Multiple sequence alignment - TraesCS5D01G545700

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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 TraesCS5D01G545700 chr5D 100.000 3653 0 0 1 3653 554522328 554518676 0.000000e+00 6746
1 TraesCS5D01G545700 chr5D 88.280 529 57 3 3130 3653 459215187 459215715 2.390000e-176 628
2 TraesCS5D01G545700 chr5D 88.280 529 57 3 3130 3653 503316789 503316261 2.390000e-176 628
3 TraesCS5D01G545700 chr5D 89.958 239 24 0 1213 1451 554577242 554577004 3.540000e-80 309
4 TraesCS5D01G545700 chr5D 86.364 154 14 4 942 1092 554577472 554577323 1.050000e-35 161
5 TraesCS5D01G545700 chr4A 91.370 2503 158 29 1178 3652 614014791 614017263 0.000000e+00 3373
6 TraesCS5D01G545700 chr4A 93.120 407 25 2 448 852 614014043 614014448 8.730000e-166 593
7 TraesCS5D01G545700 chr4A 90.735 313 13 9 846 1156 614014503 614014801 1.580000e-108 403
8 TraesCS5D01G545700 chr4A 88.430 242 28 0 1210 1451 614004664 614004905 3.570000e-75 292
9 TraesCS5D01G545700 chr5B 91.220 1606 100 22 1490 3079 696165719 696167299 0.000000e+00 2146
10 TraesCS5D01G545700 chr5B 88.302 530 55 5 3130 3653 57510758 57511286 2.390000e-176 628
11 TraesCS5D01G545700 chr5B 88.280 529 57 3 3130 3653 57511838 57512366 2.390000e-176 628
12 TraesCS5D01G545700 chr5B 92.494 413 28 2 442 852 696164638 696165049 4.060000e-164 588
13 TraesCS5D01G545700 chr5B 96.429 308 11 0 1178 1485 696165376 696165683 3.250000e-140 508
14 TraesCS5D01G545700 chr5B 89.623 318 16 6 846 1163 696165093 696165393 4.420000e-104 388
15 TraesCS5D01G545700 chr5B 89.520 229 24 0 1223 1451 696154648 696154876 1.280000e-74 291
16 TraesCS5D01G545700 chr5B 92.063 189 7 4 123 306 696164009 696164194 3.620000e-65 259
17 TraesCS5D01G545700 chr5B 83.835 266 41 2 1597 1861 696154962 696155226 6.060000e-63 252
18 TraesCS5D01G545700 chr5B 85.714 119 17 0 1985 2103 689670338 689670456 3.830000e-25 126
19 TraesCS5D01G545700 chr3A 88.469 529 56 3 3130 3653 105553673 105554201 5.150000e-178 634
20 TraesCS5D01G545700 chr3A 88.280 529 57 3 3130 3653 593309808 593309280 2.390000e-176 628
21 TraesCS5D01G545700 chr3A 90.698 86 4 3 1018 1099 647499722 647499637 1.070000e-20 111
22 TraesCS5D01G545700 chr3A 92.958 71 5 0 1018 1088 647510182 647510112 1.790000e-18 104
23 TraesCS5D01G545700 chr5A 88.280 529 57 3 3130 3653 559028663 559029191 2.390000e-176 628
24 TraesCS5D01G545700 chr1A 88.280 529 57 3 3130 3653 554485308 554484780 2.390000e-176 628
25 TraesCS5D01G545700 chr4D 90.535 243 20 3 1594 1834 477088936 477088695 5.890000e-83 318
26 TraesCS5D01G545700 chr4D 86.121 281 33 5 1210 1484 477089312 477089032 7.670000e-77 298
27 TraesCS5D01G545700 chr4D 99.174 121 1 0 1 121 412132548 412132668 6.140000e-53 219
28 TraesCS5D01G545700 chr4D 98.374 123 2 0 1 123 423728725 423728603 2.210000e-52 217
29 TraesCS5D01G545700 chr4D 77.709 323 51 13 1958 2264 477088364 477088047 1.040000e-40 178
30 TraesCS5D01G545700 chr2D 88.940 217 24 0 1234 1450 593224152 593224368 6.010000e-68 268
31 TraesCS5D01G545700 chr2D 97.600 125 3 0 1 125 621331939 621331815 7.940000e-52 215
32 TraesCS5D01G545700 chr2A 88.479 217 25 0 1234 1450 728021901 728022117 2.800000e-66 263
33 TraesCS5D01G545700 chr2A 82.869 251 38 5 2413 2659 728028539 728028788 1.710000e-53 220
34 TraesCS5D01G545700 chr2B 87.671 219 25 1 1234 1450 719496686 719496904 1.680000e-63 254
35 TraesCS5D01G545700 chr2B 83.133 249 37 5 2415 2659 719516738 719516985 4.750000e-54 222
36 TraesCS5D01G545700 chr7D 99.187 123 1 0 1 123 45792839 45792961 4.750000e-54 222
37 TraesCS5D01G545700 chr7D 99.174 121 1 0 1 121 613893081 613892961 6.140000e-53 219
38 TraesCS5D01G545700 chr7D 97.638 127 2 1 1 126 50138725 50138599 2.210000e-52 217
39 TraesCS5D01G545700 chr1D 99.180 122 1 0 1 122 46357923 46358044 1.710000e-53 220
40 TraesCS5D01G545700 chr1D 91.667 72 6 0 1018 1089 462298737 462298808 2.320000e-17 100
41 TraesCS5D01G545700 chr7A 99.174 121 1 0 1 121 722388600 722388480 6.140000e-53 219
42 TraesCS5D01G545700 chr7A 96.212 132 4 1 1 131 714410302 714410433 7.940000e-52 215
43 TraesCS5D01G545700 chr3D 90.698 86 4 3 1018 1099 511444272 511444187 1.070000e-20 111
44 TraesCS5D01G545700 chr3B 90.698 86 4 3 1018 1099 673098168 673098083 1.070000e-20 111
45 TraesCS5D01G545700 chr3B 88.043 92 11 0 998 1089 673106511 673106420 3.860000e-20 110


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 TraesCS5D01G545700 chr5D 554518676 554522328 3652 True 6746.000000 6746 100.000000 1 3653 1 chr5D.!!$R2 3652
1 TraesCS5D01G545700 chr5D 459215187 459215715 528 False 628.000000 628 88.280000 3130 3653 1 chr5D.!!$F1 523
2 TraesCS5D01G545700 chr5D 503316261 503316789 528 True 628.000000 628 88.280000 3130 3653 1 chr5D.!!$R1 523
3 TraesCS5D01G545700 chr4A 614014043 614017263 3220 False 1456.333333 3373 91.741667 448 3652 3 chr4A.!!$F2 3204
4 TraesCS5D01G545700 chr5B 696164009 696167299 3290 False 777.800000 2146 92.365800 123 3079 5 chr5B.!!$F4 2956
5 TraesCS5D01G545700 chr5B 57510758 57512366 1608 False 628.000000 628 88.291000 3130 3653 2 chr5B.!!$F2 523
