Multiple sequence alignment - TraesCS7D01G109900

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BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G109900 chr7D 100.000 5262 0 0 1 5262 66417448 66412187 0.000000e+00 9681.0
1 TraesCS7D01G109900 chr7D 98.070 1347 25 1 2824 4170 580604322 580602977 0.000000e+00 2342.0
2 TraesCS7D01G109900 chr7D 94.000 900 20 9 717 1606 68983318 68984193 0.000000e+00 1332.0
3 TraesCS7D01G109900 chr7D 96.667 540 17 1 159 697 468895151 468894612 0.000000e+00 896.0
4 TraesCS7D01G109900 chr7D 93.961 563 21 6 1642 2204 68984191 68984740 0.000000e+00 839.0
5 TraesCS7D01G109900 chr7D 85.954 655 30 22 4181 4812 68984946 68985561 1.240000e-180 643.0
6 TraesCS7D01G109900 chr7D 78.189 1082 148 53 968 2035 66508482 66507475 1.250000e-170 610.0
7 TraesCS7D01G109900 chr7D 77.526 1059 152 48 990 2035 68928627 68929612 4.600000e-155 558.0
8 TraesCS7D01G109900 chr7D 76.691 828 129 29 796 1595 85345086 85345877 8.210000e-108 401.0
9 TraesCS7D01G109900 chr7D 92.694 219 15 1 2828 3046 580602977 580603194 1.100000e-81 315.0
10 TraesCS7D01G109900 chr7D 92.237 219 17 0 2828 3046 66413279 66413497 1.420000e-80 311.0
11 TraesCS7D01G109900 chr7D 92.237 219 17 0 3952 4170 66414403 66414621 1.420000e-80 311.0
12 TraesCS7D01G109900 chr7D 92.237 219 17 0 3952 4170 580604100 580604318 1.420000e-80 311.0
13 TraesCS7D01G109900 chr7D 88.846 260 11 7 4214 4468 68930308 68930554 2.380000e-78 303.0
14 TraesCS7D01G109900 chr7D 82.919 322 49 2 1703 2021 69056086 69056404 8.620000e-73 285.0
15 TraesCS7D01G109900 chr7D 75.954 603 93 39 925 1511 73367902 73368468 4.040000e-66 263.0
16 TraesCS7D01G109900 chr7D 85.317 252 12 3 4217 4468 66506860 66506634 2.450000e-58 237.0
17 TraesCS7D01G109900 chr7D 90.511 137 12 1 4188 4324 69057112 69057247 4.190000e-41 180.0
18 TraesCS7D01G109900 chr7D 80.995 221 36 4 2828 3045 82466150 82465933 2.520000e-38 171.0
19 TraesCS7D01G109900 chr7D 90.526 95 6 2 4349 4443 66345839 66345748 7.160000e-24 122.0
20 TraesCS7D01G109900 chr7D 80.120 166 31 2 1436 1600 66547631 66547467 7.160000e-24 122.0
21 TraesCS7D01G109900 chr7D 94.595 74 4 0 2345 2418 68984845 68984918 1.200000e-21 115.0
22 TraesCS7D01G109900 chr7D 96.610 59 1 1 4411 4468 68930556 68930614 4.340000e-16 97.1
23 TraesCS7D01G109900 chr7D 92.188 64 5 0 1536 1599 68898062 68898125 2.020000e-14 91.6
24 TraesCS7D01G109900 chr7D 84.694 98 8 6 2413 2506 68984658 68984752 2.020000e-14 91.6
25 TraesCS7D01G109900 chr7D 96.364 55 1 1 4411 4464 66506632 66506578 7.260000e-14 89.8
26 TraesCS7D01G109900 chr7D 81.651 109 8 4 2704 2800 68984844 68984952 4.370000e-11 80.5
27 TraesCS7D01G109900 chr7D 85.897 78 3 5 4815 4890 68986099 68986170 5.650000e-10 76.8
28 TraesCS7D01G109900 chr7A 91.522 1557 51 15 698 2231 70890158 70888660 0.000000e+00 2069.0
29 TraesCS7D01G109900 chr7A 89.816 1522 73 23 717 2231 74642366 74643812 0.000000e+00 1877.0
30 TraesCS7D01G109900 chr7A 96.882 417 10 3 2413 2827 74643704 74644119 0.000000e+00 695.0
31 TraesCS7D01G109900 chr7A 95.174 373 18 0 4171 4543 74644110 74644482 1.630000e-164 590.0
32 TraesCS7D01G109900 chr7A 93.703 397 17 5 2439 2827 70888743 70888347 5.870000e-164 588.0
33 TraesCS7D01G109900 chr7A 75.273 1282 209 65 783 2021 74883284 74884500 3.630000e-141 512.0
34 TraesCS7D01G109900 chr7A 79.638 663 90 25 965 1619 70898537 70897912 8.090000e-118 435.0
35 TraesCS7D01G109900 chr7A 96.047 253 8 2 4217 4468 71112899 71112648 1.360000e-110 411.0
36 TraesCS7D01G109900 chr7A 79.512 615 76 27 974 1581 71114685 71114114 4.940000e-105 392.0
37 TraesCS7D01G109900 chr7A 84.434 424 24 16 4407 4812 70888163 70887764 3.850000e-101 379.0
38 TraesCS7D01G109900 chr7A 75.127 788 130 38 829 1599 70238202 70237464 5.120000e-80 309.0
39 TraesCS7D01G109900 chr7A 92.574 202 9 2 4171 4372 70888356 70888161 8.620000e-73 285.0
40 TraesCS7D01G109900 chr7A 75.788 603 94 38 925 1511 77915149 77915715 1.880000e-64 257.0
41 TraesCS7D01G109900 chr7A 84.071 226 11 14 4604 4812 74644492 74644709 1.500000e-45 195.0
42 TraesCS7D01G109900 chr7A 80.114 176 22 8 2237 2401 71113471 71113298 9.260000e-23 119.0
43 TraesCS7D01G109900 chr7B 91.808 1294 51 19 945 2219 10559005 10560262 0.000000e+00 1751.0
44 TraesCS7D01G109900 chr7B 91.170 1291 47 11 945 2219 7717619 7716380 0.000000e+00 1690.0
45 TraesCS7D01G109900 chr7B 86.592 537 30 13 4171 4687 7716002 7715488 5.950000e-154 555.0
46 TraesCS7D01G109900 chr7B 76.316 1102 175 53 947 2021 10946532 10947574 1.310000e-140 510.0
47 TraesCS7D01G109900 chr7B 93.651 252 10 3 4217 4468 7730560 7730315 6.440000e-99 372.0
48 TraesCS7D01G109900 chr7B 75.268 841 133 39 789 1598 32898704 32897908 1.090000e-86 331.0
49 TraesCS7D01G109900 chr7B 92.558 215 9 3 4171 4384 10560619 10560827 8.560000e-78 302.0
50 TraesCS7D01G109900 chr7B 100.000 146 0 0 1 146 212953770 212953915 2.420000e-68 270.0
51 TraesCS7D01G109900 chr7B 81.538 325 52 7 1686 2009 10238266 10238583 1.450000e-65 261.0
52 TraesCS7D01G109900 chr7B 75.540 556 96 28 846 1384 17507570 17508102 2.450000e-58 237.0
53 TraesCS7D01G109900 chr7B 76.327 490 81 21 1000 1485 491084216 491083758 4.100000e-56 230.0
54 TraesCS7D01G109900 chr7B 79.762 336 44 14 1689 2021 7731638 7731324 6.860000e-54 222.0
55 TraesCS7D01G109900 chr7B 82.990 194 29 4 1428 1619 10061409 10061600 7.010000e-39 172.0
56 TraesCS7D01G109900 chr7B 81.481 216 35 4 3958 4171 747374908 747374696 7.010000e-39 172.0
57 TraesCS7D01G109900 chr7B 80.784 255 15 9 693 946 10558747 10558968 9.060000e-38 169.0
58 TraesCS7D01G109900 chr7B 82.828 198 25 8 2828 3021 747374697 747374889 9.060000e-38 169.0
59 TraesCS7D01G109900 chr7B 95.098 102 5 0 4410 4511 10560827 10560928 1.520000e-35 161.0
60 TraesCS7D01G109900 chr7B 87.143 140 10 3 4192 4324 10948099 10948237 9.130000e-33 152.0
61 TraesCS7D01G109900 chr7B 92.857 98 3 1 849 946 7717749 7717656 7.110000e-29 139.0
62 TraesCS7D01G109900 chr7B 96.250 80 3 0 2748 2827 10560549 10560628 1.190000e-26 132.0
63 TraesCS7D01G109900 chr7B 83.448 145 17 5 2281 2419 7716377 7716234 1.540000e-25 128.0
64 TraesCS7D01G109900 chr7B 91.667 84 6 1 2745 2827 7716076 7715993 1.200000e-21 115.0
65 TraesCS7D01G109900 chr7B 87.629 97 6 5 2418 2510 7716474 7716380 2.000000e-19 108.0
66 TraesCS7D01G109900 chr7B 88.172 93 6 4 2421 2510 10560172 10560262 7.210000e-19 106.0
67 TraesCS7D01G109900 chr7B 80.292 137 21 2 1432 1568 10102448 10102578 1.210000e-16 99.0
68 TraesCS7D01G109900 chr7B 88.000 75 9 0 1947 2021 10069000 10069074 7.260000e-14 89.8
69 TraesCS7D01G109900 chr7B 84.211 95 10 2 718 812 7717848 7717759 2.610000e-13 87.9
70 TraesCS7D01G109900 chr7B 95.349 43 2 0 4401 4443 7730318 7730276 9.460000e-08 69.4
71 TraesCS7D01G109900 chr7B 85.294 68 8 2 1907 1973 29828941 29828875 9.460000e-08 69.4
72 TraesCS7D01G109900 chr7B 83.824 68 9 2 1907 1973 31445038 31444972 4.400000e-06 63.9
73 TraesCS7D01G109900 chr7B 83.582 67 11 0 1907 1973 31447098 31447032 4.400000e-06 63.9
74 TraesCS7D01G109900 chr7B 100.000 28 0 0 919 946 16950899 16950926 1.000000e-02 52.8
75 TraesCS7D01G109900 chr2D 97.037 540 15 1 159 697 392238218 392237679 0.000000e+00 907.0
