Multiple sequence alignment - TraesCS5D01G356000

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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 TraesCS5D01G356000 chr5D 100.000 3089 0 0 1 3089 437350663 437353751 0.000000e+00 5705.0
1 TraesCS5D01G356000 chr5D 96.296 162 6 0 1 162 217753987 217753826 1.830000e-67 267.0
2 TraesCS5D01G356000 chr5D 84.896 192 25 3 1184 1371 437456536 437456727 1.130000e-44 191.0
3 TraesCS5D01G356000 chr5D 100.000 41 0 0 1522 1562 335865026 335864986 3.300000e-10 76.8
4 TraesCS5D01G356000 chr5D 97.561 41 1 0 1522 1562 27353525 27353485 1.540000e-08 71.3
5 TraesCS5D01G356000 chr5B 92.932 948 42 9 2152 3087 531550496 531551430 0.000000e+00 1356.0
6 TraesCS5D01G356000 chr5B 85.899 1007 70 37 560 1529 531548825 531549796 0.000000e+00 1007.0
7 TraesCS5D01G356000 chr5B 92.193 602 41 5 1558 2154 531549778 531550378 0.000000e+00 846.0
8 TraesCS5D01G356000 chr5B 80.926 540 71 18 1270 1795 355616220 355616741 6.210000e-107 398.0
9 TraesCS5D01G356000 chr5B 85.864 191 22 3 1192 1377 531598467 531598657 6.760000e-47 198.0
10 TraesCS5D01G356000 chr5B 91.667 132 10 1 161 292 531548010 531548140 6.800000e-42 182.0
11 TraesCS5D01G356000 chr5B 83.333 162 18 5 401 555 531548632 531548791 1.150000e-29 141.0
12 TraesCS5D01G356000 chr5A 90.385 572 52 2 1582 2153 552546017 552546585 0.000000e+00 749.0
13 TraesCS5D01G356000 chr5A 89.308 477 27 15 898 1374 552545253 552545705 7.430000e-161 577.0
14 TraesCS5D01G356000 chr5A 85.741 526 36 19 403 921 552544737 552545230 1.270000e-143 520.0
15 TraesCS5D01G356000 chr5A 83.367 493 70 10 1620 2111 552548216 552548697 2.190000e-121 446.0
16 TraesCS5D01G356000 chr5A 86.600 403 35 8 2697 3087 552548099 552548494 7.920000e-116 427.0
17 TraesCS5D01G356000 chr5A 80.639 532 71 18 1270 1787 609200305 609200818 1.740000e-102 383.0
18 TraesCS5D01G356000 chr5A 90.608 181 17 0 2477 2657 552547922 552548102 1.110000e-59 241.0
19 TraesCS5D01G356000 chr5A 90.698 172 15 1 161 332 552544264 552544434 8.620000e-56 228.0
20 TraesCS5D01G356000 chr5A 81.229 293 35 8 2812 3087 552546052 552546341 5.190000e-53 219.0
21 TraesCS5D01G356000 chr5A 98.734 79 1 0 2152 2230 552546705 552546783 1.150000e-29 141.0
22 TraesCS5D01G356000 chr5A 91.837 98 8 0 1406 1503 552545771 552545868 1.490000e-28 137.0
23 TraesCS5D01G356000 chr5A 95.238 42 2 0 2430 2471 552547816 552547857 1.990000e-07 67.6
24 TraesCS5D01G356000 chr3D 81.212 495 67 12 1573 2059 609929254 609929730 2.910000e-100 375.0
25 TraesCS5D01G356000 chr3D 85.128 195 25 3 1936 2127 609922958 609923151 2.430000e-46 196.0
26 TraesCS5D01G356000 chr3A 79.760 499 65 17 1573 2062 743758445 743758916 2.300000e-86 329.0
27 TraesCS5D01G356000 chr3B 78.759 532 69 23 1270 1787 779516762 779517263 1.790000e-82 316.0
28 TraesCS5D01G356000 chr6D 97.531 162 4 0 1 162 183016996 183017157 8.440000e-71 278.0
29 TraesCS5D01G356000 chr6D 81.818 165 22 3 2230 2391 69942247 69942088 6.950000e-27 132.0
30 TraesCS5D01G356000 chr4D 96.296 162 6 0 1 162 281075604 281075443 1.830000e-67 267.0
31 TraesCS5D01G356000 chr4D 97.561 41 1 0 1522 1562 480505147 480505187 1.540000e-08 71.3
32 TraesCS5D01G356000 chr7D 95.732 164 7 0 1 164 230274915 230274752 6.570000e-67 265.0
33 TraesCS5D01G356000 chr7A 95.732 164 7 0 1 164 275024070 275024233 6.570000e-67 265.0
34 TraesCS5D01G356000 chr7A 97.561 41 1 0 1522 1562 191700307 191700267 1.540000e-08 71.3
35 TraesCS5D01G356000 chr6A 95.732 164 7 0 1 164 420541298 420541461 6.570000e-67 265.0
36 TraesCS5D01G356000 chr6A 95.210 167 7 1 1 166 7307819 7307653 2.360000e-66 263.0
37 TraesCS5D01G356000 chr6A 94.079 152 7 2 1918 2067 146493345 146493194 2.400000e-56 230.0
38 TraesCS5D01G356000 chr6A 82.424 165 21 3 2230 2391 87755645 87755486 1.490000e-28 137.0
39 TraesCS5D01G356000 chr6A 97.778 45 0 1 1519 1562 464506754 464506710 3.300000e-10 76.8
40 TraesCS5D01G356000 chr2D 96.273 161 6 0 1 161 339196634 339196794 6.570000e-67 265.0
41 TraesCS5D01G356000 chr2D 95.556 45 2 0 1522 1566 138766198 138766154 4.270000e-09 73.1
42 TraesCS5D01G356000 chr1A 91.146 192 14 3 1 189 506704726 506704535 1.100000e-64 257.0
43 TraesCS5D01G356000 chr6B 95.172 145 7 0 1918 2062 202353769 202353913 2.400000e-56 230.0
44 TraesCS5D01G356000 chr6B 83.251 203 27 5 1182 1377 288426988 288427190 2.450000e-41 180.0
45 TraesCS5D01G356000 chr2A 89.172 157 17 0 1960 2116 139646005 139645849 2.430000e-46 196.0
46 TraesCS5D01G356000 chr2A 85.235 149 21 1 178 326 192133971 192133824 5.340000e-33 152.0
47 TraesCS5D01G356000 chr4A 82.353 187 29 4 1182 1364 587119593 587119779 3.190000e-35 159.0
48 TraesCS5D01G356000 chr4A 91.379 58 5 0 999 1056 587119468 587119525 2.550000e-11 80.5
49 TraesCS5D01G356000 chr4B 95.556 45 1 1 1519 1562 400686189 400686233 1.540000e-08 71.3
50 TraesCS5D01G356000 chr2B 97.561 41 1 0 1522 1562 331235184 331235144 1.540000e-08 71.3
51 TraesCS5D01G356000 chr1D 95.556 45 1 1 1519 1562 454166988 454166944 1.540000e-08 71.3


