Multiple sequence alignment - TraesCS6B01G025100

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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 TraesCS6B01G025100 chr6B 100.000 7914 0 0 1 7914 15236001 15228088 0.000000e+00 14615.0
1 TraesCS6B01G025100 chr6B 96.018 2687 58 9 9 2686 16266257 16268903 0.000000e+00 4324.0
2 TraesCS6B01G025100 chr6B 96.049 1721 36 9 2718 4420 16268906 16270612 0.000000e+00 2772.0
3 TraesCS6B01G025100 chr6B 94.218 1176 24 12 3915 5062 16425939 16427098 0.000000e+00 1755.0
4 TraesCS6B01G025100 chr6B 84.983 1485 196 16 1148 2615 16433145 16434619 0.000000e+00 1482.0
5 TraesCS6B01G025100 chr6B 84.436 1285 178 11 1148 2415 52981049 52979770 0.000000e+00 1245.0
6 TraesCS6B01G025100 chr6B 84.356 1157 176 5 1174 2328 90939366 90940519 0.000000e+00 1129.0
7 TraesCS6B01G025100 chr6B 84.875 1157 120 20 3694 4821 15712722 15711592 0.000000e+00 1116.0
8 TraesCS6B01G025100 chr6B 84.824 1107 157 8 1214 2313 53062445 53061343 0.000000e+00 1103.0
9 TraesCS6B01G025100 chr6B 84.995 953 86 25 4152 5064 52578359 52577424 0.000000e+00 915.0
10 TraesCS6B01G025100 chr6B 92.357 628 27 8 6867 7486 16270900 16271514 0.000000e+00 874.0
11 TraesCS6B01G025100 chr6B 83.669 894 90 28 4152 5011 53074503 53073632 0.000000e+00 791.0
12 TraesCS6B01G025100 chr6B 90.964 498 30 8 7000 7487 16427226 16427718 0.000000e+00 656.0
13 TraesCS6B01G025100 chr6B 91.059 425 29 8 7493 7914 16427784 16428202 4.150000e-157 566.0
14 TraesCS6B01G025100 chr6B 84.436 514 43 13 4582 5064 15246836 15246329 9.300000e-129 472.0
15 TraesCS6B01G025100 chr6B 80.525 457 60 20 5300 5748 65155872 65155437 2.750000e-84 324.0
16 TraesCS6B01G025100 chr6B 84.416 308 29 9 3113 3403 15262887 15262582 1.300000e-72 285.0
17 TraesCS6B01G025100 chr6B 88.832 197 19 3 3293 3488 670590743 670590549 1.030000e-58 239.0
18 TraesCS6B01G025100 chr6B 92.025 163 13 0 3490 3652 232734819 232734981 6.180000e-56 230.0
19 TraesCS6B01G025100 chr6B 88.587 184 9 2 5068 5240 15217383 15217201 6.220000e-51 213.0
20 TraesCS6B01G025100 chr6B 88.356 146 12 2 5300 5441 16258307 16258451 3.800000e-38 171.0
21 TraesCS6B01G025100 chr6B 98.913 92 1 0 6779 6870 16270608 16270699 1.770000e-36 165.0
22 TraesCS6B01G025100 chr6B 81.000 200 26 8 5555 5753 15216986 15216798 1.780000e-31 148.0
23 TraesCS6B01G025100 chr6B 81.699 153 15 6 3747 3886 16239248 16239400 1.800000e-21 115.0
24 TraesCS6B01G025100 chr6B 81.333 150 10 9 4931 5064 16257909 16258056 1.090000e-18 106.0
25 TraesCS6B01G025100 chr6B 93.478 46 3 0 5238 5283 15230678 15230633 1.430000e-07 69.4
26 TraesCS6B01G025100 chr5B 93.748 2527 85 13 3881 6366 556618991 556616497 0.000000e+00 3723.0
27 TraesCS6B01G025100 chr5B 90.970 1783 122 18 935 2683 556628472 556626695 0.000000e+00 2364.0
28 TraesCS6B01G025100 chr5B 94.352 1204 40 14 2711 3888 556624998 556623797 0.000000e+00 1821.0
29 TraesCS6B01G025100 chr5B 80.489 1512 241 34 1144 2620 556795756 556794264 0.000000e+00 1109.0
30 TraesCS6B01G025100 chr5B 91.346 624 28 9 6867 7481 556554519 556553913 0.000000e+00 830.0
31 TraesCS6B01G025100 chr5B 91.784 426 23 5 7490 7914 556553843 556553429 4.120000e-162 582.0
32 TraesCS6B01G025100 chr5B 91.034 435 24 6 6355 6776 556616455 556616023 2.480000e-159 573.0
33 TraesCS6B01G025100 chr5B 85.575 513 61 10 2978 3488 621236541 621236040 7.040000e-145 525.0
34 TraesCS6B01G025100 chr5B 90.278 144 12 2 3694 3836 621235966 621235824 3.770000e-43 187.0
35 TraesCS6B01G025100 chr5B 93.443 61 4 0 6810 6870 556616023 556615963 3.040000e-14 91.6
36 TraesCS6B01G025100 chr5B 93.478 46 3 0 5238 5283 556617553 556617508 1.430000e-07 69.4
37 TraesCS6B01G025100 chr5B 100.000 32 0 0 3686 3717 556624162 556624131 8.580000e-05 60.2
38 TraesCS6B01G025100 chr6D 86.437 1482 187 7 1145 2615 8552801 8551323 0.000000e+00 1611.0
39 TraesCS6B01G025100 chr6D 85.692 1258 99 31 4024 5240 8804384 8805601 0.000000e+00 1251.0
40 TraesCS6B01G025100 chr6D 81.737 1462 236 21 1174 2611 8987254 8988708 0.000000e+00 1192.0
41 TraesCS6B01G025100 chr6D 83.249 1188 186 13 1142 2323 8967575 8968755 0.000000e+00 1079.0
42 TraesCS6B01G025100 chr6D 87.101 783 87 14 4152 4932 34019817 34020587 0.000000e+00 874.0
43 TraesCS6B01G025100 chr6D 81.734 1084 135 34 4030 5064 33899004 33900073 0.000000e+00 846.0
44 TraesCS6B01G025100 chr6D 84.106 906 104 17 3930 4802 8817858 8818756 0.000000e+00 839.0
45 TraesCS6B01G025100 chr6D 81.831 732 70 29 4377 5064 8815076 8815788 2.490000e-154 556.0
46 TraesCS6B01G025100 chr6D 85.882 510 49 15 4359 4855 8971703 8972202 9.100000e-144 521.0
47 TraesCS6B01G025100 chr6D 82.314 605 61 23 2899 3488 8917030 8917603 4.290000e-132 483.0
48 TraesCS6B01G025100 chr6D 82.031 512 75 6 2942 3442 8551028 8550523 3.420000e-113 420.0
49 TraesCS6B01G025100 chr6D 78.329 706 87 25 5300 5978 8972698 8973364 5.760000e-106 396.0
50 TraesCS6B01G025100 chr6D 85.174 344 41 7 4535 4873 8989648 8989986 2.110000e-90 344.0
51 TraesCS6B01G025100 chr6D 79.434 530 48 27 4581 5064 8514288 8513774 1.280000e-82 318.0
52 TraesCS6B01G025100 chr6D 79.727 439 59 13 3926 4338 8971295 8971729 2.790000e-74 291.0
53 TraesCS6B01G025100 chr6D 75.766 685 84 36 3926 4571 8577020 8576379 3.640000e-68 270.0
54 TraesCS6B01G025100 chr6D 91.617 167 13 1 3487 3652 90112403 90112237 6.180000e-56 230.0
55 TraesCS6B01G025100 chr6D 92.453 159 12 0 3493 3651 90135048 90134890 2.220000e-55 228.0
56 TraesCS6B01G025100 chr6D 79.666 359 38 15 460 783 33994431 33994789 7.990000e-55 226.0
57 TraesCS6B01G025100 chr6D 87.719 171 15 4 4326 4491 8989467 8989636 2.250000e-45 195.0
58 TraesCS6B01G025100 chr6D 87.975 158 14 2 4090 4243 8802267 8802423 1.750000e-41 182.0
59 TraesCS6B01G025100 chr6D 87.671 146 13 3 5300 5441 33900312 33900456 1.770000e-36 165.0
60 TraesCS6B01G025100 chr6D 87.143 140 13 2 5300 5435 8816039 8816177 3.820000e-33 154.0
61 TraesCS6B01G025100 chr6D 85.811 148 15 3 5298 5441 8513524 8513379 1.380000e-32 152.0
62 TraesCS6B01G025100 chr6D 85.616 146 16 2 5300 5441 8819222 8819366 1.780000e-31 148.0
63 TraesCS6B01G025100 chr6D 89.831 118 7 2 5298 5410 8805618 8805735 6.400000e-31 147.0
64 TraesCS6B01G025100 chr6D 82.667 150 8 9 4931 5064 8818823 8818970 5.020000e-22 117.0
65 TraesCS6B01G025100 chr6D 79.503 161 24 6 4320 4478 7681854 7682007 1.090000e-18 106.0
66 TraesCS6B01G025100 chr6D 80.952 105 11 7 7142 7243 318786230 318786132 3.060000e-09 75.0
67 TraesCS6B01G025100 chr6A 81.031 1571 261 24 1069 2620 9461383 9462935 0.000000e+00 1216.0
68 TraesCS6B01G025100 chr6A 87.252 957 92 12 3916 4850 9366655 9367603 0.000000e+00 1064.0
69 TraesCS6B01G025100 chr6A 90.909 748 47 8 3963 4691 9037042 9036297 0.000000e+00 985.0
70 TraesCS6B01G025100 chr6A 85.607 931 113 9 1697 2615 9474626 9475547 0.000000e+00 957.0
