Multiple sequence alignment - TraesCS7D01G148600

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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 TraesCS7D01G148600 chr7D 100.000 7605 0 0 1 7605 95857855 95865459 0.000000e+00 14044.0
1 TraesCS7D01G148600 chr7D 91.589 1498 110 14 5394 6882 600017583 600019073 0.000000e+00 2054.0
2 TraesCS7D01G148600 chr7D 91.047 860 71 6 4542 5397 399875912 399876769 0.000000e+00 1157.0
3 TraesCS7D01G148600 chr7D 96.325 653 23 1 6953 7605 95924169 95924820 0.000000e+00 1072.0
4 TraesCS7D01G148600 chr7D 82.152 1227 145 47 2987 4181 636487878 636489062 0.000000e+00 985.0
5 TraesCS7D01G148600 chr7D 89.776 401 20 8 93 489 109920820 109921203 1.910000e-135 494.0
6 TraesCS7D01G148600 chr7D 86.184 304 37 4 2399 2698 636487638 636487940 2.650000e-84 324.0
7 TraesCS7D01G148600 chr7D 84.286 280 25 11 2945 3212 95860252 95860524 9.790000e-64 255.0
8 TraesCS7D01G148600 chr7D 91.228 171 11 4 93 260 60106294 60106125 5.940000e-56 230.0
9 TraesCS7D01G148600 chr7D 90.476 63 5 1 328 390 60106130 60106069 1.760000e-11 82.4
10 TraesCS7D01G148600 chr7D 100.000 31 0 0 240 270 594703194 594703164 2.960000e-04 58.4
11 TraesCS7D01G148600 chr1D 96.799 3499 71 18 697 4181 331879935 331883406 0.000000e+00 5803.0
12 TraesCS7D01G148600 chr1D 96.559 3487 63 18 742 4190 249755948 249759415 0.000000e+00 5722.0
13 TraesCS7D01G148600 chr1D 93.628 1491 82 7 5394 6882 246872571 246874050 0.000000e+00 2215.0
14 TraesCS7D01G148600 chr1D 90.607 873 65 13 4537 5397 339671689 339672556 0.000000e+00 1142.0
15 TraesCS7D01G148600 chr1D 88.924 316 17 6 97 410 155903056 155903355 2.590000e-99 374.0
16 TraesCS7D01G148600 chr1D 80.688 378 33 24 2847 3212 331881555 331881904 2.720000e-64 257.0
17 TraesCS7D01G148600 chr1D 83.929 280 26 11 2398 2670 331882180 331882447 4.560000e-62 250.0
18 TraesCS7D01G148600 chr1D 84.825 257 25 8 2398 2652 249758169 249758413 5.890000e-61 246.0
19 TraesCS7D01G148600 chr1D 87.200 125 12 4 97 218 392994119 392993996 1.030000e-28 139.0
20 TraesCS7D01G148600 chr1D 92.000 100 6 2 121 218 393065745 393065646 1.030000e-28 139.0
21 TraesCS7D01G148600 chr1D 88.596 114 9 4 93 203 476037988 476038100 1.330000e-27 135.0
22 TraesCS7D01G148600 chr1D 86.154 130 13 5 93 218 477539601 477539473 1.330000e-27 135.0
23 TraesCS7D01G148600 chr1D 92.308 65 5 0 6885 6949 47040901 47040965 8.130000e-15 93.5
24 TraesCS7D01G148600 chr1D 100.000 32 0 0 696 727 249755916 249755947 8.240000e-05 60.2
25 TraesCS7D01G148600 chr1D 100.000 28 0 0 240 267 79794362 79794335 1.400000e-02 52.8
26 TraesCS7D01G148600 chr3D 96.286 3500 82 15 698 4182 546203285 546199819 0.000000e+00 5699.0
27 TraesCS7D01G148600 chr3D 92.508 1495 101 9 5394 6882 98390732 98392221 0.000000e+00 2130.0
28 TraesCS7D01G148600 chr3D 90.856 864 64 10 4546 5397 533930619 533931479 0.000000e+00 1144.0
29 TraesCS7D01G148600 chr3D 88.075 956 89 18 4459 5397 411176681 411175734 0.000000e+00 1110.0
30 TraesCS7D01G148600 chr3D 96.478 653 22 1 6953 7605 157571093 157570442 0.000000e+00 1077.0
31 TraesCS7D01G148600 chr3D 96.330 654 23 1 6953 7605 384126463 384125810 0.000000e+00 1074.0
32 TraesCS7D01G148600 chr3D 87.161 958 103 16 4459 5400 264386475 264385522 0.000000e+00 1070.0
33 TraesCS7D01G148600 chr3D 86.228 334 26 7 80 410 126257327 126257011 2.030000e-90 344.0
34 TraesCS7D01G148600 chr3D 86.604 321 24 6 93 410 544188807 544189111 3.400000e-88 337.0
35 TraesCS7D01G148600 chr3D 87.755 49 6 0 240 288 26600612 26600564 2.960000e-04 58.4
36 TraesCS7D01G148600 chr3D 87.755 49 6 0 240 288 578759619 578759571 2.960000e-04 58.4
37 TraesCS7D01G148600 chr5D 97.078 2259 38 6 1268 3501 481131154 481128899 0.000000e+00 3781.0
38 TraesCS7D01G148600 chr5D 93.630 1507 76 5 5394 6882 227248366 227249870 0.000000e+00 2233.0
39 TraesCS7D01G148600 chr5D 93.617 1504 81 13 5394 6885 168581989 168580489 0.000000e+00 2231.0
40 TraesCS7D01G148600 chr5D 90.782 1497 116 22 5394 6882 337736935 337738417 0.000000e+00 1980.0
41 TraesCS7D01G148600 chr5D 96.172 653 25 0 6953 7605 383524862 383524210 0.000000e+00 1068.0
42 TraesCS7D01G148600 chr5D 87.261 157 15 5 80 233 487671637 487671483 2.820000e-39 174.0
43 TraesCS7D01G148600 chr5D 89.209 139 10 5 97 233 394200122 394199987 1.310000e-37 169.0
44 TraesCS7D01G148600 chr5D 87.500 144 16 2 2945 3087 481130025 481129883 1.700000e-36 165.0
45 TraesCS7D01G148600 chr5D 94.286 70 4 0 6883 6952 232181875 232181944 2.900000e-19 108.0
46 TraesCS7D01G148600 chr7A 94.111 1885 86 13 2321 4185 51668719 51666840 0.000000e+00 2843.0
47 TraesCS7D01G148600 chr7A 94.685 1637 71 10 699 2322 51670400 51668767 0.000000e+00 2527.0
48 TraesCS7D01G148600 chr7A 82.670 427 36 20 2772 3184 51668795 51668393 2.030000e-90 344.0
49 TraesCS7D01G148600 chr7A 85.841 113 15 1 4183 4295 657231988 657231877 1.340000e-22 119.0
50 TraesCS7D01G148600 chr4D 92.757 1491 100 8 5397 6882 322448742 322447255 0.000000e+00 2148.0
51 TraesCS7D01G148600 chr4D 97.090 653 19 0 6953 7605 304812374 304813026 0.000000e+00 1101.0
52 TraesCS7D01G148600 chr4D 96.784 653 21 0 6953 7605 304806385 304807037 0.000000e+00 1090.0
53 TraesCS7D01G148600 chr4D 95.359 668 30 1 6938 7605 397704347 397705013 0.000000e+00 1061.0
54 TraesCS7D01G148600 chr4D 78.729 771 112 32 2960 3708 373845003 373844263 1.160000e-127 468.0
55 TraesCS7D01G148600 chr4D 84.722 144 17 5 69 210 212644653 212644793 1.030000e-28 139.0
56 TraesCS7D01G148600 chr4D 100.000 28 0 0 240 267 288520639 288520612 1.400000e-02 52.8
57 TraesCS7D01G148600 chr2D 92.493 1492 105 6 5394 6882 155427380 155425893 0.000000e+00 2128.0
58 TraesCS7D01G148600 chr2D 90.286 875 67 13 4537 5397 164345223 164346093 0.000000e+00 1129.0
59 TraesCS7D01G148600 chr2D 96.478 653 23 0 6953 7605 635623219 635623871 0.000000e+00 1079.0
60 TraesCS7D01G148600 chr2D 88.474 321 18 6 93 410 305470778 305470474 3.350000e-98 370.0
61 TraesCS7D01G148600 chr6D 90.909 1496 122 11 5394 6882 293133777 293135265 0.000000e+00 1997.0
62 TraesCS7D01G148600 chr6D 85.540 1639 155 38 2611 4180 148163322 148164947 0.000000e+00 1639.0
63 TraesCS7D01G148600 chr6D 96.172 653 25 0 6953 7605 202923877 202923225 0.000000e+00 1068.0
64 TraesCS7D01G148600 chr6D 84.891 1006 110 32 3042 4016 80063646 80062652 0.000000e+00 977.0
65 TraesCS7D01G148600 chr6D 85.429 350 36 8 2362 2698 80063985 80063638 4.370000e-92 350.0
66 TraesCS7D01G148600 chr6D 83.728 338 34 16 2870 3188 80064018 80063683 4.460000e-77 300.0
67 TraesCS7D01G148600 chr6D 81.944 288 37 10 2374 2652 148163639 148163920 5.940000e-56 230.0
68 TraesCS7D01G148600 chr6D 80.645 93 6 8 3093 3183 260007627 260007545 2.290000e-05 62.1
69 TraesCS7D01G148600 chr6D 100.000 29 0 0 2411 2439 260007384 260007356 4.000000e-03 54.7
70 TraesCS7D01G148600 chr6D 100.000 28 0 0 240 267 244143862 244143889 1.400000e-02 52.8
71 TraesCS7D01G148600 chr6D 100.000 28 0 0 240 267 436084411 436084384 1.400000e-02 52.8
72 TraesCS7D01G148600 chr3A 88.837 1505 131 22 5394 6891 328340028 328338554 0.000000e+00 1814.0
73 TraesCS7D01G148600 chr3A 87.398 246 16 2 165 410 92677036 92676806 1.260000e-67 268.0
74 TraesCS7D01G148600 chr3A 86.207 116 16 0 4185 4300 380668589 380668704 8.010000e-25 126.0
75 TraesCS7D01G148600 chr3A 89.706 68 7 0 6885 6952 462909360 462909293 3.780000e-13 87.9
