00 0.00 43.56 2.73
28 29 2.833631 AGGCAGTTGTAGTGTGGTAC 57.166 50.000 0.00 0.00 0.00 3.34
29 30 3.472652 CAAAGGCAGTTGTAGTGTGGTA 58.527 45.455 0.00 0.00 0.00 3.25
30 31 2.297701 CAAAGGCAGTTGTAGTGTGGT 58.702 47.619 0.00 0.00 0.00 4.16
31 32 1.608590 CCAAAGGCAGTTGTAGTGTGG 59.391 52.381 0.00 0.00 0.00 4.17
44 45 1.080772 GTACAAAGGCGCCAAAGGC 60.081 57.895 31.54 10.25 46.75 4.35
45 46 0.887933 ATGTACAAAGGCGCCAAAGG 59.112 50.000 31.54 17.30 0.00 3.11
46 47 1.135402 GGATGTACAAAGGCGCCAAAG 60.135 52.381 31.54 19.58 0.00 2.77
47 48 0.885196 GGATGTACAAAGGCGCCAAA 59.115 50.000 31.54 1.61 0.00 3.28
48 49 0.963355 GGGATGTACAAAGGCGCCAA 60.963 55.000 31.54 5.16 0.00 4.52
49 50 1.377987 GGGATGTACAAAGGCGCCA 60.378 57.895 31.54 5.89 0.00 5.69
50 51 2.119029 GGGGATGTACAAAGGCGCC 61.119 63.158 21.89 21.89 0.00 6.53
51 52 0.179468 TAGGGGATGTACAAAGGCGC 59.821 55.000 0.00 0.00 0.00 6.53
52 53 1.474498 GGTAGGGGATGTACAAAGGCG 60.474 57.143 0.00 0.00 0.00 5.52
53 54 1.562475 TGGTAGGGGATGTACAAAGGC 59.438 52.381 0.00 0.00 0.00 4.35
54 55 3.886123 CTTGGTAGGGGATGTACAAAGG 58.114 50.000 0.00 0.00 30.51 3.11
55 56 3.279434 GCTTGGTAGGGGATGTACAAAG 58.721 50.000 0.00 0.00 35.34 2.77
56 57 2.645297 TGCTTGGTAGGGGATGTACAAA 59.355 45.455 0.00 0.00 0.00 2.83
57 58 2.270858 TGCTTGGTAGGGGATGTACAA 58.729 47.619 0.00 0.00 0.00 2.41
58 59 1.959710 TGCTTGGTAGGGGATGTACA 58.040 50.000 0.00 0.00 0.00 2.90
59 60 3.359695 TTTGCTTGGTAGGGGATGTAC 57.640 47.619 0.00 0.00 0.00 2.90
60 61 3.372566 CCATTTGCTTGGTAGGGGATGTA 60.373 47.826 0.00 0.00 31.74 2.29
61 62 2.624029 CCATTTGCTTGGTAGGGGATGT 60.624 50.000 0.00 0.00 31.74 3.06
62 63 2.034124 CCATTTGCTTGGTAGGGGATG 58.966 52.381 0.00 0.00 31.74 3.51
63 64 1.062962 CCCATTTGCTTGGTAGGGGAT 60.063 52.381 0.00 0.00 36.14 3.85
64 65 0.334676 CCCATTTGCTTGGTAGGGGA 59.665 55.000 0.00 0.00 36.14 4.81
65 66 1.329913 GCCCATTTGCTTGGTAGGGG 61.330 60.000 0.00 0.00 36.79 4.79
66 67 0.614415 TGCCCATTTGCTTGGTAGGG 60.614 55.000 0.00 0.00 39.33 3.53
67 68 0.819582 CTGCCCATTTGCTTGGTAGG 59.180 55.000 0.00 0.00 34.77 3.18
68 69 1.549203 ACTGCCCATTTGCTTGGTAG 58.451 50.000 0.00 0.00 34.77 3.18
69 70 1.892474 GAACTGCCCATTTGCTTGGTA 59.108 47.619 0.00 0.00 34.77 3.25
70 71 0.681175 GAACTGCCCATTTGCTTGGT 59.319 50.000 0.00 0.00 34.77 3.67
71 72 0.971386 AGAACTGCCCATTTGCTTGG 59.029 50.000 0.00 0.00 36.46 3.61
72 73 2.825861 AAGAACTGCCCATTTGCTTG 57.174 45.000 0.00 0.00 0.00 4.01
73 74 2.699846 TGAAAGAACTGCCCATTTGCTT 59.300 40.909 0.00 0.00 0.00 3.91
