Multiple sequence alignment - TraesCS1D01G359100

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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 TraesCS1D01G359100 chr1D 100.000 3596 0 0 1 3596 442524529 442528124 0.000000e+00 6641.0
1 TraesCS1D01G359100 chr1A 93.674 2972 130 30 658 3596 536069099 536066153 0.000000e+00 4394.0
2 TraesCS1D01G359100 chr1A 95.582 249 10 1 320 568 536069370 536069123 7.230000e-107 398.0
3 TraesCS1D01G359100 chr1A 93.714 175 9 2 150 322 532321453 532321279 9.900000e-66 261.0
4 TraesCS1D01G359100 chr1B 93.453 2795 110 31 833 3596 602004772 602002020 0.000000e+00 4080.0
5 TraesCS1D01G359100 chr3B 93.785 177 9 2 146 320 795441295 795441119 7.660000e-67 265.0
6 TraesCS1D01G359100 chr3B 93.642 173 9 2 146 316 49950017 49949845 1.280000e-64 257.0
7 TraesCS1D01G359100 chr3B 92.697 178 11 2 146 321 235884179 235884002 4.610000e-64 255.0
8 TraesCS1D01G359100 chr3B 94.545 110 5 1 41 149 49950066 49949957 6.170000e-38 169.0
9 TraesCS1D01G359100 chr3B 94.545 110 5 1 43 151 523158161 523158270 6.170000e-38 169.0
10 TraesCS1D01G359100 chr5B 93.750 176 9 2 146 320 146826716 146826542 2.750000e-66 263.0
11 TraesCS1D01G359100 chr5B 94.444 108 6 0 42 149 146826764 146826657 2.220000e-37 167.0
12 TraesCS1D01G359100 chr5A 93.714 175 9 2 150 322 675426261 675426087 9.900000e-66 261.0
13 TraesCS1D01G359100 chr2A 94.186 172 8 2 150 319 101853012 101853183 9.900000e-66 261.0
14 TraesCS1D01G359100 chr7B 92.265 181 12 2 150 328 491109266 491109086 4.610000e-64 255.0
15 TraesCS1D01G359100 chr4A 92.222 180 12 2 150 327 323290640 323290461 1.660000e-63 254.0
16 TraesCS1D01G359100 chr4A 78.488 172 27 8 628 791 685783966 685783797 1.770000e-18 104.0
17 TraesCS1D01G359100 chr5D 81.227 277 36 14 37 304 352696780 352697049 3.640000e-50 209.0
18 TraesCS1D01G359100 chr5D 95.192 104 5 0 43 146 365080353 365080456 7.990000e-37 165.0
19 TraesCS1D01G359100 chr5D 78.075 187 33 7 609 788 6688749 6688934 1.060000e-20 111.0
20 TraesCS1D01G359100 chr5D 78.102 137 24 4 659 789 520858570 520858434 8.270000e-12 82.4
21 TraesCS1D01G359100 chr2B 94.690 113 4 2 40 150 711446790 711446902 1.330000e-39 174.0
22 TraesCS1D01G359100 chr2B 94.545 110 5 1 41 149 800481025 800480916 6.170000e-38 169.0
23 TraesCS1D01G359100 chr2B 74.611 193 43 4 604 790 770277142 770277334 2.980000e-11 80.5
24 TraesCS1D01G359100 chr4B 92.982 114 6 2 38 149 626017106 626017219 7.990000e-37 165.0
25 TraesCS1D01G359100 chr2D 94.444 108 5 1 43 149 298939807 298939700 7.990000e-37 165.0
26 TraesCS1D01G359100 chr2D 77.404 208 31 13 595 791 627929518 627929316 3.800000e-20 110.0
27 TraesCS1D01G359100 chr2D 76.442 208 40 8 591 791 59458257 59458462 1.770000e-18 104.0
28 TraesCS1D01G359100 chr3A 84.337 166 18 6 628 786 146558746 146558582 4.810000e-34 156.0
29 TraesCS1D01G359100 chr4D 78.537 205 37 4 603 800 111132070 111131866 1.050000e-25 128.0
30 TraesCS1D01G359100 chr7A 81.690 142 18 7 657 791 515172794 515172934 1.060000e-20 111.0
31 TraesCS1D01G359100 chr7A 76.142 197 38 6 603 791 464569558 464569363 1.060000e-15 95.3
32 TraesCS1D01G359100 chr7D 77.000 200 36 6 604 800 386350774 386350966 4.910000e-19 106.0
33 TraesCS1D01G359100 chr6A 87.500 64 8 0 728 791 453860549 453860612 1.380000e-09 75.0


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 TraesCS1D01G359100 chr1D 442524529 442528124 3595 False 6641 6641 100.000 1 3596 1 chr1D.!!$F1 3595
1 TraesCS1D01G359100 chr1A 536066153 536069370 3217 True 2396 4394 94.628 320 3596 2 chr1A.!!$R2 3276
2 TraesCS1D01G359100 chr1B 602002020 602004772 2752 True 4080 4080 93.453 833 3596 1 chr1B.!!$R1 2763

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
597 598 0.037734 GGAAACCCATCACCCGTTCT 59.962 55.0 0.00 0.0 0.00 3.01 F
788 789 0.108138 ACTATTCTGGTGCGCTGGTC 60.108 55.0 9.73 0.0 0.00 4.02 F
1998 2009 0.039764 ACGTCCTGGAGGAGATCACA 59.960 55.0 22.22 0.0 46.49 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1755 0.108329 ACGGCTTCGTGGATAACCTG 60.108 55.0 0.00 0.0 46.32 4.00 R
2553 2564 0.109735 TCTTGTCTGTAGCTGCGTCG 60.110 55.0 0.00 0.0 0.00 5.12 R
2821 2836 0.184933 TGGGACCCCACTGTTCAAAG 59.815 55.0 8.45 0.0 41.89 2.77 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
24 25 7.915293 TGAATATGACATTAACCGTCAAGTT 57.085 32.000 12.24 10.15 45.91 2.66
26 27 9.093970 TGAATATGACATTAACCGTCAAGTTAG 57.906 33.333 12.24 0.00 45.91 2.34
27 28 8.433421 AATATGACATTAACCGTCAAGTTAGG 57.567 34.615 12.24 0.00 45.91 2.69
28 29 4.571919 TGACATTAACCGTCAAGTTAGGG 58.428 43.478 7.01 0.00 40.34 3.53
29 30 4.283978 TGACATTAACCGTCAAGTTAGGGA 59.716 41.667 7.01 0.00 40.34 4.20
30 31 5.221682 TGACATTAACCGTCAAGTTAGGGAA 60.222 40.000 7.01 0.00 40.34 3.97
31 32 4.999311 ACATTAACCGTCAAGTTAGGGAAC 59.001 41.667 0.00 0.00 33.89 3.62
32 33 4.686191 TTAACCGTCAAGTTAGGGAACA 57.314 40.909 0.00 0.00 38.10 3.18
33 34 2.538512 ACCGTCAAGTTAGGGAACAC 57.461 50.000 0.00 0.00 38.10 3.32