76 TraesCS7D01G148600 chr3A 91.803 61 5 0 6885 6945 527915868 527915928 1.360000e-12 86.1
77 TraesCS7D01G148600 chr5A 88.728 967 85 18 4452 5400 577019345 577020305 0.000000e+00 1160.0
78 TraesCS7D01G148600 chr5A 88.521 967 87 18 4452 5400 577181693 577180733 0.000000e+00 1149.0
79 TraesCS7D01G148600 chr5A 88.418 967 88 18 4452 5400 577330850 577329890 0.000000e+00 1144.0
80 TraesCS7D01G148600 chr5A 83.571 1193 146 33 3006 4172 671980153 671978985 0.000000e+00 1072.0
81 TraesCS7D01G148600 chr5A 80.271 811 104 31 2403 3175 671980821 671980029 1.850000e-155 560.0
82 TraesCS7D01G148600 chr5A 86.726 113 14 1 4183 4295 121302881 121302770 2.880000e-24 124.0
83 TraesCS7D01G148600 chr5A 79.412 170 33 2 4185 4353 379933877 379934045 1.340000e-22 119.0
84 TraesCS7D01G148600 chr5A 90.698 43 3 1 2294 2336 671980441 671980400 1.000000e-03 56.5
85 TraesCS7D01G148600 chr4A 82.860 1091 139 39 2990 4051 696107579 696106508 0.000000e+00 935.0
86 TraesCS7D01G148600 chr4A 86.297 686 61 22 1 660 4713199 4713877 0.000000e+00 715.0
87 TraesCS7D01G148600 chr4A 91.082 527 46 1 1 527 157634410 157634935 0.000000e+00 712.0
88 TraesCS7D01G148600 chr4A 88.225 586 50 12 1 571 4705693 4706274 0.000000e+00 682.0
89 TraesCS7D01G148600 chr4A 85.382 301 38 5 2402 2698 696107818 696107520 2.670000e-79 307.0
90 TraesCS7D01G148600 chr3B 77.984 1240 204 60 4200 5400 543099693 543098484 0.000000e+00 713.0
91 TraesCS7D01G148600 chr3B 89.706 68 7 0 6885 6952 408530790 408530723 3.780000e-13 87.9
92 TraesCS7D01G148600 chr1A 83.411 645 79 20 3547 4174 19370535 19371168 2.380000e-159 573.0
93 TraesCS7D01G148600 chr1A 83.411 645 79 20 3547 4174 19476920 19477553 2.380000e-159 573.0
94 TraesCS7D01G148600 chr1A 90.230 174 14 3 97 268 515830471 515830299 2.760000e-54 224.0
95 TraesCS7D01G148600 chr1A 86.429 140 12 6 67 203 578178836 578178701 6.150000e-31 147.0
96 TraesCS7D01G148600 chr1A 97.059 34 0 1 240 272 575301303 575301336 1.000000e-03 56.5
97 TraesCS7D01G148600 chr1B 87.445 454 38 6 93 543 107863066 107863503 8.810000e-139 505.0
98 TraesCS7D01G148600 chr1B 90.608 181 13 4 93 270 650265640 650265819 3.550000e-58 237.0
99 TraesCS7D01G148600 chr1B 88.542 192 18 4 93 281 179582025 179581835 5.940000e-56 230.0
100 TraesCS7D01G148600 chr1B 87.273 110 11 3 4186 4295 196763081 196763187 1.040000e-23 122.0
101 TraesCS7D01G148600 chr1B 89.706 68 7 0 6885 6952 72093153 72093220 3.780000e-13 87.9
102 TraesCS7D01G148600 chr6B 85.591 347 30 8 93 436 645341549 645341220 5.650000e-91 346.0
103 TraesCS7D01G148600 chr6B 89.268 205 17 5 80 281 643030311 643030109 1.270000e-62 252.0
104 TraesCS7D01G148600 chr6B 88.235 68 8 0 6885 6952 262215408 262215475 1.760000e-11 82.4
105 TraesCS7D01G148600 chr4B 89.216 204 17 5 69 270 648972685 648972885 4.560000e-62 250.0
106 TraesCS7D01G148600 chr4B 92.908 141 9 1 121 260 205740976 205741116 3.600000e-48 204.0
107 TraesCS7D01G148600 chr4B 86.822 129 12 5 80 205 23182271 23182397 1.030000e-28 139.0
108 TraesCS7D01G148600 chr4B 86.614 127 12 5 80 203 619810408 619810284 1.330000e-27 135.0
109 TraesCS7D01G148600 chr4B 85.827 127 13 5 80 203 6423176 6423052 6.190000e-26 130.0
110 TraesCS7D01G148600 chr4B 92.857 70 5 0 6883 6952 469668615 469668684 1.350000e-17 102.0
111 TraesCS7D01G148600 chr4B 97.059 34 0 1 240 272 592372311 592372344 1.000000e-03 56.5
112 TraesCS7D01G148600 chr6A 81.868 182 26 4 3010 3184 370824242 370824423 6.150000e-31 147.0
113 TraesCS7D01G148600 chr6A 86.614 127 12 5 80 203 559300276 559300400 1.330000e-27 135.0
114 TraesCS7D01G148600 chrUn 96.471 85 2 1 120 203 40705719 40705803 1.030000e-28 139.0
115 TraesCS7D01G148600 chrUn 95.294 85 3 1 120 203 77149665 77149581 4.790000e-27 134.0
116 TraesCS7D01G148600 chrUn 86.607 112 10 5 4201 4311 446838125 446838232 1.340000e-22 119.0
117 TraesCS7D01G148600 chr2A 89.000 100 9 1 4186 4285 75527771 75527868 1.040000e-23 122.0
118 TraesCS7D01G148600 chr2A 86.364 110 15 0 4185 4294 67157596 67157705 3.730000e-23 121.0
119 TraesCS7D01G148600 chr2B 86.364 110 15 0 4185 4294 318767366 318767257 3.730000e-23 121.0
120 TraesCS7D01G148600 chr5B 92.857 70 5 0 6883 6952 202242176 202242107 1.350000e-17 102.0


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 TraesCS7D01G148600 chr7D 95857855 95865459 7604 False 14044.000000 14044 100.000000 1 7605 1 chr7D.!!$F1 7604
1 TraesCS7D01G148600 chr7D 600017583 600019073 1490 False 2054.000000 2054 91.589000 5394 6882 1 chr7D.!!$F6 1488
2 TraesCS7D01G148600 chr7D 399875912 399876769 857 False 1157.000000 1157 91.047000 4542 5397 1 chr7D.!!$F5 855
3 TraesCS7D01G148600 chr7D 95924169 95924820 651 False 1072.000000 1072 96.325000 6953 7605 1 chr7D.!!$F3 652
4 TraesCS7D01G148600 chr7D 636487638 636489062 1424 False 654.500000 985 84.168000 2399 4181 2 chr7D.!!$F7 1782
5 TraesCS7D01G148600 chr1D 246872571 246874050 1479 False 2215.000000 2215 93.628000 5394 6882 1 chr1D.!!$F3 1488
6 TraesCS7D01G148600 chr1D 331879935 331883406 3471 False 2103.333333 5803 87.138667 697 4181 3 chr1D.!!$F7 3484
7 TraesCS7D01G148600 chr1D 249755916 249759415 3499 False 2009.400000 5722 93.794667 696 4190 3 chr1D.!!$F6 3494
8 TraesCS7D01G148600 chr1D 339671689 339672556 867 False 1142.000000 1142 90.607000 4537 5397 1 chr1D.!!$F4 860
9 TraesCS7D01G148600 chr3D 546199819 546203285 3466 True 5699.000000 5699 96.286000 698 4182 1 chr3D.!!$R7 3484
10 TraesCS7D01G148600 chr3D 98390732 98392221 1489 False 2130.000000 2130 92.508000 5394 6882 1 chr3D.!!$F1 1488
11 TraesCS7D01G148600 chr3D 533930619 533931479 860 False 1144.000000 1144 90.856000 4546 5397 1 chr3D.!!$F2 851
12 TraesCS7D01G148600 chr3D 411175734 411176681 947 True 1110.000000 1110 88.075000 4459 5397 1 chr3D.!!$R6 938
13 TraesCS7D01G148600 chr3D 157570442 157571093 651 True 1077.000000 1077 96.478000 6953 7605 1 chr3D.!!$R3 652
14 TraesCS7D01G148600 chr3D 384125810 384126463 653 True 1074.000000 1074 96.330000 6953 7605 1 chr3D.!!$R5 652
15 TraesCS7D01G148600 chr3D 264385522 264386475 953 True 1070.000000 1070 87.161000 4459 5400 1 chr3D.!!$R4 941
16 TraesCS7D01G148600 chr5D 227248366 227249870 1504 False 2233.000000 2233 93.630000 5394 6882 1 chr5D.!!$F1 1488
17 TraesCS7D01G148600 chr5D 168580489 168581989 1500 True 2231.000000 2231 93.617000 5394 6885 1 chr5D.!!$R1 1491
18 TraesCS7D01G148600 chr5D 337736935 337738417 1482 False 1980.000000 1980 90.782000 5394 6882 1 chr5D.!!$F3 1488
19 TraesCS7D01G148600 chr5D 481128899 481131154 2255 True 1973.000000 3781 92.289000 1268 3501 2 chr5D.!!$R5 2233
20 TraesCS7D01G148600 chr5D 383524210 383524862 652 True 1068.000000 1068 96.172000 6953 7605 1 chr5D.!!$R2 652
21 TraesCS7D01G148600 chr7A 51666840 51670400 3560 True 1904.666667 2843 90.488667 699 4185 3 chr7A.!!$R2 3486
22 TraesCS7D01G148600 chr4D 322447255 322448742 1487 True 2148.000000 2148 92.757000 5397 6882 1 chr4D.!!$R2 1485
23 TraesCS7D01G148600 chr4D 304812374 304813026 652 False 1101.000000 1101 97.090000 6953 7605 1 chr4D.!!$F3 652
24 TraesCS7D01G148600 chr4D 304806385 304807037 652 False 1090.000000 1090 96.784000 6953 7605 1 chr4D.!!$F2 652
25 TraesCS7D01G148600 chr4D 397704347 397705013 666 False 1061.000000 1061 95.359000 6938 7605 1 chr4D.!!$F4 667
26 TraesCS7D01G148600 chr4D 373844263 373845003 740 True 468.000000 468 78.729000 2960 3708 1 chr4D.!!$R3 748
