Multiple sequence alignment - TraesCS3B01G048400

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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 TraesCS3B01G048400 chr3B 100.000 2750 0 0 1 2750 24522452 24525201 0.000000e+00 5079.0
1 TraesCS3B01G048400 chr3B 94.225 658 33 4 2097 2750 743136758 743136102 0.000000e+00 1000.0
2 TraesCS3B01G048400 chr3B 89.812 373 26 5 1434 1799 24546350 24546717 4.150000e-128 468.0
3 TraesCS3B01G048400 chr3B 84.051 395 36 16 537 925 69601599 69601226 3.370000e-94 355.0
4 TraesCS3B01G048400 chr3B 79.299 314 22 20 1794 2100 24552193 24552470 2.180000e-41 180.0
5 TraesCS3B01G048400 chr3D 89.533 1672 99 29 365 2007 17121415 17123039 0.000000e+00 2049.0
6 TraesCS3B01G048400 chr3D 93.750 48 3 0 2053 2100 17123048 17123095 3.800000e-09 73.1
7 TraesCS3B01G048400 chr3A 87.099 1589 109 48 365 1895 19761369 19759819 0.000000e+00 1711.0
8 TraesCS3B01G048400 chr3A 97.436 312 8 0 57 368 211955405 211955716 1.450000e-147 532.0
9 TraesCS3B01G048400 chr6B 94.977 657 27 6 2097 2750 537577948 537577295 0.000000e+00 1026.0
10 TraesCS3B01G048400 chr6B 96.417 307 11 0 60 366 547713649 547713955 8.790000e-140 507.0
11 TraesCS3B01G048400 chr7B 94.809 655 30 4 2099 2750 71358847 71359500 0.000000e+00 1018.0
12 TraesCS3B01G048400 chr7B 94.190 654 32 6 2099 2750 721733686 721733037 0.000000e+00 992.0
13 TraesCS3B01G048400 chr7B 81.934 393 41 13 537 922 165109147 165109516 3.440000e-79 305.0
14 TraesCS3B01G048400 chr1B 94.673 657 32 3 2097 2750 684638770 684639426 0.000000e+00 1016.0
15 TraesCS3B01G048400 chr1B 94.793 653 31 3 2099 2749 283109936 283110587 0.000000e+00 1014.0
16 TraesCS3B01G048400 chr5B 94.512 656 33 3 2096 2749 308991777 308992431 0.000000e+00 1009.0
17 TraesCS3B01G048400 chr5B 93.807 662 37 4 2091 2750 529617231 529616572 0.000000e+00 992.0
18 TraesCS3B01G048400 chr5B 93.760 657 39 2 2096 2750 73094308 73094964 0.000000e+00 985.0
19 TraesCS3B01G048400 chr5B 96.429 308 10 1 60 366 612021664 612021357 8.790000e-140 507.0
20 TraesCS3B01G048400 chr5B 82.025 395 41 14 538 925 405547201 405546830 2.660000e-80 309.0
21 TraesCS3B01G048400 chr6A 95.820 311 12 1 56 366 65071066 65071375 4.090000e-138 501.0
22 TraesCS3B01G048400 chr6A 95.484 310 14 0 57 366 410575450 410575759 1.900000e-136 496.0
23 TraesCS3B01G048400 chr4A 95.527 313 14 0 58 370 532067922 532067610 4.090000e-138 501.0
24 TraesCS3B01G048400 chr2A 95.806 310 13 0 57 366 597847811 597848120 4.090000e-138 501.0
25 TraesCS3B01G048400 chr1A 95.806 310 13 0 57 366 382255920 382256229 4.090000e-138 501.0
26 TraesCS3B01G048400 chr5A 95.513 312 14 0 58 369 404145790 404145479 1.470000e-137 499.0
27 TraesCS3B01G048400 chr5D 84.184 392 35 14 537 923 151215899 151215530 3.370000e-94 355.0
28 TraesCS3B01G048400 chr5D 83.851 322 30 10 604 925 546563961 546563662 1.250000e-73 287.0
29 TraesCS3B01G048400 chr4D 83.503 394 39 15 537 925 27524254 27524626 7.290000e-91 344.0
30 TraesCS3B01G048400 chr7D 82.822 326 33 8 604 927 24390491 24390795 1.260000e-68 270.0


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 TraesCS3B01G048400 chr3B 24522452 24525201 2749 False 5079.00 5079 100.0000 1 2750 1 chr3B.!!$F1 2749
1 TraesCS3B01G048400 chr3B 743136102 743136758 656 True 1000.00 1000 94.2250 2097 2750 1 chr3B.!!$R2 653
2 TraesCS3B01G048400 chr3D 17121415 17123095 1680 False 1061.05 2049 91.6415 365 2100 2 chr3D.!!$F1 1735
3 TraesCS3B01G048400 chr3A 19759819 19761369 1550 True 1711.00 1711 87.0990 365 1895 1 chr3A.!!$R1 1530
4 TraesCS3B01G048400 chr6B 537577295 537577948 653 True 1026.00 1026 94.9770 2097 2750 1 chr6B.!!$R1 653
5 TraesCS3B01G048400 chr7B 71358847 71359500 653 False 1018.00 1018 94.8090 2099 2750 1 chr7B.!!$F1 651
6 TraesCS3B01G048400 chr7B 721733037 721733686 649 True 992.00 992 94.1900 2099 2750 1 chr7B.!!$R1 651
7 TraesCS3B01G048400 chr1B 684638770 684639426 656 False 1016.00 1016 94.6730 2097 2750 1 chr1B.!!$F2 653
8 TraesCS3B01G048400 chr1B 283109936 283110587 651 False 1014.00 1014 94.7930 2099 2749 1 chr1B.!!$F1 650
9 TraesCS3B01G048400 chr5B 308991777 308992431 654 False 1009.00 1009 94.5120 2096 2749 1 chr5B.!!$F2 653
10 TraesCS3B01G048400 chr5B 529616572 529617231 659 True 992.00 992 93.8070 2091 2750 1 chr5B.!!$R2 659
11 TraesCS3B01G048400 chr5B 73094308 73094964 656 False 985.00 985 93.7600 2096 2750 1 chr5B.!!$F1 654

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
64 65 0.25064 CAAGTGAGTTGCTGAGGCCT 60.251 55.0 3.86 3.86 37.74 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2099 0.039618 TGCACATCCCTTTCTTCCCC 59.96 55.0 0.0 0.0 0.0 4.81 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
17 18 3.715015 GGACTGGACAGACCCCTC 58.285 66.667 6.29 0.00 37.30 4.30
18 19 2.352032 GGACTGGACAGACCCCTCG 61.352 68.421 6.29 0.00 37.30 4.63