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 TraesCS5D01G356000 chr5D 437350663 437353751 3088 False 5705.000000 5705 100.000000 1 3089 1 chr5D.!!$F1 3088
1 TraesCS5D01G356000 chr5B 531548010 531551430 3420 False 706.400000 1356 89.204800 161 3087 5 chr5B.!!$F3 2926
2 TraesCS5D01G356000 chr5B 355616220 355616741 521 False 398.000000 398 80.926000 1270 1795 1 chr5B.!!$F1 525
3 TraesCS5D01G356000 chr5A 609200305 609200818 513 False 383.000000 383 80.639000 1270 1787 1 chr5A.!!$F1 517
4 TraesCS5D01G356000 chr5A 552544264 552548697 4433 False 341.145455 749 89.431364 161 3087 11 chr5A.!!$F2 2926
5 TraesCS5D01G356000 chr3B 779516762 779517263 501 False 316.000000 316 78.759000 1270 1787 1 chr3B.!!$F1 517

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
840 1542 0.172352 CCCAGACGAGCTCTCTGAAC 59.828 60.0 29.47 10.83 37.9 3.18 F
1538 2410 0.038343 ATCAAATGCACGCCAACACC 60.038 50.0 0.00 0.00 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2713 0.401738 TTCTTGAACTGCCTCCCAGG 59.598 55.0 0.0 0.0 46.14 4.45 R
2731 4707 0.868406 CTTCTTGCCCGTTCACAGTC 59.132 55.0 0.0 0.0 0.00 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.311124 ACTGTAACATAGCGCTTCCC 57.689 50.000 18.68 0.00 0.00 3.97
21 22 1.553248 ACTGTAACATAGCGCTTCCCA 59.447 47.619 18.68 0.00 0.00 4.37
22 23 2.027561 ACTGTAACATAGCGCTTCCCAA 60.028 45.455 18.68 0.00 0.00 4.12
23 24 2.609459 CTGTAACATAGCGCTTCCCAAG 59.391 50.000 18.68 0.00 0.00 3.61
24 25 2.235155 TGTAACATAGCGCTTCCCAAGA 59.765 45.455 18.68 0.00 0.00 3.02
25 26 2.489938 AACATAGCGCTTCCCAAGAA 57.510 45.000 18.68 0.00 0.00 2.52
26 27 2.489938 ACATAGCGCTTCCCAAGAAA 57.510 45.000 18.68 0.00 0.00 2.52
27 28 2.359900 ACATAGCGCTTCCCAAGAAAG 58.640 47.619 18.68 0.00 0.00 2.62
28 29 1.672881 CATAGCGCTTCCCAAGAAAGG 59.327 52.381 18.68 0.00 0.00 3.11
29 30 0.981183 TAGCGCTTCCCAAGAAAGGA 59.019 50.000 18.68 0.00 0.00 3.36
30 31 0.329596 AGCGCTTCCCAAGAAAGGAT 59.670 50.000 2.64 0.00 32.10 3.24
31 32 0.453390 GCGCTTCCCAAGAAAGGATG 59.547 55.000 0.00 0.00 32.10 3.51
32 33 1.950484 GCGCTTCCCAAGAAAGGATGA 60.950 52.381 0.00 0.00 32.10 2.92
33 34 2.012673 CGCTTCCCAAGAAAGGATGAG 58.987 52.381 0.00 0.00 32.10 2.90
34 35 2.616510 CGCTTCCCAAGAAAGGATGAGT 60.617 50.000 0.00 0.00 32.10 3.41
35 36 3.013219 GCTTCCCAAGAAAGGATGAGTC 58.987 50.000 0.00 0.00 32.10 3.36
36 37 3.308046 GCTTCCCAAGAAAGGATGAGTCT 60.308 47.826 0.00 0.00 32.10 3.24
37 38 4.080863 GCTTCCCAAGAAAGGATGAGTCTA 60.081 45.833 0.00 0.00 32.10 2.59
38 39 5.422214 TTCCCAAGAAAGGATGAGTCTAC 57.578 43.478 0.00 0.00 32.10 2.59
39 40 4.425772 TCCCAAGAAAGGATGAGTCTACA 58.574 43.478 0.00 0.00 0.00 2.74
40 41 4.844085 TCCCAAGAAAGGATGAGTCTACAA 59.156 41.667 0.00 0.00 0.00 2.41
41 42 5.046304 TCCCAAGAAAGGATGAGTCTACAAG 60.046 44.000 0.00 0.00 0.00 3.16
42 43 4.633565 CCAAGAAAGGATGAGTCTACAAGC 59.366 45.833 0.00 0.00 0.00 4.01
43 44 5.486526 CAAGAAAGGATGAGTCTACAAGCT 58.513 41.667 0.00 0.00 0.00 3.74
44 45 6.351371 CCAAGAAAGGATGAGTCTACAAGCTA 60.351 42.308 0.00 0.00 0.00 3.32
45 46 6.859112 AGAAAGGATGAGTCTACAAGCTAA 57.141 37.500 0.00 0.00 0.00 3.09
46 47 7.430760 AGAAAGGATGAGTCTACAAGCTAAT 57.569 36.000 0.00 0.00 0.00 1.73
47 48 8.540507 AGAAAGGATGAGTCTACAAGCTAATA 57.459 34.615 0.00 0.00 0.00 0.98
48 49 8.982723 AGAAAGGATGAGTCTACAAGCTAATAA 58.017 33.333 0.00 0.00 0.00 1.40
49 50 9.601217 GAAAGGATGAGTCTACAAGCTAATAAA 57.399 33.333 0.00 0.00 0.00 1.40
51 52 9.553064 AAGGATGAGTCTACAAGCTAATAAATG 57.447 33.333 0.00 0.00 0.00 2.32
52 53 8.928448 AGGATGAGTCTACAAGCTAATAAATGA 58.072 33.333 0.00 0.00 0.00 2.57
53 54 9.547753 GGATGAGTCTACAAGCTAATAAATGAA 57.452 33.333 0.00 0.00 0.00 2.57
56 57 9.587772 TGAGTCTACAAGCTAATAAATGAAGTC 57.412 33.333 0.00 0.00 0.00 3.01
57 58 9.587772 GAGTCTACAAGCTAATAAATGAAGTCA 57.412 33.333 0.00 0.00 0.00 3.41
95 96 9.547753 ACTATTATGTTACTTTGCACTATGGAG 57.452 33.333 0.00 0.00 0.00 3.86
96 97 9.764363 CTATTATGTTACTTTGCACTATGGAGA 57.236 33.333 0.00 0.00 0.00 3.71
99 100 9.764363 TTATGTTACTTTGCACTATGGAGATAG 57.236 33.333 0.00 0.00 38.06 2.08
100 101 7.182817 TGTTACTTTGCACTATGGAGATAGT 57.817 36.000 0.00 0.00 44.86 2.12
101 102 8.301252 TGTTACTTTGCACTATGGAGATAGTA 57.699 34.615 0.00 0.00 42.55 1.82
102 103 8.755028 TGTTACTTTGCACTATGGAGATAGTAA 58.245 33.333 0.00 0.00 42.55 2.24
103 104 9.032420 GTTACTTTGCACTATGGAGATAGTAAC 57.968 37.037 0.00 0.00 42.55 2.50
104 105 7.425224 ACTTTGCACTATGGAGATAGTAACT 57.575 36.000 0.00 0.00 42.55 2.24
105 106 7.852263 ACTTTGCACTATGGAGATAGTAACTT 58.148 34.615 0.00 0.00 42.55 2.66
106 107 8.978472 ACTTTGCACTATGGAGATAGTAACTTA 58.022 33.333 0.00 0.00 42.55 2.24
107 108 9.469807 CTTTGCACTATGGAGATAGTAACTTAG 57.530 37.037 0.00 0.00 42.55 2.18
108 109 8.762481 TTGCACTATGGAGATAGTAACTTAGA 57.238 34.615 0.00 0.00 42.55 2.10
109 110 8.167605 TGCACTATGGAGATAGTAACTTAGAC 57.832 38.462 0.00 0.00 42.55 2.59
110 111 7.999545 TGCACTATGGAGATAGTAACTTAGACT 59.000 37.037 0.00 0.00 42.55 3.24
111 112 9.504708 GCACTATGGAGATAGTAACTTAGACTA 57.495 37.037 0.00 0.00 42.55 2.59