71 TraesCS6B01G025100 chr6A 82.285 954 112 30 4086 5012 30558688 30557765 0.000000e+00 773.0
72 TraesCS6B01G025100 chr6A 80.660 667 87 22 2828 3488 9356756 9357386 5.560000e-131 479.0
73 TraesCS6B01G025100 chr6A 84.176 455 56 11 4133 4583 8993099 8992657 2.040000e-115 427.0
74 TraesCS6B01G025100 chr6A 82.938 211 18 12 3691 3886 9357457 9357664 2.940000e-39 174.0
75 TraesCS6B01G025100 chr6A 86.301 146 15 2 5300 5441 30557457 30557313 3.820000e-33 154.0
76 TraesCS6B01G025100 chr6A 86.957 92 5 2 2666 2751 189573472 189573562 6.540000e-16 97.1
77 TraesCS6B01G025100 chr6A 81.250 96 9 6 7142 7234 456578118 456578029 1.430000e-07 69.4
78 TraesCS6B01G025100 chr5D 81.198 1553 246 25 1135 2661 42076046 42077578 0.000000e+00 1208.0
79 TraesCS6B01G025100 chr5D 83.499 703 73 15 2746 3442 42077575 42078240 4.060000e-172 616.0
80 TraesCS6B01G025100 chr5D 86.914 512 56 8 2978 3488 499863237 499862736 1.490000e-156 564.0
81 TraesCS6B01G025100 chr5D 80.564 674 72 28 3916 4577 499860471 499859845 1.560000e-126 464.0
82 TraesCS6B01G025100 chr5D 83.568 213 16 5 3691 3886 42078465 42078675 1.750000e-41 182.0
83 TraesCS6B01G025100 chr5D 89.744 78 6 2 2729 2805 499863421 499863345 1.820000e-16 99.0
84 TraesCS6B01G025100 chr5D 100.000 32 0 0 7202 7233 272359100 272359069 8.580000e-05 60.2
85 TraesCS6B01G025100 chr2B 85.579 1158 102 26 3904 5012 709251501 709250360 0.000000e+00 1153.0
86 TraesCS6B01G025100 chr2B 78.369 883 115 31 5300 6150 709420770 709419932 3.300000e-138 503.0
87 TraesCS6B01G025100 chr2B 79.789 663 99 22 2832 3488 709568189 709567556 4.360000e-122 449.0
88 TraesCS6B01G025100 chr2B 81.633 196 30 6 3694 3886 54014396 54014204 2.960000e-34 158.0
89 TraesCS6B01G025100 chr5A 81.879 894 118 13 1792 2661 30638332 30639205 0.000000e+00 713.0
90 TraesCS6B01G025100 chr5A 84.834 211 17 4 3690 3886 624203413 624203204 1.740000e-46 198.0
91 TraesCS6B01G025100 chr5A 97.619 42 1 0 7202 7243 362173193 362173152 1.100000e-08 73.1
92 TraesCS6B01G025100 chrUn 81.561 743 99 17 10 722 101045161 101045895 5.320000e-161 579.0
93 TraesCS6B01G025100 chrUn 88.391 379 30 8 2248 2615 42220944 42220569 2.030000e-120 444.0
94 TraesCS6B01G025100 chrUn 86.473 207 14 3 3694 3886 95439918 95440124 1.730000e-51 215.0
95 TraesCS6B01G025100 chr3D 88.161 397 45 2 2116 2511 582880863 582881258 9.300000e-129 472.0
96 TraesCS6B01G025100 chr3D 86.614 381 42 7 3111 3488 582881304 582881678 5.710000e-111 412.0
97 TraesCS6B01G025100 chr3D 91.071 168 13 2 3487 3653 549066955 549066789 7.990000e-55 226.0
98 TraesCS6B01G025100 chr3D 91.566 83 7 0 2667 2749 366988 366906 1.800000e-21 115.0
99 TraesCS6B01G025100 chr3D 83.721 86 10 3 2666 2751 381989152 381989071 2.370000e-10 78.7
100 TraesCS6B01G025100 chr1B 84.026 457 55 10 4359 4803 662155844 662156294 2.640000e-114 424.0
101 TraesCS6B01G025100 chr1B 79.279 111 17 5 7136 7244 323944357 323944251 1.100000e-08 73.1
102 TraesCS6B01G025100 chr3B 84.496 387 42 8 3111 3488 778341491 778341114 4.510000e-97 366.0
103 TraesCS6B01G025100 chr7B 92.593 162 11 1 3490 3651 156421785 156421945 1.720000e-56 231.0
104 TraesCS6B01G025100 chr7B 87.611 113 8 5 7136 7245 539218272 539218381 8.340000e-25 126.0
105 TraesCS6B01G025100 chr7B 82.143 84 3 4 7146 7229 174075872 174075943 2.380000e-05 62.1
106 TraesCS6B01G025100 chr2D 91.071 168 13 2 3490 3656 299891715 299891549 7.990000e-55 226.0
107 TraesCS6B01G025100 chr2D 86.905 84 8 2 2666 2749 78563836 78563916 3.040000e-14 91.6
108 TraesCS6B01G025100 chr2A 91.515 165 12 2 3490 3654 7920891 7921053 7.990000e-55 226.0
109 TraesCS6B01G025100 chr2A 90.625 128 8 3 3713 3836 12834685 12834812 4.910000e-37 167.0
110 TraesCS6B01G025100 chr2A 88.043 92 5 1 2666 2751 186436479 186436388 3.910000e-18 104.0
111 TraesCS6B01G025100 chr2A 84.000 100 10 3 7144 7243 537461399 537461492 3.040000e-14 91.6
112 TraesCS6B01G025100 chr7A 88.764 89 5 2 2666 2749 6953898 6953986 3.910000e-18 104.0
113 TraesCS6B01G025100 chr7A 88.043 92 5 1 2666 2751 158291513 158291422 3.910000e-18 104.0
114 TraesCS6B01G025100 chr7A 88.043 92 5 1 2666 2751 668558658 668558749 3.910000e-18 104.0
115 TraesCS6B01G025100 chr7A 100.000 28 0 0 7202 7229 237386778 237386751 1.400000e-02 52.8
116 TraesCS6B01G025100 chr7D 87.640 89 6 2 2666 2749 5569651 5569739 1.820000e-16 99.0


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 TraesCS6B01G025100 chr6B 15228088 15236001 7913 True 14615.000000 14615 100.000000 1 7914 1 chr6B.!!$R1 7913
1 TraesCS6B01G025100 chr6B 16266257 16271514 5257 False 2033.750000 4324 95.834250 9 7486 4 chr6B.!!$F6 7477
2 TraesCS6B01G025100 chr6B 16433145 16434619 1474 False 1482.000000 1482 84.983000 1148 2615 1 chr6B.!!$F2 1467
3 TraesCS6B01G025100 chr6B 52979770 52981049 1279 True 1245.000000 1245 84.436000 1148 2415 1 chr6B.!!$R7 1267
4 TraesCS6B01G025100 chr6B 90939366 90940519 1153 False 1129.000000 1129 84.356000 1174 2328 1 chr6B.!!$F3 1154
5 TraesCS6B01G025100 chr6B 15711592 15712722 1130 True 1116.000000 1116 84.875000 3694 4821 1 chr6B.!!$R5 1127
6 TraesCS6B01G025100 chr6B 53061343 53062445 1102 True 1103.000000 1103 84.824000 1214 2313 1 chr6B.!!$R8 1099
7 TraesCS6B01G025100 chr6B 16425939 16428202 2263 False 992.333333 1755 92.080333 3915 7914 3 chr6B.!!$F7 3999
8 TraesCS6B01G025100 chr6B 52577424 52578359 935 True 915.000000 915 84.995000 4152 5064 1 chr6B.!!$R6 912
9 TraesCS6B01G025100 chr6B 53073632 53074503 871 True 791.000000 791 83.669000 4152 5011 1 chr6B.!!$R9 859
10 TraesCS6B01G025100 chr6B 15246329 15246836 507 True 472.000000 472 84.436000 4582 5064 1 chr6B.!!$R3 482
11 TraesCS6B01G025100 chr5B 556623797 556628472 4675 True 1415.066667 2364 95.107333 935 3888 3 chr5B.!!$R4 2953
12 TraesCS6B01G025100 chr5B 556615963 556618991 3028 True 1114.250000 3723 92.925750 3881 6870 4 chr5B.!!$R3 2989
13 TraesCS6B01G025100 chr5B 556794264 556795756 1492 True 1109.000000 1109 80.489000 1144 2620 1 chr5B.!!$R1 1476
14 TraesCS6B01G025100 chr5B 556553429 556554519 1090 True 706.000000 830 91.565000 6867 7914 2 chr5B.!!$R2 1047
15 TraesCS6B01G025100 chr5B 621235824 621236541 717 True 356.000000 525 87.926500 2978 3836 2 chr5B.!!$R5 858
16 TraesCS6B01G025100 chr6D 8550523 8552801 2278 True 1015.500000 1611 84.234000 1145 3442 2 chr6D.!!$R6 2297
17 TraesCS6B01G025100 chr6D 34019817 34020587 770 False 874.000000 874 87.101000 4152 4932 1 chr6D.!!$F4 780
18 TraesCS6B01G025100 chr6D 8987254 8989986 2732 False 577.000000 1192 84.876667 1174 4873 3 chr6D.!!$F8 3699
19 TraesCS6B01G025100 chr6D 8967575 8973364 5789 False 571.750000 1079 81.796750 1142 5978 4 chr6D.!!$F7 4836
20 TraesCS6B01G025100 chr6D 8802267 8805735 3468 False 526.666667 1251 87.832667 4024 5410 3 chr6D.!!$F5 1386
21 TraesCS6B01G025100 chr6D 33899004 33900456 1452 False 505.500000 846 84.702500 4030 5441 2 chr6D.!!$F9 1411
