Multiple sequence alignment - TraesCS6A01G100000

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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 TraesCS6A01G100000 chr6A 100.000 4598 0 0 1 4598 67483499 67488096 0.000000e+00 8492.0
1 TraesCS6A01G100000 chr6A 100.000 2319 0 0 4985 7303 67488483 67490801 0.000000e+00 4283.0
2 TraesCS6A01G100000 chr6A 81.188 505 75 19 3347 3840 67534941 67535436 8.880000e-104 388.0
3 TraesCS6A01G100000 chr6A 86.994 346 28 11 1023 1355 67532289 67532630 2.490000e-99 374.0
4 TraesCS6A01G100000 chr6A 86.585 82 11 0 1469 1550 67532718 67532799 2.810000e-14 91.6
5 TraesCS6A01G100000 chr6D 90.204 3522 243 54 358 3840 47668552 47665094 0.000000e+00 4499.0
6 TraesCS6A01G100000 chr6D 86.327 373 37 9 1002 1364 47659031 47658663 1.910000e-105 394.0
7 TraesCS6A01G100000 chr6D 82.030 473 66 18 3347 3808 47656055 47655591 1.150000e-102 385.0
8 TraesCS6A01G100000 chr6D 87.879 66 8 0 1485 1550 47658577 47658512 2.180000e-10 78.7
9 TraesCS6A01G100000 chr7A 94.515 2352 84 13 4990 7303 245455374 245453030 0.000000e+00 3587.0
10 TraesCS6A01G100000 chr5A 94.466 2349 85 21 4990 7303 528065742 528068080 0.000000e+00 3576.0
11 TraesCS6A01G100000 chr5A 94.165 2348 94 16 4990 7303 141896521 141898859 0.000000e+00 3537.0
12 TraesCS6A01G100000 chr5A 94.768 2179 86 13 5144 7303 34948786 34946617 0.000000e+00 3367.0
13 TraesCS6A01G100000 chr5A 86.353 425 41 10 4990 5399 465648504 465648926 1.450000e-121 448.0
14 TraesCS6A01G100000 chr5A 89.008 373 26 8 4990 5347 541949196 541949568 1.450000e-121 448.0
15 TraesCS6A01G100000 chr5A 75.000 356 60 23 2252 2592 69219199 69218858 3.550000e-28 137.0
16 TraesCS6A01G100000 chr5A 77.091 275 40 10 5092 5359 184607273 184607015 3.550000e-28 137.0
17 TraesCS6A01G100000 chr2A 94.338 2349 87 21 4990 7303 384180464 384178127 0.000000e+00 3559.0
18 TraesCS6A01G100000 chr2A 94.321 2342 90 14 4995 7303 80114050 80116381 0.000000e+00 3548.0
19 TraesCS6A01G100000 chr2A 94.628 2178 91 9 5144 7303 270221452 270223621 0.000000e+00 3350.0
20 TraesCS6A01G100000 chr2A 93.802 2178 86 18 5144 7303 266684325 266686471 0.000000e+00 3229.0
21 TraesCS6A01G100000 chr2A 94.815 1543 65 14 4990 6527 176749850 176751382 0.000000e+00 2392.0
22 TraesCS6A01G100000 chr2A 91.555 521 41 3 4055 4574 777784254 777784772 0.000000e+00 715.0
23 TraesCS6A01G100000 chr2A 88.496 113 12 1 1184 1295 750065070 750065182 1.280000e-27 135.0
24 TraesCS6A01G100000 chr2A 77.119 236 43 8 2375 2606 14282102 14281874 7.690000e-25 126.0
25 TraesCS6A01G100000 chr3A 93.660 2350 102 22 4990 7303 417388051 417390389 0.000000e+00 3470.0
26 TraesCS6A01G100000 chr3A 93.742 2333 88 18 4990 7303 34473559 34471266 0.000000e+00 3446.0
27 TraesCS6A01G100000 chr3A 94.893 2154 83 10 5168 7303 662015787 662013643 0.000000e+00 3343.0
28 TraesCS6A01G100000 chr3A 93.195 1690 73 20 4990 6644 97245734 97247416 0.000000e+00 2446.0
29 TraesCS6A01G100000 chr3A 98.916 738 8 0 3861 4598 21369630 21368893 0.000000e+00 1319.0
30 TraesCS6A01G100000 chr6B 86.606 2404 217 48 1 2349 123828847 123831200 0.000000e+00 2558.0
31 TraesCS6A01G100000 chr6B 90.046 1316 95 19 2543 3840 123831913 123833210 0.000000e+00 1672.0
32 TraesCS6A01G100000 chr6B 82.087 508 66 20 3347 3840 123841332 123841828 1.900000e-110 411.0
33 TraesCS6A01G100000 chr6B 86.849 365 34 11 1001 1355 123838512 123838872 5.310000e-106 396.0
34 TraesCS6A01G100000 chr1B 99.729 737 2 0 3862 4598 685618168 685618904 0.000000e+00 1351.0
35 TraesCS6A01G100000 chr1B 100.000 513 0 0 4042 4554 11444573 11445085 0.000000e+00 948.0
36 TraesCS6A01G100000 chr3B 99.725 728 2 0 3871 4598 5431436 5432163 0.000000e+00 1334.0
37 TraesCS6A01G100000 chr3B 89.286 140 7 1 4990 5121 615122871 615123010 1.260000e-37 169.0
38 TraesCS6A01G100000 chrUn 99.713 696 2 0 3903 4598 34085479 34086174 0.000000e+00 1275.0
39 TraesCS6A01G100000 chr4A 99.711 693 2 0 3862 4554 634427849 634427157 0.000000e+00 1269.0
40 TraesCS6A01G100000 chr4A 99.847 655 1 0 3900 4554 174720803 174721457 0.000000e+00 1205.0
41 TraesCS6A01G100000 chr2B 95.758 778 29 2 6527 7303 623333494 623332720 0.000000e+00 1251.0
42 TraesCS6A01G100000 chr2B 82.243 214 35 3 1145 1358 707597551 707597761 1.620000e-41 182.0
43 TraesCS6A01G100000 chr2B 75.946 370 60 18 2252 2599 491708027 491707665 5.860000e-36 163.0
44 TraesCS6A01G100000 chr7D 90.000 520 49 3 4064 4581 181745875 181745357 0.000000e+00 669.0
45 TraesCS6A01G100000 chr4B 87.786 393 33 8 4985 5362 434965321 434965713 5.200000e-121 446.0
46 TraesCS6A01G100000 chr4B 94.643 112 3 3 4990 5101 365091258 365091366 3.500000e-38 171.0
47 TraesCS6A01G100000 chr2D 78.744 414 74 9 2276 2681 460867732 460868139 1.560000e-66 265.0
48 TraesCS6A01G100000 chr2D 83.838 198 28 4 1163 1358 586281346 586281541 1.250000e-42 185.0
