Multiple sequence alignment - TraesCS4A01G191500

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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 TraesCS4A01G191500 chr4A 100.000 6058 0 0 1 6058 471916815 471922872 0.000000e+00 11188.0
1 TraesCS4A01G191500 chr4A 90.404 198 17 2 5271 5466 471923315 471923118 6.020000e-65 259.0
2 TraesCS4A01G191500 chr4A 95.139 144 7 0 3630 3773 617326377 617326520 1.700000e-55 228.0
3 TraesCS4A01G191500 chr4D 95.501 3156 90 23 396 3540 103256352 103253238 0.000000e+00 4994.0
4 TraesCS4A01G191500 chr4D 97.868 1501 30 2 3772 5271 103253204 103251705 0.000000e+00 2593.0
5 TraesCS4A01G191500 chr4D 90.230 348 29 4 5712 6058 200716310 200715967 3.330000e-122 449.0
6 TraesCS4A01G191500 chr4D 92.800 125 7 2 3657 3781 23484233 23484355 4.820000e-41 180.0
7 TraesCS4A01G191500 chr4D 85.625 160 22 1 1 160 319383689 319383847 3.760000e-37 167.0
8 TraesCS4A01G191500 chr4D 86.822 129 17 0 7 135 269156565 269156437 1.760000e-30 145.0
9 TraesCS4A01G191500 chr4D 98.000 50 1 0 3113 3162 103253691 103253642 3.010000e-13 87.9
10 TraesCS4A01G191500 chr4D 94.737 38 0 1 3598 3633 103253238 103253201 2.360000e-04 58.4
11 TraesCS4A01G191500 chr4B 94.659 3183 142 14 1 3162 147384175 147381000 0.000000e+00 4911.0
12 TraesCS4A01G191500 chr4B 96.611 1505 31 5 3775 5271 147380518 147379026 0.000000e+00 2479.0
13 TraesCS4A01G191500 chr4B 90.635 299 23 3 5270 5566 5047055 5046760 5.690000e-105 392.0
14 TraesCS4A01G191500 chr4B 98.788 165 1 1 3158 3322 147380976 147380813 5.940000e-75 292.0
15 TraesCS4A01G191500 chr4B 98.182 165 3 0 3467 3631 147380684 147380520 7.680000e-74 289.0
16 TraesCS4A01G191500 chr4B 96.386 83 3 0 3387 3469 147380813 147380731 2.940000e-28 137.0
17 TraesCS4A01G191500 chr4B 92.958 71 5 0 5618 5688 5046602 5046532 2.990000e-18 104.0
18 TraesCS4A01G191500 chr7A 99.593 492 2 0 5567 6058 709714871 709715362 0.000000e+00 898.0
19 TraesCS4A01G191500 chr7A 100.000 296 0 0 5271 5566 709714466 709714761 1.150000e-151 547.0
20 TraesCS4A01G191500 chr7A 89.091 220 18 6 5251 5466 709715827 709715610 1.000000e-67 268.0
21 TraesCS4A01G191500 chr7A 89.950 199 17 2 5271 5466 418605207 418605405 2.800000e-63 254.0
22 TraesCS4A01G191500 chr2A 99.390 492 3 0 5567 6058 82159253 82159744 0.000000e+00 893.0
23 TraesCS4A01G191500 chr2A 100.000 296 0 0 5271 5566 82158848 82159143 1.150000e-151 547.0
24 TraesCS4A01G191500 chr2A 90.500 200 17 2 5269 5466 82160191 82159992 4.660000e-66 263.0
25 TraesCS4A01G191500 chr3B 94.764 382 20 0 5677 6058 542137301 542136920 4.040000e-166 595.0
26 TraesCS4A01G191500 chr3B 95.290 276 7 3 5293 5566 542158115 542157844 3.350000e-117 433.0
27 TraesCS4A01G191500 chr3B 88.608 158 13 2 3627 3779 133002191 133002348 2.880000e-43 187.0
28 TraesCS4A01G191500 chr3B 95.775 71 2 1 5618 5687 542157691 542157621 4.960000e-21 113.0
29 TraesCS4A01G191500 chr3B 92.958 71 4 1 163 232 330375131 330375061 1.070000e-17 102.0
30 TraesCS4A01G191500 chr7B 89.250 400 32 9 5615 6011 242511918 242512309 1.960000e-134 490.0
31 TraesCS4A01G191500 chr7B 89.884 346 30 4 5711 6055 193200036 193200377 2.000000e-119 440.0
32 TraesCS4A01G191500 chr5A 85.256 468 62 7 1910 2373 320561079 320561543 5.490000e-130 475.0
33 TraesCS4A01G191500 chr5A 83.663 404 54 4 4044 4435 320562860 320563263 2.670000e-98 370.0
34 TraesCS4A01G191500 chr5A 88.360 189 21 1 2825 3013 320562065 320562252 6.110000e-55 226.0
35 TraesCS4A01G191500 chr5A 85.926 135 19 0 1 135 278183493 278183627 1.760000e-30 145.0
36 TraesCS4A01G191500 chr5A 92.000 75 5 1 984 1057 320559815 320559889 2.990000e-18 104.0
37 TraesCS4A01G191500 chr5B 87.811 402 46 3 1910 2310 270861945 270862344 9.190000e-128 468.0
38 TraesCS4A01G191500 chr5B 82.898 421 58 8 4044 4450 270863717 270864137 3.450000e-97 366.0
39 TraesCS4A01G191500 chr5B 88.360 189 21 1 2825 3013 270862928 270863115 6.110000e-55 226.0
40 TraesCS4A01G191500 chr5B 90.805 87 5 3 973 1057 270860682 270860767 4.960000e-21 113.0
41 TraesCS4A01G191500 chr5B 93.056 72 4 1 162 232 12768910 12768839 2.990000e-18 104.0
42 TraesCS4A01G191500 chr5D 84.746 472 62 9 1910 2376 233971401 233970935 1.190000e-126 464.0
43 TraesCS4A01G191500 chr5D 88.539 349 35 4 5711 6058 489745711 489745367 9.390000e-113 418.0
44 TraesCS4A01G191500 chr5D 83.848 421 54 8 4044 4450 233969617 233969197 7.360000e-104 388.0
45 TraesCS4A01G191500 chr5D 87.500 192 22 2 2825 3016 233970410 233970221 2.840000e-53 220.0
46 TraesCS4A01G191500 chr5D 84.375 160 24 1 1 160 105489661 105489819 8.130000e-34 156.0
47 TraesCS4A01G191500 chr5D 83.750 160 25 1 1 160 69583377 69583535 3.780000e-32 150.0
48 TraesCS4A01G191500 chr5D 85.926 135 19 0 1 135 67242413 67242547 1.760000e-30 145.0
49 TraesCS4A01G191500 chr5D 93.333 75 4 1 984 1057 233972678 233972604 6.420000e-20 110.0
50 TraesCS4A01G191500 chr3D 89.914 347 30 4 5710 6055 497287871 497288213 5.570000e-120 442.0
51 TraesCS4A01G191500 chr2D 88.571 350 32 4 5711 6058 232181001 232180658 9.390000e-113 418.0
