Multiple sequence alignment - TraesCS7A01G500800

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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 TraesCS7A01G500800 chr7A 100.000 2534 0 0 1 2534 690838507 690841040 0.000000e+00 4680.0
1 TraesCS7A01G500800 chr7A 90.498 863 77 4 721 1583 690721788 690722645 0.000000e+00 1134.0
2 TraesCS7A01G500800 chr7A 87.315 607 65 10 978 1578 690861057 690861657 0.000000e+00 684.0
3 TraesCS7A01G500800 chr7A 83.037 507 35 21 402 877 690823543 690824029 1.810000e-111 412.0
4 TraesCS7A01G500800 chr7A 94.656 262 13 1 71 332 300510977 300511237 3.040000e-109 405.0
5 TraesCS7A01G500800 chr7A 84.483 406 43 12 877 1267 690776582 690776982 1.420000e-102 383.0
6 TraesCS7A01G500800 chr7A 82.804 378 45 12 493 857 690803836 690804206 1.130000e-83 320.0
7 TraesCS7A01G500800 chr7A 75.000 484 102 12 1030 1499 690790244 690790722 3.300000e-49 206.0
8 TraesCS7A01G500800 chr7A 89.157 166 13 4 2372 2534 690824390 690824553 4.270000e-48 202.0
9 TraesCS7A01G500800 chr7A 95.000 60 3 0 2465 2524 690931062 690931121 7.460000e-16 95.3
10 TraesCS7A01G500800 chr7A 90.164 61 6 0 2465 2525 690935824 690935884 2.090000e-11 80.5
11 TraesCS7A01G500800 chr7A 90.000 60 6 0 2466 2525 690976287 690976346 7.520000e-11 78.7
12 TraesCS7A01G500800 chr7D 90.476 1218 78 17 402 1582 598334955 598336171 0.000000e+00 1572.0
13 TraesCS7A01G500800 chr7D 78.679 666 97 28 877 1499 598308214 598308877 3.930000e-108 401.0
14 TraesCS7A01G500800 chr7D 79.086 569 66 26 423 970 598315003 598315539 2.410000e-90 342.0
15 TraesCS7A01G500800 chr7D 84.646 254 28 7 925 1176 598295387 598295631 2.520000e-60 243.0
16 TraesCS7A01G500800 chr7D 92.763 152 8 3 2212 2360 610417461 610417310 1.530000e-52 217.0
17 TraesCS7A01G500800 chr7D 89.375 160 15 2 2210 2367 8481534 8481693 1.540000e-47 200.0
18 TraesCS7A01G500800 chr7D 86.420 81 9 2 1688 1768 598336303 598336381 1.250000e-13 87.9
19 TraesCS7A01G500800 chr7D 96.774 31 1 0 602 632 598294777 598294807 5.000000e-03 52.8
20 TraesCS7A01G500800 chr7B 85.423 1324 127 24 402 1680 677356012 677357314 0.000000e+00 1315.0
21 TraesCS7A01G500800 chr7B 88.490 808 56 14 423 1196 677218208 677217404 0.000000e+00 942.0
22 TraesCS7A01G500800 chr7B 84.145 801 81 17 783 1580 677406526 677407283 0.000000e+00 734.0
23 TraesCS7A01G500800 chr7B 94.340 477 18 3 1736 2212 677205567 677205100 0.000000e+00 723.0
24 TraesCS7A01G500800 chr7B 95.429 350 14 1 1369 1716 677206101 677205752 7.920000e-155 556.0
25 TraesCS7A01G500800 chr7B 88.432 389 29 6 402 777 677345648 677346033 2.970000e-124 455.0
26 TraesCS7A01G500800 chr7B 79.535 645 92 24 893 1500 677400063 677400704 8.380000e-115 424.0
27 TraesCS7A01G500800 chr7B 83.596 445 43 7 1724 2148 677358539 677358973 8.500000e-105 390.0
28 TraesCS7A01G500800 chr7B 93.208 265 17 1 70 333 627876217 627876481 3.060000e-104 388.0
29 TraesCS7A01G500800 chr7B 82.118 425 56 12 877 1286 677303878 677304297 1.870000e-91 346.0
30 TraesCS7A01G500800 chr7B 83.929 336 49 3 951 1286 677188753 677189083 1.460000e-82 316.0
31 TraesCS7A01G500800 chr7B 85.971 278 31 6 402 671 677239691 677239968 8.870000e-75 291.0
32 TraesCS7A01G500800 chr7B 81.016 374 46 14 423 785 677405906 677406265 8.930000e-70 274.0
33 TraesCS7A01G500800 chr7B 95.152 165 6 2 2371 2534 677205108 677204945 2.500000e-65 259.0
34 TraesCS7A01G500800 chr7B 88.344 163 16 3 2373 2534 677360371 677360531 2.570000e-45 193.0
35 TraesCS7A01G500800 chr7B 88.136 59 7 0 2467 2525 677668702 677668760 1.260000e-08 71.3
36 TraesCS7A01G500800 chr7B 100.000 28 0 0 1704 1731 677205740 677205713 5.000000e-03 52.8
37 TraesCS7A01G500800 chr5B 98.479 263 4 0 72 334 464609838 464609576 4.940000e-127 464.0
38 TraesCS7A01G500800 chr5B 89.441 161 8 6 2202 2360 255199056 255199209 7.150000e-46 195.0
39 TraesCS7A01G500800 chr3D 95.038 262 13 0 71 332 415660802 415660541 1.810000e-111 412.0
40 TraesCS7A01G500800 chr3D 94.902 255 13 0 78 332 62813854 62813600 1.410000e-107 399.0
41 TraesCS7A01G500800 chr4B 94.253 261 15 0 72 332 398088759 398088499 1.410000e-107 399.0
42 TraesCS7A01G500800 chr4B 93.870 261 16 0 72 332 465476513 465476253 6.570000e-106 394.0
43 TraesCS7A01G500800 chr2D 93.870 261 16 0 74 334 112871208 112870948 6.570000e-106 394.0
44 TraesCS7A01G500800 chr2D 91.447 152 8 4 2213 2360 174691250 174691100 1.190000e-48 204.0
45 TraesCS7A01G500800 chr3A 93.511 262 16 1 68 329 297837471 297837731 3.060000e-104 388.0
46 TraesCS7A01G500800 chr3A 92.667 150 9 2 2211 2358 701862440 701862589 5.490000e-52 215.0
47 TraesCS7A01G500800 chr3A 86.076 158 9 5 2210 2354 735357540 735357697 9.380000e-35 158.0
48 TraesCS7A01G500800 chrUn 92.053 151 9 3 2213 2360 183017628 183017478 2.550000e-50 209.0
49 TraesCS7A01G500800 chr3B 88.679 159 13 5 2206 2360 47705954 47706111 3.330000e-44 189.0
50 TraesCS7A01G500800 chr3B 88.050 159 14 5 2206 2360 48043819 48043976 1.550000e-42 183.0
51 TraesCS7A01G500800 chr3B 87.421 159 15 5 2206 2360 47835135 47835292 7.200000e-41 178.0
52 TraesCS7A01G500800 chr4A 98.214 56 1 0 331 386 692664721 692664666 5.770000e-17 99.0


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 TraesCS7A01G500800 chr7A 690838507 690841040 2533 False 4680.000000 4680 100.000000 1 2534 1 chr7A.!!$F6 2533
