Multiple sequence alignment - TraesCS5D01G475900

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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 TraesCS5D01G475900 chr5D 100.000 5533 0 0 1 5533 515119664 515114132 0.000000e+00 10218.0
1 TraesCS5D01G475900 chr5B 93.995 2015 78 16 2917 4925 647942506 647940529 0.000000e+00 3011.0
2 TraesCS5D01G475900 chr5B 89.102 2138 100 61 210 2268 647945170 647943087 0.000000e+00 2534.0
3 TraesCS5D01G475900 chr5B 88.705 965 38 24 4209 5126 647935455 647934515 0.000000e+00 1112.0
4 TraesCS5D01G475900 chr5B 94.175 515 23 7 2324 2834 647943078 647942567 0.000000e+00 778.0
5 TraesCS5D01G475900 chr5B 85.577 520 30 14 4893 5387 647940530 647940031 2.300000e-138 503.0
6 TraesCS5D01G475900 chr5B 86.307 241 21 5 5149 5387 647934338 647934108 9.200000e-63 252.0
7 TraesCS5D01G475900 chr5B 92.562 121 9 0 5409 5529 647939933 647939813 2.050000e-39 174.0
8 TraesCS5D01G475900 chr5B 89.600 125 13 0 5409 5533 647933109 647932985 5.740000e-35 159.0
9 TraesCS5D01G475900 chr5A 94.025 1908 82 19 672 2561 643333346 643331453 0.000000e+00 2863.0
10 TraesCS5D01G475900 chr5A 92.542 1609 80 21 2572 4147 643331133 643329532 0.000000e+00 2270.0
11 TraesCS5D01G475900 chr5A 90.088 1251 58 28 4149 5387 643329369 643328173 0.000000e+00 1563.0
12 TraesCS5D01G475900 chr5A 82.353 493 48 20 97 576 643334298 643333832 5.200000e-105 392.0
13 TraesCS5D01G475900 chr5A 77.438 523 94 20 2519 3025 220456674 220456160 1.950000e-74 291.0
14 TraesCS5D01G475900 chr4B 79.726 656 108 18 2387 3025 300057403 300056756 8.450000e-123 451.0
15 TraesCS5D01G475900 chr4B 95.238 84 4 0 5163 5246 209111655 209111572 3.480000e-27 134.0
16 TraesCS5D01G475900 chr2B 79.398 665 107 22 2378 3025 268008493 268007842 5.090000e-120 442.0
17 TraesCS5D01G475900 chr2B 84.235 425 54 10 1104 1518 217793231 217792810 8.630000e-108 401.0
18 TraesCS5D01G475900 chr2B 86.452 155 16 3 1956 2109 34082948 34082798 1.230000e-36 165.0
19 TraesCS5D01G475900 chr7A 78.691 657 112 20 2387 3025 558250238 558250884 3.990000e-111 412.0
20 TraesCS5D01G475900 chr2A 83.077 455 59 10 1073 1518 172217744 172217299 1.120000e-106 398.0
21 TraesCS5D01G475900 chr2A 78.878 606 101 21 2436 3025 761151984 761152578 8.690000e-103 385.0
22 TraesCS5D01G475900 chr2A 73.401 297 61 16 1097 1387 704735473 704735757 1.640000e-15 95.3
23 TraesCS5D01G475900 chr1A 78.267 658 115 18 2387 3025 200578796 200578148 1.120000e-106 398.0
24 TraesCS5D01G475900 chr1A 85.112 356 43 7 1166 1516 487741430 487741080 6.820000e-94 355.0
25 TraesCS5D01G475900 chr1A 95.238 84 4 0 5163 5246 271755175 271755258 3.480000e-27 134.0
26 TraesCS5D01G475900 chr2D 83.765 425 56 10 1104 1518 161376773 161376352 1.870000e-104 390.0
27 TraesCS5D01G475900 chr3B 86.080 352 39 6 1166 1512 603601790 603602136 2.430000e-98 370.0
28 TraesCS5D01G475900 chr1B 85.393 356 42 7 1166 1516 522061107 522060757 1.470000e-95 361.0
29 TraesCS5D01G475900 chr1D 85.112 356 43 7 1166 1516 388651055 388650705 6.820000e-94 355.0
30 TraesCS5D01G475900 chrUn 95.489 133 6 0 5255 5387 186163737 186163605 4.340000e-51 213.0
31 TraesCS5D01G475900 chrUn 94.737 133 7 0 5255 5387 45100750 45100618 2.020000e-49 207.0
32 TraesCS5D01G475900 chrUn 94.737 133 7 0 5255 5387 261513106 261513238 2.020000e-49 207.0
33 TraesCS5D01G475900 chrUn 94.737 133 7 0 5255 5387 365031179 365031311 2.020000e-49 207.0
34 TraesCS5D01G475900 chrUn 95.238 84 4 0 5163 5246 217912797 217912714 3.480000e-27 134.0
35 TraesCS5D01G475900 chrUn 95.238 84 4 0 5163 5246 352979589 352979672 3.480000e-27 134.0
36 TraesCS5D01G475900 chrUn 95.238 84 4 0 5163 5246 433293997 433293914 3.480000e-27 134.0
37 TraesCS5D01G475900 chr4D 76.566 431 72 26 1065 1479 12408903 12409320 5.620000e-50 209.0
38 TraesCS5D01G475900 chr4D 94.737 133 7 0 5255 5387 336583482 336583614 2.020000e-49 207.0
39 TraesCS5D01G475900 chr4D 95.238 84 4 0 5163 5246 123443850 123443933 3.480000e-27 134.0
40 TraesCS5D01G475900 chr6A 94.737 133 7 0 5255 5387 375869295 375869427 2.020000e-49 207.0
41 TraesCS5D01G475900 chr6A 95.238 84 4 0 5163 5246 413573878 413573961 3.480000e-27 134.0
42 TraesCS5D01G475900 chr3D 94.737 133 7 0 5255 5387 154716385 154716253 2.020000e-49 207.0
43 TraesCS5D01G475900 chr6B 83.333 210 17 12 1900 2109 269688685 269688494 1.580000e-40 178.0


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 TraesCS5D01G475900 chr5D 515114132 515119664 5532 True 10218.000000 10218 100.0000 1 5533 1 chr5D.!!$R1 5532
1 TraesCS5D01G475900 chr5B 647939813 647945170 5357 True 1400.000000 3011 91.0822 210 5529 5 chr5B.!!$R2 5319
2 TraesCS5D01G475900 chr5B 647932985 647935455 2470 True 507.666667 1112 88.2040 4209 5533 3 chr5B.!!$R1 1324
3 TraesCS5D01G475900 chr5A 643328173 643334298 6125 True 1772.000000 2863 89.7520 97 5387 4 chr5A.!!$R2 5290
4 TraesCS5D01G475900 chr5A 220456160 220456674 514 True 291.000000 291 77.4380 2519 3025 1 chr5A.!!$R1 506