22 TraesCS6B01G025100 chr6D 8917030 8917603 573 False 483.000000 483 82.314000 2899 3488 1 chr6D.!!$F2 589
23 TraesCS6B01G025100 chr6D 8815076 8819366 4290 False 362.800000 839 84.272600 3930 5441 5 chr6D.!!$F6 1511
24 TraesCS6B01G025100 chr6D 8576379 8577020 641 True 270.000000 270 75.766000 3926 4571 1 chr6D.!!$R1 645
25 TraesCS6B01G025100 chr6D 8513379 8514288 909 True 235.000000 318 82.622500 4581 5441 2 chr6D.!!$R5 860
26 TraesCS6B01G025100 chr6A 9461383 9462935 1552 False 1216.000000 1216 81.031000 1069 2620 1 chr6A.!!$F2 1551
27 TraesCS6B01G025100 chr6A 9366655 9367603 948 False 1064.000000 1064 87.252000 3916 4850 1 chr6A.!!$F1 934
28 TraesCS6B01G025100 chr6A 9036297 9037042 745 True 985.000000 985 90.909000 3963 4691 1 chr6A.!!$R2 728
29 TraesCS6B01G025100 chr6A 9474626 9475547 921 False 957.000000 957 85.607000 1697 2615 1 chr6A.!!$F3 918
30 TraesCS6B01G025100 chr6A 30557313 30558688 1375 True 463.500000 773 84.293000 4086 5441 2 chr6A.!!$R4 1355
31 TraesCS6B01G025100 chr6A 9356756 9357664 908 False 326.500000 479 81.799000 2828 3886 2 chr6A.!!$F5 1058
32 TraesCS6B01G025100 chr5D 42076046 42078675 2629 False 668.666667 1208 82.755000 1135 3886 3 chr5D.!!$F1 2751
33 TraesCS6B01G025100 chr5D 499859845 499863421 3576 True 375.666667 564 85.740667 2729 4577 3 chr5D.!!$R2 1848
34 TraesCS6B01G025100 chr2B 709250360 709251501 1141 True 1153.000000 1153 85.579000 3904 5012 1 chr2B.!!$R2 1108
35 TraesCS6B01G025100 chr2B 709419932 709420770 838 True 503.000000 503 78.369000 5300 6150 1 chr2B.!!$R3 850
36 TraesCS6B01G025100 chr2B 709567556 709568189 633 True 449.000000 449 79.789000 2832 3488 1 chr2B.!!$R4 656
37 TraesCS6B01G025100 chr5A 30638332 30639205 873 False 713.000000 713 81.879000 1792 2661 1 chr5A.!!$F1 869
38 TraesCS6B01G025100 chrUn 101045161 101045895 734 False 579.000000 579 81.561000 10 722 1 chrUn.!!$F2 712
39 TraesCS6B01G025100 chr3D 582880863 582881678 815 False 442.000000 472 87.387500 2116 3488 2 chr3D.!!$F1 1372

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
383 388 0.179205 GTCACCTAGTCGAACGTCGG 60.179 60.0 0.00 0.0 40.88 4.79 F
533 538 0.180406 CCATACCAAAGGACTCCCCG 59.820 60.0 0.00 0.0 40.87 5.73 F
1036 1081 0.249868 CAACGCTGGACTGGAGACAA 60.250 55.0 0.00 0.0 42.06 3.18 F
2377 2499 0.180642 TGGGTTGGTCGTTGCTAACA 59.819 50.0 0.00 0.0 32.48 2.41 F
4292 6728 0.108396 GCAAAAAGTGGGTGGGCAAT 59.892 50.0 0.00 0.0 0.00 3.56 F
4297 6733 0.625849 AAGTGGGTGGGCAATAGGAG 59.374 55.0 0.00 0.0 0.00 3.69 F
4375 6811 0.682209 AGCTGGATGTTGATGGTGCC 60.682 55.0 0.00 0.0 0.00 5.01 F
5919 13391 0.036164 TTGACACCGGATGTTGGGAG 59.964 55.0 9.46 0.0 43.56 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1438 0.326927 GGTTGTCGGGGGATTTGAGA 59.673 55.000 0.00 0.00 0.00 3.27 R
2330 2452 2.677199 ACAGTCATACAACAGCAGACG 58.323 47.619 0.00 0.00 34.56 4.18 R
2810 4666 2.145865 CAGGTGACTTGACCCTGGT 58.854 57.895 0.00 0.00 41.69 4.00 R
4356 6792 0.682209 GGCACCATCAACATCCAGCT 60.682 55.000 0.00 0.00 0.00 4.24 R
5262 12707 0.521291 TAAGCACGTTGCCTTCATGC 59.479 50.000 6.39 0.00 46.52 4.06 R
5454 12903 0.816421 CATCGTGCTCATCATGGCCA 60.816 55.000 8.56 8.56 32.54 5.36 R
5937 13409 1.098050 AGTGCATCGAAGAATTGCCC 58.902 50.000 5.55 0.00 41.39 5.36 R
7373 15134 0.621609 TCCCCCGGTGGTCTAATTTG 59.378 55.000 1.78 0.00 0.00 2.32 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
79 81 0.896940 ACATCGACACCCTGTACGGT 60.897 55.000 0.00 0.00 36.18 4.83
262 264 0.770499 TCCAACTCCAATCAGCACCA 59.230 50.000 0.00 0.00 0.00 4.17
380 385 0.947244 AACGTCACCTAGTCGAACGT 59.053 50.000 3.52 3.52 33.00 3.99
383 388 0.179205 GTCACCTAGTCGAACGTCGG 60.179 60.000 0.00 0.00 40.88 4.79
396 401 2.577593 GTCGGTACCCCTCTGCAC 59.422 66.667 6.25 0.00 0.00 4.57
517 522 2.433145 CTCGTCGTGCACTGCCAT 60.433 61.111 16.19 0.00 0.00 4.40
533 538 0.180406 CCATACCAAAGGACTCCCCG 59.820 60.000 0.00 0.00 40.87 5.73
732 763 2.708325 TGGGAAAGGGGTTGATTTTTGG 59.292 45.455 0.00 0.00 0.00 3.28
733 764 2.976185 GGGAAAGGGGTTGATTTTTGGA 59.024 45.455 0.00 0.00 0.00 3.53
756 787 6.645003 GGACAGTCAACCCAAATTAAAATCAC 59.355 38.462 2.17 0.00 0.00 3.06
1005 1041 2.682494 GCGGGACCCACTCAGGTA 60.682 66.667 12.15 0.00 41.42 3.08
1006 1042 2.722201 GCGGGACCCACTCAGGTAG 61.722 68.421 12.15 0.00 41.42 3.18
1036 1081 0.249868 CAACGCTGGACTGGAGACAA 60.250 55.000 0.00 0.00 42.06 3.18
1208 1289 1.379977 TCATCTCCCTCCGCGTCTT 60.380 57.895 4.92 0.00 0.00 3.01
1234 1318 3.536917 CACCTCCGCCGCCTCATA 61.537 66.667 0.00 0.00 0.00 2.15
1351 1438 1.211456 CCTCTCCAAAGCTCTCCCAT 58.789 55.000 0.00 0.00 0.00 4.00
1801 1890 0.395311 CAGAGTGCATCCAGGGCATT 60.395 55.000 0.00 0.00 44.11 3.56
2330 2452 5.177696 GCCAAGAACGGACTATGATGTAATC 59.822 44.000 0.00 0.00 45.83 1.75
2377 2499 0.180642 TGGGTTGGTCGTTGCTAACA 59.819 50.000 0.00 0.00 32.48 2.41
2432 2554 6.780031 AGACTGGTATGTAATGCTATCACTCT 59.220 38.462 0.00 0.00 0.00 3.24
2628 2815 5.303589 CCTTCATGTGGATAATTGGAGCATT 59.696 40.000 0.00 0.00 0.00 3.56
2686 2873 3.071892 ACTCCGTCCCAAAATAAGTGTCA 59.928 43.478 0.00 0.00 0.00 3.58
2689 2876 3.128589 CCGTCCCAAAATAAGTGTCATGG 59.871 47.826 0.00 0.00 0.00 3.66
2691 2878 3.763897 GTCCCAAAATAAGTGTCATGGCT 59.236 43.478 0.00 0.00 0.00 4.75
2693 2880 4.837860 TCCCAAAATAAGTGTCATGGCTTT 59.162 37.500 0.00 0.00 0.00 3.51
2695 2882 6.152661 TCCCAAAATAAGTGTCATGGCTTTAG 59.847 38.462 0.00 0.00 0.00 1.85
2696 2883 6.071391 CCCAAAATAAGTGTCATGGCTTTAGT 60.071 38.462 0.00 0.00 0.00 2.24
2698 2885 7.542130 CCAAAATAAGTGTCATGGCTTTAGTTC 59.458 37.037 0.00 0.00 0.00 3.01
2699 2886 7.759489 AAATAAGTGTCATGGCTTTAGTTCA 57.241 32.000 0.00 0.00 0.00 3.18
2700 2887 7.759489 AATAAGTGTCATGGCTTTAGTTCAA 57.241 32.000 0.00 0.00 0.00 2.69
2701 2888 7.759489 ATAAGTGTCATGGCTTTAGTTCAAA 57.241 32.000 0.00 0.00 0.00 2.69
2703 2890 6.259550 AGTGTCATGGCTTTAGTTCAAATC 57.740 37.500 0.00 0.00 0.00 2.17
2704 2891 5.769662 AGTGTCATGGCTTTAGTTCAAATCA 59.230 36.000 0.00 0.00 0.00 2.57
2705 2892 6.265196 AGTGTCATGGCTTTAGTTCAAATCAA 59.735 34.615 0.00 0.00 0.00 2.57
2706 2893 7.039504 AGTGTCATGGCTTTAGTTCAAATCAAT 60.040 33.333 0.00 0.00 0.00 2.57
2709 4565 8.437742 GTCATGGCTTTAGTTCAAATCAATTTG 58.562 33.333 8.81 8.81 46.39 2.32
2810 4666 2.082140 TAGCGCTTCCTATTGAGGGA 57.918 50.000 18.68 0.00 43.94 4.20
3016 4970 4.591321 AGAGGTAATGATTTGGAGCCAA 57.409 40.909 0.00 0.00 0.00 4.52
3118 5072 4.000988 AGATGCCCACTTTACTAAACGTG 58.999 43.478 0.00 0.00 0.00 4.49
3198 5167 6.985645 GGTGCATCCATTCATTTTTATGCTAA 59.014 34.615 0.00 0.00 40.22 3.09
3306 5283 2.203470 TTTCATGCTCTGCACCATGA 57.797 45.000 13.18 13.18 43.04 3.07
3452 5743 4.955811 TTCTTCCTTCTGTAACTGAGCA 57.044 40.909 0.00 0.00 0.00 4.26
3564 5877 9.888878 CTACATATGGAGCAAAATAAGTGAATG 57.111 33.333 0.89 0.00 0.00 2.67
3821 6164 7.050377 CAGATTACTTCCAACTGACCACATAT 58.950 38.462 0.00 0.00 0.00 1.78