1 TraesCS7A01G500800 chr7A 690721788 690722645 857 False 1134.000000 1134 90.498000 721 1583 1 chr7A.!!$F2 862
2 TraesCS7A01G500800 chr7A 690861057 690861657 600 False 684.000000 684 87.315000 978 1578 1 chr7A.!!$F7 600
3 TraesCS7A01G500800 chr7A 690823543 690824553 1010 False 307.000000 412 86.097000 402 2534 2 chr7A.!!$F11 2132
4 TraesCS7A01G500800 chr7D 598334955 598336381 1426 False 829.950000 1572 88.448000 402 1768 2 chr7D.!!$F5 1366
5 TraesCS7A01G500800 chr7D 598308214 598308877 663 False 401.000000 401 78.679000 877 1499 1 chr7D.!!$F2 622
6 TraesCS7A01G500800 chr7D 598315003 598315539 536 False 342.000000 342 79.086000 423 970 1 chr7D.!!$F3 547
7 TraesCS7A01G500800 chr7B 677217404 677218208 804 True 942.000000 942 88.490000 423 1196 1 chr7B.!!$R1 773
8 TraesCS7A01G500800 chr7B 677356012 677360531 4519 False 632.666667 1315 85.787667 402 2534 3 chr7B.!!$F8 2132
9 TraesCS7A01G500800 chr7B 677405906 677407283 1377 False 504.000000 734 82.580500 423 1580 2 chr7B.!!$F9 1157
10 TraesCS7A01G500800 chr7B 677400063 677400704 641 False 424.000000 424 79.535000 893 1500 1 chr7B.!!$F6 607
11 TraesCS7A01G500800 chr7B 677204945 677206101 1156 True 397.700000 723 96.230250 1369 2534 4 chr7B.!!$R2 1165

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
724 794 1.317613 TCAAGTCACCAACATGCACC 58.682 50.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 5418 0.397816 AGGTCCGCCTCTAAGATGCT 60.398 55.0 0.0 0.0 42.67 3.79 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
25 26 8.974060 ATTAATATCCAACGACTATGGTTTGT 57.026 30.769 0.00 0.00 39.09 2.83
26 27 8.795842 TTAATATCCAACGACTATGGTTTGTT 57.204 30.769 0.00 0.00 39.09 2.83
27 28 9.887629 TTAATATCCAACGACTATGGTTTGTTA 57.112 29.630 0.00 0.00 39.09 2.41
28 29 8.795842 AATATCCAACGACTATGGTTTGTTAA 57.204 30.769 0.00 0.00 39.09 2.01
29 30 6.737254 ATCCAACGACTATGGTTTGTTAAG 57.263 37.500 0.00 0.00 39.09 1.85
30 31 5.856156 TCCAACGACTATGGTTTGTTAAGA 58.144 37.500 0.00 0.50 39.09 2.10
31 32 6.289834 TCCAACGACTATGGTTTGTTAAGAA 58.710 36.000 0.00 0.00 39.09 2.52
32 33 6.766944 TCCAACGACTATGGTTTGTTAAGAAA 59.233 34.615 0.00 0.00 39.09 2.52
33 34 7.282675 TCCAACGACTATGGTTTGTTAAGAAAA 59.717 33.333 0.00 0.00 39.09 2.29
34 35 7.916450 CCAACGACTATGGTTTGTTAAGAAAAA 59.084 33.333 0.00 0.00 33.08 1.94
35 36 8.953990 CAACGACTATGGTTTGTTAAGAAAAAG 58.046 33.333 0.00 0.00 0.00 2.27
36 37 8.441312 ACGACTATGGTTTGTTAAGAAAAAGA 57.559 30.769 0.00 0.00 0.00 2.52
37 38 8.895737 ACGACTATGGTTTGTTAAGAAAAAGAA 58.104 29.630 0.00 0.00 0.00 2.52
38 39 9.382244 CGACTATGGTTTGTTAAGAAAAAGAAG 57.618 33.333 0.00 0.00 0.00 2.85
39 40 9.678941 GACTATGGTTTGTTAAGAAAAAGAAGG 57.321 33.333 0.00 0.00 0.00 3.46
40 41 9.197306 ACTATGGTTTGTTAAGAAAAAGAAGGT 57.803 29.630 0.00 0.00 0.00 3.50
41 42 9.678941 CTATGGTTTGTTAAGAAAAAGAAGGTC 57.321 33.333 0.00 0.00 0.00 3.85
42 43 7.712204 TGGTTTGTTAAGAAAAAGAAGGTCT 57.288 32.000 0.00 0.00 0.00 3.85
43 44 8.810990 TGGTTTGTTAAGAAAAAGAAGGTCTA 57.189 30.769 0.00 0.00 0.00 2.59
44 45 9.416284 TGGTTTGTTAAGAAAAAGAAGGTCTAT 57.584 29.630 0.00 0.00 0.00 1.98
78 79 9.900112 ATGGTTAGATACTTCTAATTACTCCCT 57.100 33.333 0.00 0.00 44.24 4.20
79 80 9.364653 TGGTTAGATACTTCTAATTACTCCCTC 57.635 37.037 0.00 0.00 44.24 4.30
80 81 8.805175 GGTTAGATACTTCTAATTACTCCCTCC 58.195 40.741 0.00 0.00 44.24 4.30
81 82 8.513774 GTTAGATACTTCTAATTACTCCCTCCG 58.486 40.741 0.00 0.00 44.24 4.63
82 83 6.612741 AGATACTTCTAATTACTCCCTCCGT 58.387 40.000 0.00 0.00 0.00 4.69
83 84 7.068061 AGATACTTCTAATTACTCCCTCCGTT 58.932 38.462 0.00 0.00 0.00 4.44
84 85 5.595257 ACTTCTAATTACTCCCTCCGTTC 57.405 43.478 0.00 0.00 0.00 3.95
85 86 4.405036 ACTTCTAATTACTCCCTCCGTTCC 59.595 45.833 0.00 0.00 0.00 3.62
86 87 4.261411 TCTAATTACTCCCTCCGTTCCT 57.739 45.455 0.00 0.00 0.00 3.36
87 88 4.617593 TCTAATTACTCCCTCCGTTCCTT 58.382 43.478 0.00 0.00 0.00 3.36
88 89 5.028131 TCTAATTACTCCCTCCGTTCCTTT 58.972 41.667 0.00 0.00 0.00 3.11
89 90 4.652679 AATTACTCCCTCCGTTCCTTTT 57.347 40.909 0.00 0.00 0.00 2.27
90 91 4.652679 ATTACTCCCTCCGTTCCTTTTT 57.347 40.909 0.00 0.00 0.00 1.94
91 92 5.767277 ATTACTCCCTCCGTTCCTTTTTA 57.233 39.130 0.00 0.00 0.00 1.52
92 93 3.697619 ACTCCCTCCGTTCCTTTTTAG 57.302 47.619 0.00 0.00 0.00 1.85
93 94 2.977580 ACTCCCTCCGTTCCTTTTTAGT 59.022 45.455 0.00 0.00 0.00 2.24
94 95 3.007723 ACTCCCTCCGTTCCTTTTTAGTC 59.992 47.826 0.00 0.00 0.00 2.59
95 96 3.245441 TCCCTCCGTTCCTTTTTAGTCT 58.755 45.455 0.00 0.00 0.00 3.24
96 97 3.007614 TCCCTCCGTTCCTTTTTAGTCTG 59.992 47.826 0.00 0.00 0.00 3.51
97 98 2.742589 CCTCCGTTCCTTTTTAGTCTGC 59.257 50.000 0.00 0.00 0.00 4.26
98 99 3.399330 CTCCGTTCCTTTTTAGTCTGCA 58.601 45.455 0.00 0.00 0.00 4.41
99 100 4.003648 CTCCGTTCCTTTTTAGTCTGCAT 58.996 43.478 0.00 0.00 0.00 3.96
100 101 5.155278 TCCGTTCCTTTTTAGTCTGCATA 57.845 39.130 0.00 0.00 0.00 3.14
101 102 5.741011 TCCGTTCCTTTTTAGTCTGCATAT 58.259 37.500 0.00 0.00 0.00 1.78
102 103 6.880484 TCCGTTCCTTTTTAGTCTGCATATA 58.120 36.000 0.00 0.00 0.00 0.86
103 104 7.332557 TCCGTTCCTTTTTAGTCTGCATATAA 58.667 34.615 0.00 0.00 0.00 0.98
104 105 7.494625 TCCGTTCCTTTTTAGTCTGCATATAAG 59.505 37.037 0.00 0.00 0.00 1.73
105 106 7.494625 CCGTTCCTTTTTAGTCTGCATATAAGA 59.505 37.037 0.00 0.00 0.00 2.10
106 107 9.046296 CGTTCCTTTTTAGTCTGCATATAAGAT 57.954 33.333 0.00 0.00 0.00 2.40
110 111 9.956720 CCTTTTTAGTCTGCATATAAGATTTGG 57.043 33.333 0.00 0.00 0.00 3.28
