Multiple sequence alignment - TraesCS4D01G294600

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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 TraesCS4D01G294600 chr4D 100.000 3911 0 0 1 3911 464991087 464987177 0.000000e+00 7223.0
1 TraesCS4D01G294600 chr4D 82.979 188 22 10 3338 3524 22941135 22940957 1.120000e-35 161.0
2 TraesCS4D01G294600 chr4D 89.286 112 11 1 3416 3526 212159248 212159137 5.270000e-29 139.0
3 TraesCS4D01G294600 chr4B 95.121 2521 111 8 639 3152 581311247 581308732 0.000000e+00 3964.0
4 TraesCS4D01G294600 chr4B 92.230 592 18 6 3186 3768 581308654 581308082 0.000000e+00 813.0
5 TraesCS4D01G294600 chr4B 78.682 258 38 14 3269 3520 317763289 317763535 5.230000e-34 156.0
6 TraesCS4D01G294600 chr4B 95.000 80 4 0 3832 3911 581307305 581307226 4.100000e-25 126.0
7 TraesCS4D01G294600 chr4B 94.000 50 2 1 523 572 581311467 581311419 1.510000e-09 75.0
8 TraesCS4D01G294600 chr4A 94.578 2453 119 12 693 3144 5463078 5465517 0.000000e+00 3781.0
9 TraesCS4D01G294600 chr4A 89.157 249 26 1 114 361 5462582 5462830 3.800000e-80 309.0
10 TraesCS4D01G294600 chr4A 79.310 261 37 14 3269 3523 312683427 312683178 2.420000e-37 167.0
11 TraesCS4D01G294600 chr4A 82.703 185 21 11 3338 3521 579436414 579436588 1.880000e-33 154.0
12 TraesCS4D01G294600 chr2D 95.294 170 8 0 355 524 560959480 560959649 1.790000e-68 270.0
13 TraesCS4D01G294600 chr2D 95.266 169 8 0 360 528 516708476 516708308 6.440000e-68 268.0
14 TraesCS4D01G294600 chr2D 93.182 44 0 2 3268 3309 118526343 118526385 1.170000e-05 62.1
15 TraesCS4D01G294600 chr2D 90.698 43 3 1 3268 3309 118374818 118374860 5.460000e-04 56.5
16 TraesCS4D01G294600 chr5A 95.783 166 7 0 360 525 651496822 651496987 6.440000e-68 268.0
17 TraesCS4D01G294600 chr5A 95.210 167 8 0 358 524 290391863 290391697 8.330000e-67 265.0
18 TraesCS4D01G294600 chr5A 95.210 167 8 0 359 525 382566637 382566803 8.330000e-67 265.0
19 TraesCS4D01G294600 chr3B 94.767 172 9 0 353 524 120617084 120616913 6.440000e-68 268.0
20 TraesCS4D01G294600 chr3B 94.737 171 9 0 357 527 655849588 655849418 2.320000e-67 267.0
21 TraesCS4D01G294600 chr1D 94.706 170 9 0 356 525 12946805 12946974 8.330000e-67 265.0
22 TraesCS4D01G294600 chr1D 81.124 249 32 14 3278 3523 39956709 39956473 6.670000e-43 185.0
23 TraesCS4D01G294600 chr6D 93.678 174 10 1 359 532 406391524 406391352 3.880000e-65 259.0
24 TraesCS4D01G294600 chr5D 81.369 263 34 10 3266 3523 315936234 315935982 2.380000e-47 200.0
25 TraesCS4D01G294600 chr5B 79.848 263 38 11 3266 3523 364139792 364139540 1.120000e-40 178.0
26 TraesCS4D01G294600 chr2B 86.735 98 12 1 3416 3513 155044870 155044774 1.490000e-19 108.0
27 TraesCS4D01G294600 chr2A 86.441 59 4 1 3277 3331 41916624 41916682 1.170000e-05 62.1
28 TraesCS4D01G294600 chr2A 90.698 43 3 1 3268 3309 120443058 120443100 5.460000e-04 56.5


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 TraesCS4D01G294600 chr4D 464987177 464991087 3910 True 7223.0 7223 100.00000 1 3911 1 chr4D.!!$R3 3910
1 TraesCS4D01G294600 chr4B 581307226 581311467 4241 True 1244.5 3964 94.08775 523 3911 4 chr4B.!!$R1 3388
2 TraesCS4D01G294600 chr4A 5462582 5465517 2935 False 2045.0 3781 91.86750 114 3144 2 chr4A.!!$F2 3030

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
371 373 0.041386 AACCTTCTACTCCCTCCGCT 59.959 55.0 0.0 0.0 0.00 5.52 F
374 376 0.106419 CTTCTACTCCCTCCGCTCCT 60.106 60.0 0.0 0.0 0.00 3.69 F
952 1102 0.257039 CCAACCCTCCCCTCAGATTG 59.743 60.0 0.0 0.0 0.00 2.67 F
1641 1791 0.233848 CGGTGTTTGTTACCTGCGTC 59.766 55.0 0.0 0.0 36.03 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1617 0.459934 GCAGCGCAGACATCTTCTCT 60.460 55.0 11.47 0.0 28.96 3.10 R
1560 1710 0.817013 ACCCCATAAACGCTGCAATG 59.183 50.0 0.00 0.0 0.00 2.82 R
2823 2973 0.990374 AGAGAGCAATGAGGCCAACT 59.010 50.0 5.01 0.0 0.00 3.16 R
3601 3810 0.604780 CCAACTGCTCCAGTGACCAG 60.605 60.0 0.00 0.0 44.62 4.00 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
57 58 9.990360 AAAAAGAAAAACCAGTAAAGAACAAGA 57.010 25.926 0.00 0.00 0.00 3.02
58 59 9.639601 AAAAGAAAAACCAGTAAAGAACAAGAG 57.360 29.630 0.00 0.00 0.00 2.85
59 60 8.575649 AAGAAAAACCAGTAAAGAACAAGAGA 57.424 30.769 0.00 0.00 0.00 3.10
60 61 8.214721 AGAAAAACCAGTAAAGAACAAGAGAG 57.785 34.615 0.00 0.00 0.00 3.20
61 62 8.047310 AGAAAAACCAGTAAAGAACAAGAGAGA 58.953 33.333 0.00 0.00 0.00 3.10
62 63 8.753497 AAAAACCAGTAAAGAACAAGAGAGAT 57.247 30.769 0.00 0.00 0.00 2.75
63 64 9.847224 AAAAACCAGTAAAGAACAAGAGAGATA 57.153 29.630 0.00 0.00 0.00 1.98
64 65 9.847224 AAAACCAGTAAAGAACAAGAGAGATAA 57.153 29.630 0.00 0.00 0.00 1.75