4280 6716 6.313411 TGTGGAGTTTTTCATCAAGCAAAAAG 59.687 34.615 0.00 0.00 33.27 2.27
4282 6718 6.313411 TGGAGTTTTTCATCAAGCAAAAAGTG 59.687 34.615 3.32 0.00 35.97 3.16
4283 6719 6.238184 GGAGTTTTTCATCAAGCAAAAAGTGG 60.238 38.462 3.32 0.00 35.97 4.00
4284 6720 5.585844 AGTTTTTCATCAAGCAAAAAGTGGG 59.414 36.000 0.00 0.00 35.01 4.61
4285 6721 4.751767 TTTCATCAAGCAAAAAGTGGGT 57.248 36.364 0.00 0.00 0.00 4.51
4286 6722 3.731652 TCATCAAGCAAAAAGTGGGTG 57.268 42.857 0.00 0.00 0.00 4.61
4287 6723 2.364970 TCATCAAGCAAAAAGTGGGTGG 59.635 45.455 0.00 0.00 0.00 4.61
4288 6724 1.118838 TCAAGCAAAAAGTGGGTGGG 58.881 50.000 0.00 0.00 0.00 4.61
4289 6725 0.532640 CAAGCAAAAAGTGGGTGGGC 60.533 55.000 0.00 0.00 0.00 5.36
4290 6726 0.980231 AAGCAAAAAGTGGGTGGGCA 60.980 50.000 0.00 0.00 0.00 5.36
4291 6727 0.980231 AGCAAAAAGTGGGTGGGCAA 60.980 50.000 0.00 0.00 0.00 4.52
4292 6728 0.108396 GCAAAAAGTGGGTGGGCAAT 59.892 50.000 0.00 0.00 0.00 3.56
4293 6729 1.346068 GCAAAAAGTGGGTGGGCAATA 59.654 47.619 0.00 0.00 0.00 1.90
4294 6730 2.612721 GCAAAAAGTGGGTGGGCAATAG 60.613 50.000 0.00 0.00 0.00 1.73
4296 6732 1.080638 AAAGTGGGTGGGCAATAGGA 58.919 50.000 0.00 0.00 0.00 2.94
4297 6733 0.625849 AAGTGGGTGGGCAATAGGAG 59.374 55.000 0.00 0.00 0.00 3.69
4299 6735 1.928046 TGGGTGGGCAATAGGAGCA 60.928 57.895 0.00 0.00 0.00 4.26
4300 6736 1.288508 TGGGTGGGCAATAGGAGCAT 61.289 55.000 0.00 0.00 0.00 3.79
4301 6737 0.771127 GGGTGGGCAATAGGAGCATA 59.229 55.000 0.00 0.00 0.00 3.14
4302 6738 1.545651 GGGTGGGCAATAGGAGCATAC 60.546 57.143 0.00 0.00 0.00 2.39
4305 6741 2.104792 GTGGGCAATAGGAGCATACTGA 59.895 50.000 0.00 0.00 0.00 3.41
4306 6742 2.981784 TGGGCAATAGGAGCATACTGAT 59.018 45.455 0.00 0.00 0.00 2.90
4307 6743 3.395607 TGGGCAATAGGAGCATACTGATT 59.604 43.478 0.00 0.00 0.00 2.57
4308 6744 4.141181 TGGGCAATAGGAGCATACTGATTT 60.141 41.667 0.00 0.00 0.00 2.17
4309 6745 5.073008 TGGGCAATAGGAGCATACTGATTTA 59.927 40.000 0.00 0.00 0.00 1.40
4311 6747 6.234177 GGCAATAGGAGCATACTGATTTACT 58.766 40.000 0.00 0.00 0.00 2.24
4312 6748 6.148480 GGCAATAGGAGCATACTGATTTACTG 59.852 42.308 0.00 0.00 0.00 2.74
4313 6749 6.931281 GCAATAGGAGCATACTGATTTACTGA 59.069 38.462 0.00 0.00 0.00 3.41
4314 6750 7.442364 GCAATAGGAGCATACTGATTTACTGAA 59.558 37.037 0.00 0.00 0.00 3.02
4315 6751 9.499479 CAATAGGAGCATACTGATTTACTGAAT 57.501 33.333 0.00 0.00 0.00 2.57
4316 6752 9.499479 AATAGGAGCATACTGATTTACTGAATG 57.501 33.333 0.00 0.00 0.00 2.67
4317 6753 6.893583 AGGAGCATACTGATTTACTGAATGT 58.106 36.000 0.00 0.00 0.00 2.71
4318 6754 6.765036 AGGAGCATACTGATTTACTGAATGTG 59.235 38.462 0.00 0.00 0.00 3.21
4319 6755 6.017605 GGAGCATACTGATTTACTGAATGTGG 60.018 42.308 0.00 0.00 0.00 4.17
4320 6756 6.653020 AGCATACTGATTTACTGAATGTGGA 58.347 36.000 0.00 0.00 0.00 4.02
4321 6757 7.285566 AGCATACTGATTTACTGAATGTGGAT 58.714 34.615 0.00 0.00 0.00 3.41
4322 6758 7.228108 AGCATACTGATTTACTGAATGTGGATG 59.772 37.037 0.00 0.00 0.00 3.51
4323 6759 7.521099 GCATACTGATTTACTGAATGTGGATGG 60.521 40.741 0.00 0.00 0.00 3.51
4324 6760 5.819991 ACTGATTTACTGAATGTGGATGGT 58.180 37.500 0.00 0.00 0.00 3.55
4325 6761 5.649395 ACTGATTTACTGAATGTGGATGGTG 59.351 40.000 0.00 0.00 0.00 4.17
4326 6762 4.398988 TGATTTACTGAATGTGGATGGTGC 59.601 41.667 0.00 0.00 0.00 5.01
4327 6763 3.719268 TTACTGAATGTGGATGGTGCT 57.281 42.857 0.00 0.00 0.00 4.40
4328 6764 2.592102 ACTGAATGTGGATGGTGCTT 57.408 45.000 0.00 0.00 0.00 3.91
4329 6765 2.880443 ACTGAATGTGGATGGTGCTTT 58.120 42.857 0.00 0.00 0.00 3.51
4330 6766 2.821969 ACTGAATGTGGATGGTGCTTTC 59.178 45.455 0.00 0.00 0.00 2.62
4331 6767 3.087031 CTGAATGTGGATGGTGCTTTCT 58.913 45.455 0.00 0.00 0.00 2.52
4332 6768 3.499338 TGAATGTGGATGGTGCTTTCTT 58.501 40.909 0.00 0.00 0.00 2.52
4333 6769 3.896888 TGAATGTGGATGGTGCTTTCTTT 59.103 39.130 0.00 0.00 0.00 2.52
4334 6770 4.022068 TGAATGTGGATGGTGCTTTCTTTC 60.022 41.667 0.00 0.00 0.00 2.62
4335 6771 3.228188 TGTGGATGGTGCTTTCTTTCT 57.772 42.857 0.00 0.00 0.00 2.52
4336 6772 3.565307 TGTGGATGGTGCTTTCTTTCTT 58.435 40.909 0.00 0.00 0.00 2.52
4337 6773 3.569701 TGTGGATGGTGCTTTCTTTCTTC 59.430 43.478 0.00 0.00 0.00 2.87
4338 6774 3.057245 GTGGATGGTGCTTTCTTTCTTCC 60.057 47.826 0.00 0.00 0.00 3.46
4339 6775 3.157087 GGATGGTGCTTTCTTTCTTCCA 58.843 45.455 0.00 0.00 0.00 3.53
4340 6776 3.192212 GGATGGTGCTTTCTTTCTTCCAG 59.808 47.826 0.00 0.00 0.00 3.86
4341 6777 2.586425 TGGTGCTTTCTTTCTTCCAGG 58.414 47.619 0.00 0.00 0.00 4.45
4342 6778 2.091885 TGGTGCTTTCTTTCTTCCAGGT 60.092 45.455 0.00 0.00 0.00 4.00
4343 6779 2.294512 GGTGCTTTCTTTCTTCCAGGTG 59.705 50.000 0.00 0.00 0.00 4.00
4344 6780 3.214328 GTGCTTTCTTTCTTCCAGGTGA 58.786 45.455 0.00 0.00 0.00 4.02
4345 6781 3.632145 GTGCTTTCTTTCTTCCAGGTGAA 59.368 43.478 0.00 0.00 0.00 3.18
4354 6790 2.566833 TTCCAGGTGAAGATGTGTGG 57.433 50.000 0.00 0.00 0.00 4.17
4355 6791 1.728323 TCCAGGTGAAGATGTGTGGA 58.272 50.000 0.00 0.00 0.00 4.02
4356 6792 2.054021 TCCAGGTGAAGATGTGTGGAA 58.946 47.619 0.00 0.00 31.08 3.53
4357 6793 2.038952 TCCAGGTGAAGATGTGTGGAAG 59.961 50.000 0.00 0.00 31.08 3.46
4358 6794 1.808945 CAGGTGAAGATGTGTGGAAGC 59.191 52.381 0.00 0.00 0.00 3.86
4359 6795 1.701847 AGGTGAAGATGTGTGGAAGCT 59.298 47.619 0.00 0.00 0.00 3.74
4360 6796 1.808945 GGTGAAGATGTGTGGAAGCTG 59.191 52.381 0.00 0.00 0.00 4.24
4361 6797 1.808945 GTGAAGATGTGTGGAAGCTGG 59.191 52.381 0.00 0.00 0.00 4.85
4362 6798 1.699083 TGAAGATGTGTGGAAGCTGGA 59.301 47.619 0.00 0.00 0.00 3.86
4363 6799 2.306805 TGAAGATGTGTGGAAGCTGGAT 59.693 45.455 0.00 0.00 0.00 3.41
4364 6800 2.414994 AGATGTGTGGAAGCTGGATG 57.585 50.000 0.00 0.00 0.00 3.51
4365 6801 1.632409 AGATGTGTGGAAGCTGGATGT 59.368 47.619 0.00 0.00 0.00 3.06
4366 6802 2.040813 AGATGTGTGGAAGCTGGATGTT 59.959 45.455 0.00 0.00 0.00 2.71
4367 6803 1.608055 TGTGTGGAAGCTGGATGTTG 58.392 50.000 0.00 0.00 0.00 3.33
4368 6804 1.142667 TGTGTGGAAGCTGGATGTTGA 59.857 47.619 0.00 0.00 0.00 3.18
4369 6805 2.224843 TGTGTGGAAGCTGGATGTTGAT 60.225 45.455 0.00 0.00 0.00 2.57
4370 6806 2.163010 GTGTGGAAGCTGGATGTTGATG 59.837 50.000 0.00 0.00 0.00 3.07
4371 6807 1.747355 GTGGAAGCTGGATGTTGATGG 59.253 52.381 0.00 0.00 0.00 3.51
4372 6808 1.355381 TGGAAGCTGGATGTTGATGGT 59.645 47.619 0.00 0.00 0.00 3.55
4373 6809 1.747355 GGAAGCTGGATGTTGATGGTG 59.253 52.381 0.00 0.00 0.00 4.17
4374 6810 1.133790 GAAGCTGGATGTTGATGGTGC 59.866 52.381 0.00 0.00 0.00 5.01
4375 6811 0.682209 AGCTGGATGTTGATGGTGCC 60.682 55.000 0.00 0.00 0.00 5.01
4376 6812 0.682209 GCTGGATGTTGATGGTGCCT 60.682 55.000 0.00 0.00 0.00 4.75
4377 6813 1.843368 CTGGATGTTGATGGTGCCTT 58.157 50.000 0.00 0.00 0.00 4.35
4378 6814 2.173519 CTGGATGTTGATGGTGCCTTT 58.826 47.619 0.00 0.00 0.00 3.11
4379 6815 2.564062 CTGGATGTTGATGGTGCCTTTT 59.436 45.455 0.00 0.00 0.00 2.27
4380 6816 2.971330 TGGATGTTGATGGTGCCTTTTT 59.029 40.909 0.00 0.00 0.00 1.94
4381 6817 3.006752 TGGATGTTGATGGTGCCTTTTTC 59.993 43.478 0.00 0.00 0.00 2.29