34 35 1.071228 ACCGTCAAGTTAGGGAACACC 59.929 52.381 0.00 0.00 38.10 4.16
52 53 5.407407 ACACCTGTTCAATACTACCTCTG 57.593 43.478 0.00 0.00 0.00 3.35
53 54 4.838986 ACACCTGTTCAATACTACCTCTGT 59.161 41.667 0.00 0.00 0.00 3.41
54 55 5.047235 ACACCTGTTCAATACTACCTCTGTC 60.047 44.000 0.00 0.00 0.00 3.51
55 56 5.186021 CACCTGTTCAATACTACCTCTGTCT 59.814 44.000 0.00 0.00 0.00 3.41
56 57 5.780793 ACCTGTTCAATACTACCTCTGTCTT 59.219 40.000 0.00 0.00 0.00 3.01
57 58 6.102663 CCTGTTCAATACTACCTCTGTCTTG 58.897 44.000 0.00 0.00 0.00 3.02
58 59 6.037786 TGTTCAATACTACCTCTGTCTTGG 57.962 41.667 0.00 0.00 0.00 3.61
59 60 5.542635 TGTTCAATACTACCTCTGTCTTGGT 59.457 40.000 0.00 0.00 40.12 3.67
60 61 5.661056 TCAATACTACCTCTGTCTTGGTG 57.339 43.478 0.00 0.00 37.74 4.17
61 62 5.084519 TCAATACTACCTCTGTCTTGGTGT 58.915 41.667 0.00 0.00 37.74 4.16
62 63 6.250711 TCAATACTACCTCTGTCTTGGTGTA 58.749 40.000 0.00 0.00 37.74 2.90
63 64 6.895756 TCAATACTACCTCTGTCTTGGTGTAT 59.104 38.462 0.00 0.00 37.74 2.29
64 65 8.057011 TCAATACTACCTCTGTCTTGGTGTATA 58.943 37.037 0.00 0.00 37.74 1.47
65 66 8.692710 CAATACTACCTCTGTCTTGGTGTATAA 58.307 37.037 0.00 0.00 37.74 0.98
66 67 6.777213 ACTACCTCTGTCTTGGTGTATAAG 57.223 41.667 0.00 0.00 37.74 1.73
67 68 6.254522 ACTACCTCTGTCTTGGTGTATAAGT 58.745 40.000 0.00 0.00 37.74 2.24
68 69 5.662674 ACCTCTGTCTTGGTGTATAAGTC 57.337 43.478 0.00 0.00 34.90 3.01
69 70 5.084519 ACCTCTGTCTTGGTGTATAAGTCA 58.915 41.667 0.00 0.00 34.90 3.41
70 71 5.721960 ACCTCTGTCTTGGTGTATAAGTCAT 59.278 40.000 0.00 0.00 34.90 3.06
71 72 6.213600 ACCTCTGTCTTGGTGTATAAGTCATT 59.786 38.462 0.00 0.00 34.90 2.57
72 73 6.758886 CCTCTGTCTTGGTGTATAAGTCATTC 59.241 42.308 0.00 0.00 0.00 2.67
73 74 6.330278 TCTGTCTTGGTGTATAAGTCATTCG 58.670 40.000 0.00 0.00 0.00 3.34
74 75 6.032956 TGTCTTGGTGTATAAGTCATTCGT 57.967 37.500 0.00 0.00 0.00 3.85
75 76 5.867174 TGTCTTGGTGTATAAGTCATTCGTG 59.133 40.000 0.00 0.00 0.00 4.35
76 77 5.867716 GTCTTGGTGTATAAGTCATTCGTGT 59.132 40.000 0.00 0.00 0.00 4.49
77 78 7.031372 GTCTTGGTGTATAAGTCATTCGTGTA 58.969 38.462 0.00 0.00 0.00 2.90
78 79 7.220300 GTCTTGGTGTATAAGTCATTCGTGTAG 59.780 40.741 0.00 0.00 0.00 2.74
79 80 6.519679 TGGTGTATAAGTCATTCGTGTAGT 57.480 37.500 0.00 0.00 0.00 2.73
80 81 6.927416 TGGTGTATAAGTCATTCGTGTAGTT 58.073 36.000 0.00 0.00 0.00 2.24
81 82 7.380536 TGGTGTATAAGTCATTCGTGTAGTTT 58.619 34.615 0.00 0.00 0.00 2.66
82 83 7.874016 TGGTGTATAAGTCATTCGTGTAGTTTT 59.126 33.333 0.00 0.00 0.00 2.43
83 84 9.357652 GGTGTATAAGTCATTCGTGTAGTTTTA 57.642 33.333 0.00 0.00 0.00 1.52
85 86 9.577110 TGTATAAGTCATTCGTGTAGTTTTAGG 57.423 33.333 0.00 0.00 0.00 2.69
86 87 9.578439 GTATAAGTCATTCGTGTAGTTTTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
87 88 8.699283 ATAAGTCATTCGTGTAGTTTTAGGTC 57.301 34.615 0.00 0.00 0.00 3.85
88 89 5.159209 AGTCATTCGTGTAGTTTTAGGTCG 58.841 41.667 0.00 0.00 0.00 4.79
89 90 5.048504 AGTCATTCGTGTAGTTTTAGGTCGA 60.049 40.000 0.00 0.00 0.00 4.20
90 91 5.060200 GTCATTCGTGTAGTTTTAGGTCGAC 59.940 44.000 7.13 7.13 0.00 4.20
91 92 4.566545 TTCGTGTAGTTTTAGGTCGACA 57.433 40.909 18.91 0.00 0.00 4.35
92 93 4.566545 TCGTGTAGTTTTAGGTCGACAA 57.433 40.909 18.91 0.31 0.00 3.18
93 94 5.125100 TCGTGTAGTTTTAGGTCGACAAT 57.875 39.130 18.91 7.85 0.00 2.71
94 95 5.531634 TCGTGTAGTTTTAGGTCGACAATT 58.468 37.500 18.91 4.78 0.00 2.32
95 96 5.984926 TCGTGTAGTTTTAGGTCGACAATTT 59.015 36.000 18.91 2.13 0.00 1.82
96 97 7.144661 TCGTGTAGTTTTAGGTCGACAATTTA 58.855 34.615 18.91 1.12 0.00 1.40
97 98 7.651304 TCGTGTAGTTTTAGGTCGACAATTTAA 59.349 33.333 18.91 7.35 0.00 1.52
98 99 7.737311 CGTGTAGTTTTAGGTCGACAATTTAAC 59.263 37.037 18.91 13.49 0.00 2.01
99 100 8.768019 GTGTAGTTTTAGGTCGACAATTTAACT 58.232 33.333 18.91 19.05 0.00 2.24
100 101 9.979578 TGTAGTTTTAGGTCGACAATTTAACTA 57.020 29.630 18.91 18.16 0.00 2.24
103 104 9.939802 AGTTTTAGGTCGACAATTTAACTATCT 57.060 29.630 18.91 2.88 0.00 1.98
273 274 9.799106 ATATTTAATTCCTCAAATCGATGACCT 57.201 29.630 0.00 0.00 0.00 3.85
275 276 9.627123 ATTTAATTCCTCAAATCGATGACCTAA 57.373 29.630 0.00 0.00 0.00 2.69
276 277 9.456147 TTTAATTCCTCAAATCGATGACCTAAA 57.544 29.630 0.00 0.00 0.00 1.85
277 278 7.938140 AATTCCTCAAATCGATGACCTAAAA 57.062 32.000 0.00 0.00 0.00 1.52
278 279 6.737254 TTCCTCAAATCGATGACCTAAAAC 57.263 37.500 0.00 0.00 0.00 2.43
279 280 6.049955 TCCTCAAATCGATGACCTAAAACT 57.950 37.500 0.00 0.00 0.00 2.66
280 281 7.177832 TCCTCAAATCGATGACCTAAAACTA 57.822 36.000 0.00 0.00 0.00 2.24
281 282 7.039882 TCCTCAAATCGATGACCTAAAACTAC 58.960 38.462 0.00 0.00 0.00 2.73
282 283 6.019801 CCTCAAATCGATGACCTAAAACTACG 60.020 42.308 0.00 0.00 0.00 3.51
283 284 5.290158 TCAAATCGATGACCTAAAACTACGC 59.710 40.000 0.00 0.00 0.00 4.42
284 285 2.789208 TCGATGACCTAAAACTACGCG 58.211 47.619 3.53 3.53 0.00 6.01
285 286 2.419673 TCGATGACCTAAAACTACGCGA 59.580 45.455 15.93 0.00 0.00 5.87
286 287 3.119884 TCGATGACCTAAAACTACGCGAA 60.120 43.478 15.93 0.00 0.00 4.70
287 288 3.795101 CGATGACCTAAAACTACGCGAAT 59.205 43.478 15.93 0.00 0.00 3.34