6 TraesCS5D01G545700 chr5B 696154648 696155226 578 False 271.500000 291 86.677500 1223 1861 2 chr5B.!!$F3 638
7 TraesCS5D01G545700 chr3A 105553673 105554201 528 False 634.000000 634 88.469000 3130 3653 1 chr3A.!!$F1 523
8 TraesCS5D01G545700 chr3A 593309280 593309808 528 True 628.000000 628 88.280000 3130 3653 1 chr3A.!!$R1 523
9 TraesCS5D01G545700 chr5A 559028663 559029191 528 False 628.000000 628 88.280000 3130 3653 1 chr5A.!!$F1 523
10 TraesCS5D01G545700 chr1A 554484780 554485308 528 True 628.000000 628 88.280000 3130 3653 1 chr1A.!!$R1 523
11 TraesCS5D01G545700 chr4D 477088047 477089312 1265 True 264.666667 318 84.788333 1210 2264 3 chr4D.!!$R2 1054

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
65 66 0.034767 CCTTTTAGTCCCGGTTCCCC 60.035 60.0 0.00 0.00 0.0 4.81 F
99 100 0.034863 GGCCTTATGAACCGGGACAA 60.035 55.0 6.32 0.00 0.0 3.18 F
402 439 0.036765 TGGAATAGGCGACCACACAC 60.037 55.0 0.00 0.00 0.0 3.82 F
412 449 0.609131 GACCACACACCCTTCCATGG 60.609 60.0 4.97 4.97 0.0 3.66 F
1224 1602 0.748450 CCGGCCCTCATCTTACGTTA 59.252 55.0 0.00 0.00 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1772 0.108041 TCGGACCGTTTCCATAAGCC 60.108 55.0 14.79 0.0 46.29 4.35 R
1884 2423 0.165944 GATGGACGCACTTTGTTCGG 59.834 55.0 0.00 0.0 0.00 4.30 R
1885 2424 0.179250 CGATGGACGCACTTTGTTCG 60.179 55.0 0.00 0.0 34.51 3.95 R
1886 2425 0.865769 ACGATGGACGCACTTTGTTC 59.134 50.0 0.00 0.0 46.94 3.18 R
3019 3687 0.515564 GGTGGTTCAATTCGGTCACG 59.484 55.0 0.00 0.0 42.74 4.35 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
20 21 2.910199 GGTTGGTATAAGAACCGGGAC 58.090 52.381 6.32 0.00 42.91 4.46
21 22 2.502947 GGTTGGTATAAGAACCGGGACT 59.497 50.000 6.32 0.73 42.91 3.85
22 23 3.706086 GGTTGGTATAAGAACCGGGACTA 59.294 47.826 6.32 0.00 42.91 2.59
23 24 4.162131 GGTTGGTATAAGAACCGGGACTAA 59.838 45.833 6.32 0.00 42.91 2.24
24 25 5.338300 GGTTGGTATAAGAACCGGGACTAAA 60.338 44.000 6.32 0.00 42.91 1.85
25 26 5.603170 TGGTATAAGAACCGGGACTAAAG 57.397 43.478 6.32 0.00 42.91 1.85
26 27 4.406649 TGGTATAAGAACCGGGACTAAAGG 59.593 45.833 6.32 0.00 42.91 3.11
27 28 3.555527 ATAAGAACCGGGACTAAAGGC 57.444 47.619 6.32 0.00 0.00 4.35
28 29 0.327259 AAGAACCGGGACTAAAGGCC 59.673 55.000 6.32 0.00 0.00 5.19
29 30 0.546988 AGAACCGGGACTAAAGGCCT 60.547 55.000 6.32 0.00 0.00 5.19
30 31 1.197812 GAACCGGGACTAAAGGCCTA 58.802 55.000 5.16 0.00 0.00 3.93
31 32 1.138464 GAACCGGGACTAAAGGCCTAG 59.862 57.143 5.16 2.46 0.00 3.02
32 33 0.690077 ACCGGGACTAAAGGCCTAGG 60.690 60.000 5.16 3.67 0.00 3.02
33 34 1.408453 CCGGGACTAAAGGCCTAGGG 61.408 65.000 5.16 0.76 0.00 3.53
47 48 3.382048 CCTAGGGCATTAGTAACGACC 57.618 52.381 0.00 0.00 0.00 4.79
48 49 2.963782 CCTAGGGCATTAGTAACGACCT 59.036 50.000 8.71 8.71 0.00 3.85
49 50 3.387050 CCTAGGGCATTAGTAACGACCTT 59.613 47.826 9.02 0.00 0.00 3.50
50 51 3.994931 AGGGCATTAGTAACGACCTTT 57.005 42.857 0.00 0.00 0.00 3.11
51 52 4.296621 AGGGCATTAGTAACGACCTTTT 57.703 40.909 0.00 0.00 0.00 2.27
52 53 5.425196 AGGGCATTAGTAACGACCTTTTA 57.575 39.130 0.00 0.00 0.00 1.52
53 54 5.425630 AGGGCATTAGTAACGACCTTTTAG 58.574 41.667 0.00 0.00 0.00 1.85
54 55 5.046087 AGGGCATTAGTAACGACCTTTTAGT 60.046 40.000 0.00 0.00 0.00 2.24
55 56 5.292834 GGGCATTAGTAACGACCTTTTAGTC 59.707 44.000 0.00 0.00 0.00 2.59
56 57 5.292834 GGCATTAGTAACGACCTTTTAGTCC 59.707 44.000 0.00 0.00 32.91 3.85
57 58 5.292834 GCATTAGTAACGACCTTTTAGTCCC 59.707 44.000 0.00 0.00 32.91 4.46
58 59 3.582714 AGTAACGACCTTTTAGTCCCG 57.417 47.619 0.00 0.00 32.91 5.14
59 60 2.232208 AGTAACGACCTTTTAGTCCCGG 59.768 50.000 0.00 0.00 32.91 5.73
60 61 1.051008 AACGACCTTTTAGTCCCGGT 58.949 50.000 0.00 0.00 32.91 5.28
61 62 1.051008 ACGACCTTTTAGTCCCGGTT 58.949 50.000 0.00 0.00 32.91 4.44
62 63 1.001293 ACGACCTTTTAGTCCCGGTTC 59.999 52.381 0.00 0.00 32.91 3.62
63 64 1.673923 CGACCTTTTAGTCCCGGTTCC 60.674 57.143 0.00 0.00 32.91 3.62
64 65 0.694771 ACCTTTTAGTCCCGGTTCCC 59.305 55.000 0.00 0.00 0.00 3.97
65 66 0.034767 CCTTTTAGTCCCGGTTCCCC 60.035 60.000 0.00 0.00 0.00 4.81
66 67 0.694196 CTTTTAGTCCCGGTTCCCCA 59.306 55.000 0.00 0.00 0.00 4.96
67 68 1.074244 CTTTTAGTCCCGGTTCCCCAA 59.926 52.381 0.00 0.00 0.00 4.12
68 69 0.401356 TTTAGTCCCGGTTCCCCAAC 59.599 55.000 0.00 0.00 0.00 3.77
81 82 2.272146 CCAACCGGGACAGATGGG 59.728 66.667 6.32 0.00 40.01 4.00
82 83 2.438434 CAACCGGGACAGATGGGC 60.438 66.667 6.32 0.00 0.00 5.36
83 84 3.728373 AACCGGGACAGATGGGCC 61.728 66.667 6.32 0.00 0.00 5.80
84 85 4.741239 ACCGGGACAGATGGGCCT 62.741 66.667 6.32 0.00 0.00 5.19
85 86 3.411517 CCGGGACAGATGGGCCTT 61.412 66.667 4.53 0.00 0.00 4.35
86 87 2.070039 CCGGGACAGATGGGCCTTA 61.070 63.158 4.53 0.00 0.00 2.69
87 88 1.418908 CCGGGACAGATGGGCCTTAT 61.419 60.000 4.53 0.00 0.00 1.73
88 89 0.250467 CGGGACAGATGGGCCTTATG 60.250 60.000 12.06 12.06 0.00 1.90
89 90 1.140312 GGGACAGATGGGCCTTATGA 58.860 55.000 19.57 0.00 0.00 2.15
90 91 1.494721 GGGACAGATGGGCCTTATGAA 59.505 52.381 19.57 0.00 0.00 2.57
91 92 2.576615 GGACAGATGGGCCTTATGAAC 58.423 52.381 19.57 12.43 0.00 3.18
92 93 2.576615 GACAGATGGGCCTTATGAACC 58.423 52.381 19.57 5.77 0.00 3.62
93 94 1.134098 ACAGATGGGCCTTATGAACCG 60.134 52.381 19.57 0.00 0.00 4.44