52 TraesCS4A01G191500 chr2D 87.407 135 17 0 1 135 130153995 130154129 8.130000e-34 156.0
53 TraesCS4A01G191500 chr1A 100.000 193 0 0 5271 5463 574664927 574664735 2.080000e-94 357.0
54 TraesCS4A01G191500 chr1A 94.558 147 8 0 3631 3777 387472994 387472848 1.700000e-55 228.0
55 TraesCS4A01G191500 chr3A 98.701 154 2 0 3629 3782 44627660 44627507 2.150000e-69 274.0
56 TraesCS4A01G191500 chr3A 94.483 145 3 1 3631 3775 210932339 210932200 1.020000e-52 219.0
57 TraesCS4A01G191500 chr3A 94.366 71 3 1 163 232 597587911 597587981 2.310000e-19 108.0
58 TraesCS4A01G191500 chr6A 92.466 146 5 2 3632 3771 597947613 597947468 2.860000e-48 204.0
59 TraesCS4A01G191500 chr6A 89.583 144 10 2 3631 3774 38683204 38683342 1.740000e-40 178.0
60 TraesCS4A01G191500 chr7D 91.781 146 8 2 3631 3775 607049656 607049514 3.700000e-47 200.0
61 TraesCS4A01G191500 chr7D 92.958 71 4 1 163 232 319007517 319007447 1.070000e-17 102.0
62 TraesCS4A01G191500 chr6B 82.468 154 26 1 7 160 314478682 314478530 3.810000e-27 134.0
63 TraesCS4A01G191500 chr6B 93.056 72 2 3 163 232 582465581 582465511 1.070000e-17 102.0
64 TraesCS4A01G191500 chrUn 94.366 71 3 1 163 232 11282714 11282644 2.310000e-19 108.0
65 TraesCS4A01G191500 chr1B 94.286 70 3 1 164 232 151475581 151475650 8.300000e-19 106.0
66 TraesCS4A01G191500 chr2B 92.958 71 4 1 163 232 398354322 398354392 1.070000e-17 102.0


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 TraesCS4A01G191500 chr4A 471916815 471922872 6057 False 11188.000 11188 100.00000 1 6058 1 chr4A.!!$F1 6057
1 TraesCS4A01G191500 chr4D 103251705 103256352 4647 True 1933.325 4994 96.52650 396 5271 4 chr4D.!!$R3 4875
2 TraesCS4A01G191500 chr4B 147379026 147384175 5149 True 1621.600 4911 96.92520 1 5271 5 chr4B.!!$R2 5270
3 TraesCS4A01G191500 chr4B 5046532 5047055 523 True 248.000 392 91.79650 5270 5688 2 chr4B.!!$R1 418
4 TraesCS4A01G191500 chr7A 709714466 709715362 896 False 722.500 898 99.79650 5271 6058 2 chr7A.!!$F2 787
5 TraesCS4A01G191500 chr2A 82158848 82159744 896 False 720.000 893 99.69500 5271 6058 2 chr2A.!!$F1 787
6 TraesCS4A01G191500 chr5A 320559815 320563263 3448 False 293.750 475 87.31975 984 4435 4 chr5A.!!$F2 3451
7 TraesCS4A01G191500 chr5B 270860682 270864137 3455 False 293.250 468 87.46850 973 4450 4 chr5B.!!$F1 3477
8 TraesCS4A01G191500 chr5D 233969197 233972678 3481 True 295.500 464 87.35675 984 4450 4 chr5D.!!$R2 3466

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
445 447 0.540830 ACCCTCTTCTCAGCTGACGT 60.541 55.000 13.74 0.0 0.00 4.34 F
491 493 1.341080 AGGGGCTGAAAATGTTGGTG 58.659 50.000 0.00 0.0 0.00 4.17 F
600 603 2.961741 TCTTTGTGGCAAAGGCATTGTA 59.038 40.909 17.98 0.0 43.71 2.41 F
728 731 4.233789 CAAGAAGAGTCTTTCCTCACTCG 58.766 47.826 6.88 0.0 41.55 4.18 F
2337 2896 5.111293 GTGCAGGGACATCCATAAATTTTG 58.889 41.667 0.00 0.0 38.24 2.44 F
3576 4521 0.104671 CTGGTTTGCTTGGTTGTGGG 59.895 55.000 0.00 0.0 0.00 4.61 F
3756 4701 0.035439 GGATTTGAAGGAGCGGTGGA 60.035 55.000 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1579 1.107114 ATCACAGGTCAGCGGTCTAG 58.893 55.000 0.00 0.00 0.00 2.43 R
2448 3009 3.867493 TCAATGTGCGTTTTCATTGCAAA 59.133 34.783 1.71 0.00 45.76 3.68 R
2493 3054 5.885912 TCACCAAGGGTTATTCAGATTAAGC 59.114 40.000 5.92 5.92 31.02 3.09 R
2558 3149 9.642327 TTATCAACTTTCCACATTTTGATCATG 57.358 29.630 0.00 0.00 37.86 3.07 R
3737 4682 0.035439 TCCACCGCTCCTTCAAATCC 60.035 55.000 0.00 0.00 0.00 3.01 R
4787 5749 0.965866 TGACTGAGTACTGCCCCTCG 60.966 60.000 0.00 0.00 0.00 4.63 R
5125 6087 2.857448 GAAACGCGCAATCCACGA 59.143 55.556 5.73 0.00 0.00 4.35 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
30 31 2.091830 TGTCTGATCTACTCCGGATGGT 60.092 50.000 3.57 2.36 36.30 3.55
32 33 2.959030 TCTGATCTACTCCGGATGGTTG 59.041 50.000 3.57 1.21 36.30 3.77
37 38 2.039418 CTACTCCGGATGGTTGGATGA 58.961 52.381 3.57 0.00 36.30 2.92
48 49 2.108075 TGGTTGGATGACCATCTTGTGT 59.892 45.455 9.56 0.00 44.53 3.72
53 54 2.503356 GGATGACCATCTTGTGTCTCCT 59.497 50.000 9.56 0.00 37.92 3.69
58 59 1.678123 CCATCTTGTGTCTCCTGGCTG 60.678 57.143 0.00 0.00 0.00 4.85
62 63 1.002888 CTTGTGTCTCCTGGCTGACAT 59.997 52.381 19.68 0.00 43.75 3.06
69 70 2.082231 CTCCTGGCTGACATTGTTCAG 58.918 52.381 10.20 10.20 45.15 3.02
78 79 3.944015 CTGACATTGTTCAGGATCTTCCC 59.056 47.826 0.00 0.00 39.59 3.97
85 86 3.778075 TGTTCAGGATCTTCCCCGAATAA 59.222 43.478 0.00 0.00 37.19 1.40
89 90 3.118038 CAGGATCTTCCCCGAATAACCAA 60.118 47.826 0.00 0.00 37.19 3.67
90 91 3.722101 AGGATCTTCCCCGAATAACCAAT 59.278 43.478 0.00 0.00 37.19 3.16
91 92 3.821033 GGATCTTCCCCGAATAACCAATG 59.179 47.826 0.00 0.00 0.00 2.82
100 101 1.404035 GAATAACCAATGACCACCGGC 59.596 52.381 0.00 0.00 0.00 6.13
141 142 4.680237 CTGGCCGCGACAACTCCA 62.680 66.667 8.23 3.85 0.00 3.86
146 147 1.671054 CCGCGACAACTCCAACCAT 60.671 57.895 8.23 0.00 0.00 3.55
150 151 1.156736 CGACAACTCCAACCATGACC 58.843 55.000 0.00 0.00 0.00 4.02
154 155 1.423794 AACTCCAACCATGACCCCGT 61.424 55.000 0.00 0.00 0.00 5.28
156 157 1.537889 TCCAACCATGACCCCGTCT 60.538 57.895 0.00 0.00 33.15 4.18