76 TraesCS7D01G109900 chr2D 83.600 811 85 17 3367 4170 191053787 191054556 0.000000e+00 717.0
77 TraesCS7D01G109900 chr2D 86.683 413 36 9 2828 3225 191053387 191053795 1.740000e-119 440.0
78 TraesCS7D01G109900 chr2D 91.403 221 16 2 2828 3046 191054556 191054337 3.080000e-77 300.0
79 TraesCS7D01G109900 chr2D 90.411 219 19 2 3952 4170 191053603 191053387 2.400000e-73 287.0
80 TraesCS7D01G109900 chr2D 100.000 146 0 0 1 146 48064989 48064844 2.420000e-68 270.0
81 TraesCS7D01G109900 chr2D 78.670 361 56 12 923 1278 33581106 33580762 2.470000e-53 220.0
82 TraesCS7D01G109900 chr2D 83.628 226 31 5 4213 4437 326453687 326453907 1.920000e-49 207.0
83 TraesCS7D01G109900 chr2D 72.867 586 101 35 955 1517 33374157 33373607 1.180000e-31 148.0
84 TraesCS7D01G109900 chr3D 97.004 534 15 1 160 692 83041138 83041671 0.000000e+00 896.0
85 TraesCS7D01G109900 chr3D 96.822 535 16 1 159 692 433266045 433266579 0.000000e+00 893.0
86 TraesCS7D01G109900 chr3D 96.317 543 18 2 159 700 579822712 579823253 0.000000e+00 891.0
87 TraesCS7D01G109900 chr3D 100.000 146 0 0 1 146 64957081 64957226 2.420000e-68 270.0
88 TraesCS7D01G109900 chr3D 100.000 146 0 0 1 146 579823102 579823247 2.420000e-68 270.0
89 TraesCS7D01G109900 chr3D 83.794 253 37 4 3920 4170 554761276 554761026 2.450000e-58 237.0
90 TraesCS7D01G109900 chr5D 96.822 535 16 1 159 692 242862776 242862242 0.000000e+00 893.0
91 TraesCS7D01G109900 chr5D 95.487 554 20 5 161 710 454537082 454537634 0.000000e+00 880.0
92 TraesCS7D01G109900 chr5D 100.000 148 0 0 1 148 270723477 270723330 1.870000e-69 274.0
93 TraesCS7D01G109900 chr5D 100.000 146 0 0 1 146 471247738 471247883 2.420000e-68 270.0
94 TraesCS7D01G109900 chr5D 83.696 184 23 6 2829 3008 228255991 228256171 3.260000e-37 167.0
95 TraesCS7D01G109900 chr5D 81.579 152 27 1 4021 4171 189183347 189183196 1.990000e-24 124.0
96 TraesCS7D01G109900 chr4D 96.822 535 16 1 159 692 397713024 397712490 0.000000e+00 893.0
97 TraesCS7D01G109900 chr4D 85.641 390 32 8 3533 3916 484720176 484719805 6.390000e-104 388.0
98 TraesCS7D01G109900 chr4D 100.000 148 0 0 1 148 474083099 474082952 1.870000e-69 274.0
99 TraesCS7D01G109900 chr1D 96.822 535 15 2 159 692 311325030 311324497 0.000000e+00 893.0
100 TraesCS7D01G109900 chr1D 80.631 222 37 6 2827 3045 124774841 124774623 3.260000e-37 167.0
101 TraesCS7D01G109900 chr2B 77.370 791 100 40 829 1568 135794747 135795509 3.820000e-106 396.0
102 TraesCS7D01G109900 chr2B 80.923 325 52 8 1699 2021 135795661 135795977 1.130000e-61 248.0
103 TraesCS7D01G109900 chr2B 75.862 435 79 16 849 1278 55855923 55855510 1.160000e-46 198.0
104 TraesCS7D01G109900 chr4A 84.272 426 36 17 2824 3225 645073599 645074017 2.300000e-103 387.0
105 TraesCS7D01G109900 chr4A 88.341 223 17 7 3952 4170 645073819 645073602 5.230000e-65 259.0
106 TraesCS7D01G109900 chr4A 82.938 211 33 3 3962 4170 599941030 599940821 2.500000e-43 187.0
107 TraesCS7D01G109900 chr4A 84.264 197 26 4 2828 3021 599940821 599941015 2.500000e-43 187.0
108 TraesCS7D01G109900 chr1B 82.199 382 45 11 3552 3914 532661370 532660993 1.840000e-79 307.0
109 TraesCS7D01G109900 chr1B 100.000 147 0 0 1 147 152365964 152366110 6.710000e-69 272.0
110 TraesCS7D01G109900 chr6D 100.000 147 0 0 1 147 217559409 217559555 6.710000e-69 272.0
111 TraesCS7D01G109900 chr6D 86.567 134 11 4 828 961 411918497 411918371 1.980000e-29 141.0
112 TraesCS7D01G109900 chr6D 100.000 28 0 0 3685 3712 469308983 469308956 1.000000e-02 52.8
113 TraesCS7D01G109900 chr6B 100.000 146 0 0 1 146 543600393 543600248 2.420000e-68 270.0
114 TraesCS7D01G109900 chr6B 82.018 228 35 3 2828 3050 281259139 281258913 6.960000e-44 189.0
115 TraesCS7D01G109900 chr6B 82.063 223 32 5 3954 4170 281258919 281259139 3.240000e-42 183.0
116 TraesCS7D01G109900 chr5B 86.266 233 31 1 2828 3059 212206633 212206401 8.750000e-63 252.0
117 TraesCS7D01G109900 chr5B 86.364 220 29 1 3952 4170 212206414 212206633 6.810000e-59 239.0
118 TraesCS7D01G109900 chr5B 80.443 271 32 16 3905 4170 212194402 212194148 2.500000e-43 187.0
119 TraesCS7D01G109900 chr3B 85.425 247 30 4 3549 3792 780747167 780747410 8.750000e-63 252.0
120 TraesCS7D01G109900 chr3B 80.297 269 35 7 3699 3951 780747509 780747775 2.500000e-43 187.0
121 TraesCS7D01G109900 chr5A 87.500 216 25 2 3956 4170 225775829 225775615 1.130000e-61 248.0
122 TraesCS7D01G109900 chr5A 86.878 221 24 4 2827 3045 225779352 225779135 5.260000e-60 243.0
123 TraesCS7D01G109900 chrUn 82.051 195 33 2 2820 3014 61912483 61912291 1.170000e-36 165.0
124 TraesCS7D01G109900 chrUn 82.051 195 33 2 2820 3014 208958022 208957830 1.170000e-36 165.0
125 TraesCS7D01G109900 chrUn 82.051 195 33 2 2820 3014 379275200 379275008 1.170000e-36 165.0
126 TraesCS7D01G109900 chrUn 82.051 195 33 2 2820 3014 424162697 424162505 1.170000e-36 165.0
127 TraesCS7D01G109900 chrUn 81.281 203 35 3 2820 3021 206532131 206531931 1.520000e-35 161.0
128 TraesCS7D01G109900 chrUn 81.538 195 34 2 2820 3014 197808253 197808445 5.450000e-35 159.0
129 TraesCS7D01G109900 chrUn 81.538 195 34 2 2820 3014 430305216 430305408 5.450000e-35 159.0
130 TraesCS7D01G109900 chrUn 79.899 199 37 3 3974 4170 61912280 61912477 5.490000e-30 143.0
131 TraesCS7D01G109900 chrUn 79.899 199 37 3 3974 4170 206531928 206532125 5.490000e-30 143.0
132 TraesCS7D01G109900 chrUn 79.899 199 37 3 3974 4170 208957819 208958016 5.490000e-30 143.0
133 TraesCS7D01G109900 chrUn 80.423 189 35 2 3983 4170 379275007 379275194 5.490000e-30 143.0
134 TraesCS7D01G109900 chrUn 79.899 199 37 3 3974 4170 424162494 424162691 5.490000e-30 143.0
135 TraesCS7D01G109900 chrUn 79.592 196 37 3 3977 4170 197808453 197808259 2.560000e-28 137.0
136 TraesCS7D01G109900 chrUn 79.592 196 37 3 3977 4170 430305416 430305222 2.560000e-28 137.0
137 TraesCS7D01G109900 chr4B 84.667 150 23 0 2828 2977 649178154 649178303 3.280000e-32 150.0
138 TraesCS7D01G109900 chr4B 82.119 151 25 2 4021 4170 649178303 649178154 1.540000e-25 128.0
139 TraesCS7D01G109900 chr6A 89.167 120 12 1 3797 3916 59788650 59788768 1.180000e-31 148.0


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 TraesCS7D01G109900 chr7D 66412187 66417448 5261 True 9681.000000 9681 100.000000 1 5262 1 chr7D.!!$R2 5261
1 TraesCS7D01G109900 chr7D 580602977 580604322 1345 True 2342.000000 2342 98.070000 2824 4170 1 chr7D.!!$R6 1346
2 TraesCS7D01G109900 chr7D 468894612 468895151 539 True 896.000000 896 96.667000 159 697 1 chr7D.!!$R5 538
3 TraesCS7D01G109900 chr7D 68983318 68986170 2852 False 453.985714 1332 88.678857 717 4890 7 chr7D.!!$F6 4173
4 TraesCS7D01G109900 chr7D 85345086 85345877 791 False 401.000000 401 76.691000 796 1595 1 chr7D.!!$F3 799
5 TraesCS7D01G109900 chr7D 68928627 68930614 1987 False 319.366667 558 87.660667 990 4468 3 chr7D.!!$F5 3478
6 TraesCS7D01G109900 chr7D 580602977 580604318 1341 False 313.000000 315 92.465500 2828 4170 2 chr7D.!!$F8 1342
7 TraesCS7D01G109900 chr7D 66506578 66508482 1904 True 312.266667 610 86.623333 968 4468 3 chr7D.!!$R7 3500
8 TraesCS7D01G109900 chr7D 66413279 66414621 1342 False 311.000000 311 92.237000 2828 4170 2 chr7D.!!$F4 1342
9 TraesCS7D01G109900 chr7D 73367902 73368468 566 False 263.000000 263 75.954000 925 1511 1 chr7D.!!$F2 586