116 117 8.961294 TGGAGATAGTAACTTAGACTAGTGTC 57.039 38.462 0.00 0.00 43.22 3.67
117 118 8.546322 TGGAGATAGTAACTTAGACTAGTGTCA 58.454 37.037 0.00 0.00 45.20 3.58
118 119 9.563748 GGAGATAGTAACTTAGACTAGTGTCAT 57.436 37.037 0.00 0.00 45.20 3.06
123 124 8.521170 AGTAACTTAGACTAGTGTCATATGCA 57.479 34.615 0.00 0.00 45.20 3.96
124 125 9.137459 AGTAACTTAGACTAGTGTCATATGCAT 57.863 33.333 3.79 3.79 45.20 3.96
125 126 9.186323 GTAACTTAGACTAGTGTCATATGCATG 57.814 37.037 10.16 0.00 45.20 4.06
126 127 7.588497 ACTTAGACTAGTGTCATATGCATGA 57.412 36.000 10.16 0.00 45.20 3.07
145 146 7.713750 TGCATGACACTAGTATAAGTTACTCC 58.286 38.462 0.00 0.00 0.00 3.85
146 147 7.146648 GCATGACACTAGTATAAGTTACTCCC 58.853 42.308 0.00 0.00 0.00 4.30
147 148 7.659186 CATGACACTAGTATAAGTTACTCCCC 58.341 42.308 0.00 0.00 0.00 4.81
148 149 6.734532 TGACACTAGTATAAGTTACTCCCCA 58.265 40.000 0.00 0.00 0.00 4.96
149 150 6.604795 TGACACTAGTATAAGTTACTCCCCAC 59.395 42.308 0.00 0.00 0.00 4.61
150 151 6.739664 ACACTAGTATAAGTTACTCCCCACT 58.260 40.000 0.00 0.00 0.00 4.00
151 152 7.876371 ACACTAGTATAAGTTACTCCCCACTA 58.124 38.462 0.00 0.00 0.00 2.74
152 153 8.509441 ACACTAGTATAAGTTACTCCCCACTAT 58.491 37.037 0.00 0.00 0.00 2.12
153 154 8.794553 CACTAGTATAAGTTACTCCCCACTATG 58.205 40.741 0.00 0.00 0.00 2.23
154 155 8.730948 ACTAGTATAAGTTACTCCCCACTATGA 58.269 37.037 0.00 0.00 0.00 2.15
155 156 7.836479 AGTATAAGTTACTCCCCACTATGAC 57.164 40.000 0.00 0.00 0.00 3.06
156 157 6.781507 AGTATAAGTTACTCCCCACTATGACC 59.218 42.308 0.00 0.00 0.00 4.02
157 158 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
158 159 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
159 160 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
273 274 4.146616 CGTAGAGTTTCGAATATCAAGGCG 59.853 45.833 0.00 1.01 0.00 5.52
292 293 1.530031 CGCATAGCCTCGCTAGATACG 60.530 57.143 0.00 0.00 44.66 3.06
301 565 1.066114 CGCTAGATACGCGCTTAGCC 61.066 60.000 19.31 0.00 44.33 3.93
315 579 2.767505 CTTAGCCTTTCAGTTGGTCGT 58.232 47.619 0.00 0.00 0.00 4.34
348 862 2.029290 TCTTCAACGTCCAGACCTAAGC 60.029 50.000 0.00 0.00 0.00 3.09
379 901 8.420374 TGTATTCCTTCTTGAGTAATAAAGCG 57.580 34.615 0.00 0.00 0.00 4.68
381 903 6.721571 TTCCTTCTTGAGTAATAAAGCGTG 57.278 37.500 0.00 0.00 0.00 5.34
383 905 5.637810 TCCTTCTTGAGTAATAAAGCGTGTG 59.362 40.000 0.00 0.00 0.00 3.82
384 906 5.408604 CCTTCTTGAGTAATAAAGCGTGTGT 59.591 40.000 0.00 0.00 0.00 3.72
385 907 5.839262 TCTTGAGTAATAAAGCGTGTGTG 57.161 39.130 0.00 0.00 0.00 3.82
386 908 5.534407 TCTTGAGTAATAAAGCGTGTGTGA 58.466 37.500 0.00 0.00 0.00 3.58
388 910 5.839262 TGAGTAATAAAGCGTGTGTGAAG 57.161 39.130 0.00 0.00 0.00 3.02
389 911 4.151689 TGAGTAATAAAGCGTGTGTGAAGC 59.848 41.667 0.00 0.00 0.00 3.86
390 912 2.989422 AATAAAGCGTGTGTGAAGCC 57.011 45.000 0.00 0.00 0.00 4.35
391 913 2.185004 ATAAAGCGTGTGTGAAGCCT 57.815 45.000 0.00 0.00 0.00 4.58
394 916 1.961793 AAGCGTGTGTGAAGCCTAAA 58.038 45.000 0.00 0.00 0.00 1.85
544 1193 8.822652 AGAATTAAAGCACCATTTTTCTTCTG 57.177 30.769 0.00 0.00 0.00 3.02
545 1194 8.641541 AGAATTAAAGCACCATTTTTCTTCTGA 58.358 29.630 0.00 0.00 0.00 3.27
577 1257 3.462483 TGTGACGATTACACACCACTT 57.538 42.857 0.00 0.00 42.20 3.16
587 1267 3.735237 ACACACCACTTGACTGACTAG 57.265 47.619 0.00 0.00 0.00 2.57
616 1299 3.320826 CAGGGAAGGGGTTAACAAACAAG 59.679 47.826 8.10 0.00 0.00 3.16
699 1393 3.039588 GAACTTCGCGCCGTCCAA 61.040 61.111 0.00 0.00 0.00 3.53
744 1438 3.259064 GTTAATTACCAGCAGCGAGTGA 58.741 45.455 0.91 0.00 0.00 3.41
748 1442 0.391228 TACCAGCAGCGAGTGAAACA 59.609 50.000 0.91 0.00 41.43 2.83
751 1445 0.882042 CAGCAGCGAGTGAAACACCT 60.882 55.000 0.00 0.00 41.43 4.00
836 1538 1.680651 CCACCCAGACGAGCTCTCT 60.681 63.158 12.85 10.69 0.00 3.10
837 1539 1.510383 CACCCAGACGAGCTCTCTG 59.490 63.158 24.70 24.70 35.78 3.35
838 1540 0.962855 CACCCAGACGAGCTCTCTGA 60.963 60.000 29.47 0.00 37.90 3.27
839 1541 0.251386 ACCCAGACGAGCTCTCTGAA 60.251 55.000 29.47 0.00 37.90 3.02
840 1542 0.172352 CCCAGACGAGCTCTCTGAAC 59.828 60.000 29.47 10.83 37.90 3.18
841 1543 0.172352 CCAGACGAGCTCTCTGAACC 59.828 60.000 29.47 8.13 37.90 3.62
842 1544 0.172352 CAGACGAGCTCTCTGAACCC 59.828 60.000 26.28 4.59 37.90 4.11
843 1545 0.968393 AGACGAGCTCTCTGAACCCC 60.968 60.000 12.85 0.00 0.00 4.95
844 1546 2.272918 GACGAGCTCTCTGAACCCCG 62.273 65.000 12.85 0.00 0.00 5.73
845 1547 2.185608 GAGCTCTCTGAACCCCGC 59.814 66.667 6.43 0.00 0.00 6.13
846 1548 3.378399 GAGCTCTCTGAACCCCGCC 62.378 68.421 6.43 0.00 0.00 6.13
847 1549 4.821589 GCTCTCTGAACCCCGCCG 62.822 72.222 0.00 0.00 0.00 6.46
848 1550 4.148825 CTCTCTGAACCCCGCCGG 62.149 72.222 0.00 0.00 37.81 6.13
896 1634 1.630369 CAACCAATCTCACCTCCTCCA 59.370 52.381 0.00 0.00 0.00 3.86
920 1666 6.353404 TCTTCTTCTTCTTCTTCTTCCTCC 57.647 41.667 0.00 0.00 0.00 4.30
1076 1853 2.125106 CAGCTTCACCGGTAGGGC 60.125 66.667 6.87 11.88 43.47 5.19
1094 1871 0.945265 GCACCAACGCATTTGCACAT 60.945 50.000 3.13 0.00 42.21 3.21