288 289 4.317139 CGATGACCTAAAACTACGCGAATG 60.317 45.833 15.93 4.47 0.00 2.67
289 290 4.177165 TGACCTAAAACTACGCGAATGA 57.823 40.909 15.93 0.00 0.00 2.57
290 291 3.922240 TGACCTAAAACTACGCGAATGAC 59.078 43.478 15.93 0.00 0.00 3.06
291 292 4.171754 GACCTAAAACTACGCGAATGACT 58.828 43.478 15.93 0.00 0.00 3.41
292 293 4.563061 ACCTAAAACTACGCGAATGACTT 58.437 39.130 15.93 0.94 0.00 3.01
293 294 5.713025 ACCTAAAACTACGCGAATGACTTA 58.287 37.500 15.93 2.18 0.00 2.24
294 295 6.335777 ACCTAAAACTACGCGAATGACTTAT 58.664 36.000 15.93 0.00 0.00 1.73
295 296 7.483307 ACCTAAAACTACGCGAATGACTTATA 58.517 34.615 15.93 0.00 0.00 0.98
296 297 8.139989 ACCTAAAACTACGCGAATGACTTATAT 58.860 33.333 15.93 0.00 0.00 0.86
297 298 9.616634 CCTAAAACTACGCGAATGACTTATATA 57.383 33.333 15.93 0.00 0.00 0.86
299 300 7.864307 AAACTACGCGAATGACTTATATACC 57.136 36.000 15.93 0.00 0.00 2.73
300 301 5.625251 ACTACGCGAATGACTTATATACCG 58.375 41.667 15.93 0.00 0.00 4.02
301 302 3.829948 ACGCGAATGACTTATATACCGG 58.170 45.455 15.93 0.00 0.00 5.28
302 303 3.176708 CGCGAATGACTTATATACCGGG 58.823 50.000 6.32 0.00 0.00 5.73
303 304 3.119743 CGCGAATGACTTATATACCGGGA 60.120 47.826 6.32 0.00 0.00 5.14
304 305 4.171754 GCGAATGACTTATATACCGGGAC 58.828 47.826 6.32 0.00 0.00 4.46
305 306 4.321452 GCGAATGACTTATATACCGGGACA 60.321 45.833 6.32 0.00 0.00 4.02
306 307 5.399858 CGAATGACTTATATACCGGGACAG 58.600 45.833 6.32 0.00 0.00 3.51
307 308 5.182570 CGAATGACTTATATACCGGGACAGA 59.817 44.000 6.32 0.00 0.00 3.41
308 309 6.591750 AATGACTTATATACCGGGACAGAG 57.408 41.667 6.32 0.00 0.00 3.35
309 310 4.404640 TGACTTATATACCGGGACAGAGG 58.595 47.826 6.32 0.00 0.00 3.69
310 311 3.762823 GACTTATATACCGGGACAGAGGG 59.237 52.174 6.32 0.00 0.00 4.30
311 312 3.400322 ACTTATATACCGGGACAGAGGGA 59.600 47.826 6.32 0.00 0.00 4.20
312 313 2.606751 ATATACCGGGACAGAGGGAG 57.393 55.000 6.32 0.00 0.00 4.30
313 314 1.229131 TATACCGGGACAGAGGGAGT 58.771 55.000 6.32 0.00 0.00 3.85
314 315 1.229131 ATACCGGGACAGAGGGAGTA 58.771 55.000 6.32 0.00 0.00 2.59
315 316 0.549950 TACCGGGACAGAGGGAGTAG 59.450 60.000 6.32 0.00 0.00 2.57
316 317 1.306970 CCGGGACAGAGGGAGTAGT 59.693 63.158 0.00 0.00 0.00 2.73
317 318 0.549950 CCGGGACAGAGGGAGTAGTA 59.450 60.000 0.00 0.00 0.00 1.82
318 319 1.064166 CCGGGACAGAGGGAGTAGTAA 60.064 57.143 0.00 0.00 0.00 2.24
329 330 9.838339 ACAGAGGGAGTAGTAAATTTGAATATG 57.162 33.333 0.00 0.00 0.00 1.78
377 378 8.749354 AGAAAGAAAAGAACCACAATAACTGTT 58.251 29.630 0.00 0.00 35.47 3.16
419 420 8.959734 AATTAAGTTTGTAACTGCCGAATTAC 57.040 30.769 0.00 0.00 41.91 1.89
426 427 0.319083 ACTGCCGAATTACGTGACCA 59.681 50.000 0.00 0.00 40.78 4.02
430 431 2.029200 TGCCGAATTACGTGACCAGTAA 60.029 45.455 0.00 0.00 40.78 2.24
432 433 3.432933 GCCGAATTACGTGACCAGTAAAA 59.567 43.478 0.00 0.00 37.57 1.52
515 516 7.698130 GTGCACTTCAATGGTATTTAAGCTTAG 59.302 37.037 10.32 0.00 0.00 2.18
516 517 7.609918 TGCACTTCAATGGTATTTAAGCTTAGA 59.390 33.333 6.24 2.29 0.00 2.10
557 558 8.652290 AGAAACATAATCTACTAATCCTCACCC 58.348 37.037 0.00 0.00 0.00 4.61
558 559 7.931015 AACATAATCTACTAATCCTCACCCA 57.069 36.000 0.00 0.00 0.00 4.51
559 560 8.511748 AACATAATCTACTAATCCTCACCCAT 57.488 34.615 0.00 0.00 0.00 4.00
560 561 8.140112 ACATAATCTACTAATCCTCACCCATC 57.860 38.462 0.00 0.00 0.00 3.51
561 562 7.734865 ACATAATCTACTAATCCTCACCCATCA 59.265 37.037 0.00 0.00 0.00 3.07
562 563 6.426646 AATCTACTAATCCTCACCCATCAC 57.573 41.667 0.00 0.00 0.00 3.06
563 564 4.223953 TCTACTAATCCTCACCCATCACC 58.776 47.826 0.00 0.00 0.00 4.02
564 565 2.127708 ACTAATCCTCACCCATCACCC 58.872 52.381 0.00 0.00 0.00 4.61
565 566 1.070758 CTAATCCTCACCCATCACCCG 59.929 57.143 0.00 0.00 0.00 5.28
566 567 0.914417 AATCCTCACCCATCACCCGT 60.914 55.000 0.00 0.00 0.00 5.28
567 568 0.914417 ATCCTCACCCATCACCCGTT 60.914 55.000 0.00 0.00 0.00 4.44
568 569 1.131303 TCCTCACCCATCACCCGTTT 61.131 55.000 0.00 0.00 0.00 3.60
569 570 0.251165 CCTCACCCATCACCCGTTTT 60.251 55.000 0.00 0.00 0.00 2.43
570 571 1.616159 CTCACCCATCACCCGTTTTT 58.384 50.000 0.00 0.00 0.00 1.94
597 598 0.037734 GGAAACCCATCACCCGTTCT 59.962 55.000 0.00 0.00 0.00 3.01
602 603 1.746615 CCATCACCCGTTCTGGCTG 60.747 63.158 0.00 0.00 35.87 4.85
612 613 1.082690 GTTCTGGCTGTGCTTCTAGC 58.917 55.000 0.00 0.00 42.82 3.42
622 623 0.382158 TGCTTCTAGCGTCATCGGAG 59.618 55.000 0.00 0.00 46.26 4.63
624 625 1.862008 GCTTCTAGCGTCATCGGAGTG 60.862 57.143 0.00 0.00 37.56 3.51
625 626 1.402259 CTTCTAGCGTCATCGGAGTGT 59.598 52.381 0.00 0.00 37.56 3.55
628 629 2.548480 TCTAGCGTCATCGGAGTGTATG 59.452 50.000 0.00 0.00 37.56 2.39
629 630 1.103803 AGCGTCATCGGAGTGTATGT 58.896 50.000 0.00 0.00 37.56 2.29
631 632 1.840181 CGTCATCGGAGTGTATGTGG 58.160 55.000 0.00 0.00 0.00 4.17
632 633 1.404035 CGTCATCGGAGTGTATGTGGA 59.596 52.381 0.00 0.00 0.00 4.02
633 634 2.541794 CGTCATCGGAGTGTATGTGGAG 60.542 54.545 0.00 0.00 0.00 3.86
634 635 2.688446 GTCATCGGAGTGTATGTGGAGA 59.312 50.000 0.00 0.00 0.00 3.71