10 TraesCS7D01G109900 chr7D 69056086 69057247 1161 False 232.500000 285 86.715000 1703 4324 2 chr7D.!!$F7 2621
11 TraesCS7D01G109900 chr7A 74642366 74644709 2343 False 839.250000 1877 91.485750 717 4812 4 chr7A.!!$F3 4095
12 TraesCS7D01G109900 chr7A 70887764 70890158 2394 True 830.250000 2069 90.558250 698 4812 4 chr7A.!!$R3 4114
13 TraesCS7D01G109900 chr7A 74883284 74884500 1216 False 512.000000 512 75.273000 783 2021 1 chr7A.!!$F1 1238
14 TraesCS7D01G109900 chr7A 70897912 70898537 625 True 435.000000 435 79.638000 965 1619 1 chr7A.!!$R2 654
15 TraesCS7D01G109900 chr7A 70237464 70238202 738 True 309.000000 309 75.127000 829 1599 1 chr7A.!!$R1 770
16 TraesCS7D01G109900 chr7A 71112648 71114685 2037 True 307.333333 411 85.224333 974 4468 3 chr7A.!!$R4 3494
17 TraesCS7D01G109900 chr7A 77915149 77915715 566 False 257.000000 257 75.788000 925 1511 1 chr7A.!!$F2 586
18 TraesCS7D01G109900 chr7B 10558747 10560928 2181 False 436.833333 1751 90.778333 693 4511 6 chr7B.!!$F9 3818
19 TraesCS7D01G109900 chr7B 7715488 7717848 2360 True 403.271429 1690 88.224857 718 4687 7 chr7B.!!$R5 3969
20 TraesCS7D01G109900 chr7B 10946532 10948237 1705 False 331.000000 510 81.729500 947 4324 2 chr7B.!!$F10 3377
21 TraesCS7D01G109900 chr7B 32897908 32898704 796 True 331.000000 331 75.268000 789 1598 1 chr7B.!!$R2 809
22 TraesCS7D01G109900 chr7B 17507570 17508102 532 False 237.000000 237 75.540000 846 1384 1 chr7B.!!$F6 538
23 TraesCS7D01G109900 chr7B 7730276 7731638 1362 True 221.133333 372 89.587333 1689 4468 3 chr7B.!!$R6 2779
24 TraesCS7D01G109900 chr2D 392237679 392238218 539 True 907.000000 907 97.037000 159 697 1 chr2D.!!$R4 538
25 TraesCS7D01G109900 chr2D 191053387 191054556 1169 False 578.500000 717 85.141500 2828 4170 2 chr2D.!!$F2 1342
26 TraesCS7D01G109900 chr2D 191053387 191054556 1169 True 293.500000 300 90.907000 2828 4170 2 chr2D.!!$R5 1342
27 TraesCS7D01G109900 chr3D 83041138 83041671 533 False 896.000000 896 97.004000 160 692 1 chr3D.!!$F2 532
28 TraesCS7D01G109900 chr3D 433266045 433266579 534 False 893.000000 893 96.822000 159 692 1 chr3D.!!$F3 533
29 TraesCS7D01G109900 chr3D 579822712 579823253 541 False 580.500000 891 98.158500 1 700 2 chr3D.!!$F4 699
30 TraesCS7D01G109900 chr5D 242862242 242862776 534 True 893.000000 893 96.822000 159 692 1 chr5D.!!$R2 533
31 TraesCS7D01G109900 chr5D 454537082 454537634 552 False 880.000000 880 95.487000 161 710 1 chr5D.!!$F2 549
32 TraesCS7D01G109900 chr4D 397712490 397713024 534 True 893.000000 893 96.822000 159 692 1 chr4D.!!$R1 533
33 TraesCS7D01G109900 chr1D 311324497 311325030 533 True 893.000000 893 96.822000 159 692 1 chr1D.!!$R2 533
34 TraesCS7D01G109900 chr2B 135794747 135795977 1230 False 322.000000 396 79.146500 829 2021 2 chr2B.!!$F1 1192
35 TraesCS7D01G109900 chr3B 780747167 780747775 608 False 219.500000 252 82.861000 3549 3951 2 chr3B.!!$F1 402
36 TraesCS7D01G109900 chr5A 225775615 225779352 3737 True 245.500000 248 87.189000 2827 4170 2 chr5A.!!$R1 1343

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
33 34 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.0 0.00 0.00 0.00 2.90 F
769 772 0.108520 CTAACTTACGCGGGCCAAGA 60.109 55.0 12.47 0.31 0.00 3.02 F
1539 1685 0.549950 CTCCGACTAGGGTCAGGGTA 59.450 60.0 0.00 0.00 42.21 3.69 F
3359 4483 0.396435 TGCTGGTCCGATGACAGTTT 59.604 50.0 0.00 0.00 43.65 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1724 0.096976 CCAAGTCGCGCAAATTCGAT 59.903 50.0 8.75 0.0 37.06 3.59 R
1634 1819 0.179189 CACGAATTTCTCCAAGGCGC 60.179 55.0 0.00 0.0 0.00 6.53 R
3497 7301 0.032267 GGTCACCGGAGTATAGCAGC 59.968 60.0 9.46 0.0 0.00 5.25 R
4849 9937 0.108424 CAGCTGTAGCCTGTGGTCTC 60.108 60.0 5.25 0.0 43.38 3.36 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
24 25 4.755266 TTTGTCATAGAAGTAGGAGCCC 57.245 45.455 0.00 0.00 0.00 5.19
25 26 3.398318 TGTCATAGAAGTAGGAGCCCA 57.602 47.619 0.00 0.00 0.00 5.36
26 27 3.031736 TGTCATAGAAGTAGGAGCCCAC 58.968 50.000 0.00 0.00 0.00 4.61
27 28 2.365941 GTCATAGAAGTAGGAGCCCACC 59.634 54.545 0.00 0.00 0.00 4.61
28 29 2.023404 TCATAGAAGTAGGAGCCCACCA 60.023 50.000 0.00 0.00 0.00 4.17
29 30 1.861982 TAGAAGTAGGAGCCCACCAC 58.138 55.000 0.00 0.00 0.00 4.16
30 31 0.178903 AGAAGTAGGAGCCCACCACA 60.179 55.000 0.00 0.00 0.00 4.17
31 32 0.912486 GAAGTAGGAGCCCACCACAT 59.088 55.000 0.00 0.00 0.00 3.21
32 33 0.912486 AAGTAGGAGCCCACCACATC 59.088 55.000 0.00 0.00 0.00 3.06
33 34 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.000 0.00 0.00 0.00 2.90
34 35 1.291033 AGTAGGAGCCCACCACATCTA 59.709 52.381 0.00 0.00 0.00 1.98
35 36 2.090494 AGTAGGAGCCCACCACATCTAT 60.090 50.000 0.00 0.00 0.00 1.98
36 37 1.135094 AGGAGCCCACCACATCTATG 58.865 55.000 0.00 0.00 0.00 2.23
37 38 1.131638 GGAGCCCACCACATCTATGA 58.868 55.000 0.00 0.00 0.00 2.15
38 39 1.701847 GGAGCCCACCACATCTATGAT 59.298 52.381 0.00 0.00 0.00 2.45
39 40 2.551721 GGAGCCCACCACATCTATGATG 60.552 54.545 6.06 6.06 0.00 3.07
40 41 2.369860 GAGCCCACCACATCTATGATGA 59.630 50.000 13.63 0.00 0.00 2.92
41 42 2.984604 AGCCCACCACATCTATGATGAT 59.015 45.455 13.63 0.00 0.00 2.45
42 43 4.170449 AGCCCACCACATCTATGATGATA 58.830 43.478 13.63 0.00 0.00 2.15
43 44 4.019860 AGCCCACCACATCTATGATGATAC 60.020 45.833 13.63 0.00 0.00 2.24
44 45 4.836825 CCCACCACATCTATGATGATACC 58.163 47.826 13.63 0.00 0.00 2.73
45 46 4.498241 CCACCACATCTATGATGATACCG 58.502 47.826 13.63 0.06 0.00 4.02
46 47 4.498241 CACCACATCTATGATGATACCGG 58.502 47.826 13.63 0.00 0.00 5.28
47 48 3.515502 ACCACATCTATGATGATACCGGG 59.484 47.826 6.32 0.00 0.00 5.73
48 49 3.515502 CCACATCTATGATGATACCGGGT 59.484 47.826 6.32 4.46 0.00 5.28
49 50 4.020218 CCACATCTATGATGATACCGGGTT 60.020 45.833 4.31 0.00 0.00 4.11
50 51 5.513094 CCACATCTATGATGATACCGGGTTT 60.513 44.000 4.31 0.00 0.00 3.27
51 52 5.997746 CACATCTATGATGATACCGGGTTTT 59.002 40.000 4.31 0.00 0.00 2.43
52 53 5.997746 ACATCTATGATGATACCGGGTTTTG 59.002 40.000 4.31 0.00 0.00 2.44
53 54 5.623956 TCTATGATGATACCGGGTTTTGT 57.376 39.130 4.31 0.00 0.00 2.83
54 55 5.607477 TCTATGATGATACCGGGTTTTGTC 58.393 41.667 4.31 0.82 0.00 3.18
55 56 3.704800 TGATGATACCGGGTTTTGTCA 57.295 42.857 4.31 5.88 0.00 3.58
56 57 3.340034 TGATGATACCGGGTTTTGTCAC 58.660 45.455 4.31 2.17 0.00 3.67
57 58 2.932855 TGATACCGGGTTTTGTCACA 57.067 45.000 4.31 0.00 0.00 3.58
58 59 3.210232 TGATACCGGGTTTTGTCACAA 57.790 42.857 4.31 0.00 0.00 3.33
59 60 3.757270 TGATACCGGGTTTTGTCACAAT 58.243 40.909 4.31 0.00 0.00 2.71
60 61 4.145807 TGATACCGGGTTTTGTCACAATT 58.854 39.130 4.31 0.00 0.00 2.32
61 62 5.314529 TGATACCGGGTTTTGTCACAATTA 58.685 37.500 4.31 0.00 0.00 1.40
62 63 5.946972 TGATACCGGGTTTTGTCACAATTAT 59.053 36.000 4.31 0.00 0.00 1.28
63 64 4.776795 ACCGGGTTTTGTCACAATTATC 57.223 40.909 6.32 0.00 0.00 1.75
64 65 3.189702 ACCGGGTTTTGTCACAATTATCG 59.810 43.478 6.32 0.00 0.00 2.92
65 66 3.189702 CCGGGTTTTGTCACAATTATCGT 59.810 43.478 0.00 0.00 0.00 3.73
66 67 4.399978 CGGGTTTTGTCACAATTATCGTC 58.600 43.478 0.00 0.00 0.00 4.20
67 68 4.083749 CGGGTTTTGTCACAATTATCGTCA 60.084 41.667 0.00 0.00 0.00 4.35
68 69 5.391523 CGGGTTTTGTCACAATTATCGTCAT 60.392 40.000 0.00 0.00 0.00 3.06