113 114 9.679661 TTTTAGTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
114 115 9.679661 TTTAGTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
115 116 9.679661 TTAGTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
116 117 8.218338 AGTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
117 118 7.831193 AGTCTGCATATAAGATTTGGTCAAAGT 59.169 33.333 2.55 0.00 33.32 2.66
118 119 8.125448 GTCTGCATATAAGATTTGGTCAAAGTC 58.875 37.037 2.55 1.51 33.32 3.01
119 120 7.828717 TCTGCATATAAGATTTGGTCAAAGTCA 59.171 33.333 2.55 0.00 33.32 3.41
120 121 8.347004 TGCATATAAGATTTGGTCAAAGTCAA 57.653 30.769 2.55 0.00 33.32 3.18
121 122 8.801299 TGCATATAAGATTTGGTCAAAGTCAAA 58.199 29.630 2.55 0.00 37.29 2.69
122 123 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
198 199 9.573166 AGTAAAGCTATATGGTATGCAAATTCA 57.427 29.630 0.00 0.00 0.00 2.57
202 203 9.918630 AAGCTATATGGTATGCAAATTCATTTC 57.081 29.630 0.00 0.00 0.00 2.17
203 204 9.081204 AGCTATATGGTATGCAAATTCATTTCA 57.919 29.630 0.00 0.00 0.00 2.69
204 205 9.865321 GCTATATGGTATGCAAATTCATTTCAT 57.135 29.630 0.00 0.00 0.00 2.57
208 209 8.601845 ATGGTATGCAAATTCATTTCATGATG 57.398 30.769 0.00 0.00 39.39 3.07
209 210 6.480651 TGGTATGCAAATTCATTTCATGATGC 59.519 34.615 0.00 1.02 41.07 3.91
212 213 6.597262 TGCAAATTCATTTCATGATGCATC 57.403 33.333 20.14 20.14 43.74 3.91
213 214 6.345298 TGCAAATTCATTTCATGATGCATCT 58.655 32.000 26.32 10.21 43.74 2.90
214 215 7.493367 TGCAAATTCATTTCATGATGCATCTA 58.507 30.769 26.32 13.82 43.74 1.98
215 216 7.982354 TGCAAATTCATTTCATGATGCATCTAA 59.018 29.630 26.32 15.20 43.74 2.10
216 217 8.273557 GCAAATTCATTTCATGATGCATCTAAC 58.726 33.333 26.32 2.00 40.63 2.34
217 218 9.308318 CAAATTCATTTCATGATGCATCTAACA 57.692 29.630 26.32 8.26 39.39 2.41
218 219 9.878667 AAATTCATTTCATGATGCATCTAACAA 57.121 25.926 26.32 14.57 39.39 2.83
284 285 8.742554 AACTGAGTCAAAGTTAACAAAGTTTG 57.257 30.769 14.13 14.13 41.87 2.93
285 286 8.106247 ACTGAGTCAAAGTTAACAAAGTTTGA 57.894 30.769 22.23 13.70 44.97 2.69
299 300 5.738619 AAAGTTTGACTTTGACCAAACCT 57.261 34.783 12.56 0.03 45.83 3.50
300 301 6.109156 AAAGTTTGACTTTGACCAAACCTT 57.891 33.333 12.56 5.50 45.83 3.50
301 302 7.234661 AAAGTTTGACTTTGACCAAACCTTA 57.765 32.000 12.56 0.00 45.83 2.69
302 303 7.847096 AAAGTTTGACTTTGACCAAACCTTAT 58.153 30.769 12.56 0.00 45.83 1.73
303 304 8.973182 AAAGTTTGACTTTGACCAAACCTTATA 58.027 29.630 12.56 0.00 45.83 0.98
305 306 8.742554 GTTTGACTTTGACCAAACCTTATATG 57.257 34.615 0.00 0.00 43.62 1.78
306 307 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
307 308 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
308 309 6.150976 TGACTTTGACCAAACCTTATATGCAG 59.849 38.462 0.00 0.00 0.00 4.41
309 310 6.245408 ACTTTGACCAAACCTTATATGCAGA 58.755 36.000 0.00 0.00 0.00 4.26
310 311 6.151144 ACTTTGACCAAACCTTATATGCAGAC 59.849 38.462 0.00 0.00 0.00 3.51
311 312 5.435686 TGACCAAACCTTATATGCAGACT 57.564 39.130 0.00 0.00 0.00 3.24
312 313 6.553953 TGACCAAACCTTATATGCAGACTA 57.446 37.500 0.00 0.00 0.00 2.59
313 314 6.953101 TGACCAAACCTTATATGCAGACTAA 58.047 36.000 0.00 0.00 0.00 2.24
314 315 7.398829 TGACCAAACCTTATATGCAGACTAAA 58.601 34.615 0.00 0.00 0.00 1.85
315 316 7.885922 TGACCAAACCTTATATGCAGACTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
316 317 8.644374 ACCAAACCTTATATGCAGACTAAAAA 57.356 30.769 0.00 0.00 0.00 1.94
317 318 8.739972 ACCAAACCTTATATGCAGACTAAAAAG 58.260 33.333 0.00 0.00 0.00 2.27
318 319 8.956426 CCAAACCTTATATGCAGACTAAAAAGA 58.044 33.333 0.00 0.00 0.00 2.52
323 324 9.956720 CCTTATATGCAGACTAAAAAGAAATGG 57.043 33.333 0.00 0.00 0.00 3.16
326 327 5.964958 TGCAGACTAAAAAGAAATGGAGG 57.035 39.130 0.00 0.00 0.00 4.30
327 328 4.766891 TGCAGACTAAAAAGAAATGGAGGG 59.233 41.667 0.00 0.00 0.00 4.30
328 329 5.010282 GCAGACTAAAAAGAAATGGAGGGA 58.990 41.667 0.00 0.00 0.00 4.20
329 330 5.124617 GCAGACTAAAAAGAAATGGAGGGAG 59.875 44.000 0.00 0.00 0.00 4.30
330 331 6.241645 CAGACTAAAAAGAAATGGAGGGAGT 58.758 40.000 0.00 0.00 0.00 3.85
331 332 7.394816 CAGACTAAAAAGAAATGGAGGGAGTA 58.605 38.462 0.00 0.00 0.00 2.59
332 333 8.049721 CAGACTAAAAAGAAATGGAGGGAGTAT 58.950 37.037 0.00 0.00 0.00 2.12
333 334 8.615705 AGACTAAAAAGAAATGGAGGGAGTATT 58.384 33.333 0.00 0.00 0.00 1.89
334 335 8.581253 ACTAAAAAGAAATGGAGGGAGTATTG 57.419 34.615 0.00 0.00 0.00 1.90
335 336 8.170730 ACTAAAAAGAAATGGAGGGAGTATTGT 58.829 33.333 0.00 0.00 0.00 2.71
336 337 6.840780 AAAAGAAATGGAGGGAGTATTGTG 57.159 37.500 0.00 0.00 0.00 3.33
337 338 4.510167 AGAAATGGAGGGAGTATTGTGG 57.490 45.455 0.00 0.00 0.00 4.17
338 339 3.203040 AGAAATGGAGGGAGTATTGTGGG 59.797 47.826 0.00 0.00 0.00 4.61
339 340 2.587060 ATGGAGGGAGTATTGTGGGA 57.413 50.000 0.00 0.00 0.00 4.37
340 341 2.352561 TGGAGGGAGTATTGTGGGAA 57.647 50.000 0.00 0.00 0.00 3.97
341 342 2.858644 TGGAGGGAGTATTGTGGGAAT 58.141 47.619 0.00 0.00 0.00 3.01
342 343 3.197983 TGGAGGGAGTATTGTGGGAATT 58.802 45.455 0.00 0.00 0.00 2.17
343 344 3.596046 TGGAGGGAGTATTGTGGGAATTT 59.404 43.478 0.00 0.00 0.00 1.82
344 345 4.045334 TGGAGGGAGTATTGTGGGAATTTT 59.955 41.667 0.00 0.00 0.00 1.82
345 346 5.023452 GGAGGGAGTATTGTGGGAATTTTT 58.977 41.667 0.00 0.00 0.00 1.94
346 347 6.192044 GGAGGGAGTATTGTGGGAATTTTTA 58.808 40.000 0.00 0.00 0.00 1.52
347 348 6.321435 GGAGGGAGTATTGTGGGAATTTTTAG 59.679 42.308 0.00 0.00 0.00 1.85
348 349 5.656859 AGGGAGTATTGTGGGAATTTTTAGC 59.343 40.000 0.00 0.00 0.00 3.09