4382 6818 3.259123 GGATGTTGATGGTGCCTTTTTCT 59.741 43.478 0.00 0.00 0.00 2.52
4383 6819 4.262592 GGATGTTGATGGTGCCTTTTTCTT 60.263 41.667 0.00 0.00 0.00 2.52
4384 6820 4.320608 TGTTGATGGTGCCTTTTTCTTC 57.679 40.909 0.00 0.00 0.00 2.87
4385 6821 3.960102 TGTTGATGGTGCCTTTTTCTTCT 59.040 39.130 0.00 0.00 0.00 2.85
4386 6822 4.405358 TGTTGATGGTGCCTTTTTCTTCTT 59.595 37.500 0.00 0.00 0.00 2.52
4387 6823 4.853924 TGATGGTGCCTTTTTCTTCTTC 57.146 40.909 0.00 0.00 0.00 2.87
4388 6824 3.573967 TGATGGTGCCTTTTTCTTCTTCC 59.426 43.478 0.00 0.00 0.00 3.46
4389 6825 3.025322 TGGTGCCTTTTTCTTCTTCCA 57.975 42.857 0.00 0.00 0.00 3.53
4390 6826 2.958355 TGGTGCCTTTTTCTTCTTCCAG 59.042 45.455 0.00 0.00 0.00 3.86
4391 6827 2.297315 GGTGCCTTTTTCTTCTTCCAGG 59.703 50.000 0.00 0.00 0.00 4.45
4392 6828 3.222603 GTGCCTTTTTCTTCTTCCAGGA 58.777 45.455 0.00 0.00 0.00 3.86
4393 6829 3.636764 GTGCCTTTTTCTTCTTCCAGGAA 59.363 43.478 0.71 0.71 0.00 3.36
4394 6830 4.099419 GTGCCTTTTTCTTCTTCCAGGAAA 59.901 41.667 2.72 0.00 0.00 3.13
4395 6831 4.099419 TGCCTTTTTCTTCTTCCAGGAAAC 59.901 41.667 2.72 0.00 0.00 2.78
4396 6832 4.793028 GCCTTTTTCTTCTTCCAGGAAACG 60.793 45.833 2.72 0.00 0.00 3.60
4397 6833 4.578928 CCTTTTTCTTCTTCCAGGAAACGA 59.421 41.667 2.72 0.00 0.00 3.85
4398 6834 5.278022 CCTTTTTCTTCTTCCAGGAAACGAG 60.278 44.000 2.72 1.88 0.00 4.18
4399 6835 4.682778 TTTCTTCTTCCAGGAAACGAGA 57.317 40.909 2.72 4.24 0.00 4.04
4407 6843 4.286297 TCCAGGAAACGAGATGAAACAT 57.714 40.909 0.00 0.00 0.00 2.71
4411 6847 5.063944 CCAGGAAACGAGATGAAACATGTAG 59.936 44.000 0.00 0.00 0.00 2.74
4442 7044 5.277538 GCTTTGCTGTACTATACATGCTTCC 60.278 44.000 0.00 0.00 38.15 3.46
4447 7049 5.196341 TGTACTATACATGCTTCCGAAGG 57.804 43.478 10.18 0.00 41.46 3.46
4464 7066 4.437239 CGAAGGCTCTGTTAGTTGATGAT 58.563 43.478 0.00 0.00 0.00 2.45
4497 7099 5.728471 CTTCAGTGACAAGTATGGTCTGAT 58.272 41.667 0.00 0.00 34.36 2.90
4498 7100 5.745312 TCAGTGACAAGTATGGTCTGATT 57.255 39.130 0.00 0.00 31.70 2.57
4504 7106 4.380531 ACAAGTATGGTCTGATTATGGCG 58.619 43.478 0.00 0.00 0.00 5.69
4506 7108 3.995199 AGTATGGTCTGATTATGGCGTG 58.005 45.455 0.00 0.00 0.00 5.34
4542 7144 5.413213 GGGAAGCTCCTACTTTTCTCTTTTC 59.587 44.000 0.00 0.00 36.57 2.29
4545 7147 6.426646 AGCTCCTACTTTTCTCTTTTCTGA 57.573 37.500 0.00 0.00 0.00 3.27
4556 7158 7.775397 TTTCTCTTTTCTGAATTTTGCAAGG 57.225 32.000 0.00 0.00 0.00 3.61
4558 7160 6.275335 TCTCTTTTCTGAATTTTGCAAGGTG 58.725 36.000 0.00 0.00 0.00 4.00
5255 12700 9.793259 ATTTCTGGAATGAACTTAACTAGTGAA 57.207 29.630 0.00 0.00 37.12 3.18
5274 12719 3.253188 TGAACTTACTGCATGAAGGCAAC 59.747 43.478 5.47 0.00 44.40 4.17
5557 13009 2.223479 GCCTTTGTTTCGAGAGCAAACA 60.223 45.455 6.91 2.06 38.43 2.83
5712 13164 3.775316 CAGGTAAGACAGGTATGGTTCCT 59.225 47.826 0.00 0.00 35.45 3.36
5919 13391 0.036164 TTGACACCGGATGTTGGGAG 59.964 55.000 9.46 0.00 43.56 4.30
5927 13399 1.679032 CGGATGTTGGGAGGGAGAAAC 60.679 57.143 0.00 0.00 0.00 2.78
5937 13409 2.159170 GGAGGGAGAAACTGTGAGATCG 60.159 54.545 0.00 0.00 0.00 3.69
5955 13427 0.248215 CGGGCAATTCTTCGATGCAC 60.248 55.000 9.91 5.26 41.80 4.57
5957 13429 2.288666 GGGCAATTCTTCGATGCACTA 58.711 47.619 9.91 0.00 40.31 2.74
6118 13593 6.427853 CAGGAAATCTGTAGACAAATGTGTCA 59.572 38.462 18.32 1.69 45.61 3.58
6136 13611 4.627467 GTGTCATGTCTAGTTAACAGCCTG 59.373 45.833 8.61 0.00 0.00 4.85
6140 13615 5.186992 TCATGTCTAGTTAACAGCCTGCTAA 59.813 40.000 8.61 0.00 0.00 3.09
6142 13617 6.049955 TGTCTAGTTAACAGCCTGCTAATT 57.950 37.500 8.61 0.00 0.00 1.40
6143 13618 6.472887 TGTCTAGTTAACAGCCTGCTAATTT 58.527 36.000 8.61 0.00 0.00 1.82
6144 13619 6.371548 TGTCTAGTTAACAGCCTGCTAATTTG 59.628 38.462 8.61 0.00 0.00 2.32
6145 13620 5.880332 TCTAGTTAACAGCCTGCTAATTTGG 59.120 40.000 8.61 0.00 0.00 3.28
6146 13621 4.662278 AGTTAACAGCCTGCTAATTTGGA 58.338 39.130 8.61 0.00 0.00 3.53
6147 13622 5.076873 AGTTAACAGCCTGCTAATTTGGAA 58.923 37.500 8.61 0.00 0.00 3.53
6148 13623 5.716703 AGTTAACAGCCTGCTAATTTGGAAT 59.283 36.000 8.61 0.00 0.00 3.01
6149 13624 4.725790 AACAGCCTGCTAATTTGGAATC 57.274 40.909 0.00 0.00 0.00 2.52
6150 13625 2.684881 ACAGCCTGCTAATTTGGAATCG 59.315 45.455 0.00 0.00 0.00 3.34
6154 13632 4.947388 AGCCTGCTAATTTGGAATCGTTTA 59.053 37.500 0.00 0.00 0.00 2.01
6161 13639 8.085296 TGCTAATTTGGAATCGTTTATGTTTGT 58.915 29.630 0.00 0.00 0.00 2.83
6162 13640 9.562583 GCTAATTTGGAATCGTTTATGTTTGTA 57.437 29.630 0.00 0.00 0.00 2.41
6172 13650 4.611130 CGTTTATGTTTGTACACGAACCCC 60.611 45.833 9.47 0.00 39.04 4.95
6178 13656 3.389925 TTGTACACGAACCCCTGTTAG 57.610 47.619 0.00 0.00 33.97 2.34
6290 13779 5.012561 ACATATCAGTAGAATTCCAGAGGGC 59.987 44.000 0.65 0.00 0.00 5.19
6312 13801 4.630111 CTGGCTCCTAGCTTTCTTCATAG 58.370 47.826 0.00 0.00 41.99 2.23
6317 13806 6.183360 GGCTCCTAGCTTTCTTCATAGTTACT 60.183 42.308 0.00 0.00 41.99 2.24
6425 13971 3.391296 AGGTGTTGAGCTTGTTTAGAGGA 59.609 43.478 0.00 0.00 0.00 3.71
6431 13977 1.003696 AGCTTGTTTAGAGGACTGGCC 59.996 52.381 0.00 0.00 0.00 5.36
6491 14037 0.594028 TGTCTAATCCATCGCGACGC 60.594 55.000 12.93 10.49 0.00 5.19
6506 14052 1.120437 GACGCGGTGCTTTCTTTTTG 58.880 50.000 12.47 0.00 0.00 2.44
6514 14060 2.362077 GTGCTTTCTTTTTGCAGGAGGA 59.638 45.455 0.00 0.00 37.39 3.71
6566 14112 1.528129 GTGTGCTTTCTTCTCCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
6608 14154 2.743183 CGGCTTAGGTGATTCTGAAGGG 60.743 54.545 0.00 0.00 0.00 3.95
6619 14176 3.576078 TTCTGAAGGGTTTTGAGCTGA 57.424 42.857 0.00 0.00 0.00 4.26
6686 14243 7.225931 GTGGTTTTGTCACTGATTCAGTTAGTA 59.774 37.037 16.64 1.68 42.59 1.82
6694 14251 8.512956 GTCACTGATTCAGTTAGTACTTCACTA 58.487 37.037 16.64 0.00 42.59 2.74
6700 14257 5.974108 TCAGTTAGTACTTCACTATTGCCC 58.026 41.667 0.00 0.00 39.51 5.36
6707 14264 2.039879 ACTTCACTATTGCCCCGTCTTT 59.960 45.455 0.00 0.00 0.00 2.52
6740 14297 1.133216 TCAGAGCTCGCACTCATGTAC 59.867 52.381 8.37 0.00 39.26 2.90
6751 14308 3.682858 GCACTCATGTACCGTGTGTAAAT 59.317 43.478 13.09 0.00 31.99 1.40
6754 14311 6.671402 GCACTCATGTACCGTGTGTAAATAAC 60.671 42.308 13.09 0.00 31.99 1.89
6781 14338 5.828747 CTGAAATACATTCTGGAAGCATGG 58.171 41.667 0.00 0.00 42.12 3.66
6782 14339 4.098349 TGAAATACATTCTGGAAGCATGGC 59.902 41.667 0.00 0.00 42.12 4.40
6783 14340 2.804986 TACATTCTGGAAGCATGGCA 57.195 45.000 0.00 0.00 42.12 4.92
6784 14341 2.154567 ACATTCTGGAAGCATGGCAT 57.845 45.000 0.00 0.00 42.12 4.40
6785 14342 3.301794 ACATTCTGGAAGCATGGCATA 57.698 42.857 0.00 0.00 42.12 3.14
6786 14343 3.840991 ACATTCTGGAAGCATGGCATAT 58.159 40.909 0.00 0.00 42.12 1.78
6876 14433 5.949735 TGAAACTTGTCAAGAAACTGAACC 58.050 37.500 19.53 0.00 0.00 3.62
6927 14687 7.388460 AGTTTCAGCTTTAGAATGAAGATGG 57.612 36.000 2.78 0.00 40.07 3.51
6948 14708 5.953183 TGGATGTTGCAGATCAATTAACAC 58.047 37.500 9.35 0.00 36.99 3.32
6964 14724 1.165270 ACACTCCAAATGCGCTTACC 58.835 50.000 9.73 0.00 0.00 2.85