74 75 2.318908 TGAAAGAACTGCCCATTTGCT 58.681 42.857 0.00 0.00 0.00 3.91
75 76 2.818130 TGAAAGAACTGCCCATTTGC 57.182 45.000 0.00 0.00 0.00 3.68
76 77 4.692155 GGAAATGAAAGAACTGCCCATTTG 59.308 41.667 0.00 0.00 37.51 2.32
77 78 4.347583 TGGAAATGAAAGAACTGCCCATTT 59.652 37.500 0.00 0.00 39.33 2.32
78 79 3.903090 TGGAAATGAAAGAACTGCCCATT 59.097 39.130 0.00 0.00 0.00 3.16
79 80 3.509442 TGGAAATGAAAGAACTGCCCAT 58.491 40.909 0.00 0.00 0.00 4.00
80 81 2.956132 TGGAAATGAAAGAACTGCCCA 58.044 42.857 0.00 0.00 0.00 5.36
81 82 4.248058 CATTGGAAATGAAAGAACTGCCC 58.752 43.478 0.00 0.00 0.00 5.36
82 83 3.681417 GCATTGGAAATGAAAGAACTGCC 59.319 43.478 4.18 0.00 0.00 4.85
83 84 4.309099 TGCATTGGAAATGAAAGAACTGC 58.691 39.130 4.18 0.00 0.00 4.40
84 85 5.163893 GCATGCATTGGAAATGAAAGAACTG 60.164 40.000 14.21 0.00 0.00 3.16
85 86 4.933400 GCATGCATTGGAAATGAAAGAACT 59.067 37.500 14.21 0.00 0.00 3.01
86 87 4.691685 TGCATGCATTGGAAATGAAAGAAC 59.308 37.500 18.46 0.00 0.00 3.01
87 88 4.895961 TGCATGCATTGGAAATGAAAGAA 58.104 34.783 18.46 0.00 0.00 2.52
88 89 4.020928 ACTGCATGCATTGGAAATGAAAGA 60.021 37.500 22.97 0.00 0.00 2.52
89 90 4.250464 ACTGCATGCATTGGAAATGAAAG 58.750 39.130 22.97 7.02 0.00 2.62
90 91 4.247258 GACTGCATGCATTGGAAATGAAA 58.753 39.130 22.97 0.00 0.00 2.69
91 92 3.673866 CGACTGCATGCATTGGAAATGAA 60.674 43.478 22.97 0.00 0.00 2.57
92 93 2.159352 CGACTGCATGCATTGGAAATGA 60.159 45.455 22.97 0.00 0.00 2.57
93 94 2.159352 TCGACTGCATGCATTGGAAATG 60.159 45.455 22.97 9.38 0.00 2.32
94 95 2.093890 TCGACTGCATGCATTGGAAAT 58.906 42.857 22.97 0.64 0.00 2.17
95 96 1.532523 TCGACTGCATGCATTGGAAA 58.467 45.000 22.97 2.08 0.00 3.13
96 97 1.402613 CATCGACTGCATGCATTGGAA 59.597 47.619 22.97 6.61 0.00 3.53
97 98 1.018910 CATCGACTGCATGCATTGGA 58.981 50.000 22.97 22.20 0.00 3.53
98 99 3.544615 CATCGACTGCATGCATTGG 57.455 52.632 22.97 17.29 0.00 3.16
117 118 2.220653 TTTCCTGGGATGCTTGGAAG 57.779 50.000 10.16 0.00 39.39 3.46
118 119 2.925966 ATTTCCTGGGATGCTTGGAA 57.074 45.000 7.21 7.21 36.87 3.53
119 120 2.312741 AGAATTTCCTGGGATGCTTGGA 59.687 45.455 0.00 0.00 0.00 3.53
120 121 2.692041 GAGAATTTCCTGGGATGCTTGG 59.308 50.000 0.00 0.00 0.00 3.61
121 122 3.629087 AGAGAATTTCCTGGGATGCTTG 58.371 45.455 0.00 0.00 0.00 4.01
122 123 4.021916 CAAGAGAATTTCCTGGGATGCTT 58.978 43.478 0.00 0.00 0.00 3.91
123 124 3.629087 CAAGAGAATTTCCTGGGATGCT 58.371 45.455 0.00 0.00 0.00 3.79
124 125 2.100418 GCAAGAGAATTTCCTGGGATGC 59.900 50.000 0.00 0.00 0.00 3.91