19 20 2.997897 ACTGGACAGACCCCTCGC 60.998 66.667 6.29 0.00 38.00 5.03
20 21 3.775654 CTGGACAGACCCCTCGCC 61.776 72.222 0.00 0.00 38.00 5.54
21 22 4.631740 TGGACAGACCCCTCGCCA 62.632 66.667 0.00 0.00 38.00 5.69
22 23 4.083862 GGACAGACCCCTCGCCAC 62.084 72.222 0.00 0.00 0.00 5.01
23 24 4.436998 GACAGACCCCTCGCCACG 62.437 72.222 0.00 0.00 0.00 4.94
24 25 4.988716 ACAGACCCCTCGCCACGA 62.989 66.667 0.00 0.00 0.00 4.35
25 26 3.461773 CAGACCCCTCGCCACGAT 61.462 66.667 0.00 0.00 34.61 3.73
26 27 2.125326 CAGACCCCTCGCCACGATA 61.125 63.158 0.00 0.00 34.61 2.92
27 28 1.152525 AGACCCCTCGCCACGATAT 60.153 57.895 0.00 0.00 34.61 1.63
28 29 0.759436 AGACCCCTCGCCACGATATT 60.759 55.000 0.00 0.00 34.61 1.28
29 30 0.319641 GACCCCTCGCCACGATATTC 60.320 60.000 0.00 0.00 34.61 1.75
30 31 0.759436 ACCCCTCGCCACGATATTCT 60.759 55.000 0.00 0.00 34.61 2.40
31 32 0.319900 CCCCTCGCCACGATATTCTG 60.320 60.000 0.00 0.00 34.61 3.02
32 33 0.389391 CCCTCGCCACGATATTCTGT 59.611 55.000 0.00 0.00 34.61 3.41
33 34 1.202533 CCCTCGCCACGATATTCTGTT 60.203 52.381 0.00 0.00 34.61 3.16
34 35 2.128035 CCTCGCCACGATATTCTGTTC 58.872 52.381 0.00 0.00 34.61 3.18
35 36 2.128035 CTCGCCACGATATTCTGTTCC 58.872 52.381 0.00 0.00 34.61 3.62
36 37 1.478916 TCGCCACGATATTCTGTTCCA 59.521 47.619 0.00 0.00 0.00 3.53
37 38 2.102420 TCGCCACGATATTCTGTTCCAT 59.898 45.455 0.00 0.00 0.00 3.41
38 39 2.872245 CGCCACGATATTCTGTTCCATT 59.128 45.455 0.00 0.00 0.00 3.16
39 40 3.059597 CGCCACGATATTCTGTTCCATTC 60.060 47.826 0.00 0.00 0.00 2.67
40 41 3.251004 GCCACGATATTCTGTTCCATTCC 59.749 47.826 0.00 0.00 0.00 3.01
41 42 3.494626 CCACGATATTCTGTTCCATTCCG 59.505 47.826 0.00 0.00 0.00 4.30
42 43 4.368315 CACGATATTCTGTTCCATTCCGA 58.632 43.478 0.00 0.00 0.00 4.55
43 44 4.209288 CACGATATTCTGTTCCATTCCGAC 59.791 45.833 0.00 0.00 0.00 4.79
44 45 4.142026 ACGATATTCTGTTCCATTCCGACA 60.142 41.667 0.00 0.00 0.00 4.35
45 46 4.209288 CGATATTCTGTTCCATTCCGACAC 59.791 45.833 0.00 0.00 0.00 3.67
46 47 2.920724 TTCTGTTCCATTCCGACACA 57.079 45.000 0.00 0.00 0.00 3.72
47 48 2.920724 TCTGTTCCATTCCGACACAA 57.079 45.000 0.00 0.00 0.00 3.33
48 49 2.766313 TCTGTTCCATTCCGACACAAG 58.234 47.619 0.00 0.00 0.00 3.16
49 50 2.104111 TCTGTTCCATTCCGACACAAGT 59.896 45.455 0.00 0.00 0.00 3.16
50 51 2.217750 TGTTCCATTCCGACACAAGTG 58.782 47.619 0.00 0.00 0.00 3.16
51 52 2.158885 TGTTCCATTCCGACACAAGTGA 60.159 45.455 7.28 0.00 0.00 3.41
52 53 2.455674 TCCATTCCGACACAAGTGAG 57.544 50.000 7.28 0.73 0.00 3.51
53 54 1.691976 TCCATTCCGACACAAGTGAGT 59.308 47.619 7.28 0.00 0.00 3.41
54 55 2.104111 TCCATTCCGACACAAGTGAGTT 59.896 45.455 7.28 0.00 0.00 3.01
55 56 2.224079 CCATTCCGACACAAGTGAGTTG 59.776 50.000 7.28 0.00 42.48 3.16
56 57 1.295792 TTCCGACACAAGTGAGTTGC 58.704 50.000 7.28 0.00 40.15 4.17
57 58 0.464036 TCCGACACAAGTGAGTTGCT 59.536 50.000 7.28 0.00 40.15 3.91
58 59 0.583438 CCGACACAAGTGAGTTGCTG 59.417 55.000 7.28 1.07 40.15 4.41
59 60 1.570813 CGACACAAGTGAGTTGCTGA 58.429 50.000 7.28 0.00 40.15 4.26
60 61 1.524355 CGACACAAGTGAGTTGCTGAG 59.476 52.381 7.28 0.00 40.15 3.35
61 62 1.869767 GACACAAGTGAGTTGCTGAGG 59.130 52.381 7.28 0.00 40.15 3.86
62 63 0.590195 CACAAGTGAGTTGCTGAGGC 59.410 55.000 0.00 0.00 40.15 4.70
63 64 0.536006 ACAAGTGAGTTGCTGAGGCC 60.536 55.000 0.00 0.00 40.15 5.19
64 65 0.250640 CAAGTGAGTTGCTGAGGCCT 60.251 55.000 3.86 3.86 37.74 5.19
65 66 0.475906 AAGTGAGTTGCTGAGGCCTT 59.524 50.000 6.77 0.00 37.74 4.35
66 67 0.475906 AGTGAGTTGCTGAGGCCTTT 59.524 50.000 6.77 0.00 37.74 3.11
67 68 1.133668 AGTGAGTTGCTGAGGCCTTTT 60.134 47.619 6.77 0.00 37.74 2.27
68 69 1.683385 GTGAGTTGCTGAGGCCTTTTT 59.317 47.619 6.77 0.00 37.74 1.94
118 119 8.337118 AGGAATAGGAATCTTGTAGGAAATGA 57.663 34.615 0.00 0.00 0.00 2.57
119 120 8.435982 AGGAATAGGAATCTTGTAGGAAATGAG 58.564 37.037 0.00 0.00 0.00 2.90
120 121 8.432805 GGAATAGGAATCTTGTAGGAAATGAGA 58.567 37.037 0.00 0.00 0.00 3.27
122 123 9.790344 AATAGGAATCTTGTAGGAAATGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
123 124 7.443302 AGGAATCTTGTAGGAAATGAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
124 125 7.278875 AGGAATCTTGTAGGAAATGAGATGAC 58.721 38.462 0.00 0.00 0.00 3.06
125 126 7.050377 GGAATCTTGTAGGAAATGAGATGACA 58.950 38.462 0.00 0.00 0.00 3.58
126 127 7.718753 GGAATCTTGTAGGAAATGAGATGACAT 59.281 37.037 0.00 0.00 0.00 3.06
127 128 8.447924 AATCTTGTAGGAAATGAGATGACATG 57.552 34.615 0.00 0.00 0.00 3.21
128 129 6.950842 TCTTGTAGGAAATGAGATGACATGT 58.049 36.000 0.00 0.00 0.00 3.21
129 130 8.078060 TCTTGTAGGAAATGAGATGACATGTA 57.922 34.615 0.00 0.00 0.00 2.29
130 131 8.708378 TCTTGTAGGAAATGAGATGACATGTAT 58.292 33.333 0.00 0.00 0.00 2.29
131 132 8.893219 TTGTAGGAAATGAGATGACATGTATC 57.107 34.615 0.00 2.87 0.00 2.24
132 133 8.255111 TGTAGGAAATGAGATGACATGTATCT 57.745 34.615 14.05 14.05 37.59 1.98
133 134 8.363390 TGTAGGAAATGAGATGACATGTATCTC 58.637 37.037 24.04 24.04 46.82 2.75