49 TraesCS6A01G100000 chr3D 78.571 336 45 16 2342 2668 101795581 101795264 5.780000e-46 196.0
50 TraesCS6A01G100000 chr3D 77.465 355 61 14 2255 2598 5028979 5028633 2.080000e-45 195.0
51 TraesCS6A01G100000 chr3D 76.111 360 67 15 2250 2599 462807585 462807235 3.500000e-38 171.0
52 TraesCS6A01G100000 chr3D 80.714 140 25 2 2699 2837 548719985 548719847 2.790000e-19 108.0
53 TraesCS6A01G100000 chr5B 93.162 117 5 3 4985 5101 358466559 358466446 1.260000e-37 169.0
54 TraesCS6A01G100000 chr4D 74.120 483 85 23 2138 2599 459065654 459065191 5.860000e-36 163.0
55 TraesCS6A01G100000 chr7B 73.441 433 74 22 2685 3113 402851416 402851021 2.770000e-24 124.0
56 TraesCS6A01G100000 chr1A 84.259 108 14 3 2494 2599 329241006 329240900 1.300000e-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 TraesCS6A01G100000 chr6A 67483499 67490801 7302 False 6387.500000 8492 100.000000 1 7303 2 chr6A.!!$F1 7302
1 TraesCS6A01G100000 chr6A 67532289 67535436 3147 False 284.533333 388 84.922333 1023 3840 3 chr6A.!!$F2 2817
2 TraesCS6A01G100000 chr6D 47665094 47668552 3458 True 4499.000000 4499 90.204000 358 3840 1 chr6D.!!$R1 3482
3 TraesCS6A01G100000 chr6D 47655591 47659031 3440 True 285.900000 394 85.412000 1002 3808 3 chr6D.!!$R2 2806
4 TraesCS6A01G100000 chr7A 245453030 245455374 2344 True 3587.000000 3587 94.515000 4990 7303 1 chr7A.!!$R1 2313
5 TraesCS6A01G100000 chr5A 528065742 528068080 2338 False 3576.000000 3576 94.466000 4990 7303 1 chr5A.!!$F3 2313
6 TraesCS6A01G100000 chr5A 141896521 141898859 2338 False 3537.000000 3537 94.165000 4990 7303 1 chr5A.!!$F1 2313
7 TraesCS6A01G100000 chr5A 34946617 34948786 2169 True 3367.000000 3367 94.768000 5144 7303 1 chr5A.!!$R1 2159
8 TraesCS6A01G100000 chr2A 384178127 384180464 2337 True 3559.000000 3559 94.338000 4990 7303 1 chr2A.!!$R2 2313
9 TraesCS6A01G100000 chr2A 80114050 80116381 2331 False 3548.000000 3548 94.321000 4995 7303 1 chr2A.!!$F1 2308
10 TraesCS6A01G100000 chr2A 270221452 270223621 2169 False 3350.000000 3350 94.628000 5144 7303 1 chr2A.!!$F4 2159
11 TraesCS6A01G100000 chr2A 266684325 266686471 2146 False 3229.000000 3229 93.802000 5144 7303 1 chr2A.!!$F3 2159
12 TraesCS6A01G100000 chr2A 176749850 176751382 1532 False 2392.000000 2392 94.815000 4990 6527 1 chr2A.!!$F2 1537
13 TraesCS6A01G100000 chr2A 777784254 777784772 518 False 715.000000 715 91.555000 4055 4574 1 chr2A.!!$F6 519
14 TraesCS6A01G100000 chr3A 417388051 417390389 2338 False 3470.000000 3470 93.660000 4990 7303 1 chr3A.!!$F2 2313
15 TraesCS6A01G100000 chr3A 34471266 34473559 2293 True 3446.000000 3446 93.742000 4990 7303 1 chr3A.!!$R2 2313
16 TraesCS6A01G100000 chr3A 662013643 662015787 2144 True 3343.000000 3343 94.893000 5168 7303 1 chr3A.!!$R3 2135
17 TraesCS6A01G100000 chr3A 97245734 97247416 1682 False 2446.000000 2446 93.195000 4990 6644 1 chr3A.!!$F1 1654
18 TraesCS6A01G100000 chr3A 21368893 21369630 737 True 1319.000000 1319 98.916000 3861 4598 1 chr3A.!!$R1 737
19 TraesCS6A01G100000 chr6B 123828847 123833210 4363 False 2115.000000 2558 88.326000 1 3840 2 chr6B.!!$F1 3839
20 TraesCS6A01G100000 chr6B 123838512 123841828 3316 False 403.500000 411 84.468000 1001 3840 2 chr6B.!!$F2 2839
21 TraesCS6A01G100000 chr1B 685618168 685618904 736 False 1351.000000 1351 99.729000 3862 4598 1 chr1B.!!$F2 736
22 TraesCS6A01G100000 chr1B 11444573 11445085 512 False 948.000000 948 100.000000 4042 4554 1 chr1B.!!$F1 512
23 TraesCS6A01G100000 chr3B 5431436 5432163 727 False 1334.000000 1334 99.725000 3871 4598 1 chr3B.!!$F1 727
24 TraesCS6A01G100000 chrUn 34085479 34086174 695 False 1275.000000 1275 99.713000 3903 4598 1 chrUn.!!$F1 695
25 TraesCS6A01G100000 chr4A 634427157 634427849 692 True 1269.000000 1269 99.711000 3862 4554 1 chr4A.!!$R1 692
26 TraesCS6A01G100000 chr4A 174720803 174721457 654 False 1205.000000 1205 99.847000 3900 4554 1 chr4A.!!$F1 654
27 TraesCS6A01G100000 chr2B 623332720 623333494 774 True 1251.000000 1251 95.758000 6527 7303 1 chr2B.!!$R2 776
28 TraesCS6A01G100000 chr7D 181745357 181745875 518 True 669.000000 669 90.000000 4064 4581 1 chr7D.!!$R1 517

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
976 1011 0.036858 GCTCCCAACTCACTCTGGTC 60.037 60.000 0.00 0.0 0.00 4.02 F
2616 5431 0.105246 CCAGTAGCCTCCCCATCTCT 60.105 60.000 0.00 0.0 0.00 3.10 F
2922 5739 0.242825 TCCGCGAGAAAGACGACAAT 59.757 50.000 8.23 0.0 0.00 2.71 F
3152 5970 1.600511 TAATCAGTCGCTGCCCACGA 61.601 55.000 0.00 0.0 37.17 4.35 F
3188 6006 2.272146 GCGGGCATTTGAGGAGGA 59.728 61.111 0.00 0.0 0.00 3.71 F
3831 6738 6.608610 GCGGTGACAATTTTACTTTGACTAT 58.391 36.000 0.00 0.0 0.00 2.12 F
5238 8207 0.030908 GATCCATCGTCAGGGTCGTC 59.969 60.000 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2668 5483 0.035036 GCCGGCTACCCTTATCCTTC 59.965 60.000 22.15 0.0 0.00 3.46 R