5 TraesCS5D01G475900 chr4B 300056756 300057403 647 True 451.000000 451 79.7260 2387 3025 1 chr4B.!!$R2 638
6 TraesCS5D01G475900 chr2B 268007842 268008493 651 True 442.000000 442 79.3980 2378 3025 1 chr2B.!!$R3 647
7 TraesCS5D01G475900 chr7A 558250238 558250884 646 False 412.000000 412 78.6910 2387 3025 1 chr7A.!!$F1 638
8 TraesCS5D01G475900 chr2A 761151984 761152578 594 False 385.000000 385 78.8780 2436 3025 1 chr2A.!!$F2 589
9 TraesCS5D01G475900 chr1A 200578148 200578796 648 True 398.000000 398 78.2670 2387 3025 1 chr1A.!!$R1 638

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
99 100 0.103876 AACCCCCTCCTCCTGAAACT 60.104 55.000 0.0 0.0 0.00 2.66 F
512 553 0.178068 ACCGAAACGAGGGATGATGG 59.822 55.000 0.0 0.0 0.00 3.51 F
2240 2703 0.447801 GCCACTCACAGCAAATACGG 59.552 55.000 0.0 0.0 0.00 4.02 F
2816 3596 2.437281 TGGCTTTTCCTTTTCCATTGCA 59.563 40.909 0.0 0.0 35.26 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 2014 2.028420 TGGCATAGCAAGCAGTACTG 57.972 50.0 18.93 18.93 0.00 2.74 R
2356 2825 0.538287 AACCCTTCAGTTCTGCTGCC 60.538 55.0 0.00 0.00 44.66 4.85 R
3245 4053 0.599558 GCTCAGCAATCACCTGCAAA 59.400 50.0 0.00 0.00 45.18 3.68 R
4713 5708 0.680061 ACCGGAGAAAGAAACGAGCT 59.320 50.0 9.46 0.00 0.00 4.09 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
26 27 4.812308 GCCAACTGCGTAACGAAC 57.188 55.556 0.00 0.00 0.00 3.95
35 36 3.122971 GTAACGAACGGGGCAGGC 61.123 66.667 0.00 0.00 0.00 4.85
36 37 3.315949 TAACGAACGGGGCAGGCT 61.316 61.111 0.00 0.00 0.00 4.58
37 38 3.305177 TAACGAACGGGGCAGGCTC 62.305 63.158 0.00 0.00 0.00 4.70
39 40 4.473520 CGAACGGGGCAGGCTCAT 62.474 66.667 0.00 0.00 0.00 2.90
40 41 2.514824 GAACGGGGCAGGCTCATC 60.515 66.667 0.00 0.00 0.00 2.92
41 42 3.329542 GAACGGGGCAGGCTCATCA 62.330 63.158 0.00 0.00 0.00 3.07
42 43 3.628646 AACGGGGCAGGCTCATCAC 62.629 63.158 0.00 0.00 0.00 3.06
43 44 3.790437 CGGGGCAGGCTCATCACT 61.790 66.667 0.00 0.00 0.00 3.41
44 45 2.679716 GGGGCAGGCTCATCACTT 59.320 61.111 0.00 0.00 0.00 3.16
45 46 1.452833 GGGGCAGGCTCATCACTTC 60.453 63.158 0.00 0.00 0.00 3.01
46 47 1.300963 GGGCAGGCTCATCACTTCA 59.699 57.895 0.00 0.00 0.00 3.02
47 48 0.106819 GGGCAGGCTCATCACTTCAT 60.107 55.000 0.00 0.00 0.00 2.57
48 49 1.307097 GGCAGGCTCATCACTTCATC 58.693 55.000 0.00 0.00 0.00 2.92
49 50 1.407851 GGCAGGCTCATCACTTCATCA 60.408 52.381 0.00 0.00 0.00 3.07
50 51 1.941294 GCAGGCTCATCACTTCATCAG 59.059 52.381 0.00 0.00 0.00 2.90
51 52 2.562635 CAGGCTCATCACTTCATCAGG 58.437 52.381 0.00 0.00 0.00 3.86
52 53 2.169978 CAGGCTCATCACTTCATCAGGA 59.830 50.000 0.00 0.00 0.00 3.86
53 54 2.435069 AGGCTCATCACTTCATCAGGAG 59.565 50.000 0.00 0.00 0.00 3.69
54 55 2.485124 GGCTCATCACTTCATCAGGAGG 60.485 54.545 0.00 0.00 0.00 4.30
55 56 2.433604 GCTCATCACTTCATCAGGAGGA 59.566 50.000 0.00 0.00 0.00 3.71
56 57 3.071312 GCTCATCACTTCATCAGGAGGAT 59.929 47.826 0.00 0.00 36.39 3.24
57 58 4.800249 GCTCATCACTTCATCAGGAGGATC 60.800 50.000 0.00 0.00 32.57 3.36
58 59 3.320256 TCATCACTTCATCAGGAGGATCG 59.680 47.826 0.00 0.00 32.57 3.69
59 60 3.018423 TCACTTCATCAGGAGGATCGA 57.982 47.619 0.00 0.00 32.57 3.59
60 61 3.570540 TCACTTCATCAGGAGGATCGAT 58.429 45.455 0.00 0.00 32.57 3.59
61 62 3.571828 TCACTTCATCAGGAGGATCGATC 59.428 47.826 17.36 17.36 32.57 3.69
62 63 3.573538 CACTTCATCAGGAGGATCGATCT 59.426 47.826 23.96 10.82 32.57 2.75
63 64 3.826157 ACTTCATCAGGAGGATCGATCTC 59.174 47.826 23.96 17.90 32.57 2.75
64 65 2.431454 TCATCAGGAGGATCGATCTCG 58.569 52.381 23.96 9.06 41.45 4.04
65 66 1.135431 CATCAGGAGGATCGATCTCGC 60.135 57.143 23.96 15.30 39.60 5.03
66 67 0.109532 TCAGGAGGATCGATCTCGCT 59.890 55.000 23.96 13.30 39.60 4.93
67 68 1.348036 TCAGGAGGATCGATCTCGCTA 59.652 52.381 23.96 4.36 39.60 4.26
68 69 2.026729 TCAGGAGGATCGATCTCGCTAT 60.027 50.000 23.96 7.46 39.60 2.97
69 70 2.354510 CAGGAGGATCGATCTCGCTATC 59.645 54.545 23.96 12.31 39.60 2.08
71 72 0.730265 AGGATCGATCTCGCTATCGC 59.270 55.000 23.96 5.00 46.51 4.58
81 82 2.278596 GCTATCGCGCTCACCGAA 60.279 61.111 5.56 0.00 40.02 4.30
82 83 2.577785 GCTATCGCGCTCACCGAAC 61.578 63.158 5.56 0.00 40.02 3.95
83 84 1.944676 CTATCGCGCTCACCGAACC 60.945 63.158 5.56 0.00 40.02 3.62
84 85 3.420214 TATCGCGCTCACCGAACCC 62.420 63.158 5.56 0.00 40.02 4.11
88 89 4.452733 CGCTCACCGAACCCCCTC 62.453 72.222 0.00 0.00 40.02 4.30
89 90 4.097361 GCTCACCGAACCCCCTCC 62.097 72.222 0.00 0.00 0.00 4.30
90 91 2.284699 CTCACCGAACCCCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
91 92 2.284405 TCACCGAACCCCCTCCTC 60.284 66.667 0.00 0.00 0.00 3.71
92 93 3.400054 CACCGAACCCCCTCCTCC 61.400 72.222 0.00 0.00 0.00 4.30
93 94 3.612607 ACCGAACCCCCTCCTCCT 61.613 66.667 0.00 0.00 0.00 3.69
94 95 3.083997 CCGAACCCCCTCCTCCTG 61.084 72.222 0.00 0.00 0.00 3.86
95 96 2.038975 CGAACCCCCTCCTCCTGA 59.961 66.667 0.00 0.00 0.00 3.86
96 97 1.612442 CGAACCCCCTCCTCCTGAA 60.612 63.158 0.00 0.00 0.00 3.02