167 168 9.965902 ATGAGTAGGAATAAGAAACAAGATGTT 57.034 29.630 0.00 0.00 43.41 2.71
178 179 8.871686 AAGAAACAAGATGTTATTTGGTTGAC 57.128 30.769 0.00 0.00 40.14 3.18
179 180 8.006298 AGAAACAAGATGTTATTTGGTTGACA 57.994 30.769 0.00 0.00 40.14 3.58
180 181 7.920682 AGAAACAAGATGTTATTTGGTTGACAC 59.079 33.333 0.00 0.00 40.14 3.67
181 182 6.084326 ACAAGATGTTATTTGGTTGACACC 57.916 37.500 0.00 0.00 44.56 4.16
182 183 6.097554 AACAAGATGTTATTTGGTTGACACCA 59.902 34.615 0.00 0.00 44.65 4.17
194 195 5.984233 GGTTGACACCAAAGGAATTTTTC 57.016 39.130 0.00 0.00 43.61 2.29
195 196 4.814234 GGTTGACACCAAAGGAATTTTTCC 59.186 41.667 0.00 0.00 45.80 3.13
196 197 5.627968 GGTTGACACCAAAGGAATTTTTCCA 60.628 40.000 8.87 0.00 46.88 3.53
197 198 6.911529 GGTTGACACCAAAGGAATTTTTCCAT 60.912 38.462 8.87 0.00 46.88 3.41
198 199 8.334633 GGTTGACACCAAAGGAATTTTTCCATT 61.335 37.037 8.87 0.31 46.88 3.16
243 244 8.752005 TTTTCCTATGAAATGTGAAGGATAGG 57.248 34.615 0.00 0.00 40.08 2.57
244 245 7.690454 TTCCTATGAAATGTGAAGGATAGGA 57.310 36.000 0.00 0.00 39.66 2.94
245 246 7.690454 TCCTATGAAATGTGAAGGATAGGAA 57.310 36.000 0.00 0.00 38.86 3.36
246 247 7.509546 TCCTATGAAATGTGAAGGATAGGAAC 58.490 38.462 0.00 0.00 38.86 3.62
247 248 6.712547 CCTATGAAATGTGAAGGATAGGAACC 59.287 42.308 0.00 0.00 36.16 3.62
248 249 5.512942 TGAAATGTGAAGGATAGGAACCA 57.487 39.130 0.00 0.00 0.00 3.67
249 250 5.886609 TGAAATGTGAAGGATAGGAACCAA 58.113 37.500 0.00 0.00 0.00 3.67
250 251 6.493166 TGAAATGTGAAGGATAGGAACCAAT 58.507 36.000 0.00 0.00 0.00 3.16
251 252 6.603201 TGAAATGTGAAGGATAGGAACCAATC 59.397 38.462 0.00 0.00 0.00 2.67
289 290 6.396829 GAATCCATTCCTATGAACCAAAGG 57.603 41.667 0.00 0.00 33.37 3.11
290 291 4.249638 TCCATTCCTATGAACCAAAGGG 57.750 45.455 0.00 0.00 35.37 3.95
291 292 2.695147 CCATTCCTATGAACCAAAGGGC 59.305 50.000 0.00 0.00 33.50 5.19
292 293 3.628257 CCATTCCTATGAACCAAAGGGCT 60.628 47.826 0.00 0.00 33.50 5.19
293 294 3.366052 TTCCTATGAACCAAAGGGCTC 57.634 47.619 0.00 0.00 37.90 4.70
294 295 2.562296 TCCTATGAACCAAAGGGCTCT 58.438 47.619 0.00 0.00 37.90 4.09
295 296 3.731431 TCCTATGAACCAAAGGGCTCTA 58.269 45.455 0.00 0.00 37.90 2.43
296 297 4.108570 TCCTATGAACCAAAGGGCTCTAA 58.891 43.478 0.00 0.00 37.90 2.10
297 298 4.538490 TCCTATGAACCAAAGGGCTCTAAA 59.462 41.667 0.00 0.00 37.90 1.85
298 299 4.884164 CCTATGAACCAAAGGGCTCTAAAG 59.116 45.833 0.00 0.00 37.90 1.85
299 300 4.657814 ATGAACCAAAGGGCTCTAAAGA 57.342 40.909 0.00 0.00 37.90 2.52
300 301 4.447138 TGAACCAAAGGGCTCTAAAGAA 57.553 40.909 0.00 0.00 37.90 2.52
301 302 4.798882 TGAACCAAAGGGCTCTAAAGAAA 58.201 39.130 0.00 0.00 37.90 2.52
302 303 5.205056 TGAACCAAAGGGCTCTAAAGAAAA 58.795 37.500 0.00 0.00 37.90 2.29
303 304 5.659079 TGAACCAAAGGGCTCTAAAGAAAAA 59.341 36.000 0.00 0.00 37.90 1.94
347 348 8.805145 TCCTCTAGAATTCCTATGAAATTCCT 57.195 34.615 0.65 0.00 33.32 3.36
348 349 8.875168 TCCTCTAGAATTCCTATGAAATTCCTC 58.125 37.037 0.65 0.00 33.32 3.71
349 350 8.879227 CCTCTAGAATTCCTATGAAATTCCTCT 58.121 37.037 0.65 0.00 33.32 3.69
354 355 9.634021 AGAATTCCTATGAAATTCCTCTAAACC 57.366 33.333 0.65 0.00 33.32 3.27
355 356 9.408648 GAATTCCTATGAAATTCCTCTAAACCA 57.591 33.333 0.00 0.00 33.32 3.67
356 357 9.768215 AATTCCTATGAAATTCCTCTAAACCAA 57.232 29.630 0.00 0.00 33.32 3.67
357 358 9.768215 ATTCCTATGAAATTCCTCTAAACCAAA 57.232 29.630 0.00 0.00 33.32 3.28
358 359 8.807948 TCCTATGAAATTCCTCTAAACCAAAG 57.192 34.615 0.00 0.00 0.00 2.77
359 360 7.834181 TCCTATGAAATTCCTCTAAACCAAAGG 59.166 37.037 0.00 0.00 0.00 3.11
360 361 7.834181 CCTATGAAATTCCTCTAAACCAAAGGA 59.166 37.037 0.00 0.00 37.42 3.36
361 362 7.709149 ATGAAATTCCTCTAAACCAAAGGAG 57.291 36.000 0.00 0.00 40.21 3.69
362 363 6.010219 TGAAATTCCTCTAAACCAAAGGAGG 58.990 40.000 0.00 0.00 44.69 4.30
363 364 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
382 383 2.987547 TGAGCCTGCTTGCTTGCC 60.988 61.111 2.08 0.00 42.95 4.52
384 385 2.675772 AGCCTGCTTGCTTGCCTC 60.676 61.111 0.00 0.00 38.85 4.70
424 425 0.816421 CATCCATGTCGAGCCATGCA 60.816 55.000 9.85 0.00 40.72 3.96
462 463 1.534595 GCAATCTGGCATCGCGATTTT 60.535 47.619 21.14 0.00 0.00 1.82
463 464 2.801063 CAATCTGGCATCGCGATTTTT 58.199 42.857 21.14 0.00 0.00 1.94
508 509 2.418976 GGAAAACGATGTGACCTAAGCC 59.581 50.000 0.00 0.00 0.00 4.35
534 535 9.322776 CGCTTATTATTAAACTCATCAATCAGC 57.677 33.333 0.00 0.00 0.00 4.26
557 558 6.259608 AGCATCATAAAATCTTCCAACGAGAG 59.740 38.462 0.00 0.00 0.00 3.20
558 559 6.258727 GCATCATAAAATCTTCCAACGAGAGA 59.741 38.462 0.00 0.00 0.00 3.10
559 560 7.041508 GCATCATAAAATCTTCCAACGAGAGAT 60.042 37.037 0.00 0.00 0.00 2.75
560 561 8.834465 CATCATAAAATCTTCCAACGAGAGATT 58.166 33.333 0.00 0.00 40.76 2.40
561 562 8.792830 TCATAAAATCTTCCAACGAGAGATTT 57.207 30.769 5.08 5.08 46.50 2.17
562 563 8.668353 TCATAAAATCTTCCAACGAGAGATTTG 58.332 33.333 10.30 1.77 44.82 2.32
564 565 6.884280 AAATCTTCCAACGAGAGATTTGTT 57.116 33.333 9.11 0.00 44.24 2.83