3800 6705 0.884704 AAATTGTCACCGCGCACTCT 60.885 50.000 8.75 0.0 0.00 3.24 R
3805 6710 2.325509 AAGTAAAATTGTCACCGCGC 57.674 45.000 0.00 0.0 0.00 6.86 R
4988 7897 1.070289 GGGGCGAGGGTAACAGAATAG 59.930 57.143 0.00 0.0 39.74 1.73 R
5037 7946 2.285368 AGTCGGATTGGGGCTGGA 60.285 61.111 0.00 0.0 0.00 3.86 R
5746 8775 1.270094 CGGTAGCTGAACCTTGTCACA 60.270 52.381 0.00 0.0 37.39 3.58 R
7143 10214 1.002792 GTCCTGGCTGTCGTTTTGTTC 60.003 52.381 0.00 0.0 0.00 3.18 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
34 35 2.711542 ACCTTTGCCATAAGGAAGTCG 58.288 47.619 14.25 0.00 46.28 4.18
38 39 3.965379 TTGCCATAAGGAAGTCGTACA 57.035 42.857 0.00 0.00 36.89 2.90
47 48 1.618074 GGAAGTCGTACACCCCCTACT 60.618 57.143 0.00 0.00 0.00 2.57
58 59 1.497286 ACCCCCTACTTCTTTGTTGCA 59.503 47.619 0.00 0.00 0.00 4.08
64 65 4.549458 CCTACTTCTTTGTTGCAACCATG 58.451 43.478 26.14 17.18 0.00 3.66
69 70 5.127031 ACTTCTTTGTTGCAACCATGTTACT 59.873 36.000 26.14 0.57 0.00 2.24
85 86 6.456501 CATGTTACTAGCAATACCCCTACTC 58.543 44.000 0.00 0.00 0.00 2.59
89 90 7.181485 TGTTACTAGCAATACCCCTACTCTTTT 59.819 37.037 0.00 0.00 0.00 2.27
97 98 7.368059 CAATACCCCTACTCTTTTGTTGTTTC 58.632 38.462 0.00 0.00 0.00 2.78
98 99 5.125367 ACCCCTACTCTTTTGTTGTTTCT 57.875 39.130 0.00 0.00 0.00 2.52
126 134 7.411264 CGACAACTCTATCTCAAATGTGAACTG 60.411 40.741 0.00 0.00 31.88 3.16
136 144 5.255687 TCAAATGTGAACTGGATGTAGCAT 58.744 37.500 0.00 0.00 0.00 3.79
137 145 6.413892 TCAAATGTGAACTGGATGTAGCATA 58.586 36.000 0.00 0.00 0.00 3.14
160 169 2.601763 GGTCTAAACCGTAAGCATGACG 59.398 50.000 0.00 0.00 44.52 4.35
178 187 1.346395 ACGGTGCACCTATGAGAACAA 59.654 47.619 32.28 0.00 0.00 2.83
182 191 1.630369 TGCACCTATGAGAACAAGCCT 59.370 47.619 0.00 0.00 0.00 4.58
185 194 3.507622 GCACCTATGAGAACAAGCCTTTT 59.492 43.478 0.00 0.00 0.00 2.27
198 207 3.018423 AGCCTTTTAGCCCCATTGTAG 57.982 47.619 0.00 0.00 0.00 2.74
202 211 3.308832 CCTTTTAGCCCCATTGTAGACCA 60.309 47.826 0.00 0.00 0.00 4.02
207 216 1.584724 CCCCATTGTAGACCAGGAGT 58.415 55.000 0.00 0.00 0.00 3.85
208 217 1.210478 CCCCATTGTAGACCAGGAGTG 59.790 57.143 0.00 0.00 0.00 3.51
244 253 1.225704 GGGCTCCTCTGGTTCATGG 59.774 63.158 0.00 0.00 0.00 3.66
252 261 2.634940 CCTCTGGTTCATGGATATCCGT 59.365 50.000 17.04 14.13 39.43 4.69
273 282 1.538047 ACATGGATGTGAAGTGCCAC 58.462 50.000 0.00 0.00 40.03 5.01
293 302 3.996363 CACATGACATGTTTCTCCGAGAA 59.004 43.478 18.52 6.75 42.70 2.87
303 312 0.897621 TCTCCGAGAAATGCAGCTGA 59.102 50.000 20.43 2.70 0.00 4.26
308 317 4.454678 TCCGAGAAATGCAGCTGAATATT 58.545 39.130 20.43 11.44 0.00 1.28
313 322 7.308169 CCGAGAAATGCAGCTGAATATTCATTA 60.308 37.037 20.43 4.54 36.46 1.90
325 334 9.455847 GCTGAATATTCATTATGACTTTCAACC 57.544 33.333 18.26 5.84 36.46 3.77
328 337 7.807977 ATATTCATTATGACTTTCAACCGCT 57.192 32.000 0.00 0.00 0.00 5.52
331 340 5.000591 TCATTATGACTTTCAACCGCTCAA 58.999 37.500 0.00 0.00 0.00 3.02
336 345 3.003275 TGACTTTCAACCGCTCAAACATC 59.997 43.478 0.00 0.00 0.00 3.06
353 362 6.595326 TCAAACATCTATGGAAGTGCTTGTAG 59.405 38.462 0.00 0.00 0.00 2.74
356 365 6.109359 ACATCTATGGAAGTGCTTGTAGTTC 58.891 40.000 0.00 0.00 0.00 3.01
369 378 5.761234 TGCTTGTAGTTCCGATGTTTAAACT 59.239 36.000 18.72 5.10 36.09 2.66
371 380 7.441760 TGCTTGTAGTTCCGATGTTTAAACTTA 59.558 33.333 18.72 0.31 34.09 2.24
413 422 2.948979 AGCAACGGTCACAAAATTCAGA 59.051 40.909 0.00 0.00 0.00 3.27
426 435 7.010367 TCACAAAATTCAGAATGTGCACTTTTC 59.990 33.333 19.41 19.34 42.16 2.29
434 443 2.260844 TGTGCACTTTTCCCTCTGAG 57.739 50.000 19.41 0.00 0.00 3.35
450 459 0.937441 TGAGGATGGGTCTAGAGGCT 59.063 55.000 0.00 0.00 0.00 4.58
457 466 1.273267 TGGGTCTAGAGGCTGTGTCAT 60.273 52.381 0.00 0.00 0.00 3.06
484 493 1.960417 TGAAGACGCCACAAACATGA 58.040 45.000 0.00 0.00 0.00 3.07
580 591 1.135632 GCGTCACACTACAGGACTCTC 60.136 57.143 0.00 0.00 0.00 3.20
614 625 2.890474 CCCGCGGATGGAGAAACG 60.890 66.667 30.73 0.44 0.00 3.60
629 640 0.673644 AAACGTGAGCCCTCCGATTG 60.674 55.000 11.32 0.00 0.00 2.67
704 717 0.524392 TTCAGCAACGCAACCAAACG 60.524 50.000 0.00 0.00 0.00 3.60
718 731 1.066143 CCAAACGTGCTGTAGGGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
744 757 1.201825 GTGACAGCACGACGAAAGC 59.798 57.895 0.00 2.46 34.94 3.51
764 777 1.227999 TGCACGAGCTTTGGTACTGC 61.228 55.000 6.36 0.00 42.74 4.40
826 848 1.291132 GCTTGTCCGTTAGCTCCATC 58.709 55.000 0.00 0.00 34.57 3.51
827 849 1.941325 CTTGTCCGTTAGCTCCATCC 58.059 55.000 0.00 0.00 0.00 3.51
828 850 1.207089 CTTGTCCGTTAGCTCCATCCA 59.793 52.381 0.00 0.00 0.00 3.41
829 851 1.496060 TGTCCGTTAGCTCCATCCAT 58.504 50.000 0.00 0.00 0.00 3.41
830 852 1.837439 TGTCCGTTAGCTCCATCCATT 59.163 47.619 0.00 0.00 0.00 3.16
831 853 2.213499 GTCCGTTAGCTCCATCCATTG 58.787 52.381 0.00 0.00 0.00 2.82