635 636 3.319405 GTCATCGGAGTGTATGTGGAGAT 59.681 47.826 0.00 0.00 0.00 2.75
636 637 3.960755 TCATCGGAGTGTATGTGGAGATT 59.039 43.478 0.00 0.00 0.00 2.40
637 638 4.405680 TCATCGGAGTGTATGTGGAGATTT 59.594 41.667 0.00 0.00 0.00 2.17
638 639 4.819105 TCGGAGTGTATGTGGAGATTTT 57.181 40.909 0.00 0.00 0.00 1.82
639 640 5.160607 TCGGAGTGTATGTGGAGATTTTT 57.839 39.130 0.00 0.00 0.00 1.94
640 641 5.175859 TCGGAGTGTATGTGGAGATTTTTC 58.824 41.667 0.00 0.00 0.00 2.29
641 642 5.046591 TCGGAGTGTATGTGGAGATTTTTCT 60.047 40.000 0.00 0.00 0.00 2.52
642 643 5.292101 CGGAGTGTATGTGGAGATTTTTCTC 59.708 44.000 0.00 0.00 36.08 2.87
654 655 6.337853 GAGATTTTTCTCCAGTGTATCGTG 57.662 41.667 0.00 0.00 0.00 4.35
655 656 4.631813 AGATTTTTCTCCAGTGTATCGTGC 59.368 41.667 0.00 0.00 0.00 5.34
656 657 1.990799 TTTCTCCAGTGTATCGTGCG 58.009 50.000 0.00 0.00 0.00 5.34
657 658 0.172578 TTCTCCAGTGTATCGTGCGG 59.827 55.000 0.00 0.00 0.00 5.69
658 659 1.226974 CTCCAGTGTATCGTGCGGG 60.227 63.158 0.00 0.00 0.00 6.13
659 660 1.663379 CTCCAGTGTATCGTGCGGGA 61.663 60.000 0.00 0.00 0.00 5.14
660 661 1.040893 TCCAGTGTATCGTGCGGGAT 61.041 55.000 0.00 0.00 0.00 3.85
661 662 0.179084 CCAGTGTATCGTGCGGGATT 60.179 55.000 0.00 0.00 0.00 3.01
662 663 1.209128 CAGTGTATCGTGCGGGATTC 58.791 55.000 0.00 0.00 0.00 2.52
663 664 0.248907 AGTGTATCGTGCGGGATTCG 60.249 55.000 0.00 0.00 42.76 3.34
664 665 1.066752 TGTATCGTGCGGGATTCGG 59.933 57.895 0.00 0.00 39.69 4.30
665 666 1.066918 GTATCGTGCGGGATTCGGT 59.933 57.895 0.00 0.00 39.69 4.69
666 667 0.938168 GTATCGTGCGGGATTCGGTC 60.938 60.000 0.00 0.00 39.69 4.79
667 668 2.396747 TATCGTGCGGGATTCGGTCG 62.397 60.000 0.00 0.00 39.69 4.79
669 670 4.446413 GTGCGGGATTCGGTCGGT 62.446 66.667 0.00 0.00 39.69 4.69
676 677 1.232119 GGATTCGGTCGGTGTTTGTT 58.768 50.000 0.00 0.00 0.00 2.83
681 682 0.316360 CGGTCGGTGTTTGTTTTCGG 60.316 55.000 0.00 0.00 0.00 4.30
715 716 3.560068 GGATCAAGTCTTCGTTGTGTGTT 59.440 43.478 0.00 0.00 0.00 3.32
717 718 2.601314 TCAAGTCTTCGTTGTGTGTTCG 59.399 45.455 0.00 0.00 0.00 3.95
725 726 1.526184 CGTTGTGTGTTCGTGTGTCAC 60.526 52.381 0.00 0.00 0.00 3.67
750 751 6.789403 CGTTGAATCATTTCGATCTATGCTTC 59.211 38.462 10.11 10.11 34.39 3.86
752 753 8.341173 GTTGAATCATTTCGATCTATGCTTCTT 58.659 33.333 14.68 2.69 34.39 2.52
760 761 4.984785 TCGATCTATGCTTCTTTTCATCGG 59.015 41.667 0.00 0.00 34.14 4.18
763 764 0.734889 ATGCTTCTTTTCATCGGCGG 59.265 50.000 7.21 0.00 0.00 6.13
769 770 1.363145 CTTTTCATCGGCGGCGGTTA 61.363 55.000 31.73 14.01 0.00 2.85
770 771 1.637478 TTTTCATCGGCGGCGGTTAC 61.637 55.000 31.73 0.00 0.00 2.50
781 782 1.296727 GGCGGTTACTATTCTGGTGC 58.703 55.000 0.00 0.00 0.00 5.01
788 789 0.108138 ACTATTCTGGTGCGCTGGTC 60.108 55.000 9.73 0.00 0.00 4.02
800 809 2.673523 CTGGTCCTGGAGGGCTTG 59.326 66.667 0.00 0.00 40.38 4.01
813 822 3.497942 GGAGGGCTTGAGTGGTTTTCTAA 60.498 47.826 0.00 0.00 0.00 2.10
827 836 9.740710 AGTGGTTTTCTAAAATTCTATGCTAGT 57.259 29.630 0.00 0.00 0.00 2.57
927 938 1.790043 TGTCGACAAATACTGTGTGCG 59.210 47.619 17.62 0.00 38.84 5.34
1182 1193 0.818296 ACTGGTACACCGAGATGCTC 59.182 55.000 0.00 0.00 39.43 4.26
1183 1194 1.107114 CTGGTACACCGAGATGCTCT 58.893 55.000 0.00 0.00 39.43 4.09
1440 1451 2.780094 CCGTGAGCTGGAGATCGCT 61.780 63.158 0.00 0.00 38.66 4.93
1452 1463 3.423162 GATCGCTGTGCTCGAGGCT 62.423 63.158 15.58 0.00 42.39 4.58
1998 2009 0.039764 ACGTCCTGGAGGAGATCACA 59.960 55.000 22.22 0.00 46.49 3.58
2032 2043 2.668212 GCAGCAACGGCACCTACA 60.668 61.111 0.00 0.00 44.61 2.74
2531 2542 0.338120 AGGAGGAGGAAGGTGGAGAG 59.662 60.000 0.00 0.00 0.00 3.20
2532 2543 0.041982 GGAGGAGGAAGGTGGAGAGT 59.958 60.000 0.00 0.00 0.00 3.24
2533 2544 1.288335 GGAGGAGGAAGGTGGAGAGTA 59.712 57.143 0.00 0.00 0.00 2.59
2546 2557 1.004918 AGAGTACCACAGGCAACGC 60.005 57.895 0.00 0.00 46.39 4.84
2567 2578 2.126463 GCACGACGCAGCTACAGA 60.126 61.111 5.71 0.00 41.79 3.41
2569 2580 1.081442 CACGACGCAGCTACAGACA 60.081 57.895 0.00 0.00 0.00 3.41
2573 2584 1.623359 GACGCAGCTACAGACAAGAG 58.377 55.000 0.00 0.00 0.00 2.85
2608 2622 6.509418 TTTTTAGCTAGTGGTAAATGGCAG 57.491 37.500 0.00 0.00 43.05 4.85
2611 2625 2.092212 AGCTAGTGGTAAATGGCAGCAT 60.092 45.455 0.00 0.00 0.00 3.79
2612 2626 2.689983 GCTAGTGGTAAATGGCAGCATT 59.310 45.455 0.00 0.00 0.00 3.56
2763 2777 4.086706 ACCGAGTGATTCCAAGAAACTT 57.913 40.909 0.00 0.00 0.00 2.66
2770 2784 3.569701 TGATTCCAAGAAACTTGAGTGGC 59.430 43.478 12.25 0.61 0.00 5.01
2796 2810 5.467035 TGATTTCCGGCAAGAAATTTTCT 57.533 34.783 12.76 5.82 44.52 2.52
2797 2811 6.582677 TGATTTCCGGCAAGAAATTTTCTA 57.417 33.333 11.92 0.00 44.52 2.10
2821 2836 6.373759 AGGGGTCCCATCAATTCTATTTTAC 58.626 40.000 10.98 0.00 38.92 2.01
2859 2874 4.753107 TCCCATCAAAGTGAAACGAACTAC 59.247 41.667 0.00 0.00 45.86 2.73
2861 2876 5.334105 CCCATCAAAGTGAAACGAACTACTG 60.334 44.000 0.00 0.00 45.86 2.74
2862 2877 5.236478 CCATCAAAGTGAAACGAACTACTGT 59.764 40.000 0.00 0.00 45.86 3.55
2877 2896 2.787601 ACTGTTTGATGTGCTTGCAG 57.212 45.000 0.00 0.00 0.00 4.41