349 350 5.163447 GGGAGTATTGTGGGAATTTTTAGCC 60.163 44.000 0.00 0.00 0.00 3.93
350 351 5.656859 GGAGTATTGTGGGAATTTTTAGCCT 59.343 40.000 0.00 0.00 0.00 4.58
351 352 6.831868 GGAGTATTGTGGGAATTTTTAGCCTA 59.168 38.462 0.00 0.00 0.00 3.93
352 353 7.340999 GGAGTATTGTGGGAATTTTTAGCCTAA 59.659 37.037 0.00 0.00 0.00 2.69
353 354 8.838649 AGTATTGTGGGAATTTTTAGCCTAAT 57.161 30.769 0.00 0.00 0.00 1.73
354 355 9.267071 AGTATTGTGGGAATTTTTAGCCTAATT 57.733 29.630 0.00 0.00 0.00 1.40
358 359 9.487442 TTGTGGGAATTTTTAGCCTAATTATCT 57.513 29.630 0.00 0.00 0.00 1.98
359 360 9.487442 TGTGGGAATTTTTAGCCTAATTATCTT 57.513 29.630 0.00 0.00 0.00 2.40
381 382 4.846779 TTTTGTGGTTAGCCTGTCAATC 57.153 40.909 0.00 0.00 35.27 2.67
382 383 3.788227 TTGTGGTTAGCCTGTCAATCT 57.212 42.857 0.00 0.00 35.27 2.40
383 384 3.334583 TGTGGTTAGCCTGTCAATCTC 57.665 47.619 0.00 0.00 35.27 2.75
384 385 2.906389 TGTGGTTAGCCTGTCAATCTCT 59.094 45.455 0.00 0.00 35.27 3.10
385 386 3.327757 TGTGGTTAGCCTGTCAATCTCTT 59.672 43.478 0.00 0.00 35.27 2.85
386 387 4.202461 TGTGGTTAGCCTGTCAATCTCTTT 60.202 41.667 0.00 0.00 35.27 2.52
387 388 4.762251 GTGGTTAGCCTGTCAATCTCTTTT 59.238 41.667 0.00 0.00 35.27 2.27
388 389 5.241728 GTGGTTAGCCTGTCAATCTCTTTTT 59.758 40.000 0.00 0.00 35.27 1.94
484 504 6.017440 GTGTTTGGAGTACATTAAGCTTGTGA 60.017 38.462 9.86 0.00 0.00 3.58
510 530 2.150837 GCGTCGTACTTGTCGGCTC 61.151 63.158 0.00 0.00 0.00 4.70
551 590 8.562052 GCATAAGACAACACATCATTATCATGA 58.438 33.333 0.00 0.00 43.85 3.07
583 626 3.926527 ACACGCCTTCATATATACATGCG 59.073 43.478 13.85 13.85 45.59 4.73
588 631 3.623060 CCTTCATATATACATGCGTGCCC 59.377 47.826 5.64 0.00 0.00 5.36
595 638 7.391833 TCATATATACATGCGTGCCCAATTAAA 59.608 33.333 5.64 0.00 0.00 1.52
689 742 7.661040 TCATGAGTATATGACTGTATGTGGTG 58.339 38.462 0.00 0.00 39.06 4.17
724 794 1.317613 TCAAGTCACCAACATGCACC 58.682 50.000 0.00 0.00 0.00 5.01
758 828 3.223157 GTTATCGGCAACAACGACAAAG 58.777 45.455 0.00 0.00 43.78 2.77
781 851 3.434319 GCGTGCATGTGTGGGAGG 61.434 66.667 7.93 0.00 0.00 4.30
827 1160 7.039882 ACACAAGCATGTTACACCTACTATAC 58.960 38.462 0.00 0.00 37.82 1.47
834 1167 8.084073 GCATGTTACACCTACTATACGGAATAA 58.916 37.037 0.00 0.00 0.00 1.40
910 1244 3.251972 GTCATATTTAAGCAGCAGGAGCC 59.748 47.826 0.00 0.00 43.56 4.70
919 1262 2.743928 GCAGGAGCCCTTGTGTCG 60.744 66.667 0.00 0.00 33.58 4.35
1025 1388 2.200081 AGATCCTAACACCAGCACCAT 58.800 47.619 0.00 0.00 0.00 3.55
1065 1428 0.408309 TCAAGAACCTCCTCCTCGGA 59.592 55.000 0.00 0.00 40.30 4.55
1087 1450 3.550431 AGCTCCAGGCACACACGT 61.550 61.111 0.00 0.00 44.79 4.49
1253 1643 0.533032 GTGCAGAGGTGTAGGAGGAC 59.467 60.000 0.00 0.00 0.00 3.85
1353 1747 3.633609 GAGCAGCAGGACCATGGCA 62.634 63.158 13.04 0.00 0.00 4.92
1566 1961 0.961019 TGGTGGCTTGTCAATGCTTC 59.039 50.000 6.87 2.41 0.00 3.86
1653 2084 3.627577 GGATTTTATCTTGCTCTTGCGGA 59.372 43.478 0.00 0.00 43.34 5.54
1925 3684 4.522789 TCATTTAAAGGAGAAGGCCACAAC 59.477 41.667 5.01 0.00 0.00 3.32
1970 3745 1.067212 AGGTCACTGTCTTGTCACGAC 59.933 52.381 2.56 2.56 0.00 4.34
1992 3767 7.041235 ACGACGGAAACAAATGGTAAAATTCTA 60.041 33.333 0.00 0.00 0.00 2.10
2065 3862 2.199236 GCGTATTACTGCAGTACACCC 58.801 52.381 26.02 14.75 0.00 4.61
2075 3887 1.337447 GCAGTACACCCGAAACAGCTA 60.337 52.381 0.00 0.00 0.00 3.32
2076 3888 2.677037 GCAGTACACCCGAAACAGCTAT 60.677 50.000 0.00 0.00 0.00 2.97
2077 3889 3.429822 GCAGTACACCCGAAACAGCTATA 60.430 47.826 0.00 0.00 0.00 1.31
2078 3890 4.739735 GCAGTACACCCGAAACAGCTATAT 60.740 45.833 0.00 0.00 0.00 0.86
2079 3891 4.745125 CAGTACACCCGAAACAGCTATATG 59.255 45.833 0.00 0.00 0.00 1.78
2080 3892 3.194005 ACACCCGAAACAGCTATATGG 57.806 47.619 0.00 0.00 0.00 2.74
2081 3893 2.769663 ACACCCGAAACAGCTATATGGA 59.230 45.455 0.00 0.00 0.00 3.41
2082 3894 3.199071 ACACCCGAAACAGCTATATGGAA 59.801 43.478 0.00 0.00 0.00 3.53
2083 3895 4.196193 CACCCGAAACAGCTATATGGAAA 58.804 43.478 0.00 0.00 0.00 3.13
2084 3896 4.638421 CACCCGAAACAGCTATATGGAAAA 59.362 41.667 0.00 0.00 0.00 2.29
2085 3897 4.638865 ACCCGAAACAGCTATATGGAAAAC 59.361 41.667 0.00 0.00 0.00 2.43
2086 3898 4.638421 CCCGAAACAGCTATATGGAAAACA 59.362 41.667 0.00 0.00 0.00 2.83
2087 3899 5.448632 CCCGAAACAGCTATATGGAAAACAC 60.449 44.000 0.00 0.00 0.00 3.32
2088 3900 5.448632 CCGAAACAGCTATATGGAAAACACC 60.449 44.000 0.00 0.00 0.00 4.16
2089 3901 5.354234 CGAAACAGCTATATGGAAAACACCT 59.646 40.000 0.00 0.00 0.00 4.00
2090 3902 6.537301 CGAAACAGCTATATGGAAAACACCTA 59.463 38.462 0.00 0.00 0.00 3.08
2123 3935 5.357032 AGTCTAATAAAATTCACGGGCAAGG 59.643 40.000 0.00 0.00 0.00 3.61
2212 5396 9.838339 TCTTCTTTGTTTCATAGGATAGGAATC 57.162 33.333 0.00 0.00 41.37 2.52
2213 5397 9.618890 CTTCTTTGTTTCATAGGATAGGAATCA 57.381 33.333 0.00 0.00 41.37 2.57
2229 5413 9.937175 GATAGGAATCATAGTTTTAAACAGTGC 57.063 33.333 10.60 0.00 31.93 4.40
2230 5414 6.842163 AGGAATCATAGTTTTAAACAGTGCG 58.158 36.000 10.60 0.00 0.00 5.34
2231 5415 5.511729 GGAATCATAGTTTTAAACAGTGCGC 59.488 40.000 10.60 0.00 0.00 6.09
2232 5416 5.880054 ATCATAGTTTTAAACAGTGCGCT 57.120 34.783 9.73 0.00 0.00 5.92
2233 5417 6.978343 ATCATAGTTTTAAACAGTGCGCTA 57.022 33.333 9.73 0.00 0.00 4.26
2234 5418 6.788684 TCATAGTTTTAAACAGTGCGCTAA 57.211 33.333 9.73 0.00 0.00 3.09
2235 5419 6.827641 TCATAGTTTTAAACAGTGCGCTAAG 58.172 36.000 9.73 0.00 0.00 2.18