97 98 1.198759 CGAACCCCCTCCTCCTGAAA 61.199 60.000 0.00 0.00 0.00 2.69
98 99 0.328592 GAACCCCCTCCTCCTGAAAC 59.671 60.000 0.00 0.00 0.00 2.78
99 100 0.103876 AACCCCCTCCTCCTGAAACT 60.104 55.000 0.00 0.00 0.00 2.66
104 105 1.003696 CCCTCCTCCTGAAACTTCCAC 59.996 57.143 0.00 0.00 0.00 4.02
121 122 3.350612 CGCCCGTTTTCTTCGCCA 61.351 61.111 0.00 0.00 0.00 5.69
129 130 1.329599 GTTTTCTTCGCCACTTGTCGT 59.670 47.619 0.00 0.00 0.00 4.34
147 148 2.433838 CGTCTGGTCCAGCTGCAG 60.434 66.667 14.64 10.11 0.00 4.41
156 157 2.225467 GTCCAGCTGCAGAAAAAGTCT 58.775 47.619 20.43 0.00 36.88 3.24
158 159 1.538950 CCAGCTGCAGAAAAAGTCTCC 59.461 52.381 20.43 0.00 32.70 3.71
180 181 4.415512 CCCTCCCATTTTTCTACTCCCATA 59.584 45.833 0.00 0.00 0.00 2.74
181 182 5.377478 CCTCCCATTTTTCTACTCCCATAC 58.623 45.833 0.00 0.00 0.00 2.39
183 184 6.329197 CCTCCCATTTTTCTACTCCCATACTA 59.671 42.308 0.00 0.00 0.00 1.82
184 185 7.374975 TCCCATTTTTCTACTCCCATACTAG 57.625 40.000 0.00 0.00 0.00 2.57
185 186 6.329197 TCCCATTTTTCTACTCCCATACTAGG 59.671 42.308 0.00 0.00 0.00 3.02
186 187 5.998363 CCATTTTTCTACTCCCATACTAGGC 59.002 44.000 0.00 0.00 0.00 3.93
187 188 5.625568 TTTTTCTACTCCCATACTAGGCC 57.374 43.478 0.00 0.00 0.00 5.19
188 189 2.994957 TCTACTCCCATACTAGGCCC 57.005 55.000 0.00 0.00 0.00 5.80
204 205 3.006728 CCGCCCCCTTCACACCTA 61.007 66.667 0.00 0.00 0.00 3.08
205 206 2.267961 CGCCCCCTTCACACCTAC 59.732 66.667 0.00 0.00 0.00 3.18
206 207 2.589157 CGCCCCCTTCACACCTACA 61.589 63.158 0.00 0.00 0.00 2.74
207 208 1.299976 GCCCCCTTCACACCTACAG 59.700 63.158 0.00 0.00 0.00 2.74
208 209 1.299976 CCCCCTTCACACCTACAGC 59.700 63.158 0.00 0.00 0.00 4.40
240 242 2.496899 ATCCTTCAAGTCCAATGCGT 57.503 45.000 0.00 0.00 0.00 5.24
244 246 2.613977 CCTTCAAGTCCAATGCGTCTCT 60.614 50.000 0.00 0.00 0.00 3.10
270 272 4.876107 CAGCTAACCACCAATCGAATTAGT 59.124 41.667 0.00 0.00 0.00 2.24
277 281 7.696992 ACCACCAATCGAATTAGTACAAAAT 57.303 32.000 0.00 0.00 0.00 1.82
280 284 6.472163 CACCAATCGAATTAGTACAAAATGGC 59.528 38.462 0.00 0.00 0.00 4.40
281 285 6.151985 ACCAATCGAATTAGTACAAAATGGCA 59.848 34.615 0.00 0.00 0.00 4.92
285 289 5.062934 TCGAATTAGTACAAAATGGCAGTCG 59.937 40.000 0.00 1.37 0.00 4.18
302 306 3.370978 CAGTCGTATAAAACAGCACCAGG 59.629 47.826 0.00 0.00 0.00 4.45
332 336 6.829298 TCCCTCGCTAATCCTATACTAATCTG 59.171 42.308 0.00 0.00 0.00 2.90
348 353 5.711976 ACTAATCTGACACCATTCCAAAAGG 59.288 40.000 0.00 0.00 0.00 3.11
350 355 3.909732 TCTGACACCATTCCAAAAGGTT 58.090 40.909 0.00 0.00 32.15 3.50
406 434 5.025826 GGTATCGTTTTAGCCGACATTTTG 58.974 41.667 0.00 0.00 37.12 2.44
410 438 3.844099 CGTTTTAGCCGACATTTTGTAGC 59.156 43.478 0.00 0.00 31.89 3.58
435 463 8.496751 GCTATAAACCACTAAAGCTAGCATTAC 58.503 37.037 18.83 0.00 32.58 1.89
452 493 9.404348 CTAGCATTACTATAGTGTGAAGACATG 57.596 37.037 15.90 0.00 33.63 3.21
471 512 6.489361 AGACATGAGAATAAGGCATGGAAATC 59.511 38.462 0.00 0.00 0.00 2.17
495 536 1.133407 TGCGTGTGGACTTTTGAAACC 59.867 47.619 0.00 0.00 0.00 3.27
496 537 1.858399 GCGTGTGGACTTTTGAAACCG 60.858 52.381 0.00 0.00 0.00 4.44
500 541 3.855379 GTGTGGACTTTTGAAACCGAAAC 59.145 43.478 0.00 0.00 0.00 2.78
501 542 3.103007 GTGGACTTTTGAAACCGAAACG 58.897 45.455 0.00 0.00 0.00 3.60
502 543 3.008330 TGGACTTTTGAAACCGAAACGA 58.992 40.909 0.00 0.00 0.00 3.85
503 544 3.064271 TGGACTTTTGAAACCGAAACGAG 59.936 43.478 0.00 0.00 0.00 4.18
505 546 2.356695 ACTTTTGAAACCGAAACGAGGG 59.643 45.455 0.00 0.00 0.00 4.30
506 547 2.328819 TTTGAAACCGAAACGAGGGA 57.671 45.000 0.00 0.00 0.00 4.20
507 548 2.554370 TTGAAACCGAAACGAGGGAT 57.446 45.000 0.00 0.00 0.00 3.85
508 549 1.803334 TGAAACCGAAACGAGGGATG 58.197 50.000 0.00 0.00 0.00 3.51
509 550 1.345089 TGAAACCGAAACGAGGGATGA 59.655 47.619 0.00 0.00 0.00 2.92
510 551 2.027561 TGAAACCGAAACGAGGGATGAT 60.028 45.455 0.00 0.00 0.00 2.45
511 552 2.024176 AACCGAAACGAGGGATGATG 57.976 50.000 0.00 0.00 0.00 3.07
512 553 0.178068 ACCGAAACGAGGGATGATGG 59.822 55.000 0.00 0.00 0.00 3.51
513 554 0.464036 CCGAAACGAGGGATGATGGA 59.536 55.000 0.00 0.00 0.00 3.41
514 555 1.070758 CCGAAACGAGGGATGATGGAT 59.929 52.381 0.00 0.00 0.00 3.41
515 556 2.408050 CGAAACGAGGGATGATGGATC 58.592 52.381 0.00 0.00 0.00 3.36
521 562 2.743928 GGATGATGGATCGGCGGC 60.744 66.667 7.21 0.00 30.87 6.53
522 563 2.743928 GATGATGGATCGGCGGCC 60.744 66.667 9.54 9.54 0.00 6.13
586 631 1.039233 CACCAACTGCCCCATCATCC 61.039 60.000 0.00 0.00 0.00 3.51
592 637 1.004626 TGCCCCATCATCCTCCTCA 59.995 57.895 0.00 0.00 0.00 3.86
593 638 1.348008 TGCCCCATCATCCTCCTCAC 61.348 60.000 0.00 0.00 0.00 3.51
595 640 0.695462 CCCCATCATCCTCCTCACCA 60.695 60.000 0.00 0.00 0.00 4.17
596 641 0.471617 CCCATCATCCTCCTCACCAC 59.528 60.000 0.00 0.00 0.00 4.16
599 644 0.695803 ATCATCCTCCTCACCACCCC 60.696 60.000 0.00 0.00 0.00 4.95
620 686 3.356290 CCCTGCTGCTGGTTAACTTAAT 58.644 45.455 21.89 0.00 0.00 1.40
658 724 3.076032 ACAAAATCTCCACCCTAAAGGCT 59.924 43.478 0.00 0.00 40.58 4.58