832 854 0.947244 CCGTTAGCTCCATCCATTGC 59.053 55.000 0.00 0.00 0.00 3.56
833 855 0.583438 CGTTAGCTCCATCCATTGCG 59.417 55.000 0.00 0.00 0.00 4.85
836 858 1.123077 TAGCTCCATCCATTGCGAGT 58.877 50.000 0.00 0.00 0.00 4.18
837 859 1.123077 AGCTCCATCCATTGCGAGTA 58.877 50.000 0.00 0.00 0.00 2.59
839 861 2.105477 AGCTCCATCCATTGCGAGTAAT 59.895 45.455 0.00 0.00 0.00 1.89
840 862 2.225019 GCTCCATCCATTGCGAGTAATG 59.775 50.000 6.88 6.88 37.70 1.90
845 867 3.539253 CATTGCGAGTAATGGCTGC 57.461 52.632 6.09 0.00 35.03 5.25
877 906 3.203716 GAAGTGGACTGAGGTTTCGTTT 58.796 45.455 0.00 0.00 0.00 3.60
883 912 6.014840 AGTGGACTGAGGTTTCGTTTAATCTA 60.015 38.462 0.00 0.00 0.00 1.98
900 929 3.876274 TCTACTGTCAAGTCCATGAGC 57.124 47.619 0.00 0.00 37.88 4.26
964 994 0.891373 CTCTGTCTTCTCGCTCCCAA 59.109 55.000 0.00 0.00 0.00 4.12
971 1006 0.603569 TTCTCGCTCCCAACTCACTC 59.396 55.000 0.00 0.00 0.00 3.51
972 1007 0.251386 TCTCGCTCCCAACTCACTCT 60.251 55.000 0.00 0.00 0.00 3.24
973 1008 0.108898 CTCGCTCCCAACTCACTCTG 60.109 60.000 0.00 0.00 0.00 3.35
974 1009 1.079543 CGCTCCCAACTCACTCTGG 60.080 63.158 0.00 0.00 0.00 3.86
976 1011 0.036858 GCTCCCAACTCACTCTGGTC 60.037 60.000 0.00 0.00 0.00 4.02
977 1012 0.610687 CTCCCAACTCACTCTGGTCC 59.389 60.000 0.00 0.00 0.00 4.46
1158 1202 0.533032 GCGGTAGCAAGAAGAGGAGT 59.467 55.000 0.00 0.00 44.35 3.85
1233 1277 0.179000 GGAGCGTCACCATGAAGGAT 59.821 55.000 0.00 0.00 41.22 3.24
1431 1518 1.000163 TCGTGTGTCTTTCCTCTGCTC 60.000 52.381 0.00 0.00 0.00 4.26
1482 1570 0.540454 TTGGATCTGAGCTGCAGGAG 59.460 55.000 17.12 0.00 44.98 3.69
1523 1611 2.229543 GCTCATTCTGCACCACAAATCA 59.770 45.455 0.00 0.00 0.00 2.57
1524 1612 3.829948 CTCATTCTGCACCACAAATCAC 58.170 45.455 0.00 0.00 0.00 3.06
1574 3810 7.556844 TCTATATCAAAAGAGGACAGTCAACC 58.443 38.462 2.17 0.00 0.00 3.77
1587 3823 6.015434 AGGACAGTCAACCATTTGGAAAATAC 60.015 38.462 3.01 0.00 38.94 1.89
1592 3828 6.015434 AGTCAACCATTTGGAAAATACTGTCC 60.015 38.462 3.01 0.00 38.94 4.02
1593 3829 6.015434 GTCAACCATTTGGAAAATACTGTCCT 60.015 38.462 3.01 0.00 38.94 3.85
1603 3840 8.189119 TGGAAAATACTGTCCTTTTATGCTTT 57.811 30.769 2.22 0.00 34.77 3.51
1812 4083 4.829492 AGAGTATTTGAGGTTTGCTGCTTT 59.171 37.500 0.00 0.00 0.00 3.51
1829 4100 6.145535 GCTGCTTTCATATACCAGTAAATGC 58.854 40.000 0.00 0.00 0.00 3.56
1980 4255 6.725246 ACAAATCTTAAACAAGGAGACAACG 58.275 36.000 0.00 0.00 0.00 4.10
2030 4306 6.015940 GGTGGTGATTGTTTGATTCTTCTCTT 60.016 38.462 0.00 0.00 0.00 2.85
2092 4379 2.157989 AGTAGGACCTCAAACCCCTCTT 60.158 50.000 0.00 0.00 0.00 2.85
2098 4385 4.017126 GACCTCAAACCCCTCTTAAATGG 58.983 47.826 0.00 0.00 0.00 3.16
2123 4410 3.771160 GACGGCCCGGTCACTGAT 61.771 66.667 8.57 0.00 36.91 2.90
2161 4449 0.249868 CAGACGAGCACCTCAAACCA 60.250 55.000 0.00 0.00 0.00 3.67
2231 4519 3.037549 TCCAATTTGGGGTGAATATGGC 58.962 45.455 15.37 0.00 38.32 4.40
2248 4536 2.332654 GCGTTGCCCGGACAAATCT 61.333 57.895 4.17 0.00 36.94 2.40
2279 4568 3.849951 CGGTCTACGCTGGCCCAT 61.850 66.667 0.00 0.00 34.82 4.00
2280 4569 2.109181 GGTCTACGCTGGCCCATC 59.891 66.667 0.00 0.00 0.00 3.51
2281 4570 2.109181 GTCTACGCTGGCCCATCC 59.891 66.667 0.00 0.00 0.00 3.51
2282 4571 3.536917 TCTACGCTGGCCCATCCG 61.537 66.667 0.00 0.00 37.80 4.18
2283 4572 3.536917 CTACGCTGGCCCATCCGA 61.537 66.667 10.42 0.00 37.80 4.55
2289 4579 3.391665 CTGGCCCATCCGACCTCAC 62.392 68.421 0.00 0.00 37.80 3.51
2304 4594 4.442706 GACCTCACATATTCGTCCACATT 58.557 43.478 0.00 0.00 0.00 2.71
2316 4606 1.066143 GTCCACATTCGATCACCAGGT 60.066 52.381 0.00 0.00 0.00 4.00
2329 4619 1.078426 CCAGGTCAAACCCTAGCCG 60.078 63.158 0.00 0.00 39.75 5.52
2348 5006 0.902516 GCTCCACTCCAGTCCACTCT 60.903 60.000 0.00 0.00 0.00 3.24
2383 5041 4.237445 GGTGATCTCCGACTCCGA 57.763 61.111 0.00 0.00 38.22 4.55
2483 5141 3.206150 GGTGCTATGATCGTCCACATTT 58.794 45.455 16.15 0.00 0.00 2.32
2616 5431 0.105246 CCAGTAGCCTCCCCATCTCT 60.105 60.000 0.00 0.00 0.00 3.10
2719 5536 1.215673 TCGTAGAGGAGGAAGCCATCT 59.784 52.381 0.00 0.00 0.00 2.90
2745 5562 1.005340 GCATCCTCAAGAAGCGACAG 58.995 55.000 0.00 0.00 28.01 3.51
2746 5563 1.674221 GCATCCTCAAGAAGCGACAGT 60.674 52.381 0.00 0.00 28.01 3.55
2761 5578 2.029073 AGTGGAGGAACACGTGCG 59.971 61.111 17.22 0.00 45.80 5.34
2767 5584 3.284449 GGAACACGTGCGCCCTTT 61.284 61.111 17.22 0.07 0.00 3.11
2787 5604 0.740868 CCCGAGAGCAAAATCGAGCA 60.741 55.000 0.00 0.00 41.40 4.26
2792 5609 3.732169 CGAGAGCAAAATCGAGCAGTCTA 60.732 47.826 0.00 0.00 41.40 2.59
2805 5622 0.250038 CAGTCTATGCCATGGTCGGG 60.250 60.000 14.67 2.16 0.00 5.14
2839 5656 1.513622 GAGAAGGAGGACAGCGACC 59.486 63.158 0.00 0.00 0.00 4.79
2841 5658 3.358076 GAAGGAGGACAGCGACCGG 62.358 68.421 0.00 0.00 0.00 5.28
2896 5713 3.980775 CGATCCATTTTGCGTTTTTGAGT 59.019 39.130 0.00 0.00 0.00 3.41
2922 5739 0.242825 TCCGCGAGAAAGACGACAAT 59.757 50.000 8.23 0.00 0.00 2.71