2248 5432 1.413382 CGCTAAGCATCTTAGAGGCG 58.587 55.000 13.23 9.96 44.44 5.52
2249 5433 1.789506 GCTAAGCATCTTAGAGGCGG 58.210 55.000 13.23 8.81 44.44 6.13
2250 5434 1.341531 GCTAAGCATCTTAGAGGCGGA 59.658 52.381 13.23 4.56 44.44 5.54
2251 5435 2.864489 GCTAAGCATCTTAGAGGCGGAC 60.864 54.545 13.23 1.27 44.44 4.79
2252 5436 0.466124 AAGCATCTTAGAGGCGGACC 59.534 55.000 13.23 0.00 44.44 4.46
2262 5446 3.558674 AGGCGGACCTCTTCAAATG 57.441 52.632 0.00 0.00 46.34 2.32
2263 5447 0.678048 AGGCGGACCTCTTCAAATGC 60.678 55.000 0.00 0.00 46.34 3.56
2264 5448 0.678048 GGCGGACCTCTTCAAATGCT 60.678 55.000 0.00 0.00 0.00 3.79
2265 5449 1.406887 GGCGGACCTCTTCAAATGCTA 60.407 52.381 0.00 0.00 0.00 3.49
2266 5450 2.565841 GCGGACCTCTTCAAATGCTAT 58.434 47.619 0.00 0.00 0.00 2.97
2267 5451 3.494398 GGCGGACCTCTTCAAATGCTATA 60.494 47.826 0.00 0.00 0.00 1.31
2268 5452 3.743396 GCGGACCTCTTCAAATGCTATAG 59.257 47.826 0.00 0.00 0.00 1.31
2269 5453 3.743396 CGGACCTCTTCAAATGCTATAGC 59.257 47.826 18.18 18.18 42.50 2.97
2295 5479 7.490962 TGCTATAGCGTGCTATTTAAAATGT 57.509 32.000 18.62 0.00 45.83 2.71
2296 5480 7.925993 TGCTATAGCGTGCTATTTAAAATGTT 58.074 30.769 18.62 0.00 45.83 2.71
2297 5481 8.402472 TGCTATAGCGTGCTATTTAAAATGTTT 58.598 29.630 18.62 0.00 45.83 2.83
2298 5482 8.682016 GCTATAGCGTGCTATTTAAAATGTTTG 58.318 33.333 18.62 0.00 39.65 2.93
2299 5483 9.716507 CTATAGCGTGCTATTTAAAATGTTTGT 57.283 29.630 18.62 0.00 39.65 2.83
2300 5484 8.980143 ATAGCGTGCTATTTAAAATGTTTGTT 57.020 26.923 8.54 0.00 35.92 2.83
2301 5485 7.707774 AGCGTGCTATTTAAAATGTTTGTTT 57.292 28.000 0.00 0.00 0.00 2.83
2302 5486 8.804688 AGCGTGCTATTTAAAATGTTTGTTTA 57.195 26.923 0.00 0.00 0.00 2.01
2303 5487 9.418045 AGCGTGCTATTTAAAATGTTTGTTTAT 57.582 25.926 0.00 0.00 0.00 1.40
2326 5510 5.751243 TTGTTTGGACAAAGTCTCTTAGC 57.249 39.130 0.00 0.00 42.54 3.09
2327 5511 3.807622 TGTTTGGACAAAGTCTCTTAGCG 59.192 43.478 0.00 0.00 31.49 4.26
2328 5512 2.080286 TGGACAAAGTCTCTTAGCGC 57.920 50.000 0.00 0.00 32.47 5.92
2329 5513 1.343142 TGGACAAAGTCTCTTAGCGCA 59.657 47.619 11.47 0.00 32.47 6.09
2330 5514 2.224185 TGGACAAAGTCTCTTAGCGCAA 60.224 45.455 11.47 0.50 32.47 4.85
2331 5515 2.413453 GGACAAAGTCTCTTAGCGCAAG 59.587 50.000 11.47 11.67 35.38 4.01
2332 5516 3.318017 GACAAAGTCTCTTAGCGCAAGA 58.682 45.455 11.47 15.40 41.10 3.02
2333 5517 3.060602 ACAAAGTCTCTTAGCGCAAGAC 58.939 45.455 11.47 16.26 38.39 3.01
2334 5518 2.371910 AAGTCTCTTAGCGCAAGACC 57.628 50.000 21.13 13.52 40.21 3.85
2335 5519 1.551452 AGTCTCTTAGCGCAAGACCT 58.449 50.000 21.13 14.93 40.21 3.85
2336 5520 1.896465 AGTCTCTTAGCGCAAGACCTT 59.104 47.619 21.13 7.87 40.21 3.50
2337 5521 2.300437 AGTCTCTTAGCGCAAGACCTTT 59.700 45.455 21.13 7.34 40.21 3.11
2338 5522 3.067833 GTCTCTTAGCGCAAGACCTTTT 58.932 45.455 11.47 0.00 38.39 2.27
2339 5523 3.067106 TCTCTTAGCGCAAGACCTTTTG 58.933 45.455 11.47 4.34 38.39 2.44
2340 5524 2.808543 CTCTTAGCGCAAGACCTTTTGT 59.191 45.455 11.47 0.00 38.39 2.83
2341 5525 3.994392 CTCTTAGCGCAAGACCTTTTGTA 59.006 43.478 11.47 0.00 38.39 2.41
2342 5526 4.382291 TCTTAGCGCAAGACCTTTTGTAA 58.618 39.130 11.47 0.00 38.39 2.41
2343 5527 4.817464 TCTTAGCGCAAGACCTTTTGTAAA 59.183 37.500 11.47 0.00 38.39 2.01
2344 5528 3.349488 AGCGCAAGACCTTTTGTAAAC 57.651 42.857 11.47 0.00 43.02 2.01
2345 5529 2.041244 GCGCAAGACCTTTTGTAAACG 58.959 47.619 0.30 0.00 43.02 3.60
2346 5530 2.041244 CGCAAGACCTTTTGTAAACGC 58.959 47.619 0.00 0.00 43.02 4.84
2347 5531 2.286772 CGCAAGACCTTTTGTAAACGCT 60.287 45.455 0.00 0.00 43.02 5.07
2348 5532 3.059461 CGCAAGACCTTTTGTAAACGCTA 60.059 43.478 0.00 0.00 43.02 4.26
2349 5533 4.378046 CGCAAGACCTTTTGTAAACGCTAT 60.378 41.667 0.00 0.00 43.02 2.97
2350 5534 5.163933 CGCAAGACCTTTTGTAAACGCTATA 60.164 40.000 0.00 0.00 43.02 1.31
2351 5535 6.248631 GCAAGACCTTTTGTAAACGCTATAG 58.751 40.000 0.00 0.00 0.00 1.31
2352 5536 6.248631 CAAGACCTTTTGTAAACGCTATAGC 58.751 40.000 15.09 15.09 37.78 2.97
2367 5551 5.934935 GCTATAGCGGGCTATTTAAAACA 57.065 39.130 17.49 0.00 39.65 2.83
2368 5552 5.928153 GCTATAGCGGGCTATTTAAAACAG 58.072 41.667 17.49 8.76 39.65 3.16
2369 5553 5.469084 GCTATAGCGGGCTATTTAAAACAGT 59.531 40.000 17.49 0.00 39.65 3.55
2370 5554 5.751243 ATAGCGGGCTATTTAAAACAGTG 57.249 39.130 7.36 0.00 35.92 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.795842 AACAAACCATAGTCGTTGGATATTAA 57.204 30.769 0.00 0.00 37.69 1.40
2 3 9.887629 TTAACAAACCATAGTCGTTGGATATTA 57.112 29.630 0.00 0.00 37.69 0.98
3 4 8.795842 TTAACAAACCATAGTCGTTGGATATT 57.204 30.769 0.00 0.00 37.69 1.28
4 5 8.262227 TCTTAACAAACCATAGTCGTTGGATAT 58.738 33.333 0.00 0.00 37.69 1.63
5 6 7.613585 TCTTAACAAACCATAGTCGTTGGATA 58.386 34.615 0.00 0.00 37.69 2.59
7 8 5.856156 TCTTAACAAACCATAGTCGTTGGA 58.144 37.500 0.00 0.00 37.69 3.53
8 9 6.548441 TTCTTAACAAACCATAGTCGTTGG 57.452 37.500 0.00 0.00 40.26 3.77
9 10 8.844441 TTTTTCTTAACAAACCATAGTCGTTG 57.156 30.769 0.00 0.00 0.00 4.10
11 12 8.441312 TCTTTTTCTTAACAAACCATAGTCGT 57.559 30.769 0.00 0.00 0.00 4.34
12 13 9.382244 CTTCTTTTTCTTAACAAACCATAGTCG 57.618 33.333 0.00 0.00 0.00 4.18
13 14 9.678941 CCTTCTTTTTCTTAACAAACCATAGTC 57.321 33.333 0.00 0.00 0.00 2.59
14 15 9.197306 ACCTTCTTTTTCTTAACAAACCATAGT 57.803 29.630 0.00 0.00 0.00 2.12
15 16 9.678941 GACCTTCTTTTTCTTAACAAACCATAG 57.321 33.333 0.00 0.00 0.00 2.23
16 17 9.416284 AGACCTTCTTTTTCTTAACAAACCATA 57.584 29.630 0.00 0.00 0.00 2.74