669 735 3.251484 CCCTAAAGGCTGGATCCTCATA 58.749 50.000 14.23 0.00 34.82 2.15
695 1126 0.703488 TCATTGCCATCCCCAGTGAA 59.297 50.000 0.00 0.00 0.00 3.18
698 1129 2.438434 GCCATCCCCAGTGAACCG 60.438 66.667 0.00 0.00 0.00 4.44
762 1198 2.026356 TGCTGTTAATGGCTGGCTTCTA 60.026 45.455 2.00 0.00 0.00 2.10
763 1199 2.615912 GCTGTTAATGGCTGGCTTCTAG 59.384 50.000 2.00 0.00 0.00 2.43
764 1200 3.682718 GCTGTTAATGGCTGGCTTCTAGA 60.683 47.826 2.00 0.00 0.00 2.43
765 1201 4.517285 CTGTTAATGGCTGGCTTCTAGAA 58.483 43.478 4.81 4.81 0.00 2.10
768 1204 3.728385 AATGGCTGGCTTCTAGAAAGT 57.272 42.857 6.63 0.00 0.00 2.66
771 1207 2.093447 TGGCTGGCTTCTAGAAAGTAGC 60.093 50.000 18.87 18.87 43.40 3.58
772 1208 2.093447 GGCTGGCTTCTAGAAAGTAGCA 60.093 50.000 24.21 9.75 45.29 3.49
775 1211 4.621747 GCTGGCTTCTAGAAAGTAGCAGAA 60.622 45.833 20.77 6.50 45.29 3.02
903 1360 5.010617 CCCTCGATTTCCCTTTTCTTTTTCA 59.989 40.000 0.00 0.00 0.00 2.69
904 1361 6.462347 CCCTCGATTTCCCTTTTCTTTTTCAA 60.462 38.462 0.00 0.00 0.00 2.69
905 1362 6.420903 CCTCGATTTCCCTTTTCTTTTTCAAC 59.579 38.462 0.00 0.00 0.00 3.18
906 1363 6.868622 TCGATTTCCCTTTTCTTTTTCAACA 58.131 32.000 0.00 0.00 0.00 3.33
907 1364 7.496747 TCGATTTCCCTTTTCTTTTTCAACAT 58.503 30.769 0.00 0.00 0.00 2.71
908 1365 8.634444 TCGATTTCCCTTTTCTTTTTCAACATA 58.366 29.630 0.00 0.00 0.00 2.29
909 1366 8.699749 CGATTTCCCTTTTCTTTTTCAACATAC 58.300 33.333 0.00 0.00 0.00 2.39
972 1429 3.131478 CGTCCGCCCCCAAATCAC 61.131 66.667 0.00 0.00 0.00 3.06
1233 1693 0.965866 TCACCTACCTCTGCACCGAG 60.966 60.000 0.00 0.00 0.00 4.63
1909 2372 2.796593 GGTTTGCATCAGTTTCTTGCAC 59.203 45.455 0.00 0.00 45.35 4.57
1935 2398 3.882888 TGGATTGTTTTGTGACCTCTGAC 59.117 43.478 0.00 0.00 0.00 3.51
1936 2399 3.882888 GGATTGTTTTGTGACCTCTGACA 59.117 43.478 0.00 0.00 0.00 3.58
1994 2457 1.475280 CAGATGTGCCACAGAAATGGG 59.525 52.381 3.00 0.00 40.43 4.00
2018 2481 0.838554 TCCATCGGGACCTCAAACCA 60.839 55.000 0.00 0.00 38.64 3.67
2174 2637 8.087982 TGATCTAGATTTGCTAAAATAAGCGG 57.912 34.615 6.70 0.00 45.85 5.52
2178 2641 5.880341 AGATTTGCTAAAATAAGCGGTGTC 58.120 37.500 0.00 0.00 45.85 3.67
2210 2673 8.960591 TCCCATTTTTCTTCTCTGATTTATGTC 58.039 33.333 0.00 0.00 0.00 3.06
2224 2687 7.335673 TCTGATTTATGTCGTAATTTCAAGCCA 59.664 33.333 0.00 0.00 0.00 4.75
2229 2692 3.496884 TGTCGTAATTTCAAGCCACTCAC 59.503 43.478 0.00 0.00 0.00 3.51
2238 2701 2.813754 TCAAGCCACTCACAGCAAATAC 59.186 45.455 0.00 0.00 0.00 1.89
2239 2702 1.442769 AGCCACTCACAGCAAATACG 58.557 50.000 0.00 0.00 0.00 3.06
2240 2703 0.447801 GCCACTCACAGCAAATACGG 59.552 55.000 0.00 0.00 0.00 4.02
2254 2717 9.005777 ACAGCAAATACGGAAACTCTTATTAAA 57.994 29.630 0.00 0.00 0.00 1.52
2289 2758 7.899973 AGATCCACTGTATTTTGCTTGATTTT 58.100 30.769 0.00 0.00 0.00 1.82
2302 2771 3.677976 GCTTGATTTTCCATCCCTGCAAG 60.678 47.826 0.00 0.00 35.75 4.01
2313 2782 5.192327 CATCCCTGCAAGATGGATTTAAC 57.808 43.478 15.53 0.00 33.41 2.01
2316 2785 4.949856 TCCCTGCAAGATGGATTTAACTTC 59.050 41.667 0.00 0.00 34.07 3.01
2317 2786 4.098501 CCCTGCAAGATGGATTTAACTTCC 59.901 45.833 0.00 0.00 34.07 3.46
2318 2787 4.706476 CCTGCAAGATGGATTTAACTTCCA 59.294 41.667 8.41 8.41 46.86 3.53
2359 2828 9.183368 TGAGAATATATGTACAATGTTTTGGCA 57.817 29.630 0.00 0.00 37.15 4.92
2561 3030 4.082245 CCATTTTGGGCAGGTACTTAACTG 60.082 45.833 0.00 0.00 30.75 3.16
2562 3031 4.440826 TTTTGGGCAGGTACTTAACTGA 57.559 40.909 5.44 0.00 34.60 3.41
2563 3032 3.695830 TTGGGCAGGTACTTAACTGAG 57.304 47.619 5.44 0.00 34.60 3.35
2593 3371 4.677779 GCTGAATGTATGTTGCGGGAAAAT 60.678 41.667 0.00 0.00 0.00 1.82
2620 3398 5.405935 AAATCACCTTACAAATTCCTGCC 57.594 39.130 0.00 0.00 0.00 4.85
2705 3483 4.394712 GACCCGTGGCCCAGAGTG 62.395 72.222 0.00 0.00 0.00 3.51
2708 3486 4.394712 CCGTGGCCCAGAGTGTCC 62.395 72.222 0.00 0.00 0.00 4.02
2799 3579 6.378072 CAAGTACTTGGTGAGCATTATGGCT 61.378 44.000 25.19 0.00 40.84 4.75
2816 3596 2.437281 TGGCTTTTCCTTTTCCATTGCA 59.563 40.909 0.00 0.00 35.26 4.08
2880 3688 4.816385 CGGTGATATGCCTGTTTTATGTCT 59.184 41.667 0.00 0.00 0.00 3.41
2882 3690 6.498304 GGTGATATGCCTGTTTTATGTCTTG 58.502 40.000 0.00 0.00 0.00 3.02
2964 3772 7.145323 ACAATTTCCCTATTTCTTTTGTGACG 58.855 34.615 0.00 0.00 0.00 4.35
3030 3838 6.865205 CCAAAAAGAATCCTGACATTCAACTC 59.135 38.462 0.00 0.00 35.51 3.01
3144 3952 6.042781 AGTTCCAAGTTCCAACTACATCAGTA 59.957 38.462 0.00 0.00 38.57 2.74
3438 4246 6.701400 GGATGCTGTGAGTTACAAAACAAAAT 59.299 34.615 0.00 0.00 39.20 1.82
3439 4247 7.224557 GGATGCTGTGAGTTACAAAACAAAATT 59.775 33.333 0.00 0.00 39.20 1.82
3496 4305 5.254901 TGAGAGGTCTGAAGGTAGTTACTC 58.745 45.833 0.00 0.00 0.00 2.59
3589 4399 5.643379 TCCATGTGAGAAAAATAGGCAAC 57.357 39.130 0.00 0.00 0.00 4.17
3652 4462 8.519526 CAAGATAAGAGTGGGTACATAGAGATC 58.480 40.741 0.00 0.00 0.00 2.75
3676 4486 1.996191 GAGCTTAGAGTGGCTTTGACG 59.004 52.381 0.00 0.00 39.05 4.35
3765 4575 2.247635 AGGTCAGCCCTCTCATACCTTA 59.752 50.000 0.00 0.00 40.71 2.69