1103 1880 1.820519 GCATTTGCACATCCTTCCTGA 59.179 47.619 0.00 0.00 41.59 3.86
1105 1882 2.655090 TTTGCACATCCTTCCTGACA 57.345 45.000 0.00 0.00 0.00 3.58
1113 1890 3.520721 ACATCCTTCCTGACATGACATGA 59.479 43.478 22.19 0.00 0.00 3.07
1116 1893 3.776417 TCCTTCCTGACATGACATGATGA 59.224 43.478 22.19 9.15 0.00 2.92
1117 1894 3.875727 CCTTCCTGACATGACATGATGAC 59.124 47.826 22.19 10.20 0.00 3.06
1118 1895 4.510571 CTTCCTGACATGACATGATGACA 58.489 43.478 22.19 13.63 0.00 3.58
1120 1897 3.516700 TCCTGACATGACATGATGACACT 59.483 43.478 22.19 0.00 0.00 3.55
1121 1898 3.869832 CCTGACATGACATGATGACACTC 59.130 47.826 22.19 7.61 0.00 3.51
1123 1900 4.752146 TGACATGACATGATGACACTCTC 58.248 43.478 22.19 6.23 0.00 3.20
1124 1901 3.778618 ACATGACATGATGACACTCTCG 58.221 45.455 22.19 0.00 0.00 4.04
1125 1902 3.194329 ACATGACATGATGACACTCTCGT 59.806 43.478 22.19 0.00 0.00 4.18
1126 1903 3.942130 TGACATGATGACACTCTCGTT 57.058 42.857 0.00 0.00 0.00 3.85
1128 1905 3.989817 TGACATGATGACACTCTCGTTTG 59.010 43.478 0.00 0.00 0.00 2.93
1129 1906 4.237724 GACATGATGACACTCTCGTTTGA 58.762 43.478 0.00 0.00 0.00 2.69
1134 1911 5.989249 TGATGACACTCTCGTTTGATTTTG 58.011 37.500 0.00 0.00 0.00 2.44
1140 1917 4.690748 CACTCTCGTTTGATTTTGCCTCTA 59.309 41.667 0.00 0.00 0.00 2.43
1172 1949 3.702045 TGAAAAACCCTTTGATTGACGGT 59.298 39.130 0.00 0.00 0.00 4.83
1190 1967 3.006728 GACACCCGGGGACATCCA 61.007 66.667 27.92 0.00 37.91 3.41
1244 2022 4.404098 GCGGTGGGGGACGTCAAT 62.404 66.667 18.91 0.00 0.00 2.57
1377 2160 8.427902 TGAGAATCATAAGCAGGTATGTATCT 57.572 34.615 0.00 0.20 42.56 1.98
1378 2161 9.533831 TGAGAATCATAAGCAGGTATGTATCTA 57.466 33.333 0.00 0.00 42.56 1.98
1390 2173 9.765795 GCAGGTATGTATCTAGTATCTTGTTTT 57.234 33.333 0.00 0.00 0.00 2.43
1416 2236 6.437477 TCTCTAGTGCTACCTTCAGATTGAAA 59.563 38.462 0.00 0.00 35.73 2.69
1427 2247 6.150641 ACCTTCAGATTGAAAGATCATGTGTG 59.849 38.462 0.00 0.00 35.73 3.82
1466 2292 7.704899 TGTGTCATATCCAAACGAATGTACTAG 59.295 37.037 0.00 0.00 0.00 2.57
1499 2371 6.417191 TTGATATGTTCCGTACTTTGCTTC 57.583 37.500 0.00 0.00 0.00 3.86
1510 2382 5.975344 CCGTACTTTGCTTCGTAGAATGATA 59.025 40.000 0.00 0.00 45.90 2.15
1511 2383 6.474427 CCGTACTTTGCTTCGTAGAATGATAA 59.526 38.462 0.00 0.00 45.90 1.75
1512 2384 7.169308 CCGTACTTTGCTTCGTAGAATGATAAT 59.831 37.037 0.00 0.00 45.90 1.28
1513 2385 9.177304 CGTACTTTGCTTCGTAGAATGATAATA 57.823 33.333 0.00 0.00 45.90 0.98
1515 2387 8.942338 ACTTTGCTTCGTAGAATGATAATACA 57.058 30.769 0.00 0.00 45.90 2.29
1516 2388 9.035607 ACTTTGCTTCGTAGAATGATAATACAG 57.964 33.333 0.00 0.00 45.90 2.74
1517 2389 9.249457 CTTTGCTTCGTAGAATGATAATACAGA 57.751 33.333 0.00 0.00 45.90 3.41
1518 2390 8.803201 TTGCTTCGTAGAATGATAATACAGAG 57.197 34.615 0.00 0.00 45.90 3.35
1519 2391 8.166422 TGCTTCGTAGAATGATAATACAGAGA 57.834 34.615 0.00 0.00 45.90 3.10
1520 2392 8.797438 TGCTTCGTAGAATGATAATACAGAGAT 58.203 33.333 0.00 0.00 45.90 2.75
1521 2393 9.284594 GCTTCGTAGAATGATAATACAGAGATC 57.715 37.037 0.00 0.00 45.90 2.75
1528 2400 9.788889 AGAATGATAATACAGAGATCAAATGCA 57.211 29.630 0.00 0.00 33.50 3.96
1529 2401 9.823098 GAATGATAATACAGAGATCAAATGCAC 57.177 33.333 0.00 0.00 33.50 4.57
1530 2402 7.412137 TGATAATACAGAGATCAAATGCACG 57.588 36.000 0.00 0.00 0.00 5.34
1531 2403 4.542662 AATACAGAGATCAAATGCACGC 57.457 40.909 0.00 0.00 0.00 5.34
1532 2404 1.089920 ACAGAGATCAAATGCACGCC 58.910 50.000 0.00 0.00 0.00 5.68
1533 2405 1.089112 CAGAGATCAAATGCACGCCA 58.911 50.000 0.00 0.00 0.00 5.69
1534 2406 1.469703 CAGAGATCAAATGCACGCCAA 59.530 47.619 0.00 0.00 0.00 4.52
1535 2407 1.470098 AGAGATCAAATGCACGCCAAC 59.530 47.619 0.00 0.00 0.00 3.77
1536 2408 1.199789 GAGATCAAATGCACGCCAACA 59.800 47.619 0.00 0.00 0.00 3.33
1537 2409 1.068333 AGATCAAATGCACGCCAACAC 60.068 47.619 0.00 0.00 0.00 3.32
1538 2410 0.038343 ATCAAATGCACGCCAACACC 60.038 50.000 0.00 0.00 0.00 4.16
1539 2411 1.067084 CAAATGCACGCCAACACCA 59.933 52.632 0.00 0.00 0.00 4.17
1540 2412 1.067250 AAATGCACGCCAACACCAC 59.933 52.632 0.00 0.00 0.00 4.16
1541 2413 1.670949 AAATGCACGCCAACACCACA 61.671 50.000 0.00 0.00 0.00 4.17
1542 2414 2.348605 AATGCACGCCAACACCACAC 62.349 55.000 0.00 0.00 0.00 3.82
1543 2415 3.513438 GCACGCCAACACCACACA 61.513 61.111 0.00 0.00 0.00 3.72
1544 2416 2.407210 CACGCCAACACCACACAC 59.593 61.111 0.00 0.00 0.00 3.82
1545 2417 2.045829 ACGCCAACACCACACACA 60.046 55.556 0.00 0.00 0.00 3.72
1546 2418 2.403378 ACGCCAACACCACACACAC 61.403 57.895 0.00 0.00 0.00 3.82
1547 2419 2.804856 GCCAACACCACACACACC 59.195 61.111 0.00 0.00 0.00 4.16
1548 2420 2.781158 GCCAACACCACACACACCC 61.781 63.158 0.00 0.00 0.00 4.61
1549 2421 1.379176 CCAACACCACACACACCCA 60.379 57.895 0.00 0.00 0.00 4.51
1550 2422 0.967887 CCAACACCACACACACCCAA 60.968 55.000 0.00 0.00 0.00 4.12
1551 2423 0.455410 CAACACCACACACACCCAAG 59.545 55.000 0.00 0.00 0.00 3.61
1552 2424 0.682855 AACACCACACACACCCAAGG 60.683 55.000 0.00 0.00 0.00 3.61
1553 2425 2.123897 ACCACACACACCCAAGGC 60.124 61.111 0.00 0.00 0.00 4.35
1554 2426 2.123939 CCACACACACCCAAGGCA 60.124 61.111 0.00 0.00 0.00 4.75