565 566 6.884280 AATCTTCCAACGAGAGATTTGTTT 57.116 33.333 0.00 0.00 36.92 2.83
569 570 8.215926 TCTTCCAACGAGAGATTTGTTTAAAA 57.784 30.769 0.00 0.00 30.68 1.52
570 571 8.679100 TCTTCCAACGAGAGATTTGTTTAAAAA 58.321 29.630 0.00 0.00 30.68 1.94
595 596 7.548196 TTACAACAAGGTCAGAAGTAAACTG 57.452 36.000 0.00 0.00 36.80 3.16
607 608 6.430925 TCAGAAGTAAACTGGGATCAATTGTG 59.569 38.462 5.13 0.00 36.22 3.33
621 626 1.269012 ATTGTGGGTTGATGCTTGGG 58.731 50.000 0.00 0.00 0.00 4.12
657 662 5.558083 GCCAAAAATTCACGTTCAATGAACC 60.558 40.000 19.16 3.44 39.14 3.62
658 663 5.521735 CCAAAAATTCACGTTCAATGAACCA 59.478 36.000 19.16 2.14 39.14 3.67
684 689 0.885196 GGAGCTACTCCTCCTATGCG 59.115 60.000 6.38 0.00 46.41 4.73
685 690 0.885196 GAGCTACTCCTCCTATGCGG 59.115 60.000 0.00 0.00 0.00 5.69
826 835 1.866925 GAGGTTTGTACAGCACGGC 59.133 57.895 0.00 0.00 0.00 5.68
828 837 1.957186 GGTTTGTACAGCACGGCGA 60.957 57.895 16.62 0.00 0.00 5.54
881 894 4.742201 CCCTCCGCACCACACTCG 62.742 72.222 0.00 0.00 0.00 4.18
886 899 3.792047 CGCACCACACTCGCCATG 61.792 66.667 0.00 0.00 0.00 3.66
915 928 7.667557 CCTATTTATATCCACGTTCCTCTCAA 58.332 38.462 0.00 0.00 0.00 3.02
928 941 3.714144 TCCTCTCAACCTTCTTCTAGGG 58.286 50.000 0.00 0.00 39.76 3.53
949 962 2.202716 AGCAGCTCTCACATCGCG 60.203 61.111 0.00 0.00 0.00 5.87
955 968 1.994467 CTCTCACATCGCGTTCTGC 59.006 57.895 5.77 0.00 41.47 4.26
966 979 0.997932 GCGTTCTGCATCTCTGACAG 59.002 55.000 0.00 0.00 45.45 3.51
999 1018 2.103263 CCCTTGCTGATCCAGTAGTACC 59.897 54.545 0.00 0.00 33.43 3.34
1002 1021 4.375272 CTTGCTGATCCAGTAGTACCATG 58.625 47.826 0.00 0.00 33.43 3.66
1003 1022 2.700371 TGCTGATCCAGTAGTACCATGG 59.300 50.000 11.19 11.19 33.43 3.66
1004 1023 2.965831 GCTGATCCAGTAGTACCATGGA 59.034 50.000 21.47 12.35 46.69 3.41
1007 1026 3.206639 TGATCCAGTAGTACCATGGAGGA 59.793 47.826 21.47 13.13 45.89 3.71
1020 1039 0.855855 TGGAGGAGGAGGAGGAGGAA 60.856 60.000 0.00 0.00 0.00 3.36
1532 1593 4.025401 CAACGGGAACAGCGGTGC 62.025 66.667 15.82 0.00 0.00 5.01
1718 1779 3.441290 CAAGCAGCAGAGCAGGGC 61.441 66.667 0.00 0.00 36.85 5.19
1722 1783 2.750637 CAGCAGAGCAGGGCCTTG 60.751 66.667 11.24 11.24 0.00 3.61
1793 1854 2.746269 ACAAGTTAAGCGCACTCGTTA 58.254 42.857 11.47 0.00 38.14 3.18
1794 1855 3.125316 ACAAGTTAAGCGCACTCGTTAA 58.875 40.909 11.47 1.95 38.14 2.01
1804 1865 4.079710 GCGCACTCGTTAAAATTACTGAC 58.920 43.478 0.30 0.00 38.14 3.51
1807 1868 5.618561 GCACTCGTTAAAATTACTGACTGG 58.381 41.667 0.00 0.00 0.00 4.00
1822 1883 0.539986 ACTGGTTGTCCACTTGTCGT 59.460 50.000 0.00 0.00 39.03 4.34
1875 1939 7.820872 GGAAAGATGAATCAAACCATGTGAATT 59.179 33.333 0.00 0.00 0.00 2.17
1878 1942 5.058149 TGAATCAAACCATGTGAATTCGG 57.942 39.130 0.04 0.00 0.00 4.30
1883 1947 0.695924 ACCATGTGAATTCGGGACCA 59.304 50.000 10.95 0.00 0.00 4.02
1894 1958 3.275617 TTCGGGACCAATTGATCGATT 57.724 42.857 7.12 2.01 0.00 3.34
1935 1999 2.287373 CGACGGACAGAGTATGAGTACC 59.713 54.545 0.00 0.00 0.00 3.34
1953 2017 2.991250 ACCACAGTAGGCTTATTGCTG 58.009 47.619 0.00 0.00 42.39 4.41
1979 2043 2.842058 CATGGGATGGGAGGAGGC 59.158 66.667 0.00 0.00 0.00 4.70
1989 2053 1.000771 GGAGGAGGCCCTTTTGGTC 60.001 63.158 0.00 0.00 44.53 4.02
1995 2059 1.527380 GGCCCTTTTGGTCGTGTCA 60.527 57.895 0.00 0.00 38.10 3.58
2007 2071 1.463444 GTCGTGTCATTGGTTAGTGGC 59.537 52.381 0.00 0.00 0.00 5.01
2008 2072 1.070914 TCGTGTCATTGGTTAGTGGCA 59.929 47.619 0.00 0.00 0.00 4.92
2009 2073 1.876799 CGTGTCATTGGTTAGTGGCAA 59.123 47.619 0.00 0.00 30.89 4.52
2011 2075 2.228822 GTGTCATTGGTTAGTGGCAAGG 59.771 50.000 0.00 0.00 30.89 3.61
2012 2076 1.202348 GTCATTGGTTAGTGGCAAGGC 59.798 52.381 0.00 0.00 0.00 4.35
2014 2078 1.826720 CATTGGTTAGTGGCAAGGCAT 59.173 47.619 0.00 0.00 0.00 4.40
2015 2079 1.255882 TTGGTTAGTGGCAAGGCATG 58.744 50.000 0.00 0.00 0.00 4.06
2016 2080 0.611618 TGGTTAGTGGCAAGGCATGG 60.612 55.000 0.00 0.00 0.00 3.66
2017 2081 0.323360 GGTTAGTGGCAAGGCATGGA 60.323 55.000 0.00 0.00 0.00 3.41
2018 2082 1.686115 GGTTAGTGGCAAGGCATGGAT 60.686 52.381 0.00 0.00 0.00 3.41
2019 2083 1.406539 GTTAGTGGCAAGGCATGGATG 59.593 52.381 0.00 0.00 0.00 3.51
2020 2084 0.106569 TAGTGGCAAGGCATGGATGG 60.107 55.000 0.00 0.00 0.00 3.51
2021 2085 1.380246 GTGGCAAGGCATGGATGGA 60.380 57.895 0.00 0.00 0.00 3.41
2022 2086 1.076559 TGGCAAGGCATGGATGGAG 60.077 57.895 0.00 0.00 0.00 3.86
2023 2087 2.496291 GGCAAGGCATGGATGGAGC 61.496 63.158 0.00 0.00 0.00 4.70
2024 2088 2.842256 GCAAGGCATGGATGGAGCG 61.842 63.158 0.00 0.00 0.00 5.03
2025 2089 2.191513 CAAGGCATGGATGGAGCGG 61.192 63.158 0.00 0.00 0.00 5.52
2026 2090 3.426309 AAGGCATGGATGGAGCGGG 62.426 63.158 0.00 0.00 0.00 6.13
2027 2091 4.962836 GGCATGGATGGAGCGGGG 62.963 72.222 0.00 0.00 0.00 5.73
2028 2092 4.962836 GCATGGATGGAGCGGGGG 62.963 72.222 0.00 0.00 0.00 5.40
2029 2093 3.492353 CATGGATGGAGCGGGGGT 61.492 66.667 0.00 0.00 0.00 4.95