3801 4611 7.484035 AACTGTACAACATCTTTCTCAGAAC 57.516 36.000 0.00 0.00 34.16 3.01
3823 4633 7.925483 AGAACTCAGAACATATGCTAATGACTC 59.075 37.037 1.58 1.19 0.00 3.36
3857 4667 5.824097 TGAAAACTGAAACCAACCTACTACC 59.176 40.000 0.00 0.00 0.00 3.18
3931 4741 1.539827 CCGGTGGTTCAGGATTCAAAC 59.460 52.381 0.00 0.00 33.18 2.93
4161 5142 5.618056 AGCAACATGTATGACTTGTTCAG 57.382 39.130 0.00 1.40 42.29 3.02
4264 5253 5.104527 CCAGACCAGGTCACAAGGATAAATA 60.105 44.000 22.31 0.00 34.60 1.40
4544 5533 1.403679 CAGAAGTAGACCGAGCAGAGG 59.596 57.143 0.00 0.00 0.00 3.69
4624 5618 4.286320 ATCGTGATCGCCCCGAGC 62.286 66.667 0.00 0.00 42.86 5.03
4674 5669 1.002468 GTCATGTTGTTTCGCTGTGCT 60.002 47.619 0.00 0.00 0.00 4.40
4713 5708 3.314080 GGTTTTGTCGTCAGATTTCACCA 59.686 43.478 0.00 0.00 0.00 4.17
4718 5713 0.994995 CGTCAGATTTCACCAGCTCG 59.005 55.000 0.00 0.00 0.00 5.03
4877 5872 4.323868 GGGAAATGCTTAACAGAGGAGTCT 60.324 45.833 0.00 0.00 0.00 3.24
4895 5890 2.481952 GTCTTGGTCTTGCACTCATCAC 59.518 50.000 0.00 0.00 0.00 3.06
4899 5956 1.446907 GTCTTGCACTCATCACCCTG 58.553 55.000 0.00 0.00 0.00 4.45
5077 6143 1.202463 ACTGTGAGCGCACCTATCATC 60.202 52.381 18.33 0.00 44.51 2.92
5078 6144 0.249031 TGTGAGCGCACCTATCATCG 60.249 55.000 18.33 0.00 44.51 3.84
5079 6145 0.249073 GTGAGCGCACCTATCATCGT 60.249 55.000 11.47 0.00 39.14 3.73
5080 6146 0.030773 TGAGCGCACCTATCATCGTC 59.969 55.000 11.47 0.00 0.00 4.20
5081 6147 0.030773 GAGCGCACCTATCATCGTCA 59.969 55.000 11.47 0.00 0.00 4.35
5082 6148 0.676184 AGCGCACCTATCATCGTCAT 59.324 50.000 11.47 0.00 0.00 3.06
5083 6149 1.063806 GCGCACCTATCATCGTCATC 58.936 55.000 0.30 0.00 0.00 2.92
5084 6150 1.602920 GCGCACCTATCATCGTCATCA 60.603 52.381 0.30 0.00 0.00 3.07
5085 6151 2.928301 GCGCACCTATCATCGTCATCAT 60.928 50.000 0.30 0.00 0.00 2.45
5158 6393 1.331756 CTGGCCTATGCTTAGTTTGCG 59.668 52.381 3.32 0.00 37.74 4.85
5217 6457 5.329399 TGTTCTTGTATGCCCAATACCTTT 58.671 37.500 0.00 0.00 40.53 3.11
5246 6486 6.240894 AGCAGTGATTTCAAATCCAGAAGTA 58.759 36.000 7.68 0.00 0.00 2.24
5250 6490 6.151817 AGTGATTTCAAATCCAGAAGTAAGGC 59.848 38.462 7.68 0.00 0.00 4.35
5252 6492 5.964958 TTTCAAATCCAGAAGTAAGGCTG 57.035 39.130 0.00 0.00 0.00 4.85
5253 6493 4.908601 TCAAATCCAGAAGTAAGGCTGA 57.091 40.909 0.00 0.00 34.06 4.26
5254 6494 4.579869 TCAAATCCAGAAGTAAGGCTGAC 58.420 43.478 0.00 0.00 34.06 3.51
5255 6495 4.287067 TCAAATCCAGAAGTAAGGCTGACT 59.713 41.667 0.00 0.00 34.06 3.41
5256 6496 5.483937 TCAAATCCAGAAGTAAGGCTGACTA 59.516 40.000 4.55 0.00 34.06 2.59
5257 6497 5.346181 AATCCAGAAGTAAGGCTGACTAC 57.654 43.478 4.55 0.00 34.06 2.73
5345 6587 2.417379 CCTGGAGAACGTGTGATACTGG 60.417 54.545 0.00 0.00 0.00 4.00
5387 6629 4.532834 ACAGGTTGCTCCTTTAGTTGAAA 58.467 39.130 0.00 0.00 45.67 2.69
5388 6630 4.953579 ACAGGTTGCTCCTTTAGTTGAAAA 59.046 37.500 0.00 0.00 45.67 2.29
5389 6631 5.067805 ACAGGTTGCTCCTTTAGTTGAAAAG 59.932 40.000 0.00 0.00 45.67 2.27
5392 6634 6.486993 AGGTTGCTCCTTTAGTTGAAAAGTAG 59.513 38.462 0.00 0.00 45.67 2.57
5393 6635 5.941948 TGCTCCTTTAGTTGAAAAGTAGC 57.058 39.130 6.89 6.89 44.34 3.58
5394 6636 5.941948 GCTCCTTTAGTTGAAAAGTAGCA 57.058 39.130 8.48 0.00 43.84 3.49
5396 6638 6.374578 GCTCCTTTAGTTGAAAAGTAGCAAG 58.625 40.000 8.48 0.00 43.84 4.01
5398 6640 7.172703 GCTCCTTTAGTTGAAAAGTAGCAAGTA 59.827 37.037 8.48 0.00 43.84 2.24
5399 6641 9.220767 CTCCTTTAGTTGAAAAGTAGCAAGTAT 57.779 33.333 0.00 0.00 35.16 2.12
5400 6642 9.216117 TCCTTTAGTTGAAAAGTAGCAAGTATC 57.784 33.333 0.00 0.00 35.16 2.24
5401 6643 8.169268 CCTTTAGTTGAAAAGTAGCAAGTATCG 58.831 37.037 0.00 0.00 35.16 2.92
5403 6645 5.790593 AGTTGAAAAGTAGCAAGTATCGGA 58.209 37.500 0.00 0.00 0.00 4.55
5404 6646 5.638234 AGTTGAAAAGTAGCAAGTATCGGAC 59.362 40.000 0.00 0.00 0.00 4.79
5405 6647 5.401531 TGAAAAGTAGCAAGTATCGGACT 57.598 39.130 0.00 0.00 41.56 3.85
5454 7674 5.009410 AGAGAATGCAAACTTTCTGTCAAGG 59.991 40.000 5.04 0.00 39.63 3.61
5456 7676 3.011566 TGCAAACTTTCTGTCAAGGGA 57.988 42.857 0.00 0.00 0.00 4.20
5529 7749 1.609210 TGGACCGCCAGAGATGACA 60.609 57.895 0.00 0.00 39.92 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.154727 CGTTCGTTACGCAGTTGGC 60.155 57.895 0.00 0.00 37.78 4.52
18 19 3.122971 GCCTGCCCCGTTCGTTAC 61.123 66.667 0.00 0.00 0.00 2.50
19 20 3.305177 GAGCCTGCCCCGTTCGTTA 62.305 63.158 0.00 0.00 0.00 3.18
20 21 4.699522 GAGCCTGCCCCGTTCGTT 62.700 66.667 0.00 0.00 0.00 3.85
22 23 4.473520 ATGAGCCTGCCCCGTTCG 62.474 66.667 0.00 0.00 0.00 3.95
23 24 2.514824 GATGAGCCTGCCCCGTTC 60.515 66.667 0.00 0.00 0.00 3.95
24 25 3.329889 TGATGAGCCTGCCCCGTT 61.330 61.111 0.00 0.00 0.00 4.44
25 26 4.101448 GTGATGAGCCTGCCCCGT 62.101 66.667 0.00 0.00 0.00 5.28
26 27 3.335356 AAGTGATGAGCCTGCCCCG 62.335 63.158 0.00 0.00 0.00 5.73
27 28 1.452833 GAAGTGATGAGCCTGCCCC 60.453 63.158 0.00 0.00 0.00 5.80
28 29 0.106819 ATGAAGTGATGAGCCTGCCC 60.107 55.000 0.00 0.00 0.00 5.36
29 30 1.307097 GATGAAGTGATGAGCCTGCC 58.693 55.000 0.00 0.00 0.00 4.85