94 95 0.474184 AGATGGGCCTTATGAACCGG 59.526 55.000 4.53 0.00 0.00 5.28
95 96 0.537371 GATGGGCCTTATGAACCGGG 60.537 60.000 6.32 0.00 0.00 5.73
96 97 0.991355 ATGGGCCTTATGAACCGGGA 60.991 55.000 6.32 0.00 0.00 5.14
97 98 1.153025 GGGCCTTATGAACCGGGAC 60.153 63.158 6.32 0.00 0.00 4.46
98 99 1.605453 GGCCTTATGAACCGGGACA 59.395 57.895 6.32 5.75 0.00 4.02
99 100 0.034863 GGCCTTATGAACCGGGACAA 60.035 55.000 6.32 0.00 0.00 3.18
100 101 1.614850 GGCCTTATGAACCGGGACAAA 60.615 52.381 6.32 2.62 0.00 2.83
101 102 2.375146 GCCTTATGAACCGGGACAAAT 58.625 47.619 6.32 0.00 0.00 2.32
102 103 2.099098 GCCTTATGAACCGGGACAAATG 59.901 50.000 6.32 0.20 0.00 2.32
103 104 2.687935 CCTTATGAACCGGGACAAATGG 59.312 50.000 6.32 5.49 0.00 3.16
104 105 1.757682 TATGAACCGGGACAAATGGC 58.242 50.000 6.32 0.00 0.00 4.40
105 106 0.970427 ATGAACCGGGACAAATGGCC 60.970 55.000 6.32 0.00 44.61 5.36
115 116 4.188247 GGACAAATGGCCCTTTTTCTAC 57.812 45.455 16.22 1.38 37.19 2.59
116 117 3.832490 GGACAAATGGCCCTTTTTCTACT 59.168 43.478 16.22 0.00 37.19 2.57
117 118 5.014202 GGACAAATGGCCCTTTTTCTACTA 58.986 41.667 16.22 0.00 37.19 1.82
118 119 5.125578 GGACAAATGGCCCTTTTTCTACTAG 59.874 44.000 16.22 1.81 37.19 2.57
119 120 5.641155 ACAAATGGCCCTTTTTCTACTAGT 58.359 37.500 2.87 0.00 0.00 2.57
120 121 5.476945 ACAAATGGCCCTTTTTCTACTAGTG 59.523 40.000 5.39 0.00 0.00 2.74
121 122 3.067684 TGGCCCTTTTTCTACTAGTGC 57.932 47.619 5.39 0.00 0.00 4.40
172 173 6.485648 ACCCTAAGTTCATGGAAATTATACGC 59.514 38.462 0.00 0.00 32.93 4.42
238 243 2.572104 GAGGGGACATCAACCTAACACT 59.428 50.000 0.00 0.00 34.02 3.55
244 249 2.884639 ACATCAACCTAACACTTGGTGC 59.115 45.455 0.00 0.00 36.98 5.01
248 253 2.332654 CCTAACACTTGGTGCGCCC 61.333 63.158 15.15 6.44 36.98 6.13
252 257 4.025401 CACTTGGTGCGCCCGAAC 62.025 66.667 15.15 0.00 35.15 3.95
279 284 5.163561 CCGGATAGATGAATAGAGCTTCTCC 60.164 48.000 0.00 0.00 0.00 3.71
280 285 5.163561 CGGATAGATGAATAGAGCTTCTCCC 60.164 48.000 0.00 0.00 0.00 4.30
281 286 5.957774 GGATAGATGAATAGAGCTTCTCCCT 59.042 44.000 0.00 0.00 0.00 4.20
282 287 6.440328 GGATAGATGAATAGAGCTTCTCCCTT 59.560 42.308 0.00 0.00 0.00 3.95
283 288 5.806654 AGATGAATAGAGCTTCTCCCTTC 57.193 43.478 0.00 0.00 0.00 3.46
286 291 6.386635 AGATGAATAGAGCTTCTCCCTTCTTT 59.613 38.462 0.00 0.00 0.00 2.52
312 317 7.713764 TTTTGGAATAGAGCTTTTCTTTTGC 57.286 32.000 0.00 0.00 36.31 3.68
314 319 6.403866 TGGAATAGAGCTTTTCTTTTGCAA 57.596 33.333 0.00 0.00 40.37 4.08
315 320 6.449698 TGGAATAGAGCTTTTCTTTTGCAAG 58.550 36.000 0.00 0.00 40.37 4.01
316 321 6.265196 TGGAATAGAGCTTTTCTTTTGCAAGA 59.735 34.615 0.00 0.00 40.37 3.02
317 322 6.805760 GGAATAGAGCTTTTCTTTTGCAAGAG 59.194 38.462 10.67 10.67 40.28 2.85
319 324 4.929781 AGAGCTTTTCTTTTGCAAGAGTG 58.070 39.130 15.90 7.13 40.28 3.51
328 365 7.566760 TTCTTTTGCAAGAGTGATCACTTAA 57.433 32.000 28.46 15.55 42.66 1.85
339 376 4.829492 AGTGATCACTTAAAGCTTTGCCTT 59.171 37.500 22.89 0.00 38.83 4.35
345 382 5.359576 TCACTTAAAGCTTTGCCTTCAAGAA 59.640 36.000 22.02 3.66 33.12 2.52
354 391 2.378038 TGCCTTCAAGAAAAGCAGTGT 58.622 42.857 3.78 0.00 0.00 3.55
358 395 3.303395 CCTTCAAGAAAAGCAGTGTCGAC 60.303 47.826 9.11 9.11 0.00 4.20
373 410 3.791887 GTGTCGACGATGTAGATGAAAGG 59.208 47.826 11.62 0.00 0.00 3.11
377 414 3.521560 GACGATGTAGATGAAAGGCACA 58.478 45.455 0.00 0.00 0.00 4.57
392 429 1.678101 GGCACAGTCATTGGAATAGGC 59.322 52.381 0.00 0.00 0.00 3.93
400 437 1.670811 CATTGGAATAGGCGACCACAC 59.329 52.381 0.00 0.00 33.20 3.82
401 438 0.687920 TTGGAATAGGCGACCACACA 59.312 50.000 0.00 0.00 33.20 3.72
402 439 0.036765 TGGAATAGGCGACCACACAC 60.037 55.000 0.00 0.00 0.00 3.82
403 440 0.743345 GGAATAGGCGACCACACACC 60.743 60.000 0.00 0.00 0.00 4.16
404 441 0.743345 GAATAGGCGACCACACACCC 60.743 60.000 0.00 0.00 0.00 4.61
405 442 1.198759 AATAGGCGACCACACACCCT 61.199 55.000 0.00 0.00 0.00 4.34
406 443 1.198759 ATAGGCGACCACACACCCTT 61.199 55.000 0.00 0.00 0.00 3.95
407 444 1.823169 TAGGCGACCACACACCCTTC 61.823 60.000 0.00 0.00 0.00 3.46
408 445 2.668550 GCGACCACACACCCTTCC 60.669 66.667 0.00 0.00 0.00 3.46
409 446 2.825982 CGACCACACACCCTTCCA 59.174 61.111 0.00 0.00 0.00 3.53
410 447 1.374947 CGACCACACACCCTTCCAT 59.625 57.895 0.00 0.00 0.00 3.41
411 448 0.955428 CGACCACACACCCTTCCATG 60.955 60.000 0.00 0.00 0.00 3.66
412 449 0.609131 GACCACACACCCTTCCATGG 60.609 60.000 4.97 4.97 0.00 3.66
413 450 1.978617 CCACACACCCTTCCATGGC 60.979 63.158 6.96 0.00 0.00 4.40
414 451 1.978617 CACACACCCTTCCATGGCC 60.979 63.158 6.96 0.00 0.00 5.36
415 452 2.362889 CACACCCTTCCATGGCCC 60.363 66.667 6.96 0.00 0.00 5.80
416 453 2.863484 ACACCCTTCCATGGCCCA 60.863 61.111 6.96 0.00 0.00 5.36
417 454 2.444696 CACCCTTCCATGGCCCAA 59.555 61.111 6.96 0.00 0.00 4.12
418 455 1.002017 CACCCTTCCATGGCCCAAT 59.998 57.895 6.96 0.00 0.00 3.16
419 456 1.002017 ACCCTTCCATGGCCCAATG 59.998 57.895 6.96 0.00 0.00 2.82
420 457 1.310715 CCCTTCCATGGCCCAATGA 59.689 57.895 6.96 0.00 0.00 2.57
421 458 0.757935 CCCTTCCATGGCCCAATGAG 60.758 60.000 6.96 0.00 0.00 2.90
422 459 0.757935 CCTTCCATGGCCCAATGAGG 60.758 60.000 6.96 0.00 37.03 3.86
544 858 4.511454 GCACGTGGAGCATGAGATTATTTA 59.489 41.667 18.88 0.00 0.00 1.40