2030 2094 2.696125 ATGGATGGAGCGGGGGTT 60.696 61.111 0.00 0.00 0.00 4.11
2031 2095 3.060614 ATGGATGGAGCGGGGGTTG 62.061 63.158 0.00 0.00 0.00 3.77
2032 2096 3.407967 GGATGGAGCGGGGGTTGA 61.408 66.667 0.00 0.00 0.00 3.18
2033 2097 2.674754 GATGGAGCGGGGGTTGAA 59.325 61.111 0.00 0.00 0.00 2.69
2034 2098 1.001393 GATGGAGCGGGGGTTGAAA 60.001 57.895 0.00 0.00 0.00 2.69
2035 2099 1.000896 ATGGAGCGGGGGTTGAAAG 60.001 57.895 0.00 0.00 0.00 2.62
2036 2100 2.361230 GGAGCGGGGGTTGAAAGG 60.361 66.667 0.00 0.00 0.00 3.11
2037 2101 2.361230 GAGCGGGGGTTGAAAGGG 60.361 66.667 0.00 0.00 0.00 3.95
2038 2102 3.938637 GAGCGGGGGTTGAAAGGGG 62.939 68.421 0.00 0.00 0.00 4.79
2039 2103 3.974293 GCGGGGGTTGAAAGGGGA 61.974 66.667 0.00 0.00 0.00 4.81
2040 2104 2.848032 CGGGGGTTGAAAGGGGAA 59.152 61.111 0.00 0.00 0.00 3.97
2041 2105 1.304134 CGGGGGTTGAAAGGGGAAG 60.304 63.158 0.00 0.00 0.00 3.46
2042 2106 1.785353 CGGGGGTTGAAAGGGGAAGA 61.785 60.000 0.00 0.00 0.00 2.87
2043 2107 0.485543 GGGGGTTGAAAGGGGAAGAA 59.514 55.000 0.00 0.00 0.00 2.52
2044 2108 1.132977 GGGGGTTGAAAGGGGAAGAAA 60.133 52.381 0.00 0.00 0.00 2.52
2045 2109 2.248248 GGGGTTGAAAGGGGAAGAAAG 58.752 52.381 0.00 0.00 0.00 2.62
2046 2110 2.248248 GGGTTGAAAGGGGAAGAAAGG 58.752 52.381 0.00 0.00 0.00 3.11
2047 2111 2.248248 GGTTGAAAGGGGAAGAAAGGG 58.752 52.381 0.00 0.00 0.00 3.95
2048 2112 2.158370 GGTTGAAAGGGGAAGAAAGGGA 60.158 50.000 0.00 0.00 0.00 4.20
2049 2113 3.502303 GGTTGAAAGGGGAAGAAAGGGAT 60.502 47.826 0.00 0.00 0.00 3.85
2050 2114 3.456380 TGAAAGGGGAAGAAAGGGATG 57.544 47.619 0.00 0.00 0.00 3.51
2051 2115 2.721906 TGAAAGGGGAAGAAAGGGATGT 59.278 45.455 0.00 0.00 0.00 3.06
2082 2146 3.140144 TGTTGTGGGGAGGAAAGAAAGAT 59.860 43.478 0.00 0.00 0.00 2.40
2083 2147 3.439857 TGTGGGGAGGAAAGAAAGATG 57.560 47.619 0.00 0.00 0.00 2.90
2087 2151 4.642437 GTGGGGAGGAAAGAAAGATGATTC 59.358 45.833 0.00 0.00 0.00 2.52
2155 2219 1.542987 CCGTCCGTTTGGGGTAAAAGA 60.543 52.381 0.00 0.00 36.01 2.52
2198 2262 2.395654 GCGGGCACAAACGAATTTTTA 58.604 42.857 0.00 0.00 0.00 1.52
2266 2331 3.446310 GTTTTTGGGTGAAACGGACAT 57.554 42.857 0.00 0.00 38.12 3.06
2349 2417 0.395173 GGGCCTTTTTCTATCCGCCA 60.395 55.000 0.84 0.00 38.16 5.69
2353 2421 1.064685 CCTTTTTCTATCCGCCACCCT 60.065 52.381 0.00 0.00 0.00 4.34
2358 2428 0.326238 TCTATCCGCCACCCTTCCTT 60.326 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.352032 CGAGGGGTCTGTCCAGTCC 61.352 68.421 2.41 2.41 38.11 3.85
1 2 3.007973 GCGAGGGGTCTGTCCAGTC 62.008 68.421 0.00 0.00 38.11 3.51
2 3 2.997897 GCGAGGGGTCTGTCCAGT 60.998 66.667 0.00 0.00 38.11 4.00
3 4 3.775654 GGCGAGGGGTCTGTCCAG 61.776 72.222 0.00 0.00 38.11 3.86
4 5 4.631740 TGGCGAGGGGTCTGTCCA 62.632 66.667 0.00 0.00 38.11 4.02
5 6 4.083862 GTGGCGAGGGGTCTGTCC 62.084 72.222 0.00 0.00 0.00 4.02
6 7 4.436998 CGTGGCGAGGGGTCTGTC 62.437 72.222 0.00 0.00 0.00 3.51
7 8 2.849096 TATCGTGGCGAGGGGTCTGT 62.849 60.000 0.00 0.00 39.91 3.41
8 9 1.464376 ATATCGTGGCGAGGGGTCTG 61.464 60.000 0.00 0.00 39.91 3.51
9 10 0.759436 AATATCGTGGCGAGGGGTCT 60.759 55.000 0.00 0.00 39.91 3.85
10 11 0.319641 GAATATCGTGGCGAGGGGTC 60.320 60.000 0.00 0.00 39.91 4.46
11 12 0.759436 AGAATATCGTGGCGAGGGGT 60.759 55.000 0.00 0.00 39.91 4.95
12 13 0.319900 CAGAATATCGTGGCGAGGGG 60.320 60.000 0.00 0.00 39.91 4.79
13 14 0.389391 ACAGAATATCGTGGCGAGGG 59.611 55.000 0.00 0.00 39.91 4.30
14 15 2.128035 GAACAGAATATCGTGGCGAGG 58.872 52.381 0.00 0.00 39.91 4.63
15 16 2.128035 GGAACAGAATATCGTGGCGAG 58.872 52.381 0.00 0.00 39.91 5.03
16 17 1.478916 TGGAACAGAATATCGTGGCGA 59.521 47.619 0.00 0.00 41.13 5.54
17 18 1.934589 TGGAACAGAATATCGTGGCG 58.065 50.000 0.00 0.00 0.00 5.69
31 32 2.480419 CTCACTTGTGTCGGAATGGAAC 59.520 50.000 0.46 0.00 0.00 3.62
32 33 2.104111 ACTCACTTGTGTCGGAATGGAA 59.896 45.455 0.46 0.00 0.00 3.53
33 34 1.691976 ACTCACTTGTGTCGGAATGGA 59.308 47.619 0.46 0.00 0.00 3.41
34 35 2.169832 ACTCACTTGTGTCGGAATGG 57.830 50.000 0.46 0.00 0.00 3.16
35 36 2.349817 GCAACTCACTTGTGTCGGAATG 60.350 50.000 0.46 0.00 31.73 2.67
36 37 1.873591 GCAACTCACTTGTGTCGGAAT 59.126 47.619 0.46 0.00 31.73 3.01
37 38 1.134521 AGCAACTCACTTGTGTCGGAA 60.135 47.619 0.46 0.00 31.73 4.30
38 39 0.464036 AGCAACTCACTTGTGTCGGA 59.536 50.000 0.46 0.00 31.73 4.55
39 40 0.583438 CAGCAACTCACTTGTGTCGG 59.417 55.000 0.46 0.00 31.73 4.79
40 41 1.524355 CTCAGCAACTCACTTGTGTCG 59.476 52.381 0.46 0.00 31.73 4.35
41 42 1.869767 CCTCAGCAACTCACTTGTGTC 59.130 52.381 0.46 0.00 31.73 3.67
42 43 1.959042 CCTCAGCAACTCACTTGTGT 58.041 50.000 0.46 0.00 31.73 3.72
43 44 0.590195 GCCTCAGCAACTCACTTGTG 59.410 55.000 0.00 0.00 39.53 3.33
44 45 0.536006 GGCCTCAGCAACTCACTTGT 60.536 55.000 0.00 0.00 42.56 3.16
45 46 0.250640 AGGCCTCAGCAACTCACTTG 60.251 55.000 0.00 0.00 42.56 3.16
46 47 0.475906 AAGGCCTCAGCAACTCACTT 59.524 50.000 5.23 0.00 42.56 3.16