69 70 6.183360 CGGGTTTTGTCACAATTATCGTCATA 60.183 38.462 0.00 0.00 0.00 2.15
70 71 7.186804 GGGTTTTGTCACAATTATCGTCATAG 58.813 38.462 0.00 0.00 0.00 2.23
71 72 7.065324 GGGTTTTGTCACAATTATCGTCATAGA 59.935 37.037 0.00 0.00 0.00 1.98
72 73 8.447833 GGTTTTGTCACAATTATCGTCATAGAA 58.552 33.333 0.00 0.00 0.00 2.10
73 74 9.478019 GTTTTGTCACAATTATCGTCATAGAAG 57.522 33.333 0.00 0.00 0.00 2.85
74 75 8.771920 TTTGTCACAATTATCGTCATAGAAGT 57.228 30.769 0.00 0.00 0.00 3.01
75 76 7.755582 TGTCACAATTATCGTCATAGAAGTG 57.244 36.000 0.00 0.00 0.00 3.16
76 77 7.320399 TGTCACAATTATCGTCATAGAAGTGT 58.680 34.615 0.00 0.00 0.00 3.55
77 78 7.488150 TGTCACAATTATCGTCATAGAAGTGTC 59.512 37.037 0.00 0.00 0.00 3.67
78 79 7.488150 GTCACAATTATCGTCATAGAAGTGTCA 59.512 37.037 0.00 0.00 0.00 3.58
79 80 8.197439 TCACAATTATCGTCATAGAAGTGTCAT 58.803 33.333 0.00 0.00 0.00 3.06
80 81 9.463443 CACAATTATCGTCATAGAAGTGTCATA 57.537 33.333 0.00 0.00 0.00 2.15
87 88 8.391075 TCGTCATAGAAGTGTCATATGTATGA 57.609 34.615 1.90 4.48 40.19 2.15
112 113 2.892784 AAAAATTTCGTTCGGCCCAA 57.107 40.000 0.00 0.00 0.00 4.12
113 114 2.892784 AAAATTTCGTTCGGCCCAAA 57.107 40.000 0.00 0.00 0.00 3.28
114 115 2.892784 AAATTTCGTTCGGCCCAAAA 57.107 40.000 0.00 0.00 0.00 2.44
115 116 3.394674 AAATTTCGTTCGGCCCAAAAT 57.605 38.095 0.00 0.00 0.00 1.82
116 117 2.362169 ATTTCGTTCGGCCCAAAATG 57.638 45.000 0.00 0.00 0.00 2.32
117 118 1.033574 TTTCGTTCGGCCCAAAATGT 58.966 45.000 0.00 0.00 0.00 2.71
118 119 0.594110 TTCGTTCGGCCCAAAATGTC 59.406 50.000 0.00 0.00 0.00 3.06
119 120 0.535328 TCGTTCGGCCCAAAATGTCA 60.535 50.000 0.00 0.00 0.00 3.58
120 121 0.386731 CGTTCGGCCCAAAATGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
121 122 0.386731 GTTCGGCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
122 123 1.519751 TTCGGCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
123 124 1.969064 CGGCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
124 125 1.312371 CGGCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
125 126 0.173255 GGCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
126 127 0.887933 GCCCAAAATGTCACGGATGT 59.112 50.000 0.00 0.00 0.00 3.06
128 129 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
129 130 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
130 131 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
131 132 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
132 133 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
133 134 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
134 135 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
180 181 0.687354 AACGCTCACTGTTCATCCCT 59.313 50.000 0.00 0.00 0.00 4.20
201 202 2.182842 GGCAGCATCGATCGGCTTT 61.183 57.895 16.41 0.00 38.56 3.51
248 249 2.182825 CTCGATCGGGTTCAGTTAACG 58.817 52.381 16.41 0.00 39.13 3.18
346 347 0.526662 CGCTCGGGTTCAGTTAGAGT 59.473 55.000 0.00 0.00 0.00 3.24
357 358 1.199327 CAGTTAGAGTCAACGCCTCGA 59.801 52.381 0.00 0.00 34.08 4.04
533 534 1.966451 CCGCCCAGAACGAAAAGCT 60.966 57.895 0.00 0.00 0.00 3.74
763 766 0.938168 GCGGATCTAACTTACGCGGG 60.938 60.000 12.47 0.00 40.84 6.13
769 772 0.108520 CTAACTTACGCGGGCCAAGA 60.109 55.000 12.47 0.31 0.00 3.02
773 776 1.918868 CTTACGCGGGCCAAGAAACC 61.919 60.000 12.47 0.00 0.00 3.27
776 779 2.396157 CGCGGGCCAAGAAACCTAC 61.396 63.158 4.39 0.00 0.00 3.18
777 780 1.302993 GCGGGCCAAGAAACCTACA 60.303 57.895 4.39 0.00 0.00 2.74
778 781 1.305930 GCGGGCCAAGAAACCTACAG 61.306 60.000 4.39 0.00 0.00 2.74
783 786 3.597255 GGCCAAGAAACCTACAGTACTC 58.403 50.000 0.00 0.00 0.00 2.59
817 820 3.081554 CAAGCCCACCTAGTGCCT 58.918 61.111 0.00 0.00 31.34 4.75
1539 1685 0.549950 CTCCGACTAGGGTCAGGGTA 59.450 60.000 0.00 0.00 42.21 3.69
1568 1724 2.779755 TGCCCGCTTCTTGATTCTTA 57.220 45.000 0.00 0.00 0.00 2.10
1634 1819 7.036829 TGACTGCAAATCATGTTAATTCCATG 58.963 34.615 10.37 10.37 40.82 3.66
1711 1962 4.357142 GCATCATGATGTTTCTTTGCGAT 58.643 39.130 31.09 0.00 40.80 4.58
1901 2161 4.101448 GCCACCATGGGCGTCTCT 62.101 66.667 18.09 0.00 45.40 3.10
2127 2412 1.000607 GTACTGTCTGCCTCGTGTTGA 60.001 52.381 0.00 0.00 0.00 3.18
2155 2440 7.859325 ACAGTGTACTGAATTTGTTACAGTT 57.141 32.000 18.18 0.00 46.59 3.16
2213 2498 2.040278 TCAGCTAGGACTTGGCAATTGT 59.960 45.455 7.40 0.00 0.00 2.71
2219 2504 4.058721 AGGACTTGGCAATTGTTTGAAC 57.941 40.909 7.40 0.00 34.60 3.18
2220 2505 3.706086 AGGACTTGGCAATTGTTTGAACT 59.294 39.130 7.40 0.00 34.60 3.01
2231 2519 7.201600 GGCAATTGTTTGAACTGTTGTATTTGT 60.202 33.333 7.40 0.00 34.60 2.83
2254 2626 3.996480 ACAGTCTGAAGCTTAGTTGGTC 58.004 45.455 6.91 0.00 0.00 4.02
2259 2631 4.621886 GTCTGAAGCTTAGTTGGTCGTTAG 59.378 45.833 0.00 0.00 0.00 2.34
2262 2634 5.790593 TGAAGCTTAGTTGGTCGTTAGATT 58.209 37.500 0.00 0.00 0.00 2.40
2301 2673 5.598417 ACTTAAAAGCCCAAATCAGTTCAGT 59.402 36.000 0.00 0.00 0.00 3.41
2302 2674 4.590850 AAAAGCCCAAATCAGTTCAGTC 57.409 40.909 0.00 0.00 0.00 3.51
2303 2675 2.957402 AGCCCAAATCAGTTCAGTCA 57.043 45.000 0.00 0.00 0.00 3.41
2304 2676 3.446442 AGCCCAAATCAGTTCAGTCAT 57.554 42.857 0.00 0.00 0.00 3.06
2306 2678 5.121380 AGCCCAAATCAGTTCAGTCATAT 57.879 39.130 0.00 0.00 0.00 1.78
2307 2679 5.128919 AGCCCAAATCAGTTCAGTCATATC 58.871 41.667 0.00 0.00 0.00 1.63
2308 2680 4.883585 GCCCAAATCAGTTCAGTCATATCA 59.116 41.667 0.00 0.00 0.00 2.15
2309 2681 5.008415 GCCCAAATCAGTTCAGTCATATCAG 59.992 44.000 0.00 0.00 0.00 2.90
2310 2682 6.118170 CCCAAATCAGTTCAGTCATATCAGT 58.882 40.000 0.00 0.00 0.00 3.41
2311 2683 6.600822 CCCAAATCAGTTCAGTCATATCAGTT 59.399 38.462 0.00 0.00 0.00 3.16
2313 2690 7.335171 CCAAATCAGTTCAGTCATATCAGTTCA 59.665 37.037 0.00 0.00 0.00 3.18
2315 2692 5.414360 TCAGTTCAGTCATATCAGTTCAGC 58.586 41.667 0.00 0.00 0.00 4.26
2318 2695 6.035866 CAGTTCAGTCATATCAGTTCAGCTTC 59.964 42.308 0.00 0.00 0.00 3.86
2319 2696 5.665916 TCAGTCATATCAGTTCAGCTTCA 57.334 39.130 0.00 0.00 0.00 3.02
2320 2697 5.414360 TCAGTCATATCAGTTCAGCTTCAC 58.586 41.667 0.00 0.00 0.00 3.18
2325 2702 7.656542 AGTCATATCAGTTCAGCTTCACATATG 59.343 37.037 0.00 0.00 0.00 1.78
2334 2711 5.683681 TCAGCTTCACATATGATTTAGCCA 58.316 37.500 10.38 0.52 37.04 4.75
2335 2712 6.121590 TCAGCTTCACATATGATTTAGCCAA 58.878 36.000 10.38 1.75 37.04 4.52
2337 2714 6.861572 CAGCTTCACATATGATTTAGCCAATG 59.138 38.462 10.38 4.10 37.04 2.82
2348 2726 6.186957 TGATTTAGCCAATGGTGTAATCAGT 58.813 36.000 15.70 0.00 33.39 3.41
2361 2739 8.335532 TGGTGTAATCAGTAAGAAAATTCAGG 57.664 34.615 0.00 0.00 0.00 3.86
2372 2750 6.840780 AAGAAAATTCAGGTTGTATCCCAG 57.159 37.500 0.00 0.00 0.00 4.45
2425 2803 4.930963 CACATTACAGTGCTTGGAAAACA 58.069 39.130 0.00 0.00 32.05 2.83
2426 2804 4.977963 CACATTACAGTGCTTGGAAAACAG 59.022 41.667 0.00 0.00 32.05 3.16
2427 2805 4.644685 ACATTACAGTGCTTGGAAAACAGT 59.355 37.500 0.00 0.00 32.05 3.55
2428 2806 4.630894 TTACAGTGCTTGGAAAACAGTG 57.369 40.909 0.00 0.00 39.97 3.66
2478 2856 3.142174 GTTCACTGAAGCTTAGCTGGTT 58.858 45.455 7.77 0.00 39.62 3.67
2728 3173 8.862325 TTCAGAAAGAAAAATCAGGCTGTATA 57.138 30.769 15.27 0.00 32.05 1.47
2856 3729 2.828520 TGCAAGAAACCACCACTTTGAA 59.171 40.909 0.00 0.00 0.00 2.69
3163 4287 2.475466 GCGACGGTGATCGAGGGTA 61.475 63.158 0.00 0.00 45.13 3.69
3211 4335 1.605738 AACCGAGGGTGTAGAGCGT 60.606 57.895 0.00 0.00 35.34 5.07