546 860 6.653183 CACGTGGAGCATGAGATTATTTAAG 58.347 40.000 7.95 0.00 0.00 1.85
556 870 6.985188 TGAGATTATTTAAGAGCACACACC 57.015 37.500 0.00 0.00 0.00 4.16
580 894 5.896922 CAGAAGCCTGTGTATAATTCTCG 57.103 43.478 0.00 0.00 35.70 4.04
581 895 4.747108 CAGAAGCCTGTGTATAATTCTCGG 59.253 45.833 0.00 0.00 35.70 4.63
589 903 4.110482 GTGTATAATTCTCGGTCGTTGCT 58.890 43.478 0.00 0.00 0.00 3.91
646 960 2.649531 TTCCAAACCGACCAAGTCAT 57.350 45.000 0.00 0.00 32.09 3.06
684 998 2.198406 TCTTTCACTGTTGGTTCGTCG 58.802 47.619 0.00 0.00 0.00 5.12
771 1087 8.313292 ACAATGTTATCACCTGCAAATTATGTT 58.687 29.630 0.00 0.00 0.00 2.71
850 1226 5.842907 TGAAATACATTCATCGTCGGAGAT 58.157 37.500 0.00 0.00 43.08 2.75
872 1248 7.715657 AGATGTTGACAGCTTAATTTGTTGAA 58.284 30.769 0.00 0.00 40.00 2.69
878 1254 9.598517 TTGACAGCTTAATTTGTTGAATTCTTT 57.401 25.926 7.05 0.00 38.80 2.52
885 1261 6.900568 AATTTGTTGAATTCTTTTGCGTGA 57.099 29.167 7.05 0.00 32.49 4.35
887 1263 4.362932 TGTTGAATTCTTTTGCGTGACA 57.637 36.364 7.05 0.00 0.00 3.58
888 1264 4.350346 TGTTGAATTCTTTTGCGTGACAG 58.650 39.130 7.05 0.00 0.00 3.51
889 1265 2.998772 TGAATTCTTTTGCGTGACAGC 58.001 42.857 7.05 0.00 37.71 4.40
890 1266 2.618241 TGAATTCTTTTGCGTGACAGCT 59.382 40.909 7.05 0.00 38.13 4.24
891 1267 3.066621 TGAATTCTTTTGCGTGACAGCTT 59.933 39.130 7.05 0.00 38.13 3.74
892 1268 4.274705 TGAATTCTTTTGCGTGACAGCTTA 59.725 37.500 7.05 0.00 38.13 3.09
893 1269 4.829064 ATTCTTTTGCGTGACAGCTTAA 57.171 36.364 0.00 0.00 38.13 1.85
926 1304 8.254508 CCTGTCCTAGCTATAAAATGGATCTAC 58.745 40.741 0.00 0.00 0.00 2.59
961 1339 2.290641 GCAACAACCAACAGACGATTCT 59.709 45.455 0.00 0.00 0.00 2.40
1129 1507 1.339055 ACGCATGCCTTTCTTCTGCTA 60.339 47.619 13.15 0.00 0.00 3.49
1147 1525 7.628769 TCTGCTATTCATTCTACAAATGCAA 57.371 32.000 0.00 0.00 0.00 4.08
1148 1526 8.229253 TCTGCTATTCATTCTACAAATGCAAT 57.771 30.769 0.00 0.00 0.00 3.56
1149 1527 8.689061 TCTGCTATTCATTCTACAAATGCAATT 58.311 29.630 0.00 0.00 38.98 2.32
1150 1528 9.955208 CTGCTATTCATTCTACAAATGCAATTA 57.045 29.630 0.00 0.00 33.67 1.40
1151 1529 9.955208 TGCTATTCATTCTACAAATGCAATTAG 57.045 29.630 0.00 0.00 33.67 1.73
1152 1530 9.956720 GCTATTCATTCTACAAATGCAATTAGT 57.043 29.630 0.00 0.00 33.67 2.24
1157 1535 9.890629 TCATTCTACAAATGCAATTAGTAGTCT 57.109 29.630 16.68 8.35 33.67 3.24
1160 1538 9.944376 TTCTACAAATGCAATTAGTAGTCTTCT 57.056 29.630 16.68 0.00 33.67 2.85
1161 1539 9.944376 TCTACAAATGCAATTAGTAGTCTTCTT 57.056 29.630 16.68 0.00 33.67 2.52
1208 1586 5.721232 AGTCTTCTTTACATGTTACTCCGG 58.279 41.667 2.30 0.00 0.00 5.14
1220 1598 1.700955 TACTCCGGCCCTCATCTTAC 58.299 55.000 0.00 0.00 0.00 2.34
1224 1602 0.748450 CCGGCCCTCATCTTACGTTA 59.252 55.000 0.00 0.00 0.00 3.18
1297 1675 2.847234 ACACCTGCTCCCGGAACA 60.847 61.111 0.73 0.00 0.00 3.18
1394 1772 0.757188 ATAGGTGCCGACAGGGAGAG 60.757 60.000 0.00 0.00 39.06 3.20
1557 1985 1.846648 GCCTCGACGCGACATTATG 59.153 57.895 15.93 0.00 0.00 1.90
1587 2015 8.560903 AGTTAGTAAAATCTCCCTTCATCCAAT 58.439 33.333 0.00 0.00 0.00 3.16
1598 2026 9.182642 TCTCCCTTCATCCAATTAATATAGGTT 57.817 33.333 0.00 0.00 0.00 3.50
1628 2056 2.584791 GCACAATTGTTCTACAAGCCG 58.415 47.619 8.77 0.00 41.94 5.52
1817 2245 4.036380 GGCTACACAATTTATGCTACCACC 59.964 45.833 0.00 0.00 0.00 4.61
1885 2424 8.984891 TGACATTTGTTTTCATACAATCATCC 57.015 30.769 0.00 0.00 37.81 3.51
1886 2425 7.754475 TGACATTTGTTTTCATACAATCATCCG 59.246 33.333 0.00 0.00 37.81 4.18
1889 2528 8.586273 CATTTGTTTTCATACAATCATCCGAAC 58.414 33.333 0.00 0.00 37.81 3.95
1955 2595 9.374838 TGGTACCTAAAATTAAGTCGAATCTTC 57.625 33.333 14.36 0.00 0.00 2.87
2025 2671 1.002087 CTTACGAGGAGTTTGGCCACT 59.998 52.381 3.88 0.00 0.00 4.00
2107 2753 9.088512 CCGATATGATTAAAGATGTAAGTAGCC 57.911 37.037 0.00 0.00 0.00 3.93
2208 2864 3.714798 AGTCGCTTTATATTGGGAGGGAA 59.285 43.478 0.00 0.00 33.68 3.97
2215 2872 8.417884 CGCTTTATATTGGGAGGGAAAAATTAA 58.582 33.333 0.00 0.00 0.00 1.40
2272 2929 5.871396 AGCCATCTCTTAATAGACCGAAA 57.129 39.130 0.00 0.00 0.00 3.46
2333 2990 7.870509 AAGAGCTTGTCAGATTTATATTGCA 57.129 32.000 0.00 0.00 0.00 4.08
2338 2995 7.859377 AGCTTGTCAGATTTATATTGCAAATCG 59.141 33.333 1.71 0.00 43.86 3.34
2348 3005 9.964303 ATTTATATTGCAAATCGCTAATTCACA 57.036 25.926 1.71 0.00 43.06 3.58
2380 3037 7.545362 AAACTGTATAGCATAGCTTGTTCTG 57.455 36.000 0.00 0.00 40.44 3.02
2441 3102 7.090173 TCAAACTGCTAGCAATTTTTACATCC 58.910 34.615 20.76 0.00 0.00 3.51
2446 3107 8.802267 ACTGCTAGCAATTTTTACATCCTTTTA 58.198 29.630 19.86 0.00 0.00 1.52
2509 3171 9.914131 CATAGATTGATACCGAGTTTATGAAGA 57.086 33.333 0.00 0.00 0.00 2.87
2530 3192 2.032681 AGCACTTGAAGACCCCGC 59.967 61.111 0.00 0.00 0.00 6.13
2674 3336 2.664402 ATCAATTCCCCCGAATCAGG 57.336 50.000 0.00 0.00 37.76 3.86
2675 3337 1.590591 TCAATTCCCCCGAATCAGGA 58.409 50.000 0.00 0.00 37.76 3.86
2676 3338 1.211949 TCAATTCCCCCGAATCAGGAC 59.788 52.381 0.00 0.00 37.76 3.85
2677 3339 1.212935 CAATTCCCCCGAATCAGGACT 59.787 52.381 0.00 0.00 37.76 3.85
2678 3340 0.839946 ATTCCCCCGAATCAGGACTG 59.160 55.000 0.00 0.00 33.15 3.51
2687 3349 0.693049 AATCAGGACTGGACCGCTTT 59.307 50.000 0.00 0.00 34.73 3.51