30 31 1.941294 CTGATGAAGTGATGAGCCTGC 59.059 52.381 0.00 0.00 0.00 4.85
31 32 2.169978 TCCTGATGAAGTGATGAGCCTG 59.830 50.000 0.00 0.00 0.00 4.85
32 33 2.435069 CTCCTGATGAAGTGATGAGCCT 59.565 50.000 0.00 0.00 0.00 4.58
33 34 2.485124 CCTCCTGATGAAGTGATGAGCC 60.485 54.545 0.00 0.00 0.00 4.70
34 35 2.433604 TCCTCCTGATGAAGTGATGAGC 59.566 50.000 0.00 0.00 0.00 4.26
35 36 4.559099 CGATCCTCCTGATGAAGTGATGAG 60.559 50.000 0.00 0.00 32.41 2.90
36 37 3.320256 CGATCCTCCTGATGAAGTGATGA 59.680 47.826 0.00 0.00 32.41 2.92
37 38 3.320256 TCGATCCTCCTGATGAAGTGATG 59.680 47.826 0.00 0.00 32.41 3.07
38 39 3.570540 TCGATCCTCCTGATGAAGTGAT 58.429 45.455 0.00 0.00 32.41 3.06
39 40 3.018423 TCGATCCTCCTGATGAAGTGA 57.982 47.619 0.00 0.00 32.41 3.41
40 41 3.573538 AGATCGATCCTCCTGATGAAGTG 59.426 47.826 21.66 0.00 32.41 3.16
41 42 3.826157 GAGATCGATCCTCCTGATGAAGT 59.174 47.826 21.66 0.00 32.41 3.01
42 43 3.119884 CGAGATCGATCCTCCTGATGAAG 60.120 52.174 21.66 1.06 43.02 3.02
43 44 2.816672 CGAGATCGATCCTCCTGATGAA 59.183 50.000 21.66 0.00 43.02 2.57
44 45 2.431454 CGAGATCGATCCTCCTGATGA 58.569 52.381 21.66 0.00 43.02 2.92
45 46 1.135431 GCGAGATCGATCCTCCTGATG 60.135 57.143 21.66 6.96 43.02 3.07
46 47 1.173043 GCGAGATCGATCCTCCTGAT 58.827 55.000 21.66 0.92 43.02 2.90
47 48 0.109532 AGCGAGATCGATCCTCCTGA 59.890 55.000 21.66 0.00 43.02 3.86
48 49 1.814793 TAGCGAGATCGATCCTCCTG 58.185 55.000 21.66 8.44 43.02 3.86
49 50 2.639065 GATAGCGAGATCGATCCTCCT 58.361 52.381 21.66 16.12 43.02 3.69
65 66 1.944676 GGTTCGGTGAGCGCGATAG 60.945 63.158 12.10 0.00 0.00 2.08
66 67 2.103538 GGTTCGGTGAGCGCGATA 59.896 61.111 12.10 0.00 0.00 2.92
67 68 4.814294 GGGTTCGGTGAGCGCGAT 62.814 66.667 12.10 1.23 0.00 4.58
71 72 4.452733 GAGGGGGTTCGGTGAGCG 62.453 72.222 0.00 0.00 0.00 5.03
72 73 4.097361 GGAGGGGGTTCGGTGAGC 62.097 72.222 0.00 0.00 0.00 4.26
73 74 2.284699 AGGAGGGGGTTCGGTGAG 60.285 66.667 0.00 0.00 0.00 3.51
74 75 2.284405 GAGGAGGGGGTTCGGTGA 60.284 66.667 0.00 0.00 0.00 4.02
75 76 3.400054 GGAGGAGGGGGTTCGGTG 61.400 72.222 0.00 0.00 0.00 4.94
76 77 3.612607 AGGAGGAGGGGGTTCGGT 61.613 66.667 0.00 0.00 0.00 4.69
77 78 3.083997 CAGGAGGAGGGGGTTCGG 61.084 72.222 0.00 0.00 0.00 4.30
78 79 1.198759 TTTCAGGAGGAGGGGGTTCG 61.199 60.000 0.00 0.00 0.00 3.95
79 80 0.328592 GTTTCAGGAGGAGGGGGTTC 59.671 60.000 0.00 0.00 0.00 3.62
80 81 0.103876 AGTTTCAGGAGGAGGGGGTT 60.104 55.000 0.00 0.00 0.00 4.11
81 82 0.103876 AAGTTTCAGGAGGAGGGGGT 60.104 55.000 0.00 0.00 0.00 4.95
82 83 0.621082 GAAGTTTCAGGAGGAGGGGG 59.379 60.000 0.00 0.00 0.00 5.40
83 84 0.621082 GGAAGTTTCAGGAGGAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
84 85 1.003696 GTGGAAGTTTCAGGAGGAGGG 59.996 57.143 0.00 0.00 0.00 4.30
85 86 1.338200 CGTGGAAGTTTCAGGAGGAGG 60.338 57.143 0.00 0.00 0.00 4.30
86 87 1.941668 GCGTGGAAGTTTCAGGAGGAG 60.942 57.143 8.06 0.00 0.00 3.69
87 88 0.034896 GCGTGGAAGTTTCAGGAGGA 59.965 55.000 8.06 0.00 0.00 3.71
88 89 0.955919 GGCGTGGAAGTTTCAGGAGG 60.956 60.000 8.06 0.00 0.00 4.30
89 90 0.955919 GGGCGTGGAAGTTTCAGGAG 60.956 60.000 8.06 0.00 0.00 3.69
90 91 1.072505 GGGCGTGGAAGTTTCAGGA 59.927 57.895 8.06 0.00 0.00 3.86
91 92 2.325082 CGGGCGTGGAAGTTTCAGG 61.325 63.158 0.00 0.00 0.00 3.86
92 93 1.164041 AACGGGCGTGGAAGTTTCAG 61.164 55.000 0.00 0.00 0.00 3.02
93 94 0.748729 AAACGGGCGTGGAAGTTTCA 60.749 50.000 0.00 0.00 32.05 2.69
94 95 0.382873 AAAACGGGCGTGGAAGTTTC 59.617 50.000 0.00 0.00 35.99 2.78
95 96 0.382873 GAAAACGGGCGTGGAAGTTT 59.617 50.000 0.00 0.00 38.30 2.66
96 97 0.464916 AGAAAACGGGCGTGGAAGTT 60.465 50.000 0.00 0.00 0.00 2.66
97 98 0.464916 AAGAAAACGGGCGTGGAAGT 60.465 50.000 0.00 0.00 0.00 3.01
98 99 0.237498 GAAGAAAACGGGCGTGGAAG 59.763 55.000 0.00 0.00 0.00 3.46
99 100 1.500512 CGAAGAAAACGGGCGTGGAA 61.501 55.000 0.00 0.00 0.00 3.53
104 105 3.350612 TGGCGAAGAAAACGGGCG 61.351 61.111 0.00 0.00 0.00 6.13
121 122 1.105167 TGGACCAGACGACGACAAGT 61.105 55.000 0.00 0.00 0.00 3.16
129 130 2.917227 TGCAGCTGGACCAGACGA 60.917 61.111 26.25 2.23 32.44 4.20
147 148 5.540337 AGAAAAATGGGAGGGAGACTTTTTC 59.460 40.000 9.22 9.22 40.37 2.29
156 157 2.850568 GGGAGTAGAAAAATGGGAGGGA 59.149 50.000 0.00 0.00 0.00 4.20
158 159 4.526438 ATGGGAGTAGAAAAATGGGAGG 57.474 45.455 0.00 0.00 0.00 4.30
187 188 3.006728 TAGGTGTGAAGGGGGCGG 61.007 66.667 0.00 0.00 0.00 6.13
188 189 2.267961 GTAGGTGTGAAGGGGGCG 59.732 66.667 0.00 0.00 0.00 6.13
199 200 6.238484 GGATAAAGTAAAGCATGCTGTAGGTG 60.238 42.308 23.48 0.00 0.00 4.00
200 201 5.823045 GGATAAAGTAAAGCATGCTGTAGGT 59.177 40.000 23.48 7.45 0.00 3.08
201 202 6.058183 AGGATAAAGTAAAGCATGCTGTAGG 58.942 40.000 23.48 0.00 0.00 3.18
202 203 7.280876 TGAAGGATAAAGTAAAGCATGCTGTAG 59.719 37.037 23.48 0.00 0.00 2.74
203 204 7.109501 TGAAGGATAAAGTAAAGCATGCTGTA 58.890 34.615 23.48 18.40 0.00 2.74
204 205 5.945784 TGAAGGATAAAGTAAAGCATGCTGT 59.054 36.000 23.48 19.70 0.00 4.40
205 206 6.441093 TGAAGGATAAAGTAAAGCATGCTG 57.559 37.500 23.48 0.00 0.00 4.41