65 66 9.495572 AAACCAGTAAAGAACAAGAGAGATAAG 57.504 33.333 0.00 0.00 0.00 1.73
66 67 8.423906 ACCAGTAAAGAACAAGAGAGATAAGA 57.576 34.615 0.00 0.00 0.00 2.10
67 68 8.871125 ACCAGTAAAGAACAAGAGAGATAAGAA 58.129 33.333 0.00 0.00 0.00 2.52
68 69 9.712305 CCAGTAAAGAACAAGAGAGATAAGAAA 57.288 33.333 0.00 0.00 0.00 2.52
73 74 8.840833 AAGAACAAGAGAGATAAGAAAAGGAC 57.159 34.615 0.00 0.00 0.00 3.85
74 75 7.390823 AGAACAAGAGAGATAAGAAAAGGACC 58.609 38.462 0.00 0.00 0.00 4.46
75 76 5.725362 ACAAGAGAGATAAGAAAAGGACCG 58.275 41.667 0.00 0.00 0.00 4.79
76 77 5.480772 ACAAGAGAGATAAGAAAAGGACCGA 59.519 40.000 0.00 0.00 0.00 4.69
77 78 6.014499 ACAAGAGAGATAAGAAAAGGACCGAA 60.014 38.462 0.00 0.00 0.00 4.30
78 79 6.215495 AGAGAGATAAGAAAAGGACCGAAG 57.785 41.667 0.00 0.00 0.00 3.79
79 80 5.717654 AGAGAGATAAGAAAAGGACCGAAGT 59.282 40.000 0.00 0.00 0.00 3.01
80 81 6.890814 AGAGAGATAAGAAAAGGACCGAAGTA 59.109 38.462 0.00 0.00 0.00 2.24
81 82 7.396623 AGAGAGATAAGAAAAGGACCGAAGTAA 59.603 37.037 0.00 0.00 0.00 2.24
82 83 7.904205 AGAGATAAGAAAAGGACCGAAGTAAA 58.096 34.615 0.00 0.00 0.00 2.01
83 84 8.541234 AGAGATAAGAAAAGGACCGAAGTAAAT 58.459 33.333 0.00 0.00 0.00 1.40
84 85 8.719560 AGATAAGAAAAGGACCGAAGTAAATC 57.280 34.615 0.00 0.00 0.00 2.17
85 86 8.541234 AGATAAGAAAAGGACCGAAGTAAATCT 58.459 33.333 0.00 0.00 0.00 2.40
86 87 9.163899 GATAAGAAAAGGACCGAAGTAAATCTT 57.836 33.333 0.00 0.00 39.32 2.40
87 88 7.436430 AAGAAAAGGACCGAAGTAAATCTTC 57.564 36.000 0.00 0.00 46.39 2.87
88 89 5.938710 AGAAAAGGACCGAAGTAAATCTTCC 59.061 40.000 2.65 0.00 46.97 3.46
89 90 3.908643 AGGACCGAAGTAAATCTTCCC 57.091 47.619 2.65 0.00 46.97 3.97
90 91 2.167900 AGGACCGAAGTAAATCTTCCCG 59.832 50.000 2.65 0.00 46.97 5.14
91 92 2.167075 GGACCGAAGTAAATCTTCCCGA 59.833 50.000 2.65 0.00 46.97 5.14
92 93 3.368739 GGACCGAAGTAAATCTTCCCGAA 60.369 47.826 2.65 0.00 46.97 4.30
93 94 4.248058 GACCGAAGTAAATCTTCCCGAAA 58.752 43.478 2.65 0.00 46.97 3.46
94 95 3.999001 ACCGAAGTAAATCTTCCCGAAAC 59.001 43.478 2.65 0.00 46.97 2.78
95 96 4.251268 CCGAAGTAAATCTTCCCGAAACT 58.749 43.478 2.65 0.00 46.97 2.66
96 97 4.092968 CCGAAGTAAATCTTCCCGAAACTG 59.907 45.833 2.65 0.00 46.97 3.16
97 98 4.092968 CGAAGTAAATCTTCCCGAAACTGG 59.907 45.833 2.65 0.00 46.97 4.00
98 99 4.635699 AGTAAATCTTCCCGAAACTGGT 57.364 40.909 0.00 0.00 0.00 4.00
99 100 4.981812 AGTAAATCTTCCCGAAACTGGTT 58.018 39.130 0.00 0.00 0.00 3.67
100 101 5.382616 AGTAAATCTTCCCGAAACTGGTTT 58.617 37.500 0.00 0.00 35.14 3.27
101 102 5.831525 AGTAAATCTTCCCGAAACTGGTTTT 59.168 36.000 0.13 0.00 32.11 2.43
102 103 5.607939 AAATCTTCCCGAAACTGGTTTTT 57.392 34.783 0.13 0.00 32.11 1.94
151 152 3.775065 GAAGGTTTCCAAAGCGAGC 57.225 52.632 0.00 0.00 41.06 5.03
154 155 0.179018 AGGTTTCCAAAGCGAGCACT 60.179 50.000 0.00 0.00 41.06 4.40
156 157 1.197036 GGTTTCCAAAGCGAGCACTAC 59.803 52.381 0.00 0.00 0.00 2.73
157 158 1.871039 GTTTCCAAAGCGAGCACTACA 59.129 47.619 0.00 0.00 0.00 2.74
160 161 2.346803 TCCAAAGCGAGCACTACATTC 58.653 47.619 0.00 0.00 0.00 2.67
161 162 1.398390 CCAAAGCGAGCACTACATTCC 59.602 52.381 0.00 0.00 0.00 3.01
164 165 0.530744 AGCGAGCACTACATTCCGAA 59.469 50.000 0.00 0.00 0.00 4.30
172 173 3.424962 GCACTACATTCCGAAAACTGCTC 60.425 47.826 0.00 0.00 0.00 4.26
181 182 2.073816 CGAAAACTGCTCGGGTACAAT 58.926 47.619 0.00 0.00 32.62 2.71
221 222 2.566997 CGCGAGGAATGTCGTAGTG 58.433 57.895 0.00 0.00 42.17 2.74
241 242 1.067669 GCAGAGCTCCATACATCGTGA 59.932 52.381 10.93 0.00 0.00 4.35
253 254 3.452755 ACATCGTGAATCCTATTCGCA 57.547 42.857 12.26 2.36 0.00 5.10
256 257 1.202486 TCGTGAATCCTATTCGCACCC 60.202 52.381 12.26 0.00 0.00 4.61
274 275 1.217882 CCCATTGCGTCGAACTATCC 58.782 55.000 0.00 0.00 0.00 2.59
276 277 2.483876 CCATTGCGTCGAACTATCCAT 58.516 47.619 0.00 0.00 0.00 3.41
282 283 1.781429 CGTCGAACTATCCATGCTTCG 59.219 52.381 0.00 0.00 37.45 3.79
287 288 1.656652 ACTATCCATGCTTCGCACAC 58.343 50.000 0.00 0.00 43.04 3.82
294 295 0.819259 ATGCTTCGCACACAGTTGGT 60.819 50.000 0.00 0.00 43.04 3.67
343 345 3.074281 GGTGTTCCACCGATCCCA 58.926 61.111 0.00 0.00 44.95 4.37
344 346 1.078426 GGTGTTCCACCGATCCCAG 60.078 63.158 0.00 0.00 44.95 4.45
369 371 1.112950 GGAACCTTCTACTCCCTCCG 58.887 60.000 0.00 0.00 0.00 4.63
370 372 0.460722 GAACCTTCTACTCCCTCCGC 59.539 60.000 0.00 0.00 0.00 5.54
371 373 0.041386 AACCTTCTACTCCCTCCGCT 59.959 55.000 0.00 0.00 0.00 5.52
372 374 0.396001 ACCTTCTACTCCCTCCGCTC 60.396 60.000 0.00 0.00 0.00 5.03
373 375 1.110518 CCTTCTACTCCCTCCGCTCC 61.111 65.000 0.00 0.00 0.00 4.70
374 376 0.106419 CTTCTACTCCCTCCGCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