1555 2427 2.195567 CCACACACACCCAAGGCAG 61.196 63.158 0.00 0.00 0.00 4.85
1591 2534 6.640499 TCAAATTGCATGAAAAGTAGAAACCG 59.360 34.615 0.00 0.00 0.00 4.44
1602 2545 7.386848 TGAAAAGTAGAAACCGGAGAACTTATG 59.613 37.037 9.46 0.00 0.00 1.90
1606 2549 4.098894 AGAAACCGGAGAACTTATGGGTA 58.901 43.478 9.46 0.00 0.00 3.69
1648 2591 5.819991 AGAGATAAATCTGCAGGTCCAAAA 58.180 37.500 15.13 0.00 37.25 2.44
1649 2592 5.884792 AGAGATAAATCTGCAGGTCCAAAAG 59.115 40.000 15.13 0.00 37.25 2.27
1684 2628 9.288576 TGATTGACAGATTTTACAAGTTCAGAT 57.711 29.630 0.00 0.00 0.00 2.90
1720 2665 5.319043 TCCAGTTTCCACAATTACTTCCT 57.681 39.130 0.00 0.00 0.00 3.36
1727 2672 4.566004 TCCACAATTACTTCCTCAACTCG 58.434 43.478 0.00 0.00 0.00 4.18
1737 2682 2.885616 TCCTCAACTCGGACTAAACCT 58.114 47.619 0.00 0.00 0.00 3.50
1767 2713 6.012658 TGTTTGCAGAAAATGATACTGGTC 57.987 37.500 0.00 0.00 33.00 4.02
1774 2720 4.164988 AGAAAATGATACTGGTCCTGGGAG 59.835 45.833 0.33 0.00 0.00 4.30
1787 2733 1.005215 CCTGGGAGGCAGTTCAAGAAT 59.995 52.381 0.00 0.00 0.00 2.40
1790 2736 1.066143 GGGAGGCAGTTCAAGAATCGA 60.066 52.381 0.00 0.00 0.00 3.59
1797 2743 3.743396 GCAGTTCAAGAATCGAGAACACT 59.257 43.478 18.01 1.69 43.00 3.55
1800 2746 5.920840 CAGTTCAAGAATCGAGAACACTACA 59.079 40.000 18.01 0.00 43.00 2.74
1865 2811 1.905215 ACCATCAGGAGTTCAGTCTGG 59.095 52.381 0.00 0.00 38.69 3.86
2127 3073 1.084289 GGTTTCGCCGTTATGCTCTT 58.916 50.000 0.00 0.00 0.00 2.85
2300 3372 7.533900 CCTTGTAACAAATCAAACTGTGTATCG 59.466 37.037 0.00 0.00 0.00 2.92
2568 4544 0.340208 AGGGGAAGACGAGGAAGGAT 59.660 55.000 0.00 0.00 0.00 3.24
2679 4655 6.538742 ACTGTGGTGTTCTGTGTAATATATGC 59.461 38.462 0.00 0.00 0.00 3.14
2741 4717 7.324322 TGTACTTTATTAACGACTGTGAACG 57.676 36.000 0.00 0.00 0.00 3.95
2742 4718 5.834239 ACTTTATTAACGACTGTGAACGG 57.166 39.130 0.00 0.00 0.00 4.44
2754 4730 1.202879 TGTGAACGGGCAAGAAGGATT 60.203 47.619 0.00 0.00 0.00 3.01
2880 4863 8.207545 ACAGTTTTTAGAAGTTCAGAGAGTGAT 58.792 33.333 5.50 0.00 34.17 3.06
2885 4868 8.594881 TTTAGAAGTTCAGAGAGTGATTTGTC 57.405 34.615 5.50 0.00 34.17 3.18
2902 4885 7.004086 TGATTTGTCTCCTATTTCCACAACTT 58.996 34.615 0.00 0.00 0.00 2.66
2940 4928 9.844790 CTACTTGTTTGCAGAAAATGATATTGA 57.155 29.630 0.00 0.00 0.00 2.57
2953 4941 4.104383 TGATATTGATTCTGGGAAGCCC 57.896 45.455 0.00 0.00 45.71 5.19
3005 4993 1.001158 CCACCGTTACCGCAACATTTT 60.001 47.619 0.03 0.00 36.92 1.82
3032 5020 3.220110 CGCTCTACCACCATTAGGAGTA 58.780 50.000 0.00 0.00 38.69 2.59
3033 5021 3.253677 CGCTCTACCACCATTAGGAGTAG 59.746 52.174 0.00 0.00 42.01 2.57
3034 5022 4.216708 GCTCTACCACCATTAGGAGTAGT 58.783 47.826 12.63 0.00 41.68 2.73
3079 5067 4.791411 GCACCTGATCGAGTAGAAGATCAC 60.791 50.000 4.26 0.00 45.61 3.06
3087 5075 3.280295 GAGTAGAAGATCACGGACCTCA 58.720 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.761767 TGGGAAGCGCTATGTTACAGTA 59.238 45.455 12.05 0.00 0.00 2.74
1 2 1.553248 TGGGAAGCGCTATGTTACAGT 59.447 47.619 12.05 0.00 0.00 3.55
2 3 2.309528 TGGGAAGCGCTATGTTACAG 57.690 50.000 12.05 0.00 0.00 2.74
3 4 2.235155 TCTTGGGAAGCGCTATGTTACA 59.765 45.455 12.05 1.24 0.00 2.41
4 5 2.901249 TCTTGGGAAGCGCTATGTTAC 58.099 47.619 12.05 0.00 0.00 2.50
5 6 3.620427 TTCTTGGGAAGCGCTATGTTA 57.380 42.857 12.05 0.00 0.00 2.41
6 7 2.489938 TTCTTGGGAAGCGCTATGTT 57.510 45.000 12.05 0.00 0.00 2.71
7 8 2.359900 CTTTCTTGGGAAGCGCTATGT 58.640 47.619 12.05 0.00 32.61 2.29
8 9 1.672881 CCTTTCTTGGGAAGCGCTATG 59.327 52.381 12.05 0.00 32.61 2.23
9 10 1.559682 TCCTTTCTTGGGAAGCGCTAT 59.440 47.619 12.05 0.00 32.61 2.97
10 11 0.981183 TCCTTTCTTGGGAAGCGCTA 59.019 50.000 12.05 0.00 32.61 4.26
11 12 0.329596 ATCCTTTCTTGGGAAGCGCT 59.670 50.000 2.64 2.64 36.37 5.92
12 13 0.453390 CATCCTTTCTTGGGAAGCGC 59.547 55.000 0.00 0.00 36.37 5.92
13 14 2.012673 CTCATCCTTTCTTGGGAAGCG 58.987 52.381 0.00 0.00 36.37 4.68
14 15 3.013219 GACTCATCCTTTCTTGGGAAGC 58.987 50.000 0.00 0.00 36.37 3.86
15 16 4.566426 AGACTCATCCTTTCTTGGGAAG 57.434 45.455 0.00 0.00 36.37 3.46
16 17 4.844085 TGTAGACTCATCCTTTCTTGGGAA 59.156 41.667 0.00 0.00 36.37 3.97
17 18 4.425772 TGTAGACTCATCCTTTCTTGGGA 58.574 43.478 0.00 0.00 37.26 4.37
18 19 4.826274 TGTAGACTCATCCTTTCTTGGG 57.174 45.455 0.00 0.00 0.00 4.12
19 20 4.633565 GCTTGTAGACTCATCCTTTCTTGG 59.366 45.833 0.00 0.00 0.00 3.61
20 21 5.486526 AGCTTGTAGACTCATCCTTTCTTG 58.513 41.667 0.00 0.00 0.00 3.02
21 22 5.753721 AGCTTGTAGACTCATCCTTTCTT 57.246 39.130 0.00 0.00 0.00 2.52
22 23 6.859112 TTAGCTTGTAGACTCATCCTTTCT 57.141 37.500 0.00 0.00 0.00 2.52
23 24 9.601217 TTTATTAGCTTGTAGACTCATCCTTTC 57.399 33.333 0.00 0.00 0.00 2.62
25 26 9.553064 CATTTATTAGCTTGTAGACTCATCCTT 57.447 33.333 0.00 0.00 0.00 3.36
26 27 8.928448 TCATTTATTAGCTTGTAGACTCATCCT 58.072 33.333 0.00 0.00 0.00 3.24
27 28 9.547753 TTCATTTATTAGCTTGTAGACTCATCC 57.452 33.333 0.00 0.00 0.00 3.51
30 31 9.587772 GACTTCATTTATTAGCTTGTAGACTCA 57.412 33.333 0.00 0.00 0.00 3.41
31 32 9.587772 TGACTTCATTTATTAGCTTGTAGACTC 57.412 33.333 0.00 0.00 0.00 3.36