206 207 6.660949 ACTTGAAGGATAAAGTAAAGCATGCT 59.339 34.615 16.30 16.30 34.90 3.79
207 208 6.856895 ACTTGAAGGATAAAGTAAAGCATGC 58.143 36.000 10.51 10.51 34.90 4.06
208 209 7.121168 TGGACTTGAAGGATAAAGTAAAGCATG 59.879 37.037 0.00 0.00 36.77 4.06
240 242 0.835971 TGGTGGTTAGCTGGCAGAGA 60.836 55.000 20.86 0.89 0.00 3.10
244 246 0.676466 CGATTGGTGGTTAGCTGGCA 60.676 55.000 0.00 0.00 0.00 4.92
270 272 7.436430 TGTTTTATACGACTGCCATTTTGTA 57.564 32.000 0.00 0.00 0.00 2.41
277 281 2.739913 GTGCTGTTTTATACGACTGCCA 59.260 45.455 11.54 1.91 39.19 4.92
280 284 3.370978 CCTGGTGCTGTTTTATACGACTG 59.629 47.826 0.00 0.00 0.00 3.51
281 285 3.259876 TCCTGGTGCTGTTTTATACGACT 59.740 43.478 0.00 0.00 0.00 4.18
285 289 6.330278 GGAATTTCCTGGTGCTGTTTTATAC 58.670 40.000 8.25 0.00 32.53 1.47
302 306 6.937392 AGTATAGGATTAGCGAGGGAATTTC 58.063 40.000 0.00 0.00 0.00 2.17
332 336 4.145052 AGAGAACCTTTTGGAATGGTGTC 58.855 43.478 0.00 1.39 44.07 3.67
358 363 7.344871 CCCCTACCTGTAGAAATCTCTCTTTAA 59.655 40.741 5.89 0.00 35.21 1.52
359 364 6.839657 CCCCTACCTGTAGAAATCTCTCTTTA 59.160 42.308 5.89 0.00 35.21 1.85
379 407 2.362077 GTCGGCTAAAACGATACCCCTA 59.638 50.000 0.00 0.00 42.82 3.53
406 434 7.208080 TGCTAGCTTTAGTGGTTTATAGCTAC 58.792 38.462 17.23 0.00 38.40 3.58
410 438 9.765795 AGTAATGCTAGCTTTAGTGGTTTATAG 57.234 33.333 23.07 0.00 0.00 1.31
435 463 9.689976 CCTTATTCTCATGTCTTCACACTATAG 57.310 37.037 0.00 0.00 34.48 1.31
452 493 4.473444 TGGGATTTCCATGCCTTATTCTC 58.527 43.478 0.00 0.00 41.60 2.87
471 512 0.039256 CAAAAGTCCACACGCATGGG 60.039 55.000 8.44 8.44 40.49 4.00
495 536 2.408050 GATCCATCATCCCTCGTTTCG 58.592 52.381 0.00 0.00 0.00 3.46
496 537 2.408050 CGATCCATCATCCCTCGTTTC 58.592 52.381 0.00 0.00 0.00 2.78
500 541 1.079543 GCCGATCCATCATCCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
501 542 1.079543 CGCCGATCCATCATCCCTC 60.080 63.158 0.00 0.00 0.00 4.30
502 543 2.587247 CCGCCGATCCATCATCCCT 61.587 63.158 0.00 0.00 0.00 4.20
503 544 2.046892 CCGCCGATCCATCATCCC 60.047 66.667 0.00 0.00 0.00 3.85
505 546 2.743928 GGCCGCCGATCCATCATC 60.744 66.667 0.00 0.00 0.00 2.92
522 563 1.312371 ATTGTCCGGGAAATGGCACG 61.312 55.000 0.00 0.00 0.00 5.34
527 568 2.099098 GGCAGTTATTGTCCGGGAAATG 59.901 50.000 0.00 0.00 0.00 2.32
528 569 2.375146 GGCAGTTATTGTCCGGGAAAT 58.625 47.619 0.00 4.58 0.00 2.17
599 644 2.489938 TAAGTTAACCAGCAGCAGGG 57.510 50.000 8.98 5.14 0.00 4.45
603 648 3.621558 AGGGATTAAGTTAACCAGCAGC 58.378 45.455 0.88 0.00 0.00 5.25
604 649 5.104259 AGAGGGATTAAGTTAACCAGCAG 57.896 43.478 0.88 0.00 0.00 4.24
605 650 4.534500 TGAGAGGGATTAAGTTAACCAGCA 59.466 41.667 0.88 3.64 0.00 4.41
606 651 5.099042 TGAGAGGGATTAAGTTAACCAGC 57.901 43.478 0.88 6.87 0.00 4.85
608 653 7.335924 CGAATTTGAGAGGGATTAAGTTAACCA 59.664 37.037 0.88 0.00 0.00 3.67
620 686 2.559698 TTGTGCGAATTTGAGAGGGA 57.440 45.000 0.00 0.00 0.00 4.20
658 724 3.059051 TGATGGTGGTATGAGGATCCA 57.941 47.619 15.82 0.00 0.00 3.41
669 735 0.397535 GGGATGGCAATGATGGTGGT 60.398 55.000 0.00 0.00 0.00 4.16
748 1184 3.728385 ACTTTCTAGAAGCCAGCCATT 57.272 42.857 5.12 0.00 0.00 3.16
762 1198 2.028112 TGGATGCGTTCTGCTACTTTCT 60.028 45.455 0.00 0.00 46.63 2.52
763 1199 2.346803 TGGATGCGTTCTGCTACTTTC 58.653 47.619 0.00 0.00 46.63 2.62
764 1200 2.350522 CTGGATGCGTTCTGCTACTTT 58.649 47.619 0.00 0.00 46.63 2.66
765 1201 2.009042 GCTGGATGCGTTCTGCTACTT 61.009 52.381 8.76 0.00 46.63 2.24
768 1204 1.153369 GGCTGGATGCGTTCTGCTA 60.153 57.895 14.98 0.00 46.63 3.49
771 1207 3.197790 CCGGCTGGATGCGTTCTG 61.198 66.667 5.28 0.00 44.05 3.02
1553 2014 2.028420 TGGCATAGCAAGCAGTACTG 57.972 50.000 18.93 18.93 0.00 2.74
1849 2312 8.438513 CCTGCATGAACATATACTTAGAAATCG 58.561 37.037 0.00 0.00 0.00 3.34
1888 2351 3.096489 TGCAAGAAACTGATGCAAACC 57.904 42.857 0.00 0.00 46.23 3.27
1909 2372 6.430925 TCAGAGGTCACAAAACAATCCAATAG 59.569 38.462 0.00 0.00 0.00 1.73
1935 2398 6.312487 CAAAGCAAGAGTACATGTCAGATTG 58.688 40.000 0.00 5.55 0.00 2.67
1936 2399 5.106396 GCAAAGCAAGAGTACATGTCAGATT 60.106 40.000 0.00 0.00 0.00 2.40
2174 2637 5.412904 AGAAGAAAAATGGGAAGATCGACAC 59.587 40.000 0.00 0.00 0.00 3.67
2178 2641 5.877012 TCAGAGAAGAAAAATGGGAAGATCG 59.123 40.000 0.00 0.00 0.00 3.69
2210 2673 3.667960 GCTGTGAGTGGCTTGAAATTACG 60.668 47.826 0.00 0.00 0.00 3.18
2224 2687 3.740115 AGTTTCCGTATTTGCTGTGAGT 58.260 40.909 0.00 0.00 0.00 3.41
2261 2724 7.792374 TCAAGCAAAATACAGTGGATCTATC 57.208 36.000 0.00 0.00 0.00 2.08
2311 2780 9.739276 TCTCAATAAACTGTATCAATGGAAGTT 57.261 29.630 0.00 0.00 32.60 2.66
2347 2816 2.798283 CAGTTCTGCTGCCAAAACATTG 59.202 45.455 0.00 0.00 38.52 2.82
2348 2817 2.694628 TCAGTTCTGCTGCCAAAACATT 59.305 40.909 0.00 0.00 44.66 2.71
2350 2819 1.761449 TCAGTTCTGCTGCCAAAACA 58.239 45.000 0.00 0.00 44.66 2.83
2351 2820 2.544486 CCTTCAGTTCTGCTGCCAAAAC 60.544 50.000 0.00 0.00 44.66 2.43
2356 2825 0.538287 AACCCTTCAGTTCTGCTGCC 60.538 55.000 0.00 0.00 44.66 4.85