47 48 0.475906 AAAGGCCTCAGCAACTCACT 59.524 50.000 5.23 0.00 42.56 3.41
48 49 1.322442 AAAAGGCCTCAGCAACTCAC 58.678 50.000 5.23 0.00 42.56 3.51
49 50 2.071778 AAAAAGGCCTCAGCAACTCA 57.928 45.000 5.23 0.00 42.56 3.41
92 93 9.447279 TCATTTCCTACAAGATTCCTATTCCTA 57.553 33.333 0.00 0.00 0.00 2.94
93 94 8.337118 TCATTTCCTACAAGATTCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
94 95 8.432805 TCTCATTTCCTACAAGATTCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
96 97 9.790344 CATCTCATTTCCTACAAGATTCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
97 98 9.163894 TCATCTCATTTCCTACAAGATTCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
98 99 8.424918 GTCATCTCATTTCCTACAAGATTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
99 100 7.092712 TGTCATCTCATTTCCTACAAGATTCCT 60.093 37.037 0.00 0.00 0.00 3.36
100 101 7.050377 TGTCATCTCATTTCCTACAAGATTCC 58.950 38.462 0.00 0.00 0.00 3.01
101 102 8.557864 CATGTCATCTCATTTCCTACAAGATTC 58.442 37.037 0.00 0.00 0.00 2.52
102 103 8.051535 ACATGTCATCTCATTTCCTACAAGATT 58.948 33.333 0.00 0.00 0.00 2.40
103 104 7.571919 ACATGTCATCTCATTTCCTACAAGAT 58.428 34.615 0.00 0.00 0.00 2.40
104 105 6.950842 ACATGTCATCTCATTTCCTACAAGA 58.049 36.000 0.00 0.00 0.00 3.02
105 106 8.899427 ATACATGTCATCTCATTTCCTACAAG 57.101 34.615 0.00 0.00 0.00 3.16
106 107 8.708378 AGATACATGTCATCTCATTTCCTACAA 58.292 33.333 0.00 0.00 0.00 2.41
107 108 8.255111 AGATACATGTCATCTCATTTCCTACA 57.745 34.615 0.00 0.00 0.00 2.74
108 109 8.755696 GAGATACATGTCATCTCATTTCCTAC 57.244 38.462 24.95 8.46 45.17 3.18
141 142 9.965902 AACATCTTGTTTCTTATTCCTACTCAT 57.034 29.630 0.00 0.00 37.26 2.90
152 153 9.959749 GTCAACCAAATAACATCTTGTTTCTTA 57.040 29.630 0.00 0.00 41.45 2.10
153 154 8.474025 TGTCAACCAAATAACATCTTGTTTCTT 58.526 29.630 0.00 0.00 41.45 2.52
154 155 7.920682 GTGTCAACCAAATAACATCTTGTTTCT 59.079 33.333 0.00 0.00 41.45 2.52
155 156 7.169140 GGTGTCAACCAAATAACATCTTGTTTC 59.831 37.037 0.00 0.00 46.75 2.78
156 157 6.983890 GGTGTCAACCAAATAACATCTTGTTT 59.016 34.615 0.00 0.00 46.75 2.83
157 158 6.512297 GGTGTCAACCAAATAACATCTTGTT 58.488 36.000 0.00 0.00 46.75 2.83
158 159 6.084326 GGTGTCAACCAAATAACATCTTGT 57.916 37.500 0.00 0.00 46.75 3.16
172 173 4.814234 GGAAAAATTCCTTTGGTGTCAACC 59.186 41.667 1.86 0.00 46.57 3.77
173 174 5.984233 GGAAAAATTCCTTTGGTGTCAAC 57.016 39.130 1.86 0.00 46.57 3.18
183 184 8.166726 AGTCTAGACTCAATGGAAAAATTCCTT 58.833 33.333 20.00 1.58 43.58 3.36
184 185 7.694093 AGTCTAGACTCAATGGAAAAATTCCT 58.306 34.615 20.00 0.00 43.58 3.36
185 186 7.929941 AGTCTAGACTCAATGGAAAAATTCC 57.070 36.000 20.00 2.12 43.52 3.01
217 218 9.359653 CCTATCCTTCACATTTCATAGGAAAAT 57.640 33.333 6.65 0.00 45.52 1.82
218 219 8.556589 TCCTATCCTTCACATTTCATAGGAAAA 58.443 33.333 6.65 0.00 45.52 2.29
219 220 8.101309 TCCTATCCTTCACATTTCATAGGAAA 57.899 34.615 4.85 4.85 46.36 3.13
220 221 7.690454 TCCTATCCTTCACATTTCATAGGAA 57.310 36.000 3.47 0.00 39.17 3.36
221 222 7.420214 GGTTCCTATCCTTCACATTTCATAGGA 60.420 40.741 2.01 2.01 39.98 2.94
222 223 6.712547 GGTTCCTATCCTTCACATTTCATAGG 59.287 42.308 0.00 0.00 35.93 2.57
223 224 7.282585 TGGTTCCTATCCTTCACATTTCATAG 58.717 38.462 0.00 0.00 0.00 2.23
224 225 7.206789 TGGTTCCTATCCTTCACATTTCATA 57.793 36.000 0.00 0.00 0.00 2.15
225 226 6.078456 TGGTTCCTATCCTTCACATTTCAT 57.922 37.500 0.00 0.00 0.00 2.57
226 227 5.512942 TGGTTCCTATCCTTCACATTTCA 57.487 39.130 0.00 0.00 0.00 2.69
227 228 6.039829 GGATTGGTTCCTATCCTTCACATTTC 59.960 42.308 19.71 0.00 41.78 2.17
228 229 5.893824 GGATTGGTTCCTATCCTTCACATTT 59.106 40.000 19.71 0.00 41.78 2.32
229 230 5.449553 GGATTGGTTCCTATCCTTCACATT 58.550 41.667 19.71 0.00 41.78 2.71
230 231 5.053978 GGATTGGTTCCTATCCTTCACAT 57.946 43.478 19.71 0.00 41.78 3.21
231 232 4.503714 GGATTGGTTCCTATCCTTCACA 57.496 45.455 19.71 0.00 41.78 3.58
266 267 5.302823 CCCTTTGGTTCATAGGAATGGATTC 59.697 44.000 6.07 0.00 35.14 2.52
267 268 5.211201 CCCTTTGGTTCATAGGAATGGATT 58.789 41.667 6.07 0.00 35.14 3.01
268 269 4.808042 CCCTTTGGTTCATAGGAATGGAT 58.192 43.478 6.07 0.00 35.14 3.41
269 270 3.627237 GCCCTTTGGTTCATAGGAATGGA 60.627 47.826 6.07 0.00 35.14 3.41
270 271 2.695147 GCCCTTTGGTTCATAGGAATGG 59.305 50.000 6.07 0.00 35.14 3.16
271 272 3.633986 GAGCCCTTTGGTTCATAGGAATG 59.366 47.826 6.07 0.00 41.28 2.67
272 273 3.529319 AGAGCCCTTTGGTTCATAGGAAT 59.471 43.478 6.07 0.00 43.89 3.01
273 274 2.919602 AGAGCCCTTTGGTTCATAGGAA 59.080 45.455 6.07 0.00 43.89 3.36
274 275 2.562296 AGAGCCCTTTGGTTCATAGGA 58.438 47.619 6.07 0.00 43.89 2.94
275 276 4.503714 TTAGAGCCCTTTGGTTCATAGG 57.496 45.455 0.00 0.00 43.89 2.57
276 277 5.745227 TCTTTAGAGCCCTTTGGTTCATAG 58.255 41.667 0.00 0.00 43.89 2.23
277 278 5.772393 TCTTTAGAGCCCTTTGGTTCATA 57.228 39.130 0.00 0.00 43.89 2.15
278 279 4.657814 TCTTTAGAGCCCTTTGGTTCAT 57.342 40.909 0.00 0.00 43.89 2.57
279 280 4.447138 TTCTTTAGAGCCCTTTGGTTCA 57.553 40.909 0.00 0.00 43.89 3.18