2717 3379 8.897752 AGCTCTTGATTACTTGGAAAATACATC 58.102 33.333 0.00 0.00 0.00 3.06
2810 3477 0.466372 TGGCACATTTCACGGGACAA 60.466 50.000 0.00 0.00 0.00 3.18
2811 3478 0.671251 GGCACATTTCACGGGACAAA 59.329 50.000 0.00 0.00 0.00 2.83
2845 3512 2.485038 GTGCAAATTTGGGCCTCATTTG 59.515 45.455 25.04 25.04 39.78 2.32
2875 3543 6.889301 ATATATGAGTCATGCTGGTTTTGG 57.111 37.500 16.15 0.00 0.00 3.28
2878 3546 3.146066 TGAGTCATGCTGGTTTTGGTAC 58.854 45.455 0.00 0.00 0.00 3.34
2882 3550 3.190535 GTCATGCTGGTTTTGGTACGAAT 59.809 43.478 0.00 0.00 0.00 3.34
2959 3627 3.377346 GATGAGAGCATCCTTCGCTTA 57.623 47.619 0.00 0.00 44.12 3.09
2963 3631 3.684788 TGAGAGCATCCTTCGCTTAAAAC 59.315 43.478 0.00 0.00 40.63 2.43
3042 3710 1.268625 GACCGAATTGAACCACCCAAC 59.731 52.381 0.00 0.00 0.00 3.77
3070 3738 2.104111 GCAGCATATACCTACACACCCA 59.896 50.000 0.00 0.00 0.00 4.51
3073 3741 5.376625 CAGCATATACCTACACACCCAAAT 58.623 41.667 0.00 0.00 0.00 2.32
3100 3770 6.943718 TGATAAGATATTGGATCATGCAAGCA 59.056 34.615 0.00 0.00 29.36 3.91
3102 3772 3.501062 AGATATTGGATCATGCAAGCACG 59.499 43.478 0.00 0.00 29.36 5.34
3125 3795 1.813178 GGCCTTGTTCCTCAGCTTAAC 59.187 52.381 0.00 0.00 0.00 2.01
3301 4510 9.924650 CTTGTTCCGGTATAAATAGTAGCTATT 57.075 33.333 0.00 0.00 38.17 1.73
3315 4524 4.710375 AGTAGCTATTTTCTCTTCCACCGA 59.290 41.667 0.00 0.00 0.00 4.69
3329 4538 0.462759 CACCGAGAGAGGATTTGCCC 60.463 60.000 0.00 0.00 37.37 5.36
3330 4539 0.909610 ACCGAGAGAGGATTTGCCCA 60.910 55.000 0.00 0.00 37.37 5.36
3331 4540 0.253044 CCGAGAGAGGATTTGCCCAA 59.747 55.000 0.00 0.00 37.37 4.12
3334 4543 2.637947 GAGAGAGGATTTGCCCAAGAC 58.362 52.381 0.00 0.00 37.37 3.01
3336 4545 3.452627 GAGAGAGGATTTGCCCAAGACTA 59.547 47.826 0.00 0.00 37.37 2.59
3362 4571 7.496529 TTAAGCAATTCCCTTAATCATCGAG 57.503 36.000 0.00 0.00 31.72 4.04
3366 4575 1.056660 TCCCTTAATCATCGAGCCCC 58.943 55.000 0.00 0.00 0.00 5.80
3431 4640 4.079980 TGTGCAAAGGCTTGTAACTCTA 57.920 40.909 0.00 0.00 41.91 2.43
3467 4676 6.917533 AGTTCCAATTAAGATTTGTCAGCTG 58.082 36.000 7.63 7.63 0.00 4.24
3473 4682 3.637998 AAGATTTGTCAGCTGCTTGTG 57.362 42.857 9.47 0.00 0.00 3.33
3487 4696 4.418392 CTGCTTGTGTCATGGCTTTAATC 58.582 43.478 0.00 0.00 0.00 1.75
3504 4713 2.317371 ATCTGAGCCGTGGATCCTAT 57.683 50.000 14.23 0.00 0.00 2.57
3505 4714 2.971901 TCTGAGCCGTGGATCCTATA 57.028 50.000 14.23 0.00 0.00 1.31
3506 4715 2.796557 TCTGAGCCGTGGATCCTATAG 58.203 52.381 14.23 0.18 0.00 1.31
3547 5297 3.823281 TTAATAGCGGGTCGAATTCCA 57.177 42.857 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.502947 AGTCCCGGTTCTTATACCAACC 59.497 50.000 0.00 2.87 38.12 3.77
1 2 3.900966 AGTCCCGGTTCTTATACCAAC 57.099 47.619 0.00 0.00 38.12 3.77
2 3 5.104817 CCTTTAGTCCCGGTTCTTATACCAA 60.105 44.000 0.00 0.00 38.12 3.67
3 4 4.406649 CCTTTAGTCCCGGTTCTTATACCA 59.593 45.833 0.00 0.00 38.12 3.25
4 5 4.741837 GCCTTTAGTCCCGGTTCTTATACC 60.742 50.000 0.00 0.00 34.72 2.73
5 6 4.375272 GCCTTTAGTCCCGGTTCTTATAC 58.625 47.826 0.00 0.00 0.00 1.47
6 7 3.389002 GGCCTTTAGTCCCGGTTCTTATA 59.611 47.826 0.00 0.00 0.00 0.98
7 8 2.172082 GGCCTTTAGTCCCGGTTCTTAT 59.828 50.000 0.00 0.00 0.00 1.73
8 9 1.556451 GGCCTTTAGTCCCGGTTCTTA 59.444 52.381 0.00 0.00 0.00 2.10
9 10 0.327259 GGCCTTTAGTCCCGGTTCTT 59.673 55.000 0.00 0.00 0.00 2.52
10 11 0.546988 AGGCCTTTAGTCCCGGTTCT 60.547 55.000 0.00 0.15 0.00 3.01
11 12 1.138464 CTAGGCCTTTAGTCCCGGTTC 59.862 57.143 12.58 0.00 0.00 3.62
12 13 1.201424 CTAGGCCTTTAGTCCCGGTT 58.799 55.000 12.58 0.00 0.00 4.44
13 14 0.690077 CCTAGGCCTTTAGTCCCGGT 60.690 60.000 12.58 0.00 0.00 5.28
14 15 1.408453 CCCTAGGCCTTTAGTCCCGG 61.408 65.000 12.58 0.00 0.00 5.73
15 16 2.041206 GCCCTAGGCCTTTAGTCCCG 62.041 65.000 12.58 0.00 44.06 5.14
16 17 1.837789 GCCCTAGGCCTTTAGTCCC 59.162 63.158 12.58 0.00 44.06 4.46
27 28 2.963782 AGGTCGTTACTAATGCCCTAGG 59.036 50.000 0.06 0.06 0.00 3.02
28 29 4.667519 AAGGTCGTTACTAATGCCCTAG 57.332 45.455 0.00 0.00 0.00 3.02
29 30 5.425196 AAAAGGTCGTTACTAATGCCCTA 57.575 39.130 0.00 0.00 0.00 3.53
30 31 3.994931 AAAGGTCGTTACTAATGCCCT 57.005 42.857 0.00 0.00 0.00 5.19
31 32 5.181009 ACTAAAAGGTCGTTACTAATGCCC 58.819 41.667 0.00 0.00 0.00 5.36
32 33 5.292834 GGACTAAAAGGTCGTTACTAATGCC 59.707 44.000 0.00 0.00 37.12 4.40
33 34 5.292834 GGGACTAAAAGGTCGTTACTAATGC 59.707 44.000 0.00 0.00 37.12 3.56
34 35 5.517770 CGGGACTAAAAGGTCGTTACTAATG 59.482 44.000 0.00 0.00 37.12 1.90
35 36 5.394553 CCGGGACTAAAAGGTCGTTACTAAT 60.395 44.000 0.00 0.00 37.12 1.73
36 37 4.082245 CCGGGACTAAAAGGTCGTTACTAA 60.082 45.833 0.00 0.00 37.12 2.24
37 38 3.443681 CCGGGACTAAAAGGTCGTTACTA 59.556 47.826 0.00 0.00 37.12 1.82
38 39 2.232208 CCGGGACTAAAAGGTCGTTACT 59.768 50.000 0.00 0.00 37.12 2.24
39 40 2.029020 ACCGGGACTAAAAGGTCGTTAC 60.029 50.000 6.32 0.00 37.12 2.50
40 41 2.247358 ACCGGGACTAAAAGGTCGTTA 58.753 47.619 6.32 0.00 37.12 3.18
41 42 1.051008 ACCGGGACTAAAAGGTCGTT 58.949 50.000 6.32 0.00 37.12 3.85
42 43 1.001293 GAACCGGGACTAAAAGGTCGT 59.999 52.381 6.32 0.00 35.68 4.34
43 44 1.673923 GGAACCGGGACTAAAAGGTCG 60.674 57.143 6.32 0.00 35.68 4.79
44 45 1.339438 GGGAACCGGGACTAAAAGGTC 60.339 57.143 6.32 0.00 40.86 3.85
45 46 0.694771 GGGAACCGGGACTAAAAGGT 59.305 55.000 6.32 0.00 40.86 3.50