2359 2828 2.972713 TGAGTAACCCTTCAGTTCTGCT 59.027 45.455 0.00 0.00 0.00 4.24
2561 3030 5.049129 GCAACATACATTCAGCCTAATCCTC 60.049 44.000 0.00 0.00 0.00 3.71
2562 3031 4.823989 GCAACATACATTCAGCCTAATCCT 59.176 41.667 0.00 0.00 0.00 3.24
2563 3032 4.319766 CGCAACATACATTCAGCCTAATCC 60.320 45.833 0.00 0.00 0.00 3.01
2619 3397 3.181488 TGTTCAGTTTCTGCACAACATGG 60.181 43.478 0.00 0.00 35.02 3.66
2620 3398 4.031418 TGTTCAGTTTCTGCACAACATG 57.969 40.909 6.76 0.00 35.02 3.21
2705 3483 0.460459 GGTCTTTAGCAGGCTCGGAC 60.460 60.000 0.00 5.03 0.00 4.79
2708 3486 1.338200 ACAAGGTCTTTAGCAGGCTCG 60.338 52.381 0.00 0.00 0.00 5.03
2757 3536 3.049674 TGCTGCAGTAAGCCGTGC 61.050 61.111 16.64 0.00 44.83 5.34
2799 3579 5.700373 GCTGTTATGCAATGGAAAAGGAAAA 59.300 36.000 0.00 0.00 0.00 2.29
2816 3596 9.135189 ACAATTCACCATTATGTATGCTGTTAT 57.865 29.630 0.00 0.00 32.60 1.89
2844 3650 7.817478 CAGGCATATCACCGTATAAGATACAAA 59.183 37.037 0.00 0.00 0.00 2.83
2880 3688 1.073025 ATCAACTGCTCACGGCCAA 59.927 52.632 2.24 0.00 40.92 4.52
2882 3690 0.955428 TTCATCAACTGCTCACGGCC 60.955 55.000 0.00 0.00 40.92 6.13
3030 3838 2.353607 GCTCGGACAGTATCGCCG 60.354 66.667 0.00 0.00 46.08 6.46
3144 3952 7.599998 GCATAAATGTTTTTGTTCAGTGAGGAT 59.400 33.333 0.00 0.00 0.00 3.24
3245 4053 0.599558 GCTCAGCAATCACCTGCAAA 59.400 50.000 0.00 0.00 45.18 3.68
3496 4305 1.202440 TCAGCCTGCAAAAGCAAAGTG 60.202 47.619 5.89 0.00 0.00 3.16
3589 4399 5.505173 AAGCCTTTTGGATATGTTCATCG 57.495 39.130 0.00 0.00 44.07 3.84
3652 4462 2.663826 AAGCCACTCTAAGCTCTTCG 57.336 50.000 0.00 0.00 38.74 3.79
3676 4486 0.842635 AAGCTCCATCCACCTCATCC 59.157 55.000 0.00 0.00 0.00 3.51
3765 4575 5.254901 TGTTGTACAGTTTAGTGGGTTGTT 58.745 37.500 0.00 0.00 0.00 2.83
3801 4611 8.089597 AGATGAGTCATTAGCATATGTTCTGAG 58.910 37.037 7.16 0.00 0.00 3.35
3823 4633 7.962964 TGGTTTCAGTTTTCAGTAGTAGATG 57.037 36.000 0.00 0.00 0.00 2.90
3890 4700 2.036387 CATGGGTCATGCATGTGGAAT 58.964 47.619 25.43 12.94 35.02 3.01
3931 4741 0.936297 GAACAAGCCTTGCAGCAACG 60.936 55.000 2.83 1.22 34.23 4.10
4118 4938 7.270757 TGCTACTTTCAACTGCTATTTTCAA 57.729 32.000 0.00 0.00 0.00 2.69
4288 5277 4.171663 TGCAGCTTTCAATCGCAAATTA 57.828 36.364 0.00 0.00 0.00 1.40
4321 5310 3.154710 GGTTGAACTTAGGGGGTTTGAG 58.845 50.000 0.00 0.00 0.00 3.02
4544 5533 2.552743 GCACCCCTTCTGTTTCTTACAC 59.447 50.000 0.00 0.00 32.10 2.90
4624 5618 1.551430 TCAATATATACCCCGCCCGTG 59.449 52.381 0.00 0.00 0.00 4.94
4625 5619 1.551883 GTCAATATATACCCCGCCCGT 59.448 52.381 0.00 0.00 0.00 5.28
4674 5669 1.455959 CCCCGACAACAAAACCCCA 60.456 57.895 0.00 0.00 0.00 4.96
4713 5708 0.680061 ACCGGAGAAAGAAACGAGCT 59.320 50.000 9.46 0.00 0.00 4.09
4718 5713 4.895224 ACAAAGAACCGGAGAAAGAAAC 57.105 40.909 9.46 0.00 0.00 2.78
4877 5872 1.545428 GGGTGATGAGTGCAAGACCAA 60.545 52.381 0.00 0.00 33.23 3.67
4895 5890 3.054503 GCACTCAGCAGCACAGGG 61.055 66.667 0.00 0.00 44.79 4.45
5077 6143 3.060895 CAGCGATGATGATGATGATGACG 59.939 47.826 0.00 0.00 0.00 4.35
5078 6144 3.995048 ACAGCGATGATGATGATGATGAC 59.005 43.478 8.12 0.00 0.00 3.06
5079 6145 3.994392 CACAGCGATGATGATGATGATGA 59.006 43.478 8.12 0.00 0.00 2.92
5080 6146 3.994392 TCACAGCGATGATGATGATGATG 59.006 43.478 8.12 0.00 0.00 3.07
5081 6147 4.246458 CTCACAGCGATGATGATGATGAT 58.754 43.478 8.12 0.00 0.00 2.45
5082 6148 3.650139 CTCACAGCGATGATGATGATGA 58.350 45.455 8.12 0.00 0.00 2.92
5083 6149 2.157863 GCTCACAGCGATGATGATGATG 59.842 50.000 8.12 0.00 0.00 3.07
5084 6150 2.224209 TGCTCACAGCGATGATGATGAT 60.224 45.455 8.12 0.00 46.26 2.45
5085 6151 1.137479 TGCTCACAGCGATGATGATGA 59.863 47.619 8.12 0.00 46.26 2.92
5158 6393 3.948473 GCAAGAGGAGGAAGGGTTATTTC 59.052 47.826 0.00 0.00 0.00 2.17
5217 6457 8.806429 TCTGGATTTGAAATCACTGCTTATAA 57.194 30.769 18.55 0.00 0.00 0.98
5246 6486 0.252467 AGCCAGGAGTAGTCAGCCTT 60.252 55.000 0.00 0.00 0.00 4.35
5250 6490 0.107945 GGCAAGCCAGGAGTAGTCAG 60.108 60.000 6.14 0.00 35.81 3.51
5252 6492 0.176910 GAGGCAAGCCAGGAGTAGTC 59.823 60.000 14.40 0.00 38.92 2.59
5253 6493 1.268283 GGAGGCAAGCCAGGAGTAGT 61.268 60.000 14.40 0.00 38.92 2.73
5254 6494 1.524482 GGAGGCAAGCCAGGAGTAG 59.476 63.158 14.40 0.00 38.92 2.57
5255 6495 2.359169 CGGAGGCAAGCCAGGAGTA 61.359 63.158 14.40 0.00 38.92 2.59
5256 6496 3.710722 CGGAGGCAAGCCAGGAGT 61.711 66.667 14.40 0.00 38.92 3.85
5257 6497 1.402896 TATCGGAGGCAAGCCAGGAG 61.403 60.000 14.40 1.91 38.92 3.69
5345 6587 3.754068 GTTCACCAAACCCCGACC 58.246 61.111 0.00 0.00 31.20 4.79
5426 7646 8.169977 TGACAGAAAGTTTGCATTCTCTTAAT 57.830 30.769 0.00 0.00 33.73 1.40
5446 7666 2.158608 AGAACCCACTTTCCCTTGACAG 60.159 50.000 0.00 0.00 0.00 3.51
5450 7670 2.887152 CAGAAGAACCCACTTTCCCTTG 59.113 50.000 0.00 0.00 0.00 3.61
5454 7674 1.981256 TGCAGAAGAACCCACTTTCC 58.019 50.000 0.00 0.00 0.00 3.13
5456 7676 3.217626 CTCTTGCAGAAGAACCCACTTT 58.782 45.455 0.00 0.00 37.77 2.66


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

AutoCloner maintained by Alex Coulton.