7215 14976 6.610020 TGTACATAGGCTTGTATAGAGGTTGT 59.390 38.462 11.04 0.00 34.76 3.32
7292 15053 2.818130 TGCACCTTCCATTTTCTTGC 57.182 45.000 0.00 0.00 0.00 4.01
7356 15117 4.816048 ACATAGTACTCCCTCTGATCCA 57.184 45.455 0.00 0.00 0.00 3.41
7357 15118 5.346782 ACATAGTACTCCCTCTGATCCAT 57.653 43.478 0.00 0.00 0.00 3.41
7358 15119 6.470456 ACATAGTACTCCCTCTGATCCATA 57.530 41.667 0.00 0.00 0.00 2.74
7361 15122 7.958583 ACATAGTACTCCCTCTGATCCATAATT 59.041 37.037 0.00 0.00 0.00 1.40
7438 15207 5.621193 TGTGAGACATAGATATCGACCTGA 58.379 41.667 0.00 0.00 0.00 3.86
7487 15256 2.153547 GAAACCACAACGCCCCCATG 62.154 60.000 0.00 0.00 0.00 3.66
7488 15257 2.937959 AAACCACAACGCCCCCATGT 62.938 55.000 0.00 0.00 0.00 3.21
7500 15330 0.245539 CCCCATGTTCAGCAAGCAAG 59.754 55.000 0.00 0.00 0.00 4.01
7781 15614 9.781633 TTGAAGAATGTTCATGATTCCAAAAAT 57.218 25.926 0.00 0.00 31.22 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.904649 ATGATGAGGAGGTGTTGCGA 59.095 50.000 0.00 0.00 0.00 5.10
97 99 2.100879 GACCGTGCAAGAGGTGGAGT 62.101 60.000 13.62 0.00 41.51 3.85
213 215 2.765807 CGATCTGGGTCCCTGGCT 60.766 66.667 14.48 3.05 0.00 4.75
214 216 2.764128 TCGATCTGGGTCCCTGGC 60.764 66.667 14.48 6.71 0.00 4.85
215 217 2.435693 GGTCGATCTGGGTCCCTGG 61.436 68.421 14.48 5.15 0.00 4.45
216 218 2.435693 GGGTCGATCTGGGTCCCTG 61.436 68.421 10.00 9.21 35.63 4.45
217 219 2.041819 GGGTCGATCTGGGTCCCT 60.042 66.667 10.00 0.00 35.63 4.20
218 220 3.162154 GGGGTCGATCTGGGTCCC 61.162 72.222 0.00 0.00 37.59 4.46
219 221 3.537874 CGGGGTCGATCTGGGTCC 61.538 72.222 0.00 0.00 39.00 4.46
220 222 3.537874 CCGGGGTCGATCTGGGTC 61.538 72.222 0.00 0.00 39.00 4.46
262 264 3.370231 GCGGGAATTGTTGGCGGT 61.370 61.111 0.00 0.00 0.00 5.68
360 365 1.334869 ACGTTCGACTAGGTGACGTTT 59.665 47.619 3.52 0.00 35.51 3.60
363 368 0.517946 CGACGTTCGACTAGGTGACG 60.518 60.000 2.25 2.25 43.74 4.35
383 388 2.269241 GGCTGTGCAGAGGGGTAC 59.731 66.667 13.44 0.00 0.00 3.34
396 401 3.443045 GGCGACATGGTTGGGCTG 61.443 66.667 0.00 0.00 0.00 4.85
517 522 2.652095 CGCGGGGAGTCCTTTGGTA 61.652 63.158 9.58 0.00 0.00 3.25
732 763 6.362283 CGTGATTTTAATTTGGGTTGACTGTC 59.638 38.462 0.00 0.00 0.00 3.51
733 764 6.039941 TCGTGATTTTAATTTGGGTTGACTGT 59.960 34.615 0.00 0.00 0.00 3.55
791 823 2.936498 CCTTCAAAGGCGTACACCATAG 59.064 50.000 2.11 0.00 39.76 2.23
817 849 5.101628 TCATTTGAGTTCAACAAAGTGTGC 58.898 37.500 0.00 0.00 39.90 4.57
897 929 2.417719 GGAGGCACACACTTCAGTTAG 58.582 52.381 0.00 0.00 0.00 2.34
902 934 0.179020 CAAGGGAGGCACACACTTCA 60.179 55.000 0.00 0.00 38.56 3.02
999 1035 3.491964 CGTTGTTCAACCTGACTACCTGA 60.492 47.826 9.62 0.00 0.00 3.86
1000 1036 2.800544 CGTTGTTCAACCTGACTACCTG 59.199 50.000 9.62 0.00 0.00 4.00
1001 1037 2.805657 GCGTTGTTCAACCTGACTACCT 60.806 50.000 9.62 0.00 0.00 3.08
1002 1038 1.529865 GCGTTGTTCAACCTGACTACC 59.470 52.381 9.62 0.00 0.00 3.18
1003 1039 2.221055 CAGCGTTGTTCAACCTGACTAC 59.779 50.000 19.43 0.00 0.00 2.73
1004 1040 2.479837 CAGCGTTGTTCAACCTGACTA 58.520 47.619 19.43 0.00 0.00 2.59
1005 1041 1.299541 CAGCGTTGTTCAACCTGACT 58.700 50.000 19.43 8.07 0.00 3.41
1006 1042 0.307760 CCAGCGTTGTTCAACCTGAC 59.692 55.000 22.78 8.87 0.00 3.51
1351 1438 0.326927 GGTTGTCGGGGGATTTGAGA 59.673 55.000 0.00 0.00 0.00 3.27
1801 1890 3.205536 TTTTGAGCGCGTGCCACA 61.206 55.556 19.02 15.56 44.31 4.17
2330 2452 2.677199 ACAGTCATACAACAGCAGACG 58.323 47.619 0.00 0.00 34.56 4.18
2377 2499 8.591072 GGGATCAAATTATCAATTCCATCACAT 58.409 33.333 0.00 0.00 29.20 3.21
2432 2554 3.726557 ATCCATGGTTTCTTCTCTGCA 57.273 42.857 12.58 0.00 0.00 4.41
2628 2815 6.839124 AAATTTGTGACTGGCATCAGATTA 57.161 33.333 0.00 0.00 43.49 1.75
2698 2885 6.640499 TCGTGGCTTTAGTTCAAATTGATTTG 59.360 34.615 9.61 9.61 46.39 2.32
2699 2886 6.640907 GTCGTGGCTTTAGTTCAAATTGATTT 59.359 34.615 0.00 0.00 0.00 2.17
2700 2887 6.149633 GTCGTGGCTTTAGTTCAAATTGATT 58.850 36.000 0.00 0.00 0.00 2.57
2701 2888 5.240623 TGTCGTGGCTTTAGTTCAAATTGAT 59.759 36.000 0.00 0.00 0.00 2.57
2703 2890 4.675114 GTGTCGTGGCTTTAGTTCAAATTG 59.325 41.667 0.00 0.00 0.00 2.32
2704 2891 4.578928 AGTGTCGTGGCTTTAGTTCAAATT 59.421 37.500 0.00 0.00 0.00 1.82
2705 2892 4.134563 AGTGTCGTGGCTTTAGTTCAAAT 58.865 39.130 0.00 0.00 0.00 2.32
2706 2893 3.537580 AGTGTCGTGGCTTTAGTTCAAA 58.462 40.909 0.00 0.00 0.00 2.69
2709 4565 5.857822 AATAAGTGTCGTGGCTTTAGTTC 57.142 39.130 0.00 0.00 0.00 3.01
2810 4666 2.145865 CAGGTGACTTGACCCTGGT 58.854 57.895 0.00 0.00 41.69 4.00
3016 4970 8.677871 TCCAATAGGTATTTCCAATATGACCAT 58.322 33.333 0.00 0.00 39.02 3.55
3038 4992 1.820519 GCATTTCATCCTGCAGTCCAA 59.179 47.619 13.81 0.00 38.28 3.53
3306 5283 9.995003 ATTCACAACAAACACATAATTTATGGT 57.005 25.926 18.24 11.34 40.47 3.55
3452 5743 3.797559 AGCCAAACTAAAGAAGAGGCT 57.202 42.857 0.00 0.00 42.49 4.58
3524 5815 9.890629 GCTCCATATGTAGTCCATATTGAAATA 57.109 33.333 1.24 0.00 42.87 1.40
3589 5902 8.818141 ATTTCAATACGGACTACATACAGATG 57.182 34.615 0.00 0.00 39.16 2.90
3744 6083 8.819974 CAGCATTTTGAACAAACAAGAATACTT 58.180 29.630 0.00 0.00 36.73 2.24
3821 6164 7.227873 TGAACACCCAATAATCAAGTACAGAA 58.772 34.615 0.00 0.00 0.00 3.02
4280 6716 1.453928 GCTCCTATTGCCCACCCAC 60.454 63.158 0.00 0.00 0.00 4.61
4282 6718 0.771127 TATGCTCCTATTGCCCACCC 59.229 55.000 0.00 0.00 0.00 4.61
4283 6719 1.421646 AGTATGCTCCTATTGCCCACC 59.578 52.381 0.00 0.00 0.00 4.61
4284 6720 2.104792 TCAGTATGCTCCTATTGCCCAC 59.895 50.000 0.00 0.00 34.76 4.61
4285 6721 2.407562 TCAGTATGCTCCTATTGCCCA 58.592 47.619 0.00 0.00 34.76 5.36
4286 6722 3.710209 ATCAGTATGCTCCTATTGCCC 57.290 47.619 0.00 0.00 34.76 5.36
4287 6723 6.148480 CAGTAAATCAGTATGCTCCTATTGCC 59.852 42.308 0.00 0.00 34.76 4.52
4288 6724 6.931281 TCAGTAAATCAGTATGCTCCTATTGC 59.069 38.462 0.00 0.00 34.76 3.56
4289 6725 8.893219 TTCAGTAAATCAGTATGCTCCTATTG 57.107 34.615 0.00 0.00 34.76 1.90
4290 6726 9.499479 CATTCAGTAAATCAGTATGCTCCTATT 57.501 33.333 0.00 0.00 34.76 1.73
4291 6727 8.654997 ACATTCAGTAAATCAGTATGCTCCTAT 58.345 33.333 0.00 0.00 34.76 2.57
4292 6728 7.928167 CACATTCAGTAAATCAGTATGCTCCTA 59.072 37.037 0.00 0.00 34.76 2.94
4293 6729 6.765036 CACATTCAGTAAATCAGTATGCTCCT 59.235 38.462 0.00 0.00 34.76 3.69
4294 6730 6.017605 CCACATTCAGTAAATCAGTATGCTCC 60.018 42.308 0.00 0.00 34.76 4.70
4296 6732 6.653020 TCCACATTCAGTAAATCAGTATGCT 58.347 36.000 0.00 0.00 34.76 3.79
4297 6733 6.925610 TCCACATTCAGTAAATCAGTATGC 57.074 37.500 0.00 0.00 34.76 3.14
4299 6735 7.500227 CACCATCCACATTCAGTAAATCAGTAT 59.500 37.037 0.00 0.00 0.00 2.12
4300 6736 6.823182 CACCATCCACATTCAGTAAATCAGTA 59.177 38.462 0.00 0.00 0.00 2.74
4301 6737 5.649395 CACCATCCACATTCAGTAAATCAGT 59.351 40.000 0.00 0.00 0.00 3.41
4302 6738 5.449588 GCACCATCCACATTCAGTAAATCAG 60.450 44.000 0.00 0.00 0.00 2.90
4305 6741 4.603131 AGCACCATCCACATTCAGTAAAT 58.397 39.130 0.00 0.00 0.00 1.40
4306 6742 4.032960 AGCACCATCCACATTCAGTAAA 57.967 40.909 0.00 0.00 0.00 2.01