27 TraesCS7D01G148600 chr2D 155425893 155427380 1487 True 2128.000000 2128 92.493000 5394 6882 1 chr2D.!!$R1 1488
28 TraesCS7D01G148600 chr2D 164345223 164346093 870 False 1129.000000 1129 90.286000 4537 5397 1 chr2D.!!$F1 860
29 TraesCS7D01G148600 chr2D 635623219 635623871 652 False 1079.000000 1079 96.478000 6953 7605 1 chr2D.!!$F2 652
30 TraesCS7D01G148600 chr6D 293133777 293135265 1488 False 1997.000000 1997 90.909000 5394 6882 1 chr6D.!!$F2 1488
31 TraesCS7D01G148600 chr6D 202923225 202923877 652 True 1068.000000 1068 96.172000 6953 7605 1 chr6D.!!$R1 652
32 TraesCS7D01G148600 chr6D 148163322 148164947 1625 False 934.500000 1639 83.742000 2374 4180 2 chr6D.!!$F3 1806
33 TraesCS7D01G148600 chr6D 80062652 80064018 1366 True 542.333333 977 84.682667 2362 4016 3 chr6D.!!$R3 1654
34 TraesCS7D01G148600 chr3A 328338554 328340028 1474 True 1814.000000 1814 88.837000 5394 6891 1 chr3A.!!$R2 1497
35 TraesCS7D01G148600 chr5A 577019345 577020305 960 False 1160.000000 1160 88.728000 4452 5400 1 chr5A.!!$F2 948
36 TraesCS7D01G148600 chr5A 577180733 577181693 960 True 1149.000000 1149 88.521000 4452 5400 1 chr5A.!!$R2 948
37 TraesCS7D01G148600 chr5A 577329890 577330850 960 True 1144.000000 1144 88.418000 4452 5400 1 chr5A.!!$R3 948
38 TraesCS7D01G148600 chr5A 671978985 671980821 1836 True 562.833333 1072 84.846667 2294 4172 3 chr5A.!!$R4 1878
39 TraesCS7D01G148600 chr4A 4713199 4713877 678 False 715.000000 715 86.297000 1 660 1 chr4A.!!$F2 659
40 TraesCS7D01G148600 chr4A 157634410 157634935 525 False 712.000000 712 91.082000 1 527 1 chr4A.!!$F3 526
41 TraesCS7D01G148600 chr4A 4705693 4706274 581 False 682.000000 682 88.225000 1 571 1 chr4A.!!$F1 570
42 TraesCS7D01G148600 chr4A 696106508 696107818 1310 True 621.000000 935 84.121000 2402 4051 2 chr4A.!!$R1 1649
43 TraesCS7D01G148600 chr3B 543098484 543099693 1209 True 713.000000 713 77.984000 4200 5400 1 chr3B.!!$R2 1200
44 TraesCS7D01G148600 chr1A 19370535 19371168 633 False 573.000000 573 83.411000 3547 4174 1 chr1A.!!$F1 627
45 TraesCS7D01G148600 chr1A 19476920 19477553 633 False 573.000000 573 83.411000 3547 4174 1 chr1A.!!$F2 627

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
643 688 0.036732 TTCTGCCGCTTCAACCTGAT 59.963 50.000 0.00 0.00 0.00 2.90 F
672 717 0.039256 GGTCAGCAGCAAAATCGCAA 60.039 50.000 0.00 0.00 0.00 4.85 F
1188 1234 0.389166 CGCCAGCTCGAGAAAGTCTT 60.389 55.000 18.75 0.00 0.00 3.01 F
1970 2021 0.323908 TACATTTTTGCCCCCGGGAG 60.324 55.000 26.32 11.12 37.50 4.30 F
2390 3108 2.341168 CGTGACATGGCAATTTTTACGC 59.659 45.455 0.58 0.00 0.00 4.42 F
2398 3116 3.192422 TGGCAATTTTTACGCTGTAGCAT 59.808 39.130 4.59 0.00 42.21 3.79 F
4182 5065 1.046204 GGGTGTTATCGGGGTCCTAG 58.954 60.000 0.00 0.00 0.00 3.02 F
4406 5296 0.107214 GGCATGGCCTTGTAGTGCTA 60.107 55.000 19.05 0.00 46.69 3.49 F
5325 6251 0.172803 GTGGAGCTATTCGGTCGTGT 59.827 55.000 0.00 0.00 41.03 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2016 0.107831 TTCCAAGGTGTGTTCTCCCG 59.892 55.000 0.00 0.00 0.00 5.14 R
1970 2021 2.024414 AGCACTTTCCAAGGTGTGTTC 58.976 47.619 3.78 0.00 36.03 3.18 R
2705 3439 2.768253 TGCCATGGTCTACAGACAAG 57.232 50.000 14.67 0.82 46.47 3.16 R
3037 3802 7.141363 GCCATGATTCATTAACTAAATTCGCT 58.859 34.615 0.00 0.00 0.00 4.93 R
4028 4907 1.450312 CCTCGTTAGCTGGGCCTTG 60.450 63.158 4.53 0.00 0.00 3.61 R
4391 5281 1.281867 AGCAATAGCACTACAAGGCCA 59.718 47.619 5.01 0.00 45.49 5.36 R
5309 6235 0.454600 TGGACACGACCGAATAGCTC 59.545 55.000 0.00 0.00 0.00 4.09 R
5812 6739 0.834687 AGCTTACCAGTCCAACCCGA 60.835 55.000 0.00 0.00 0.00 5.14 R
6883 7844 0.040067 CGTTCCTGCCAAGTTGCTTC 60.040 55.000 0.00 0.00 0.00 3.86 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
48 49 1.129326 GTCTGTGACGAAGAACACGG 58.871 55.000 0.00 0.00 42.16 4.94
76 79 3.833645 CCTTCGTCGCCGGATCCA 61.834 66.667 13.41 0.00 33.95 3.41
203 206 1.725182 TCCTCTCCCCTCTTCCTTCTT 59.275 52.381 0.00 0.00 0.00 2.52
336 339 4.849329 GCGCAGTCGTAGGACCCG 62.849 72.222 11.83 14.86 44.54 5.28
339 342 1.153881 GCAGTCGTAGGACCCGAAC 60.154 63.158 11.83 0.00 44.54 3.95
360 363 2.280389 CTAGCCCATGCGCATCGT 60.280 61.111 22.51 7.73 44.33 3.73
571 590 2.043450 CTCCCCTGCTCCTCTCGT 60.043 66.667 0.00 0.00 0.00 4.18
572 591 2.043852 TCCCCTGCTCCTCTCGTC 60.044 66.667 0.00 0.00 0.00 4.20
573 592 3.151022 CCCCTGCTCCTCTCGTCC 61.151 72.222 0.00 0.00 0.00 4.79
574 593 3.151022 CCCTGCTCCTCTCGTCCC 61.151 72.222 0.00 0.00 0.00 4.46
575 594 2.043450 CCTGCTCCTCTCGTCCCT 60.043 66.667 0.00 0.00 0.00 4.20
576 595 2.422231 CCTGCTCCTCTCGTCCCTG 61.422 68.421 0.00 0.00 0.00 4.45
577 596 3.071206 TGCTCCTCTCGTCCCTGC 61.071 66.667 0.00 0.00 0.00 4.85
578 597 2.757917 GCTCCTCTCGTCCCTGCT 60.758 66.667 0.00 0.00 0.00 4.24
579 598 1.454111 GCTCCTCTCGTCCCTGCTA 60.454 63.158 0.00 0.00 0.00 3.49
580 599 1.730451 GCTCCTCTCGTCCCTGCTAC 61.730 65.000 0.00 0.00 0.00 3.58
581 600 1.076923 TCCTCTCGTCCCTGCTACC 60.077 63.158 0.00 0.00 0.00 3.18
582 601 1.076632 CCTCTCGTCCCTGCTACCT 60.077 63.158 0.00 0.00 0.00 3.08
583 602 1.388065 CCTCTCGTCCCTGCTACCTG 61.388 65.000 0.00 0.00 0.00 4.00
584 603 2.010582 CTCTCGTCCCTGCTACCTGC 62.011 65.000 0.00 0.00 43.25 4.85
585 604 2.037367 TCGTCCCTGCTACCTGCT 59.963 61.111 0.00 0.00 43.37 4.24
586 605 2.185350 CGTCCCTGCTACCTGCTG 59.815 66.667 0.00 0.00 43.37 4.41
587 606 2.124942 GTCCCTGCTACCTGCTGC 60.125 66.667 0.00 0.00 43.37 5.25
588 607 2.284921 TCCCTGCTACCTGCTGCT 60.285 61.111 0.00 0.00 43.37 4.24
612 631 3.191539 GCTCTGCCTGCACTACGC 61.192 66.667 0.00 0.00 42.89 4.42
621 666 3.854459 GCACTACGCCGCTTGCTC 61.854 66.667 0.00 0.00 38.05 4.26
631 676 4.157958 GCTTGCTCGCTTCTGCCG 62.158 66.667 0.00 0.00 35.36 5.69
643 688 0.036732 TTCTGCCGCTTCAACCTGAT 59.963 50.000 0.00 0.00 0.00 2.90
650 695 1.407437 CGCTTCAACCTGATTAGCCCT 60.407 52.381 0.00 0.00 28.90 5.19
653 698 3.539604 CTTCAACCTGATTAGCCCTCTG 58.460 50.000 0.00 0.00 0.00 3.35
654 699 1.839994 TCAACCTGATTAGCCCTCTGG 59.160 52.381 3.17 3.17 37.64 3.86
655 700 1.561542 CAACCTGATTAGCCCTCTGGT 59.438 52.381 4.21 4.21 44.13 4.00
656 701 1.501582 ACCTGATTAGCCCTCTGGTC 58.498 55.000 4.21 0.00 39.86 4.02
657 702 1.273838 ACCTGATTAGCCCTCTGGTCA 60.274 52.381 4.21 0.00 39.86 4.02
658 703 1.415659 CCTGATTAGCCCTCTGGTCAG 59.584 57.143 0.00 0.00 36.11 3.51
659 704 0.833287 TGATTAGCCCTCTGGTCAGC 59.167 55.000 0.00 0.00 0.00 4.26
660 705 0.833287 GATTAGCCCTCTGGTCAGCA 59.167 55.000 0.00 0.00 0.00 4.41
661 706 0.835941 ATTAGCCCTCTGGTCAGCAG 59.164 55.000 0.00 0.00 0.00 4.24
662 707 1.903877 TTAGCCCTCTGGTCAGCAGC 61.904 60.000 0.00 0.00 0.00 5.25
663 708 4.025858 GCCCTCTGGTCAGCAGCA 62.026 66.667 0.00 0.00 0.00 4.41
664 709 2.752358 CCCTCTGGTCAGCAGCAA 59.248 61.111 0.00 0.00 0.00 3.91
665 710 1.073722 CCCTCTGGTCAGCAGCAAA 59.926 57.895 0.00 0.00 0.00 3.68
666 711 0.538057 CCCTCTGGTCAGCAGCAAAA 60.538 55.000 0.00 0.00 0.00 2.44
667 712 1.542492 CCTCTGGTCAGCAGCAAAAT 58.458 50.000 0.00 0.00 0.00 1.82
668 713 1.471684 CCTCTGGTCAGCAGCAAAATC 59.528 52.381 0.00 0.00 0.00 2.17
669 714 1.129998 CTCTGGTCAGCAGCAAAATCG 59.870 52.381 0.00 0.00 0.00 3.34
670 715 0.455633 CTGGTCAGCAGCAAAATCGC 60.456 55.000 0.00 0.00 0.00 4.58
671 716 1.171549 TGGTCAGCAGCAAAATCGCA 61.172 50.000 0.00 0.00 0.00 5.10
672 717 0.039256 GGTCAGCAGCAAAATCGCAA 60.039 50.000 0.00 0.00 0.00 4.85
673 718 1.403249 GGTCAGCAGCAAAATCGCAAT 60.403 47.619 0.00 0.00 0.00 3.56