17 18 8.306313 AGACCTTCTTTTTCTTAACAAACCAT 57.694 30.769 0.00 0.00 0.00 3.55
18 19 7.712204 AGACCTTCTTTTTCTTAACAAACCA 57.288 32.000 0.00 0.00 0.00 3.67
57 58 7.753630 ACGGAGGGAGTAATTAGAAGTATCTA 58.246 38.462 0.00 0.00 37.10 1.98
58 59 6.612741 ACGGAGGGAGTAATTAGAAGTATCT 58.387 40.000 0.00 0.00 39.82 1.98
59 60 6.897706 ACGGAGGGAGTAATTAGAAGTATC 57.102 41.667 0.00 0.00 0.00 2.24
60 61 6.267242 GGAACGGAGGGAGTAATTAGAAGTAT 59.733 42.308 0.00 0.00 0.00 2.12
61 62 5.595952 GGAACGGAGGGAGTAATTAGAAGTA 59.404 44.000 0.00 0.00 0.00 2.24
62 63 4.405036 GGAACGGAGGGAGTAATTAGAAGT 59.595 45.833 0.00 0.00 0.00 3.01
63 64 4.650131 AGGAACGGAGGGAGTAATTAGAAG 59.350 45.833 0.00 0.00 0.00 2.85
64 65 4.617593 AGGAACGGAGGGAGTAATTAGAA 58.382 43.478 0.00 0.00 0.00 2.10
65 66 4.261411 AGGAACGGAGGGAGTAATTAGA 57.739 45.455 0.00 0.00 0.00 2.10
66 67 5.354842 AAAGGAACGGAGGGAGTAATTAG 57.645 43.478 0.00 0.00 0.00 1.73
67 68 5.767277 AAAAGGAACGGAGGGAGTAATTA 57.233 39.130 0.00 0.00 0.00 1.40
68 69 4.652679 AAAAGGAACGGAGGGAGTAATT 57.347 40.909 0.00 0.00 0.00 1.40
69 70 4.652679 AAAAAGGAACGGAGGGAGTAAT 57.347 40.909 0.00 0.00 0.00 1.89
70 71 4.594491 ACTAAAAAGGAACGGAGGGAGTAA 59.406 41.667 0.00 0.00 0.00 2.24
71 72 4.162651 ACTAAAAAGGAACGGAGGGAGTA 58.837 43.478 0.00 0.00 0.00 2.59
72 73 2.977580 ACTAAAAAGGAACGGAGGGAGT 59.022 45.455 0.00 0.00 0.00 3.85
73 74 3.261137 AGACTAAAAAGGAACGGAGGGAG 59.739 47.826 0.00 0.00 0.00 4.30
74 75 3.007614 CAGACTAAAAAGGAACGGAGGGA 59.992 47.826 0.00 0.00 0.00 4.20
75 76 3.335579 CAGACTAAAAAGGAACGGAGGG 58.664 50.000 0.00 0.00 0.00 4.30
76 77 2.742589 GCAGACTAAAAAGGAACGGAGG 59.257 50.000 0.00 0.00 0.00 4.30
77 78 3.399330 TGCAGACTAAAAAGGAACGGAG 58.601 45.455 0.00 0.00 0.00 4.63
78 79 3.478857 TGCAGACTAAAAAGGAACGGA 57.521 42.857 0.00 0.00 0.00 4.69
79 80 7.494625 TCTTATATGCAGACTAAAAAGGAACGG 59.505 37.037 0.00 0.00 0.00 4.44
80 81 8.420374 TCTTATATGCAGACTAAAAAGGAACG 57.580 34.615 0.00 0.00 0.00 3.95
84 85 9.956720 CCAAATCTTATATGCAGACTAAAAAGG 57.043 33.333 0.00 0.00 0.00 3.11
87 88 9.679661 TGACCAAATCTTATATGCAGACTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
88 89 9.679661 TTGACCAAATCTTATATGCAGACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
89 90 9.679661 TTTGACCAAATCTTATATGCAGACTAA 57.320 29.630 0.00 0.00 0.00 2.24
90 91 9.330063 CTTTGACCAAATCTTATATGCAGACTA 57.670 33.333 0.00 0.00 0.00 2.59
91 92 7.831193 ACTTTGACCAAATCTTATATGCAGACT 59.169 33.333 0.00 0.00 0.00 3.24
92 93 7.989826 ACTTTGACCAAATCTTATATGCAGAC 58.010 34.615 0.00 0.00 0.00 3.51
93 94 7.828717 TGACTTTGACCAAATCTTATATGCAGA 59.171 33.333 0.00 0.00 0.00 4.26
94 95 7.988737 TGACTTTGACCAAATCTTATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
95 96 7.936496 TGACTTTGACCAAATCTTATATGCA 57.064 32.000 0.00 0.00 0.00 3.96
96 97 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
172 173 9.573166 TGAATTTGCATACCATATAGCTTTACT 57.427 29.630 0.00 0.00 0.00 2.24
176 177 9.918630 GAAATGAATTTGCATACCATATAGCTT 57.081 29.630 0.00 0.00 0.00 3.74
177 178 9.081204 TGAAATGAATTTGCATACCATATAGCT 57.919 29.630 0.00 0.00 0.00 3.32
178 179 9.865321 ATGAAATGAATTTGCATACCATATAGC 57.135 29.630 0.00 0.00 0.00 2.97
258 259 9.191995 CAAACTTTGTTAACTTTGACTCAGTTT 57.808 29.630 7.22 6.67 35.95 2.66
259 260 8.573035 TCAAACTTTGTTAACTTTGACTCAGTT 58.427 29.630 13.70 5.56 38.13 3.16
260 261 8.021396 GTCAAACTTTGTTAACTTTGACTCAGT 58.979 33.333 27.39 10.29 44.69 3.41
261 262 8.382003 GTCAAACTTTGTTAACTTTGACTCAG 57.618 34.615 27.39 9.84 44.69 3.35
278 279 5.738619 AAGGTTTGGTCAAAGTCAAACTT 57.261 34.783 15.43 7.93 46.86 2.66
279 280 8.576442 CATATAAGGTTTGGTCAAAGTCAAACT 58.424 33.333 15.43 3.50 46.86 2.66
280 281 7.328493 GCATATAAGGTTTGGTCAAAGTCAAAC 59.672 37.037 9.59 9.59 46.92 2.93
281 282 7.014711 TGCATATAAGGTTTGGTCAAAGTCAAA 59.985 33.333 0.00 0.00 0.00 2.69
282 283 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
283 284 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
284 285 6.374333 TCTGCATATAAGGTTTGGTCAAAGTC 59.626 38.462 0.00 0.00 0.00 3.01
285 286 6.151144 GTCTGCATATAAGGTTTGGTCAAAGT 59.849 38.462 0.00 0.00 0.00 2.66
286 287 6.375455 AGTCTGCATATAAGGTTTGGTCAAAG 59.625 38.462 0.00 0.00 0.00 2.77
287 288 6.245408 AGTCTGCATATAAGGTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
288 289 5.815581 AGTCTGCATATAAGGTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
289 290 5.435686 AGTCTGCATATAAGGTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
290 291 7.859325 TTTAGTCTGCATATAAGGTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
291 292 8.644374 TTTTTAGTCTGCATATAAGGTTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
292 293 8.956426 TCTTTTTAGTCTGCATATAAGGTTTGG 58.044 33.333 0.00 0.00 0.00 3.28
297 298 9.956720 CCATTTCTTTTTAGTCTGCATATAAGG 57.043 33.333 0.00 0.00 0.00 2.69
300 301 9.342308 CCTCCATTTCTTTTTAGTCTGCATATA 57.658 33.333 0.00 0.00 0.00 0.86
301 302 7.286316 CCCTCCATTTCTTTTTAGTCTGCATAT 59.714 37.037 0.00 0.00 0.00 1.78
302 303 6.603201 CCCTCCATTTCTTTTTAGTCTGCATA 59.397 38.462 0.00 0.00 0.00 3.14
303 304 5.420104 CCCTCCATTTCTTTTTAGTCTGCAT 59.580 40.000 0.00 0.00 0.00 3.96
304 305 4.766891 CCCTCCATTTCTTTTTAGTCTGCA 59.233 41.667 0.00 0.00 0.00 4.41
305 306 5.010282 TCCCTCCATTTCTTTTTAGTCTGC 58.990 41.667 0.00 0.00 0.00 4.26
306 307 6.241645 ACTCCCTCCATTTCTTTTTAGTCTG 58.758 40.000 0.00 0.00 0.00 3.51