159 160 2.298661 AACCATGACCCCGTCTCCC 61.299 63.158 0.00 0.00 33.15 4.30
161 162 3.075005 CATGACCCCGTCTCCCGT 61.075 66.667 0.00 0.00 33.15 5.28
179 180 2.545952 CCGTCTGCTACTTGTGAGTTGT 60.546 50.000 0.00 0.00 37.33 3.32
185 186 2.290641 GCTACTTGTGAGTTGTGTTGGG 59.709 50.000 0.00 0.00 37.33 4.12
196 197 2.882137 GTTGTGTTGGGATTTCTCCGAA 59.118 45.455 0.00 0.00 43.11 4.30
197 198 2.778299 TGTGTTGGGATTTCTCCGAAG 58.222 47.619 0.00 0.00 43.11 3.79
212 213 2.363680 TCCGAAGAGGAGAAGATGATGC 59.636 50.000 0.00 0.00 45.98 3.91
214 215 3.431346 CCGAAGAGGAGAAGATGATGCAA 60.431 47.826 0.00 0.00 45.00 4.08
219 220 5.856156 AGAGGAGAAGATGATGCAATACAG 58.144 41.667 0.00 0.00 0.00 2.74
224 225 6.867816 GGAGAAGATGATGCAATACAGTAGAG 59.132 42.308 0.00 0.00 0.00 2.43
228 229 9.571810 GAAGATGATGCAATACAGTAGAGATAG 57.428 37.037 0.00 0.00 0.00 2.08
230 231 9.746457 AGATGATGCAATACAGTAGAGATAGTA 57.254 33.333 0.00 0.00 0.00 1.82
260 261 9.451002 GAAAAATTAGGGACTCTTTTAGCTAGT 57.549 33.333 0.00 0.00 41.75 2.57
272 273 6.611381 TCTTTTAGCTAGTAAACGTTCGCTA 58.389 36.000 0.00 6.44 29.89 4.26
278 279 3.227810 AGTAAACGTTCGCTAGAAGGG 57.772 47.619 0.00 0.00 44.10 3.95
296 297 2.804931 GGTGGCATTTGCGAACGC 60.805 61.111 12.33 12.33 43.26 4.84
303 304 2.286833 GGCATTTGCGAACGCTTAGATA 59.713 45.455 19.32 0.00 43.26 1.98
312 313 5.792962 TGCGAACGCTTAGATAACAATTTTG 59.207 36.000 19.32 0.00 42.51 2.44
313 314 5.227184 GCGAACGCTTAGATAACAATTTTGG 59.773 40.000 11.97 0.00 38.26 3.28
319 320 8.736244 ACGCTTAGATAACAATTTTGGTTGTAT 58.264 29.630 0.00 0.00 41.22 2.29
323 324 9.535170 TTAGATAACAATTTTGGTTGTATGGGA 57.465 29.630 0.00 0.00 41.22 4.37
328 330 7.256494 ACAATTTTGGTTGTATGGGATTGAT 57.744 32.000 0.00 0.00 40.35 2.57
330 332 8.477256 ACAATTTTGGTTGTATGGGATTGATAG 58.523 33.333 0.00 0.00 40.35 2.08
351 353 9.554395 TGATAGTTTCTTGAGAACAACATAACA 57.446 29.630 0.00 0.00 33.13 2.41
385 387 4.174009 ACTGTTATCACCGTTTGATCTCG 58.826 43.478 0.24 0.00 41.53 4.04
386 388 4.174009 CTGTTATCACCGTTTGATCTCGT 58.826 43.478 0.24 0.00 41.53 4.18
389 391 2.060326 TCACCGTTTGATCTCGTGTC 57.940 50.000 0.00 0.00 0.00 3.67
394 396 1.390123 CGTTTGATCTCGTGTCGCAAT 59.610 47.619 0.00 0.00 0.00 3.56
398 400 4.840401 TTGATCTCGTGTCGCAATTAAG 57.160 40.909 0.00 0.00 0.00 1.85
407 409 2.736721 TGTCGCAATTAAGACTGTCAGC 59.263 45.455 10.88 3.41 38.16 4.26
420 422 4.997395 AGACTGTCAGCAAAATACATTCGT 59.003 37.500 10.88 0.00 30.60 3.85
422 424 6.017109 AGACTGTCAGCAAAATACATTCGTTT 60.017 34.615 10.88 0.00 30.60 3.60
423 425 7.172532 AGACTGTCAGCAAAATACATTCGTTTA 59.827 33.333 10.88 0.00 30.60 2.01
424 426 7.816640 ACTGTCAGCAAAATACATTCGTTTAT 58.183 30.769 0.00 0.00 0.00 1.40
427 429 7.748683 TGTCAGCAAAATACATTCGTTTATCAC 59.251 33.333 0.00 0.00 0.00 3.06
435 437 5.422214 ACATTCGTTTATCACCCTCTTCT 57.578 39.130 0.00 0.00 0.00 2.85
445 447 0.540830 ACCCTCTTCTCAGCTGACGT 60.541 55.000 13.74 0.00 0.00 4.34
462 464 5.063944 GCTGACGTTTGTGAGATAACATCAT 59.936 40.000 0.00 0.00 29.85 2.45
475 477 7.710907 TGAGATAACATCATCGAAAAACTAGGG 59.289 37.037 0.00 0.00 0.00 3.53
476 478 6.992715 AGATAACATCATCGAAAAACTAGGGG 59.007 38.462 0.00 0.00 0.00 4.79
487 489 5.508994 CGAAAAACTAGGGGCTGAAAATGTT 60.509 40.000 0.00 0.00 0.00 2.71
491 493 1.341080 AGGGGCTGAAAATGTTGGTG 58.659 50.000 0.00 0.00 0.00 4.17
540 543 4.196193 TGGTGAAAGTCGTGATCTTTTGT 58.804 39.130 0.00 0.00 35.62 2.83
558 561 9.835389 ATCTTTTGTTGGAAATTCAAAGAATCA 57.165 25.926 8.74 0.00 34.10 2.57
600 603 2.961741 TCTTTGTGGCAAAGGCATTGTA 59.038 40.909 17.98 0.00 43.71 2.41
728 731 4.233789 CAAGAAGAGTCTTTCCTCACTCG 58.766 47.826 6.88 0.00 41.55 4.18
1113 1121 8.621286 GTTTGTTGGAGATTTCTGTTTTCTAGA 58.379 33.333 0.00 0.00 0.00 2.43
1322 1443 8.225603 TCTGCTCTACATTTTTGTCTTTCTTT 57.774 30.769 0.00 0.00 0.00 2.52
1843 2002 9.905713 TTATACTGCCTATGAGAATTTCTTGTT 57.094 29.630 0.00 0.00 0.00 2.83
1884 2043 9.181061 ACATGTATAATAACACCTTGTAAACCC 57.819 33.333 0.00 0.00 30.75 4.11
2056 2614 8.655935 AAATTGAAGATACCAAGGACATTTCT 57.344 30.769 0.00 0.00 0.00 2.52
2337 2896 5.111293 GTGCAGGGACATCCATAAATTTTG 58.889 41.667 0.00 0.00 38.24 2.44
2373 2934 9.676195 CAGAATCTGATATATCCTACTTATGCG 57.324 37.037 3.77 0.00 32.44 4.73
2448 3009 7.718314 TCATGCTCATGTTTCTAATAAGCATCT 59.282 33.333 9.14 0.00 44.67 2.90
2493 3054 7.546358 TGAGGACTATATGCAAAATTTGGTTG 58.454 34.615 7.89 0.00 0.00 3.77
2558 3149 4.718961 ACACTTTATGCTGGGTATCCATC 58.281 43.478 0.00 0.00 43.11 3.51
2688 3389 9.529325 CCAATCAATGAGACTTAACTTCGTATA 57.471 33.333 0.00 0.00 0.00 1.47
2788 3518 6.668323 TGTTAAGTCATTACTTTGCTGAAGC 58.332 36.000 0.00 0.00 43.60 3.86
2820 3550 9.624697 TTTTGCTAATGAGTTGTCAATATGTTC 57.375 29.630 0.00 0.00 35.88 3.18
2821 3551 8.565896 TTGCTAATGAGTTGTCAATATGTTCT 57.434 30.769 0.00 0.00 35.88 3.01
2897 3627 5.128919 CAGCTAAGGCATCCAAATCTAGTT 58.871 41.667 0.00 0.00 41.70 2.24
3027 3779 2.354109 TAGCAACTTCTCTCGCACAG 57.646 50.000 0.00 0.00 0.00 3.66
3061 3813 0.762418 TTGTCGCCTCCCTTTTCTCA 59.238 50.000 0.00 0.00 0.00 3.27