4307 6743 3.719268 AGCACCATCCACATTCAGTAA 57.281 42.857 0.00 0.00 0.00 2.24
4308 6744 3.719268 AAGCACCATCCACATTCAGTA 57.281 42.857 0.00 0.00 0.00 2.74
4309 6745 2.592102 AAGCACCATCCACATTCAGT 57.408 45.000 0.00 0.00 0.00 3.41
4311 6747 3.159213 AGAAAGCACCATCCACATTCA 57.841 42.857 0.00 0.00 0.00 2.57
4312 6748 4.219288 AGAAAGAAAGCACCATCCACATTC 59.781 41.667 0.00 0.00 0.00 2.67
4313 6749 4.154942 AGAAAGAAAGCACCATCCACATT 58.845 39.130 0.00 0.00 0.00 2.71
4314 6750 3.771216 AGAAAGAAAGCACCATCCACAT 58.229 40.909 0.00 0.00 0.00 3.21
4315 6751 3.228188 AGAAAGAAAGCACCATCCACA 57.772 42.857 0.00 0.00 0.00 4.17
4316 6752 3.057245 GGAAGAAAGAAAGCACCATCCAC 60.057 47.826 0.00 0.00 0.00 4.02
4317 6753 3.157087 GGAAGAAAGAAAGCACCATCCA 58.843 45.455 0.00 0.00 0.00 3.41
4318 6754 3.157087 TGGAAGAAAGAAAGCACCATCC 58.843 45.455 0.00 0.00 0.00 3.51
4319 6755 3.192212 CCTGGAAGAAAGAAAGCACCATC 59.808 47.826 0.00 0.00 34.07 3.51
4320 6756 3.160269 CCTGGAAGAAAGAAAGCACCAT 58.840 45.455 0.00 0.00 34.07 3.55
4321 6757 2.091885 ACCTGGAAGAAAGAAAGCACCA 60.092 45.455 0.00 0.00 34.07 4.17
4322 6758 2.294512 CACCTGGAAGAAAGAAAGCACC 59.705 50.000 0.00 0.00 34.07 5.01
4323 6759 3.214328 TCACCTGGAAGAAAGAAAGCAC 58.786 45.455 0.00 0.00 34.07 4.40
4324 6760 3.576078 TCACCTGGAAGAAAGAAAGCA 57.424 42.857 0.00 0.00 34.07 3.91
4335 6771 2.054021 TCCACACATCTTCACCTGGAA 58.946 47.619 0.00 0.00 0.00 3.53
4336 6772 1.728323 TCCACACATCTTCACCTGGA 58.272 50.000 0.00 0.00 0.00 3.86
4337 6773 2.430465 CTTCCACACATCTTCACCTGG 58.570 52.381 0.00 0.00 0.00 4.45
4338 6774 1.808945 GCTTCCACACATCTTCACCTG 59.191 52.381 0.00 0.00 0.00 4.00
4339 6775 1.701847 AGCTTCCACACATCTTCACCT 59.298 47.619 0.00 0.00 0.00 4.00
4340 6776 1.808945 CAGCTTCCACACATCTTCACC 59.191 52.381 0.00 0.00 0.00 4.02
4341 6777 1.808945 CCAGCTTCCACACATCTTCAC 59.191 52.381 0.00 0.00 0.00 3.18
4342 6778 1.699083 TCCAGCTTCCACACATCTTCA 59.301 47.619 0.00 0.00 0.00 3.02
4343 6779 2.479566 TCCAGCTTCCACACATCTTC 57.520 50.000 0.00 0.00 0.00 2.87
4344 6780 2.040813 ACATCCAGCTTCCACACATCTT 59.959 45.455 0.00 0.00 0.00 2.40
4345 6781 1.632409 ACATCCAGCTTCCACACATCT 59.368 47.619 0.00 0.00 0.00 2.90
4346 6782 2.119801 ACATCCAGCTTCCACACATC 57.880 50.000 0.00 0.00 0.00 3.06
4347 6783 2.165167 CAACATCCAGCTTCCACACAT 58.835 47.619 0.00 0.00 0.00 3.21
4348 6784 1.142667 TCAACATCCAGCTTCCACACA 59.857 47.619 0.00 0.00 0.00 3.72
4349 6785 1.896220 TCAACATCCAGCTTCCACAC 58.104 50.000 0.00 0.00 0.00 3.82
4350 6786 2.439409 CATCAACATCCAGCTTCCACA 58.561 47.619 0.00 0.00 0.00 4.17
4351 6787 1.747355 CCATCAACATCCAGCTTCCAC 59.253 52.381 0.00 0.00 0.00 4.02
4352 6788 1.355381 ACCATCAACATCCAGCTTCCA 59.645 47.619 0.00 0.00 0.00 3.53
4353 6789 1.747355 CACCATCAACATCCAGCTTCC 59.253 52.381 0.00 0.00 0.00 3.46
4354 6790 1.133790 GCACCATCAACATCCAGCTTC 59.866 52.381 0.00 0.00 0.00 3.86
4355 6791 1.180029 GCACCATCAACATCCAGCTT 58.820 50.000 0.00 0.00 0.00 3.74
4356 6792 0.682209 GGCACCATCAACATCCAGCT 60.682 55.000 0.00 0.00 0.00 4.24
4357 6793 0.682209 AGGCACCATCAACATCCAGC 60.682 55.000 0.00 0.00 0.00 4.85
4358 6794 1.843368 AAGGCACCATCAACATCCAG 58.157 50.000 0.00 0.00 0.00 3.86
4359 6795 2.307496 AAAGGCACCATCAACATCCA 57.693 45.000 0.00 0.00 0.00 3.41
4360 6796 3.259123 AGAAAAAGGCACCATCAACATCC 59.741 43.478 0.00 0.00 0.00 3.51
4361 6797 4.525912 AGAAAAAGGCACCATCAACATC 57.474 40.909 0.00 0.00 0.00 3.06
4362 6798 4.590222 AGAAGAAAAAGGCACCATCAACAT 59.410 37.500 0.00 0.00 0.00 2.71
4363 6799 3.960102 AGAAGAAAAAGGCACCATCAACA 59.040 39.130 0.00 0.00 0.00 3.33
4364 6800 4.590850 AGAAGAAAAAGGCACCATCAAC 57.409 40.909 0.00 0.00 0.00 3.18
4365 6801 4.039124 GGAAGAAGAAAAAGGCACCATCAA 59.961 41.667 0.00 0.00 0.00 2.57
4366 6802 3.573967 GGAAGAAGAAAAAGGCACCATCA 59.426 43.478 0.00 0.00 0.00 3.07
4367 6803 3.573967 TGGAAGAAGAAAAAGGCACCATC 59.426 43.478 0.00 0.00 0.00 3.51
4368 6804 3.575687 CTGGAAGAAGAAAAAGGCACCAT 59.424 43.478 0.00 0.00 34.07 3.55
4369 6805 2.958355 CTGGAAGAAGAAAAAGGCACCA 59.042 45.455 0.00 0.00 34.07 4.17
4370 6806 2.297315 CCTGGAAGAAGAAAAAGGCACC 59.703 50.000 0.00 0.00 34.07 5.01
4371 6807 3.222603 TCCTGGAAGAAGAAAAAGGCAC 58.777 45.455 0.00 0.00 34.07 5.01
4372 6808 3.593442 TCCTGGAAGAAGAAAAAGGCA 57.407 42.857 0.00 0.00 34.07 4.75
4373 6809 4.621991 GTTTCCTGGAAGAAGAAAAAGGC 58.378 43.478 9.42 0.00 34.07 4.35
4374 6810 4.578928 TCGTTTCCTGGAAGAAGAAAAAGG 59.421 41.667 9.42 0.00 34.07 3.11
4375 6811 5.527582 TCTCGTTTCCTGGAAGAAGAAAAAG 59.472 40.000 9.42 0.00 34.07 2.27
4376 6812 5.433526 TCTCGTTTCCTGGAAGAAGAAAAA 58.566 37.500 9.42 0.00 34.07 1.94
4377 6813 5.031066 TCTCGTTTCCTGGAAGAAGAAAA 57.969 39.130 9.42 0.00 34.07 2.29
4378 6814 4.682778 TCTCGTTTCCTGGAAGAAGAAA 57.317 40.909 9.42 0.00 34.07 2.52
4379 6815 4.283467 TCATCTCGTTTCCTGGAAGAAGAA 59.717 41.667 9.42 0.00 34.07 2.52
4380 6816 3.832490 TCATCTCGTTTCCTGGAAGAAGA 59.168 43.478 9.42 13.13 34.07 2.87
4381 6817 4.193826 TCATCTCGTTTCCTGGAAGAAG 57.806 45.455 9.42 8.52 34.07 2.85
4382 6818 4.617253 TTCATCTCGTTTCCTGGAAGAA 57.383 40.909 9.42 5.21 34.07 2.52
4383 6819 4.202315 TGTTTCATCTCGTTTCCTGGAAGA 60.202 41.667 9.42 3.72 34.07 2.87
4384 6820 4.065088 TGTTTCATCTCGTTTCCTGGAAG 58.935 43.478 9.42 0.00 0.00 3.46
4385 6821 4.079980 TGTTTCATCTCGTTTCCTGGAA 57.920 40.909 4.68 4.68 0.00 3.53
4386 6822 3.762407 TGTTTCATCTCGTTTCCTGGA 57.238 42.857 0.00 0.00 0.00 3.86
4387 6823 3.753272 ACATGTTTCATCTCGTTTCCTGG 59.247 43.478 0.00 0.00 0.00 4.45
4388 6824 5.063944 CCTACATGTTTCATCTCGTTTCCTG 59.936 44.000 2.30 0.00 0.00 3.86
4389 6825 5.178797 CCTACATGTTTCATCTCGTTTCCT 58.821 41.667 2.30 0.00 0.00 3.36
4390 6826 4.201822 GCCTACATGTTTCATCTCGTTTCC 60.202 45.833 2.30 0.00 0.00 3.13
4391 6827 4.391830 TGCCTACATGTTTCATCTCGTTTC 59.608 41.667 2.30 0.00 0.00 2.78
4392 6828 4.323417 TGCCTACATGTTTCATCTCGTTT 58.677 39.130 2.30 0.00 0.00 3.60
4393 6829 3.937814 TGCCTACATGTTTCATCTCGTT 58.062 40.909 2.30 0.00 0.00 3.85
4394 6830 3.610040 TGCCTACATGTTTCATCTCGT 57.390 42.857 2.30 0.00 0.00 4.18
4395 6831 4.260907 CCATTGCCTACATGTTTCATCTCG 60.261 45.833 2.30 0.00 0.00 4.04
4396 6832 4.498682 GCCATTGCCTACATGTTTCATCTC 60.499 45.833 2.30 0.00 0.00 2.75
4397 6833 3.382546 GCCATTGCCTACATGTTTCATCT 59.617 43.478 2.30 0.00 0.00 2.90
4398 6834 3.382546 AGCCATTGCCTACATGTTTCATC 59.617 43.478 2.30 0.00 38.69 2.92
4399 6835 3.368248 AGCCATTGCCTACATGTTTCAT 58.632 40.909 2.30 0.00 38.69 2.57
4428 7030 2.700897 AGCCTTCGGAAGCATGTATAGT 59.299 45.455 12.29 0.00 0.00 2.12
4442 7044 3.849911 TCATCAACTAACAGAGCCTTCG 58.150 45.455 0.00 0.00 0.00 3.79
4447 7049 2.615912 GGGCATCATCAACTAACAGAGC 59.384 50.000 0.00 0.00 0.00 4.09
4480 7082 5.368145 GCCATAATCAGACCATACTTGTCA 58.632 41.667 0.00 0.00 35.15 3.58
4481 7083 4.449068 CGCCATAATCAGACCATACTTGTC 59.551 45.833 0.00 0.00 0.00 3.18
4497 7099 4.638421 CCCTGAATAAAACTCACGCCATAA 59.362 41.667 0.00 0.00 0.00 1.90