46 47 3.564262 GGGAACCGGGACTAAAAGG 57.436 57.895 6.32 0.00 40.86 3.11
64 65 2.272146 CCCATCTGTCCCGGTTGG 59.728 66.667 0.00 0.00 31.38 3.77
65 66 2.438434 GCCCATCTGTCCCGGTTG 60.438 66.667 0.00 0.00 0.00 3.77
66 67 3.728373 GGCCCATCTGTCCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
67 68 2.833151 TAAGGCCCATCTGTCCCGGT 62.833 60.000 0.00 0.00 0.00 5.28
68 69 1.418908 ATAAGGCCCATCTGTCCCGG 61.419 60.000 0.00 0.00 0.00 5.73
69 70 0.250467 CATAAGGCCCATCTGTCCCG 60.250 60.000 0.00 0.00 0.00 5.14
70 71 1.140312 TCATAAGGCCCATCTGTCCC 58.860 55.000 0.00 0.00 0.00 4.46
71 72 2.576615 GTTCATAAGGCCCATCTGTCC 58.423 52.381 0.00 0.00 0.00 4.02
72 73 2.576615 GGTTCATAAGGCCCATCTGTC 58.423 52.381 0.00 0.00 0.00 3.51
73 74 1.134098 CGGTTCATAAGGCCCATCTGT 60.134 52.381 0.00 0.00 0.00 3.41
74 75 1.597742 CGGTTCATAAGGCCCATCTG 58.402 55.000 0.00 0.00 0.00 2.90
75 76 0.474184 CCGGTTCATAAGGCCCATCT 59.526 55.000 0.00 0.00 0.00 2.90
76 77 0.537371 CCCGGTTCATAAGGCCCATC 60.537 60.000 0.00 0.00 0.00 3.51
77 78 0.991355 TCCCGGTTCATAAGGCCCAT 60.991 55.000 0.00 0.00 0.00 4.00
78 79 1.616930 TCCCGGTTCATAAGGCCCA 60.617 57.895 0.00 0.00 0.00 5.36
79 80 1.153025 GTCCCGGTTCATAAGGCCC 60.153 63.158 0.00 0.00 0.00 5.80
80 81 0.034863 TTGTCCCGGTTCATAAGGCC 60.035 55.000 0.00 0.00 0.00 5.19
81 82 1.828979 TTTGTCCCGGTTCATAAGGC 58.171 50.000 0.00 0.00 0.00 4.35
82 83 2.687935 CCATTTGTCCCGGTTCATAAGG 59.312 50.000 0.00 0.00 0.00 2.69
83 84 2.099098 GCCATTTGTCCCGGTTCATAAG 59.901 50.000 0.00 0.00 0.00 1.73
84 85 2.096248 GCCATTTGTCCCGGTTCATAA 58.904 47.619 0.00 0.00 0.00 1.90
85 86 1.683629 GGCCATTTGTCCCGGTTCATA 60.684 52.381 0.00 0.00 0.00 2.15
86 87 0.970427 GGCCATTTGTCCCGGTTCAT 60.970 55.000 0.00 0.00 0.00 2.57
87 88 1.605165 GGCCATTTGTCCCGGTTCA 60.605 57.895 0.00 0.00 0.00 3.18
88 89 2.348104 GGGCCATTTGTCCCGGTTC 61.348 63.158 4.39 0.00 32.00 3.62
89 90 2.283604 GGGCCATTTGTCCCGGTT 60.284 61.111 4.39 0.00 32.00 4.44
93 94 1.977854 AGAAAAAGGGCCATTTGTCCC 59.022 47.619 25.73 11.52 42.94 4.46
94 95 3.832490 AGTAGAAAAAGGGCCATTTGTCC 59.168 43.478 25.73 13.84 28.13 4.02
95 96 5.710567 ACTAGTAGAAAAAGGGCCATTTGTC 59.289 40.000 22.82 22.82 0.00 3.18
96 97 5.476945 CACTAGTAGAAAAAGGGCCATTTGT 59.523 40.000 17.44 11.46 0.00 2.83
97 98 5.622233 GCACTAGTAGAAAAAGGGCCATTTG 60.622 44.000 17.44 3.54 33.42 2.32
98 99 4.462834 GCACTAGTAGAAAAAGGGCCATTT 59.537 41.667 10.16 10.16 33.42 2.32
99 100 4.017126 GCACTAGTAGAAAAAGGGCCATT 58.983 43.478 6.18 0.00 33.42 3.16
100 101 3.010138 TGCACTAGTAGAAAAAGGGCCAT 59.990 43.478 6.18 0.00 38.95 4.40
101 102 2.373836 TGCACTAGTAGAAAAAGGGCCA 59.626 45.455 6.18 0.00 38.95 5.36
102 103 3.067684 TGCACTAGTAGAAAAAGGGCC 57.932 47.619 3.59 0.00 38.95 5.80
103 104 4.010349 ACATGCACTAGTAGAAAAAGGGC 58.990 43.478 3.59 0.00 40.16 5.19
104 105 5.705441 TGAACATGCACTAGTAGAAAAAGGG 59.295 40.000 3.59 0.00 0.00 3.95
105 106 6.348540 GGTGAACATGCACTAGTAGAAAAAGG 60.349 42.308 3.59 0.00 38.78 3.11
106 107 6.428159 AGGTGAACATGCACTAGTAGAAAAAG 59.572 38.462 3.59 0.00 38.78 2.27
107 108 6.296026 AGGTGAACATGCACTAGTAGAAAAA 58.704 36.000 3.59 0.00 38.78 1.94
108 109 5.865085 AGGTGAACATGCACTAGTAGAAAA 58.135 37.500 3.59 0.00 38.78 2.29
109 110 5.483685 AGGTGAACATGCACTAGTAGAAA 57.516 39.130 3.59 0.00 38.78 2.52
110 111 5.483685 AAGGTGAACATGCACTAGTAGAA 57.516 39.130 3.59 0.00 38.78 2.10
111 112 5.483685 AAAGGTGAACATGCACTAGTAGA 57.516 39.130 3.59 0.00 38.78 2.59
112 113 5.122396 GGAAAAGGTGAACATGCACTAGTAG 59.878 44.000 0.00 0.00 38.78 2.57
113 114 5.001232 GGAAAAGGTGAACATGCACTAGTA 58.999 41.667 0.00 0.00 38.78 1.82
114 115 3.821033 GGAAAAGGTGAACATGCACTAGT 59.179 43.478 0.00 0.00 38.78 2.57
115 116 4.074970 AGGAAAAGGTGAACATGCACTAG 58.925 43.478 0.00 0.00 38.78 2.57
116 117 4.098914 AGGAAAAGGTGAACATGCACTA 57.901 40.909 0.00 0.00 38.78 2.74
117 118 2.949447 AGGAAAAGGTGAACATGCACT 58.051 42.857 0.00 0.00 38.78 4.40
118 119 3.733443 AAGGAAAAGGTGAACATGCAC 57.267 42.857 0.00 0.00 38.05 4.57
119 120 4.751767 AAAAGGAAAAGGTGAACATGCA 57.248 36.364 0.00 0.00 0.00 3.96
120 121 4.875536 ACAAAAAGGAAAAGGTGAACATGC 59.124 37.500 0.00 0.00 0.00 4.06
121 122 6.983474 AACAAAAAGGAAAAGGTGAACATG 57.017 33.333 0.00 0.00 0.00 3.21
248 253 2.768833 TTCATCTATCCGGACGTTCG 57.231 50.000 6.12 9.95 0.00 3.95
252 257 3.692101 AGCTCTATTCATCTATCCGGACG 59.308 47.826 6.12 0.01 0.00 4.79
264 269 6.380079 AAAAGAAGGGAGAAGCTCTATTCA 57.620 37.500 0.00 0.00 32.00 2.57
302 307 6.455360 AGTGATCACTCTTGCAAAAGAAAA 57.545 33.333 22.89 0.00 36.92 2.29
306 311 6.361748 GCTTTAAGTGATCACTCTTGCAAAAG 59.638 38.462 28.01 24.64 41.58 2.27
308 313 5.532406 AGCTTTAAGTGATCACTCTTGCAAA 59.468 36.000 28.01 19.18 41.58 3.68
309 314 5.065914 AGCTTTAAGTGATCACTCTTGCAA 58.934 37.500 28.01 14.69 41.58 4.08
310 315 4.645535 AGCTTTAAGTGATCACTCTTGCA 58.354 39.130 28.01 10.27 41.58 4.08
311 316 5.619625 AAGCTTTAAGTGATCACTCTTGC 57.380 39.130 28.01 25.24 41.58 4.01
312 317 5.855395 GCAAAGCTTTAAGTGATCACTCTTG 59.145 40.000 28.01 19.94 41.58 3.02
314 319 4.457257 GGCAAAGCTTTAAGTGATCACTCT 59.543 41.667 28.01 17.24 41.58 3.24