3332 4228 5.818136 CCAGTAAATGGTGATTTCGACAT 57.182 39.130 0.00 0.00 44.91 3.06
3333 4229 5.572211 CCAGTAAATGGTGATTTCGACATG 58.428 41.667 0.00 0.00 44.91 3.21
3334 4230 5.123820 CCAGTAAATGGTGATTTCGACATGT 59.876 40.000 0.00 0.00 44.91 3.21
3335 4231 6.315144 CCAGTAAATGGTGATTTCGACATGTA 59.685 38.462 0.00 0.00 44.91 2.29
3336 4232 7.148323 CCAGTAAATGGTGATTTCGACATGTAA 60.148 37.037 0.00 0.00 44.91 2.41
3337 4233 8.397906 CAGTAAATGGTGATTTCGACATGTAAT 58.602 33.333 0.00 0.00 33.63 1.89
3338 4234 8.956426 AGTAAATGGTGATTTCGACATGTAATT 58.044 29.630 0.00 0.00 33.63 1.40
3339 4235 9.009327 GTAAATGGTGATTTCGACATGTAATTG 57.991 33.333 0.00 0.00 33.63 2.32
3340 4236 4.980590 TGGTGATTTCGACATGTAATTGC 58.019 39.130 0.00 0.00 0.00 3.56
3341 4237 4.699735 TGGTGATTTCGACATGTAATTGCT 59.300 37.500 0.00 0.00 0.00 3.91
3342 4238 5.877564 TGGTGATTTCGACATGTAATTGCTA 59.122 36.000 0.00 0.00 0.00 3.49
3343 4239 6.183360 TGGTGATTTCGACATGTAATTGCTAC 60.183 38.462 0.00 0.00 0.00 3.58
3344 4240 6.037172 GGTGATTTCGACATGTAATTGCTACT 59.963 38.462 0.00 0.00 0.00 2.57
3345 4241 6.901887 GTGATTTCGACATGTAATTGCTACTG 59.098 38.462 0.00 0.00 0.00 2.74
3346 4242 4.857871 TTCGACATGTAATTGCTACTGC 57.142 40.909 0.00 0.00 40.20 4.40
3347 4243 4.123497 TCGACATGTAATTGCTACTGCT 57.877 40.909 0.00 0.00 40.48 4.24
3348 4244 3.865164 TCGACATGTAATTGCTACTGCTG 59.135 43.478 0.00 0.00 40.48 4.41
3349 4245 3.544834 CGACATGTAATTGCTACTGCTGC 60.545 47.826 0.00 0.00 40.48 5.25
3350 4246 3.346315 ACATGTAATTGCTACTGCTGCA 58.654 40.909 0.88 0.88 40.48 4.41
3370 4266 3.861689 GCAATCAGCAGTAGAATTTTGGC 59.138 43.478 0.00 0.00 44.79 4.52
3371 4267 4.427312 CAATCAGCAGTAGAATTTTGGCC 58.573 43.478 0.00 0.00 0.00 5.36
3372 4268 3.439857 TCAGCAGTAGAATTTTGGCCT 57.560 42.857 3.32 0.00 0.00 5.19
3373 4269 3.084039 TCAGCAGTAGAATTTTGGCCTG 58.916 45.455 3.32 0.00 0.00 4.85
3374 4270 2.821969 CAGCAGTAGAATTTTGGCCTGT 59.178 45.455 3.32 0.00 0.00 4.00
3375 4271 3.256631 CAGCAGTAGAATTTTGGCCTGTT 59.743 43.478 3.32 0.00 0.00 3.16
3376 4272 3.897505 AGCAGTAGAATTTTGGCCTGTTT 59.102 39.130 3.32 0.00 0.00 2.83
3377 4273 4.344968 AGCAGTAGAATTTTGGCCTGTTTT 59.655 37.500 3.32 0.00 0.00 2.43
3378 4274 4.448732 GCAGTAGAATTTTGGCCTGTTTTG 59.551 41.667 3.32 0.00 0.00 2.44
3379 4275 5.738783 GCAGTAGAATTTTGGCCTGTTTTGA 60.739 40.000 3.32 0.00 0.00 2.69
3380 4276 6.279882 CAGTAGAATTTTGGCCTGTTTTGAA 58.720 36.000 3.32 0.00 0.00 2.69
3381 4277 6.930722 CAGTAGAATTTTGGCCTGTTTTGAAT 59.069 34.615 3.32 0.00 0.00 2.57
3382 4278 7.442062 CAGTAGAATTTTGGCCTGTTTTGAATT 59.558 33.333 3.32 0.04 0.00 2.17
3383 4279 6.622833 AGAATTTTGGCCTGTTTTGAATTG 57.377 33.333 3.32 0.00 0.00 2.32
3384 4280 6.355747 AGAATTTTGGCCTGTTTTGAATTGA 58.644 32.000 3.32 0.00 0.00 2.57
3385 4281 6.827762 AGAATTTTGGCCTGTTTTGAATTGAA 59.172 30.769 3.32 0.00 0.00 2.69
3386 4282 7.503230 AGAATTTTGGCCTGTTTTGAATTGAAT 59.497 29.630 3.32 0.00 0.00 2.57
3392 4288 7.322664 TGGCCTGTTTTGAATTGAATATCTTC 58.677 34.615 3.32 0.00 0.00 2.87
3421 4317 7.639113 TTTGAACTGAGTACAATTTGGTCTT 57.361 32.000 0.78 0.00 0.00 3.01
3576 4521 0.104671 CTGGTTTGCTTGGTTGTGGG 59.895 55.000 0.00 0.00 0.00 4.61
3632 4577 3.913799 TCTGGTTCCCAATTGGAGTCTAA 59.086 43.478 26.60 8.77 46.24 2.10
3633 4578 4.019321 TCTGGTTCCCAATTGGAGTCTAAG 60.019 45.833 26.60 14.75 46.24 2.18
3634 4579 3.010138 TGGTTCCCAATTGGAGTCTAAGG 59.990 47.826 26.60 6.41 46.24 2.69
3635 4580 3.621558 GTTCCCAATTGGAGTCTAAGGG 58.378 50.000 26.60 5.68 46.24 3.95
3636 4581 1.564348 TCCCAATTGGAGTCTAAGGGC 59.436 52.381 26.60 0.00 38.61 5.19
3637 4582 1.668419 CCAATTGGAGTCTAAGGGCG 58.332 55.000 20.50 0.00 37.39 6.13
3638 4583 1.017387 CAATTGGAGTCTAAGGGCGC 58.983 55.000 0.00 0.00 0.00 6.53
3639 4584 0.462047 AATTGGAGTCTAAGGGCGCG 60.462 55.000 0.00 0.00 0.00 6.86
3640 4585 1.614241 ATTGGAGTCTAAGGGCGCGT 61.614 55.000 8.43 0.00 0.00 6.01
3641 4586 1.823169 TTGGAGTCTAAGGGCGCGTT 61.823 55.000 8.43 0.00 0.00 4.84
3642 4587 1.518792 GGAGTCTAAGGGCGCGTTC 60.519 63.158 8.43 0.00 0.00 3.95
3643 4588 1.872679 GAGTCTAAGGGCGCGTTCG 60.873 63.158 8.43 0.00 39.07 3.95
3644 4589 2.884207 GTCTAAGGGCGCGTTCGG 60.884 66.667 8.43 0.00 35.95 4.30
3645 4590 3.376078 TCTAAGGGCGCGTTCGGT 61.376 61.111 8.43 0.00 35.95 4.69
3646 4591 3.186047 CTAAGGGCGCGTTCGGTG 61.186 66.667 8.43 0.00 35.95 4.94
3647 4592 4.745751 TAAGGGCGCGTTCGGTGG 62.746 66.667 8.43 0.00 35.95 4.61
3672 4617 4.567385 CTCCGCTCCGCTCTGCTC 62.567 72.222 0.00 0.00 0.00 4.26
3675 4620 4.869440 CGCTCCGCTCTGCTCCTG 62.869 72.222 0.00 0.00 0.00 3.86
3676 4621 4.527583 GCTCCGCTCTGCTCCTGG 62.528 72.222 0.00 0.00 0.00 4.45
3677 4622 2.757508 CTCCGCTCTGCTCCTGGA 60.758 66.667 0.00 0.00 0.00 3.86
3678 4623 2.757508 TCCGCTCTGCTCCTGGAG 60.758 66.667 19.55 19.55 0.00 3.86
3687 4632 3.522731 CTCCTGGAGCGGACGGAG 61.523 72.222 11.42 0.00 37.33 4.63
3690 4635 4.504916 CTGGAGCGGACGGAGCTG 62.505 72.222 6.28 0.00 46.13 4.24
3693 4638 4.200283 GAGCGGACGGAGCTGGAG 62.200 72.222 6.28 0.00 46.13 3.86
3695 4640 4.070552 GCGGACGGAGCTGGAGTT 62.071 66.667 0.00 0.00 0.00 3.01