307 308 6.455690 ACTCCCTCCATTTCTTTTTAGTCT 57.544 37.500 0.00 0.00 0.00 3.24
308 309 8.678199 CAATACTCCCTCCATTTCTTTTTAGTC 58.322 37.037 0.00 0.00 0.00 2.59
309 310 8.170730 ACAATACTCCCTCCATTTCTTTTTAGT 58.829 33.333 0.00 0.00 0.00 2.24
310 311 8.462016 CACAATACTCCCTCCATTTCTTTTTAG 58.538 37.037 0.00 0.00 0.00 1.85
311 312 7.396055 CCACAATACTCCCTCCATTTCTTTTTA 59.604 37.037 0.00 0.00 0.00 1.52
312 313 6.211384 CCACAATACTCCCTCCATTTCTTTTT 59.789 38.462 0.00 0.00 0.00 1.94
313 314 5.716703 CCACAATACTCCCTCCATTTCTTTT 59.283 40.000 0.00 0.00 0.00 2.27
314 315 5.264395 CCACAATACTCCCTCCATTTCTTT 58.736 41.667 0.00 0.00 0.00 2.52
315 316 4.325344 CCCACAATACTCCCTCCATTTCTT 60.325 45.833 0.00 0.00 0.00 2.52
316 317 3.203040 CCCACAATACTCCCTCCATTTCT 59.797 47.826 0.00 0.00 0.00 2.52
317 318 3.202151 TCCCACAATACTCCCTCCATTTC 59.798 47.826 0.00 0.00 0.00 2.17
318 319 3.197983 TCCCACAATACTCCCTCCATTT 58.802 45.455 0.00 0.00 0.00 2.32
319 320 2.858644 TCCCACAATACTCCCTCCATT 58.141 47.619 0.00 0.00 0.00 3.16
320 321 2.587060 TCCCACAATACTCCCTCCAT 57.413 50.000 0.00 0.00 0.00 3.41
321 322 2.352561 TTCCCACAATACTCCCTCCA 57.647 50.000 0.00 0.00 0.00 3.86
322 323 3.953542 AATTCCCACAATACTCCCTCC 57.046 47.619 0.00 0.00 0.00 4.30
323 324 6.183360 GCTAAAAATTCCCACAATACTCCCTC 60.183 42.308 0.00 0.00 0.00 4.30
324 325 5.656859 GCTAAAAATTCCCACAATACTCCCT 59.343 40.000 0.00 0.00 0.00 4.20
325 326 5.163447 GGCTAAAAATTCCCACAATACTCCC 60.163 44.000 0.00 0.00 0.00 4.30
326 327 5.656859 AGGCTAAAAATTCCCACAATACTCC 59.343 40.000 0.00 0.00 0.00 3.85
327 328 6.775594 AGGCTAAAAATTCCCACAATACTC 57.224 37.500 0.00 0.00 0.00 2.59
328 329 8.838649 ATTAGGCTAAAAATTCCCACAATACT 57.161 30.769 11.59 0.00 0.00 2.12
332 333 9.487442 AGATAATTAGGCTAAAAATTCCCACAA 57.513 29.630 11.59 0.00 0.00 3.33
333 334 9.487442 AAGATAATTAGGCTAAAAATTCCCACA 57.513 29.630 11.59 0.00 0.00 4.17
359 360 4.892934 AGATTGACAGGCTAACCACAAAAA 59.107 37.500 0.00 0.00 39.06 1.94
360 361 4.469657 AGATTGACAGGCTAACCACAAAA 58.530 39.130 0.00 0.00 39.06 2.44
361 362 4.072131 GAGATTGACAGGCTAACCACAAA 58.928 43.478 0.00 0.00 39.06 2.83
362 363 3.327757 AGAGATTGACAGGCTAACCACAA 59.672 43.478 0.00 0.00 39.06 3.33
363 364 2.906389 AGAGATTGACAGGCTAACCACA 59.094 45.455 0.00 0.00 39.06 4.17
364 365 3.618690 AGAGATTGACAGGCTAACCAC 57.381 47.619 0.00 0.00 39.06 4.16
365 366 4.640771 AAAGAGATTGACAGGCTAACCA 57.359 40.909 0.00 0.00 39.06 3.67
366 367 5.966742 AAAAAGAGATTGACAGGCTAACC 57.033 39.130 0.00 0.00 0.00 2.85
394 395 9.889128 TGTCATGATCACACAGAAATCTATTTA 57.111 29.630 0.00 0.00 0.00 1.40
395 396 8.797350 TGTCATGATCACACAGAAATCTATTT 57.203 30.769 0.00 0.00 0.00 1.40
396 397 8.837389 CATGTCATGATCACACAGAAATCTATT 58.163 33.333 7.04 0.00 0.00 1.73
397 398 7.444487 CCATGTCATGATCACACAGAAATCTAT 59.556 37.037 14.67 0.00 0.00 1.98
398 399 6.764560 CCATGTCATGATCACACAGAAATCTA 59.235 38.462 14.67 0.00 0.00 1.98
399 400 5.589050 CCATGTCATGATCACACAGAAATCT 59.411 40.000 14.67 0.00 0.00 2.40
400 401 5.587443 TCCATGTCATGATCACACAGAAATC 59.413 40.000 14.67 0.00 0.00 2.17
484 504 1.000506 ACAAGTACGACGCCAGATGTT 59.999 47.619 0.00 0.00 0.00 2.71
577 620 1.404047 GCTTTAATTGGGCACGCATGT 60.404 47.619 0.00 0.00 0.00 3.21
583 626 2.479560 GGTGATCGCTTTAATTGGGCAC 60.480 50.000 6.18 0.00 0.00 5.01
588 631 6.063640 TGATGATGGTGATCGCTTTAATTG 57.936 37.500 6.18 0.00 0.00 2.32
595 638 2.180432 CCATGATGATGGTGATCGCT 57.820 50.000 2.51 0.00 43.98 4.93
689 742 6.322491 GTGACTTGAAGCCAAAATGTATACC 58.678 40.000 0.00 0.00 0.00 2.73
724 794 1.966563 CCGATAACAACGTTTTGTGCG 59.033 47.619 0.00 0.05 45.69 5.34
781 851 1.331756 CACCGGCAGCTGAATCATAAC 59.668 52.381 20.43 0.00 0.00 1.89
827 1160 3.485743 GCGCCTTGCTTAAAATTATTCCG 59.514 43.478 0.00 0.00 41.73 4.30
834 1167 3.401033 AAAAGGCGCCTTGCTTAAAAT 57.599 38.095 40.75 20.86 45.43 1.82
840 1173 0.250727 TCACTAAAAGGCGCCTTGCT 60.251 50.000 40.75 30.94 45.43 3.91
910 1244 1.411612 GGATAGGTACCCGACACAAGG 59.588 57.143 8.74 0.00 0.00 3.61
919 1262 2.496470 GTCGATGGATGGATAGGTACCC 59.504 54.545 8.74 0.00 0.00 3.69
1065 1428 3.563224 TGTGCCTGGAGCTGCAGT 61.563 61.111 30.32 1.59 44.23 4.40
1253 1643 4.767255 GGCAGCACCTCCTCACGG 62.767 72.222 0.00 0.00 34.51 4.94
1274 1664 0.261991 TCTCCCCGAGCACCTCTTAT 59.738 55.000 0.00 0.00 0.00 1.73
1275 1665 0.261991 ATCTCCCCGAGCACCTCTTA 59.738 55.000 0.00 0.00 0.00 2.10
1338 1732 2.044555 CAGTGCCATGGTCCTGCTG 61.045 63.158 14.67 10.56 0.00 4.41
1353 1747 0.397254 CCGGTATCACCTCCCTCAGT 60.397 60.000 0.00 0.00 35.66 3.41
1566 1961 0.514691 GCTTGTCCTTCTGTTCGCAG 59.485 55.000 0.00 0.00 46.29 5.18
1644 2075 3.118956 ACTGATAGGAACTTCCGCAAGAG 60.119 47.826 0.00 0.00 42.75 2.85
1653 2084 5.020132 AGCACTCTACACTGATAGGAACTT 58.980 41.667 0.00 0.00 41.75 2.66
1692 2408 4.063689 CTCTGCTGATCAACAAAGAGTGT 58.936 43.478 0.00 0.00 44.64 3.55
1855 3614 5.065731 GGTTCTGCAGATTTCCTGACTAATG 59.934 44.000 19.04 0.00 45.78 1.90
1925 3684 1.032794 TGGAGCCTATGTACGAGCAG 58.967 55.000 0.00 0.00 0.00 4.24
2009 3784 6.156256 TGCCAGGTCTCAGTTATTTACATACT 59.844 38.462 0.00 0.00 0.00 2.12
2010 3785 6.346096 TGCCAGGTCTCAGTTATTTACATAC 58.654 40.000 0.00 0.00 0.00 2.39
2011 3786 6.553953 TGCCAGGTCTCAGTTATTTACATA 57.446 37.500 0.00 0.00 0.00 2.29
2012 3787 5.435686 TGCCAGGTCTCAGTTATTTACAT 57.564 39.130 0.00 0.00 0.00 2.29
2065 3862 5.354234 AGGTGTTTTCCATATAGCTGTTTCG 59.646 40.000 0.00 0.00 0.00 3.46