2955 5772 1.745890 CAATGGCTGCCATGGATGG 59.254 57.895 33.13 16.82 44.40 3.51
3014 5831 7.201609 GCTAATTTTTGATAGTCCGATGACACA 60.202 37.037 0.00 0.00 44.33 3.72
3037 5854 3.635373 TCCTGATGTAGTAACCGGATGAC 59.365 47.826 9.46 2.20 0.00 3.06
3091 5909 7.821652 TGCGTTTTGTATGGATTTGAGATTTA 58.178 30.769 0.00 0.00 0.00 1.40
3118 5936 1.671845 GAGGTGTGCGGTTGTACAAAA 59.328 47.619 10.51 0.00 42.53 2.44
3120 5938 2.691011 AGGTGTGCGGTTGTACAAAAAT 59.309 40.909 10.51 0.00 42.53 1.82
3122 5940 4.521256 AGGTGTGCGGTTGTACAAAAATAT 59.479 37.500 10.51 0.00 42.53 1.28
3124 5942 6.376018 AGGTGTGCGGTTGTACAAAAATATAT 59.624 34.615 10.51 0.00 42.53 0.86
3147 5965 1.726853 AAGTGTAATCAGTCGCTGCC 58.273 50.000 0.00 0.00 0.00 4.85
3152 5970 1.600511 TAATCAGTCGCTGCCCACGA 61.601 55.000 0.00 0.00 37.17 4.35
3188 6006 2.272146 GCGGGCATTTGAGGAGGA 59.728 61.111 0.00 0.00 0.00 3.71
3244 6062 8.786898 TGCTCTTATGCATTTCCTATGTTTATC 58.213 33.333 3.54 0.00 38.12 1.75
3298 6124 7.111466 TGAGGATTCATTGTATGATCACAACA 58.889 34.615 0.00 2.73 41.02 3.33
3352 6220 7.636259 TTTTTAGCTTACATCACATTTGCAC 57.364 32.000 0.00 0.00 0.00 4.57
3831 6738 6.608610 GCGGTGACAATTTTACTTTGACTAT 58.391 36.000 0.00 0.00 0.00 2.12
5037 7946 4.471726 GACGCGTCCACGACCGAT 62.472 66.667 28.61 0.00 43.02 4.18
5160 8129 1.077429 GCCGCCTCCTCATTCCTTT 60.077 57.895 0.00 0.00 0.00 3.11
5161 8130 1.098129 GCCGCCTCCTCATTCCTTTC 61.098 60.000 0.00 0.00 0.00 2.62
5176 8145 0.810031 CTTTCGTCGCCGGATCCATT 60.810 55.000 13.41 0.00 33.95 3.16
5194 8163 2.758737 GTCGGGGTCGTCATCCCT 60.759 66.667 0.96 0.00 44.07 4.20
5238 8207 0.030908 GATCCATCGTCAGGGTCGTC 59.969 60.000 0.00 0.00 0.00 4.20
5253 8222 2.191641 GTCATCCCTGCCTCCTGC 59.808 66.667 0.00 0.00 41.77 4.85
5263 8237 4.787280 CCTCCTGCCTCCCTCCGT 62.787 72.222 0.00 0.00 0.00 4.69
5278 8252 4.266070 CGTCGCCGGATCCATCGT 62.266 66.667 13.41 0.00 0.00 3.73
5280 8254 3.961197 TCGCCGGATCCATCGTCG 61.961 66.667 13.41 7.12 0.00 5.12
5284 8258 3.224324 CGGATCCATCGTCGGGGT 61.224 66.667 13.41 0.00 0.00 4.95
5288 8262 2.403671 GATCCATCGTCGGGGTCGTC 62.404 65.000 0.00 0.00 37.69 4.20
5294 8268 2.758737 GTCGGGGTCGTCATCCCT 60.759 66.667 0.96 0.00 44.07 4.20
5305 8279 3.414193 CATCCCTGCCTCCTGCCA 61.414 66.667 0.00 0.00 40.16 4.92
5494 8520 1.001974 AGAACATGCCAGTAAGACGCA 59.998 47.619 0.00 0.00 36.84 5.24
5746 8775 3.388024 ACATATGCGTCAGTCCAGGTATT 59.612 43.478 1.58 0.00 0.00 1.89
5964 9006 7.182817 AGGTTACTGTCAGTGCATCTAAATA 57.817 36.000 16.03 0.00 0.00 1.40
6162 9208 7.030768 GTCCAGTTTACAAAACAGTGCTAAAA 58.969 34.615 5.42 0.00 0.00 1.52
6163 9209 7.542824 GTCCAGTTTACAAAACAGTGCTAAAAA 59.457 33.333 5.42 0.00 0.00 1.94
6401 9450 5.895636 TTTGAAGATACACCGCAATCATT 57.104 34.783 0.00 0.00 0.00 2.57
6550 9616 2.659610 GCTTCCACCAGTCGCTCT 59.340 61.111 0.00 0.00 0.00 4.09
6826 9894 1.109323 AACAAACACCAGAGGCAGCC 61.109 55.000 1.84 1.84 0.00 4.85
6929 10000 9.743057 CCATCTAACATTTTTGTTTTGTCACTA 57.257 29.630 0.00 0.00 33.59 2.74
6937 10008 8.655092 CATTTTTGTTTTGTCACTATTGTGTGT 58.345 29.630 7.18 0.00 44.14 3.72
7129 10200 8.463930 AGTTTATGAATCAAAGGTGTCTGAAA 57.536 30.769 0.00 0.00 0.00 2.69
7143 10214 3.745975 TGTCTGAAACAAATAGACAGCGG 59.254 43.478 0.00 0.00 44.10 5.52
7149 10220 5.066634 TGAAACAAATAGACAGCGGAACAAA 59.933 36.000 0.00 0.00 0.00 2.83
7161 10232 0.310854 GGAACAAAACGACAGCCAGG 59.689 55.000 0.00 0.00 0.00 4.45
7165 10236 0.588252 CAAAACGACAGCCAGGACTG 59.412 55.000 8.82 8.82 43.59 3.51
7169 10240 0.251209 ACGACAGCCAGGACTGACTA 60.251 55.000 15.48 0.00 40.25 2.59
7193 10264 3.203934 AGGGCTAAAATGAGGCTGAAGAT 59.796 43.478 0.00 0.00 41.63 2.40
7194 10265 3.956848 GGGCTAAAATGAGGCTGAAGATT 59.043 43.478 0.00 0.00 41.63 2.40
7260 10331 0.833834 ACCACAGGCTACAGCTCACT 60.834 55.000 0.54 0.00 41.70 3.41
7261 10332 0.108424 CCACAGGCTACAGCTCACTC 60.108 60.000 0.54 0.00 41.70 3.51
7264 10335 0.108424 CAGGCTACAGCTCACTCCAC 60.108 60.000 0.54 0.00 41.70 4.02
7296 10367 3.960102 TCTTCTTGCACTCCCACAAAAAT 59.040 39.130 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.092968 GTGTACGACTTCCTTATGGCAAAG 59.907 45.833 0.00 0.00 0.00 2.77
26 27 0.706433 TAGGGGGTGTACGACTTCCT 59.294 55.000 0.00 0.00 33.51 3.36
29 30 2.174360 GAAGTAGGGGGTGTACGACTT 58.826 52.381 0.00 0.00 35.67 3.01
34 35 4.070009 CAACAAAGAAGTAGGGGGTGTAC 58.930 47.826 0.00 0.00 0.00 2.90
38 39 1.497286 TGCAACAAAGAAGTAGGGGGT 59.503 47.619 0.00 0.00 0.00 4.95
47 48 5.590530 AGTAACATGGTTGCAACAAAGAA 57.409 34.783 29.55 10.71 0.00 2.52
58 59 4.477213 AGGGGTATTGCTAGTAACATGGTT 59.523 41.667 0.00 0.00 0.00 3.67
64 65 6.728089 AAGAGTAGGGGTATTGCTAGTAAC 57.272 41.667 0.00 0.00 0.00 2.50
69 70 6.177610 CAACAAAAGAGTAGGGGTATTGCTA 58.822 40.000 0.00 0.00 0.00 3.49
97 98 6.808704 TCACATTTGAGATAGAGTTGTCGAAG 59.191 38.462 0.00 0.00 0.00 3.79