3359 4483 0.396435 TGCTGGTCCGATGACAGTTT 59.604 50.000 0.00 0.00 43.65 2.66
3497 7301 0.750546 TAGGACGTGACGGGGATGAG 60.751 60.000 10.66 0.00 0.00 2.90
3733 8091 1.455773 ATCCAGATCGAGGTCGGCA 60.456 57.895 7.06 0.00 40.29 5.69
3780 8169 3.876589 GACACGAAGGCGGCTCCAA 62.877 63.158 13.70 0.00 43.17 3.53
4071 8495 6.018589 TCCGTCAATCAATGTTATTTGCAA 57.981 33.333 0.00 0.00 0.00 4.08
4125 8549 7.693120 TGTCACAAAAATGTAACGTAGTGTTTC 59.307 33.333 0.00 0.00 45.00 2.78
4170 8594 4.646945 TGGTGGTTTCTTGCAATTTACTCA 59.353 37.500 0.00 0.00 0.00 3.41
4171 8595 5.221224 TGGTGGTTTCTTGCAATTTACTCAG 60.221 40.000 0.00 0.00 0.00 3.35
4172 8596 4.681483 GTGGTTTCTTGCAATTTACTCAGC 59.319 41.667 0.00 0.00 0.00 4.26
4173 8597 4.340666 TGGTTTCTTGCAATTTACTCAGCA 59.659 37.500 0.00 0.00 34.79 4.41
4174 8598 5.163468 TGGTTTCTTGCAATTTACTCAGCAA 60.163 36.000 0.00 0.00 43.90 3.91
4175 8599 5.928264 GGTTTCTTGCAATTTACTCAGCAAT 59.072 36.000 0.00 0.00 44.85 3.56
4176 8600 7.090173 GGTTTCTTGCAATTTACTCAGCAATA 58.910 34.615 0.00 0.00 44.85 1.90
4177 8601 7.761249 GGTTTCTTGCAATTTACTCAGCAATAT 59.239 33.333 0.00 0.00 44.85 1.28
4178 8602 8.589629 GTTTCTTGCAATTTACTCAGCAATATG 58.410 33.333 0.00 0.00 44.85 1.78
4179 8603 7.628769 TCTTGCAATTTACTCAGCAATATGA 57.371 32.000 0.00 0.00 44.85 2.15
4277 8706 3.898123 AGTGTAGAGAAAGACCAGAGCAA 59.102 43.478 0.00 0.00 0.00 3.91
4364 8801 0.753262 CAGTGAGATAGGGGTTCGGG 59.247 60.000 0.00 0.00 0.00 5.14
4455 8952 7.025963 CCTATTTGCTGTTCTCAAATTCAGAC 58.974 38.462 6.32 0.00 42.27 3.51
4497 8994 2.194271 GCGGTGACATTAGTCTGTAGC 58.806 52.381 0.00 0.00 45.20 3.58
4543 9040 7.549488 CCACTTAAAGTTTCAGTCCTACCTATG 59.451 40.741 0.00 0.00 0.00 2.23
4544 9041 8.311836 CACTTAAAGTTTCAGTCCTACCTATGA 58.688 37.037 0.00 0.00 0.00 2.15
4545 9042 9.047947 ACTTAAAGTTTCAGTCCTACCTATGAT 57.952 33.333 0.00 0.00 0.00 2.45
4546 9043 9.319143 CTTAAAGTTTCAGTCCTACCTATGATG 57.681 37.037 0.00 0.00 0.00 3.07
4547 9044 7.496346 AAAGTTTCAGTCCTACCTATGATGA 57.504 36.000 0.00 0.00 0.00 2.92
4548 9045 7.496346 AAGTTTCAGTCCTACCTATGATGAA 57.504 36.000 0.00 0.00 0.00 2.57
4549 9046 7.682787 AGTTTCAGTCCTACCTATGATGAAT 57.317 36.000 0.00 0.00 0.00 2.57
4550 9047 8.095452 AGTTTCAGTCCTACCTATGATGAATT 57.905 34.615 0.00 0.00 0.00 2.17
4551 9048 9.213777 AGTTTCAGTCCTACCTATGATGAATTA 57.786 33.333 0.00 0.00 0.00 1.40
4558 9062 7.547370 GTCCTACCTATGATGAATTATGCAGAC 59.453 40.741 0.00 0.00 0.00 3.51
4559 9063 7.235399 TCCTACCTATGATGAATTATGCAGACA 59.765 37.037 0.00 0.00 0.00 3.41
4700 9246 3.092334 AGGACGGTTTTGTGCAAATTC 57.908 42.857 0.00 0.00 31.86 2.17
4762 9315 3.670105 GGGGGAACTGAGCAATTGA 57.330 52.632 10.34 0.00 0.00 2.57
4763 9316 1.467920 GGGGGAACTGAGCAATTGAG 58.532 55.000 10.34 0.00 0.00 3.02
4764 9317 0.813821 GGGGAACTGAGCAATTGAGC 59.186 55.000 10.34 0.00 0.00 4.26
4798 9351 4.410492 AGCAACTTCTGAATAGTTTGCG 57.590 40.909 14.86 0.00 38.78 4.85
4856 9944 2.863153 GCACACATGCGAGACCAC 59.137 61.111 0.00 0.00 43.33 4.16
4857 9945 1.960763 GCACACATGCGAGACCACA 60.961 57.895 0.00 0.00 43.33 4.17
4858 9946 1.904852 GCACACATGCGAGACCACAG 61.905 60.000 0.00 0.00 43.33 3.66
4859 9947 1.004560 ACACATGCGAGACCACAGG 60.005 57.895 0.00 0.00 0.00 4.00
4877 9965 0.322906 GGCTACAGCTGGGCTTTTCT 60.323 55.000 25.39 4.47 36.40 2.52
5123 10211 5.987777 TTGCACATTCTCAAACATTTTGG 57.012 34.783 0.00 0.00 0.00 3.28
5124 10212 5.273674 TGCACATTCTCAAACATTTTGGA 57.726 34.783 0.00 0.00 0.00 3.53
5125 10213 5.668471 TGCACATTCTCAAACATTTTGGAA 58.332 33.333 0.00 2.92 0.00 3.53
5126 10214 5.754406 TGCACATTCTCAAACATTTTGGAAG 59.246 36.000 0.00 0.00 0.00 3.46
5127 10215 5.754890 GCACATTCTCAAACATTTTGGAAGT 59.245 36.000 0.00 1.46 0.00 3.01
5128 10216 6.074142 GCACATTCTCAAACATTTTGGAAGTC 60.074 38.462 0.00 0.00 0.00 3.01
5129 10217 6.979817 CACATTCTCAAACATTTTGGAAGTCA 59.020 34.615 0.00 0.00 0.00 3.41
5130 10218 7.654520 CACATTCTCAAACATTTTGGAAGTCAT 59.345 33.333 0.00 0.00 0.00 3.06
5131 10219 7.654520 ACATTCTCAAACATTTTGGAAGTCATG 59.345 33.333 0.00 0.00 0.00 3.07
5132 10220 6.088016 TCTCAAACATTTTGGAAGTCATGG 57.912 37.500 0.00 0.00 0.00 3.66
5133 10221 5.832595 TCTCAAACATTTTGGAAGTCATGGA 59.167 36.000 0.00 0.00 0.00 3.41
5134 10222 6.494491 TCTCAAACATTTTGGAAGTCATGGAT 59.506 34.615 0.00 0.00 0.00 3.41
5135 10223 7.669304 TCTCAAACATTTTGGAAGTCATGGATA 59.331 33.333 0.00 0.00 0.00 2.59
5136 10224 7.601856 TCAAACATTTTGGAAGTCATGGATAC 58.398 34.615 0.00 0.00 0.00 2.24
5191 10279 9.447157 TCATGAATAATTTTCCAATTTGGGAAC 57.553 29.630 15.37 1.06 46.28 3.62
5192 10280 9.228949 CATGAATAATTTTCCAATTTGGGAACA 57.771 29.630 15.37 6.62 46.28 3.18
5193 10281 9.978336 ATGAATAATTTTCCAATTTGGGAACAT 57.022 25.926 15.37 8.52 46.28 2.71
5194 10282 9.804977 TGAATAATTTTCCAATTTGGGAACATT 57.195 25.926 15.37 15.33 46.28 2.71
5200 10288 8.807948 TTTTCCAATTTGGGAACATTTTTACA 57.192 26.923 15.37 0.00 46.28 2.41
5201 10289 8.807948 TTTCCAATTTGGGAACATTTTTACAA 57.192 26.923 15.37 0.00 46.28 2.41
5202 10290 8.443953 TTCCAATTTGGGAACATTTTTACAAG 57.556 30.769 15.37 0.00 41.92 3.16
5203 10291 7.569240 TCCAATTTGGGAACATTTTTACAAGT 58.431 30.769 15.37 0.00 42.32 3.16
5204 10292 7.713073 TCCAATTTGGGAACATTTTTACAAGTC 59.287 33.333 15.37 0.00 42.32 3.01
5205 10293 7.497249 CCAATTTGGGAACATTTTTACAAGTCA 59.503 33.333 7.60 0.00 42.32 3.41
5206 10294 9.054922 CAATTTGGGAACATTTTTACAAGTCAT 57.945 29.630 0.00 0.00 42.32 3.06
5207 10295 8.606040 ATTTGGGAACATTTTTACAAGTCATG 57.394 30.769 0.00 0.00 42.32 3.07
5208 10296 6.968263 TGGGAACATTTTTACAAGTCATGA 57.032 33.333 0.00 0.00 33.40 3.07
5209 10297 7.353414 TGGGAACATTTTTACAAGTCATGAA 57.647 32.000 0.00 0.00 33.40 2.57
5210 10298 7.206687 TGGGAACATTTTTACAAGTCATGAAC 58.793 34.615 0.00 0.00 33.40 3.18
5211 10299 7.147828 TGGGAACATTTTTACAAGTCATGAACA 60.148 33.333 0.00 0.00 33.40 3.18
5212 10300 7.872483 GGGAACATTTTTACAAGTCATGAACAT 59.128 33.333 0.00 0.00 0.00 2.71
5213 10301 9.260002 GGAACATTTTTACAAGTCATGAACATT 57.740 29.630 0.00 0.00 0.00 2.71
5239 10327 8.783833 TTTTGGAATTGTGAACATTCTTTTCA 57.216 26.923 0.00 0.00 0.00 2.69
5240 10328 8.422973 TTTGGAATTGTGAACATTCTTTTCAG 57.577 30.769 0.00 0.00 33.63 3.02
5241 10329 7.345422 TGGAATTGTGAACATTCTTTTCAGA 57.655 32.000 0.00 0.00 33.63 3.27
5242 10330 7.780064 TGGAATTGTGAACATTCTTTTCAGAA 58.220 30.769 0.00 0.00 43.45 3.02
5244 10332 8.919661 GGAATTGTGAACATTCTTTTCAGAATC 58.080 33.333 7.63 3.42 45.26 2.52
5245 10333 8.511465 AATTGTGAACATTCTTTTCAGAATCG 57.489 30.769 7.63 0.00 45.26 3.34
5246 10334 5.451908 TGTGAACATTCTTTTCAGAATCGC 58.548 37.500 0.00 0.00 45.26 4.58
5247 10335 5.239306 TGTGAACATTCTTTTCAGAATCGCT 59.761 36.000 0.00 0.00 45.26 4.93
5248 10336 6.426633 TGTGAACATTCTTTTCAGAATCGCTA 59.573 34.615 0.00 0.00 45.26 4.26
5249 10337 7.041440 TGTGAACATTCTTTTCAGAATCGCTAA 60.041 33.333 0.00 0.00 45.26 3.09
5250 10338 7.269297 GTGAACATTCTTTTCAGAATCGCTAAC 59.731 37.037 0.00 0.00 45.26 2.34
5251 10339 6.801539 ACATTCTTTTCAGAATCGCTAACA 57.198 33.333 0.00 0.00 45.26 2.41
5252 10340 7.202016 ACATTCTTTTCAGAATCGCTAACAA 57.798 32.000 0.00 0.00 45.26 2.83
5253 10341 7.820648 ACATTCTTTTCAGAATCGCTAACAAT 58.179 30.769 0.00 0.00 45.26 2.71
5254 10342 8.299570 ACATTCTTTTCAGAATCGCTAACAATT 58.700 29.630 0.00 0.00 45.26 2.32