125 126 3.380637 CAGCAAGAGAATTTCCTGGGATG 59.619 47.826 0.00 0.00 0.00 3.51
126 127 3.629087 CAGCAAGAGAATTTCCTGGGAT 58.371 45.455 0.00 0.00 0.00 3.85
127 128 2.881403 GCAGCAAGAGAATTTCCTGGGA 60.881 50.000 0.00 0.00 0.00 4.37
128 129 1.475682 GCAGCAAGAGAATTTCCTGGG 59.524 52.381 0.00 0.00 0.00 4.45
129 130 2.165167 TGCAGCAAGAGAATTTCCTGG 58.835 47.619 0.00 0.00 0.00 4.45
130 131 4.158025 AGAATGCAGCAAGAGAATTTCCTG 59.842 41.667 0.00 0.00 0.00 3.86
131 132 4.158025 CAGAATGCAGCAAGAGAATTTCCT 59.842 41.667 0.00 0.00 0.00 3.36
132 133 4.082354 ACAGAATGCAGCAAGAGAATTTCC 60.082 41.667 0.00 0.00 42.53 3.13
133 134 5.056894 ACAGAATGCAGCAAGAGAATTTC 57.943 39.130 0.00 0.00 42.53 2.17
134 135 5.709164 AGTACAGAATGCAGCAAGAGAATTT 59.291 36.000 0.00 0.00 42.53 1.82
135 136 5.251764 AGTACAGAATGCAGCAAGAGAATT 58.748 37.500 0.00 0.00 42.53 2.17
136 137 4.841422 AGTACAGAATGCAGCAAGAGAAT 58.159 39.130 0.00 0.00 42.53 2.40
137 138 4.277515 AGTACAGAATGCAGCAAGAGAA 57.722 40.909 0.00 0.00 42.53 2.87
138 139 3.969287 AGTACAGAATGCAGCAAGAGA 57.031 42.857 0.00 0.00 42.53 3.10
139 140 4.118410 CCTAGTACAGAATGCAGCAAGAG 58.882 47.826 0.00 0.00 42.53 2.85
140 141 3.769300 TCCTAGTACAGAATGCAGCAAGA 59.231 43.478 0.00 0.00 42.53 3.02
141 142 4.128925 TCCTAGTACAGAATGCAGCAAG 57.871 45.455 0.00 0.00 42.53 4.01
142 143 4.443457 GGATCCTAGTACAGAATGCAGCAA 60.443 45.833 3.84 0.00 42.53 3.91
143 144 3.070159 GGATCCTAGTACAGAATGCAGCA 59.930 47.826 3.84 0.00 42.53 4.41
144 145 3.070159 TGGATCCTAGTACAGAATGCAGC 59.930 47.826 14.23 0.00 42.53 5.25
145 146 4.944619 TGGATCCTAGTACAGAATGCAG 57.055 45.455 14.23 0.00 42.53 4.41
146 147 4.443457 GCTTGGATCCTAGTACAGAATGCA 60.443 45.833 21.99 0.00 42.53 3.96
147 148 4.061596 GCTTGGATCCTAGTACAGAATGC 58.938 47.826 21.99 5.28 42.53 3.56
148 149 5.163364 ACTGCTTGGATCCTAGTACAGAATG 60.163 44.000 25.95 13.18 46.00 2.67
149 150 4.965532 ACTGCTTGGATCCTAGTACAGAAT 59.034 41.667 25.95 10.83 0.00 2.40
150 151 4.160439 CACTGCTTGGATCCTAGTACAGAA 59.840 45.833 25.95 7.13 0.00 3.02
151 152 3.701542 CACTGCTTGGATCCTAGTACAGA 59.298 47.826 25.95 8.46 0.00 3.41
152 153 3.449018 ACACTGCTTGGATCCTAGTACAG 59.551 47.826 21.99 21.40 0.00 2.74
153 154 3.441101 ACACTGCTTGGATCCTAGTACA 58.559 45.455 21.99 12.68 0.00 2.90
154 155 3.702045 AGACACTGCTTGGATCCTAGTAC 59.298 47.826 21.99 9.02 0.00 2.73
155 156 3.982516 AGACACTGCTTGGATCCTAGTA 58.017 45.455 21.99 17.55 0.00 1.82
156 157 2.826488 AGACACTGCTTGGATCCTAGT 58.174 47.619 21.99 13.56 0.00 2.57