69 70 9.547753 CTCCATAGTGCAAAGTAACATAATAGT 57.452 33.333 0.00 0.00 0.00 2.12
70 71 9.764363 TCTCCATAGTGCAAAGTAACATAATAG 57.236 33.333 0.00 0.00 0.00 1.73
73 74 9.764363 CTATCTCCATAGTGCAAAGTAACATAA 57.236 33.333 0.00 0.00 0.00 1.90
74 75 8.924303 ACTATCTCCATAGTGCAAAGTAACATA 58.076 33.333 0.00 0.00 43.21 2.29
75 76 7.796054 ACTATCTCCATAGTGCAAAGTAACAT 58.204 34.615 0.00 0.00 43.21 2.71
76 77 7.182817 ACTATCTCCATAGTGCAAAGTAACA 57.817 36.000 0.00 0.00 43.21 2.41
77 78 9.032420 GTTACTATCTCCATAGTGCAAAGTAAC 57.968 37.037 5.12 0.00 44.33 2.50
78 79 8.978472 AGTTACTATCTCCATAGTGCAAAGTAA 58.022 33.333 5.12 0.00 44.33 2.24
79 80 8.534954 AGTTACTATCTCCATAGTGCAAAGTA 57.465 34.615 5.12 0.00 44.33 2.24
80 81 7.425224 AGTTACTATCTCCATAGTGCAAAGT 57.575 36.000 5.12 0.00 44.33 2.66
81 82 9.469807 CTAAGTTACTATCTCCATAGTGCAAAG 57.530 37.037 5.12 0.00 44.33 2.77
82 83 9.197306 TCTAAGTTACTATCTCCATAGTGCAAA 57.803 33.333 5.12 0.00 44.33 3.68
83 84 8.630917 GTCTAAGTTACTATCTCCATAGTGCAA 58.369 37.037 5.12 0.00 44.33 4.08
84 85 7.999545 AGTCTAAGTTACTATCTCCATAGTGCA 59.000 37.037 5.12 0.00 44.33 4.57
85 86 8.398878 AGTCTAAGTTACTATCTCCATAGTGC 57.601 38.462 5.12 0.00 44.33 4.40
90 91 9.563748 GACACTAGTCTAAGTTACTATCTCCAT 57.436 37.037 0.00 0.00 41.64 3.41
91 92 8.546322 TGACACTAGTCTAAGTTACTATCTCCA 58.454 37.037 0.00 0.00 45.20 3.86
92 93 8.961294 TGACACTAGTCTAAGTTACTATCTCC 57.039 38.462 0.00 0.00 45.20 3.71
97 98 9.623000 TGCATATGACACTAGTCTAAGTTACTA 57.377 33.333 6.97 0.00 45.20 1.82
98 99 8.521170 TGCATATGACACTAGTCTAAGTTACT 57.479 34.615 6.97 0.00 45.20 2.24
99 100 9.186323 CATGCATATGACACTAGTCTAAGTTAC 57.814 37.037 6.97 0.00 45.20 2.50
100 101 9.131791 TCATGCATATGACACTAGTCTAAGTTA 57.868 33.333 6.97 0.00 45.20 2.24
101 102 8.011844 TCATGCATATGACACTAGTCTAAGTT 57.988 34.615 6.97 0.00 45.20 2.66
102 103 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
119 120 8.361139 GGAGTAACTTATACTAGTGTCATGCAT 58.639 37.037 5.39 0.00 0.00 3.96
120 121 7.201884 GGGAGTAACTTATACTAGTGTCATGCA 60.202 40.741 5.39 0.00 0.00 3.96
121 122 7.146648 GGGAGTAACTTATACTAGTGTCATGC 58.853 42.308 5.39 0.00 0.00 4.06
122 123 7.287005 TGGGGAGTAACTTATACTAGTGTCATG 59.713 40.741 5.39 0.00 0.00 3.07
123 124 7.287235 GTGGGGAGTAACTTATACTAGTGTCAT 59.713 40.741 5.39 0.00 0.00 3.06
124 125 6.604795 GTGGGGAGTAACTTATACTAGTGTCA 59.395 42.308 5.39 0.00 0.00 3.58
125 126 6.832900 AGTGGGGAGTAACTTATACTAGTGTC 59.167 42.308 5.39 0.00 0.00 3.67
126 127 6.739664 AGTGGGGAGTAACTTATACTAGTGT 58.260 40.000 5.39 0.39 0.00 3.55
127 128 8.794553 CATAGTGGGGAGTAACTTATACTAGTG 58.205 40.741 5.39 0.00 0.00 2.74
128 129 8.730948 TCATAGTGGGGAGTAACTTATACTAGT 58.269 37.037 0.00 0.00 0.00 2.57
129 130 9.012161 GTCATAGTGGGGAGTAACTTATACTAG 57.988 40.741 0.00 0.00 0.00 2.57
130 131 7.946776 GGTCATAGTGGGGAGTAACTTATACTA 59.053 40.741 0.00 0.00 0.00 1.82
131 132 6.781507 GGTCATAGTGGGGAGTAACTTATACT 59.218 42.308 0.00 0.00 0.00 2.12
132 133 6.552350 TGGTCATAGTGGGGAGTAACTTATAC 59.448 42.308 0.00 0.00 0.00 1.47
133 134 6.685541 TGGTCATAGTGGGGAGTAACTTATA 58.314 40.000 0.00 0.00 0.00 0.98
134 135 5.535029 TGGTCATAGTGGGGAGTAACTTAT 58.465 41.667 0.00 0.00 0.00 1.73
135 136 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
136 137 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
137 138 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
138 139 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
139 140 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
140 141 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
141 142 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
142 143 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
143 144 0.639943 TAGGCTGGTCATAGTGGGGA 59.360 55.000 0.00 0.00 0.00 4.81
144 145 1.507140 TTAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
145 146 2.158755 CCTTTAGGCTGGTCATAGTGGG 60.159 54.545 0.00 0.00 0.00 4.61
146 147 3.199880 CCTTTAGGCTGGTCATAGTGG 57.800 52.381 0.00 0.00 0.00 4.00
159 160 3.888930 TGTTTTCCTTCAGTGCCTTTAGG 59.111 43.478 0.00 0.00 38.53 2.69
169 170 6.688637 TGATATGAGCATGTTTTCCTTCAG 57.311 37.500 0.00 0.00 0.00 3.02
172 173 7.201884 CCTTGATGATATGAGCATGTTTTCCTT 60.202 37.037 0.00 0.00 0.00 3.36
240 241 7.801547 ATTCGAAACTCTACGTTCGAAAATA 57.198 32.000 20.36 2.85 42.48 1.40
246 247 6.075519 CCTTGATATTCGAAACTCTACGTTCG 60.076 42.308 0.00 0.00 33.90 3.95
273 274 1.795889 GCGTATCTAGCGAGGCTATGC 60.796 57.143 3.14 3.14 40.54 3.14
292 293 0.169009 CCAACTGAAAGGCTAAGCGC 59.831 55.000 0.00 0.00 39.30 5.92
301 565 4.282068 CAAACATGACGACCAACTGAAAG 58.718 43.478 0.00 0.00 42.29 2.62
315 579 2.948979 ACGTTGAAGAAGCCAAACATGA 59.051 40.909 0.00 0.00 0.00 3.07
452 1098 9.628500 GGTCCAACTAATGAATTAATACTCCTT 57.372 33.333 0.00 0.00 0.00 3.36
454 1100 8.974060 TGGTCCAACTAATGAATTAATACTCC 57.026 34.615 0.00 0.00 0.00 3.85
459 1105 7.893302 TGGTCTTGGTCCAACTAATGAATTAAT 59.107 33.333 0.00 0.00 31.50 1.40
460 1106 7.235079 TGGTCTTGGTCCAACTAATGAATTAA 58.765 34.615 0.00 0.00 31.50 1.40