4498 7100 4.080807 TCCCTGAATAAAACTCACGCCATA 60.081 41.667 0.00 0.00 0.00 2.74
4504 7106 4.396478 GGAGCTTCCCTGAATAAAACTCAC 59.604 45.833 0.00 0.00 0.00 3.51
4506 7108 4.849518 AGGAGCTTCCCTGAATAAAACTC 58.150 43.478 0.00 0.00 37.19 3.01
4542 7144 6.071728 AGGATTACTCACCTTGCAAAATTCAG 60.072 38.462 0.00 0.00 31.95 3.02
4545 7147 6.494835 AGAAGGATTACTCACCTTGCAAAATT 59.505 34.615 0.00 0.00 45.08 1.82
4874 12108 0.179156 CTGGCCGCATTGCTGTTAAG 60.179 55.000 7.12 0.00 0.00 1.85
5169 12599 4.508551 TCCTCACATGCCTTCAATACAT 57.491 40.909 0.00 0.00 0.00 2.29
5188 12619 1.620323 AGCCTTTGCACTTGGAATTCC 59.380 47.619 18.17 18.17 41.13 3.01
5251 12696 2.813754 TGCCTTCATGCAGTAAGTTCAC 59.186 45.455 9.31 0.00 36.04 3.18
5255 12700 1.806542 CGTTGCCTTCATGCAGTAAGT 59.193 47.619 9.31 0.00 43.21 2.24
5262 12707 0.521291 TAAGCACGTTGCCTTCATGC 59.479 50.000 6.39 0.00 46.52 4.06
5454 12903 0.816421 CATCGTGCTCATCATGGCCA 60.816 55.000 8.56 8.56 32.54 5.36
5569 13021 8.437443 TTTTTGTGTAAAGTTCAGTTGTTACG 57.563 30.769 0.00 0.00 30.61 3.18
5570 13022 8.856247 CCTTTTTGTGTAAAGTTCAGTTGTTAC 58.144 33.333 0.00 0.00 34.11 2.50
5649 13101 3.458189 CAGCCCCTGTTTATTAGACTCG 58.542 50.000 0.00 0.00 0.00 4.18
5712 13164 5.486735 TTAGTTGAACTGAATCCCCGTAA 57.513 39.130 8.33 0.00 0.00 3.18
5919 13391 1.134670 CCCGATCTCACAGTTTCTCCC 60.135 57.143 0.00 0.00 0.00 4.30
5927 13399 2.322355 AGAATTGCCCGATCTCACAG 57.678 50.000 0.00 0.00 0.00 3.66
5937 13409 1.098050 AGTGCATCGAAGAATTGCCC 58.902 50.000 5.55 0.00 41.39 5.36
5965 13437 8.509690 GGAACCACCTACTAAACTGAAAATAAC 58.490 37.037 0.00 0.00 35.41 1.89
6118 13593 5.677319 TTAGCAGGCTGTTAACTAGACAT 57.323 39.130 18.31 0.00 0.00 3.06
6136 13611 8.460831 ACAAACATAAACGATTCCAAATTAGC 57.539 30.769 0.00 0.00 0.00 3.09
6140 13615 7.535940 CGTGTACAAACATAAACGATTCCAAAT 59.464 33.333 0.00 0.00 37.90 2.32
6142 13617 6.202379 TCGTGTACAAACATAAACGATTCCAA 59.798 34.615 0.00 0.00 39.36 3.53
6143 13618 5.695363 TCGTGTACAAACATAAACGATTCCA 59.305 36.000 0.00 0.00 39.36 3.53
6144 13619 6.155691 TCGTGTACAAACATAAACGATTCC 57.844 37.500 0.00 0.00 39.36 3.01
6145 13620 6.517374 GGTTCGTGTACAAACATAAACGATTC 59.483 38.462 11.52 4.82 42.78 2.52
6146 13621 6.365050 GGTTCGTGTACAAACATAAACGATT 58.635 36.000 11.52 0.00 42.78 3.34
6147 13622 5.106987 GGGTTCGTGTACAAACATAAACGAT 60.107 40.000 11.52 0.00 42.78 3.73
6148 13623 4.210955 GGGTTCGTGTACAAACATAAACGA 59.789 41.667 11.52 5.07 41.85 3.85
6149 13624 4.456914 GGGTTCGTGTACAAACATAAACG 58.543 43.478 11.52 2.89 38.08 3.60
6150 13625 4.516321 AGGGGTTCGTGTACAAACATAAAC 59.484 41.667 11.52 4.46 38.08 2.01
6154 13632 2.158726 ACAGGGGTTCGTGTACAAACAT 60.159 45.455 11.52 0.00 39.83 2.71
6161 13639 2.880443 ACTCTAACAGGGGTTCGTGTA 58.120 47.619 0.00 0.00 40.61 2.90
6162 13640 1.713297 ACTCTAACAGGGGTTCGTGT 58.287 50.000 0.00 0.00 42.95 4.49
6178 13656 9.771534 AGTTGCCTCTAATTATCTATTCAACTC 57.228 33.333 0.00 0.00 34.06 3.01
6290 13779 3.557228 ATGAAGAAAGCTAGGAGCCAG 57.443 47.619 0.00 0.00 43.77 4.85
6294 13783 9.959749 CTTAGTAACTATGAAGAAAGCTAGGAG 57.040 37.037 0.00 0.00 0.00 3.69
6326 13815 8.978874 TGCCATGCTCTCTAATATAAAGAAAA 57.021 30.769 0.00 0.00 0.00 2.29
6398 13942 7.201785 CCTCTAAACAAGCTCAACACCTTAAAA 60.202 37.037 0.00 0.00 0.00 1.52
6402 13946 4.137543 CCTCTAAACAAGCTCAACACCTT 58.862 43.478 0.00 0.00 0.00 3.50
6403 13947 3.391296 TCCTCTAAACAAGCTCAACACCT 59.609 43.478 0.00 0.00 0.00 4.00
6425 13971 1.149101 TTCAGGGAAGAAAGGCCAGT 58.851 50.000 5.01 0.00 0.00 4.00
6471 14017 1.399572 CGTCGCGATGGATTAGACAG 58.600 55.000 20.66 0.00 32.57 3.51
6491 14037 1.066908 TCCTGCAAAAAGAAAGCACCG 59.933 47.619 0.00 0.00 34.13 4.94
6506 14052 1.979155 GCCCACCTTTTCCTCCTGC 60.979 63.158 0.00 0.00 0.00 4.85
6514 14060 1.063266 TCCAGTTTCAGCCCACCTTTT 60.063 47.619 0.00 0.00 0.00 2.27
6608 14154 4.322567 AGACCATCTTCTCAGCTCAAAAC 58.677 43.478 0.00 0.00 0.00 2.43
6619 14176 5.960811 TCCATGAGAAACTAGACCATCTTCT 59.039 40.000 0.00 0.00 0.00 2.85
6686 14243 1.276622 AGACGGGGCAATAGTGAAGT 58.723 50.000 0.00 0.00 0.00 3.01
6694 14251 1.202879 TGTCAAGAAAGACGGGGCAAT 60.203 47.619 0.00 0.00 41.41 3.56
6700 14257 1.202651 ACCTGGTGTCAAGAAAGACGG 60.203 52.381 0.00 0.00 41.41 4.79
6721 14278 1.554392 GTACATGAGTGCGAGCTCTG 58.446 55.000 12.85 6.68 36.51 3.35
6728 14285 0.666274 ACACACGGTACATGAGTGCG 60.666 55.000 0.00 1.09 33.69 5.34
6740 14297 5.676532 TTCAGGTTGTTATTTACACACGG 57.323 39.130 0.00 0.00 36.21 4.94
6751 14308 7.094377 GCTTCCAGAATGTATTTCAGGTTGTTA 60.094 37.037 0.00 0.00 40.83 2.41
6754 14311 5.183713 TGCTTCCAGAATGTATTTCAGGTTG 59.816 40.000 0.00 0.00 40.83 3.77
6775 14332 3.559069 ACAGCAAGTAATATGCCATGCT 58.441 40.909 0.00 0.00 44.91 3.79
6776 14333 3.996150 ACAGCAAGTAATATGCCATGC 57.004 42.857 0.00 0.00 44.91 4.06
6777 14334 8.552083 TCTAATACAGCAAGTAATATGCCATG 57.448 34.615 0.00 0.00 44.91 3.66
6778 14335 8.597167 TCTCTAATACAGCAAGTAATATGCCAT 58.403 33.333 0.00 0.00 44.91 4.40
6779 14336 7.962441 TCTCTAATACAGCAAGTAATATGCCA 58.038 34.615 0.00 0.00 44.91 4.92
6780 14337 8.091449 ACTCTCTAATACAGCAAGTAATATGCC 58.909 37.037 0.00 0.00 44.91 4.40
6781 14338 9.482627 AACTCTCTAATACAGCAAGTAATATGC 57.517 33.333 0.00 0.00 44.15 3.14
6785 14342 8.754080 AGTGAACTCTCTAATACAGCAAGTAAT 58.246 33.333 0.00 0.00 36.05 1.89
6786 14343 8.123639 AGTGAACTCTCTAATACAGCAAGTAA 57.876 34.615 0.00 0.00 36.05 2.24
6876 14433 2.291741 GGTTCAGGCTTCAACTGTCAAG 59.708 50.000 6.15 0.00 37.25 3.02
6927 14687 6.127925 TGGAGTGTTAATTGATCTGCAACATC 60.128 38.462 0.00 0.00 39.78 3.06
6948 14708 1.453155 ACAGGTAAGCGCATTTGGAG 58.547 50.000 11.47 0.00 0.00 3.86
6964 14724 9.138062 CCATTCTCTATATTTCGAGATGAACAG 57.862 37.037 0.00 0.00 36.29 3.16
7018 14778 1.337823 CCCTCGACCGATTTGAGTTGT 60.338 52.381 0.00 0.00 34.12 3.32
7215 14976 5.130311 TCCCTCTGATCCGAATTAATTGACA 59.870 40.000 5.17 0.00 0.00 3.58
7292 15053 9.655769 CATATCGATTTGTTGAAGTATCAAAGG 57.344 33.333 1.71 0.00 46.66 3.11
7361 15122 9.680315 CGGTGGTCTAATTTGTTTGTTTTTATA 57.320 29.630 0.00 0.00 0.00 0.98
7369 15130 2.230266 CCCCGGTGGTCTAATTTGTTTG 59.770 50.000 0.00 0.00 0.00 2.93
7373 15134 0.621609 TCCCCCGGTGGTCTAATTTG 59.378 55.000 1.78 0.00 0.00 2.32
7424 15193 4.140994 ACCCCTCTTTCAGGTCGATATCTA 60.141 45.833 0.34 0.00 41.51 1.98
7428 15197 2.500098 CAACCCCTCTTTCAGGTCGATA 59.500 50.000 0.00 0.00 41.51 2.92
7429 15198 1.279271 CAACCCCTCTTTCAGGTCGAT 59.721 52.381 0.00 0.00 41.51 3.59
7438 15207 2.106684 GACCAGAGTTCAACCCCTCTTT 59.893 50.000 0.00 0.00 35.90 2.52
7487 15256 2.012948 GCGTGCTTGCTTGCTGAAC 61.013 57.895 3.47 0.00 0.00 3.18
7488 15257 2.332514 GCGTGCTTGCTTGCTGAA 59.667 55.556 3.47 0.00 0.00 3.02
7750 15583 9.781633 TGGAATCATGAACATTCTTCAAATTTT 57.218 25.926 0.00 0.00 31.82 1.82


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

AutoCloner maintained by Alex Coulton.