280 281 5.784578 TTTTCTTTAGAGCCCTTTGGTTC 57.215 39.130 0.00 0.00 41.91 3.62
321 322 9.404077 AGGAATTTCATAGGAATTCTAGAGGAT 57.596 33.333 5.23 0.00 31.93 3.24
322 323 8.805145 AGGAATTTCATAGGAATTCTAGAGGA 57.195 34.615 5.23 0.00 31.93 3.71
323 324 8.879227 AGAGGAATTTCATAGGAATTCTAGAGG 58.121 37.037 5.23 0.00 31.93 3.69
328 329 9.634021 GGTTTAGAGGAATTTCATAGGAATTCT 57.366 33.333 5.23 0.00 31.93 2.40
329 330 9.408648 TGGTTTAGAGGAATTTCATAGGAATTC 57.591 33.333 0.00 0.00 31.93 2.17
330 331 9.768215 TTGGTTTAGAGGAATTTCATAGGAATT 57.232 29.630 0.00 0.00 31.93 2.17
331 332 9.768215 TTTGGTTTAGAGGAATTTCATAGGAAT 57.232 29.630 0.00 0.00 31.93 3.01
332 333 9.243105 CTTTGGTTTAGAGGAATTTCATAGGAA 57.757 33.333 0.00 0.00 0.00 3.36
333 334 7.834181 CCTTTGGTTTAGAGGAATTTCATAGGA 59.166 37.037 0.00 0.00 32.11 2.94
334 335 7.834181 TCCTTTGGTTTAGAGGAATTTCATAGG 59.166 37.037 0.00 0.00 36.67 2.57
335 336 8.807948 TCCTTTGGTTTAGAGGAATTTCATAG 57.192 34.615 0.00 0.00 36.67 2.23
336 337 8.807948 CTCCTTTGGTTTAGAGGAATTTCATA 57.192 34.615 0.00 0.00 39.00 2.15
337 338 7.709149 CTCCTTTGGTTTAGAGGAATTTCAT 57.291 36.000 0.00 0.00 39.00 2.57
346 347 2.305927 TCAGGCCTCCTTTGGTTTAGAG 59.694 50.000 0.00 0.00 0.00 2.43
347 348 2.305927 CTCAGGCCTCCTTTGGTTTAGA 59.694 50.000 0.00 0.00 0.00 2.10
348 349 2.716217 CTCAGGCCTCCTTTGGTTTAG 58.284 52.381 0.00 0.00 0.00 1.85
349 350 1.271926 GCTCAGGCCTCCTTTGGTTTA 60.272 52.381 0.00 0.00 0.00 2.01
350 351 0.540597 GCTCAGGCCTCCTTTGGTTT 60.541 55.000 0.00 0.00 0.00 3.27
351 352 1.075659 GCTCAGGCCTCCTTTGGTT 59.924 57.895 0.00 0.00 0.00 3.67
352 353 2.759795 GCTCAGGCCTCCTTTGGT 59.240 61.111 0.00 0.00 0.00 3.67
362 363 2.675772 AAGCAAGCAGGCTCAGGC 60.676 61.111 2.41 0.00 45.07 4.85
363 364 2.991076 GCAAGCAAGCAGGCTCAGG 61.991 63.158 2.41 0.00 45.07 3.86
382 383 2.202810 GAAAGGAGCCCGAGCGAG 60.203 66.667 0.00 0.00 46.67 5.03
384 385 4.436998 ACGAAAGGAGCCCGAGCG 62.437 66.667 0.00 0.00 46.67 5.03
392 393 2.283298 CATGGATGGACACGAAAGGAG 58.717 52.381 0.00 0.00 0.00 3.69
463 464 8.171400 TCCCAATTAGTTGTGTAGGGATAAAAA 58.829 33.333 0.00 0.00 38.84 1.94
464 465 7.700846 TCCCAATTAGTTGTGTAGGGATAAAA 58.299 34.615 0.00 0.00 38.84 1.52
465 466 7.273457 TCCCAATTAGTTGTGTAGGGATAAA 57.727 36.000 0.00 0.00 38.84 1.40
466 467 6.894735 TCCCAATTAGTTGTGTAGGGATAA 57.105 37.500 0.00 0.00 38.84 1.75
472 473 6.548441 TCGTTTTCCCAATTAGTTGTGTAG 57.452 37.500 0.00 0.00 33.36 2.74
476 477 5.533154 TCACATCGTTTTCCCAATTAGTTGT 59.467 36.000 0.00 0.00 33.36 3.32
508 509 9.322776 GCTGATTGATGAGTTTAATAATAAGCG 57.677 33.333 0.00 0.00 0.00 4.68
534 535 7.776933 TCTCTCGTTGGAAGATTTTATGATG 57.223 36.000 0.00 0.00 0.00 3.07
535 536 8.970859 AATCTCTCGTTGGAAGATTTTATGAT 57.029 30.769 0.00 0.00 0.00 2.45
540 541 6.884280 ACAAATCTCTCGTTGGAAGATTTT 57.116 33.333 6.80 0.00 37.17 1.82
569 570 8.621286 CAGTTTACTTCTGACCTTGTTGTAATT 58.379 33.333 0.00 0.00 35.20 1.40
570 571 7.228706 CCAGTTTACTTCTGACCTTGTTGTAAT 59.771 37.037 0.00 0.00 35.20 1.89
576 577 3.714798 TCCCAGTTTACTTCTGACCTTGT 59.285 43.478 0.00 0.00 35.20 3.16
583 584 6.349611 CCACAATTGATCCCAGTTTACTTCTG 60.350 42.308 13.59 0.00 0.00 3.02
595 596 2.159057 GCATCAACCCACAATTGATCCC 60.159 50.000 13.59 0.00 43.39 3.85
628 633 4.686972 TGAACGTGAATTTTTGGCAATCA 58.313 34.783 0.00 0.00 0.00 2.57
685 690 0.588252 ACGCGAATGAATGGCATAGC 59.412 50.000 15.93 0.00 35.78 2.97
851 860 2.443577 GAGGGTCCGGGGAGGTAC 60.444 72.222 0.00 0.00 41.99 3.34
852 861 3.759101 GGAGGGTCCGGGGAGGTA 61.759 72.222 0.00 0.00 41.99 3.08
862 875 3.591254 GAGTGTGGTGCGGAGGGTC 62.591 68.421 0.00 0.00 0.00 4.46
881 894 2.618709 GGATATAAATAGGCGGCATGGC 59.381 50.000 13.08 9.69 45.27 4.40
885 898 2.300723 ACGTGGATATAAATAGGCGGCA 59.699 45.455 13.08 0.00 0.00 5.69
886 899 2.968675 ACGTGGATATAAATAGGCGGC 58.031 47.619 0.00 0.00 0.00 6.53
889 902 6.038997 AGAGGAACGTGGATATAAATAGGC 57.961 41.667 0.00 0.00 0.00 3.93
915 928 1.199615 GCTGCTCCCTAGAAGAAGGT 58.800 55.000 0.00 0.00 34.56 3.50
949 962 2.090400 TGCTGTCAGAGATGCAGAAC 57.910 50.000 3.32 0.00 32.39 3.01
955 968 2.896243 GCAAGTTGCTGTCAGAGATG 57.104 50.000 20.71 0.00 40.96 2.90
966 979 1.005748 GCAAGGGGAAGCAAGTTGC 60.006 57.895 20.44 20.44 45.46 4.17
999 1018 0.471591 CCTCCTCCTCCTCCTCCATG 60.472 65.000 0.00 0.00 0.00 3.66
1002 1021 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1003 1022 0.759060 GCTTCCTCCTCCTCCTCCTC 60.759 65.000 0.00 0.00 0.00 3.71
1004 1023 1.228215 AGCTTCCTCCTCCTCCTCCT 61.228 60.000 0.00 0.00 0.00 3.69
1007 1026 0.686112 CGAAGCTTCCTCCTCCTCCT 60.686 60.000 20.62 0.00 0.00 3.69
1090 1121 3.812019 CTCGGGCTGCGTAGTCGT 61.812 66.667 14.87 0.00 39.49 4.34
1095 1126 4.451150 CTTGGCTCGGGCTGCGTA 62.451 66.667 7.48 0.00 38.73 4.42
1469 1518 1.198637 GAGCGACTTTCTTGCAATGCT 59.801 47.619 6.82 1.00 0.00 3.79
1532 1593 1.135083 AGTAAACCGATCTCGCACCAG 60.135 52.381 0.00 0.00 38.18 4.00