98 99 6.687604 TCACATTTGAGATAGAGTTGTCGAA 58.312 36.000 0.00 0.00 0.00 3.71
126 134 4.304939 GGTTTAGACCGTATGCTACATCC 58.695 47.826 0.00 0.00 35.91 3.51
154 163 1.136891 TCTCATAGGTGCACCGTCATG 59.863 52.381 29.68 28.85 42.08 3.07
160 169 1.740025 GCTTGTTCTCATAGGTGCACC 59.260 52.381 29.22 29.22 0.00 5.01
161 170 1.740025 GGCTTGTTCTCATAGGTGCAC 59.260 52.381 8.80 8.80 0.00 4.57
164 173 5.163713 GCTAAAAGGCTTGTTCTCATAGGTG 60.164 44.000 0.00 0.00 0.00 4.00
167 176 4.336713 GGGCTAAAAGGCTTGTTCTCATAG 59.663 45.833 0.00 0.00 41.09 2.23
169 178 3.092301 GGGCTAAAAGGCTTGTTCTCAT 58.908 45.455 0.00 0.00 41.09 2.90
178 187 2.580783 TCTACAATGGGGCTAAAAGGCT 59.419 45.455 0.25 0.00 41.09 4.58
182 191 3.308832 CCTGGTCTACAATGGGGCTAAAA 60.309 47.826 0.00 0.00 0.00 1.52
185 194 1.009060 TCCTGGTCTACAATGGGGCTA 59.991 52.381 0.00 0.00 0.00 3.93
198 207 3.196685 AGAAGCTTATCACACTCCTGGTC 59.803 47.826 0.00 0.00 0.00 4.02
202 211 6.239543 CCATGATAGAAGCTTATCACACTCCT 60.240 42.308 12.96 0.00 41.46 3.69
207 216 4.349048 AGCCCATGATAGAAGCTTATCACA 59.651 41.667 12.96 8.03 41.46 3.58
208 217 4.904241 AGCCCATGATAGAAGCTTATCAC 58.096 43.478 12.96 2.87 41.46 3.06
269 278 1.131126 CGGAGAAACATGTCATGTGGC 59.869 52.381 19.08 13.47 44.07 5.01
270 279 2.674852 CTCGGAGAAACATGTCATGTGG 59.325 50.000 19.08 5.40 44.07 4.17
273 282 5.566623 CATTTCTCGGAGAAACATGTCATG 58.433 41.667 29.73 19.84 45.83 3.07
293 302 8.405418 AGTCATAATGAATATTCAGCTGCATT 57.595 30.769 21.97 13.72 41.08 3.56
303 312 8.225603 AGCGGTTGAAAGTCATAATGAATATT 57.774 30.769 0.00 0.00 0.00 1.28
308 317 4.574892 TGAGCGGTTGAAAGTCATAATGA 58.425 39.130 0.00 0.00 0.00 2.57
313 322 2.948979 TGTTTGAGCGGTTGAAAGTCAT 59.051 40.909 0.00 0.00 0.00 3.06
325 334 3.242543 GCACTTCCATAGATGTTTGAGCG 60.243 47.826 0.00 0.00 0.00 5.03
328 337 5.316167 ACAAGCACTTCCATAGATGTTTGA 58.684 37.500 6.66 0.00 29.25 2.69
331 340 6.054860 ACTACAAGCACTTCCATAGATGTT 57.945 37.500 0.00 0.00 0.00 2.71
336 345 3.865745 CGGAACTACAAGCACTTCCATAG 59.134 47.826 0.00 0.00 33.04 2.23
353 362 6.247791 GCACGAATAAGTTTAAACATCGGAAC 59.752 38.462 25.41 16.63 33.45 3.62
356 365 5.864986 AGCACGAATAAGTTTAAACATCGG 58.135 37.500 25.41 19.12 33.45 4.18
369 378 8.454894 TGCTGAAAATTTACATAGCACGAATAA 58.545 29.630 11.95 0.00 36.37 1.40
371 380 6.851609 TGCTGAAAATTTACATAGCACGAAT 58.148 32.000 11.95 0.00 36.37 3.34
374 383 5.002468 CGTTGCTGAAAATTTACATAGCACG 59.998 40.000 14.32 15.41 40.45 5.34
413 422 3.152341 CTCAGAGGGAAAAGTGCACATT 58.848 45.455 21.04 11.14 0.00 2.71
434 443 0.755686 CACAGCCTCTAGACCCATCC 59.244 60.000 0.00 0.00 0.00 3.51
457 466 2.839975 TGTGGCGTCTTCATGTGTTTA 58.160 42.857 0.00 0.00 0.00 2.01
484 493 6.835174 AGCTCTGGACATGTTTATATCACAT 58.165 36.000 0.00 0.00 35.10 3.21
614 625 2.514824 GGCAATCGGAGGGCTCAC 60.515 66.667 4.06 0.00 0.00 3.51
704 717 1.335496 GTCTCGATCTCCCTACAGCAC 59.665 57.143 0.00 0.00 0.00 4.40
718 731 2.643272 GTGCTGTCACGGTCTCGA 59.357 61.111 0.00 0.00 40.11 4.04
744 757 0.792640 CAGTACCAAAGCTCGTGCAG 59.207 55.000 12.58 1.11 42.74 4.41
746 759 1.227999 TGCAGTACCAAAGCTCGTGC 61.228 55.000 0.07 0.07 40.05 5.34
764 777 5.233050 GCACTACTACTGACATGTGCTATTG 59.767 44.000 1.15 0.00 44.80 1.90
778 796 2.248248 TGCCAGACAAGCACTACTACT 58.752 47.619 0.00 0.00 34.69 2.57
827 849 0.734309 TGCAGCCATTACTCGCAATG 59.266 50.000 0.00 0.00 35.97 2.82
828 850 0.734889 GTGCAGCCATTACTCGCAAT 59.265 50.000 0.00 0.00 33.76 3.56
829 851 0.605050 TGTGCAGCCATTACTCGCAA 60.605 50.000 0.00 0.00 33.76 4.85
830 852 1.003959 TGTGCAGCCATTACTCGCA 60.004 52.632 0.00 0.00 0.00 5.10
831 853 1.021390 ACTGTGCAGCCATTACTCGC 61.021 55.000 0.00 0.00 0.00 5.03
832 854 2.293677 TACTGTGCAGCCATTACTCG 57.706 50.000 0.00 0.00 0.00 4.18
833 855 3.310774 CACATACTGTGCAGCCATTACTC 59.689 47.826 0.00 0.00 41.89 2.59
836 858 2.238395 TCCACATACTGTGCAGCCATTA 59.762 45.455 1.71 0.00 46.51 1.90
837 859 1.004628 TCCACATACTGTGCAGCCATT 59.995 47.619 1.71 0.00 46.51 3.16
839 861 0.399833 TTCCACATACTGTGCAGCCA 59.600 50.000 1.71 0.00 46.51 4.75
840 862 1.089920 CTTCCACATACTGTGCAGCC 58.910 55.000 1.71 0.00 46.51 4.85
841 863 1.466167 CACTTCCACATACTGTGCAGC 59.534 52.381 1.71 0.00 46.51 5.25
842 864 2.079158 CCACTTCCACATACTGTGCAG 58.921 52.381 1.71 0.00 46.51 4.41
843 865 1.696884 TCCACTTCCACATACTGTGCA 59.303 47.619 1.71 0.00 46.51 4.57
844 866 2.076863 GTCCACTTCCACATACTGTGC 58.923 52.381 1.71 0.00 46.51 4.57
877 906 5.658634 AGCTCATGGACTTGACAGTAGATTA 59.341 40.000 0.00 0.00 31.22 1.75
883 912 1.973515 TCAGCTCATGGACTTGACAGT 59.026 47.619 0.00 0.00 35.17 3.55
900 929 2.703416 TGTAGATGGTTTGCAGCTCAG 58.297 47.619 0.00 0.00 0.00 3.35
964 994 1.079438 GGGAGGGACCAGAGTGAGT 59.921 63.158 0.00 0.00 41.20 3.41
971 1006 1.229984 AAAGGGAGGGAGGGACCAG 60.230 63.158 0.00 0.00 41.20 4.00