375 377 1.143277 CTTCTACTCCCTCCGCTCCTA 59.857 57.143 0.00 0.00 0.00 2.94
376 378 1.219773 TCTACTCCCTCCGCTCCTAA 58.780 55.000 0.00 0.00 0.00 2.69
377 379 1.567649 TCTACTCCCTCCGCTCCTAAA 59.432 52.381 0.00 0.00 0.00 1.85
378 380 2.177233 TCTACTCCCTCCGCTCCTAAAT 59.823 50.000 0.00 0.00 0.00 1.40
379 381 2.769602 ACTCCCTCCGCTCCTAAATA 57.230 50.000 0.00 0.00 0.00 1.40
380 382 3.261818 ACTCCCTCCGCTCCTAAATAT 57.738 47.619 0.00 0.00 0.00 1.28
381 383 3.588569 ACTCCCTCCGCTCCTAAATATT 58.411 45.455 0.00 0.00 0.00 1.28
382 384 3.974642 ACTCCCTCCGCTCCTAAATATTT 59.025 43.478 5.89 5.89 0.00 1.40
383 385 4.202367 ACTCCCTCCGCTCCTAAATATTTG 60.202 45.833 11.05 1.40 0.00 2.32
384 386 3.714798 TCCCTCCGCTCCTAAATATTTGT 59.285 43.478 11.05 0.00 0.00 2.83
385 387 4.065789 CCCTCCGCTCCTAAATATTTGTC 58.934 47.826 11.05 0.00 0.00 3.18
386 388 4.202367 CCCTCCGCTCCTAAATATTTGTCT 60.202 45.833 11.05 0.00 0.00 3.41
387 389 5.368989 CCTCCGCTCCTAAATATTTGTCTT 58.631 41.667 11.05 0.00 0.00 3.01
388 390 5.823045 CCTCCGCTCCTAAATATTTGTCTTT 59.177 40.000 11.05 0.00 0.00 2.52
389 391 6.318900 CCTCCGCTCCTAAATATTTGTCTTTT 59.681 38.462 11.05 0.00 0.00 2.27
390 392 7.148069 CCTCCGCTCCTAAATATTTGTCTTTTT 60.148 37.037 11.05 0.00 0.00 1.94
391 393 8.795842 TCCGCTCCTAAATATTTGTCTTTTTA 57.204 30.769 11.05 0.00 0.00 1.52
392 394 8.889717 TCCGCTCCTAAATATTTGTCTTTTTAG 58.110 33.333 11.05 0.00 33.47 1.85
393 395 8.889717 CCGCTCCTAAATATTTGTCTTTTTAGA 58.110 33.333 11.05 0.00 34.90 2.10
394 396 9.922305 CGCTCCTAAATATTTGTCTTTTTAGAG 57.078 33.333 11.05 4.94 34.90 2.43
407 409 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
408 410 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
424 426 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
425 427 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
426 428 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
427 429 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
428 430 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
429 431 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
430 432 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
431 433 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
432 434 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
433 435 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
435 437 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
463 465 7.986085 ATAGTGTAGTTTCACTCATTTTGCT 57.014 32.000 2.59 0.00 45.79 3.91
464 466 6.699575 AGTGTAGTTTCACTCATTTTGCTT 57.300 33.333 0.00 0.00 44.07 3.91
465 467 6.729187 AGTGTAGTTTCACTCATTTTGCTTC 58.271 36.000 0.00 0.00 44.07 3.86
466 468 6.318648 AGTGTAGTTTCACTCATTTTGCTTCA 59.681 34.615 0.00 0.00 44.07 3.02
467 469 7.013655 AGTGTAGTTTCACTCATTTTGCTTCAT 59.986 33.333 0.00 0.00 44.07 2.57
468 470 8.289618 GTGTAGTTTCACTCATTTTGCTTCATA 58.710 33.333 0.00 0.00 35.68 2.15
469 471 8.289618 TGTAGTTTCACTCATTTTGCTTCATAC 58.710 33.333 0.00 0.00 0.00 2.39
470 472 6.373779 AGTTTCACTCATTTTGCTTCATACG 58.626 36.000 0.00 0.00 0.00 3.06
471 473 5.940192 TTCACTCATTTTGCTTCATACGT 57.060 34.783 0.00 0.00 0.00 3.57
472 474 7.172532 AGTTTCACTCATTTTGCTTCATACGTA 59.827 33.333 0.00 0.00 0.00 3.57
473 475 6.647212 TCACTCATTTTGCTTCATACGTAG 57.353 37.500 0.08 0.00 0.00 3.51
475 477 6.310467 TCACTCATTTTGCTTCATACGTAGTC 59.690 38.462 0.08 0.00 43.93 2.59
476 478 6.090763 CACTCATTTTGCTTCATACGTAGTCA 59.909 38.462 0.08 0.00 43.93 3.41
477 479 6.090898 ACTCATTTTGCTTCATACGTAGTCAC 59.909 38.462 0.08 0.00 43.93 3.67
490 492 4.547956 CGTAGTCACGTGTTGAAATCTC 57.452 45.455 16.51 0.00 43.31 2.75
491 493 4.227538 CGTAGTCACGTGTTGAAATCTCT 58.772 43.478 16.51 4.33 43.31 3.10
492 494 5.388111 CGTAGTCACGTGTTGAAATCTCTA 58.612 41.667 16.51 3.48 43.31 2.43
493 495 5.508573 CGTAGTCACGTGTTGAAATCTCTAG 59.491 44.000 16.51 0.00 43.31 2.43
494 496 5.707242 AGTCACGTGTTGAAATCTCTAGA 57.293 39.130 16.51 0.00 35.39 2.43
495 497 6.085555 AGTCACGTGTTGAAATCTCTAGAA 57.914 37.500 16.51 0.00 35.39 2.10
496 498 6.513180 AGTCACGTGTTGAAATCTCTAGAAA 58.487 36.000 16.51 0.00 35.39 2.52
497 499 6.642950 AGTCACGTGTTGAAATCTCTAGAAAG 59.357 38.462 16.51 0.00 35.39 2.62
498 500 6.641314 GTCACGTGTTGAAATCTCTAGAAAGA 59.359 38.462 16.51 0.00 35.39 2.52
499 501 6.641314 TCACGTGTTGAAATCTCTAGAAAGAC 59.359 38.462 16.51 0.00 0.00 3.01
500 502 6.420903 CACGTGTTGAAATCTCTAGAAAGACA 59.579 38.462 7.58 0.00 0.00 3.41
501 503 6.984474 ACGTGTTGAAATCTCTAGAAAGACAA 59.016 34.615 0.00 0.00 0.00 3.18
502 504 7.494625 ACGTGTTGAAATCTCTAGAAAGACAAA 59.505 33.333 0.00 0.00 0.00 2.83