3696 4641 2.707849 GCGGACGGAGCTGGAGTTA 61.708 63.158 0.00 0.00 0.00 2.24
3697 4642 2.017559 GCGGACGGAGCTGGAGTTAT 62.018 60.000 0.00 0.00 0.00 1.89
3698 4643 1.315690 CGGACGGAGCTGGAGTTATA 58.684 55.000 0.00 0.00 0.00 0.98
3699 4644 1.679680 CGGACGGAGCTGGAGTTATAA 59.320 52.381 0.00 0.00 0.00 0.98
3700 4645 2.296471 CGGACGGAGCTGGAGTTATAAT 59.704 50.000 0.00 0.00 0.00 1.28
3701 4646 3.612004 CGGACGGAGCTGGAGTTATAATC 60.612 52.174 0.00 0.00 0.00 1.75
3702 4647 3.306156 GGACGGAGCTGGAGTTATAATCC 60.306 52.174 0.00 6.88 37.35 3.01
3703 4648 2.633481 ACGGAGCTGGAGTTATAATCCC 59.367 50.000 0.00 5.66 35.86 3.85
3704 4649 2.900546 CGGAGCTGGAGTTATAATCCCT 59.099 50.000 0.00 3.51 35.86 4.20
3705 4650 3.306364 CGGAGCTGGAGTTATAATCCCTG 60.306 52.174 0.00 8.91 35.86 4.45
3706 4651 3.008485 GGAGCTGGAGTTATAATCCCTGG 59.992 52.174 0.00 0.00 35.86 4.45
3707 4652 3.904339 GAGCTGGAGTTATAATCCCTGGA 59.096 47.826 0.00 0.00 35.86 3.86
3708 4653 3.906846 AGCTGGAGTTATAATCCCTGGAG 59.093 47.826 0.00 4.34 35.86 3.86
3709 4654 3.558109 GCTGGAGTTATAATCCCTGGAGC 60.558 52.174 0.00 8.63 35.86 4.70
3710 4655 2.632996 TGGAGTTATAATCCCTGGAGCG 59.367 50.000 0.00 0.00 35.86 5.03
3711 4656 2.897969 GGAGTTATAATCCCTGGAGCGA 59.102 50.000 0.00 0.00 0.00 4.93
3712 4657 3.056465 GGAGTTATAATCCCTGGAGCGAG 60.056 52.174 0.00 0.00 0.00 5.03
3713 4658 2.300437 AGTTATAATCCCTGGAGCGAGC 59.700 50.000 0.00 0.00 0.00 5.03
3714 4659 2.300437 GTTATAATCCCTGGAGCGAGCT 59.700 50.000 0.00 0.00 0.00 4.09
3715 4660 2.310779 ATAATCCCTGGAGCGAGCTA 57.689 50.000 0.00 0.00 0.00 3.32
3716 4661 2.082140 TAATCCCTGGAGCGAGCTAA 57.918 50.000 0.00 0.00 0.00 3.09
3717 4662 0.466124 AATCCCTGGAGCGAGCTAAC 59.534 55.000 0.00 0.00 0.00 2.34
3718 4663 0.687757 ATCCCTGGAGCGAGCTAACA 60.688 55.000 0.00 0.00 0.00 2.41
3719 4664 1.142748 CCCTGGAGCGAGCTAACAG 59.857 63.158 17.19 17.19 33.58 3.16
3720 4665 1.520342 CCTGGAGCGAGCTAACAGC 60.520 63.158 18.16 0.00 42.84 4.40
3730 4675 2.964911 GCTAACAGCTGCTCCGTAG 58.035 57.895 15.27 8.87 38.45 3.51
3731 4676 0.456221 GCTAACAGCTGCTCCGTAGA 59.544 55.000 15.27 0.00 38.45 2.59
3732 4677 1.067821 GCTAACAGCTGCTCCGTAGAT 59.932 52.381 15.27 0.00 38.45 1.98
3733 4678 2.482142 GCTAACAGCTGCTCCGTAGATT 60.482 50.000 15.27 0.00 38.45 2.40
3734 4679 2.301577 AACAGCTGCTCCGTAGATTC 57.698 50.000 15.27 0.00 0.00 2.52
3735 4680 1.479709 ACAGCTGCTCCGTAGATTCT 58.520 50.000 15.27 0.00 0.00 2.40
3736 4681 1.827969 ACAGCTGCTCCGTAGATTCTT 59.172 47.619 15.27 0.00 0.00 2.52
3737 4682 2.200067 CAGCTGCTCCGTAGATTCTTG 58.800 52.381 0.00 0.00 0.00 3.02
3738 4683 1.137872 AGCTGCTCCGTAGATTCTTGG 59.862 52.381 0.00 0.00 0.00 3.61
3739 4684 1.137086 GCTGCTCCGTAGATTCTTGGA 59.863 52.381 7.03 7.03 0.00 3.53
3740 4685 2.224161 GCTGCTCCGTAGATTCTTGGAT 60.224 50.000 7.55 0.00 0.00 3.41
3741 4686 3.742640 GCTGCTCCGTAGATTCTTGGATT 60.743 47.826 7.55 0.00 0.00 3.01
3742 4687 4.446371 CTGCTCCGTAGATTCTTGGATTT 58.554 43.478 7.55 0.00 0.00 2.17
3743 4688 4.191544 TGCTCCGTAGATTCTTGGATTTG 58.808 43.478 7.55 0.13 0.00 2.32
3744 4689 4.081142 TGCTCCGTAGATTCTTGGATTTGA 60.081 41.667 7.55 0.00 0.00 2.69
3745 4690 4.876107 GCTCCGTAGATTCTTGGATTTGAA 59.124 41.667 7.55 0.00 0.00 2.69
3746 4691 5.007136 GCTCCGTAGATTCTTGGATTTGAAG 59.993 44.000 7.55 0.00 0.00 3.02
3747 4692 5.428253 TCCGTAGATTCTTGGATTTGAAGG 58.572 41.667 3.83 0.00 0.00 3.46
3748 4693 5.188948 TCCGTAGATTCTTGGATTTGAAGGA 59.811 40.000 3.83 0.00 0.00 3.36
3749 4694 5.525378 CCGTAGATTCTTGGATTTGAAGGAG 59.475 44.000 0.00 0.00 0.00 3.69
3750 4695 5.007136 CGTAGATTCTTGGATTTGAAGGAGC 59.993 44.000 0.00 0.00 0.00 4.70
3751 4696 3.944015 AGATTCTTGGATTTGAAGGAGCG 59.056 43.478 0.00 0.00 0.00 5.03
3752 4697 2.113860 TCTTGGATTTGAAGGAGCGG 57.886 50.000 0.00 0.00 0.00 5.52
3753 4698 1.351017 TCTTGGATTTGAAGGAGCGGT 59.649 47.619 0.00 0.00 0.00 5.68
3754 4699 1.470098 CTTGGATTTGAAGGAGCGGTG 59.530 52.381 0.00 0.00 0.00 4.94
3755 4700 0.322456 TGGATTTGAAGGAGCGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
3756 4701 0.035439 GGATTTGAAGGAGCGGTGGA 60.035 55.000 0.00 0.00 0.00 4.02
3757 4702 1.373570 GATTTGAAGGAGCGGTGGAG 58.626 55.000 0.00 0.00 0.00 3.86
3758 4703 0.693049 ATTTGAAGGAGCGGTGGAGT 59.307 50.000 0.00 0.00 0.00 3.85
3759 4704 0.250295 TTTGAAGGAGCGGTGGAGTG 60.250 55.000 0.00 0.00 0.00 3.51
3760 4705 2.435059 GAAGGAGCGGTGGAGTGC 60.435 66.667 0.00 0.00 0.00 4.40
3761 4706 3.959991 GAAGGAGCGGTGGAGTGCC 62.960 68.421 0.00 0.00 0.00 5.01
3848 4793 0.738389 CCCACCCGTTGTTATGCATC 59.262 55.000 0.19 0.00 0.00 3.91
4325 5287 1.602311 CAAGCTGTCTGACTTTGGCT 58.398 50.000 9.51 10.09 0.00 4.75
4547 5509 2.715046 ACCACACATCATTTGCTCGAT 58.285 42.857 0.00 0.00 0.00 3.59
4724 5686 3.325753 AGGGAGCACAGCCTGGTC 61.326 66.667 0.00 3.14 45.32 4.02
4766 5728 3.269178 GAATGACAAGAGGAGGCTTCTG 58.731 50.000 0.00 0.00 0.00 3.02
4778 5740 3.478509 GAGGCTTCTGCAGATCATTGAT 58.521 45.455 19.04 0.00 41.91 2.57
4787 5749 2.686235 CAGATCATTGATCCGAGGCTC 58.314 52.381 20.49 3.87 39.66 4.70
5093 6055 1.457346 GTTCATGTTGCCTGGAGGAG 58.543 55.000 0.00 0.00 37.39 3.69