674 719 2.159393 GGTCAGCAGCAAAATCGCAATA 60.159 45.455 0.00 0.00 0.00 1.90
675 720 3.500982 GTCAGCAGCAAAATCGCAATAA 58.499 40.909 0.00 0.00 0.00 1.40
676 721 3.545078 GTCAGCAGCAAAATCGCAATAAG 59.455 43.478 0.00 0.00 0.00 1.73
677 722 3.191162 TCAGCAGCAAAATCGCAATAAGT 59.809 39.130 0.00 0.00 0.00 2.24
678 723 3.545078 CAGCAGCAAAATCGCAATAAGTC 59.455 43.478 0.00 0.00 0.00 3.01
679 724 3.191162 AGCAGCAAAATCGCAATAAGTCA 59.809 39.130 0.00 0.00 0.00 3.41
680 725 3.545078 GCAGCAAAATCGCAATAAGTCAG 59.455 43.478 0.00 0.00 0.00 3.51
681 726 4.100529 CAGCAAAATCGCAATAAGTCAGG 58.899 43.478 0.00 0.00 0.00 3.86
682 727 3.129287 AGCAAAATCGCAATAAGTCAGGG 59.871 43.478 0.00 0.00 0.00 4.45
683 728 3.734902 GCAAAATCGCAATAAGTCAGGGG 60.735 47.826 0.00 0.00 0.00 4.79
684 729 3.366052 AAATCGCAATAAGTCAGGGGT 57.634 42.857 0.00 0.00 0.00 4.95
685 730 3.366052 AATCGCAATAAGTCAGGGGTT 57.634 42.857 0.00 0.00 0.00 4.11
686 731 4.497291 AATCGCAATAAGTCAGGGGTTA 57.503 40.909 0.00 0.00 0.00 2.85
687 732 4.706842 ATCGCAATAAGTCAGGGGTTAT 57.293 40.909 0.00 0.00 0.00 1.89
688 733 4.067972 TCGCAATAAGTCAGGGGTTATC 57.932 45.455 0.00 0.00 0.00 1.75
689 734 3.452990 TCGCAATAAGTCAGGGGTTATCA 59.547 43.478 0.00 0.00 0.00 2.15
690 735 4.102524 TCGCAATAAGTCAGGGGTTATCAT 59.897 41.667 0.00 0.00 0.00 2.45
691 736 5.305902 TCGCAATAAGTCAGGGGTTATCATA 59.694 40.000 0.00 0.00 0.00 2.15
692 737 5.639506 CGCAATAAGTCAGGGGTTATCATAG 59.360 44.000 0.00 0.00 0.00 2.23
693 738 6.518369 CGCAATAAGTCAGGGGTTATCATAGA 60.518 42.308 0.00 0.00 0.00 1.98
694 739 7.398024 GCAATAAGTCAGGGGTTATCATAGAT 58.602 38.462 0.00 0.00 0.00 1.98
939 984 1.810151 CCCGACCACACAAATCGATTT 59.190 47.619 17.60 17.60 38.10 2.17
1075 1120 2.441164 AGCAGAGCCGTCTCCGAT 60.441 61.111 0.00 0.00 40.22 4.18
1112 1158 2.844839 GGCGCAGAGGGGGATAGT 60.845 66.667 10.83 0.00 0.00 2.12
1144 1190 3.910490 GCAAGGGTGTTGCGGCAA 61.910 61.111 12.11 12.11 35.58 4.52
1187 1233 1.214062 CGCCAGCTCGAGAAAGTCT 59.786 57.895 18.75 0.00 0.00 3.24
1188 1234 0.389166 CGCCAGCTCGAGAAAGTCTT 60.389 55.000 18.75 0.00 0.00 3.01
1230 1276 2.284478 AGGGAGAGAGCAGCAGCA 60.284 61.111 3.17 0.00 45.49 4.41
1522 1570 0.527817 CGCCGCCGTAAGAATCTCTT 60.528 55.000 0.00 0.00 40.35 2.85
1625 1673 7.231317 TGAACTAGGATTTCTGTTTCTTTGCAT 59.769 33.333 0.00 0.00 0.00 3.96
1875 1923 1.743772 GCAAGCGTCCTGTCCATATGT 60.744 52.381 1.24 0.00 0.00 2.29
1960 2010 2.983136 TGGCATTTCGCGTACATTTTTG 59.017 40.909 5.77 0.00 43.84 2.44
1965 2016 1.153920 CGCGTACATTTTTGCCCCC 60.154 57.895 0.00 0.00 0.00 5.40
1970 2021 0.323908 TACATTTTTGCCCCCGGGAG 60.324 55.000 26.32 11.12 37.50 4.30
2323 2433 3.595709 TTTTTCCGTAGCACGACAAAG 57.404 42.857 9.75 0.00 46.05 2.77
2389 3107 3.816091 TCGTGACATGGCAATTTTTACG 58.184 40.909 0.58 0.00 0.00 3.18
2390 3108 2.341168 CGTGACATGGCAATTTTTACGC 59.659 45.455 0.58 0.00 0.00 4.42
2398 3116 3.192422 TGGCAATTTTTACGCTGTAGCAT 59.808 39.130 4.59 0.00 42.21 3.79
2400 3118 4.031652 GGCAATTTTTACGCTGTAGCATTG 59.968 41.667 4.59 6.38 42.21 2.82
2402 3120 5.516339 GCAATTTTTACGCTGTAGCATTGAT 59.484 36.000 13.32 0.00 42.21 2.57
2403 3121 6.034898 GCAATTTTTACGCTGTAGCATTGATT 59.965 34.615 13.32 1.13 42.21 2.57
2404 3122 7.411804 GCAATTTTTACGCTGTAGCATTGATTT 60.412 33.333 13.32 0.00 42.21 2.17
2405 3123 8.434661 CAATTTTTACGCTGTAGCATTGATTTT 58.565 29.630 4.59 0.00 42.21 1.82
2407 3125 9.801873 ATTTTTACGCTGTAGCATTGATTTTAT 57.198 25.926 4.59 0.00 42.21 1.40
2409 3127 8.613613 TTTACGCTGTAGCATTGATTTTATTG 57.386 30.769 4.59 0.00 42.21 1.90
2410 3128 5.036737 ACGCTGTAGCATTGATTTTATTGC 58.963 37.500 4.59 0.00 42.21 3.56
2484 3216 5.047660 AGCCATGGCAAATTTAGTTAACGAA 60.048 36.000 37.18 0.00 44.88 3.85
2486 3218 6.237808 GCCATGGCAAATTTAGTTAACGAATG 60.238 38.462 32.08 0.00 41.49 2.67
2518 3250 9.651913 AAATTTAGTTAACGAATCATGGCAAAT 57.348 25.926 1.80 0.00 0.00 2.32
2536 3268 9.814899 ATGGCAAATTTATTTTCGTTGATCATA 57.185 25.926 0.00 0.00 0.00 2.15
2601 3334 6.012658 TCATGGCAAATTGTAGTTTCTCAC 57.987 37.500 0.00 0.00 0.00 3.51
2615 3348 8.598916 TGTAGTTTCTCACTAATTAACCATGGA 58.401 33.333 21.47 0.00 39.86 3.41
2621 3354 9.667107 TTCTCACTAATTAACCATGGAAACTAG 57.333 33.333 21.47 16.84 0.00 2.57
2622 3355 9.042450 TCTCACTAATTAACCATGGAAACTAGA 57.958 33.333 21.47 4.90 0.00 2.43
2623 3356 9.667107 CTCACTAATTAACCATGGAAACTAGAA 57.333 33.333 21.47 8.63 0.00 2.10
2633 3366 7.886338 ACCATGGAAACTAGAATTTTCACTTC 58.114 34.615 21.47 0.00 35.08 3.01
2651 3384 8.918202 TTCACTTCATCATGGTAAGTTTAGTT 57.082 30.769 0.00 0.00 31.21 2.24
2730 3464 4.832266 TGTCTGTAGACCATGGCAAATTTT 59.168 37.500 13.04 0.00 44.15 1.82
2904 3646 7.984002 TGTTTTTATCCGCATAACATGATTG 57.016 32.000 0.00 0.00 0.00 2.67
3037 3802 9.729023 CATGGCAAATTTAGTTAACGAATGATA 57.271 29.630 1.80 0.00 0.00 2.15
3040 3805 7.111593 GGCAAATTTAGTTAACGAATGATAGCG 59.888 37.037 1.80 0.00 0.00 4.26
3511 4340 4.684877 ACAAACGGAAAATTTACACCACC 58.315 39.130 0.00 0.00 0.00 4.61
3967 4841 6.090763 CAGTTGGGTTTTCTTCACTGTTTTTC 59.909 38.462 0.00 0.00 0.00 2.29
3968 4842 4.739195 TGGGTTTTCTTCACTGTTTTTCG 58.261 39.130 0.00 0.00 0.00 3.46
3969 4843 4.218852 TGGGTTTTCTTCACTGTTTTTCGT 59.781 37.500 0.00 0.00 0.00 3.85
3970 4844 4.561213 GGGTTTTCTTCACTGTTTTTCGTG 59.439 41.667 0.00 0.00 0.00 4.35
3983 4862 6.147000 ACTGTTTTTCGTGTTTTTCTGCATTT 59.853 30.769 0.00 0.00 0.00 2.32
4182 5065 1.046204 GGGTGTTATCGGGGTCCTAG 58.954 60.000 0.00 0.00 0.00 3.02
4188 5071 5.070847 GGTGTTATCGGGGTCCTAGATAAAA 59.929 44.000 15.99 11.10 38.21 1.52
4189 5072 6.408434 GGTGTTATCGGGGTCCTAGATAAAAA 60.408 42.308 15.99 8.87 38.21 1.94
4190 5073 7.222161 GTGTTATCGGGGTCCTAGATAAAAAT 58.778 38.462 15.99 0.00 38.21 1.82
4191 5074 7.172703 GTGTTATCGGGGTCCTAGATAAAAATG 59.827 40.741 15.99 0.00 38.21 2.32
4192 5075 7.071447 TGTTATCGGGGTCCTAGATAAAAATGA 59.929 37.037 15.99 0.00 38.21 2.57
4193 5076 6.704056 ATCGGGGTCCTAGATAAAAATGAT 57.296 37.500 0.00 0.00 0.00 2.45
4194 5077 5.865085 TCGGGGTCCTAGATAAAAATGATG 58.135 41.667 0.00 0.00 0.00 3.07
4195 5078 5.368523 TCGGGGTCCTAGATAAAAATGATGT 59.631 40.000 0.00 0.00 0.00 3.06
4196 5079 5.470098 CGGGGTCCTAGATAAAAATGATGTG 59.530 44.000 0.00 0.00 0.00 3.21
4197 5080 6.601332 GGGGTCCTAGATAAAAATGATGTGA 58.399 40.000 0.00 0.00 0.00 3.58
4198 5081 7.060421 GGGGTCCTAGATAAAAATGATGTGAA 58.940 38.462 0.00 0.00 0.00 3.18
4214 5097 5.303333 TGATGTGAACAGGTAGTACACTTGA 59.697 40.000 12.25 0.00 37.65 3.02
4218 5101 5.462398 GTGAACAGGTAGTACACTTGACAAG 59.538 44.000 13.77 13.77 37.65 3.16
4221 5104 4.238514 CAGGTAGTACACTTGACAAGCTC 58.761 47.826 15.24 3.68 36.35 4.09
4224 5107 3.838244 AGTACACTTGACAAGCTCCAA 57.162 42.857 15.24 0.00 0.00 3.53
4225 5108 3.733337 AGTACACTTGACAAGCTCCAAG 58.267 45.455 15.24 16.93 43.84 3.61
4234 5117 4.973168 TGACAAGCTCCAAGTTACTTCAT 58.027 39.130 0.00 0.00 0.00 2.57
4236 5119 5.239306 TGACAAGCTCCAAGTTACTTCATTG 59.761 40.000 0.00 0.00 0.00 2.82
4240 5123 3.125316 GCTCCAAGTTACTTCATTGGACG 59.875 47.826 1.84 1.33 45.76 4.79
4245 5128 6.488683 TCCAAGTTACTTCATTGGACGAAATT 59.511 34.615 1.84 0.00 45.76 1.82
4248 5131 7.504924 AGTTACTTCATTGGACGAAATTCAA 57.495 32.000 0.00 0.00 0.00 2.69
4249 5132 7.936584 AGTTACTTCATTGGACGAAATTCAAA 58.063 30.769 0.00 0.00 0.00 2.69
4251 5134 9.834628 GTTACTTCATTGGACGAAATTCAAATA 57.165 29.630 0.00 0.00 0.00 1.40
4252 5135 9.834628 TTACTTCATTGGACGAAATTCAAATAC 57.165 29.630 0.00 0.00 0.00 1.89
4253 5136 7.021196 ACTTCATTGGACGAAATTCAAATACG 58.979 34.615 0.00 0.00 0.00 3.06