503 505 8.499162 CGTGTTGAAATCTCTAGAAAGACAAAT 58.501 33.333 0.00 0.00 0.00 2.32
514 516 9.672086 CTCTAGAAAGACAAATATCTAGGAACG 57.328 37.037 8.37 0.00 41.00 3.95
515 517 8.630917 TCTAGAAAGACAAATATCTAGGAACGG 58.369 37.037 8.37 0.00 41.00 4.44
516 518 7.419711 AGAAAGACAAATATCTAGGAACGGA 57.580 36.000 0.00 0.00 0.00 4.69
517 519 7.493367 AGAAAGACAAATATCTAGGAACGGAG 58.507 38.462 0.00 0.00 0.00 4.63
518 520 5.793030 AGACAAATATCTAGGAACGGAGG 57.207 43.478 0.00 0.00 0.00 4.30
519 521 4.589374 AGACAAATATCTAGGAACGGAGGG 59.411 45.833 0.00 0.00 0.00 4.30
520 522 4.553678 ACAAATATCTAGGAACGGAGGGA 58.446 43.478 0.00 0.00 0.00 4.20
521 523 4.589374 ACAAATATCTAGGAACGGAGGGAG 59.411 45.833 0.00 0.00 0.00 4.30
556 558 0.313987 CCGGTTCAGGTGCCTTTTTC 59.686 55.000 0.00 0.00 0.00 2.29
770 919 3.306364 CGAGATCGAGGCCTAATCCAATT 60.306 47.826 19.38 5.66 43.02 2.32
932 1082 1.511887 CGGAAGCACGCCAAATTCG 60.512 57.895 0.00 0.00 0.00 3.34
952 1102 0.257039 CCAACCCTCCCCTCAGATTG 59.743 60.000 0.00 0.00 0.00 2.67
1410 1560 2.641559 GTGCTTGCAGTGTGCCTC 59.358 61.111 0.00 0.00 44.23 4.70
1458 1608 2.572284 GCCGCGGACTACTTCTGT 59.428 61.111 33.48 0.00 32.41 3.41
1467 1617 2.233922 GGACTACTTCTGTTGCAGCCTA 59.766 50.000 0.00 0.00 0.00 3.93
1479 1629 2.744760 TGCAGCCTAGAGAAGATGTCT 58.255 47.619 0.00 0.00 40.25 3.41
1560 1710 0.524862 CTCCTGATGTGTTTGCCAGC 59.475 55.000 0.00 0.00 0.00 4.85
1641 1791 0.233848 CGGTGTTTGTTACCTGCGTC 59.766 55.000 0.00 0.00 36.03 5.19
1656 1806 1.301087 CGTCGTTGTTGGGGCAGTA 60.301 57.895 0.00 0.00 0.00 2.74
1734 1884 4.916041 TGTTGGATTCTTCCTGATCACT 57.084 40.909 0.00 0.00 43.07 3.41
1857 2007 7.408756 TGCAAATGAGTTATTAAGGAAGCAT 57.591 32.000 0.00 0.00 0.00 3.79
1899 2049 1.732259 GTAGTCACACCATTGCTTCCG 59.268 52.381 0.00 0.00 0.00 4.30
1935 2085 3.054287 TCTTCTCACACGGACTAGAGGAT 60.054 47.826 0.00 0.00 0.00 3.24
1983 2133 5.127845 TCTTGAGGAGGATACAAGTGATGAC 59.872 44.000 0.00 0.00 40.89 3.06
2052 2202 6.888105 TCATGTGGCTATCTACTCAAATCAA 58.112 36.000 0.00 0.00 0.00 2.57
2103 2253 2.069775 TGGGGTTGGAATGAAGAAGGA 58.930 47.619 0.00 0.00 0.00 3.36
2517 2667 9.136323 GTGATACTTGGGATTAATCCTTCAATT 57.864 33.333 29.24 21.45 46.35 2.32
2520 2670 7.888250 ACTTGGGATTAATCCTTCAATTCTC 57.112 36.000 29.24 13.03 46.35 2.87
2523 2673 5.104109 TGGGATTAATCCTTCAATTCTCGGT 60.104 40.000 29.24 0.00 46.35 4.69
2562 2712 2.639065 GGCAATTCGATGGGTGACTTA 58.361 47.619 0.00 0.00 0.00 2.24
2592 2742 0.544833 TGGCCTTGGCAATGAATGGT 60.545 50.000 14.04 0.00 34.49 3.55
2598 2748 2.832643 TGGCAATGAATGGTGGAGAT 57.167 45.000 0.00 0.00 0.00 2.75
2634 2784 0.983467 TGTCTGGCTGTTATGCAGGA 59.017 50.000 0.00 0.00 45.14 3.86
2643 2793 3.947834 GCTGTTATGCAGGACCTATGTTT 59.052 43.478 0.00 0.00 45.14 2.83
2655 2805 6.823689 CAGGACCTATGTTTAATACACTTGCT 59.176 38.462 0.00 0.00 40.19 3.91
2659 2809 4.718940 ATGTTTAATACACTTGCTGGCC 57.281 40.909 0.00 0.00 40.19 5.36
2676 2826 3.701542 CTGGCCTAGGAATATCGATGCTA 59.298 47.826 14.75 0.00 0.00 3.49
2694 2844 0.242825 TACTTGGAGCTTGGTCGACG 59.757 55.000 9.92 0.00 0.00 5.12
2793 2943 2.314647 GCTTGTTACGCTGCCACGA 61.315 57.895 2.16 0.00 36.70 4.35
2823 2973 1.336517 CGACCTAACAAGACGCTTGGA 60.337 52.381 19.13 9.22 0.00 3.53
2958 3108 7.861629 ACTGTCCTTTATACAGATGAAATGGA 58.138 34.615 10.02 0.00 45.89 3.41
2996 3149 4.318332 TCTGTTCTGTTGTTATGCCTCAG 58.682 43.478 0.00 0.00 0.00 3.35
3000 3153 5.412594 TGTTCTGTTGTTATGCCTCAGATTC 59.587 40.000 0.00 0.00 35.54 2.52
3004 3157 3.179443 TGTTATGCCTCAGATTCGGTC 57.821 47.619 0.00 0.00 0.00 4.79
3080 3234 8.350722 TGGTCTACTTATCTGTAAGCTTAATCG 58.649 37.037 7.99 0.00 40.82 3.34
3177 3372 1.400242 GCAGCGTGACCTTTTGTGATC 60.400 52.381 0.00 0.00 0.00 2.92
3226 3426 3.129287 CAGTTTGGCACTCTCACTTGTTT 59.871 43.478 0.00 0.00 30.92 2.83
3227 3427 3.129287 AGTTTGGCACTCTCACTTGTTTG 59.871 43.478 0.00 0.00 0.00 2.93
3228 3428 1.024271 TGGCACTCTCACTTGTTTGC 58.976 50.000 0.00 0.00 0.00 3.68
3229 3429 1.312815 GGCACTCTCACTTGTTTGCT 58.687 50.000 0.00 0.00 0.00 3.91
3230 3430 1.002033 GGCACTCTCACTTGTTTGCTG 60.002 52.381 0.00 0.00 0.00 4.41
3231 3431 1.942657 GCACTCTCACTTGTTTGCTGA 59.057 47.619 0.00 0.00 0.00 4.26
3232 3432 2.032204 GCACTCTCACTTGTTTGCTGAG 60.032 50.000 0.00 0.00 33.94 3.35
3233 3433 3.201290 CACTCTCACTTGTTTGCTGAGT 58.799 45.455 0.00 0.00 34.26 3.41
3234 3434 4.371786 CACTCTCACTTGTTTGCTGAGTA 58.628 43.478 0.00 0.00 34.26 2.59
3235 3435 4.447054 CACTCTCACTTGTTTGCTGAGTAG 59.553 45.833 0.00 0.00 34.26 2.57
3236 3436 4.100189 ACTCTCACTTGTTTGCTGAGTAGT 59.900 41.667 0.00 0.00 34.26 2.73