5125 6087 6.220726 AGGTTCAGTTGTAAATTTGCAAGT 57.779 33.333 20.19 20.00 36.98 3.16
5182 6146 4.034742 ACTTGTGTCGTGCGTATTTTCTTT 59.965 37.500 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.498894 TCCGGAGTAGATCAGACAGTAA 57.501 45.455 0.00 0.00 0.00 2.24
13 14 2.039418 CCAACCATCCGGAGTAGATCA 58.961 52.381 11.34 0.00 35.59 2.92
21 22 0.912006 TGGTCATCCAACCATCCGGA 60.912 55.000 6.61 6.61 44.40 5.14
32 33 2.503356 AGGAGACACAAGATGGTCATCC 59.497 50.000 7.28 0.00 38.58 3.51
37 38 0.326264 GCCAGGAGACACAAGATGGT 59.674 55.000 0.00 0.00 0.00 3.55
48 49 1.699083 TGAACAATGTCAGCCAGGAGA 59.301 47.619 0.00 0.00 0.00 3.71
53 54 2.306805 AGATCCTGAACAATGTCAGCCA 59.693 45.455 7.13 0.00 43.18 4.75
58 59 3.282885 GGGGAAGATCCTGAACAATGTC 58.717 50.000 0.00 0.00 36.57 3.06
62 63 1.651737 TCGGGGAAGATCCTGAACAA 58.348 50.000 0.00 0.00 39.11 2.83
69 70 3.570912 TTGGTTATTCGGGGAAGATCC 57.429 47.619 0.00 0.00 35.23 3.36
78 79 1.668751 CGGTGGTCATTGGTTATTCGG 59.331 52.381 0.00 0.00 0.00 4.30
85 86 2.034066 CTGCCGGTGGTCATTGGT 59.966 61.111 1.90 0.00 0.00 3.67
89 90 3.320879 CTGCTCTGCCGGTGGTCAT 62.321 63.158 1.90 0.00 0.00 3.06
90 91 4.007644 CTGCTCTGCCGGTGGTCA 62.008 66.667 1.90 0.00 0.00 4.02
100 101 4.834453 CGGAGGCAGGCTGCTCTG 62.834 72.222 35.73 28.73 44.28 3.35
136 137 1.838073 GACGGGGTCATGGTTGGAGT 61.838 60.000 0.00 0.00 32.09 3.85
141 142 2.298661 GGGAGACGGGGTCATGGTT 61.299 63.158 0.00 0.00 34.60 3.67
154 155 0.888619 CACAAGTAGCAGACGGGAGA 59.111 55.000 0.00 0.00 0.00 3.71
156 157 0.888619 CTCACAAGTAGCAGACGGGA 59.111 55.000 0.00 0.00 0.00 5.14
159 160 2.472861 CACAACTCACAAGTAGCAGACG 59.527 50.000 0.00 0.00 33.48 4.18
161 162 3.819564 ACACAACTCACAAGTAGCAGA 57.180 42.857 0.00 0.00 33.48 4.26
179 180 2.027192 CCTCTTCGGAGAAATCCCAACA 60.027 50.000 0.00 0.00 45.90 3.33
196 197 5.366186 ACTGTATTGCATCATCTTCTCCTCT 59.634 40.000 0.00 0.00 0.00 3.69
197 198 5.609423 ACTGTATTGCATCATCTTCTCCTC 58.391 41.667 0.00 0.00 0.00 3.71
204 205 8.648698 ACTATCTCTACTGTATTGCATCATCT 57.351 34.615 0.00 0.00 0.00 2.90
243 244 5.718146 ACGTTTACTAGCTAAAAGAGTCCC 58.282 41.667 13.38 0.00 30.67 4.46
260 261 1.205417 CCCCCTTCTAGCGAACGTTTA 59.795 52.381 0.46 0.00 0.00 2.01
272 273 1.610379 GCAAATGCCACCCCCTTCT 60.610 57.895 0.00 0.00 34.31 2.85
278 279 2.126502 CGTTCGCAAATGCCACCC 60.127 61.111 0.00 0.00 37.91 4.61
296 297 9.801873 CCCATACAACCAAAATTGTTATCTAAG 57.198 33.333 0.00 0.00 39.86 2.18
303 304 7.072263 TCAATCCCATACAACCAAAATTGTT 57.928 32.000 0.00 0.00 39.86 2.83
312 313 7.556275 TCAAGAAACTATCAATCCCATACAACC 59.444 37.037 0.00 0.00 0.00 3.77
313 314 8.506168 TCAAGAAACTATCAATCCCATACAAC 57.494 34.615 0.00 0.00 0.00 3.32
319 320 6.778821 TGTTCTCAAGAAACTATCAATCCCA 58.221 36.000 0.00 0.00 35.58 4.37
350 352 8.504005 ACGGTGATAACAGTAAAGAAGAAATTG 58.496 33.333 0.00 0.00 0.00 2.32
351 353 8.617290 ACGGTGATAACAGTAAAGAAGAAATT 57.383 30.769 0.00 0.00 0.00 1.82
352 354 8.617290 AACGGTGATAACAGTAAAGAAGAAAT 57.383 30.769 0.00 0.00 0.00 2.17
356 358 7.416154 TCAAACGGTGATAACAGTAAAGAAG 57.584 36.000 0.00 0.00 0.00 2.85
385 387 3.423645 GCTGACAGTCTTAATTGCGACAC 60.424 47.826 3.99 4.07 32.68 3.67
386 388 2.736721 GCTGACAGTCTTAATTGCGACA 59.263 45.455 3.99 0.00 32.68 4.35
389 391 3.811722 TTGCTGACAGTCTTAATTGCG 57.188 42.857 3.99 0.00 0.00 4.85
394 396 7.172532 ACGAATGTATTTTGCTGACAGTCTTAA 59.827 33.333 3.99 0.00 36.35 1.85
398 400 5.283060 ACGAATGTATTTTGCTGACAGTC 57.717 39.130 3.99 0.00 35.43 3.51
407 409 7.985476 AGAGGGTGATAAACGAATGTATTTTG 58.015 34.615 0.00 0.00 0.00 2.44
420 422 4.081420 GTCAGCTGAGAAGAGGGTGATAAA 60.081 45.833 18.89 0.00 39.18 1.40
422 424 3.027412 GTCAGCTGAGAAGAGGGTGATA 58.973 50.000 18.89 0.00 39.18 2.15
423 425 1.830477 GTCAGCTGAGAAGAGGGTGAT 59.170 52.381 18.89 0.00 39.18 3.06
424 426 1.261480 GTCAGCTGAGAAGAGGGTGA 58.739 55.000 18.89 0.00 35.54 4.02
427 429 0.605589 AACGTCAGCTGAGAAGAGGG 59.394 55.000 18.89 3.24 0.00 4.30
435 437 2.820059 ATCTCACAAACGTCAGCTGA 57.180 45.000 13.74 13.74 0.00 4.26
445 447 8.783093 AGTTTTTCGATGATGTTATCTCACAAA 58.217 29.630 0.00 0.00 0.00 2.83
462 464 3.495434 TTTCAGCCCCTAGTTTTTCGA 57.505 42.857 0.00 0.00 0.00 3.71
475 477 6.859420 AATTTAACACCAACATTTTCAGCC 57.141 33.333 0.00 0.00 0.00 4.85
476 478 8.279800 GGTAAATTTAACACCAACATTTTCAGC 58.720 33.333 8.41 0.00 32.32 4.26
487 489 7.057894 ACAGTCTTGAGGTAAATTTAACACCA 58.942 34.615 15.47 9.62 34.62 4.17
558 561 9.025041 CAAAGAAACCCCAGTTCTAGATTATTT 57.975 33.333 0.00 0.00 34.19 1.40
600 603 2.564947 CAGTAGTGCTCCCTTTCACTCT 59.435 50.000 0.00 0.00 42.06 3.24
871 874 2.751036 CATGCGGTCATGCCACCA 60.751 61.111 4.59 2.68 43.00 4.17
1322 1443 6.586344 TCTGCTGAAGAAGAAGAAGAAGAAA 58.414 36.000 0.00 0.00 37.67 2.52
1458 1579 1.107114 ATCACAGGTCAGCGGTCTAG 58.893 55.000 0.00 0.00 0.00 2.43
1884 2043 7.630924 ACAACAAGAGTGAGAAAATAAAGACG 58.369 34.615 0.00 0.00 0.00 4.18
2056 2614 8.744568 TGAAGGCAATCACATTGTTGTATATA 57.255 30.769 0.00 0.00 42.20 0.86
2448 3009 3.867493 TCAATGTGCGTTTTCATTGCAAA 59.133 34.783 1.71 0.00 45.76 3.68