5255 10343 9.132521 CATTCTTTTCAGAATCGCTAACAATTT 57.867 29.630 0.00 0.00 45.26 1.82
5256 10344 9.696917 ATTCTTTTCAGAATCGCTAACAATTTT 57.303 25.926 0.00 0.00 45.26 1.82
5257 10345 9.528018 TTCTTTTCAGAATCGCTAACAATTTTT 57.472 25.926 0.00 0.00 33.80 1.94
5258 10346 8.967218 TCTTTTCAGAATCGCTAACAATTTTTG 58.033 29.630 0.00 0.00 0.00 2.44
5259 10347 8.864069 TTTTCAGAATCGCTAACAATTTTTGA 57.136 26.923 0.00 0.00 0.00 2.69
5260 10348 8.864069 TTTCAGAATCGCTAACAATTTTTGAA 57.136 26.923 0.00 0.00 0.00 2.69
5261 10349 9.474920 TTTCAGAATCGCTAACAATTTTTGAAT 57.525 25.926 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.534500 TGGGCTCCTACTTCTATGACAAAA 59.466 41.667 0.00 0.00 0.00 2.44
3 4 4.081087 GTGGGCTCCTACTTCTATGACAAA 60.081 45.833 0.00 0.00 0.00 2.83
9 10 2.292918 TGTGGTGGGCTCCTACTTCTAT 60.293 50.000 2.46 0.00 0.00 1.98
10 11 1.078159 TGTGGTGGGCTCCTACTTCTA 59.922 52.381 2.46 0.00 0.00 2.10
11 12 0.178903 TGTGGTGGGCTCCTACTTCT 60.179 55.000 2.46 0.00 0.00 2.85
12 13 0.912486 ATGTGGTGGGCTCCTACTTC 59.088 55.000 2.46 0.00 0.00 3.01
13 14 0.912486 GATGTGGTGGGCTCCTACTT 59.088 55.000 2.46 0.00 0.00 2.24
14 15 0.043334 AGATGTGGTGGGCTCCTACT 59.957 55.000 2.46 0.00 0.00 2.57
15 16 1.789523 TAGATGTGGTGGGCTCCTAC 58.210 55.000 0.00 0.00 0.00 3.18
16 17 2.090775 TCATAGATGTGGTGGGCTCCTA 60.091 50.000 0.00 0.00 0.00 2.94
17 18 1.135094 CATAGATGTGGTGGGCTCCT 58.865 55.000 0.00 0.00 0.00 3.69
18 19 1.131638 TCATAGATGTGGTGGGCTCC 58.868 55.000 0.00 0.00 0.00 4.70
19 20 2.369860 TCATCATAGATGTGGTGGGCTC 59.630 50.000 6.86 0.00 0.00 4.70
20 21 2.411583 TCATCATAGATGTGGTGGGCT 58.588 47.619 6.86 0.00 0.00 5.19
21 22 2.936919 TCATCATAGATGTGGTGGGC 57.063 50.000 6.86 0.00 0.00 5.36
22 23 4.621510 CGGTATCATCATAGATGTGGTGGG 60.622 50.000 6.86 0.00 0.00 4.61
23 24 4.498241 CGGTATCATCATAGATGTGGTGG 58.502 47.826 6.86 0.00 0.00 4.61
24 25 4.498241 CCGGTATCATCATAGATGTGGTG 58.502 47.826 6.86 0.00 0.00 4.17
25 26 3.515502 CCCGGTATCATCATAGATGTGGT 59.484 47.826 0.00 0.00 0.00 4.16
26 27 3.515502 ACCCGGTATCATCATAGATGTGG 59.484 47.826 0.00 3.53 0.00 4.17
27 28 4.808414 ACCCGGTATCATCATAGATGTG 57.192 45.455 0.00 0.00 0.00 3.21
28 29 5.825593 AAACCCGGTATCATCATAGATGT 57.174 39.130 0.00 0.00 0.00 3.06
29 30 5.997746 ACAAAACCCGGTATCATCATAGATG 59.002 40.000 0.00 0.62 0.00 2.90
30 31 6.183361 TGACAAAACCCGGTATCATCATAGAT 60.183 38.462 0.00 0.00 0.00 1.98
31 32 5.129650 TGACAAAACCCGGTATCATCATAGA 59.870 40.000 0.00 0.00 0.00 1.98
32 33 5.236478 GTGACAAAACCCGGTATCATCATAG 59.764 44.000 0.00 0.00 0.00 2.23
33 34 5.120399 GTGACAAAACCCGGTATCATCATA 58.880 41.667 0.00 0.00 0.00 2.15
34 35 3.945285 GTGACAAAACCCGGTATCATCAT 59.055 43.478 0.00 0.00 0.00 2.45
35 36 3.244596 TGTGACAAAACCCGGTATCATCA 60.245 43.478 0.00 0.00 0.00 3.07
36 37 3.340034 TGTGACAAAACCCGGTATCATC 58.660 45.455 0.00 0.00 0.00 2.92
37 38 3.426787 TGTGACAAAACCCGGTATCAT 57.573 42.857 0.00 0.00 0.00 2.45
38 39 2.932855 TGTGACAAAACCCGGTATCA 57.067 45.000 0.00 0.00 0.00 2.15
39 40 4.776795 AATTGTGACAAAACCCGGTATC 57.223 40.909 0.62 0.00 0.00 2.24
40 41 5.065474 CGATAATTGTGACAAAACCCGGTAT 59.935 40.000 0.62 0.00 0.00 2.73
41 42 4.392445 CGATAATTGTGACAAAACCCGGTA 59.608 41.667 0.62 0.00 0.00 4.02
42 43 3.189702 CGATAATTGTGACAAAACCCGGT 59.810 43.478 0.62 0.00 0.00 5.28
43 44 3.189702 ACGATAATTGTGACAAAACCCGG 59.810 43.478 0.62 0.00 0.00 5.73
44 45 4.083749 TGACGATAATTGTGACAAAACCCG 60.084 41.667 0.62 7.01 0.00 5.28
45 46 5.365403 TGACGATAATTGTGACAAAACCC 57.635 39.130 0.62 0.00 0.00 4.11
46 47 7.970384 TCTATGACGATAATTGTGACAAAACC 58.030 34.615 0.62 0.00 0.00 3.27
47 48 9.478019 CTTCTATGACGATAATTGTGACAAAAC 57.522 33.333 0.62 0.00 0.00 2.43
48 49 9.214957 ACTTCTATGACGATAATTGTGACAAAA 57.785 29.630 0.62 0.00 0.00 2.44
49 50 8.655970 CACTTCTATGACGATAATTGTGACAAA 58.344 33.333 0.62 0.00 0.00 2.83
50 51 7.817478 ACACTTCTATGACGATAATTGTGACAA 59.183 33.333 0.00 0.00 0.00 3.18
51 52 7.320399 ACACTTCTATGACGATAATTGTGACA 58.680 34.615 0.00 0.00 0.00 3.58
52 53 7.488150 TGACACTTCTATGACGATAATTGTGAC 59.512 37.037 0.00 0.00 0.00 3.67
53 54 7.543756 TGACACTTCTATGACGATAATTGTGA 58.456 34.615 0.00 0.00 0.00 3.58
54 55 7.755582 TGACACTTCTATGACGATAATTGTG 57.244 36.000 0.00 0.00 0.00 3.33
61 62 9.014297 TCATACATATGACACTTCTATGACGAT 57.986 33.333 10.38 0.00 37.76 3.73
62 63 8.391075 TCATACATATGACACTTCTATGACGA 57.609 34.615 10.38 0.00 37.76 4.20
93 94 2.892784 TTGGGCCGAACGAAATTTTT 57.107 40.000 0.00 0.00 0.00 1.94
94 95 2.892784 TTTGGGCCGAACGAAATTTT 57.107 40.000 0.79 0.00 0.00 1.82
95 96 2.892784 TTTTGGGCCGAACGAAATTT 57.107 40.000 5.46 0.00 0.00 1.82
96 97 2.036604 ACATTTTGGGCCGAACGAAATT 59.963 40.909 5.46 0.00 31.28 1.82
97 98 1.616374 ACATTTTGGGCCGAACGAAAT 59.384 42.857 5.46 0.00 33.33 2.17
98 99 1.001158 GACATTTTGGGCCGAACGAAA 60.001 47.619 5.46 0.00 0.00 3.46
99 100 0.594110 GACATTTTGGGCCGAACGAA 59.406 50.000 5.46 0.00 0.00 3.85
100 101 0.535328 TGACATTTTGGGCCGAACGA 60.535 50.000 5.46 0.00 0.00 3.85
101 102 0.386731 GTGACATTTTGGGCCGAACG 60.387 55.000 5.46 3.01 0.00 3.95
102 103 0.386731 CGTGACATTTTGGGCCGAAC 60.387 55.000 5.46 0.00 0.00 3.95
103 104 1.519751 CCGTGACATTTTGGGCCGAA 61.520 55.000 0.79 0.79 0.00 4.30
104 105 1.969064 CCGTGACATTTTGGGCCGA 60.969 57.895 0.00 0.00 0.00 5.54
105 106 1.312371 ATCCGTGACATTTTGGGCCG 61.312 55.000 0.00 0.00 0.00 6.13
106 107 0.173255 CATCCGTGACATTTTGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
107 108 0.887933 ACATCCGTGACATTTTGGGC 59.112 50.000 0.00 0.00 0.00 5.36
108 109 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
109 110 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
110 111 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
111 112 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
112 113 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
180 181 2.418777 CCGATCGATGCTGCCTCA 59.581 61.111 18.66 0.00 0.00 3.86
201 202 2.099263 CCTTCGCTACTGCTGCTAACTA 59.901 50.000 0.00 0.00 36.97 2.24
346 347 1.947146 CGTGTGTTCGAGGCGTTGA 60.947 57.895 0.00 0.00 0.00 3.18
377 378 2.161486 GCGATGCGCGTTTCTCTCT 61.161 57.895 8.43 0.00 44.55 3.10
471 472 0.916086 TATTTGGGCCGTCCATGACT 59.084 50.000 0.00 0.00 46.52 3.41
489 490 1.009078 GACGCAGCTGCATGACATTA 58.991 50.000 36.03 0.00 42.21 1.90
656 658 8.408043 AAAAGACACATCCATGACATTTTAGA 57.592 30.769 0.00 0.00 0.00 2.10
717 719 6.395629 GTCTAATGTCCACAGCAAACTACTA 58.604 40.000 0.00 0.00 0.00 1.82
718 720 5.238583 GTCTAATGTCCACAGCAAACTACT 58.761 41.667 0.00 0.00 0.00 2.57
719 721 4.091509 CGTCTAATGTCCACAGCAAACTAC 59.908 45.833 0.00 0.00 0.00 2.73
720 722 4.242475 CGTCTAATGTCCACAGCAAACTA 58.758 43.478 0.00 0.00 0.00 2.24
727 730 0.992072 CGCACGTCTAATGTCCACAG 59.008 55.000 0.00 0.00 0.00 3.66
763 766 4.538746 AGAGTACTGTAGGTTTCTTGGC 57.461 45.455 0.00 0.00 0.00 4.52
769 772 3.306571 GGCCGAAAGAGTACTGTAGGTTT 60.307 47.826 0.00 0.00 30.29 3.27
773 776 1.798079 GCGGCCGAAAGAGTACTGTAG 60.798 57.143 33.48 0.00 0.00 2.74
776 779 2.158959 CGCGGCCGAAAGAGTACTG 61.159 63.158 33.48 0.95 36.29 2.74
777 780 2.181021 CGCGGCCGAAAGAGTACT 59.819 61.111 33.48 0.00 36.29 2.73
778 781 2.884207 CCGCGGCCGAAAGAGTAC 60.884 66.667 33.48 7.28 36.29 2.73