3237 3437 4.371786 TCTCACTTGTTTGCTGAGTAGTG 58.628 43.478 0.00 0.00 34.26 2.74
3238 3438 4.099419 TCTCACTTGTTTGCTGAGTAGTGA 59.901 41.667 0.00 0.00 39.53 3.41
3266 3466 7.331026 TGTAGTCATGCTTAGCTTGTTATCTT 58.669 34.615 17.57 4.00 35.60 2.40
3275 3475 6.614694 TTAGCTTGTTATCTTGTACTCCCA 57.385 37.500 0.00 0.00 0.00 4.37
3349 3549 9.220767 AGTTTGACAGAGTGTATAGAAAAATCC 57.779 33.333 0.00 0.00 0.00 3.01
3369 3569 5.982890 TCCGCAATGATCTATGATACTCA 57.017 39.130 0.00 0.00 0.00 3.41
3373 3573 7.879677 TCCGCAATGATCTATGATACTCAAAAT 59.120 33.333 0.00 0.00 0.00 1.82
3405 3605 9.481340 GACACAGCAGAATCAAATATATGTAGA 57.519 33.333 0.00 0.00 0.00 2.59
3575 3784 3.133542 CCTCCATAAGATGCTCACTGTGA 59.866 47.826 10.50 10.50 0.00 3.58
3601 3810 3.386543 ACGCAGTGAGGATAATGGC 57.613 52.632 0.00 0.00 42.51 4.40
3681 3890 1.593750 GGAGCAGAGTAGCGGCATG 60.594 63.158 1.45 0.00 40.40 4.06
3736 3945 5.752955 CGTCTTTTCATTTGTTTGGGTTGAT 59.247 36.000 0.00 0.00 0.00 2.57
3737 3946 6.292274 CGTCTTTTCATTTGTTTGGGTTGATG 60.292 38.462 0.00 0.00 0.00 3.07
3740 3949 7.826252 TCTTTTCATTTGTTTGGGTTGATGAAA 59.174 29.630 5.49 5.49 40.01 2.69
3748 3957 2.238521 TGGGTTGATGAAAGAAGTGGC 58.761 47.619 0.00 0.00 0.00 5.01
3791 4730 0.249238 TTGGCATTGCGTTCAACCAC 60.249 50.000 1.91 0.00 34.60 4.16
3814 4753 2.359900 GTCGATTCATTTGGTCTGCCT 58.640 47.619 0.00 0.00 35.27 4.75
3815 4754 2.096496 GTCGATTCATTTGGTCTGCCTG 59.904 50.000 0.00 0.00 35.27 4.85
3816 4755 2.086869 CGATTCATTTGGTCTGCCTGT 58.913 47.619 0.00 0.00 35.27 4.00
3817 4756 2.096496 CGATTCATTTGGTCTGCCTGTC 59.904 50.000 0.00 0.00 35.27 3.51
3818 4757 1.909700 TTCATTTGGTCTGCCTGTCC 58.090 50.000 0.00 0.00 35.27 4.02
3819 4758 0.321564 TCATTTGGTCTGCCTGTCCG 60.322 55.000 0.00 0.00 35.27 4.79
3820 4759 1.002134 ATTTGGTCTGCCTGTCCGG 60.002 57.895 0.00 0.00 35.27 5.14
3821 4760 1.779061 ATTTGGTCTGCCTGTCCGGT 61.779 55.000 0.00 0.00 35.27 5.28
3822 4761 2.391724 TTTGGTCTGCCTGTCCGGTC 62.392 60.000 0.00 0.00 35.27 4.79
3823 4762 4.436998 GGTCTGCCTGTCCGGTCG 62.437 72.222 0.00 0.00 34.25 4.79
3824 4763 4.436998 GTCTGCCTGTCCGGTCGG 62.437 72.222 0.00 0.00 34.25 4.79
3875 4814 7.475015 TGCATGCATCTAACTAAAAGAACATC 58.525 34.615 18.46 0.00 0.00 3.06
3883 4822 8.407457 TCTAACTAAAAGAACATCGCACATAG 57.593 34.615 0.00 0.00 0.00 2.23
3884 4823 8.033038 TCTAACTAAAAGAACATCGCACATAGT 58.967 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.990360 TCTTGTTCTTTACTGGTTTTTCTTTTT 57.010 25.926 0.00 0.00 0.00 1.94
32 33 9.639601 CTCTTGTTCTTTACTGGTTTTTCTTTT 57.360 29.630 0.00 0.00 0.00 2.27
33 34 9.020731 TCTCTTGTTCTTTACTGGTTTTTCTTT 57.979 29.630 0.00 0.00 0.00 2.52
34 35 8.575649 TCTCTTGTTCTTTACTGGTTTTTCTT 57.424 30.769 0.00 0.00 0.00 2.52
35 36 8.047310 TCTCTCTTGTTCTTTACTGGTTTTTCT 58.953 33.333 0.00 0.00 0.00 2.52
36 37 8.209917 TCTCTCTTGTTCTTTACTGGTTTTTC 57.790 34.615 0.00 0.00 0.00 2.29
37 38 8.753497 ATCTCTCTTGTTCTTTACTGGTTTTT 57.247 30.769 0.00 0.00 0.00 1.94
38 39 9.847224 TTATCTCTCTTGTTCTTTACTGGTTTT 57.153 29.630 0.00 0.00 0.00 2.43
39 40 9.495572 CTTATCTCTCTTGTTCTTTACTGGTTT 57.504 33.333 0.00 0.00 0.00 3.27
40 41 8.871125 TCTTATCTCTCTTGTTCTTTACTGGTT 58.129 33.333 0.00 0.00 0.00 3.67
41 42 8.423906 TCTTATCTCTCTTGTTCTTTACTGGT 57.576 34.615 0.00 0.00 0.00 4.00
42 43 9.712305 TTTCTTATCTCTCTTGTTCTTTACTGG 57.288 33.333 0.00 0.00 0.00 4.00
47 48 9.278978 GTCCTTTTCTTATCTCTCTTGTTCTTT 57.721 33.333 0.00 0.00 0.00 2.52
48 49 7.880713 GGTCCTTTTCTTATCTCTCTTGTTCTT 59.119 37.037 0.00 0.00 0.00 2.52
49 50 7.390823 GGTCCTTTTCTTATCTCTCTTGTTCT 58.609 38.462 0.00 0.00 0.00 3.01
50 51 6.311690 CGGTCCTTTTCTTATCTCTCTTGTTC 59.688 42.308 0.00 0.00 0.00 3.18
51 52 6.014499 TCGGTCCTTTTCTTATCTCTCTTGTT 60.014 38.462 0.00 0.00 0.00 2.83
52 53 5.480772 TCGGTCCTTTTCTTATCTCTCTTGT 59.519 40.000 0.00 0.00 0.00 3.16
53 54 5.967088 TCGGTCCTTTTCTTATCTCTCTTG 58.033 41.667 0.00 0.00 0.00 3.02
54 55 6.211785 ACTTCGGTCCTTTTCTTATCTCTCTT 59.788 38.462 0.00 0.00 0.00 2.85
55 56 5.717654 ACTTCGGTCCTTTTCTTATCTCTCT 59.282 40.000 0.00 0.00 0.00 3.10
56 57 5.968254 ACTTCGGTCCTTTTCTTATCTCTC 58.032 41.667 0.00 0.00 0.00 3.20
57 58 7.477945 TTACTTCGGTCCTTTTCTTATCTCT 57.522 36.000 0.00 0.00 0.00 3.10
58 59 8.719560 ATTTACTTCGGTCCTTTTCTTATCTC 57.280 34.615 0.00 0.00 0.00 2.75
59 60 8.541234 AGATTTACTTCGGTCCTTTTCTTATCT 58.459 33.333 0.00 0.00 0.00 1.98
60 61 8.719560 AGATTTACTTCGGTCCTTTTCTTATC 57.280 34.615 0.00 0.00 0.00 1.75
61 62 9.163899 GAAGATTTACTTCGGTCCTTTTCTTAT 57.836 33.333 0.00 0.00 44.15 1.73
62 63 8.543862 GAAGATTTACTTCGGTCCTTTTCTTA 57.456 34.615 0.00 0.00 44.15 2.10