2878 2897 2.026641 ACTGTTTGATGTGCTTGCAGT 58.973 42.857 0.00 0.00 0.00 4.40
2881 2900 4.097741 ACTGTTTGATGTGCTTGCAGTAAA 59.902 37.500 0.00 0.00 34.47 2.01
2882 2901 4.358851 TGTTTGATGTGCTTGCAGTAAAC 58.641 39.130 0.00 6.33 33.07 2.01
2912 2934 0.817654 GGGGATGCTTGCAGTAAACC 59.182 55.000 0.87 0.00 0.00 3.27
2913 2935 1.544724 GGGATGCTTGCAGTAAACCA 58.455 50.000 0.87 0.00 0.00 3.67
2925 2947 6.716934 TGCAGTAAACCAAAAACCAAGATA 57.283 33.333 0.00 0.00 0.00 1.98
2973 2995 4.297510 CTGTGAACTTGTCAGAGTCAGAG 58.702 47.826 0.00 0.00 41.66 3.35
2975 2997 2.036475 TGAACTTGTCAGAGTCAGAGGC 59.964 50.000 0.00 0.00 0.00 4.70
3009 3031 2.680339 GGAAAGTTCAGGCAGATGCTAC 59.320 50.000 4.59 0.00 41.70 3.58
3169 3201 2.017049 AGTTAAGATGGGCGCATCAAC 58.983 47.619 36.23 30.90 34.19 3.18
3246 3278 0.870307 CACGTAGCTATCGGGTGCAC 60.870 60.000 8.80 8.80 0.00 4.57
3248 3280 1.436336 GTAGCTATCGGGTGCACGT 59.564 57.895 11.45 0.00 34.94 4.49
3249 3281 0.664761 GTAGCTATCGGGTGCACGTA 59.335 55.000 11.45 0.00 34.94 3.57
3250 3282 0.949397 TAGCTATCGGGTGCACGTAG 59.051 55.000 11.45 11.07 34.94 3.51
3251 3283 1.949631 GCTATCGGGTGCACGTAGC 60.950 63.158 19.32 19.32 45.96 3.58
3252 3284 1.734137 CTATCGGGTGCACGTAGCT 59.266 57.895 11.45 0.00 45.94 3.32
3253 3285 0.949397 CTATCGGGTGCACGTAGCTA 59.051 55.000 11.45 0.00 45.94 3.32
3254 3286 1.540267 CTATCGGGTGCACGTAGCTAT 59.460 52.381 11.45 1.20 45.94 2.97
3255 3287 0.314302 ATCGGGTGCACGTAGCTATC 59.686 55.000 11.45 0.00 45.94 2.08
3256 3288 1.657487 CGGGTGCACGTAGCTATCG 60.657 63.158 11.45 12.26 45.94 2.92
3419 3465 3.314541 AGATATATTCCGGCGGTTCAC 57.685 47.619 27.32 11.75 0.00 3.18
3554 3602 1.710013 TTCTTGGAGAACGACATCGC 58.290 50.000 0.14 0.00 44.43 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.915293 AACTTGACGGTTAATGTCATATTCA 57.085 32.000 12.53 0.21 45.10 2.57
1 2 8.548721 CCTAACTTGACGGTTAATGTCATATTC 58.451 37.037 12.53 0.00 45.10 1.75
2 3 7.497909 CCCTAACTTGACGGTTAATGTCATATT 59.502 37.037 12.53 11.89 45.10 1.28
3 4 6.990349 CCCTAACTTGACGGTTAATGTCATAT 59.010 38.462 12.53 6.56 45.10 1.78
4 5 6.154877 TCCCTAACTTGACGGTTAATGTCATA 59.845 38.462 12.53 4.33 45.10 2.15
5 6 5.046159 TCCCTAACTTGACGGTTAATGTCAT 60.046 40.000 12.53 3.55 45.10 3.06
6 7 4.283978 TCCCTAACTTGACGGTTAATGTCA 59.716 41.667 8.85 8.85 44.17 3.58
7 8 4.824289 TCCCTAACTTGACGGTTAATGTC 58.176 43.478 4.37 4.37 36.88 3.06
8 9 4.895668 TCCCTAACTTGACGGTTAATGT 57.104 40.909 0.00 0.00 32.27 2.71
9 10 4.998672 TGTTCCCTAACTTGACGGTTAATG 59.001 41.667 0.00 0.00 36.51 1.90
10 11 4.999311 GTGTTCCCTAACTTGACGGTTAAT 59.001 41.667 0.00 0.00 36.51 1.40
11 12 4.379652 GTGTTCCCTAACTTGACGGTTAA 58.620 43.478 0.00 0.00 36.51 2.01
12 13 3.244181 GGTGTTCCCTAACTTGACGGTTA 60.244 47.826 0.00 0.00 36.51 2.85
13 14 2.486013 GGTGTTCCCTAACTTGACGGTT 60.486 50.000 0.00 0.00 36.51 4.44
14 15 1.071228 GGTGTTCCCTAACTTGACGGT 59.929 52.381 0.00 0.00 36.51 4.83
15 16 1.346722 AGGTGTTCCCTAACTTGACGG 59.653 52.381 0.00 0.00 43.87 4.79
16 17 2.224209 ACAGGTGTTCCCTAACTTGACG 60.224 50.000 0.00 0.00 43.86 4.35
17 18 3.487120 ACAGGTGTTCCCTAACTTGAC 57.513 47.619 0.00 0.00 43.86 3.18
18 19 4.081322 GAACAGGTGTTCCCTAACTTGA 57.919 45.455 11.17 0.00 46.42 3.02
29 30 5.307196 ACAGAGGTAGTATTGAACAGGTGTT 59.693 40.000 0.00 0.00 41.64 3.32
30 31 4.838986 ACAGAGGTAGTATTGAACAGGTGT 59.161 41.667 0.00 0.00 0.00 4.16
31 32 5.186021 AGACAGAGGTAGTATTGAACAGGTG 59.814 44.000 0.00 0.00 0.00 4.00
32 33 5.334421 AGACAGAGGTAGTATTGAACAGGT 58.666 41.667 0.00 0.00 0.00 4.00
33 34 5.923733 AGACAGAGGTAGTATTGAACAGG 57.076 43.478 0.00 0.00 0.00 4.00
34 35 6.102663 CCAAGACAGAGGTAGTATTGAACAG 58.897 44.000 0.00 0.00 39.78 3.16
35 36 5.542635 ACCAAGACAGAGGTAGTATTGAACA 59.457 40.000 0.00 0.00 39.78 3.18
36 37 5.869888 CACCAAGACAGAGGTAGTATTGAAC 59.130 44.000 0.00 0.00 39.78 3.18
37 38 5.542635 ACACCAAGACAGAGGTAGTATTGAA 59.457 40.000 0.00 0.00 39.78 2.69
38 39 5.084519 ACACCAAGACAGAGGTAGTATTGA 58.915 41.667 0.00 0.00 39.78 2.57
39 40 5.407407 ACACCAAGACAGAGGTAGTATTG 57.593 43.478 0.00 0.00 37.79 1.90
40 41 8.834004 TTATACACCAAGACAGAGGTAGTATT 57.166 34.615 0.00 0.00 36.07 1.89
41 42 8.060075 ACTTATACACCAAGACAGAGGTAGTAT 58.940 37.037 0.00 0.00 36.07 2.12
42 43 7.408543 ACTTATACACCAAGACAGAGGTAGTA 58.591 38.462 0.00 0.00 36.07 1.82
43 44 6.254522 ACTTATACACCAAGACAGAGGTAGT 58.745 40.000 0.00 0.00 36.07 2.73
44 45 6.377429 TGACTTATACACCAAGACAGAGGTAG 59.623 42.308 0.00 0.00 36.07 3.18
45 46 6.250711 TGACTTATACACCAAGACAGAGGTA 58.749 40.000 0.00 0.00 36.07 3.08
46 47 5.084519 TGACTTATACACCAAGACAGAGGT 58.915 41.667 0.00 0.00 39.10 3.85
47 48 5.661056 TGACTTATACACCAAGACAGAGG 57.339 43.478 0.00 0.00 0.00 3.69
48 49 6.473778 CGAATGACTTATACACCAAGACAGAG 59.526 42.308 0.00 0.00 32.66 3.35
49 50 6.071560 ACGAATGACTTATACACCAAGACAGA 60.072 38.462 0.00 0.00 32.66 3.41
50 51 6.035005 CACGAATGACTTATACACCAAGACAG 59.965 42.308 0.00 0.00 32.66 3.51
51 52 5.867174 CACGAATGACTTATACACCAAGACA 59.133 40.000 0.00 0.00 33.44 3.41