157 158 3.431486 GGAAGACACTGCTTGGATCCTAG 60.431 52.174 17.84 17.84 0.00 3.02
158 159 2.501723 GGAAGACACTGCTTGGATCCTA 59.498 50.000 14.23 4.17 0.00 2.94
159 160 1.280421 GGAAGACACTGCTTGGATCCT 59.720 52.381 14.23 0.00 0.00 3.24
160 161 1.743996 GGAAGACACTGCTTGGATCC 58.256 55.000 4.20 4.20 0.00 3.36
161 162 1.363744 CGGAAGACACTGCTTGGATC 58.636 55.000 0.00 0.00 0.00 3.36
162 163 0.674895 GCGGAAGACACTGCTTGGAT 60.675 55.000 0.00 0.00 38.89 3.41
163 164 1.301716 GCGGAAGACACTGCTTGGA 60.302 57.895 0.00 0.00 38.89 3.53
164 165 0.957395 ATGCGGAAGACACTGCTTGG 60.957 55.000 0.00 0.00 42.03 3.61
165 166 0.877071 AATGCGGAAGACACTGCTTG 59.123 50.000 0.00 0.00 42.03 4.01
166 167 0.877071 CAATGCGGAAGACACTGCTT 59.123 50.000 0.00 0.00 42.03 3.91
167 168 0.957395 CCAATGCGGAAGACACTGCT 60.957 55.000 0.00 0.00 42.03 4.24
168 169 1.503542 CCAATGCGGAAGACACTGC 59.496 57.895 0.00 0.00 41.89 4.40
169 170 0.606401 ACCCAATGCGGAAGACACTG 60.606 55.000 0.00 0.00 36.56 3.66
170 171 0.606401 CACCCAATGCGGAAGACACT 60.606 55.000 0.00 0.00 36.56 3.55
171 172 0.889186 ACACCCAATGCGGAAGACAC 60.889 55.000 0.00 0.00 36.56 3.67
172 173 0.179004 AACACCCAATGCGGAAGACA 60.179 50.000 0.00 0.00 36.56 3.41
173 174 0.521735 GAACACCCAATGCGGAAGAC 59.478 55.000 0.00 0.00 36.56 3.01
174 175 0.953471 CGAACACCCAATGCGGAAGA 60.953 55.000 0.00 0.00 36.56 2.87
175 176 1.501741 CGAACACCCAATGCGGAAG 59.498 57.895 0.00 0.00 36.56 3.46
176 177 2.622011 GCGAACACCCAATGCGGAA 61.622 57.895 0.00 0.00 36.56 4.30
177 178 3.053291 GCGAACACCCAATGCGGA 61.053 61.111 0.00 0.00 36.56 5.54
178 179 2.801113 CTTGCGAACACCCAATGCGG 62.801 60.000 0.00 0.00 0.00 5.69
179 180 1.442520 CTTGCGAACACCCAATGCG 60.443 57.895 0.00 0.00 0.00 4.73
180 181 0.387239 GACTTGCGAACACCCAATGC 60.387 55.000 0.00 0.00 0.00 3.56
181 182 0.110238 CGACTTGCGAACACCCAATG 60.110 55.000 0.00 0.00 44.57 2.82
182 183 1.234615 CCGACTTGCGAACACCCAAT 61.235 55.000 0.00 0.00 44.57 3.16
183 184 1.890041 CCGACTTGCGAACACCCAA 60.890 57.895 0.00 0.00 44.57 4.12
184 185 2.280524 CCGACTTGCGAACACCCA 60.281 61.111 0.00 0.00 44.57 4.51
185 186 2.027625 CTCCGACTTGCGAACACCC 61.028 63.158 0.00 0.00 44.57 4.61
186 187 0.038892 TACTCCGACTTGCGAACACC 60.039 55.000 0.00 0.00 44.57 4.16
187 188 1.068748 TCTACTCCGACTTGCGAACAC 60.069 52.381 0.00 0.00 44.57 3.32
188 189 1.199327 CTCTACTCCGACTTGCGAACA 59.801 52.381 0.00 0.00 44.57 3.18
189 190 1.897641 CTCTACTCCGACTTGCGAAC 58.102 55.000 0.00 0.00 44.57 3.95