2075 3887 9.990868 ACTTAATTTCCTAGGTGTTTTCCATAT 57.009 29.630 9.08 0.00 0.00 1.78
2076 3888 9.457436 GACTTAATTTCCTAGGTGTTTTCCATA 57.543 33.333 9.08 0.00 0.00 2.74
2077 3889 8.170730 AGACTTAATTTCCTAGGTGTTTTCCAT 58.829 33.333 9.08 0.00 0.00 3.41
2078 3890 7.523415 AGACTTAATTTCCTAGGTGTTTTCCA 58.477 34.615 9.08 0.00 0.00 3.53
2079 3891 7.997773 AGACTTAATTTCCTAGGTGTTTTCC 57.002 36.000 9.08 0.00 0.00 3.13
2116 3928 1.762957 TCACTAGCTACATCCTTGCCC 59.237 52.381 0.00 0.00 0.00 5.36
2123 3935 6.109359 ACAATTTCCTGTCACTAGCTACATC 58.891 40.000 0.00 0.00 0.00 3.06
2212 5396 5.508224 GCTTAGCGCACTGTTTAAAACTATG 59.492 40.000 11.47 0.00 38.92 2.23
2213 5397 5.180492 TGCTTAGCGCACTGTTTAAAACTAT 59.820 36.000 11.47 0.00 45.47 2.12
2214 5398 4.512198 TGCTTAGCGCACTGTTTAAAACTA 59.488 37.500 11.47 0.00 45.47 2.24
2215 5399 3.314080 TGCTTAGCGCACTGTTTAAAACT 59.686 39.130 11.47 0.00 45.47 2.66
2216 5400 3.623863 TGCTTAGCGCACTGTTTAAAAC 58.376 40.909 11.47 0.00 45.47 2.43
2217 5401 3.972950 TGCTTAGCGCACTGTTTAAAA 57.027 38.095 11.47 0.00 45.47 1.52
2228 5412 1.144136 GCCTCTAAGATGCTTAGCGC 58.856 55.000 0.00 0.00 39.77 5.92
2229 5413 1.413382 CGCCTCTAAGATGCTTAGCG 58.587 55.000 8.89 7.01 36.06 4.26
2230 5414 1.341531 TCCGCCTCTAAGATGCTTAGC 59.658 52.381 8.89 0.00 0.00 3.09
2231 5415 2.288518 GGTCCGCCTCTAAGATGCTTAG 60.289 54.545 7.68 7.68 0.00 2.18
2232 5416 1.687123 GGTCCGCCTCTAAGATGCTTA 59.313 52.381 0.00 0.00 0.00 3.09
2233 5417 0.466124 GGTCCGCCTCTAAGATGCTT 59.534 55.000 0.00 0.00 0.00 3.91
2234 5418 0.397816 AGGTCCGCCTCTAAGATGCT 60.398 55.000 0.00 0.00 42.67 3.79
2235 5419 2.128729 AGGTCCGCCTCTAAGATGC 58.871 57.895 0.00 0.00 42.67 3.91
2245 5429 0.678048 AGCATTTGAAGAGGTCCGCC 60.678 55.000 0.00 0.00 0.00 6.13
2246 5430 2.024176 TAGCATTTGAAGAGGTCCGC 57.976 50.000 0.00 0.00 0.00 5.54
2247 5431 3.743396 GCTATAGCATTTGAAGAGGTCCG 59.257 47.826 20.01 0.00 41.59 4.79
2269 5453 8.017373 ACATTTTAAATAGCACGCTATAGCATG 58.983 33.333 23.99 20.27 42.21 4.06
2270 5454 8.099364 ACATTTTAAATAGCACGCTATAGCAT 57.901 30.769 23.99 6.50 42.21 3.79
2271 5455 7.490962 ACATTTTAAATAGCACGCTATAGCA 57.509 32.000 23.99 4.83 42.21 3.49
2272 5456 8.682016 CAAACATTTTAAATAGCACGCTATAGC 58.318 33.333 15.09 15.09 38.20 2.97
2273 5457 9.716507 ACAAACATTTTAAATAGCACGCTATAG 57.283 29.630 11.80 0.00 38.20 1.31
2275 5459 8.980143 AACAAACATTTTAAATAGCACGCTAT 57.020 26.923 5.72 5.72 40.63 2.97
2276 5460 8.804688 AAACAAACATTTTAAATAGCACGCTA 57.195 26.923 0.39 0.39 0.00 4.26
2277 5461 7.707774 AAACAAACATTTTAAATAGCACGCT 57.292 28.000 0.00 0.00 0.00 5.07
2304 5488 4.272504 CGCTAAGAGACTTTGTCCAAACAA 59.727 41.667 0.00 0.00 43.58 2.83
2305 5489 3.807622 CGCTAAGAGACTTTGTCCAAACA 59.192 43.478 0.00 0.00 32.18 2.83
2306 5490 3.364068 GCGCTAAGAGACTTTGTCCAAAC 60.364 47.826 0.00 0.00 32.18 2.93
2307 5491 2.806244 GCGCTAAGAGACTTTGTCCAAA 59.194 45.455 0.00 0.00 32.18 3.28
2308 5492 2.224185 TGCGCTAAGAGACTTTGTCCAA 60.224 45.455 9.73 0.00 32.18 3.53
2309 5493 1.343142 TGCGCTAAGAGACTTTGTCCA 59.657 47.619 9.73 0.00 32.18 4.02
2310 5494 2.080286 TGCGCTAAGAGACTTTGTCC 57.920 50.000 9.73 0.00 32.18 4.02
2311 5495 3.122111 GTCTTGCGCTAAGAGACTTTGTC 59.878 47.826 18.44 5.22 45.71 3.18
2312 5496 3.060602 GTCTTGCGCTAAGAGACTTTGT 58.939 45.455 18.44 0.00 45.71 2.83
2313 5497 2.413453 GGTCTTGCGCTAAGAGACTTTG 59.587 50.000 22.91 0.00 45.71 2.77
2314 5498 2.300437 AGGTCTTGCGCTAAGAGACTTT 59.700 45.455 22.91 14.31 45.71 2.66
2315 5499 1.896465 AGGTCTTGCGCTAAGAGACTT 59.104 47.619 22.91 17.23 45.71 3.01
2316 5500 1.551452 AGGTCTTGCGCTAAGAGACT 58.449 50.000 22.91 18.83 45.71 3.24
2317 5501 2.371910 AAGGTCTTGCGCTAAGAGAC 57.628 50.000 18.44 18.59 45.71 3.36
2318 5502 3.067106 CAAAAGGTCTTGCGCTAAGAGA 58.933 45.455 18.44 9.99 45.71 3.10
2319 5503 2.808543 ACAAAAGGTCTTGCGCTAAGAG 59.191 45.455 18.44 10.73 45.71 2.85
2320 5504 2.846193 ACAAAAGGTCTTGCGCTAAGA 58.154 42.857 9.73 13.31 43.01 2.10
2321 5505 4.742438 TTACAAAAGGTCTTGCGCTAAG 57.258 40.909 9.73 11.02 37.76 2.18
2322 5506 4.553156 CGTTTACAAAAGGTCTTGCGCTAA 60.553 41.667 9.73 0.00 0.00 3.09
2323 5507 3.059461 CGTTTACAAAAGGTCTTGCGCTA 60.059 43.478 9.73 0.00 0.00 4.26
2324 5508 2.286772 CGTTTACAAAAGGTCTTGCGCT 60.287 45.455 9.73 0.00 0.00 5.92
2325 5509 2.041244 CGTTTACAAAAGGTCTTGCGC 58.959 47.619 0.00 0.00 0.00 6.09
2326 5510 2.041244 GCGTTTACAAAAGGTCTTGCG 58.959 47.619 0.00 0.00 0.00 4.85
2327 5511 3.349488 AGCGTTTACAAAAGGTCTTGC 57.651 42.857 0.00 0.00 0.00 4.01
2328 5512 6.248631 GCTATAGCGTTTACAAAAGGTCTTG 58.751 40.000 9.40 0.00 31.10 3.02
2329 5513 6.418585 GCTATAGCGTTTACAAAAGGTCTT 57.581 37.500 9.40 0.00 31.10 3.01
2345 5529 5.469084 ACTGTTTTAAATAGCCCGCTATAGC 59.531 40.000 15.09 15.09 38.20 2.97
2346 5530 6.704493 TCACTGTTTTAAATAGCCCGCTATAG 59.296 38.462 9.56 4.62 38.20 1.31
2347 5531 6.584488 TCACTGTTTTAAATAGCCCGCTATA 58.416 36.000 9.56 0.00 38.20 1.31
2348 5532 5.433526 TCACTGTTTTAAATAGCCCGCTAT 58.566 37.500 3.31 3.31 40.63 2.97
2349 5533 4.834534 TCACTGTTTTAAATAGCCCGCTA 58.165 39.130 0.00 0.00 0.00 4.26
2350 5534 3.681593 TCACTGTTTTAAATAGCCCGCT 58.318 40.909 1.36 0.00 0.00 5.52
2351 5535 4.632538 ATCACTGTTTTAAATAGCCCGC 57.367 40.909 1.36 0.00 0.00 6.13
2352 5536 7.548196 TTCTATCACTGTTTTAAATAGCCCG 57.452 36.000 1.36 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.