4254 5137 6.729391 TCATTGGACGAAATTCAAATACGA 57.271 33.333 0.00 0.00 0.00 3.43
4300 5183 9.683069 AAATGACAAAAAGCTATGTTCTGTTAG 57.317 29.630 0.00 0.00 0.00 2.34
4301 5184 7.801716 TGACAAAAAGCTATGTTCTGTTAGT 57.198 32.000 0.00 0.00 0.00 2.24
4302 5185 8.220755 TGACAAAAAGCTATGTTCTGTTAGTT 57.779 30.769 0.00 0.00 0.00 2.24
4303 5186 8.128582 TGACAAAAAGCTATGTTCTGTTAGTTG 58.871 33.333 0.00 0.00 0.00 3.16
4304 5187 8.220755 ACAAAAAGCTATGTTCTGTTAGTTGA 57.779 30.769 0.00 0.00 0.00 3.18
4305 5188 8.682710 ACAAAAAGCTATGTTCTGTTAGTTGAA 58.317 29.630 0.00 0.00 0.00 2.69
4306 5189 9.173939 CAAAAAGCTATGTTCTGTTAGTTGAAG 57.826 33.333 0.00 0.00 0.00 3.02
4319 5202 7.083875 TGTTAGTTGAAGAACAGAAAACCAG 57.916 36.000 0.00 0.00 34.17 4.00
4320 5203 6.882140 TGTTAGTTGAAGAACAGAAAACCAGA 59.118 34.615 0.00 0.00 34.17 3.86
4321 5204 7.556275 TGTTAGTTGAAGAACAGAAAACCAGAT 59.444 33.333 0.00 0.00 34.17 2.90
4323 5206 9.793259 TTAGTTGAAGAACAGAAAACCAGATAT 57.207 29.630 0.00 0.00 34.17 1.63
4325 5208 9.965902 AGTTGAAGAACAGAAAACCAGATATAT 57.034 29.630 0.00 0.00 34.17 0.86
4328 5211 8.677300 TGAAGAACAGAAAACCAGATATATTGC 58.323 33.333 0.00 0.00 0.00 3.56
4329 5212 7.573968 AGAACAGAAAACCAGATATATTGCC 57.426 36.000 0.00 0.00 0.00 4.52
4330 5213 7.118723 AGAACAGAAAACCAGATATATTGCCA 58.881 34.615 0.00 0.00 0.00 4.92
4368 5258 7.287810 AGTAGAAAATGAACAAGTTACAGGGT 58.712 34.615 0.00 0.00 0.00 4.34
4369 5259 6.635030 AGAAAATGAACAAGTTACAGGGTC 57.365 37.500 0.00 0.00 0.00 4.46
4385 5275 1.971167 GTCCTGGCGTGCCATCAAA 60.971 57.895 15.00 0.00 46.15 2.69
4386 5276 1.675310 TCCTGGCGTGCCATCAAAG 60.675 57.895 15.00 1.87 46.15 2.77
4388 5278 2.676121 TGGCGTGCCATCAAAGGG 60.676 61.111 10.06 0.00 41.89 3.95
4405 5295 1.379044 GGCATGGCCTTGTAGTGCT 60.379 57.895 19.05 0.00 46.69 4.40
4406 5296 0.107214 GGCATGGCCTTGTAGTGCTA 60.107 55.000 19.05 0.00 46.69 3.49
4407 5297 1.477558 GGCATGGCCTTGTAGTGCTAT 60.478 52.381 19.05 0.00 46.69 2.97
4408 5298 2.301346 GCATGGCCTTGTAGTGCTATT 58.699 47.619 19.05 0.00 33.25 1.73
4409 5299 2.033801 GCATGGCCTTGTAGTGCTATTG 59.966 50.000 19.05 0.00 33.25 1.90
4410 5300 1.750193 TGGCCTTGTAGTGCTATTGC 58.250 50.000 3.32 0.00 40.20 3.56
4411 5301 1.281867 TGGCCTTGTAGTGCTATTGCT 59.718 47.619 3.32 0.00 40.48 3.91
4412 5302 1.672881 GGCCTTGTAGTGCTATTGCTG 59.327 52.381 0.00 0.00 40.48 4.41
4414 5304 3.531538 GCCTTGTAGTGCTATTGCTGTA 58.468 45.455 0.00 0.00 40.48 2.74
4417 5307 5.046529 CCTTGTAGTGCTATTGCTGTAGAG 58.953 45.833 0.00 0.00 40.48 2.43
4418 5308 5.394663 CCTTGTAGTGCTATTGCTGTAGAGT 60.395 44.000 0.00 0.00 40.48 3.24
4421 5311 7.165460 TGTAGTGCTATTGCTGTAGAGTAAA 57.835 36.000 0.00 0.00 40.48 2.01
4423 5313 6.969828 AGTGCTATTGCTGTAGAGTAAAAC 57.030 37.500 0.00 0.00 40.48 2.43
4424 5314 6.464222 AGTGCTATTGCTGTAGAGTAAAACA 58.536 36.000 0.00 0.00 40.48 2.83
4425 5315 6.369065 AGTGCTATTGCTGTAGAGTAAAACAC 59.631 38.462 10.73 10.73 40.48 3.32
4426 5316 6.369065 GTGCTATTGCTGTAGAGTAAAACACT 59.631 38.462 0.00 0.00 39.26 3.55
4454 5344 6.679843 AGAAAGTGTCTCCTTTAGAACTACG 58.320 40.000 0.00 0.00 35.47 3.51
4457 5347 4.701171 AGTGTCTCCTTTAGAACTACGGAG 59.299 45.833 14.80 14.80 42.00 4.63
4491 5381 4.051237 GCCTTTGAAAAACAGCTAAGTGG 58.949 43.478 0.00 0.00 0.00 4.00
4505 5400 6.970484 CAGCTAAGTGGTGTTAAAACTGAAT 58.030 36.000 0.00 0.00 39.17 2.57
4523 5418 6.276847 ACTGAATAATTCTCAGACTTAGCCG 58.723 40.000 19.35 0.00 42.51 5.52
4534 5429 2.572104 AGACTTAGCCGATTTTCAGGGT 59.428 45.455 0.00 0.00 41.59 4.34
4625 5524 6.882610 TGTACATGAAAGTTGCTCAGAATT 57.117 33.333 0.00 0.00 0.00 2.17
4626 5525 7.275888 TGTACATGAAAGTTGCTCAGAATTT 57.724 32.000 0.00 0.00 0.00 1.82
4637 5536 4.245660 TGCTCAGAATTTCGAGACGAATT 58.754 39.130 16.93 1.99 45.28 2.17
4713 5613 1.904287 TCCCTTTCCGGTCATTTGTG 58.096 50.000 0.00 0.00 0.00 3.33
4769 5669 3.951563 TGAATTCCCCCTTCACCTATG 57.048 47.619 2.27 0.00 0.00 2.23
4845 5746 5.178067 GCTTTGTGATGCTATGTTTGCTTTT 59.822 36.000 0.00 0.00 0.00 2.27
4849 5750 9.920133 TTTGTGATGCTATGTTTGCTTTTATAA 57.080 25.926 0.00 0.00 0.00 0.98
4875 5776 5.388599 TTGTTTCTTTCCCCTCTTCTCTT 57.611 39.130 0.00 0.00 0.00 2.85
4886 5787 2.357361 CCTCTTCTCTTCGGTAGACCCT 60.357 54.545 0.00 0.00 0.00 4.34
4936 5844 1.325355 TCGACAACGACCCTTCTTCT 58.675 50.000 0.00 0.00 43.81 2.85
4985 5895 3.264193 CCCCTTTGATCATCCCGATATCA 59.736 47.826 3.12 0.00 33.17 2.15
4990 5900 2.833943 TGATCATCCCGATATCACCCAG 59.166 50.000 3.12 0.00 33.17 4.45
5004 5914 3.994317 TCACCCAGTCCATTCTCTCATA 58.006 45.455 0.00 0.00 0.00 2.15
5015 5925 6.426328 GTCCATTCTCTCATACTTGCATTAGG 59.574 42.308 0.00 0.00 0.00 2.69
5137 6050 5.431765 GTTGGTTAGTGATCCATCAGTGAT 58.568 41.667 0.00 0.00 40.49 3.06
5309 6235 3.515502 TCCTGATGAGGTCTTTGTAGTGG 59.484 47.826 0.00 0.00 40.76 4.00
5325 6251 0.172803 GTGGAGCTATTCGGTCGTGT 59.827 55.000 0.00 0.00 41.03 4.49
5326 6252 0.454600 TGGAGCTATTCGGTCGTGTC 59.545 55.000 0.00 0.00 41.03 3.67
5490 6416 6.403200 CGGATACTTGGACTTTACCATTGTTG 60.403 42.308 0.00 0.00 39.82 3.33
5671 6597 1.841663 CTGCTTGTTACCGCGTGCTT 61.842 55.000 4.92 0.00 0.00 3.91
5805 6732 3.310253 GACGTCAGCGACTGAGCGA 62.310 63.158 23.47 2.28 41.46 4.93
5806 6733 2.101185 CGTCAGCGACTGAGCGAT 59.899 61.111 17.58 0.00 41.46 4.58
5977 6905 1.648116 TTAAGCCTAGGTCGGGTTGT 58.352 50.000 11.31 0.00 43.99 3.32
6068 6996 0.694196 GGTAAGTTGGTGCACCCCTA 59.306 55.000 32.62 15.50 34.29 3.53
6071 6999 0.777446 AAGTTGGTGCACCCCTACAT 59.223 50.000 32.62 17.44 33.34 2.29
6088 7016 7.062957 CCCCTACATGGAAGAAAACATCTATT 58.937 38.462 0.00 0.00 37.42 1.73
6153 7081 5.206299 CGATCGATACAACTAGAACTGGAC 58.794 45.833 10.26 0.00 0.00 4.02
6197 7125 0.677731 TGGCTCTGGGATTGCTTTCG 60.678 55.000 0.00 0.00 0.00 3.46
6244 7175 2.093869 GGCCGAGGTTGATAACACTACA 60.094 50.000 0.00 0.00 0.00 2.74
6428 7366 1.661112 GTGTAGATCCTTGCTTGCGAC 59.339 52.381 0.00 0.00 0.00 5.19
6476 7417 1.000486 GCTCCCCCTTTCCCCTTTC 60.000 63.158 0.00 0.00 0.00 2.62
6488 7429 2.642982 TCCCCTTTCCCATTCTTCTCA 58.357 47.619 0.00 0.00 0.00 3.27
6556 7497 2.926200 GACGACGACTGCTACTACACTA 59.074 50.000 0.00 0.00 0.00 2.74
6652 7596 5.221880 CCTTTTCGATCATGTTGCTTTTGA 58.778 37.500 0.00 0.00 0.00 2.69
6658 7602 4.093998 CGATCATGTTGCTTTTGAGCTAGT 59.906 41.667 0.00 0.00 35.49 2.57
6669 7613 5.935206 GCTTTTGAGCTAGTCTTCTTAAGGT 59.065 40.000 1.85 0.00 0.00 3.50
6713 7657 7.394016 TCTGTACTCAGATATTTTTGCTTCCA 58.606 34.615 0.00 0.00 44.58 3.53
6715 7659 6.939730 TGTACTCAGATATTTTTGCTTCCACA 59.060 34.615 0.00 0.00 0.00 4.17
6819 7780 2.357952 TGTGATATCTTCCCGTGAGTCG 59.642 50.000 3.98 0.00 39.52 4.18
6867 7828 7.377662 TGCGTGTATTATTAGTGTACGATTGAG 59.622 37.037 0.00 0.00 32.36 3.02
6882 7843 1.532604 TTGAGTCGAGGGCGTCACAT 61.533 55.000 8.06 0.00 38.98 3.21
6883 7844 1.517257 GAGTCGAGGGCGTCACATG 60.517 63.158 8.06 0.00 38.98 3.21
6884 7845 1.934220 GAGTCGAGGGCGTCACATGA 61.934 60.000 8.06 0.00 38.98 3.07
6893 7854 1.678360 GCGTCACATGAAGCAACTTG 58.322 50.000 13.89 0.00 46.36 3.16
6894 7855 1.664016 GCGTCACATGAAGCAACTTGG 60.664 52.381 13.89 0.00 46.36 3.61
6895 7856 1.664016 CGTCACATGAAGCAACTTGGC 60.664 52.381 0.00 0.00 0.00 4.52
6896 7857 1.337703 GTCACATGAAGCAACTTGGCA 59.662 47.619 0.00 0.00 35.83 4.92
6897 7858 1.610038 TCACATGAAGCAACTTGGCAG 59.390 47.619 0.00 0.00 35.83 4.85
6898 7859 0.963962 ACATGAAGCAACTTGGCAGG 59.036 50.000 0.00 0.00 35.83 4.85