315 320 4.457257 AGGCAAAGCTTTAAGTGATCACTC 59.543 41.667 28.01 15.25 41.58 3.51
316 321 4.401925 AGGCAAAGCTTTAAGTGATCACT 58.598 39.130 22.89 22.89 44.94 3.41
317 322 4.773323 AGGCAAAGCTTTAAGTGATCAC 57.227 40.909 18.47 18.47 0.00 3.06
319 324 5.376854 TGAAGGCAAAGCTTTAAGTGATC 57.623 39.130 12.25 6.65 0.00 2.92
328 365 3.118665 TGCTTTTCTTGAAGGCAAAGCTT 60.119 39.130 27.55 0.00 45.94 3.74
339 376 1.858458 CGTCGACACTGCTTTTCTTGA 59.142 47.619 17.16 0.00 0.00 3.02
345 382 2.228103 TCTACATCGTCGACACTGCTTT 59.772 45.455 17.16 0.00 0.00 3.51
354 391 2.425668 TGCCTTTCATCTACATCGTCGA 59.574 45.455 0.00 0.00 0.00 4.20
358 395 3.525537 ACTGTGCCTTTCATCTACATCG 58.474 45.455 0.00 0.00 0.00 3.84
373 410 1.331756 CGCCTATTCCAATGACTGTGC 59.668 52.381 0.00 0.00 0.00 4.57
377 414 1.837439 TGGTCGCCTATTCCAATGACT 59.163 47.619 0.00 0.00 0.00 3.41
392 429 0.955428 CATGGAAGGGTGTGTGGTCG 60.955 60.000 0.00 0.00 0.00 4.79
400 437 1.002017 ATTGGGCCATGGAAGGGTG 59.998 57.895 18.40 0.00 42.11 4.61
401 438 1.002017 CATTGGGCCATGGAAGGGT 59.998 57.895 18.40 0.00 42.11 4.34
402 439 0.757935 CTCATTGGGCCATGGAAGGG 60.758 60.000 18.40 0.00 43.76 3.95
403 440 0.757935 CCTCATTGGGCCATGGAAGG 60.758 60.000 18.40 8.73 0.00 3.46
404 441 2.816746 CCTCATTGGGCCATGGAAG 58.183 57.895 18.40 2.73 0.00 3.46
422 459 3.774216 TGATCAACAATTGGAATTCCCCC 59.226 43.478 21.90 0.00 34.29 5.40
423 460 4.677779 CGTGATCAACAATTGGAATTCCCC 60.678 45.833 21.90 0.00 34.29 4.81
424 461 4.157656 TCGTGATCAACAATTGGAATTCCC 59.842 41.667 21.90 4.57 34.29 3.97
425 462 5.309323 TCGTGATCAACAATTGGAATTCC 57.691 39.130 18.17 18.17 0.00 3.01
426 463 5.678483 CGATCGTGATCAACAATTGGAATTC 59.322 40.000 10.83 0.00 37.69 2.17
427 464 5.353956 TCGATCGTGATCAACAATTGGAATT 59.646 36.000 15.94 0.00 37.69 2.17
428 465 4.875536 TCGATCGTGATCAACAATTGGAAT 59.124 37.500 15.94 0.00 37.69 3.01
429 466 4.249661 TCGATCGTGATCAACAATTGGAA 58.750 39.130 15.94 0.00 37.69 3.53
430 467 3.855858 TCGATCGTGATCAACAATTGGA 58.144 40.909 15.94 0.00 37.69 3.53
431 468 3.865164 TCTCGATCGTGATCAACAATTGG 59.135 43.478 15.94 0.00 37.69 3.16
432 469 4.549680 GCTCTCGATCGTGATCAACAATTG 60.550 45.833 19.13 3.24 37.69 2.32
433 470 3.553511 GCTCTCGATCGTGATCAACAATT 59.446 43.478 19.13 0.00 37.69 2.32
434 471 3.119291 GCTCTCGATCGTGATCAACAAT 58.881 45.455 19.13 0.00 37.69 2.71
435 472 2.530177 GCTCTCGATCGTGATCAACAA 58.470 47.619 19.13 0.00 37.69 2.83
436 473 1.531883 CGCTCTCGATCGTGATCAACA 60.532 52.381 19.13 0.00 37.69 3.33
437 474 1.116436 CGCTCTCGATCGTGATCAAC 58.884 55.000 19.13 9.23 37.69 3.18
438 475 1.014352 TCGCTCTCGATCGTGATCAA 58.986 50.000 19.13 0.00 40.21 2.57
439 476 2.690326 TCGCTCTCGATCGTGATCA 58.310 52.632 19.13 4.83 40.21 2.92
518 832 1.812922 CTCATGCTCCACGTGCTCC 60.813 63.158 10.91 0.02 35.07 4.70
544 858 1.959042 CTTCTGTGGTGTGTGCTCTT 58.041 50.000 0.00 0.00 0.00 2.85
546 860 1.510480 GGCTTCTGTGGTGTGTGCTC 61.510 60.000 0.00 0.00 0.00 4.26
574 888 1.741770 GCCAGCAACGACCGAGAAT 60.742 57.895 0.00 0.00 0.00 2.40
575 889 2.357034 GCCAGCAACGACCGAGAA 60.357 61.111 0.00 0.00 0.00 2.87
576 890 4.373116 GGCCAGCAACGACCGAGA 62.373 66.667 0.00 0.00 0.00 4.04
579 893 3.599285 TTAGGGCCAGCAACGACCG 62.599 63.158 6.18 0.00 0.00 4.79
580 894 1.745489 CTTAGGGCCAGCAACGACC 60.745 63.158 6.18 0.00 0.00 4.79
581 895 0.321298 TTCTTAGGGCCAGCAACGAC 60.321 55.000 6.18 0.00 0.00 4.34
646 960 8.717717 AGTGAAAGATGGAGACCATTATCATAA 58.282 33.333 4.74 0.00 45.26 1.90
684 998 6.579865 ACCATTAACTATATATACGGCCAGC 58.420 40.000 2.24 0.00 0.00 4.85
768 1084 3.124270 CATGCCGCTACGCCAACA 61.124 61.111 0.00 0.00 0.00 3.33
771 1087 4.075854 TGACATGCCGCTACGCCA 62.076 61.111 0.00 0.00 0.00 5.69
820 1136 4.274069 CGATGAATGTATTTCACCGCTTG 58.726 43.478 0.00 0.00 44.04 4.01
850 1226 8.196771 AGAATTCAACAAATTAAGCTGTCAACA 58.803 29.630 8.44 0.00 37.70 3.33
872 1248 4.829064 TTAAGCTGTCACGCAAAAGAAT 57.171 36.364 0.00 0.00 0.00 2.40
878 1254 1.164411 CCCATTAAGCTGTCACGCAA 58.836 50.000 0.00 0.00 0.00 4.85
885 1261 2.290960 GGACAGGAACCCATTAAGCTGT 60.291 50.000 0.00 0.00 0.00 4.40
887 1263 2.279173 AGGACAGGAACCCATTAAGCT 58.721 47.619 0.00 0.00 0.00 3.74
888 1264 2.808906 AGGACAGGAACCCATTAAGC 57.191 50.000 0.00 0.00 0.00 3.09
889 1265 3.456277 AGCTAGGACAGGAACCCATTAAG 59.544 47.826 0.00 0.00 0.00 1.85
890 1266 3.460825 AGCTAGGACAGGAACCCATTAA 58.539 45.455 0.00 0.00 0.00 1.40
891 1267 3.130734 AGCTAGGACAGGAACCCATTA 57.869 47.619 0.00 0.00 0.00 1.90
892 1268 1.972588 AGCTAGGACAGGAACCCATT 58.027 50.000 0.00 0.00 0.00 3.16
893 1269 2.868964 TAGCTAGGACAGGAACCCAT 57.131 50.000 0.00 0.00 0.00 4.00
926 1304 1.741770 GTTGCCACGGACAGCTAGG 60.742 63.158 0.00 0.00 0.00 3.02
961 1339 0.243636 TGTCGCTCGCTCAAATGAGA 59.756 50.000 14.43 0.00 44.74 3.27
1119 1497 8.400947 GCATTTGTAGAATGAATAGCAGAAGAA 58.599 33.333 3.12 0.00 0.00 2.52
1164 1542 6.261381 AGACTACTAATTGTTGCGGTCAAAAA 59.739 34.615 0.00 0.00 34.19 1.94
1165 1543 5.761234 AGACTACTAATTGTTGCGGTCAAAA 59.239 36.000 0.00 0.00 33.37 2.44
1166 1544 5.302360 AGACTACTAATTGTTGCGGTCAAA 58.698 37.500 0.00 0.00 33.37 2.69
1167 1545 4.890088 AGACTACTAATTGTTGCGGTCAA 58.110 39.130 0.00 0.00 0.00 3.18