63 64 7.436430 GAAGATTTACTTCGGTCCTTTTCTT 57.564 36.000 0.00 0.00 44.15 2.52
75 76 7.469594 AAAACCAGTTTCGGGAAGATTTACTTC 60.470 37.037 0.00 0.00 41.50 3.01
76 77 4.981812 ACCAGTTTCGGGAAGATTTACTT 58.018 39.130 0.00 0.00 42.03 2.24
77 78 4.635699 ACCAGTTTCGGGAAGATTTACT 57.364 40.909 0.00 0.00 0.00 2.24
78 79 5.700722 AAACCAGTTTCGGGAAGATTTAC 57.299 39.130 0.00 0.00 0.00 2.01
79 80 6.718522 AAAAACCAGTTTCGGGAAGATTTA 57.281 33.333 0.00 0.00 31.45 1.40
80 81 5.607939 AAAAACCAGTTTCGGGAAGATTT 57.392 34.783 0.00 0.00 31.45 2.17
102 103 8.909923 AGTTTCGGGAAGATTTCTTTCTAAAAA 58.090 29.630 0.00 0.00 36.11 1.94
103 104 8.349983 CAGTTTCGGGAAGATTTCTTTCTAAAA 58.650 33.333 0.00 0.00 36.11 1.52
104 105 7.040686 CCAGTTTCGGGAAGATTTCTTTCTAAA 60.041 37.037 0.00 0.00 36.11 1.85
105 106 6.430000 CCAGTTTCGGGAAGATTTCTTTCTAA 59.570 38.462 0.00 0.00 36.11 2.10
106 107 5.938125 CCAGTTTCGGGAAGATTTCTTTCTA 59.062 40.000 0.00 0.00 36.11 2.10
107 108 4.762251 CCAGTTTCGGGAAGATTTCTTTCT 59.238 41.667 0.00 0.00 36.11 2.52
108 109 4.519350 ACCAGTTTCGGGAAGATTTCTTTC 59.481 41.667 0.00 0.00 36.11 2.62
109 110 4.278419 CACCAGTTTCGGGAAGATTTCTTT 59.722 41.667 0.00 0.00 36.11 2.52
110 111 3.821033 CACCAGTTTCGGGAAGATTTCTT 59.179 43.478 0.00 0.00 39.23 2.52
111 112 3.412386 CACCAGTTTCGGGAAGATTTCT 58.588 45.455 0.00 0.00 0.00 2.52
112 113 2.488153 CCACCAGTTTCGGGAAGATTTC 59.512 50.000 0.00 0.00 0.00 2.17
143 144 1.067142 TCGGAATGTAGTGCTCGCTTT 60.067 47.619 0.00 0.00 0.00 3.51
151 152 3.181530 CGAGCAGTTTTCGGAATGTAGTG 60.182 47.826 0.00 0.00 34.56 2.74
161 162 1.504359 TTGTACCCGAGCAGTTTTCG 58.496 50.000 0.00 0.00 37.78 3.46
164 165 1.722011 CGATTGTACCCGAGCAGTTT 58.278 50.000 0.00 0.00 0.00 2.66
172 173 3.004419 TCTCAATAGAGCGATTGTACCCG 59.996 47.826 8.33 0.00 41.81 5.28
181 182 0.681733 GGGCCATCTCAATAGAGCGA 59.318 55.000 4.39 0.00 41.81 4.93
221 222 1.067669 TCACGATGTATGGAGCTCTGC 59.932 52.381 14.64 0.00 0.00 4.26
241 242 2.586425 CAATGGGGTGCGAATAGGATT 58.414 47.619 0.00 0.00 0.00 3.01
253 254 0.539986 ATAGTTCGACGCAATGGGGT 59.460 50.000 1.62 0.00 43.72 4.95
256 257 1.934589 TGGATAGTTCGACGCAATGG 58.065 50.000 0.00 0.00 0.00 3.16
282 283 1.202580 ACTCTCTCACCAACTGTGTGC 60.203 52.381 0.00 0.00 45.61 4.57
287 288 6.405286 CCAGTTAGATACTCTCTCACCAACTG 60.405 46.154 0.00 0.00 41.93 3.16
294 295 5.194432 GTGACCCAGTTAGATACTCTCTCA 58.806 45.833 0.00 0.00 33.85 3.27
343 345 4.368565 GGAGTAGAAGGTTCCCAAAACT 57.631 45.455 0.00 0.00 32.29 2.66
361 363 4.202367 ACAAATATTTAGGAGCGGAGGGAG 60.202 45.833 0.00 0.00 0.00 4.30
362 364 3.714798 ACAAATATTTAGGAGCGGAGGGA 59.285 43.478 0.00 0.00 0.00 4.20
363 365 4.065789 GACAAATATTTAGGAGCGGAGGG 58.934 47.826 0.00 0.00 0.00 4.30
364 366 4.962155 AGACAAATATTTAGGAGCGGAGG 58.038 43.478 0.00 0.00 0.00 4.30
365 367 6.927294 AAAGACAAATATTTAGGAGCGGAG 57.073 37.500 0.00 0.00 0.00 4.63
366 368 7.696992 AAAAAGACAAATATTTAGGAGCGGA 57.303 32.000 0.00 0.00 0.00 5.54
367 369 8.889717 TCTAAAAAGACAAATATTTAGGAGCGG 58.110 33.333 0.00 0.00 36.48 5.52
368 370 9.922305 CTCTAAAAAGACAAATATTTAGGAGCG 57.078 33.333 0.00 0.00 36.48 5.03
381 383 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
382 384 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
386 388 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
387 389 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
388 390 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
389 391 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
390 392 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
391 393 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
392 394 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
393 395 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
394 396 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
395 397 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
396 398 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
397 399 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
398 400 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
399 401 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
400 402 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
401 403 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
402 404 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
403 405 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
404 406 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
405 407 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
406 408 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
407 409 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