190 191 0.170561 GCTCTACTCCGACTTGCGAA 59.829 55.000 0.00 0.00 44.57 4.70
191 192 0.958876 TGCTCTACTCCGACTTGCGA 60.959 55.000 0.00 0.00 44.57 5.10
192 193 0.101399 ATGCTCTACTCCGACTTGCG 59.899 55.000 0.00 0.00 40.47 4.85
193 194 1.565305 CATGCTCTACTCCGACTTGC 58.435 55.000 0.00 0.00 0.00 4.01
194 195 1.134995 TGCATGCTCTACTCCGACTTG 60.135 52.381 20.33 0.00 0.00 3.16
195 196 1.186200 TGCATGCTCTACTCCGACTT 58.814 50.000 20.33 0.00 0.00 3.01
346 348 1.219124 GAGGAAGCTGATGCCGACA 59.781 57.895 0.00 0.00 40.80 4.35
356 358 2.669849 CTGCTGCAGGAGGAAGCT 59.330 61.111 26.30 0.00 37.82 3.74
409 412 2.307309 CGGCGTTTTGTCTGCTCGA 61.307 57.895 0.00 0.00 0.00 4.04
527 530 0.534412 ATGAGAGAAGGTGTCGCCAG 59.466 55.000 4.97 0.00 40.61 4.85
528 531 0.976641 AATGAGAGAAGGTGTCGCCA 59.023 50.000 4.97 0.00 40.61 5.69
534 537 2.263077 CGTCGGAAATGAGAGAAGGTG 58.737 52.381 0.00 0.00 0.00 4.00
557 560 1.543429 GCACCGCTAGATAGGCCATTT 60.543 52.381 5.01 0.00 0.00 2.32
646 658 2.213499 CTGTCAGGCGAAAAGTCAAGT 58.787 47.619 0.00 0.00 0.00 3.16
668 681 2.203625 AAAACACGCCTGGGCCAT 60.204 55.556 6.72 0.00 37.98 4.40
738 755 4.693525 CGTTTTTGGGCCGGCGAC 62.694 66.667 22.54 16.89 0.00 5.19
762 780 0.102481 AGACGTCGAAATCCATCGGG 59.898 55.000 10.46 0.00 42.92 5.14
823 842 2.895372 GATACCGCGCCCCAACAG 60.895 66.667 0.00 0.00 0.00 3.16
824 843 4.823419 CGATACCGCGCCCCAACA 62.823 66.667 0.00 0.00 0.00 3.33
835 854 4.910585 CCTGTGGGCCGCGATACC 62.911 72.222 8.23 7.28 0.00 2.73
1045 1070 4.812476 CATCTCCGCCAACGCCGA 62.812 66.667 0.00 0.00 38.22 5.54
1908 1934 6.869913 CCTACATCAAATGCAATTGTTCAAGT 59.130 34.615 14.00 9.06 36.10 3.16
1946 1972 6.769822 CACATTGATTTAGCCTATCCTTCACT 59.230 38.462 0.00 0.00 0.00 3.41
1957 1983 8.986477 AACTATTTTGTCACATTGATTTAGCC 57.014 30.769 0.00 0.00 0.00 3.93
2075 2102 3.105937 GACGAAACAAGCAGGTCAAAAC 58.894 45.455 0.00 0.00 0.00 2.43
2827 6232 0.535335 TAGTACGCAGCCTTTCCCTG 59.465 55.000 0.00 0.00 0.00 4.45
2908 6324 9.013229 ACTAGCAAGTCAATGACATGATAAAAA 57.987 29.630 20.94 0.37 33.10 1.94
2909 6325 8.565896 ACTAGCAAGTCAATGACATGATAAAA 57.434 30.769 20.94 0.71 33.10 1.52
2910 6326 9.836864 ATACTAGCAAGTCAATGACATGATAAA 57.163 29.630 20.94 10.83 33.10 1.40
3849 7268 5.624281 CGTTACGGAGGGAGTACCAAATAAA 60.624 44.000 0.00 0.00 43.89 1.40
3872 7291 6.363626 AGTGATCTAAGCGCACTTATATTTCG 59.636 38.462 11.47 0.00 39.69 3.46
3957 7469 6.817765 TTTTACCTTGCAATCACCTAAGAG 57.182 37.500 0.00 0.00 0.00 2.85
4290 7804 5.852827 TCCTTGGGCTAGAAAAACATTTTG 58.147 37.500 0.00 0.00 0.00 2.44