52 53 5.867716 ACACGAATGACTTATACACCAAGAC 59.132 40.000 0.00 0.00 0.00 3.01
53 54 6.032956 ACACGAATGACTTATACACCAAGA 57.967 37.500 0.00 0.00 0.00 3.02
54 55 7.033791 ACTACACGAATGACTTATACACCAAG 58.966 38.462 0.00 0.00 0.00 3.61
55 56 6.927416 ACTACACGAATGACTTATACACCAA 58.073 36.000 0.00 0.00 0.00 3.67
56 57 6.519679 ACTACACGAATGACTTATACACCA 57.480 37.500 0.00 0.00 0.00 4.17
57 58 7.823149 AAACTACACGAATGACTTATACACC 57.177 36.000 0.00 0.00 0.00 4.16
59 60 9.577110 CCTAAAACTACACGAATGACTTATACA 57.423 33.333 0.00 0.00 0.00 2.29
60 61 9.578439 ACCTAAAACTACACGAATGACTTATAC 57.422 33.333 0.00 0.00 0.00 1.47
61 62 9.793252 GACCTAAAACTACACGAATGACTTATA 57.207 33.333 0.00 0.00 0.00 0.98
62 63 7.487189 CGACCTAAAACTACACGAATGACTTAT 59.513 37.037 0.00 0.00 0.00 1.73
63 64 6.803320 CGACCTAAAACTACACGAATGACTTA 59.197 38.462 0.00 0.00 0.00 2.24
64 65 5.632347 CGACCTAAAACTACACGAATGACTT 59.368 40.000 0.00 0.00 0.00 3.01
65 66 5.048504 TCGACCTAAAACTACACGAATGACT 60.049 40.000 0.00 0.00 0.00 3.41
66 67 5.060200 GTCGACCTAAAACTACACGAATGAC 59.940 44.000 3.51 0.00 0.00 3.06
67 68 5.156355 GTCGACCTAAAACTACACGAATGA 58.844 41.667 3.51 0.00 0.00 2.57
68 69 4.919168 TGTCGACCTAAAACTACACGAATG 59.081 41.667 14.12 0.00 0.00 2.67
69 70 5.125100 TGTCGACCTAAAACTACACGAAT 57.875 39.130 14.12 0.00 0.00 3.34
70 71 4.566545 TGTCGACCTAAAACTACACGAA 57.433 40.909 14.12 0.00 0.00 3.85
71 72 4.566545 TTGTCGACCTAAAACTACACGA 57.433 40.909 14.12 0.00 0.00 4.35
72 73 5.834239 AATTGTCGACCTAAAACTACACG 57.166 39.130 14.12 0.00 0.00 4.49
73 74 8.768019 AGTTAAATTGTCGACCTAAAACTACAC 58.232 33.333 14.12 0.00 0.00 2.90
74 75 8.891671 AGTTAAATTGTCGACCTAAAACTACA 57.108 30.769 14.12 0.00 0.00 2.74
77 78 9.939802 AGATAGTTAAATTGTCGACCTAAAACT 57.060 29.630 14.12 16.81 0.00 2.66
247 248 9.799106 AGGTCATCGATTTGAGGAATTAAATAT 57.201 29.630 0.00 0.00 39.46 1.28
249 250 9.627123 TTAGGTCATCGATTTGAGGAATTAAAT 57.373 29.630 0.00 0.00 39.46 1.40
250 251 9.456147 TTTAGGTCATCGATTTGAGGAATTAAA 57.544 29.630 0.00 0.00 39.46 1.52
251 252 9.456147 TTTTAGGTCATCGATTTGAGGAATTAA 57.544 29.630 0.00 0.00 39.46 1.40
252 253 8.889717 GTTTTAGGTCATCGATTTGAGGAATTA 58.110 33.333 0.00 0.00 39.46 1.40
253 254 7.611855 AGTTTTAGGTCATCGATTTGAGGAATT 59.388 33.333 0.00 0.00 39.46 2.17
254 255 7.112779 AGTTTTAGGTCATCGATTTGAGGAAT 58.887 34.615 0.00 0.00 39.46 3.01
255 256 6.472887 AGTTTTAGGTCATCGATTTGAGGAA 58.527 36.000 0.00 0.00 39.46 3.36
256 257 6.049955 AGTTTTAGGTCATCGATTTGAGGA 57.950 37.500 0.00 0.00 34.44 3.71
257 258 6.019801 CGTAGTTTTAGGTCATCGATTTGAGG 60.020 42.308 0.00 0.00 0.00 3.86
258 259 6.508088 GCGTAGTTTTAGGTCATCGATTTGAG 60.508 42.308 0.00 0.00 0.00 3.02
259 260 5.290158 GCGTAGTTTTAGGTCATCGATTTGA 59.710 40.000 0.00 0.00 0.00 2.69
260 261 5.490213 GCGTAGTTTTAGGTCATCGATTTG 58.510 41.667 0.00 0.00 0.00 2.32
261 262 4.266976 CGCGTAGTTTTAGGTCATCGATTT 59.733 41.667 0.00 0.00 0.00 2.17
262 263 3.795101 CGCGTAGTTTTAGGTCATCGATT 59.205 43.478 0.00 0.00 0.00 3.34
263 264 3.065786 TCGCGTAGTTTTAGGTCATCGAT 59.934 43.478 5.77 0.00 0.00 3.59
264 265 2.419673 TCGCGTAGTTTTAGGTCATCGA 59.580 45.455 5.77 0.00 0.00 3.59
265 266 2.789208 TCGCGTAGTTTTAGGTCATCG 58.211 47.619 5.77 0.00 0.00 3.84
266 267 4.802039 TCATTCGCGTAGTTTTAGGTCATC 59.198 41.667 5.77 0.00 0.00 2.92
267 268 4.565564 GTCATTCGCGTAGTTTTAGGTCAT 59.434 41.667 5.77 0.00 0.00 3.06
268 269 3.922240 GTCATTCGCGTAGTTTTAGGTCA 59.078 43.478 5.77 0.00 0.00 4.02
269 270 4.171754 AGTCATTCGCGTAGTTTTAGGTC 58.828 43.478 5.77 0.00 0.00 3.85
270 271 4.184079 AGTCATTCGCGTAGTTTTAGGT 57.816 40.909 5.77 0.00 0.00 3.08
271 272 6.823678 ATAAGTCATTCGCGTAGTTTTAGG 57.176 37.500 5.77 0.00 0.00 2.69
273 274 9.398170 GGTATATAAGTCATTCGCGTAGTTTTA 57.602 33.333 5.77 0.20 0.00 1.52
274 275 7.113965 CGGTATATAAGTCATTCGCGTAGTTTT 59.886 37.037 5.77 0.00 0.00 2.43
275 276 6.580041 CGGTATATAAGTCATTCGCGTAGTTT 59.420 38.462 5.77 0.00 0.00 2.66
276 277 6.082338 CGGTATATAAGTCATTCGCGTAGTT 58.918 40.000 5.77 2.59 0.00 2.24
277 278 5.391310 CCGGTATATAAGTCATTCGCGTAGT 60.391 44.000 5.77 0.00 0.00 2.73
278 279 5.026462 CCGGTATATAAGTCATTCGCGTAG 58.974 45.833 5.77 0.00 0.00 3.51
279 280 4.142622 CCCGGTATATAAGTCATTCGCGTA 60.143 45.833 5.77 0.00 0.00 4.42
280 281 3.366679 CCCGGTATATAAGTCATTCGCGT 60.367 47.826 5.77 0.00 0.00 6.01
281 282 3.119743 TCCCGGTATATAAGTCATTCGCG 60.120 47.826 0.00 0.00 0.00 5.87
282 283 4.171754 GTCCCGGTATATAAGTCATTCGC 58.828 47.826 0.00 0.00 0.00 4.70
283 284 5.182570 TCTGTCCCGGTATATAAGTCATTCG 59.817 44.000 0.00 0.00 0.00 3.34
284 285 6.350277 CCTCTGTCCCGGTATATAAGTCATTC 60.350 46.154 0.00 0.00 0.00 2.67
285 286 5.480772 CCTCTGTCCCGGTATATAAGTCATT 59.519 44.000 0.00 0.00 0.00 2.57
286 287 5.017490 CCTCTGTCCCGGTATATAAGTCAT 58.983 45.833 0.00 0.00 0.00 3.06
287 288 4.404640 CCTCTGTCCCGGTATATAAGTCA 58.595 47.826 0.00 0.00 0.00 3.41
288 289 3.762823 CCCTCTGTCCCGGTATATAAGTC 59.237 52.174 0.00 0.00 0.00 3.01
289 290 3.400322 TCCCTCTGTCCCGGTATATAAGT 59.600 47.826 0.00 0.00 0.00 2.24