461 1107 6.785076 TGGTCTTGGTCCAACTAATGAATTA 58.215 36.000 0.00 0.00 31.50 1.40
462 1108 5.640147 TGGTCTTGGTCCAACTAATGAATT 58.360 37.500 0.00 0.00 31.50 2.17
505 1152 6.128007 TGCTTTAATTCTCCTTCACGGATTTC 60.128 38.462 0.00 0.00 42.12 2.17
508 1155 4.636206 GTGCTTTAATTCTCCTTCACGGAT 59.364 41.667 0.00 0.00 42.12 4.18
509 1156 4.000988 GTGCTTTAATTCTCCTTCACGGA 58.999 43.478 0.00 0.00 40.30 4.69
510 1157 3.127030 GGTGCTTTAATTCTCCTTCACGG 59.873 47.826 0.00 0.00 0.00 4.94
511 1158 3.751175 TGGTGCTTTAATTCTCCTTCACG 59.249 43.478 0.00 0.00 0.00 4.35
512 1159 5.904362 ATGGTGCTTTAATTCTCCTTCAC 57.096 39.130 0.00 0.00 0.00 3.18
513 1160 6.916360 AAATGGTGCTTTAATTCTCCTTCA 57.084 33.333 0.00 0.00 0.00 3.02
544 1193 4.778842 ATCGTCACATCGTATGCTTTTC 57.221 40.909 0.00 0.00 0.00 2.29
545 1194 5.579119 TGTAATCGTCACATCGTATGCTTTT 59.421 36.000 0.00 0.00 0.00 2.27
556 1205 3.678056 AGTGGTGTGTAATCGTCACAT 57.322 42.857 2.23 0.00 45.43 3.21
558 1207 3.183775 GTCAAGTGGTGTGTAATCGTCAC 59.816 47.826 0.00 0.00 36.48 3.67
577 1257 4.930696 TCCCTGTTCATACTAGTCAGTCA 58.069 43.478 0.00 0.00 36.14 3.41
587 1267 4.263594 TGTTAACCCCTTCCCTGTTCATAC 60.264 45.833 2.48 0.00 0.00 2.39
616 1299 2.262211 GGCATTCAAGGATCGTTTTGC 58.738 47.619 14.52 14.52 0.00 3.68
698 1392 3.233507 CCGGATTGGATTGGATTGGATT 58.766 45.455 0.00 0.00 42.00 3.01
699 1393 2.491455 CCCGGATTGGATTGGATTGGAT 60.491 50.000 0.73 0.00 42.00 3.41
739 1433 3.181469 TGGTCTACACAGGTGTTTCACTC 60.181 47.826 10.70 1.63 41.83 3.51
896 1634 6.350949 CGGAGGAAGAAGAAGAAGAAGAAGAT 60.351 42.308 0.00 0.00 0.00 2.40
920 1666 1.718396 CATGGACGGATCATGGATCG 58.282 55.000 0.00 0.00 39.72 3.69
990 1767 2.338015 GCACTGCATGTCCACCTGG 61.338 63.158 0.00 0.00 0.00 4.45
1076 1853 1.062258 GATGTGCAAATGCGTTGGTG 58.938 50.000 0.00 0.00 45.83 4.17
1094 1871 3.776417 TCATCATGTCATGTCAGGAAGGA 59.224 43.478 11.10 9.18 32.10 3.36
1103 1880 3.194329 ACGAGAGTGTCATCATGTCATGT 59.806 43.478 12.54 0.00 46.97 3.21
1120 1897 6.817765 AAATAGAGGCAAAATCAAACGAGA 57.182 33.333 0.00 0.00 0.00 4.04
1121 1898 7.308435 AGAAAATAGAGGCAAAATCAAACGAG 58.692 34.615 0.00 0.00 0.00 4.18
1123 1900 6.528072 GGAGAAAATAGAGGCAAAATCAAACG 59.472 38.462 0.00 0.00 0.00 3.60
1124 1901 6.813649 GGGAGAAAATAGAGGCAAAATCAAAC 59.186 38.462 0.00 0.00 0.00 2.93
1125 1902 6.725834 AGGGAGAAAATAGAGGCAAAATCAAA 59.274 34.615 0.00 0.00 0.00 2.69
1126 1903 6.153340 CAGGGAGAAAATAGAGGCAAAATCAA 59.847 38.462 0.00 0.00 0.00 2.57
1128 1905 5.888161 TCAGGGAGAAAATAGAGGCAAAATC 59.112 40.000 0.00 0.00 0.00 2.17
1129 1906 5.831103 TCAGGGAGAAAATAGAGGCAAAAT 58.169 37.500 0.00 0.00 0.00 1.82
1159 1936 1.535462 GGGTGTCACCGTCAATCAAAG 59.465 52.381 15.93 0.00 39.83 2.77
1172 1949 3.006728 GGATGTCCCCGGGTGTCA 61.007 66.667 21.85 15.50 0.00 3.58
1184 1961 4.057432 CGAAAACCAAGCAAAATGGATGT 58.943 39.130 0.00 0.00 40.56 3.06
1190 1967 3.120041 CGAACCGAAAACCAAGCAAAAT 58.880 40.909 0.00 0.00 0.00 1.82
1227 2005 4.404098 ATTGACGTCCCCCACCGC 62.404 66.667 14.12 0.00 0.00 5.68
1242 2020 4.740822 GGCCACGACCCCAGCATT 62.741 66.667 0.00 0.00 0.00 3.56
1378 2161 8.035984 GGTAGCACTAGAGAAAAACAAGATACT 58.964 37.037 0.00 0.00 0.00 2.12
1379 2162 8.035984 AGGTAGCACTAGAGAAAAACAAGATAC 58.964 37.037 0.00 0.00 0.00 2.24
1390 2173 5.952347 TCAATCTGAAGGTAGCACTAGAGAA 59.048 40.000 0.00 0.00 0.00 2.87
1427 2247 0.463654 TGACACAGAACACTGGTGGC 60.464 55.000 5.70 0.00 36.12 5.01
1466 2292 6.481954 ACGGAACATATCAAACTTCAGAAC 57.518 37.500 0.00 0.00 0.00 3.01
1510 2382 3.313526 GGCGTGCATTTGATCTCTGTATT 59.686 43.478 0.00 0.00 0.00 1.89
1511 2383 2.874701 GGCGTGCATTTGATCTCTGTAT 59.125 45.455 0.00 0.00 0.00 2.29
1512 2384 2.279741 GGCGTGCATTTGATCTCTGTA 58.720 47.619 0.00 0.00 0.00 2.74
1513 2385 1.089920 GGCGTGCATTTGATCTCTGT 58.910 50.000 0.00 0.00 0.00 3.41
1514 2386 1.089112 TGGCGTGCATTTGATCTCTG 58.911 50.000 0.00 0.00 0.00 3.35
1515 2387 1.470098 GTTGGCGTGCATTTGATCTCT 59.530 47.619 0.00 0.00 0.00 3.10
1516 2388 1.199789 TGTTGGCGTGCATTTGATCTC 59.800 47.619 0.00 0.00 0.00 2.75
1517 2389 1.068333 GTGTTGGCGTGCATTTGATCT 60.068 47.619 0.00 0.00 0.00 2.75
1518 2390 1.339711 GTGTTGGCGTGCATTTGATC 58.660 50.000 0.00 0.00 0.00 2.92
1519 2391 0.038343 GGTGTTGGCGTGCATTTGAT 60.038 50.000 0.00 0.00 0.00 2.57
1520 2392 1.361993 GGTGTTGGCGTGCATTTGA 59.638 52.632 0.00 0.00 0.00 2.69
1521 2393 1.067084 TGGTGTTGGCGTGCATTTG 59.933 52.632 0.00 0.00 0.00 2.32
1522 2394 1.067250 GTGGTGTTGGCGTGCATTT 59.933 52.632 0.00 0.00 0.00 2.32
1523 2395 2.124060 TGTGGTGTTGGCGTGCATT 61.124 52.632 0.00 0.00 0.00 3.56
1524 2396 2.518112 TGTGGTGTTGGCGTGCAT 60.518 55.556 0.00 0.00 0.00 3.96
1525 2397 3.513438 GTGTGGTGTTGGCGTGCA 61.513 61.111 0.00 0.00 0.00 4.57
1526 2398 3.513438 TGTGTGGTGTTGGCGTGC 61.513 61.111 0.00 0.00 0.00 5.34
1527 2399 2.402572 TGTGTGTGGTGTTGGCGTG 61.403 57.895 0.00 0.00 0.00 5.34
1528 2400 2.045829 TGTGTGTGGTGTTGGCGT 60.046 55.556 0.00 0.00 0.00 5.68
1529 2401 2.407210 GTGTGTGTGGTGTTGGCG 59.593 61.111 0.00 0.00 0.00 5.69