817 820 2.506217 CGTCGCCGCTCAGCTTTA 60.506 61.111 0.00 0.00 0.00 1.85
847 852 2.883888 GCCAAGGCAGGGTATTTCAAGA 60.884 50.000 6.14 0.00 41.49 3.02
1568 1724 0.096976 CCAAGTCGCGCAAATTCGAT 59.903 50.000 8.75 0.00 37.06 3.59
1621 1806 2.101249 CCAAGGCGCATGGAATTAACAT 59.899 45.455 22.98 0.00 40.56 2.71
1634 1819 0.179189 CACGAATTTCTCCAAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
1711 1962 1.133823 TGAAGGGAAGCTGCAGTTGAA 60.134 47.619 16.64 0.00 0.00 2.69
1942 2202 2.034879 TCGACGACGAGTGGGGTAC 61.035 63.158 5.75 0.00 43.81 3.34
2127 2412 9.567848 CTGTAACAAATTCAGTACACTGTTTTT 57.432 29.630 9.11 7.58 44.12 1.94
2155 2440 7.701924 CAGCAGTTTCAGTGAACTATTTTTCAA 59.298 33.333 4.68 0.00 37.76 2.69
2196 2481 5.010012 AGTTCAAACAATTGCCAAGTCCTAG 59.990 40.000 5.05 0.00 36.45 3.02
2219 2504 7.041780 AGCTTCAGACTGTAACAAATACAACAG 60.042 37.037 1.59 0.00 43.75 3.16
2220 2505 6.765989 AGCTTCAGACTGTAACAAATACAACA 59.234 34.615 1.59 0.00 43.75 3.33
2231 2519 5.539048 GACCAACTAAGCTTCAGACTGTAA 58.461 41.667 0.00 0.00 0.00 2.41
2233 2521 3.553096 CGACCAACTAAGCTTCAGACTGT 60.553 47.826 0.00 0.00 0.00 3.55
2254 2626 6.202954 AGTTCCAAGAGTGTGAAAATCTAACG 59.797 38.462 0.00 0.00 0.00 3.18
2259 2631 9.237846 CTTTTAAGTTCCAAGAGTGTGAAAATC 57.762 33.333 0.00 0.00 0.00 2.17
2262 2634 6.405397 GGCTTTTAAGTTCCAAGAGTGTGAAA 60.405 38.462 0.00 0.00 0.00 2.69
2301 2673 7.729116 TCATATGTGAAGCTGAACTGATATGA 58.271 34.615 1.90 13.04 32.01 2.15
2302 2674 7.958053 TCATATGTGAAGCTGAACTGATATG 57.042 36.000 1.90 0.56 0.00 1.78
2303 2675 9.570468 AAATCATATGTGAAGCTGAACTGATAT 57.430 29.630 1.90 0.00 38.01 1.63
2304 2676 8.969260 AAATCATATGTGAAGCTGAACTGATA 57.031 30.769 1.90 0.00 38.01 2.15
2306 2678 7.011763 GCTAAATCATATGTGAAGCTGAACTGA 59.988 37.037 1.90 0.00 38.01 3.41
2307 2679 7.130917 GCTAAATCATATGTGAAGCTGAACTG 58.869 38.462 1.90 0.00 38.01 3.16
2308 2680 6.261826 GGCTAAATCATATGTGAAGCTGAACT 59.738 38.462 12.57 0.00 36.45 3.01
2309 2681 6.038603 TGGCTAAATCATATGTGAAGCTGAAC 59.961 38.462 12.57 0.00 36.45 3.18
2310 2682 6.121590 TGGCTAAATCATATGTGAAGCTGAA 58.878 36.000 12.57 0.17 36.45 3.02
2311 2683 5.683681 TGGCTAAATCATATGTGAAGCTGA 58.316 37.500 12.57 0.69 36.45 4.26
2313 2690 6.015688 CCATTGGCTAAATCATATGTGAAGCT 60.016 38.462 12.57 0.00 36.45 3.74
2315 2692 7.143340 CACCATTGGCTAAATCATATGTGAAG 58.857 38.462 1.54 0.00 38.01 3.02
2318 2695 6.395426 ACACCATTGGCTAAATCATATGTG 57.605 37.500 1.54 0.00 0.00 3.21
2319 2696 8.710749 ATTACACCATTGGCTAAATCATATGT 57.289 30.769 1.54 0.00 0.00 2.29
2320 2697 8.795513 TGATTACACCATTGGCTAAATCATATG 58.204 33.333 16.98 0.00 0.00 1.78
2325 2702 6.699575 ACTGATTACACCATTGGCTAAATC 57.300 37.500 1.54 9.55 0.00 2.17
2335 2712 8.960591 CCTGAATTTTCTTACTGATTACACCAT 58.039 33.333 0.00 0.00 0.00 3.55
2337 2714 8.336801 ACCTGAATTTTCTTACTGATTACACC 57.663 34.615 0.00 0.00 0.00 4.16
2348 2726 7.695055 TCTGGGATACAACCTGAATTTTCTTA 58.305 34.615 0.00 0.00 33.69 2.10
2361 2739 6.377327 CATGTAATGGTTCTGGGATACAAC 57.623 41.667 0.00 0.00 41.79 3.32
2417 2795 6.767524 ACAAATTCAGTACACTGTTTTCCA 57.232 33.333 9.11 0.00 44.12 3.53
2418 2796 8.185505 TGTAACAAATTCAGTACACTGTTTTCC 58.814 33.333 9.11 1.61 44.12 3.13
2419 2797 9.221775 CTGTAACAAATTCAGTACACTGTTTTC 57.778 33.333 9.11 1.62 44.12 2.29
2420 2798 8.736244 ACTGTAACAAATTCAGTACACTGTTTT 58.264 29.630 9.11 7.88 44.12 2.43
2421 2799 8.276252 ACTGTAACAAATTCAGTACACTGTTT 57.724 30.769 9.11 1.41 44.12 2.83
2424 2802 7.438160 TCAGACTGTAACAAATTCAGTACACTG 59.562 37.037 1.59 2.84 41.58 3.66
2425 2803 7.497595 TCAGACTGTAACAAATTCAGTACACT 58.502 34.615 1.59 0.00 41.58 3.55
2426 2804 7.709269 TCAGACTGTAACAAATTCAGTACAC 57.291 36.000 1.59 0.00 41.58 2.90
2427 2805 8.725405 TTTCAGACTGTAACAAATTCAGTACA 57.275 30.769 1.59 0.00 41.58 2.90
2428 2806 9.997482 TTTTTCAGACTGTAACAAATTCAGTAC 57.003 29.630 1.59 0.00 41.58 2.73
2478 2856 6.959639 ATTGCAAAGTCCTAACTGAAGAAA 57.040 33.333 1.71 0.00 35.36 2.52
2583 3016 3.809832 TCTTTCAAGTTCCAAGAGCGAAG 59.190 43.478 0.00 0.00 0.00 3.79
2587 3020 6.758416 ACAATTTTCTTTCAAGTTCCAAGAGC 59.242 34.615 0.00 0.00 0.00 4.09
2728 3173 6.303839 ACTAATTTCCATGTAGTGTTGTGGT 58.696 36.000 0.00 0.00 33.47 4.16
2856 3729 5.763876 AGTGTTTTCTGATAACCTAGCCT 57.236 39.130 8.23 0.00 0.00 4.58
3163 4287 2.278206 CGCGTCGCTGCACTCTAT 60.278 61.111 16.36 0.00 34.15 1.98
3189 4313 0.108615 CTCTACACCCTCGGTTGCTG 60.109 60.000 0.00 0.00 31.02 4.41
3211 4335 1.002430 GATATCCTGGATGCTTCGCCA 59.998 52.381 19.42 0.00 0.00 5.69
3434 5286 6.862711 AGTACTTGAGAAGTAAAAACAGCC 57.137 37.500 0.00 0.00 44.95 4.85
3497 7301 0.032267 GGTCACCGGAGTATAGCAGC 59.968 60.000 9.46 0.00 0.00 5.25
3780 8169 1.753463 GGACCGTCCTCGATCTGGT 60.753 63.158 10.59 0.00 39.71 4.00
4125 8549 3.456277 ACTTTGAGGGCTAGGTTATCAGG 59.544 47.826 0.00 0.00 0.00 3.86
4170 8594 4.910304 AGGAGGTAAGGTCATCATATTGCT 59.090 41.667 0.00 0.00 0.00 3.91
4171 8595 5.221722 TGAGGAGGTAAGGTCATCATATTGC 60.222 44.000 0.00 0.00 30.09 3.56
4172 8596 6.226787 GTGAGGAGGTAAGGTCATCATATTG 58.773 44.000 0.00 0.00 37.11 1.90
4173 8597 5.308237 GGTGAGGAGGTAAGGTCATCATATT 59.692 44.000 0.00 0.00 37.11 1.28
4174 8598 4.841246 GGTGAGGAGGTAAGGTCATCATAT 59.159 45.833 0.00 0.00 37.11 1.78
4175 8599 4.223953 GGTGAGGAGGTAAGGTCATCATA 58.776 47.826 0.00 0.00 37.11 2.15
4176 8600 3.041946 GGTGAGGAGGTAAGGTCATCAT 58.958 50.000 0.00 0.00 37.11 2.45
4177 8601 2.467880 GGTGAGGAGGTAAGGTCATCA 58.532 52.381 0.00 0.00 32.54 3.07
4178 8602 1.409427 CGGTGAGGAGGTAAGGTCATC 59.591 57.143 0.00 0.00 0.00 2.92
4179 8603 1.273098 ACGGTGAGGAGGTAAGGTCAT 60.273 52.381 0.00 0.00 0.00 3.06
4277 8706 1.587933 GAAGCGACGGTCAGGACTCT 61.588 60.000 9.10 0.00 0.00 3.24
4364 8801 4.450082 ACACAACAACTTCTGGGTTTTC 57.550 40.909 0.00 0.00 0.00 2.29
4455 8952 5.200454 GCATCGTTGTTCAAGCAGTATATG 58.800 41.667 0.00 0.00 0.00 1.78
4497 8994 1.006832 CCGGAATAAGAGTGCAACCG 58.993 55.000 0.00 0.00 37.80 4.44
4543 9040 7.259882 TGGAAACATTGTCTGCATAATTCATC 58.740 34.615 0.00 0.00 33.40 2.92
4544 9041 7.172868 TGGAAACATTGTCTGCATAATTCAT 57.827 32.000 0.00 0.00 33.40 2.57
4545 9042 6.587206 TGGAAACATTGTCTGCATAATTCA 57.413 33.333 0.00 0.00 33.40 2.57
4546 9043 5.517770 GCTGGAAACATTGTCTGCATAATTC 59.482 40.000 0.00 0.00 41.51 2.17
4547 9044 5.047164 TGCTGGAAACATTGTCTGCATAATT 60.047 36.000 4.97 0.00 41.51 1.40
4548 9045 4.463539 TGCTGGAAACATTGTCTGCATAAT 59.536 37.500 4.97 0.00 41.51 1.28
4549 9046 3.825585 TGCTGGAAACATTGTCTGCATAA 59.174 39.130 4.97 0.00 41.51 1.90
4550 9047 3.419943 TGCTGGAAACATTGTCTGCATA 58.580 40.909 4.97 0.00 41.51 3.14
4551 9048 2.230508 CTGCTGGAAACATTGTCTGCAT 59.769 45.455 8.34 0.00 41.51 3.96
4552 9049 1.610038 CTGCTGGAAACATTGTCTGCA 59.390 47.619 7.84 7.84 41.51 4.41
4558 9062 1.411394 CAACGCTGCTGGAAACATTG 58.589 50.000 0.00 0.00 41.51 2.82
4559 9063 0.318955 GCAACGCTGCTGGAAACATT 60.319 50.000 2.93 0.00 45.74 2.71
4632 9164 7.862372 TGAAAACACAAATTCATTCTCTGCTAC 59.138 33.333 0.00 0.00 30.94 3.58
4707 9253 0.326264 AACATTCTCAGGCTTCGGCT 59.674 50.000 0.00 0.00 41.44 5.52
4756 9309 8.642020 GTTGCTAAAAGAAACTATGCTCAATTG 58.358 33.333 0.00 0.00 30.88 2.32
4757 9310 8.579863 AGTTGCTAAAAGAAACTATGCTCAATT 58.420 29.630 0.00 0.00 42.22 2.32