4995 8688 4.537433 GCGGCGAGGCAGAGGATT 62.537 66.667 12.98 0.00 0.00 3.01
5042 8735 2.203788 AGGCAGAGTTCGGGTGGA 60.204 61.111 0.00 0.00 0.00 4.02
5249 9220 3.550431 ACCGGGCGATGAGGGATG 61.550 66.667 6.32 0.00 0.00 3.51
5510 9505 1.414181 CGATACATCTCAAGGGCCACT 59.586 52.381 6.18 0.00 0.00 4.00
6219 11171 4.467438 TCACAATATCCTGCTCAGTCAAGA 59.533 41.667 0.00 0.00 0.00 3.02
6292 11247 4.697352 GCCAGAAGCATTAGTCAAAGAAGA 59.303 41.667 0.00 0.00 42.97 2.87
6293 11248 4.979388 GCCAGAAGCATTAGTCAAAGAAG 58.021 43.478 0.00 0.00 42.97 2.85
6476 11431 3.303135 CTCTAGGGCGCGGGCATA 61.303 66.667 26.61 16.37 42.47 3.14
6579 11534 2.289694 GGCAATATAGATCACGCCAGGT 60.290 50.000 0.00 0.00 39.38 4.00
6654 11630 4.275936 GGGGTAATTTGAGAATGGATGACG 59.724 45.833 0.00 0.00 0.00 4.35
6811 11788 1.340889 TGCAGGCAATTCAGTGAAACC 59.659 47.619 10.14 11.70 37.80 3.27
6991 11968 6.554228 TCTTCTCCTAGACCTAGAATACTCGA 59.446 42.308 5.67 0.00 35.21 4.04
7008 11985 5.710646 TCATAAGCAGGTCTATCTTCTCCT 58.289 41.667 0.00 0.00 0.00 3.69
7009 11986 5.538433 ACTCATAAGCAGGTCTATCTTCTCC 59.462 44.000 0.00 0.00 0.00 3.71
7010 11987 6.648879 ACTCATAAGCAGGTCTATCTTCTC 57.351 41.667 0.00 0.00 0.00 2.87
7020 11997 5.307976 TGGAGCAATATACTCATAAGCAGGT 59.692 40.000 7.71 0.00 35.79 4.00
7246 12227 4.680708 GCTGAGATCCCGAGTGTGATTAAA 60.681 45.833 0.00 0.00 0.00 1.52
7580 12562 1.705873 ACCGAGTGTCAGAAAGGTCT 58.294 50.000 0.00 0.00 32.85 3.85
7588 12570 3.060602 GAGAAAAGGAACCGAGTGTCAG 58.939 50.000 0.00 0.00 0.00 3.51
7655 12637 3.503363 CAGTGTTACTTCACATGCCATGT 59.497 43.478 4.03 4.03 46.22 3.21
7674 12656 4.099573 CCCATATCCTCGTAGTGAAACAGT 59.900 45.833 0.00 0.00 41.43 3.55
8295 13277 7.015226 TGTTGTTAACAGAACTCACATCTTG 57.985 36.000 8.56 0.00 36.25 3.02
8402 13386 0.592637 CAATTCAGCACCGCACAAGA 59.407 50.000 0.00 0.00 0.00 3.02
8405 13389 0.592637 CTTCAATTCAGCACCGCACA 59.407 50.000 0.00 0.00 0.00 4.57
8429 13413 2.301870 ACAGGTTCTTCCGCAGTCAATA 59.698 45.455 0.00 0.00 41.99 1.90
8763 13747 3.723348 AAACGCCTTCGCCTTCGC 61.723 61.111 0.00 0.00 39.84 4.70
8764 13748 2.173382 CAAACGCCTTCGCCTTCG 59.827 61.111 0.00 0.00 39.84 3.79
8765 13749 1.082104 CACAAACGCCTTCGCCTTC 60.082 57.895 0.00 0.00 39.84 3.46
8766 13750 2.551912 CCACAAACGCCTTCGCCTT 61.552 57.895 0.00 0.00 39.84 4.35
8767 13751 2.978010 CCACAAACGCCTTCGCCT 60.978 61.111 0.00 0.00 39.84 5.52
8768 13752 3.284449 ACCACAAACGCCTTCGCC 61.284 61.111 0.00 0.00 39.84 5.54