2493 3054 5.885912 TCACCAAGGGTTATTCAGATTAAGC 59.114 40.000 5.92 5.92 31.02 3.09
2558 3149 9.642327 TTATCAACTTTCCACATTTTGATCATG 57.358 29.630 0.00 0.00 37.86 3.07
2820 3550 7.065894 CGAAACAGAGAATGAGTTAACAACAG 58.934 38.462 8.61 0.00 0.00 3.16
2821 3551 6.537301 ACGAAACAGAGAATGAGTTAACAACA 59.463 34.615 8.61 8.08 0.00 3.33
2897 3627 7.828717 TCTTCACAGCAATATCCAATCAACTTA 59.171 33.333 0.00 0.00 0.00 2.24
3001 3731 3.608939 GCGAGAGAAGTTGCTAACAGTAC 59.391 47.826 0.00 0.00 0.00 2.73
3027 3779 6.178239 AGGCGACAAAATGAGTAAACATAC 57.822 37.500 0.00 0.00 0.00 2.39
3044 3796 1.892209 TTTGAGAAAAGGGAGGCGAC 58.108 50.000 0.00 0.00 0.00 5.19
3061 3813 5.378230 TCTTATCAGTGGAGATGGCATTT 57.622 39.130 0.00 0.00 0.00 2.32
3322 4218 5.904080 GCAGTAGCAATTACATGTCGAAATC 59.096 40.000 0.00 0.00 41.58 2.17
3323 4219 5.586243 AGCAGTAGCAATTACATGTCGAAAT 59.414 36.000 0.00 0.00 45.49 2.17
3324 4220 4.935205 AGCAGTAGCAATTACATGTCGAAA 59.065 37.500 0.00 0.00 45.49 3.46
3325 4221 4.329801 CAGCAGTAGCAATTACATGTCGAA 59.670 41.667 0.00 0.00 45.49 3.71
3326 4222 3.865164 CAGCAGTAGCAATTACATGTCGA 59.135 43.478 0.00 0.00 45.49 4.20
3327 4223 3.544834 GCAGCAGTAGCAATTACATGTCG 60.545 47.826 0.00 0.00 45.49 4.35
3328 4224 3.374988 TGCAGCAGTAGCAATTACATGTC 59.625 43.478 0.00 0.00 45.49 3.06
3329 4225 3.346315 TGCAGCAGTAGCAATTACATGT 58.654 40.909 2.69 2.69 45.49 3.21
3330 4226 4.359971 TTGCAGCAGTAGCAATTACATG 57.640 40.909 0.00 0.00 46.13 3.21
3348 4244 3.861689 GCCAAAATTCTACTGCTGATTGC 59.138 43.478 0.00 0.00 43.25 3.56
3349 4245 4.159135 AGGCCAAAATTCTACTGCTGATTG 59.841 41.667 5.01 0.00 0.00 2.67
3350 4246 4.159135 CAGGCCAAAATTCTACTGCTGATT 59.841 41.667 5.01 0.00 0.00 2.57
3351 4247 3.698040 CAGGCCAAAATTCTACTGCTGAT 59.302 43.478 5.01 0.00 0.00 2.90
3352 4248 3.084039 CAGGCCAAAATTCTACTGCTGA 58.916 45.455 5.01 0.00 0.00 4.26
3353 4249 2.821969 ACAGGCCAAAATTCTACTGCTG 59.178 45.455 5.01 0.00 0.00 4.41
3354 4250 3.160679 ACAGGCCAAAATTCTACTGCT 57.839 42.857 5.01 0.00 0.00 4.24
3355 4251 3.942130 AACAGGCCAAAATTCTACTGC 57.058 42.857 5.01 0.00 0.00 4.40
3356 4252 5.841810 TCAAAACAGGCCAAAATTCTACTG 58.158 37.500 5.01 0.00 0.00 2.74
3357 4253 6.478512 TTCAAAACAGGCCAAAATTCTACT 57.521 33.333 5.01 0.00 0.00 2.57
3358 4254 7.440856 TCAATTCAAAACAGGCCAAAATTCTAC 59.559 33.333 5.01 0.00 0.00 2.59
3359 4255 7.504403 TCAATTCAAAACAGGCCAAAATTCTA 58.496 30.769 5.01 0.00 0.00 2.10
3360 4256 6.355747 TCAATTCAAAACAGGCCAAAATTCT 58.644 32.000 5.01 0.00 0.00 2.40
3361 4257 6.616774 TCAATTCAAAACAGGCCAAAATTC 57.383 33.333 5.01 0.00 0.00 2.17
3362 4258 7.585579 ATTCAATTCAAAACAGGCCAAAATT 57.414 28.000 5.01 0.00 0.00 1.82
3363 4259 8.866970 ATATTCAATTCAAAACAGGCCAAAAT 57.133 26.923 5.01 0.00 0.00 1.82
3364 4260 8.156165 AGATATTCAATTCAAAACAGGCCAAAA 58.844 29.630 5.01 0.00 0.00 2.44
3365 4261 7.678837 AGATATTCAATTCAAAACAGGCCAAA 58.321 30.769 5.01 0.00 0.00 3.28
3366 4262 7.243604 AGATATTCAATTCAAAACAGGCCAA 57.756 32.000 5.01 0.00 0.00 4.52
3367 4263 6.855763 AGATATTCAATTCAAAACAGGCCA 57.144 33.333 5.01 0.00 0.00 5.36
3368 4264 7.490402 CAGAAGATATTCAATTCAAAACAGGCC 59.510 37.037 2.42 0.00 0.00 5.19
3369 4265 8.031277 ACAGAAGATATTCAATTCAAAACAGGC 58.969 33.333 2.42 0.00 0.00 4.85
3370 4266 9.918630 AACAGAAGATATTCAATTCAAAACAGG 57.081 29.630 2.42 0.00 0.00 4.00
3382 4278 9.342308 ACTCAGTTCAAAAACAGAAGATATTCA 57.658 29.630 2.42 0.00 37.88 2.57
3385 4281 9.778741 TGTACTCAGTTCAAAAACAGAAGATAT 57.221 29.630 0.00 0.00 37.88 1.63
3386 4282 9.607988 TTGTACTCAGTTCAAAAACAGAAGATA 57.392 29.630 0.00 0.00 37.88 1.98
3392 4288 7.759433 ACCAAATTGTACTCAGTTCAAAAACAG 59.241 33.333 0.44 0.00 37.88 3.16
3592 4537 1.032014 GAAAGACTGCCAAGTGCCAA 58.968 50.000 0.00 0.00 40.16 4.52
3660 4605 2.757508 TCCAGGAGCAGAGCGGAG 60.758 66.667 0.00 0.00 0.00 4.63
3661 4606 2.757508 CTCCAGGAGCAGAGCGGA 60.758 66.667 2.60 0.00 0.00 5.54
3670 4615 3.522731 CTCCGTCCGCTCCAGGAG 61.523 72.222 12.81 12.81 41.68 3.69
3673 4618 4.504916 CAGCTCCGTCCGCTCCAG 62.505 72.222 0.00 0.00 35.07 3.86
3676 4621 4.200283 CTCCAGCTCCGTCCGCTC 62.200 72.222 0.00 0.00 35.07 5.03
3677 4622 4.979611 TATAACTCCAGCTCCGTCCGCT 62.980 54.545 0.00 0.00 38.49 5.52
3678 4623 2.017559 ATAACTCCAGCTCCGTCCGC 62.018 60.000 0.00 0.00 0.00 5.54
3679 4624 1.315690 TATAACTCCAGCTCCGTCCG 58.684 55.000 0.00 0.00 0.00 4.79
3680 4625 3.306156 GGATTATAACTCCAGCTCCGTCC 60.306 52.174 8.31 0.00 32.72 4.79
3681 4626 3.306156 GGGATTATAACTCCAGCTCCGTC 60.306 52.174 12.91 0.00 34.24 4.79
3682 4627 2.633481 GGGATTATAACTCCAGCTCCGT 59.367 50.000 12.91 0.00 34.24 4.69
3683 4628 2.900546 AGGGATTATAACTCCAGCTCCG 59.099 50.000 12.91 0.00 34.24 4.63
3684 4629 3.008485 CCAGGGATTATAACTCCAGCTCC 59.992 52.174 12.91 4.15 34.24 4.70
3685 4630 3.904339 TCCAGGGATTATAACTCCAGCTC 59.096 47.826 12.91 0.00 34.24 4.09
3686 4631 3.906846 CTCCAGGGATTATAACTCCAGCT 59.093 47.826 12.91 0.00 34.24 4.24
3687 4632 3.558109 GCTCCAGGGATTATAACTCCAGC 60.558 52.174 12.91 10.07 34.24 4.85
3688 4633 3.306364 CGCTCCAGGGATTATAACTCCAG 60.306 52.174 12.91 4.62 34.24 3.86