290 291 4.017808 CTCCCTCTGTCCCGGTATATAAG 58.982 52.174 0.00 0.00 0.00 1.73
291 292 3.400322 ACTCCCTCTGTCCCGGTATATAA 59.600 47.826 0.00 0.00 0.00 0.98
292 293 2.991713 ACTCCCTCTGTCCCGGTATATA 59.008 50.000 0.00 0.00 0.00 0.86
293 294 1.787676 ACTCCCTCTGTCCCGGTATAT 59.212 52.381 0.00 0.00 0.00 0.86
294 295 1.229131 ACTCCCTCTGTCCCGGTATA 58.771 55.000 0.00 0.00 0.00 1.47
295 296 1.145325 CTACTCCCTCTGTCCCGGTAT 59.855 57.143 0.00 0.00 0.00 2.73
296 297 0.549950 CTACTCCCTCTGTCCCGGTA 59.450 60.000 0.00 0.00 0.00 4.02
297 298 1.306970 CTACTCCCTCTGTCCCGGT 59.693 63.158 0.00 0.00 0.00 5.28
298 299 0.549950 TACTACTCCCTCTGTCCCGG 59.450 60.000 0.00 0.00 0.00 5.73
299 300 2.431954 TTACTACTCCCTCTGTCCCG 57.568 55.000 0.00 0.00 0.00 5.14
300 301 5.189145 TCAAATTTACTACTCCCTCTGTCCC 59.811 44.000 0.00 0.00 0.00 4.46
301 302 6.295719 TCAAATTTACTACTCCCTCTGTCC 57.704 41.667 0.00 0.00 0.00 4.02
303 304 9.838339 CATATTCAAATTTACTACTCCCTCTGT 57.162 33.333 0.00 0.00 0.00 3.41
304 305 9.277783 CCATATTCAAATTTACTACTCCCTCTG 57.722 37.037 0.00 0.00 0.00 3.35
305 306 9.225682 TCCATATTCAAATTTACTACTCCCTCT 57.774 33.333 0.00 0.00 0.00 3.69
306 307 9.274206 GTCCATATTCAAATTTACTACTCCCTC 57.726 37.037 0.00 0.00 0.00 4.30
307 308 8.778059 TGTCCATATTCAAATTTACTACTCCCT 58.222 33.333 0.00 0.00 0.00 4.20
308 309 8.974060 TGTCCATATTCAAATTTACTACTCCC 57.026 34.615 0.00 0.00 0.00 4.30
329 330 6.272698 CTTTGCAACAATACAAAGTTGTCC 57.727 37.500 0.00 0.00 44.90 4.02
537 538 7.181125 GGTGATGGGTGAGGATTAGTAGATTAT 59.819 40.741 0.00 0.00 0.00 1.28
571 572 1.069358 GGTGATGGGTTTCCGCAAAAA 59.931 47.619 0.00 0.00 37.06 1.94
572 573 0.676736 GGTGATGGGTTTCCGCAAAA 59.323 50.000 0.00 0.00 37.06 2.44
573 574 1.182385 GGGTGATGGGTTTCCGCAAA 61.182 55.000 0.00 0.00 37.06 3.68
574 575 1.605165 GGGTGATGGGTTTCCGCAA 60.605 57.895 0.00 0.00 37.06 4.85
575 576 2.034999 GGGTGATGGGTTTCCGCA 59.965 61.111 0.00 0.00 37.98 5.69
576 577 3.131478 CGGGTGATGGGTTTCCGC 61.131 66.667 0.00 0.00 34.17 5.54
577 578 1.302993 AACGGGTGATGGGTTTCCG 60.303 57.895 0.00 0.00 45.42 4.30
578 579 0.037734 AGAACGGGTGATGGGTTTCC 59.962 55.000 0.00 0.00 0.00 3.13
579 580 1.165270 CAGAACGGGTGATGGGTTTC 58.835 55.000 0.00 0.00 0.00 2.78
580 581 0.251165 CCAGAACGGGTGATGGGTTT 60.251 55.000 0.00 0.00 0.00 3.27
581 582 1.378762 CCAGAACGGGTGATGGGTT 59.621 57.895 0.00 0.00 0.00 4.11
582 583 3.077907 CCAGAACGGGTGATGGGT 58.922 61.111 0.00 0.00 0.00 4.51
583 584 2.438434 GCCAGAACGGGTGATGGG 60.438 66.667 5.13 0.00 33.23 4.00
584 585 2.671070 AGCCAGAACGGGTGATGG 59.329 61.111 0.00 0.00 46.40 3.51
597 598 1.079819 GACGCTAGAAGCACAGCCA 60.080 57.895 0.00 0.00 42.58 4.75
602 603 0.100682 TCCGATGACGCTAGAAGCAC 59.899 55.000 0.00 0.00 42.58 4.40
612 613 1.404035 TCCACATACACTCCGATGACG 59.596 52.381 0.00 0.00 39.43 4.35
631 632 5.220491 GCACGATACACTGGAGAAAAATCTC 60.220 44.000 0.00 0.00 36.08 2.75
632 633 4.631813 GCACGATACACTGGAGAAAAATCT 59.368 41.667 0.00 0.00 0.00 2.40
633 634 4.492570 CGCACGATACACTGGAGAAAAATC 60.493 45.833 0.00 0.00 0.00 2.17
634 635 3.370978 CGCACGATACACTGGAGAAAAAT 59.629 43.478 0.00 0.00 0.00 1.82
635 636 2.734606 CGCACGATACACTGGAGAAAAA 59.265 45.455 0.00 0.00 0.00 1.94
636 637 2.333926 CGCACGATACACTGGAGAAAA 58.666 47.619 0.00 0.00 0.00 2.29
637 638 1.403647 CCGCACGATACACTGGAGAAA 60.404 52.381 0.00 0.00 0.00 2.52
638 639 0.172578 CCGCACGATACACTGGAGAA 59.827 55.000 0.00 0.00 0.00 2.87
639 640 1.663379 CCCGCACGATACACTGGAGA 61.663 60.000 0.00 0.00 0.00 3.71
640 641 1.226974 CCCGCACGATACACTGGAG 60.227 63.158 0.00 0.00 0.00 3.86
641 642 1.040893 ATCCCGCACGATACACTGGA 61.041 55.000 0.00 0.00 0.00 3.86
642 643 0.179084 AATCCCGCACGATACACTGG 60.179 55.000 0.00 0.00 0.00 4.00
643 644 1.209128 GAATCCCGCACGATACACTG 58.791 55.000 0.00 0.00 0.00 3.66
644 645 0.248907 CGAATCCCGCACGATACACT 60.249 55.000 0.00 0.00 0.00 3.55
645 646 1.213094 CCGAATCCCGCACGATACAC 61.213 60.000 0.00 0.00 36.84 2.90
646 647 1.066752 CCGAATCCCGCACGATACA 59.933 57.895 0.00 0.00 36.84 2.29
647 648 0.938168 GACCGAATCCCGCACGATAC 60.938 60.000 0.00 0.00 36.84 2.24
648 649 1.361271 GACCGAATCCCGCACGATA 59.639 57.895 0.00 0.00 36.84 2.92
649 650 2.106332 GACCGAATCCCGCACGAT 59.894 61.111 0.00 0.00 36.84 3.73
650 651 4.485834 CGACCGAATCCCGCACGA 62.486 66.667 0.00 0.00 37.43 4.35
652 653 4.446413 ACCGACCGAATCCCGCAC 62.446 66.667 0.00 0.00 36.84 5.34
653 654 4.444838 CACCGACCGAATCCCGCA 62.445 66.667 0.00 0.00 36.84 5.69
654 655 3.945304 AACACCGACCGAATCCCGC 62.945 63.158 0.00 0.00 36.84 6.13
655 656 1.375013 AAACACCGACCGAATCCCG 60.375 57.895 0.00 0.00 38.18 5.14
656 657 0.604511 ACAAACACCGACCGAATCCC 60.605 55.000 0.00 0.00 0.00 3.85
657 658 1.232119 AACAAACACCGACCGAATCC 58.768 50.000 0.00 0.00 0.00 3.01
658 659 3.294102 GAAAACAAACACCGACCGAATC 58.706 45.455 0.00 0.00 0.00 2.52
659 660 2.286536 CGAAAACAAACACCGACCGAAT 60.287 45.455 0.00 0.00 0.00 3.34
660 661 1.062294 CGAAAACAAACACCGACCGAA 59.938 47.619 0.00 0.00 0.00 4.30