8794 13778 7.614494 TCAGTCAACACATCATCTTGAGATTA 58.386 34.615 0.00 0.00 31.21 1.75
8800 13784 5.236282 AGACTCAGTCAACACATCATCTTG 58.764 41.667 7.77 0.00 34.60 3.02
8812 13796 4.155709 ACATCTCCAAGAGACTCAGTCAA 58.844 43.478 7.77 0.00 41.76 3.18
8818 13802 5.221422 CCCTATGAACATCTCCAAGAGACTC 60.221 48.000 0.00 0.00 41.76 3.36
8890 13874 3.672808 AGAAGTTTGGTCTGATGCTCAG 58.327 45.455 6.79 6.79 45.59 3.35
8896 13880 2.641815 AGCCTGAGAAGTTTGGTCTGAT 59.358 45.455 0.00 0.00 0.00 2.90
8910 13894 2.166459 TGATTAGTCGGTCAAGCCTGAG 59.834 50.000 0.00 0.00 34.25 3.35
8999 13987 5.018809 ACAAATAAGGACGGAGGTAGTACA 58.981 41.667 2.06 0.00 0.00 2.90
9000 13988 5.588958 ACAAATAAGGACGGAGGTAGTAC 57.411 43.478 0.00 0.00 0.00 2.73
9001 13989 6.426587 AGTACAAATAAGGACGGAGGTAGTA 58.573 40.000 0.00 0.00 0.00 1.82
9002 13990 5.267587 AGTACAAATAAGGACGGAGGTAGT 58.732 41.667 0.00 0.00 0.00 2.73
9003 13991 5.848833 AGTACAAATAAGGACGGAGGTAG 57.151 43.478 0.00 0.00 0.00 3.18
9004 13992 5.594317 GGTAGTACAAATAAGGACGGAGGTA 59.406 44.000 2.06 0.00 0.00 3.08
9005 13993 4.403752 GGTAGTACAAATAAGGACGGAGGT 59.596 45.833 2.06 0.00 0.00 3.85
9006 13994 4.648307 AGGTAGTACAAATAAGGACGGAGG 59.352 45.833 2.06 0.00 0.00 4.30
9007 13995 5.221204 GGAGGTAGTACAAATAAGGACGGAG 60.221 48.000 2.06 0.00 0.00 4.63
9008 13996 4.646492 GGAGGTAGTACAAATAAGGACGGA 59.354 45.833 2.06 0.00 0.00 4.69
9009 13997 4.498682 CGGAGGTAGTACAAATAAGGACGG 60.499 50.000 2.06 0.00 0.00 4.79
9010 13998 4.096984 ACGGAGGTAGTACAAATAAGGACG 59.903 45.833 2.06 0.00 0.00 4.79
9011 13999 5.451103 GGACGGAGGTAGTACAAATAAGGAC 60.451 48.000 2.06 0.00 0.00 3.85
9012 14000 4.646492 GGACGGAGGTAGTACAAATAAGGA 59.354 45.833 2.06 0.00 0.00 3.36
9013 14001 4.648307 AGGACGGAGGTAGTACAAATAAGG 59.352 45.833 2.06 0.00 0.00 2.69
9014 14002 5.848833 AGGACGGAGGTAGTACAAATAAG 57.151 43.478 2.06 0.00 0.00 1.73
9015 14003 5.481473 ACAAGGACGGAGGTAGTACAAATAA 59.519 40.000 2.06 0.00 0.00 1.40
9016 14004 5.018809 ACAAGGACGGAGGTAGTACAAATA 58.981 41.667 2.06 0.00 0.00 1.40
9017 14005 3.836562 ACAAGGACGGAGGTAGTACAAAT 59.163 43.478 2.06 0.00 0.00 2.32
9018 14006 3.233507 ACAAGGACGGAGGTAGTACAAA 58.766 45.455 2.06 0.00 0.00 2.83
9019 14007 2.880443 ACAAGGACGGAGGTAGTACAA 58.120 47.619 2.06 0.00 0.00 2.41
9020 14008 2.592102 ACAAGGACGGAGGTAGTACA 57.408 50.000 2.06 0.00 0.00 2.90
9030 14018 4.482952 AGGGACTAATAAACAAGGACGG 57.517 45.455 0.00 0.00 36.02 4.79


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

AutoCloner maintained by Alex Coulton.