1647 1708 0.950555 TCAGCATGTTCACCACGCTC 60.951 55.000 0.00 0.00 37.40 5.03
1718 1779 4.711949 AGCAGCGCACTCCCAAGG 62.712 66.667 11.47 0.00 0.00 3.61
1746 1807 5.679601 AGTACTACTGCCTGGTACTACTAC 58.320 45.833 0.00 0.00 42.61 2.73
1807 1868 1.531149 CCATGACGACAAGTGGACAAC 59.469 52.381 1.86 0.00 33.53 3.32
1822 1883 7.446769 TCTTACTTACTTACAAGCAACCATGA 58.553 34.615 0.00 0.00 0.00 3.07
1864 1928 0.695924 TGGTCCCGAATTCACATGGT 59.304 50.000 6.22 0.00 0.00 3.55
1875 1939 3.202906 GAAATCGATCAATTGGTCCCGA 58.797 45.455 13.10 8.91 0.00 5.14
1878 1942 4.731773 GCACTGAAATCGATCAATTGGTCC 60.732 45.833 13.10 0.00 0.00 4.46
1883 1947 3.935203 AGACGCACTGAAATCGATCAATT 59.065 39.130 0.00 0.00 0.00 2.32
1914 1978 2.287373 GGTACTCATACTCTGTCCGTCG 59.713 54.545 0.00 0.00 0.00 5.12
1953 2017 1.440060 CCATCCCATGCATGCACAC 59.560 57.895 25.37 0.00 0.00 3.82
1979 2043 1.269448 CCAATGACACGACCAAAAGGG 59.731 52.381 0.00 0.00 44.81 3.95
1984 2048 3.135225 CACTAACCAATGACACGACCAA 58.865 45.455 0.00 0.00 0.00 3.67
1989 2053 1.518325 TGCCACTAACCAATGACACG 58.482 50.000 0.00 0.00 0.00 4.49
1995 2059 1.826720 CATGCCTTGCCACTAACCAAT 59.173 47.619 0.00 0.00 0.00 3.16
2007 2071 2.191513 CCGCTCCATCCATGCCTTG 61.192 63.158 0.00 0.00 0.00 3.61
2008 2072 2.194056 CCGCTCCATCCATGCCTT 59.806 61.111 0.00 0.00 0.00 4.35
2009 2073 3.882326 CCCGCTCCATCCATGCCT 61.882 66.667 0.00 0.00 0.00 4.75
2011 2075 4.962836 CCCCCGCTCCATCCATGC 62.963 72.222 0.00 0.00 0.00 4.06
2012 2076 3.060614 AACCCCCGCTCCATCCATG 62.061 63.158 0.00 0.00 0.00 3.66
2014 2078 3.727258 CAACCCCCGCTCCATCCA 61.727 66.667 0.00 0.00 0.00 3.41
2015 2079 2.493273 TTTCAACCCCCGCTCCATCC 62.493 60.000 0.00 0.00 0.00 3.51
2016 2080 1.001393 TTTCAACCCCCGCTCCATC 60.001 57.895 0.00 0.00 0.00 3.51
2017 2081 1.000896 CTTTCAACCCCCGCTCCAT 60.001 57.895 0.00 0.00 0.00 3.41
2018 2082 2.434331 CTTTCAACCCCCGCTCCA 59.566 61.111 0.00 0.00 0.00 3.86
2019 2083 2.361230 CCTTTCAACCCCCGCTCC 60.361 66.667 0.00 0.00 0.00 4.70
2020 2084 2.361230 CCCTTTCAACCCCCGCTC 60.361 66.667 0.00 0.00 0.00 5.03
2021 2085 3.979497 CCCCTTTCAACCCCCGCT 61.979 66.667 0.00 0.00 0.00 5.52
2022 2086 3.516949 TTCCCCTTTCAACCCCCGC 62.517 63.158 0.00 0.00 0.00 6.13
2023 2087 1.304134 CTTCCCCTTTCAACCCCCG 60.304 63.158 0.00 0.00 0.00 5.73
2024 2088 0.485543 TTCTTCCCCTTTCAACCCCC 59.514 55.000 0.00 0.00 0.00 5.40
2025 2089 2.248248 CTTTCTTCCCCTTTCAACCCC 58.752 52.381 0.00 0.00 0.00 4.95
2026 2090 2.248248 CCTTTCTTCCCCTTTCAACCC 58.752 52.381 0.00 0.00 0.00 4.11
2027 2091 2.158370 TCCCTTTCTTCCCCTTTCAACC 60.158 50.000 0.00 0.00 0.00 3.77
2028 2092 3.238788 TCCCTTTCTTCCCCTTTCAAC 57.761 47.619 0.00 0.00 0.00 3.18
2029 2093 3.142028 ACATCCCTTTCTTCCCCTTTCAA 59.858 43.478 0.00 0.00 0.00 2.69
2030 2094 2.721906 ACATCCCTTTCTTCCCCTTTCA 59.278 45.455 0.00 0.00 0.00 2.69
2031 2095 3.092301 CACATCCCTTTCTTCCCCTTTC 58.908 50.000 0.00 0.00 0.00 2.62
2032 2096 2.823152 GCACATCCCTTTCTTCCCCTTT 60.823 50.000 0.00 0.00 0.00 3.11
2033 2097 1.272704 GCACATCCCTTTCTTCCCCTT 60.273 52.381 0.00 0.00 0.00 3.95
2034 2098 0.332972 GCACATCCCTTTCTTCCCCT 59.667 55.000 0.00 0.00 0.00 4.79
2035 2099 0.039618 TGCACATCCCTTTCTTCCCC 59.960 55.000 0.00 0.00 0.00 4.81
2036 2100 1.753073 CATGCACATCCCTTTCTTCCC 59.247 52.381 0.00 0.00 0.00 3.97
2037 2101 2.165030 CACATGCACATCCCTTTCTTCC 59.835 50.000 0.00 0.00 0.00 3.46
2038 2102 2.165030 CCACATGCACATCCCTTTCTTC 59.835 50.000 0.00 0.00 0.00 2.87
2039 2103 2.173519 CCACATGCACATCCCTTTCTT 58.826 47.619 0.00 0.00 0.00 2.52
2040 2104 1.076024 ACCACATGCACATCCCTTTCT 59.924 47.619 0.00 0.00 0.00 2.52
2041 2105 1.203052 CACCACATGCACATCCCTTTC 59.797 52.381 0.00 0.00 0.00 2.62
2042 2106 1.259609 CACCACATGCACATCCCTTT 58.740 50.000 0.00 0.00 0.00 3.11
2043 2107 0.112995 ACACCACATGCACATCCCTT 59.887 50.000 0.00 0.00 0.00 3.95
2044 2108 0.112995 AACACCACATGCACATCCCT 59.887 50.000 0.00 0.00 0.00 4.20
2045 2109 0.244450 CAACACCACATGCACATCCC 59.756 55.000 0.00 0.00 0.00 3.85
2046 2110 0.961019 ACAACACCACATGCACATCC 59.039 50.000 0.00 0.00 0.00 3.51
2047 2111 1.336148 CCACAACACCACATGCACATC 60.336 52.381 0.00 0.00 0.00 3.06
2048 2112 0.675083 CCACAACACCACATGCACAT 59.325 50.000 0.00 0.00 0.00 3.21
2049 2113 1.390383 CCCACAACACCACATGCACA 61.390 55.000 0.00 0.00 0.00 4.57
2050 2114 1.363443 CCCACAACACCACATGCAC 59.637 57.895 0.00 0.00 0.00 4.57
2051 2115 1.831726 CCCCACAACACCACATGCA 60.832 57.895 0.00 0.00 0.00 3.96
2082 2146 0.535780 GCCTCATGCCGGATGAATCA 60.536 55.000 5.05 0.00 40.73 2.57
2083 2147 2.251600 GCCTCATGCCGGATGAATC 58.748 57.895 5.05 2.87 40.73 2.52
2155 2219 1.692749 TGGGCCGCCTCCTTTATCT 60.693 57.895 9.86 0.00 0.00 1.98
2198 2262 1.265905 GAAAGCGGACACAAAACGGAT 59.734 47.619 0.00 0.00 0.00 4.18
2285 2350 4.148825 GGGAGGACACGCGCAGAT 62.149 66.667 5.73 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.