4758 9311 8.115490 AGTTGCTAAAAGAAACTATGCTCAAT 57.885 30.769 0.00 0.00 42.22 2.57
4759 9312 7.510549 AGTTGCTAAAAGAAACTATGCTCAA 57.489 32.000 0.00 0.00 42.22 3.02
4760 9313 7.445402 AGAAGTTGCTAAAAGAAACTATGCTCA 59.555 33.333 0.70 0.00 43.21 4.26
4761 9314 7.748241 CAGAAGTTGCTAAAAGAAACTATGCTC 59.252 37.037 0.70 0.00 43.21 4.26
4762 9315 7.445402 TCAGAAGTTGCTAAAAGAAACTATGCT 59.555 33.333 0.70 0.00 43.21 3.79
4763 9316 7.584987 TCAGAAGTTGCTAAAAGAAACTATGC 58.415 34.615 0.70 0.00 43.21 3.14
4798 9351 0.452987 TCGCGACCACATACTGTACC 59.547 55.000 3.71 0.00 0.00 3.34
4846 9934 1.877576 CTGTAGCCTGTGGTCTCGCA 61.878 60.000 0.00 0.00 0.00 5.10
4849 9937 0.108424 CAGCTGTAGCCTGTGGTCTC 60.108 60.000 5.25 0.00 43.38 3.36
4852 9940 2.596851 CCCAGCTGTAGCCTGTGGT 61.597 63.158 13.81 0.00 43.38 4.16
4854 9942 2.437359 GCCCAGCTGTAGCCTGTG 60.437 66.667 13.81 0.00 43.38 3.66
4855 9943 1.783250 AAAGCCCAGCTGTAGCCTGT 61.783 55.000 19.28 5.70 39.62 4.00
4856 9944 0.610232 AAAAGCCCAGCTGTAGCCTG 60.610 55.000 19.28 0.73 39.62 4.85
4857 9945 0.322906 GAAAAGCCCAGCTGTAGCCT 60.323 55.000 19.28 6.79 39.62 4.58
4858 9946 0.322906 AGAAAAGCCCAGCTGTAGCC 60.323 55.000 19.28 7.00 39.62 3.93
4859 9947 1.539157 AAGAAAAGCCCAGCTGTAGC 58.461 50.000 13.81 15.15 39.62 3.58
5098 10186 7.120285 TCCAAAATGTTTGAGAATGTGCAAAAA 59.880 29.630 2.30 0.00 35.95 1.94
5099 10187 6.596888 TCCAAAATGTTTGAGAATGTGCAAAA 59.403 30.769 2.30 0.00 35.95 2.44
5100 10188 6.111382 TCCAAAATGTTTGAGAATGTGCAAA 58.889 32.000 2.30 0.00 0.00 3.68
5101 10189 5.668471 TCCAAAATGTTTGAGAATGTGCAA 58.332 33.333 2.30 0.00 0.00 4.08
5102 10190 5.273674 TCCAAAATGTTTGAGAATGTGCA 57.726 34.783 2.30 0.00 0.00 4.57
5103 10191 5.754890 ACTTCCAAAATGTTTGAGAATGTGC 59.245 36.000 2.30 0.00 0.00 4.57
5104 10192 6.979817 TGACTTCCAAAATGTTTGAGAATGTG 59.020 34.615 2.30 0.00 0.00 3.21
5105 10193 7.111247 TGACTTCCAAAATGTTTGAGAATGT 57.889 32.000 2.30 5.20 0.00 2.71
5106 10194 7.117236 CCATGACTTCCAAAATGTTTGAGAATG 59.883 37.037 0.00 3.83 0.00 2.67
5107 10195 7.015487 TCCATGACTTCCAAAATGTTTGAGAAT 59.985 33.333 0.00 0.00 0.00 2.40
5108 10196 6.323482 TCCATGACTTCCAAAATGTTTGAGAA 59.677 34.615 0.00 4.11 0.00 2.87
5109 10197 5.832595 TCCATGACTTCCAAAATGTTTGAGA 59.167 36.000 0.00 0.00 0.00 3.27
5110 10198 6.088016 TCCATGACTTCCAAAATGTTTGAG 57.912 37.500 0.00 0.00 0.00 3.02
5111 10199 6.669125 ATCCATGACTTCCAAAATGTTTGA 57.331 33.333 0.00 0.00 0.00 2.69
5112 10200 7.377398 TGTATCCATGACTTCCAAAATGTTTG 58.623 34.615 0.00 0.00 0.00 2.93
5113 10201 7.537596 TGTATCCATGACTTCCAAAATGTTT 57.462 32.000 0.00 0.00 0.00 2.83
5114 10202 7.722949 ATGTATCCATGACTTCCAAAATGTT 57.277 32.000 0.00 0.00 0.00 2.71
5115 10203 7.722949 AATGTATCCATGACTTCCAAAATGT 57.277 32.000 0.00 0.00 0.00 2.71
5116 10204 8.875803 CAAAATGTATCCATGACTTCCAAAATG 58.124 33.333 0.00 0.00 0.00 2.32
5117 10205 8.814931 TCAAAATGTATCCATGACTTCCAAAAT 58.185 29.630 0.00 0.00 0.00 1.82
5118 10206 8.187913 TCAAAATGTATCCATGACTTCCAAAA 57.812 30.769 0.00 0.00 0.00 2.44
5119 10207 7.773489 TCAAAATGTATCCATGACTTCCAAA 57.227 32.000 0.00 0.00 0.00 3.28
5120 10208 7.773489 TTCAAAATGTATCCATGACTTCCAA 57.227 32.000 0.00 0.00 0.00 3.53
5121 10209 7.959658 ATTCAAAATGTATCCATGACTTCCA 57.040 32.000 0.00 0.00 0.00 3.53
5122 10210 8.469200 TGAATTCAAAATGTATCCATGACTTCC 58.531 33.333 5.45 0.00 32.13 3.46
5123 10211 9.294030 GTGAATTCAAAATGTATCCATGACTTC 57.706 33.333 10.35 0.00 33.11 3.01
5124 10212 8.805175 TGTGAATTCAAAATGTATCCATGACTT 58.195 29.630 10.35 0.00 0.00 3.01
5125 10213 8.352137 TGTGAATTCAAAATGTATCCATGACT 57.648 30.769 10.35 0.00 0.00 3.41
5126 10214 8.984891 TTGTGAATTCAAAATGTATCCATGAC 57.015 30.769 10.35 0.00 0.00 3.06
5165 10253 9.447157 GTTCCCAAATTGGAAAATTATTCATGA 57.553 29.630 14.62 0.00 45.67 3.07
5166 10254 9.228949 TGTTCCCAAATTGGAAAATTATTCATG 57.771 29.630 14.62 0.00 45.67 3.07
5167 10255 9.978336 ATGTTCCCAAATTGGAAAATTATTCAT 57.022 25.926 14.62 4.43 45.67 2.57
5168 10256 9.804977 AATGTTCCCAAATTGGAAAATTATTCA 57.195 25.926 14.62 2.37 46.13 2.57
5174 10262 9.413734 TGTAAAAATGTTCCCAAATTGGAAAAT 57.586 25.926 14.62 4.05 45.67 1.82
5175 10263 8.807948 TGTAAAAATGTTCCCAAATTGGAAAA 57.192 26.923 14.62 4.66 45.67 2.29
5176 10264 8.807948 TTGTAAAAATGTTCCCAAATTGGAAA 57.192 26.923 14.62 0.00 45.67 3.13
5177 10265 8.049721 ACTTGTAAAAATGTTCCCAAATTGGAA 58.950 29.630 14.62 3.26 40.96 3.53
5178 10266 7.569240 ACTTGTAAAAATGTTCCCAAATTGGA 58.431 30.769 14.62 0.00 40.96 3.53
5179 10267 7.497249 TGACTTGTAAAAATGTTCCCAAATTGG 59.503 33.333 4.74 4.74 37.25 3.16
5180 10268 8.430801 TGACTTGTAAAAATGTTCCCAAATTG 57.569 30.769 0.00 0.00 0.00 2.32
5181 10269 9.054922 CATGACTTGTAAAAATGTTCCCAAATT 57.945 29.630 0.00 0.00 0.00 1.82
5182 10270 8.428063 TCATGACTTGTAAAAATGTTCCCAAAT 58.572 29.630 0.00 0.00 0.00 2.32
5183 10271 7.786030 TCATGACTTGTAAAAATGTTCCCAAA 58.214 30.769 0.00 0.00 0.00 3.28
5184 10272 7.353414 TCATGACTTGTAAAAATGTTCCCAA 57.647 32.000 0.00 0.00 0.00 4.12
5185 10273 6.968263 TCATGACTTGTAAAAATGTTCCCA 57.032 33.333 0.00 0.00 0.00 4.37
5186 10274 7.206687 TGTTCATGACTTGTAAAAATGTTCCC 58.793 34.615 0.00 0.00 0.00 3.97
5187 10275 8.816640 ATGTTCATGACTTGTAAAAATGTTCC 57.183 30.769 0.00 0.00 0.00 3.62
5213 10301 9.224267 TGAAAAGAATGTTCACAATTCCAAAAA 57.776 25.926 0.00 0.00 37.43 1.94
5214 10302 8.783833 TGAAAAGAATGTTCACAATTCCAAAA 57.216 26.923 0.00 0.00 37.43 2.44
5215 10303 8.256605 TCTGAAAAGAATGTTCACAATTCCAAA 58.743 29.630 0.00 0.00 37.43 3.28
5216 10304 7.780064 TCTGAAAAGAATGTTCACAATTCCAA 58.220 30.769 0.00 0.00 37.43 3.53
5217 10305 7.345422 TCTGAAAAGAATGTTCACAATTCCA 57.655 32.000 0.00 0.00 37.43 3.53
5218 10306 8.822652 ATTCTGAAAAGAATGTTCACAATTCC 57.177 30.769 0.27 0.00 37.43 3.01
5219 10307 8.633408 CGATTCTGAAAAGAATGTTCACAATTC 58.367 33.333 5.72 0.00 37.43 2.17
5220 10308 7.115378 GCGATTCTGAAAAGAATGTTCACAATT 59.885 33.333 5.72 0.00 37.43 2.32
5221 10309 6.583806 GCGATTCTGAAAAGAATGTTCACAAT 59.416 34.615 5.72 0.00 37.43 2.71
5222 10310 5.914635 GCGATTCTGAAAAGAATGTTCACAA 59.085 36.000 5.72 0.00 37.43 3.33
5223 10311 5.239306 AGCGATTCTGAAAAGAATGTTCACA 59.761 36.000 5.72 0.00 37.43 3.58
5224 10312 5.693814 AGCGATTCTGAAAAGAATGTTCAC 58.306 37.500 5.72 0.00 37.43 3.18
5225 10313 5.947228 AGCGATTCTGAAAAGAATGTTCA 57.053 34.783 5.72 0.00 40.79 3.18
5226 10314 7.298122 TGTTAGCGATTCTGAAAAGAATGTTC 58.702 34.615 5.72 0.00 38.50 3.18
5227 10315 7.202016 TGTTAGCGATTCTGAAAAGAATGTT 57.798 32.000 5.72 0.81 38.50 2.71
5228 10316 6.801539 TGTTAGCGATTCTGAAAAGAATGT 57.198 33.333 5.72 0.00 38.50 2.71
5229 10317 8.679288 AATTGTTAGCGATTCTGAAAAGAATG 57.321 30.769 5.72 1.01 38.50 2.67
5230 10318 9.696917 AAAATTGTTAGCGATTCTGAAAAGAAT 57.303 25.926 0.67 0.67 40.81 2.40
5231 10319 9.528018 AAAAATTGTTAGCGATTCTGAAAAGAA 57.472 25.926 0.00 0.00 0.00 2.52
5232 10320 8.967218 CAAAAATTGTTAGCGATTCTGAAAAGA 58.033 29.630 0.00 0.00 0.00 2.52
5233 10321 8.967218 TCAAAAATTGTTAGCGATTCTGAAAAG 58.033 29.630 0.00 0.00 0.00 2.27
5234 10322 8.864069 TCAAAAATTGTTAGCGATTCTGAAAA 57.136 26.923 0.00 0.00 0.00 2.29
5235 10323 8.864069 TTCAAAAATTGTTAGCGATTCTGAAA 57.136 26.923 11.50 0.00 32.76 2.69


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

AutoCloner maintained by Alex Coulton.