1168 1546 4.530710 AGACTACTAATTGTTGCGGTCA 57.469 40.909 0.00 0.00 0.00 4.02
1169 1547 5.169295 AGAAGACTACTAATTGTTGCGGTC 58.831 41.667 0.00 0.00 0.00 4.79
1170 1548 5.148651 AGAAGACTACTAATTGTTGCGGT 57.851 39.130 0.00 0.00 0.00 5.68
1171 1549 6.481954 AAAGAAGACTACTAATTGTTGCGG 57.518 37.500 0.00 0.00 0.00 5.69
1172 1550 8.014322 TGTAAAGAAGACTACTAATTGTTGCG 57.986 34.615 0.00 0.00 0.00 4.85
1173 1551 9.760660 CATGTAAAGAAGACTACTAATTGTTGC 57.239 33.333 0.00 0.00 0.00 4.17
1208 1586 3.612004 CGAGGATAACGTAAGATGAGGGC 60.612 52.174 0.00 0.00 43.62 5.19
1220 1598 3.921021 GGCATGTCTATTCGAGGATAACG 59.079 47.826 0.00 0.00 0.00 3.18
1224 1602 3.367806 CGATGGCATGTCTATTCGAGGAT 60.368 47.826 3.81 0.00 0.00 3.24
1297 1675 2.043450 CTCCTCCAGCTCCTCCGT 60.043 66.667 0.00 0.00 0.00 4.69
1301 1679 2.686835 GGCACTCCTCCAGCTCCT 60.687 66.667 0.00 0.00 0.00 3.69
1394 1772 0.108041 TCGGACCGTTTCCATAAGCC 60.108 55.000 14.79 0.00 46.29 4.35
1557 1985 9.267084 GATGAAGGGAGATTTTACTAACTCATC 57.733 37.037 0.00 0.00 0.00 2.92
1587 2015 6.542735 TGTGCCGCATTGTTAACCTATATTAA 59.457 34.615 2.48 0.00 0.00 1.40
1598 2026 3.005261 AGAACAATTGTGCCGCATTGTTA 59.995 39.130 18.82 0.00 44.30 2.41
1628 2056 1.067142 TCCGCTGTACATCCAACAGTC 60.067 52.381 0.00 0.00 45.01 3.51
1817 2245 8.948631 ATTCAGTACACATGTAGATACCTTTG 57.051 34.615 0.00 0.00 0.00 2.77
1872 2411 5.163764 GCACTTTGTTCGGATGATTGTATGA 60.164 40.000 0.00 0.00 0.00 2.15
1873 2412 5.030295 GCACTTTGTTCGGATGATTGTATG 58.970 41.667 0.00 0.00 0.00 2.39
1876 2415 2.095768 CGCACTTTGTTCGGATGATTGT 60.096 45.455 0.00 0.00 0.00 2.71
1877 2416 2.095768 ACGCACTTTGTTCGGATGATTG 60.096 45.455 0.00 0.00 0.00 2.67
1878 2417 2.151202 ACGCACTTTGTTCGGATGATT 58.849 42.857 0.00 0.00 0.00 2.57
1879 2418 1.732259 GACGCACTTTGTTCGGATGAT 59.268 47.619 0.00 0.00 0.00 2.45
1883 2422 0.250124 ATGGACGCACTTTGTTCGGA 60.250 50.000 0.00 0.00 0.00 4.55
1884 2423 0.165944 GATGGACGCACTTTGTTCGG 59.834 55.000 0.00 0.00 0.00 4.30
1885 2424 0.179250 CGATGGACGCACTTTGTTCG 60.179 55.000 0.00 0.00 34.51 3.95
1886 2425 0.865769 ACGATGGACGCACTTTGTTC 59.134 50.000 0.00 0.00 46.94 3.18
1889 2528 2.399396 AAAACGATGGACGCACTTTG 57.601 45.000 0.00 0.00 46.94 2.77
1927 2567 9.379791 AGATTCGACTTAATTTTAGGTACCAAG 57.620 33.333 15.94 9.41 0.00 3.61
1947 2587 5.772521 ACAACCATCCAAAAAGAAGATTCG 58.227 37.500 0.00 0.00 0.00 3.34
1955 2595 7.232118 AGGAGAAATACAACCATCCAAAAAG 57.768 36.000 0.00 0.00 0.00 2.27
2107 2753 2.762327 ACAAGGAAAATGCATGCTAGGG 59.238 45.455 20.33 1.53 0.00 3.53
2222 2879 6.502136 TGGTGCAAATAATACATCGTTTGA 57.498 33.333 0.00 0.00 34.38 2.69
2358 3015 6.227298 ACAGAACAAGCTATGCTATACAGT 57.773 37.500 0.00 0.00 38.25 3.55
2380 3037 7.612677 TCTAATTTCTTGGTTGGAGAGACTAC 58.387 38.462 0.00 0.00 0.00 2.73
2509 3171 1.543429 CGGGGTCTTCAAGTGCTCTTT 60.543 52.381 0.00 0.00 0.00 2.52
2666 3328 1.519455 GCGGTCCAGTCCTGATTCG 60.519 63.158 0.00 0.00 0.00 3.34
2717 3379 3.634397 TTTTGCTCCACTCTCCTATGG 57.366 47.619 0.00 0.00 37.32 2.74
2767 3434 3.081061 GTGTCCACAATGATGCCACTTA 58.919 45.455 0.00 0.00 0.00 2.24
2810 3477 6.806249 CCAAATTTGCACATTCATACGTACTT 59.194 34.615 12.92 0.00 0.00 2.24
2811 3478 6.321717 CCAAATTTGCACATTCATACGTACT 58.678 36.000 12.92 0.00 0.00 2.73
2845 3512 7.382110 ACCAGCATGACTCATATATTCAGTAC 58.618 38.462 0.00 0.00 39.69 2.73
2991 3659 1.923356 ATTGGGTGGTCGAATTGCTT 58.077 45.000 0.00 0.00 0.00 3.91
3019 3687 0.515564 GGTGGTTCAATTCGGTCACG 59.484 55.000 0.00 0.00 42.74 4.35
3020 3688 0.879090 GGGTGGTTCAATTCGGTCAC 59.121 55.000 0.00 0.00 0.00 3.67
3042 3710 0.601558 AGGTATATGCTGCCCGTACG 59.398 55.000 8.69 8.69 0.00 3.67
3070 3738 9.304335 TGCATGATCCAATATCTTATCACATTT 57.696 29.630 0.00 0.00 31.56 2.32
3073 3741 7.094506 GCTTGCATGATCCAATATCTTATCACA 60.095 37.037 3.33 0.00 31.56 3.58
3100 3770 2.397413 CTGAGGAACAAGGCCCACGT 62.397 60.000 0.00 0.00 0.00 4.49
3102 3772 1.973812 GCTGAGGAACAAGGCCCAC 60.974 63.158 0.00 0.00 0.00 4.61
3243 4452 7.532571 TCTCGATTCGTTAGAAATTGTACAGA 58.467 34.615 5.89 0.00 40.15 3.41
3265 4474 5.986501 ATACCGGAACAAGAGGATATCTC 57.013 43.478 9.46 0.00 37.23 2.75
3301 4510 2.171840 CCTCTCTCGGTGGAAGAGAAA 58.828 52.381 4.56 0.00 43.30 2.52
3315 4524 2.273619 AGTCTTGGGCAAATCCTCTCT 58.726 47.619 0.00 0.00 34.39 3.10
3331 4540 9.920946 TGATTAAGGGAATTGCTTAAATAGTCT 57.079 29.630 0.00 0.00 0.00 3.24
3334 4543 9.831737 CGATGATTAAGGGAATTGCTTAAATAG 57.168 33.333 0.00 0.00 0.00 1.73
3336 4545 8.463930 TCGATGATTAAGGGAATTGCTTAAAT 57.536 30.769 0.00 0.00 0.00 1.40
3362 4571 2.071778 TAGAATCAATTGGCAGGGGC 57.928 50.000 5.42 0.00 40.13 5.80
3431 4640 7.103641 TCTTAATTGGAACTAGCTCAATTCGT 58.896 34.615 16.60 3.14 40.33 3.85
3467 4676 4.156556 TCAGATTAAAGCCATGACACAAGC 59.843 41.667 0.00 0.00 0.00 4.01
3487 4696 2.520069 ACTATAGGATCCACGGCTCAG 58.480 52.381 15.82 3.46 0.00 3.35
3547 5297 1.889170 TCTGCGGATCTATTCATCGCT 59.111 47.619 10.74 0.00 45.59 4.93
3617 5376 6.233434 AGTTGAGACTCAATCTGCAAACATA 58.767 36.000 20.43 0.00 38.79 2.29
3624 5383 9.587772 TTTACTAATAGTTGAGACTCAATCTGC 57.412 33.333 20.43 8.14 38.79 4.26


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

AutoCloner maintained by Alex Coulton.