972 1007 1.229853 GAAAGGGAGGGAGGGACCA 60.230 63.158 0.00 0.00 41.20 4.02
973 1008 0.550393 AAGAAAGGGAGGGAGGGACC 60.550 60.000 0.00 0.00 38.08 4.46
974 1009 0.913205 GAAGAAAGGGAGGGAGGGAC 59.087 60.000 0.00 0.00 0.00 4.46
976 1011 1.208706 GAGAAGAAAGGGAGGGAGGG 58.791 60.000 0.00 0.00 0.00 4.30
977 1012 1.208706 GGAGAAGAAAGGGAGGGAGG 58.791 60.000 0.00 0.00 0.00 4.30
1158 1202 4.452251 TCCGCCGGCCTCTTCCTA 62.452 66.667 23.46 0.00 0.00 2.94
1482 1570 2.009774 CTCCATTCCAACACCATCGAC 58.990 52.381 0.00 0.00 0.00 4.20
1509 1597 0.599558 CCCAGTGATTTGTGGTGCAG 59.400 55.000 0.00 0.00 31.17 4.41
1523 1611 1.362224 ACCATACTCACTTGCCCAGT 58.638 50.000 0.00 0.00 35.35 4.00
1524 1612 2.496899 AACCATACTCACTTGCCCAG 57.503 50.000 0.00 0.00 0.00 4.45
1540 1628 9.841880 GTCCTCTTTTGATATAGAAACAAAACC 57.158 33.333 0.00 0.00 38.17 3.27
1574 3810 8.872845 GCATAAAAGGACAGTATTTTCCAAATG 58.127 33.333 0.30 1.50 33.92 2.32
1587 3823 9.313118 ACAACTTTTTAAAGCATAAAAGGACAG 57.687 29.630 17.73 10.81 42.71 3.51
1593 3829 9.823647 TGATGGACAACTTTTTAAAGCATAAAA 57.176 25.926 2.23 4.01 39.63 1.52
1603 3840 9.685276 ATGACTATCATGATGGACAACTTTTTA 57.315 29.630 24.25 1.84 35.43 1.52
1637 3902 9.672673 AAGCAAGAAATGACAGTGTAATATAGT 57.327 29.630 0.00 0.00 0.00 2.12
1638 3903 9.926751 CAAGCAAGAAATGACAGTGTAATATAG 57.073 33.333 0.00 0.00 0.00 1.31
1812 4083 3.071747 TGCGGGCATTTACTGGTATATGA 59.928 43.478 12.84 0.00 29.63 2.15
1829 4100 1.178534 ACCTTCAAATGGTGTGCGGG 61.179 55.000 0.00 0.00 36.30 6.13
1882 4155 5.528690 GGCATAGAGATGTCAAGCAAATGTA 59.471 40.000 0.00 0.00 37.63 2.29
1894 4167 2.826337 TGCGAGGGCATAGAGATGT 58.174 52.632 0.00 0.00 46.21 3.06
2005 4280 5.474876 AGAGAAGAATCAAACAATCACCACC 59.525 40.000 0.00 0.00 0.00 4.61
2054 4340 8.951541 AGGTCCTACTATAGATGTTCTAACTCT 58.048 37.037 6.78 0.00 31.96 3.24
2055 4341 9.223099 GAGGTCCTACTATAGATGTTCTAACTC 57.777 40.741 6.78 0.00 31.96 3.01
2056 4342 8.725256 TGAGGTCCTACTATAGATGTTCTAACT 58.275 37.037 6.78 0.00 31.96 2.24
2057 4343 8.921353 TGAGGTCCTACTATAGATGTTCTAAC 57.079 38.462 6.78 0.00 31.96 2.34
2063 4349 5.839606 GGGTTTGAGGTCCTACTATAGATGT 59.160 44.000 6.78 0.00 0.00 3.06
2070 4356 2.658489 AGAGGGGTTTGAGGTCCTACTA 59.342 50.000 0.00 0.00 0.00 1.82
2073 4359 2.735259 AAGAGGGGTTTGAGGTCCTA 57.265 50.000 0.00 0.00 0.00 2.94
2074 4360 2.735259 TAAGAGGGGTTTGAGGTCCT 57.265 50.000 0.00 0.00 0.00 3.85
2077 4364 3.817931 GCCATTTAAGAGGGGTTTGAGGT 60.818 47.826 0.00 0.00 0.00 3.85
2092 4379 1.743623 CCGTCCGCACAGCCATTTA 60.744 57.895 0.00 0.00 0.00 1.40
2123 4410 3.057104 TCTGAGTCGCTTATTTTGACCGA 60.057 43.478 0.00 0.00 33.09 4.69
2161 4449 0.896940 TAGCCCGGACGTTTGAGACT 60.897 55.000 0.73 0.00 0.00 3.24
2231 4519 0.725117 GTAGATTTGTCCGGGCAACG 59.275 55.000 23.74 0.00 43.80 4.10
2243 4531 1.066605 CGGATCCGACGTGGTAGATTT 59.933 52.381 30.62 0.00 42.83 2.17
2248 4536 2.045045 ACCGGATCCGACGTGGTA 60.045 61.111 35.42 0.00 42.83 3.25
2277 4566 3.309388 GACGAATATGTGAGGTCGGATG 58.691 50.000 0.00 0.00 37.81 3.51
2279 4568 1.679680 GGACGAATATGTGAGGTCGGA 59.320 52.381 0.00 0.00 37.81 4.55
2280 4569 1.407618 TGGACGAATATGTGAGGTCGG 59.592 52.381 0.00 0.00 37.81 4.79
2281 4570 2.159296 TGTGGACGAATATGTGAGGTCG 60.159 50.000 0.00 0.00 39.37 4.79
2282 4571 3.520290 TGTGGACGAATATGTGAGGTC 57.480 47.619 0.00 0.00 0.00 3.85
2283 4572 4.442706 GAATGTGGACGAATATGTGAGGT 58.557 43.478 0.00 0.00 0.00 3.85
2285 4574 4.359706 TCGAATGTGGACGAATATGTGAG 58.640 43.478 0.00 0.00 35.62 3.51
2286 4575 4.379339 TCGAATGTGGACGAATATGTGA 57.621 40.909 0.00 0.00 35.62 3.58
2289 4579 4.150627 GGTGATCGAATGTGGACGAATATG 59.849 45.833 0.00 0.00 41.65 1.78
2304 4594 0.323629 GGGTTTGACCTGGTGATCGA 59.676 55.000 2.82 0.00 38.64 3.59
2316 4606 1.916273 TGGAGCGGCTAGGGTTTGA 60.916 57.895 0.60 0.00 0.00 2.69
2329 4619 0.902516 AGAGTGGACTGGAGTGGAGC 60.903 60.000 0.00 0.00 0.00 4.70
2348 5006 3.650950 GGACAGGAGCTTGGGGCA 61.651 66.667 0.00 0.00 44.79 5.36
2401 5059 3.362262 CGGACTGGTCGGAGTCAA 58.638 61.111 10.88 0.00 43.70 3.18
2454 5112 0.402121 GATCATAGCACCCCTTCCCC 59.598 60.000 0.00 0.00 0.00 4.81
2457 5115 1.270358 GGACGATCATAGCACCCCTTC 60.270 57.143 0.00 0.00 0.00 3.46
2458 5116 0.759346 GGACGATCATAGCACCCCTT 59.241 55.000 0.00 0.00 0.00 3.95
2459 5117 0.398522 TGGACGATCATAGCACCCCT 60.399 55.000 0.00 0.00 0.00 4.79
2460 5118 0.249911 GTGGACGATCATAGCACCCC 60.250 60.000 0.00 0.00 0.00 4.95
2461 5119 0.464036 TGTGGACGATCATAGCACCC 59.536 55.000 0.00 0.00 0.00 4.61
2462 5120 2.533266 ATGTGGACGATCATAGCACC 57.467 50.000 0.00 0.00 0.00 5.01
2463 5121 3.248602 GGAAATGTGGACGATCATAGCAC 59.751 47.826 0.00 0.00 0.00 4.40
2541 5199 3.507924 TGCGCCGATGCAATGGAC 61.508 61.111 4.18 3.45 43.02 4.02
2569 5384 3.758133 ATCCAGCCCCGACGGATCT 62.758 63.158 17.49 8.81 34.31 2.75
2599 5414 0.105246 CCAGAGATGGGGAGGCTACT 60.105 60.000 0.00 0.00 0.00 2.57