6899 7860 1.250328 CATGAAGCAACTTGGCAGGA 58.750 50.000 2.65 0.00 35.83 3.86
6900 7861 1.614903 CATGAAGCAACTTGGCAGGAA 59.385 47.619 2.65 0.00 35.83 3.36
6901 7862 1.032014 TGAAGCAACTTGGCAGGAAC 58.968 50.000 2.65 0.00 35.83 3.62
6902 7863 0.040067 GAAGCAACTTGGCAGGAACG 60.040 55.000 2.65 0.00 35.83 3.95
6903 7864 2.050077 GCAACTTGGCAGGAACGC 60.050 61.111 2.65 0.00 0.00 4.84
6911 7872 2.045926 GCAGGAACGCCCATGTCT 60.046 61.111 0.00 0.00 37.41 3.41
6912 7873 1.220749 GCAGGAACGCCCATGTCTA 59.779 57.895 0.00 0.00 37.41 2.59
6913 7874 0.179045 GCAGGAACGCCCATGTCTAT 60.179 55.000 0.00 0.00 37.41 1.98
6914 7875 1.586422 CAGGAACGCCCATGTCTATG 58.414 55.000 0.00 0.00 37.41 2.23
6915 7876 1.134401 CAGGAACGCCCATGTCTATGT 60.134 52.381 0.00 0.00 37.41 2.29
6916 7877 1.134401 AGGAACGCCCATGTCTATGTG 60.134 52.381 0.00 0.00 37.41 3.21
6917 7878 1.299541 GAACGCCCATGTCTATGTGG 58.700 55.000 0.00 0.00 35.22 4.17
6918 7879 0.908910 AACGCCCATGTCTATGTGGA 59.091 50.000 0.00 0.00 37.72 4.02
6919 7880 1.131638 ACGCCCATGTCTATGTGGAT 58.868 50.000 0.00 0.00 37.72 3.41
6920 7881 1.202687 ACGCCCATGTCTATGTGGATG 60.203 52.381 0.00 0.00 37.72 3.51
6921 7882 1.070601 CGCCCATGTCTATGTGGATGA 59.929 52.381 0.00 0.00 37.72 2.92
6922 7883 2.498167 GCCCATGTCTATGTGGATGAC 58.502 52.381 0.00 0.00 37.72 3.06
6923 7884 2.158769 GCCCATGTCTATGTGGATGACA 60.159 50.000 0.00 0.00 43.53 3.58
6925 7886 4.263025 GCCCATGTCTATGTGGATGACATA 60.263 45.833 7.39 0.00 45.95 2.29
6935 7896 6.560003 ATGTGGATGACATAGTGGTAAAGA 57.440 37.500 0.00 0.00 43.96 2.52
6936 7897 5.730550 TGTGGATGACATAGTGGTAAAGAC 58.269 41.667 0.00 0.00 0.00 3.01
6937 7898 4.804139 GTGGATGACATAGTGGTAAAGACG 59.196 45.833 0.00 0.00 0.00 4.18
6938 7899 4.142026 TGGATGACATAGTGGTAAAGACGG 60.142 45.833 0.00 0.00 0.00 4.79
6939 7900 4.098960 GGATGACATAGTGGTAAAGACGGA 59.901 45.833 0.00 0.00 0.00 4.69
6940 7901 4.713824 TGACATAGTGGTAAAGACGGAG 57.286 45.455 0.00 0.00 0.00 4.63
6941 7902 4.338012 TGACATAGTGGTAAAGACGGAGA 58.662 43.478 0.00 0.00 0.00 3.71
6942 7903 4.768448 TGACATAGTGGTAAAGACGGAGAA 59.232 41.667 0.00 0.00 0.00 2.87
6943 7904 5.105877 TGACATAGTGGTAAAGACGGAGAAG 60.106 44.000 0.00 0.00 0.00 2.85
6944 7905 2.745515 AGTGGTAAAGACGGAGAAGC 57.254 50.000 0.00 0.00 0.00 3.86
6945 7906 1.067776 AGTGGTAAAGACGGAGAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
6946 7907 0.389426 TGGTAAAGACGGAGAAGCGC 60.389 55.000 0.00 0.00 0.00 5.92
6947 7908 1.411493 GGTAAAGACGGAGAAGCGCG 61.411 60.000 0.00 0.00 0.00 6.86
6948 7909 1.153901 TAAAGACGGAGAAGCGCGG 60.154 57.895 8.83 0.00 0.00 6.46
7017 7978 4.411256 AAGTAAGAGTGTCGAACCCAAA 57.589 40.909 0.00 0.00 0.00 3.28
7065 8026 2.761208 CCCTCAAGTTCTATCGACCACT 59.239 50.000 0.00 0.00 0.00 4.00
7082 8043 3.447586 ACCACTGATACAACTCTACGCAT 59.552 43.478 0.00 0.00 0.00 4.73
7151 8112 6.489022 ACTTTGTAGGTGTTTTTGGATAGGTC 59.511 38.462 0.00 0.00 0.00 3.85
7157 8118 4.220602 GGTGTTTTTGGATAGGTCTGCAAT 59.779 41.667 0.00 0.00 0.00 3.56
7370 8332 8.701908 ATCATATGCACTTATGATTGGAACTT 57.298 30.769 14.44 0.00 43.52 2.66
7441 8403 6.040166 CCATAGCATTAAAGCATCAAGTCCTT 59.960 38.462 5.36 0.00 36.85 3.36
7486 8448 3.628487 CCTTACTCGGGTTTGTGTTTCAA 59.372 43.478 0.00 0.00 0.00 2.69
7499 8461 3.127721 TGTGTTTCAATCACTCACGCAAA 59.872 39.130 0.41 0.00 36.83 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 284 1.081376 AGTCGAACTTGACGGCGAG 60.081 57.895 16.62 3.14 43.70 5.03
325 328 3.803082 CGCGTTCGGGTCCTACGA 61.803 66.667 13.43 1.63 37.47 3.43
336 339 3.941836 GCATGGGCTAGCGCGTTC 61.942 66.667 22.76 15.27 36.88 3.95
552 571 3.535962 GAGAGGAGCAGGGGAGCG 61.536 72.222 0.00 0.00 40.15 5.03
561 580 1.454111 TAGCAGGGACGAGAGGAGC 60.454 63.158 0.00 0.00 0.00 4.70
565 584 2.010582 GCAGGTAGCAGGGACGAGAG 62.011 65.000 0.00 0.00 44.79 3.20
577 596 4.463879 AGCGGCAGCAGCAGGTAG 62.464 66.667 20.27 0.00 44.63 3.18
578 597 4.765449 CAGCGGCAGCAGCAGGTA 62.765 66.667 20.27 0.00 44.66 3.08
593 612 1.808799 CGTAGTGCAGGCAGAGCAG 60.809 63.158 0.00 0.00 43.63 4.24
612 631 4.157958 GCAGAAGCGAGCAAGCGG 62.158 66.667 0.00 0.00 43.00 5.52
621 666 2.174349 GTTGAAGCGGCAGAAGCG 59.826 61.111 1.45 0.00 43.41 4.68
631 676 2.092699 AGAGGGCTAATCAGGTTGAAGC 60.093 50.000 0.00 0.00 31.30 3.86
643 688 1.903877 GCTGCTGACCAGAGGGCTAA 61.904 60.000 0.47 0.00 44.64 3.09
650 695 1.159285 CGATTTTGCTGCTGACCAGA 58.841 50.000 0.00 0.00 44.64 3.86
653 698 0.039256 TTGCGATTTTGCTGCTGACC 60.039 50.000 0.00 0.00 35.36 4.02
654 699 1.986698 ATTGCGATTTTGCTGCTGAC 58.013 45.000 0.00 0.00 35.36 3.51
655 700 3.191162 ACTTATTGCGATTTTGCTGCTGA 59.809 39.130 0.00 0.00 35.36 4.26
656 701 3.504863 ACTTATTGCGATTTTGCTGCTG 58.495 40.909 0.00 0.00 35.36 4.41
657 702 3.191162 TGACTTATTGCGATTTTGCTGCT 59.809 39.130 0.00 0.00 35.36 4.24
658 703 3.500982 TGACTTATTGCGATTTTGCTGC 58.499 40.909 0.00 0.00 35.36 5.25
659 704 4.100529 CCTGACTTATTGCGATTTTGCTG 58.899 43.478 0.00 0.00 35.36 4.41
660 705 3.129287 CCCTGACTTATTGCGATTTTGCT 59.871 43.478 0.00 0.00 35.36 3.91
661 706 3.438360 CCCTGACTTATTGCGATTTTGC 58.562 45.455 0.00 0.00 0.00 3.68
662 707 3.443681 ACCCCTGACTTATTGCGATTTTG 59.556 43.478 0.00 0.00 0.00 2.44
663 708 3.697166 ACCCCTGACTTATTGCGATTTT 58.303 40.909 0.00 0.00 0.00 1.82
664 709 3.366052 ACCCCTGACTTATTGCGATTT 57.634 42.857 0.00 0.00 0.00 2.17
665 710 3.366052 AACCCCTGACTTATTGCGATT 57.634 42.857 0.00 0.00 0.00 3.34
666 711 4.102524 TGATAACCCCTGACTTATTGCGAT 59.897 41.667 0.00 0.00 0.00 4.58
667 712 3.452990 TGATAACCCCTGACTTATTGCGA 59.547 43.478 0.00 0.00 0.00 5.10
668 713 3.804036 TGATAACCCCTGACTTATTGCG 58.196 45.455 0.00 0.00 0.00 4.85
669 714 6.769512 TCTATGATAACCCCTGACTTATTGC 58.230 40.000 0.00 0.00 0.00 3.56
673 718 8.582437 CGTTTATCTATGATAACCCCTGACTTA 58.418 37.037 0.11 0.00 0.00 2.24
674 719 7.442656 CGTTTATCTATGATAACCCCTGACTT 58.557 38.462 0.11 0.00 0.00 3.01
675 720 6.014499 CCGTTTATCTATGATAACCCCTGACT 60.014 42.308 0.11 0.00 0.00 3.41
676 721 6.014840 TCCGTTTATCTATGATAACCCCTGAC 60.015 42.308 0.11 0.00 0.00 3.51
677 722 6.079336 TCCGTTTATCTATGATAACCCCTGA 58.921 40.000 0.11 0.00 0.00 3.86
678 723 6.354794 TCCGTTTATCTATGATAACCCCTG 57.645 41.667 0.11 0.00 0.00 4.45
679 724 7.147444 TGTTTCCGTTTATCTATGATAACCCCT 60.147 37.037 0.11 0.00 0.00 4.79
680 725 6.993902 TGTTTCCGTTTATCTATGATAACCCC 59.006 38.462 0.11 0.00 0.00 4.95
681 726 8.441312 TTGTTTCCGTTTATCTATGATAACCC 57.559 34.615 0.11 0.00 0.00 4.11
686 731 8.280497 GCGTTATTGTTTCCGTTTATCTATGAT 58.720 33.333 0.00 0.00 0.00 2.45
687 732 7.254522 GGCGTTATTGTTTCCGTTTATCTATGA 60.255 37.037 0.00 0.00 0.00 2.15
688 733 6.849305 GGCGTTATTGTTTCCGTTTATCTATG 59.151 38.462 0.00 0.00 0.00 2.23
689 734 6.017687 GGGCGTTATTGTTTCCGTTTATCTAT 60.018 38.462 0.00 0.00 0.00 1.98
690 735 5.294060 GGGCGTTATTGTTTCCGTTTATCTA 59.706 40.000 0.00 0.00 0.00 1.98
691 736 4.095334 GGGCGTTATTGTTTCCGTTTATCT 59.905 41.667 0.00 0.00 0.00 1.98
692 737 4.345288 GGGCGTTATTGTTTCCGTTTATC 58.655 43.478 0.00 0.00 0.00 1.75
693 738 3.181508 CGGGCGTTATTGTTTCCGTTTAT 60.182 43.478 0.00 0.00 33.63 1.40
694 739 2.159234 CGGGCGTTATTGTTTCCGTTTA 59.841 45.455 0.00 0.00 33.63 2.01
869 914 7.617723 AGTCTAGAAATGGATAGTGAAGTGAGT 59.382 37.037 0.00 0.00 0.00 3.41
871 916 7.962995 AGTCTAGAAATGGATAGTGAAGTGA 57.037 36.000 0.00 0.00 0.00 3.41
939 984 2.668632 GCGATCTGGTTGGGGTGA 59.331 61.111 0.00 0.00 0.00 4.02
1075 1120 2.571757 CCTCTTAGACACGCCGCA 59.428 61.111 0.00 0.00 0.00 5.69