409 411 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
447 449 6.142817 ACGTATGAAGCAAAATGAGTGAAAC 58.857 36.000 0.00 0.00 0.00 2.78
448 450 6.312399 ACGTATGAAGCAAAATGAGTGAAA 57.688 33.333 0.00 0.00 0.00 2.69
449 451 5.940192 ACGTATGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
450 452 6.163476 ACTACGTATGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
451 453 6.090763 TGACTACGTATGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
452 454 6.090898 GTGACTACGTATGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
453 455 6.470160 GTGACTACGTATGAAGCAAAATGAG 58.530 40.000 0.00 0.00 0.00 2.90
454 456 5.061684 CGTGACTACGTATGAAGCAAAATGA 59.938 40.000 0.00 0.00 44.99 2.57
455 457 5.248087 CGTGACTACGTATGAAGCAAAATG 58.752 41.667 0.00 0.00 44.99 2.32
456 458 5.450376 CGTGACTACGTATGAAGCAAAAT 57.550 39.130 0.00 0.00 44.99 1.82
457 459 4.896562 CGTGACTACGTATGAAGCAAAA 57.103 40.909 0.00 0.00 44.99 2.44
470 472 6.609533 TCTAGAGATTTCAACACGTGACTAC 58.390 40.000 25.01 6.63 35.39 2.73
471 473 6.812879 TCTAGAGATTTCAACACGTGACTA 57.187 37.500 25.01 3.25 35.39 2.59
472 474 5.707242 TCTAGAGATTTCAACACGTGACT 57.293 39.130 25.01 5.75 35.39 3.41
473 475 6.641314 TCTTTCTAGAGATTTCAACACGTGAC 59.359 38.462 25.01 4.36 35.39 3.67
474 476 6.641314 GTCTTTCTAGAGATTTCAACACGTGA 59.359 38.462 25.01 0.00 0.00 4.35
475 477 6.420903 TGTCTTTCTAGAGATTTCAACACGTG 59.579 38.462 15.48 15.48 0.00 4.49
476 478 6.513180 TGTCTTTCTAGAGATTTCAACACGT 58.487 36.000 0.00 0.00 0.00 4.49
477 479 7.408132 TTGTCTTTCTAGAGATTTCAACACG 57.592 36.000 0.00 0.00 0.00 4.49
488 490 9.672086 CGTTCCTAGATATTTGTCTTTCTAGAG 57.328 37.037 7.26 0.00 39.92 2.43
489 491 8.630917 CCGTTCCTAGATATTTGTCTTTCTAGA 58.369 37.037 7.26 0.00 39.92 2.43
490 492 8.630917 TCCGTTCCTAGATATTTGTCTTTCTAG 58.369 37.037 0.00 0.00 38.15 2.43
491 493 8.529424 TCCGTTCCTAGATATTTGTCTTTCTA 57.471 34.615 0.00 0.00 0.00 2.10
492 494 7.418025 CCTCCGTTCCTAGATATTTGTCTTTCT 60.418 40.741 0.00 0.00 0.00 2.52
493 495 6.702282 CCTCCGTTCCTAGATATTTGTCTTTC 59.298 42.308 0.00 0.00 0.00 2.62
494 496 6.408206 CCCTCCGTTCCTAGATATTTGTCTTT 60.408 42.308 0.00 0.00 0.00 2.52
495 497 5.070580 CCCTCCGTTCCTAGATATTTGTCTT 59.929 44.000 0.00 0.00 0.00 3.01
496 498 4.589374 CCCTCCGTTCCTAGATATTTGTCT 59.411 45.833 0.00 0.00 0.00 3.41
497 499 4.587684 TCCCTCCGTTCCTAGATATTTGTC 59.412 45.833 0.00 0.00 0.00 3.18
498 500 4.553678 TCCCTCCGTTCCTAGATATTTGT 58.446 43.478 0.00 0.00 0.00 2.83
499 501 4.589374 ACTCCCTCCGTTCCTAGATATTTG 59.411 45.833 0.00 0.00 0.00 2.32
500 502 4.817286 ACTCCCTCCGTTCCTAGATATTT 58.183 43.478 0.00 0.00 0.00 1.40
501 503 4.472690 ACTCCCTCCGTTCCTAGATATT 57.527 45.455 0.00 0.00 0.00 1.28
502 504 4.018233 CCTACTCCCTCCGTTCCTAGATAT 60.018 50.000 0.00 0.00 0.00 1.63
503 505 3.330110 CCTACTCCCTCCGTTCCTAGATA 59.670 52.174 0.00 0.00 0.00 1.98
504 506 2.108601 CCTACTCCCTCCGTTCCTAGAT 59.891 54.545 0.00 0.00 0.00 1.98
505 507 1.493871 CCTACTCCCTCCGTTCCTAGA 59.506 57.143 0.00 0.00 0.00 2.43
506 508 1.493871 TCCTACTCCCTCCGTTCCTAG 59.506 57.143 0.00 0.00 0.00 3.02
507 509 1.493871 CTCCTACTCCCTCCGTTCCTA 59.506 57.143 0.00 0.00 0.00 2.94
508 510 0.259356 CTCCTACTCCCTCCGTTCCT 59.741 60.000 0.00 0.00 0.00 3.36
509 511 0.756070 CCTCCTACTCCCTCCGTTCC 60.756 65.000 0.00 0.00 0.00 3.62
510 512 0.033306 ACCTCCTACTCCCTCCGTTC 60.033 60.000 0.00 0.00 0.00 3.95
511 513 0.412640 AACCTCCTACTCCCTCCGTT 59.587 55.000 0.00 0.00 0.00 4.44
512 514 0.412640 AAACCTCCTACTCCCTCCGT 59.587 55.000 0.00 0.00 0.00 4.69
513 515 1.112950 GAAACCTCCTACTCCCTCCG 58.887 60.000 0.00 0.00 0.00 4.63
514 516 2.292323 TGAGAAACCTCCTACTCCCTCC 60.292 54.545 0.00 0.00 0.00 4.30
515 517 2.761767 GTGAGAAACCTCCTACTCCCTC 59.238 54.545 0.00 0.00 0.00 4.30
516 518 2.560158 GGTGAGAAACCTCCTACTCCCT 60.560 54.545 0.00 0.00 46.55 4.20
517 519 1.832366 GGTGAGAAACCTCCTACTCCC 59.168 57.143 0.00 0.00 46.55 4.30
700 849 1.199327 GCCTCGGCTTTTAGAAACACC 59.801 52.381 0.00 0.00 38.26 4.16
722 871 1.546476 CTAGCCGTTTCCTGACAGAGT 59.454 52.381 3.32 0.00 0.00 3.24
770 919 0.600782 GTCGTTGTTAAGTGGGCCGA 60.601 55.000 0.00 0.00 0.00 5.54
932 1082 1.575447 AATCTGAGGGGAGGGTTGGC 61.575 60.000 0.00 0.00 0.00 4.52
1046 1196 4.664267 AGAGCACCAGGGAGGCCA 62.664 66.667 5.01 0.00 43.14 5.36
1262 1412 4.675029 CGAAACCCTCGTGGCGGT 62.675 66.667 0.00 0.00 42.89 5.68
1410 1560 2.885644 ATGTAGAACAGCGCCGCG 60.886 61.111 8.83 8.83 0.00 6.46
1458 1608 3.102972 AGACATCTTCTCTAGGCTGCAA 58.897 45.455 0.50 0.00 0.00 4.08
1467 1617 0.459934 GCAGCGCAGACATCTTCTCT 60.460 55.000 11.47 0.00 28.96 3.10