2616 5431 2.043752 TCATACTCCGGCGGACCA 60.044 61.111 27.46 16.13 34.57 4.02
2657 5472 3.056080 CCTTATCCTTCCCTTCCCATGA 58.944 50.000 0.00 0.00 0.00 3.07
2668 5483 0.035036 GCCGGCTACCCTTATCCTTC 59.965 60.000 22.15 0.00 0.00 3.46
2669 5484 1.755393 CGCCGGCTACCCTTATCCTT 61.755 60.000 26.68 0.00 0.00 3.36
2719 5536 2.046023 CTTGAGGATGCGGGCACA 60.046 61.111 0.00 0.00 0.00 4.57
2745 5562 3.712881 GCGCACGTGTTCCTCCAC 61.713 66.667 18.38 0.00 0.00 4.02
2746 5563 4.980805 GGCGCACGTGTTCCTCCA 62.981 66.667 18.38 0.00 0.00 3.86
2761 5578 0.893727 TTTTGCTCTCGGGAAAGGGC 60.894 55.000 0.00 0.00 43.43 5.19
2767 5584 0.460284 GCTCGATTTTGCTCTCGGGA 60.460 55.000 0.00 0.00 37.57 5.14
2787 5604 2.136791 CCCGACCATGGCATAGACT 58.863 57.895 13.04 0.00 0.00 3.24
2812 5629 0.836400 TCCTCCTTCTCGCCTTTGGT 60.836 55.000 0.00 0.00 0.00 3.67
2820 5637 1.137825 GTCGCTGTCCTCCTTCTCG 59.862 63.158 0.00 0.00 0.00 4.04
2849 5666 1.888436 AATCTGCTCGTTGCCGGAGA 61.888 55.000 5.05 0.00 42.00 3.71
2871 5688 3.915437 AAAACGCAAAATGGATCGAGT 57.085 38.095 0.00 0.00 0.00 4.18
2896 5713 0.885879 TCTTTCTCGCGGAAGTAGCA 59.114 50.000 6.13 0.00 35.16 3.49
2999 5816 3.566351 TCAGGATGTGTCATCGGACTAT 58.434 45.455 4.08 0.00 38.99 2.12
3014 5831 4.281182 GTCATCCGGTTACTACATCAGGAT 59.719 45.833 0.00 0.00 37.48 3.24
3091 5909 2.151202 CAACCGCACACCTCAATTAGT 58.849 47.619 0.00 0.00 0.00 2.24
3120 5938 8.761497 GCAGCGACTGATTACACTTTAAATATA 58.239 33.333 10.46 0.00 32.44 0.86
3122 5940 6.036735 GGCAGCGACTGATTACACTTTAAATA 59.963 38.462 10.46 0.00 32.44 1.40
3124 5942 4.153475 GGCAGCGACTGATTACACTTTAAA 59.847 41.667 10.46 0.00 32.44 1.52
3170 5988 2.045045 CCTCCTCAAATGCCCGCA 60.045 61.111 0.00 0.00 0.00 5.69
3188 6006 2.570302 ACAGCCACGGTAGGTAAATCTT 59.430 45.455 0.00 0.00 0.00 2.40
3800 6705 0.884704 AAATTGTCACCGCGCACTCT 60.885 50.000 8.75 0.00 0.00 3.24
3805 6710 2.325509 AAGTAAAATTGTCACCGCGC 57.674 45.000 0.00 0.00 0.00 6.86
3806 6711 3.662186 GTCAAAGTAAAATTGTCACCGCG 59.338 43.478 0.00 0.00 0.00 6.46
4984 7893 2.429610 GCGAGGGTAACAGAATAGTCCA 59.570 50.000 0.00 0.00 39.74 4.02
4985 7894 2.223994 GGCGAGGGTAACAGAATAGTCC 60.224 54.545 0.00 0.00 39.74 3.85
4986 7895 2.223994 GGGCGAGGGTAACAGAATAGTC 60.224 54.545 0.00 0.00 39.74 2.59
4987 7896 1.761198 GGGCGAGGGTAACAGAATAGT 59.239 52.381 0.00 0.00 39.74 2.12
4988 7897 1.070289 GGGGCGAGGGTAACAGAATAG 59.930 57.143 0.00 0.00 39.74 1.73
5037 7946 2.285368 AGTCGGATTGGGGCTGGA 60.285 61.111 0.00 0.00 0.00 3.86
5176 8145 3.072468 GGGATGACGACCCCGACA 61.072 66.667 0.00 0.00 43.58 4.35
5267 8241 3.208884 GACCCCGACGATGGATCCG 62.209 68.421 7.39 0.00 0.00 4.18
5284 8258 2.060383 CAGGAGGCAGGGATGACGA 61.060 63.158 0.00 0.00 0.00 4.20
5288 8262 3.414193 TGGCAGGAGGCAGGGATG 61.414 66.667 0.00 0.00 46.46 3.51
5320 8294 1.300233 GACGGCTCCGATGATGGAC 60.300 63.158 15.95 0.00 42.83 4.02
5494 8520 4.456566 GTCTTCTTCTTCTACCTCTCGTGT 59.543 45.833 0.00 0.00 0.00 4.49
5713 8740 7.377766 ACTGACGCATATGTGTTATTTTTCT 57.622 32.000 22.18 0.00 39.12 2.52
5714 8741 6.687105 GGACTGACGCATATGTGTTATTTTTC 59.313 38.462 22.18 12.59 39.12 2.29
5746 8775 1.270094 CGGTAGCTGAACCTTGTCACA 60.270 52.381 0.00 0.00 37.39 3.58
6081 9127 8.148351 TCTTCTGTAACTTATGCAACTACACTT 58.852 33.333 0.00 0.00 0.00 3.16
6162 9208 5.637810 CACGGATGTACTGATGTACTGTTTT 59.362 40.000 7.67 0.00 46.70 2.43
6163 9209 5.168569 CACGGATGTACTGATGTACTGTTT 58.831 41.667 7.67 0.00 46.70 2.83
6217 9265 6.658188 TGGGATTAATCTGGTTTCGTTTTT 57.342 33.333 14.95 0.00 0.00 1.94
6401 9450 2.273908 GGACCTGTCCGTGCTTCTA 58.726 57.895 0.00 0.00 40.36 2.10
6550 9616 2.419673 GCACGGATGATTGATGTTGACA 59.580 45.455 0.00 0.00 0.00 3.58
6586 9653 3.319198 GCCCTGGTCTTCCCGTCA 61.319 66.667 0.00 0.00 35.15 4.35
6826 9894 7.039714 TGGATACTTACATGTGTATAGCTCTGG 60.040 40.741 9.11 0.00 37.61 3.86
6937 10008 1.630369 AGCTTCAATGTCAGGTGGCTA 59.370 47.619 0.00 0.00 0.00 3.93
7129 10200 4.553938 CGTTTTGTTCCGCTGTCTATTTGT 60.554 41.667 0.00 0.00 0.00 2.83
7143 10214 1.002792 GTCCTGGCTGTCGTTTTGTTC 60.003 52.381 0.00 0.00 0.00 3.18
7149 10220 1.115930 AGTCAGTCCTGGCTGTCGTT 61.116 55.000 14.79 1.62 44.94 3.85
7161 10232 5.086104 TCATTTTAGCCCTGTAGTCAGTC 57.914 43.478 0.00 0.00 39.82 3.51
7165 10236 3.118223 AGCCTCATTTTAGCCCTGTAGTC 60.118 47.826 0.00 0.00 0.00 2.59
7169 10240 1.635487 TCAGCCTCATTTTAGCCCTGT 59.365 47.619 0.00 0.00 0.00 4.00
7193 10264 4.036262 CGACAAGTGTTCCATCCTTTTCAA 59.964 41.667 0.00 0.00 0.00 2.69
7194 10265 3.563808 CGACAAGTGTTCCATCCTTTTCA 59.436 43.478 0.00 0.00 0.00 2.69
7210 10281 6.037098 CCCAGACTATCTCTTTTACGACAAG 58.963 44.000 0.00 0.00 0.00 3.16
7264 10335 3.973657 AGTGCAAGAAGACAAGCATTTG 58.026 40.909 0.00 0.00 39.43 2.32


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

AutoCloner maintained by Alex Coulton.