1129 1175 3.223589 GGTTGCCGCAACACCCTT 61.224 61.111 31.72 0.00 45.11 3.95
1144 1190 3.461773 CGAGATCCGTGGGCAGGT 61.462 66.667 0.00 0.00 0.00 4.00
1474 1522 1.194121 AAGGGGTTAACGTACCGGCT 61.194 55.000 0.00 0.00 39.18 5.52
1522 1570 2.684001 AGGTGTGACTCGTTCAAACA 57.316 45.000 10.85 0.00 43.66 2.83
1625 1673 6.840780 TCGATCAAGATGCTATGGAATCTA 57.159 37.500 0.00 0.00 36.86 1.98
1960 2010 4.717313 GTGTGTTCTCCCGGGGGC 62.717 72.222 23.50 5.69 34.68 5.80
1965 2016 0.107831 TTCCAAGGTGTGTTCTCCCG 59.892 55.000 0.00 0.00 0.00 5.14
1970 2021 2.024414 AGCACTTTCCAAGGTGTGTTC 58.976 47.619 3.78 0.00 36.03 3.18
2389 3107 5.350633 TGGCAATAAAATCAATGCTACAGC 58.649 37.500 0.00 0.00 38.79 4.40
2390 3108 6.422701 CCATGGCAATAAAATCAATGCTACAG 59.577 38.462 0.00 0.00 38.79 2.74
2409 3127 6.257423 GCAATAAAAGTAAATTTGCCATGGC 58.743 36.000 30.54 30.54 37.34 4.40
2439 3169 5.811613 GGCTGTTTGCTAATAATTGCAATCA 59.188 36.000 13.38 0.00 46.55 2.57
2443 3173 4.797800 TGGCTGTTTGCTAATAATTGCA 57.202 36.364 0.00 0.00 42.39 4.08
2461 3193 4.739195 TCGTTAACTAAATTTGCCATGGC 58.261 39.130 30.54 30.54 42.35 4.40
2484 3216 8.465999 TGATTCGTTAACTAAATTTGCCATCAT 58.534 29.630 3.71 0.00 0.00 2.45
2486 3218 8.745837 CATGATTCGTTAACTAAATTTGCCATC 58.254 33.333 3.71 0.00 0.00 3.51
2564 3297 9.976511 CAATTTGCCATGATCTATGAACTAAAT 57.023 29.630 0.00 0.00 39.21 1.40
2576 3309 6.749118 GTGAGAAACTACAATTTGCCATGATC 59.251 38.462 0.00 0.00 0.00 2.92
2615 3348 9.082313 ACCATGATGAAGTGAAAATTCTAGTTT 57.918 29.630 0.00 0.00 42.30 2.66
2620 3353 8.641498 ACTTACCATGATGAAGTGAAAATTCT 57.359 30.769 0.00 0.00 42.30 2.40
2621 3354 9.696917 AAACTTACCATGATGAAGTGAAAATTC 57.303 29.630 0.00 0.00 42.13 2.17
2705 3439 2.768253 TGCCATGGTCTACAGACAAG 57.232 50.000 14.67 0.82 46.47 3.16
2730 3464 6.587990 CCAAATATAAATTGTTGTGGTCGCAA 59.412 34.615 0.00 0.00 0.00 4.85
2904 3646 7.158697 AGTAAAAATTGCCATGTTCCTAAACC 58.841 34.615 0.00 0.00 34.28 3.27
2987 3729 8.354711 TGGTTGTTTGCTAATAATTACCATCA 57.645 30.769 0.00 0.00 0.00 3.07
3037 3802 7.141363 GCCATGATTCATTAACTAAATTCGCT 58.859 34.615 0.00 0.00 0.00 4.93
3749 4602 8.491331 AATAAATTGCCATGGTTTGTATGAAC 57.509 30.769 14.67 0.00 0.00 3.18
4028 4907 1.450312 CCTCGTTAGCTGGGCCTTG 60.450 63.158 4.53 0.00 0.00 3.61
4188 5071 6.360370 AGTGTACTACCTGTTCACATCATT 57.640 37.500 7.94 0.00 45.52 2.57
4189 5072 6.014584 TCAAGTGTACTACCTGTTCACATCAT 60.015 38.462 7.94 0.00 45.52 2.45
4190 5073 5.303333 TCAAGTGTACTACCTGTTCACATCA 59.697 40.000 7.94 0.00 45.52 3.07
4191 5074 5.634020 GTCAAGTGTACTACCTGTTCACATC 59.366 44.000 7.94 0.00 45.52 3.06
4192 5075 5.069914 TGTCAAGTGTACTACCTGTTCACAT 59.930 40.000 7.94 0.00 45.52 3.21
4193 5076 4.403113 TGTCAAGTGTACTACCTGTTCACA 59.597 41.667 7.94 0.00 45.52 3.58
4194 5077 4.940463 TGTCAAGTGTACTACCTGTTCAC 58.060 43.478 0.00 0.00 44.11 3.18
4195 5078 5.597806 CTTGTCAAGTGTACTACCTGTTCA 58.402 41.667 4.27 0.00 0.00 3.18
4196 5079 4.448060 GCTTGTCAAGTGTACTACCTGTTC 59.552 45.833 14.03 0.00 0.00 3.18
4197 5080 4.101119 AGCTTGTCAAGTGTACTACCTGTT 59.899 41.667 14.03 0.00 0.00 3.16
4198 5081 3.641906 AGCTTGTCAAGTGTACTACCTGT 59.358 43.478 14.03 0.00 0.00 4.00
4214 5097 4.520492 CCAATGAAGTAACTTGGAGCTTGT 59.480 41.667 0.00 0.00 41.61 3.16
4218 5101 3.125316 CGTCCAATGAAGTAACTTGGAGC 59.875 47.826 3.59 0.00 46.74 4.70
4221 5104 5.682943 TTTCGTCCAATGAAGTAACTTGG 57.317 39.130 0.00 0.00 40.66 3.61
4224 5107 7.504924 TTGAATTTCGTCCAATGAAGTAACT 57.495 32.000 0.00 0.00 0.00 2.24
4225 5108 8.742554 ATTTGAATTTCGTCCAATGAAGTAAC 57.257 30.769 0.00 0.00 0.00 2.50
4230 5113 7.018826 GTCGTATTTGAATTTCGTCCAATGAA 58.981 34.615 0.00 0.00 0.00 2.57
4231 5114 6.147985 TGTCGTATTTGAATTTCGTCCAATGA 59.852 34.615 0.00 0.00 0.00 2.57
4234 5117 5.926214 TGTCGTATTTGAATTTCGTCCAA 57.074 34.783 0.00 0.00 0.00 3.53
4236 5119 5.064198 TCCATGTCGTATTTGAATTTCGTCC 59.936 40.000 0.00 0.00 0.00 4.79
4238 5121 6.677781 ATCCATGTCGTATTTGAATTTCGT 57.322 33.333 0.00 0.00 0.00 3.85
4285 5168 7.659652 GTTCTTCAACTAACAGAACATAGCT 57.340 36.000 6.44 0.00 43.98 3.32
4299 5182 9.965902 ATATATCTGGTTTTCTGTTCTTCAACT 57.034 29.630 0.00 0.00 33.17 3.16
4302 5185 8.677300 GCAATATATCTGGTTTTCTGTTCTTCA 58.323 33.333 0.00 0.00 0.00 3.02
4303 5186 8.131731 GGCAATATATCTGGTTTTCTGTTCTTC 58.868 37.037 0.00 0.00 0.00 2.87
4304 5187 7.615365 TGGCAATATATCTGGTTTTCTGTTCTT 59.385 33.333 0.00 0.00 0.00 2.52
4305 5188 7.118723 TGGCAATATATCTGGTTTTCTGTTCT 58.881 34.615 0.00 0.00 0.00 3.01
4306 5189 7.333528 TGGCAATATATCTGGTTTTCTGTTC 57.666 36.000 0.00 0.00 0.00 3.18
4327 5210 4.592485 TCTACTCTAAAGCTGCTATGGC 57.408 45.455 0.90 0.00 39.26 4.40
4328 5211 7.712639 TCATTTTCTACTCTAAAGCTGCTATGG 59.287 37.037 0.90 0.00 0.00 2.74
4329 5212 8.654230 TCATTTTCTACTCTAAAGCTGCTATG 57.346 34.615 0.90 0.00 0.00 2.23
4330 5213 9.103861 GTTCATTTTCTACTCTAAAGCTGCTAT 57.896 33.333 0.90 0.00 0.00 2.97
4335 5225 8.910351 ACTTGTTCATTTTCTACTCTAAAGCT 57.090 30.769 0.00 0.00 0.00 3.74
4345 5235 6.713450 GGACCCTGTAACTTGTTCATTTTCTA 59.287 38.462 0.00 0.00 0.00 2.10
4378 5268 3.223226 GGCCATGCCCTTTGATGG 58.777 61.111 0.00 0.00 44.06 3.51
4388 5278 1.972872 ATAGCACTACAAGGCCATGC 58.027 50.000 8.15 5.97 36.52 4.06
4389 5279 2.033801 GCAATAGCACTACAAGGCCATG 59.966 50.000 5.01 5.77 41.58 3.66
4391 5281 1.281867 AGCAATAGCACTACAAGGCCA 59.718 47.619 5.01 0.00 45.49 5.36
4392 5282 1.672881 CAGCAATAGCACTACAAGGCC 59.327 52.381 0.00 0.00 45.49 5.19
4393 5283 2.359900 ACAGCAATAGCACTACAAGGC 58.640 47.619 0.00 0.00 45.49 4.35
4394 5284 5.011090 TCTACAGCAATAGCACTACAAGG 57.989 43.478 0.00 0.00 45.49 3.61
4402 5292 6.464222 AGTGTTTTACTCTACAGCAATAGCA 58.536 36.000 0.00 0.00 38.12 3.49
4403 5293 6.969828 AGTGTTTTACTCTACAGCAATAGC 57.030 37.500 0.00 0.00 33.17 2.97
4431 5321 5.862860 CCGTAGTTCTAAAGGAGACACTTTC 59.137 44.000 0.00 0.00 40.82 2.62
4432 5322 5.537674 TCCGTAGTTCTAAAGGAGACACTTT 59.462 40.000 0.00 0.00 42.83 2.66
4444 5334 8.295288 GCTATAACTATTGCTCCGTAGTTCTAA 58.705 37.037 1.46 0.00 40.53 2.10
4445 5335 7.094463 GGCTATAACTATTGCTCCGTAGTTCTA 60.094 40.741 1.46 0.00 40.53 2.10
4446 5336 6.294620 GGCTATAACTATTGCTCCGTAGTTCT 60.295 42.308 1.46 0.00 40.53 3.01
4449 5339 5.078256 AGGCTATAACTATTGCTCCGTAGT 58.922 41.667 0.00 0.00 35.32 2.73
4450 5340 5.646577 AGGCTATAACTATTGCTCCGTAG 57.353 43.478 0.00 0.00 35.32 3.51
4451 5341 6.041182 TCAAAGGCTATAACTATTGCTCCGTA 59.959 38.462 0.00 0.00 35.32 4.02
4452 5342 4.957684 AAGGCTATAACTATTGCTCCGT 57.042 40.909 0.00 0.00 35.32 4.69
4454 5344 7.568199 TTTCAAAGGCTATAACTATTGCTCC 57.432 36.000 0.00 0.00 35.32 4.70
4457 5347 8.980143 TGTTTTTCAAAGGCTATAACTATTGC 57.020 30.769 0.00 0.00 34.43 3.56
4505 5400 7.327975 TGAAAATCGGCTAAGTCTGAGAATTA 58.672 34.615 2.21 2.21 0.00 1.40
4523 5418 9.283768 ACAATTATTTGGAAAACCCTGAAAATC 57.716 29.630 2.66 0.00 37.15 2.17
4603 5502 6.521133 CGAAATTCTGAGCAACTTTCATGTAC 59.479 38.462 0.00 0.00 0.00 2.90
4626 5525 2.369600 GCGTATTCGAATTCGTCTCGA 58.630 47.619 29.50 4.96 43.25 4.04
4637 5536 0.449786 TAAACGGACCGCGTATTCGA 59.550 50.000 15.39 0.00 39.71 3.71
4698 5597 3.945921 TGTGTTACACAAATGACCGGAAA 59.054 39.130 16.40 0.00 41.69 3.13
4699 5598 3.542648 TGTGTTACACAAATGACCGGAA 58.457 40.909 16.40 0.00 41.69 4.30
4713 5613 0.668401 CGGTTCCGGACCTGTGTTAC 60.668 60.000 1.83 0.00 46.92 2.50
4739 5639 1.215924 GGGGGAATTCAACCGGGAATA 59.784 52.381 6.32 0.00 36.51 1.75
4769 5669 2.098117 ACCTAACGTATGGCTACACGAC 59.902 50.000 8.22 0.00 40.56 4.34