1530 2402 2.781158 GGGTGTGTGTGGTGTTGGC 61.781 63.158 0.00 0.00 0.00 4.52
1531 2403 0.967887 TTGGGTGTGTGTGGTGTTGG 60.968 55.000 0.00 0.00 0.00 3.77
1532 2404 0.455410 CTTGGGTGTGTGTGGTGTTG 59.545 55.000 0.00 0.00 0.00 3.33
1533 2405 0.682855 CCTTGGGTGTGTGTGGTGTT 60.683 55.000 0.00 0.00 0.00 3.32
1534 2406 1.077068 CCTTGGGTGTGTGTGGTGT 60.077 57.895 0.00 0.00 0.00 4.16
1535 2407 2.489275 GCCTTGGGTGTGTGTGGTG 61.489 63.158 0.00 0.00 0.00 4.17
1536 2408 2.123897 GCCTTGGGTGTGTGTGGT 60.124 61.111 0.00 0.00 0.00 4.16
1537 2409 2.123939 TGCCTTGGGTGTGTGTGG 60.124 61.111 0.00 0.00 0.00 4.17
1538 2410 2.195567 CCTGCCTTGGGTGTGTGTG 61.196 63.158 0.00 0.00 0.00 3.82
1539 2411 1.719063 ATCCTGCCTTGGGTGTGTGT 61.719 55.000 0.00 0.00 0.00 3.72
1540 2412 0.327924 TATCCTGCCTTGGGTGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
1541 2413 0.328258 GTATCCTGCCTTGGGTGTGT 59.672 55.000 0.00 0.00 0.00 3.72
1542 2414 0.327924 TGTATCCTGCCTTGGGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
1543 2415 0.620556 CTGTATCCTGCCTTGGGTGT 59.379 55.000 0.00 0.00 0.00 4.16
1544 2416 0.911769 TCTGTATCCTGCCTTGGGTG 59.088 55.000 0.00 0.00 0.00 4.61
1545 2417 1.207791 CTCTGTATCCTGCCTTGGGT 58.792 55.000 0.00 0.00 0.00 4.51
1546 2418 1.500474 TCTCTGTATCCTGCCTTGGG 58.500 55.000 0.00 0.00 0.00 4.12
1547 2419 2.702478 TGATCTCTGTATCCTGCCTTGG 59.298 50.000 0.00 0.00 0.00 3.61
1548 2420 4.412796 TTGATCTCTGTATCCTGCCTTG 57.587 45.455 0.00 0.00 0.00 3.61
1549 2421 5.643421 ATTTGATCTCTGTATCCTGCCTT 57.357 39.130 0.00 0.00 0.00 4.35
1550 2422 5.374921 CAATTTGATCTCTGTATCCTGCCT 58.625 41.667 0.00 0.00 0.00 4.75
1551 2423 4.023365 GCAATTTGATCTCTGTATCCTGCC 60.023 45.833 0.00 0.00 0.00 4.85
1552 2424 4.577693 TGCAATTTGATCTCTGTATCCTGC 59.422 41.667 0.00 0.00 0.00 4.85
1553 2425 6.485648 TCATGCAATTTGATCTCTGTATCCTG 59.514 38.462 0.00 0.00 0.00 3.86
1554 2426 6.598503 TCATGCAATTTGATCTCTGTATCCT 58.401 36.000 0.00 0.00 0.00 3.24
1555 2427 6.872628 TCATGCAATTTGATCTCTGTATCC 57.127 37.500 0.00 0.00 0.00 2.59
1591 2534 6.351711 ACGGTTTTATACCCATAAGTTCTCC 58.648 40.000 0.00 0.00 44.70 3.71
1602 2545 8.962884 TCTTCCTTTATAACGGTTTTATACCC 57.037 34.615 7.80 0.00 44.70 3.69
1617 2560 7.810260 ACCTGCAGATTTATCTCTTCCTTTAT 58.190 34.615 17.39 0.00 34.22 1.40
1622 2565 4.141620 TGGACCTGCAGATTTATCTCTTCC 60.142 45.833 17.39 5.31 34.22 3.46
1649 2592 9.897744 TGTAAAATCTGTCAATCAAATTCACTC 57.102 29.630 0.00 0.00 0.00 3.51
1716 2661 3.006537 CAGGTTTAGTCCGAGTTGAGGAA 59.993 47.826 0.00 0.00 39.84 3.36
1720 2665 1.968493 AGCAGGTTTAGTCCGAGTTGA 59.032 47.619 0.00 0.00 0.00 3.18
1727 2672 4.320275 GCAAACAAGTAGCAGGTTTAGTCC 60.320 45.833 0.00 0.00 33.72 3.85
1737 2682 5.512753 TCATTTTCTGCAAACAAGTAGCA 57.487 34.783 0.00 0.00 36.72 3.49
1767 2713 0.401738 TTCTTGAACTGCCTCCCAGG 59.598 55.000 0.00 0.00 46.14 4.45
1774 2720 3.067106 TGTTCTCGATTCTTGAACTGCC 58.933 45.455 13.58 0.00 40.27 4.85
1787 2733 2.030185 GCTGAAGGTGTAGTGTTCTCGA 60.030 50.000 0.00 0.00 0.00 4.04
1790 2736 2.300437 GGAGCTGAAGGTGTAGTGTTCT 59.700 50.000 0.00 0.00 0.00 3.01
1797 2743 1.972198 CGGTGGAGCTGAAGGTGTA 59.028 57.895 0.00 0.00 0.00 2.90
1865 2811 2.512515 GATGCAGGTCCTCGTGGC 60.513 66.667 0.00 0.00 0.00 5.01
2300 3372 6.929606 ACCAGTGAACATCTACAGAGTAAAAC 59.070 38.462 0.00 0.00 0.00 2.43
2414 3673 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2416 3675 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
2417 3676 1.437625 TCTGTGTGTGTGTGTGTGTG 58.562 50.000 0.00 0.00 0.00 3.82
2418 3677 2.009051 CATCTGTGTGTGTGTGTGTGT 58.991 47.619 0.00 0.00 0.00 3.72
2419 3678 2.030823 GTCATCTGTGTGTGTGTGTGTG 59.969 50.000 0.00 0.00 0.00 3.82
2568 4544 2.184322 GAGCGGGCGATCTTGACA 59.816 61.111 0.00 0.00 0.00 3.58
2609 4585 1.818674 CAAAAGGGACACATACCTGCC 59.181 52.381 0.00 0.00 38.81 4.85
2679 4655 6.276832 AGAAGTGGAATCATTTGGTCATTG 57.723 37.500 0.00 0.00 0.00 2.82
2731 4707 0.868406 CTTCTTGCCCGTTCACAGTC 59.132 55.000 0.00 0.00 0.00 3.51
2740 4716 2.643551 ACACATAATCCTTCTTGCCCG 58.356 47.619 0.00 0.00 0.00 6.13
2741 4717 4.781934 AGTACACATAATCCTTCTTGCCC 58.218 43.478 0.00 0.00 0.00 5.36
2742 4718 5.525378 CAGAGTACACATAATCCTTCTTGCC 59.475 44.000 0.00 0.00 0.00 4.52
2754 4730 8.683615 CATTCTGGTAAGTACAGAGTACACATA 58.316 37.037 9.68 0.00 44.91 2.29
2880 4863 6.633500 CAAGTTGTGGAAATAGGAGACAAA 57.367 37.500 0.00 0.00 0.00 2.83
2902 4885 4.196193 CAAACAAGTAGTGGTTCAGTCCA 58.804 43.478 0.00 0.00 33.71 4.02
2908 4891 4.893424 TTCTGCAAACAAGTAGTGGTTC 57.107 40.909 0.00 0.00 33.71 3.62
2953 4941 0.949105 CGTGTCCCCGGTTCTTGAAG 60.949 60.000 0.00 0.00 0.00 3.02
3005 4993 1.264749 ATGGTGGTAGAGCGCTGGAA 61.265 55.000 18.48 0.00 0.00 3.53
3032 5020 0.962489 CCTCGTGGTCAGACTGAACT 59.038 55.000 20.91 0.00 34.53 3.01
3033 5021 0.959553 TCCTCGTGGTCAGACTGAAC 59.040 55.000 13.89 13.89 33.88 3.18
3034 5022 1.819288 GATCCTCGTGGTCAGACTGAA 59.181 52.381 6.76 0.00 34.23 3.02


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

AutoCloner maintained by Alex Coulton.