1503 1653 1.761174 CAGGGTAACACCAGCCACT 59.239 57.895 0.00 0.00 41.02 4.00
1560 1710 0.817013 ACCCCATAAACGCTGCAATG 59.183 50.000 0.00 0.00 0.00 2.82
1641 1791 1.750193 ATGATACTGCCCCAACAACG 58.250 50.000 0.00 0.00 0.00 4.10
1734 1884 4.917385 ACATAATAGACAGTGCCACCAAA 58.083 39.130 0.00 0.00 0.00 3.28
1899 2049 3.133183 GTGAGAAGATACTTCCCCTCACC 59.867 52.174 15.22 4.84 41.33 4.02
1935 2085 6.101650 AGTGAACTGTACACAGAATCATCA 57.898 37.500 16.05 8.74 46.59 3.07
1983 2133 3.428282 GTGTTTACCTGGGCCGCG 61.428 66.667 0.00 0.00 0.00 6.46
2052 2202 1.079490 TCAGGTGAACCATCTCTCCCT 59.921 52.381 1.62 0.00 38.89 4.20
2322 2472 2.902486 TGCAATCCCAAAAATACCAGCA 59.098 40.909 0.00 0.00 0.00 4.41
2517 2667 2.035704 TGCTAACACCGTTAAACCGAGA 59.964 45.455 0.00 0.00 0.00 4.04
2520 2670 2.159626 CCATGCTAACACCGTTAAACCG 60.160 50.000 0.00 0.00 0.00 4.44
2523 2673 2.438411 CCCCATGCTAACACCGTTAAA 58.562 47.619 0.00 0.00 0.00 1.52
2562 2712 1.002315 GCCAAGGCCACATTTGACATT 59.998 47.619 5.01 0.00 34.56 2.71
2592 2742 2.840038 AGCAATCTGTACACCATCTCCA 59.160 45.455 0.00 0.00 0.00 3.86
2598 2748 4.383010 CCAGACATAGCAATCTGTACACCA 60.383 45.833 0.00 0.00 40.70 4.17
2634 2784 5.357032 GCCAGCAAGTGTATTAAACATAGGT 59.643 40.000 0.00 0.00 41.10 3.08
2643 2793 3.380393 TCCTAGGCCAGCAAGTGTATTA 58.620 45.455 5.01 0.00 0.00 0.98
2655 2805 2.540383 AGCATCGATATTCCTAGGCCA 58.460 47.619 5.01 0.00 0.00 5.36
2659 2809 6.516739 TCCAAGTAGCATCGATATTCCTAG 57.483 41.667 0.00 0.00 0.00 3.02
2676 2826 1.006102 CGTCGACCAAGCTCCAAGT 60.006 57.895 10.58 0.00 0.00 3.16
2694 2844 3.073274 AGAACATAAGAGTTGGGTGCC 57.927 47.619 0.00 0.00 0.00 5.01
2793 2943 2.106683 GTTAGGTCGCATGCCGCTT 61.107 57.895 13.15 4.03 39.08 4.68
2805 2955 1.692519 ACTCCAAGCGTCTTGTTAGGT 59.307 47.619 15.28 7.83 0.00 3.08
2823 2973 0.990374 AGAGAGCAATGAGGCCAACT 59.010 50.000 5.01 0.00 0.00 3.16
2958 3108 5.760253 CAGAACAGAGGAACAATGTACAACT 59.240 40.000 0.00 0.00 0.00 3.16
2996 3149 1.202371 TGACAGGCATACGACCGAATC 60.202 52.381 0.00 0.00 0.00 2.52
3000 3153 1.226974 CCTGACAGGCATACGACCG 60.227 63.158 8.99 0.00 0.00 4.79
3024 3177 3.879295 GCATGCTCTGGCTTTATTGTCTA 59.121 43.478 11.37 0.00 39.59 2.59
3164 3328 7.379529 CACATACAAAACAGATCACAAAAGGTC 59.620 37.037 0.00 0.00 0.00 3.85
3166 3330 7.379529 GTCACATACAAAACAGATCACAAAAGG 59.620 37.037 0.00 0.00 0.00 3.11
3226 3426 4.768130 GACTACAAGTCACTACTCAGCA 57.232 45.455 2.22 0.00 44.45 4.41
3237 3437 4.932200 ACAAGCTAAGCATGACTACAAGTC 59.068 41.667 0.00 0.01 45.26 3.01
3238 3438 4.899502 ACAAGCTAAGCATGACTACAAGT 58.100 39.130 0.00 0.00 31.38 3.16
3266 3466 3.773418 TTTTGGAACGATGGGAGTACA 57.227 42.857 0.00 0.00 0.00 2.90
3333 3533 7.716998 AGATCATTGCGGATTTTTCTATACACT 59.283 33.333 0.00 0.00 0.00 3.55
3334 3534 7.865707 AGATCATTGCGGATTTTTCTATACAC 58.134 34.615 0.00 0.00 0.00 2.90
3369 3569 7.218228 TGATTCTGCTGTGTCAATGTATTTT 57.782 32.000 0.00 0.00 0.00 1.82
3373 3573 6.822667 ATTTGATTCTGCTGTGTCAATGTA 57.177 33.333 11.69 2.28 31.39 2.29
3520 3729 6.919721 TGCGAAATAGCCTAGAAACATTTTT 58.080 32.000 0.00 0.00 36.02 1.94
3529 3738 2.908688 TGCATGCGAAATAGCCTAGA 57.091 45.000 14.09 0.00 36.02 2.43
3530 3739 3.304257 CCTTTGCATGCGAAATAGCCTAG 60.304 47.826 20.68 6.89 36.02 3.02
3531 3740 2.618241 CCTTTGCATGCGAAATAGCCTA 59.382 45.455 20.68 0.00 36.02 3.93
3532 3741 1.406539 CCTTTGCATGCGAAATAGCCT 59.593 47.619 20.68 0.00 36.02 4.58
3575 3784 0.827925 TCCTCACTGCGTCTCAACCT 60.828 55.000 0.00 0.00 0.00 3.50
3601 3810 0.604780 CCAACTGCTCCAGTGACCAG 60.605 60.000 0.00 0.00 44.62 4.00
3636 3845 2.430694 TGACTGCATACCGCTACTCATT 59.569 45.455 0.00 0.00 43.06 2.57
3666 3875 2.512286 TGCATGCCGCTACTCTGC 60.512 61.111 16.68 0.00 43.06 4.26
3681 3890 1.154225 CGTTTGGATTCGGCACTGC 60.154 57.895 0.00 0.00 0.00 4.40
3736 3945 1.301401 CCGGACGCCACTTCTTTCA 60.301 57.895 0.00 0.00 0.00 2.69
3737 3946 2.677979 GCCGGACGCCACTTCTTTC 61.678 63.158 5.05 0.00 0.00 2.62
3759 3968 1.431440 TGCCAACGCAAACACAGAC 59.569 52.632 0.00 0.00 43.74 3.51
3791 4730 1.665679 CAGACCAAATGAATCGACCGG 59.334 52.381 0.00 0.00 0.00 5.28
3818 4757 1.010125 CATATTTTGCCGCCGACCG 60.010 57.895 0.00 0.00 0.00 4.79
3819 4758 1.299089 GCATATTTTGCCGCCGACC 60.299 57.895 0.00 0.00 46.15 4.79
3820 4759 4.302154 GCATATTTTGCCGCCGAC 57.698 55.556 0.00 0.00 46.15 4.79
3828 4767 8.729529 TGCATGAAAATTTTGTGCATATTTTG 57.270 26.923 25.26 9.14 40.51 2.44
3843 4782 9.309516 CTTTTAGTTAGATGCATGCATGAAAAT 57.690 29.630 36.73 27.38 36.70 1.82
3875 4814 6.656314 TTGGTTGTATTAGAACTATGTGCG 57.344 37.500 3.98 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.