3689 4634 2.632996 CGCTCCAGGGATTATAACTCCA 59.367 50.000 12.91 0.00 34.24 3.86
3690 4635 2.897969 TCGCTCCAGGGATTATAACTCC 59.102 50.000 0.00 0.00 31.73 3.85
3691 4636 3.615351 GCTCGCTCCAGGGATTATAACTC 60.615 52.174 0.00 0.00 36.39 3.01
3692 4637 2.300437 GCTCGCTCCAGGGATTATAACT 59.700 50.000 0.00 0.00 36.39 2.24
3693 4638 2.300437 AGCTCGCTCCAGGGATTATAAC 59.700 50.000 0.00 0.00 36.39 1.89
3694 4639 2.609747 AGCTCGCTCCAGGGATTATAA 58.390 47.619 0.00 0.00 36.39 0.98
3695 4640 2.310779 AGCTCGCTCCAGGGATTATA 57.689 50.000 0.00 0.00 36.39 0.98
3696 4641 2.300437 GTTAGCTCGCTCCAGGGATTAT 59.700 50.000 0.00 0.00 36.39 1.28
3697 4642 1.687123 GTTAGCTCGCTCCAGGGATTA 59.313 52.381 0.00 0.00 36.39 1.75
3698 4643 0.466124 GTTAGCTCGCTCCAGGGATT 59.534 55.000 0.00 0.00 36.39 3.01
3699 4644 0.687757 TGTTAGCTCGCTCCAGGGAT 60.688 55.000 0.00 0.00 36.39 3.85
3700 4645 1.304962 TGTTAGCTCGCTCCAGGGA 60.305 57.895 0.00 0.00 35.61 4.20
3701 4646 1.142748 CTGTTAGCTCGCTCCAGGG 59.857 63.158 0.00 0.00 0.00 4.45
3702 4647 1.520342 GCTGTTAGCTCGCTCCAGG 60.520 63.158 15.78 0.00 38.45 4.45
3703 4648 4.100981 GCTGTTAGCTCGCTCCAG 57.899 61.111 11.86 11.86 38.45 3.86
3712 4657 0.456221 TCTACGGAGCAGCTGTTAGC 59.544 55.000 16.64 0.00 42.84 3.09
3713 4658 3.067461 AGAATCTACGGAGCAGCTGTTAG 59.933 47.826 16.64 9.65 37.31 2.34
3714 4659 3.024547 AGAATCTACGGAGCAGCTGTTA 58.975 45.455 16.64 0.00 37.31 2.41
3715 4660 1.827969 AGAATCTACGGAGCAGCTGTT 59.172 47.619 16.64 9.79 37.31 3.16
3716 4661 1.479709 AGAATCTACGGAGCAGCTGT 58.520 50.000 16.64 1.59 39.97 4.40
3717 4662 2.200067 CAAGAATCTACGGAGCAGCTG 58.800 52.381 10.11 10.11 0.00 4.24
3718 4663 1.137872 CCAAGAATCTACGGAGCAGCT 59.862 52.381 0.00 0.00 0.00 4.24
3719 4664 1.137086 TCCAAGAATCTACGGAGCAGC 59.863 52.381 0.00 0.00 0.00 5.25
3720 4665 3.742433 ATCCAAGAATCTACGGAGCAG 57.258 47.619 7.32 0.00 0.00 4.24
3721 4666 4.081142 TCAAATCCAAGAATCTACGGAGCA 60.081 41.667 7.32 0.00 0.00 4.26
3722 4667 4.442706 TCAAATCCAAGAATCTACGGAGC 58.557 43.478 7.32 0.00 0.00 4.70
3723 4668 5.525378 CCTTCAAATCCAAGAATCTACGGAG 59.475 44.000 7.32 0.00 0.00 4.63
3724 4669 5.188948 TCCTTCAAATCCAAGAATCTACGGA 59.811 40.000 4.10 4.10 0.00 4.69
3725 4670 5.428253 TCCTTCAAATCCAAGAATCTACGG 58.572 41.667 0.00 0.00 0.00 4.02
3726 4671 5.007136 GCTCCTTCAAATCCAAGAATCTACG 59.993 44.000 0.00 0.00 0.00 3.51
3727 4672 5.007136 CGCTCCTTCAAATCCAAGAATCTAC 59.993 44.000 0.00 0.00 0.00 2.59
3728 4673 5.118990 CGCTCCTTCAAATCCAAGAATCTA 58.881 41.667 0.00 0.00 0.00 1.98
3729 4674 3.944015 CGCTCCTTCAAATCCAAGAATCT 59.056 43.478 0.00 0.00 0.00 2.40
3730 4675 3.065925 CCGCTCCTTCAAATCCAAGAATC 59.934 47.826 0.00 0.00 0.00 2.52
3731 4676 3.019564 CCGCTCCTTCAAATCCAAGAAT 58.980 45.455 0.00 0.00 0.00 2.40
3732 4677 2.224769 ACCGCTCCTTCAAATCCAAGAA 60.225 45.455 0.00 0.00 0.00 2.52
3733 4678 1.351017 ACCGCTCCTTCAAATCCAAGA 59.649 47.619 0.00 0.00 0.00 3.02
3734 4679 1.470098 CACCGCTCCTTCAAATCCAAG 59.530 52.381 0.00 0.00 0.00 3.61
3735 4680 1.533625 CACCGCTCCTTCAAATCCAA 58.466 50.000 0.00 0.00 0.00 3.53
3736 4681 0.322456 CCACCGCTCCTTCAAATCCA 60.322 55.000 0.00 0.00 0.00 3.41
3737 4682 0.035439 TCCACCGCTCCTTCAAATCC 60.035 55.000 0.00 0.00 0.00 3.01
3738 4683 1.339151 ACTCCACCGCTCCTTCAAATC 60.339 52.381 0.00 0.00 0.00 2.17
3739 4684 0.693049 ACTCCACCGCTCCTTCAAAT 59.307 50.000 0.00 0.00 0.00 2.32
3740 4685 0.250295 CACTCCACCGCTCCTTCAAA 60.250 55.000 0.00 0.00 0.00 2.69
3741 4686 1.371183 CACTCCACCGCTCCTTCAA 59.629 57.895 0.00 0.00 0.00 2.69
3742 4687 3.059982 CACTCCACCGCTCCTTCA 58.940 61.111 0.00 0.00 0.00 3.02
3743 4688 2.435059 GCACTCCACCGCTCCTTC 60.435 66.667 0.00 0.00 0.00 3.46
3744 4689 4.021925 GGCACTCCACCGCTCCTT 62.022 66.667 0.00 0.00 0.00 3.36
3761 4706 1.521423 CTTAGATTTAGGCCGCGTTCG 59.479 52.381 4.92 0.00 0.00 3.95
3762 4707 2.538861 GTCTTAGATTTAGGCCGCGTTC 59.461 50.000 4.92 0.00 0.00 3.95
3763 4708 2.547826 GTCTTAGATTTAGGCCGCGTT 58.452 47.619 4.92 0.00 0.00 4.84
3764 4709 1.202498 GGTCTTAGATTTAGGCCGCGT 60.202 52.381 4.92 0.00 0.00 6.01
3765 4710 1.068741 AGGTCTTAGATTTAGGCCGCG 59.931 52.381 0.00 0.00 42.31 6.46
3766 4711 2.158943 ACAGGTCTTAGATTTAGGCCGC 60.159 50.000 0.00 0.00 42.31 6.53
3767 4712 3.821421 ACAGGTCTTAGATTTAGGCCG 57.179 47.619 0.00 0.00 42.31 6.13
3768 4713 9.794719 AATATTTACAGGTCTTAGATTTAGGCC 57.205 33.333 0.00 0.00 37.67 5.19
3848 4793 1.086696 CACCGTAACATGCAGAAGGG 58.913 55.000 0.00 0.00 0.00 3.95
3969 4915 5.934935 ACCAATACAAGTTTACTCCAACG 57.065 39.130 0.00 0.00 0.00 4.10
4547 5509 9.981460 TCAGATTCTGCTAATGATACTCCTATA 57.019 33.333 8.89 0.00 0.00 1.31
4719 5681 4.767255 GCAGGCCCAGTCGACCAG 62.767 72.222 13.01 5.19 0.00 4.00
4766 5728 1.155042 GCCTCGGATCAATGATCTGC 58.845 55.000 23.52 16.08 43.08 4.26
4787 5749 0.965866 TGACTGAGTACTGCCCCTCG 60.966 60.000 0.00 0.00 0.00 4.63
4811 5773 2.960170 CTGCAAGCCTTGTGAGCC 59.040 61.111 6.28 0.00 0.00 4.70
5125 6087 2.857448 GAAACGCGCAATCCACGA 59.143 55.556 5.73 0.00 0.00 4.35
5182 6146 4.878397 ACAAATCGGAAAACCATGCAAAAA 59.122 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.