4849 5750 7.703755 AGAGAAGAGGGGAAAGAAACAATAAT 58.296 34.615 0.00 0.00 0.00 1.28
4862 5763 1.921049 TCTACCGAAGAGAAGAGGGGA 59.079 52.381 0.00 0.00 0.00 4.81
4886 5787 2.362503 AGGGCGACATCGGTCTCA 60.363 61.111 3.08 0.00 42.05 3.27
4936 5844 1.002888 CCTGGAAGCTCTGCTGAAAGA 59.997 52.381 0.00 0.00 39.62 2.52
4985 5895 4.000928 AGTATGAGAGAATGGACTGGGT 57.999 45.455 0.00 0.00 0.00 4.51
4990 5900 6.426328 CCTAATGCAAGTATGAGAGAATGGAC 59.574 42.308 0.00 0.00 0.00 4.02
5004 5914 4.827284 ACAGTAGCAAAACCTAATGCAAGT 59.173 37.500 0.00 0.00 44.95 3.16
5015 5925 6.143919 GGAGCAAACAATAACAGTAGCAAAAC 59.856 38.462 0.00 0.00 0.00 2.43
5137 6050 2.448931 AACCGGGACAAGTGGGGA 60.449 61.111 6.32 0.00 0.00 4.81
5297 6223 4.113354 CCGAATAGCTCCACTACAAAGAC 58.887 47.826 0.00 0.00 32.32 3.01
5309 6235 0.454600 TGGACACGACCGAATAGCTC 59.545 55.000 0.00 0.00 0.00 4.09
5325 6251 1.762957 GAGGAAATCACCCTCGATGGA 59.237 52.381 14.21 0.00 40.58 3.41
5326 6252 2.246719 GAGGAAATCACCCTCGATGG 57.753 55.000 5.04 5.04 40.58 3.51
5448 6374 2.644676 TCCGTGTGTCCAAACATCAAA 58.355 42.857 0.00 0.00 37.81 2.69
5490 6416 3.431725 CGACCCGCCTTTCCAAGC 61.432 66.667 0.00 0.00 0.00 4.01
5805 6732 2.824041 GTCCAACCCGATGCGCAT 60.824 61.111 25.66 25.66 0.00 4.73
5806 6733 4.015406 AGTCCAACCCGATGCGCA 62.015 61.111 14.96 14.96 0.00 6.09
5812 6739 0.834687 AGCTTACCAGTCCAACCCGA 60.835 55.000 0.00 0.00 0.00 5.14
5977 6905 1.302383 CTCGGCCAAACAATACGCCA 61.302 55.000 2.24 0.00 41.71 5.69
6068 6996 8.844244 GCTATCAATAGATGTTTTCTTCCATGT 58.156 33.333 1.15 0.00 35.79 3.21
6071 6999 7.500227 CAGGCTATCAATAGATGTTTTCTTCCA 59.500 37.037 1.15 0.00 35.79 3.53
6153 7081 7.348080 TACTATCCAGTTATCACCTCAAGTG 57.652 40.000 0.00 0.00 40.98 3.16
6197 7125 1.807573 CTTTCTCGACTCCCTGCGC 60.808 63.158 0.00 0.00 0.00 6.09
6270 7203 2.398252 TCTTGCAGCATCAGAAGAGG 57.602 50.000 0.00 0.00 0.00 3.69
6428 7366 4.158025 ACCGTGAGTACTCATCCAAAGTAG 59.842 45.833 27.54 11.30 42.18 2.57
6476 7417 3.349927 TGCAACATCTGAGAAGAATGGG 58.650 45.455 0.00 0.00 0.00 4.00
6514 7455 2.836360 GGTGGCGTCGGGATCCTA 60.836 66.667 12.58 0.00 0.00 2.94
6522 7463 4.394078 TCGTCGAAGGTGGCGTCG 62.394 66.667 0.00 0.00 40.53 5.12
6556 7497 2.097825 CACGTAGTAGTAGGCACCCTT 58.902 52.381 0.00 0.00 41.61 3.95
6627 7568 1.131126 AGCAACATGATCGAAAAGGCG 59.869 47.619 0.00 0.00 0.00 5.52
6658 7602 7.949006 AGGTTAGACAAGTCTACCTTAAGAAGA 59.051 37.037 17.87 3.76 41.48 2.87
6669 7613 8.327271 AGTACAGACATAGGTTAGACAAGTCTA 58.673 37.037 5.86 5.86 40.93 2.59
6704 7648 2.945008 CACAAGAGTCTGTGGAAGCAAA 59.055 45.455 12.34 0.00 42.52 3.68
6713 7657 3.367498 GGCTCGAATACACAAGAGTCTGT 60.367 47.826 0.00 0.00 33.04 3.41
6715 7659 2.166664 GGGCTCGAATACACAAGAGTCT 59.833 50.000 0.00 0.00 35.82 3.24
6819 7780 5.734498 GCAAATGTGTACGATCAAGATCAAC 59.266 40.000 10.39 7.89 37.69 3.18
6867 7828 1.078759 CTTCATGTGACGCCCTCGAC 61.079 60.000 0.00 0.00 39.41 4.20
6882 7843 1.032014 GTTCCTGCCAAGTTGCTTCA 58.968 50.000 0.00 0.00 0.00 3.02
6883 7844 0.040067 CGTTCCTGCCAAGTTGCTTC 60.040 55.000 0.00 0.00 0.00 3.86
6884 7845 2.032981 CGTTCCTGCCAAGTTGCTT 58.967 52.632 0.00 0.00 0.00 3.91
6894 7855 0.179045 ATAGACATGGGCGTTCCTGC 60.179 55.000 0.00 0.00 36.20 4.85
6895 7856 1.134401 ACATAGACATGGGCGTTCCTG 60.134 52.381 0.00 0.00 36.39 3.86
6896 7857 1.134401 CACATAGACATGGGCGTTCCT 60.134 52.381 0.00 0.00 36.39 3.36
6897 7858 1.299541 CACATAGACATGGGCGTTCC 58.700 55.000 0.00 0.00 36.39 3.62
6898 7859 1.134521 TCCACATAGACATGGGCGTTC 60.135 52.381 0.00 0.00 33.89 3.95
6899 7860 0.908910 TCCACATAGACATGGGCGTT 59.091 50.000 0.00 0.00 33.89 4.84
6900 7861 1.131638 ATCCACATAGACATGGGCGT 58.868 50.000 0.00 0.00 33.89 5.68
6901 7862 1.070601 TCATCCACATAGACATGGGCG 59.929 52.381 0.00 0.00 33.89 6.13
6902 7863 2.158769 TGTCATCCACATAGACATGGGC 60.159 50.000 0.00 0.00 37.36 5.36
6903 7864 3.843893 TGTCATCCACATAGACATGGG 57.156 47.619 0.00 0.00 37.36 4.00
6911 7872 7.497595 GTCTTTACCACTATGTCATCCACATA 58.502 38.462 0.00 0.00 44.56 2.29
6913 7874 5.623596 CGTCTTTACCACTATGTCATCCACA 60.624 44.000 0.00 0.00 40.18 4.17
6914 7875 4.804139 CGTCTTTACCACTATGTCATCCAC 59.196 45.833 0.00 0.00 0.00 4.02
6915 7876 4.142026 CCGTCTTTACCACTATGTCATCCA 60.142 45.833 0.00 0.00 0.00 3.41
6916 7877 4.098960 TCCGTCTTTACCACTATGTCATCC 59.901 45.833 0.00 0.00 0.00 3.51
6917 7878 5.067413 TCTCCGTCTTTACCACTATGTCATC 59.933 44.000 0.00 0.00 0.00 2.92
6918 7879 4.954202 TCTCCGTCTTTACCACTATGTCAT 59.046 41.667 0.00 0.00 0.00 3.06
6919 7880 4.338012 TCTCCGTCTTTACCACTATGTCA 58.662 43.478 0.00 0.00 0.00 3.58
6920 7881 4.978083 TCTCCGTCTTTACCACTATGTC 57.022 45.455 0.00 0.00 0.00 3.06
6921 7882 4.381718 GCTTCTCCGTCTTTACCACTATGT 60.382 45.833 0.00 0.00 0.00 2.29
6922 7883 4.113354 GCTTCTCCGTCTTTACCACTATG 58.887 47.826 0.00 0.00 0.00 2.23
6923 7884 3.181489 CGCTTCTCCGTCTTTACCACTAT 60.181 47.826 0.00 0.00 0.00 2.12
6924 7885 2.163010 CGCTTCTCCGTCTTTACCACTA 59.837 50.000 0.00 0.00 0.00 2.74
6925 7886 1.067776 CGCTTCTCCGTCTTTACCACT 60.068 52.381 0.00 0.00 0.00 4.00
6926 7887 1.347320 CGCTTCTCCGTCTTTACCAC 58.653 55.000 0.00 0.00 0.00 4.16
6927 7888 0.389426 GCGCTTCTCCGTCTTTACCA 60.389 55.000 0.00 0.00 0.00 3.25
6928 7889 1.411493 CGCGCTTCTCCGTCTTTACC 61.411 60.000 5.56 0.00 0.00 2.85
6929 7890 1.411493 CCGCGCTTCTCCGTCTTTAC 61.411 60.000 5.56 0.00 0.00 2.01
6930 7891 1.153901 CCGCGCTTCTCCGTCTTTA 60.154 57.895 5.56 0.00 0.00 1.85
6931 7892 2.432628 CCGCGCTTCTCCGTCTTT 60.433 61.111 5.56 0.00 0.00 2.52
6937 7898 2.629050 TATCAGTGCCGCGCTTCTCC 62.629 60.000 5.56 0.00 0.00 3.71
6938 7899 0.806102 TTATCAGTGCCGCGCTTCTC 60.806 55.000 5.56 0.00 0.00 2.87
6939 7900 1.084370 GTTATCAGTGCCGCGCTTCT 61.084 55.000 5.56 0.00 0.00 2.85
6940 7901 1.348594 GTTATCAGTGCCGCGCTTC 59.651 57.895 5.56 0.00 0.00 3.86
6941 7902 2.106683 GGTTATCAGTGCCGCGCTT 61.107 57.895 5.56 0.00 0.00 4.68
6942 7903 2.511600 GGTTATCAGTGCCGCGCT 60.512 61.111 5.56 0.00 0.00 5.92
6943 7904 3.573491 GGGTTATCAGTGCCGCGC 61.573 66.667 0.00 0.00 0.00 6.86
6944 7905 2.125310 TGGGTTATCAGTGCCGCG 60.125 61.111 0.00 0.00 0.00 6.46
6945 7906 0.958382 TTGTGGGTTATCAGTGCCGC 60.958 55.000 0.00 0.00 0.00 6.53
6946 7907 1.086696 CTTGTGGGTTATCAGTGCCG 58.913 55.000 0.00 0.00 0.00 5.69
6947 7908 2.200373 ACTTGTGGGTTATCAGTGCC 57.800 50.000 0.00 0.00 0.00 5.01
6948 7909 5.057149 CCTATACTTGTGGGTTATCAGTGC 58.943 45.833 0.00 0.00 0.00 4.40
6949 7910 5.454755 CCCCTATACTTGTGGGTTATCAGTG 60.455 48.000 0.00 0.00 39.31 3.66
6950 7911 4.658901 CCCCTATACTTGTGGGTTATCAGT 59.341 45.833 0.00 0.00 39.31 3.41
7017 7978 6.628644 ATTTGTTCTACCTTTAGCTCCTCT 57.371 37.500 0.00 0.00 0.00 3.69
7065 8026 3.801114 AGCATGCGTAGAGTTGTATCA 57.199 42.857 13.01 0.00 0.00 2.15
7082 8043 2.778299 AGGTAAAGCGAATGTCAAGCA 58.222 42.857 0.00 0.00 0.00 3.91
7151 8112 3.246226 ACGCGCTCTTTATCTTATTGCAG 59.754 43.478 5.73 0.00 0.00 4.41
7157 8118 8.545420 CCTTTTATTTACGCGCTCTTTATCTTA 58.455 33.333 5.73 0.00 0.00 2.10
7370 8332 2.006888 GTAGTTGCGGATGCTTGCTAA 58.993 47.619 0.00 0.00 43.34 3.09
7441 8403 3.444388 GGGTTGTTGCGTATGGGATAAAA 59.556 43.478 0.00 0.00 0.00 1.52
7486 8448 2.831685 TAGTGGTTTGCGTGAGTGAT 57.168 45.000 0.00 0.00 0.00 3.06
7499 8461 4.745125 CGTTCATGATTCGCTTATAGTGGT 59.255 41.667 0.00 0.00 0.00 4.16
7576 8538 9.521841 TGTTTTATTATTGGTGTTGTCCTATGA 57.478 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.