661 662 0.651551 CGAAAACAAACACCGACCGA 59.348 50.000 0.00 0.00 0.00 4.69
662 663 0.316360 CCGAAAACAAACACCGACCG 60.316 55.000 0.00 0.00 0.00 4.79
663 664 0.734309 ACCGAAAACAAACACCGACC 59.266 50.000 0.00 0.00 0.00 4.79
664 665 1.532298 CCACCGAAAACAAACACCGAC 60.532 52.381 0.00 0.00 0.00 4.79
665 666 0.733729 CCACCGAAAACAAACACCGA 59.266 50.000 0.00 0.00 0.00 4.69
666 667 0.733729 TCCACCGAAAACAAACACCG 59.266 50.000 0.00 0.00 0.00 4.94
667 668 2.287970 GGATCCACCGAAAACAAACACC 60.288 50.000 6.95 0.00 0.00 4.16
668 669 2.359531 TGGATCCACCGAAAACAAACAC 59.640 45.455 11.44 0.00 42.61 3.32
669 670 2.359531 GTGGATCCACCGAAAACAAACA 59.640 45.455 31.37 0.00 42.61 2.83
676 677 1.004320 CCACGTGGATCCACCGAAA 60.004 57.895 34.05 0.64 43.49 3.46
715 716 4.318475 GAAATGATTCAACGTGACACACGA 60.318 41.667 26.54 8.29 45.89 4.35
717 718 3.900116 CGAAATGATTCAACGTGACACAC 59.100 43.478 6.37 0.00 35.15 3.82
725 726 6.220579 AGCATAGATCGAAATGATTCAACG 57.779 37.500 9.27 0.00 37.47 4.10
729 730 9.379811 GAAAAGAAGCATAGATCGAAATGATTC 57.620 33.333 20.29 20.29 44.75 2.52
733 734 7.529854 CGATGAAAAGAAGCATAGATCGAAATG 59.470 37.037 0.00 0.00 34.75 2.32
750 751 1.363145 TAACCGCCGCCGATGAAAAG 61.363 55.000 0.00 0.00 36.29 2.27
752 753 2.101835 GTAACCGCCGCCGATGAAA 61.102 57.895 0.00 0.00 36.29 2.69
760 761 0.179092 ACCAGAATAGTAACCGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
763 764 0.928229 CGCACCAGAATAGTAACCGC 59.072 55.000 0.00 0.00 0.00 5.68
769 770 0.108138 GACCAGCGCACCAGAATAGT 60.108 55.000 11.47 0.00 0.00 2.12
770 771 0.811616 GGACCAGCGCACCAGAATAG 60.812 60.000 11.47 0.00 0.00 1.73
788 789 1.783250 AACCACTCAAGCCCTCCAGG 61.783 60.000 0.00 0.00 39.47 4.45
798 807 9.077885 AGCATAGAATTTTAGAAAACCACTCAA 57.922 29.630 0.00 0.00 0.00 3.02
827 836 9.899661 AAGCGATGGCCATATATTTATTAAGTA 57.100 29.630 20.84 0.00 41.24 2.24
927 938 0.179070 GAGAAAGGATGGACGAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
1158 1169 1.136984 CTCGGTGTACCAGTCGAGC 59.863 63.158 1.50 0.00 41.69 5.03
1744 1755 0.108329 ACGGCTTCGTGGATAACCTG 60.108 55.000 0.00 0.00 46.32 4.00
1998 2009 0.605083 TGCTGTCTCGTCTCATGCTT 59.395 50.000 0.00 0.00 0.00 3.91
2553 2564 0.109735 TCTTGTCTGTAGCTGCGTCG 60.110 55.000 0.00 0.00 0.00 5.12
2740 2754 5.422214 AGTTTCTTGGAATCACTCGGTAT 57.578 39.130 0.00 0.00 0.00 2.73
2741 2755 4.884668 AGTTTCTTGGAATCACTCGGTA 57.115 40.909 0.00 0.00 0.00 4.02
2744 2758 4.752101 ACTCAAGTTTCTTGGAATCACTCG 59.248 41.667 9.18 0.00 0.00 4.18
2763 2777 1.522668 CGGAAATCAAGTGCCACTCA 58.477 50.000 0.00 0.00 0.00 3.41
2770 2784 3.641437 TTTCTTGCCGGAAATCAAGTG 57.359 42.857 5.05 0.00 40.27 3.16
2796 2810 6.606241 AAAATAGAATTGATGGGACCCCTA 57.394 37.500 8.45 0.10 36.94 3.53
2797 2811 5.487861 AAAATAGAATTGATGGGACCCCT 57.512 39.130 8.45 0.00 36.94 4.79
2821 2836 0.184933 TGGGACCCCACTGTTCAAAG 59.815 55.000 8.45 0.00 41.89 2.77
2859 2874 2.787601 ACTGCAAGCACATCAAACAG 57.212 45.000 0.00 0.00 37.60 3.16
2861 2876 4.610945 AGTTTACTGCAAGCACATCAAAC 58.389 39.130 0.00 0.15 37.60 2.93
2862 2877 4.916983 AGTTTACTGCAAGCACATCAAA 57.083 36.364 0.00 0.00 37.60 2.69
2877 2896 5.243954 AGCATCCCCTGAAGAAAAAGTTTAC 59.756 40.000 0.00 0.00 0.00 2.01
2878 2897 5.393866 AGCATCCCCTGAAGAAAAAGTTTA 58.606 37.500 0.00 0.00 0.00 2.01
2881 2900 3.532641 AGCATCCCCTGAAGAAAAAGT 57.467 42.857 0.00 0.00 0.00 2.66
2882 2901 3.615834 GCAAGCATCCCCTGAAGAAAAAG 60.616 47.826 0.00 0.00 0.00 2.27
2912 2934 7.257722 ACAGTGTTCAACTATCTTGGTTTTTG 58.742 34.615 0.00 0.00 36.83 2.44
2913 2935 7.404671 ACAGTGTTCAACTATCTTGGTTTTT 57.595 32.000 0.00 0.00 36.83 1.94
2942 2964 2.285977 ACAAGTTCACAGTCCCGTTTC 58.714 47.619 0.00 0.00 0.00 2.78
2949 2971 4.046938 TGACTCTGACAAGTTCACAGTC 57.953 45.455 3.50 3.50 45.76 3.51
2973 2995 5.048991 TGAACTTTCCTTGAAGTTTATCGCC 60.049 40.000 4.70 0.00 46.73 5.54
2975 2997 6.603095 CCTGAACTTTCCTTGAAGTTTATCG 58.397 40.000 4.70 0.00 46.73 2.92
3039 3067 4.727235 CGTCCCGCTTTATTCTAATTCC 57.273 45.455 0.00 0.00 0.00 3.01
3169 3201 1.247567 AAAAACCCACATGCTCCTCG 58.752 50.000 0.00 0.00 0.00 4.63
3248 3280 7.419134 AAGTTGATCTTGCAGCCGATAGCTA 62.419 44.000 0.00 0.00 42.04 3.32
3249 3281 6.727587 AAGTTGATCTTGCAGCCGATAGCT 62.728 45.833 0.00 0.00 43.70 3.32
3250 3282 1.262683 GTTGATCTTGCAGCCGATAGC 59.737 52.381 0.00 0.00 44.25 2.97
3251 3283 2.831333 AGTTGATCTTGCAGCCGATAG 58.169 47.619 0.00 0.00 0.00 2.08
3252 3284 2.988010 AGTTGATCTTGCAGCCGATA 57.012 45.000 0.00 0.00 0.00 2.92
3253 3285 2.119801 AAGTTGATCTTGCAGCCGAT 57.880 45.000 0.00 0.00 34.77 4.18
3254 3286 1.896220 AAAGTTGATCTTGCAGCCGA 58.104 45.000 0.00 0.00 36.40 5.54
3255 3287 2.712057 AAAAGTTGATCTTGCAGCCG 57.288 45.000 0.00 0.00 36.40 5.52
3419 3465 2.048222 ACGTGGTCCATGACGCAG 60.048 61.111 18.36 0.00 39.22 5.18
3482 3528 2.919494 CGGTGTGAAAGCAAGGGGC 61.919 63.158 0.00 0.00 45.30 5.80
3554 3602 4.698304 TCCAGCTCCCAAAGTAATAAAACG 59.302 41.667 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.