Multiple sequence alignment - TraesCS3D01G501300

Loading Multiple Alignment...

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 TraesCS3D01G501300 chr3D 100.000 4878 0 0 1 4878 590237489 590242366 0.000000e+00 9009.0
1 TraesCS3D01G501300 chr3D 90.655 1787 136 24 2373 4137 590202920 590204697 0.000000e+00 2346.0
2 TraesCS3D01G501300 chr3D 87.117 1894 145 40 1 1857 590199650 590201481 0.000000e+00 2054.0
3 TraesCS3D01G501300 chr3D 82.126 1035 143 24 871 1875 590306093 590307115 0.000000e+00 848.0
4 TraesCS3D01G501300 chr3D 89.231 650 60 8 3495 4135 589000712 589000064 0.000000e+00 804.0
5 TraesCS3D01G501300 chr3D 99.091 440 3 1 4439 4878 603060265 603060703 0.000000e+00 789.0
6 TraesCS3D01G501300 chr3D 82.366 930 110 43 2507 3401 590307381 590308291 0.000000e+00 760.0
7 TraesCS3D01G501300 chr3D 94.322 317 18 0 4135 4451 590205096 590205412 2.040000e-133 486.0
8 TraesCS3D01G501300 chr3D 87.342 316 25 1 4136 4451 590309391 590309691 1.000000e-91 348.0
9 TraesCS3D01G501300 chr3D 93.077 130 9 0 2260 2389 590201961 590202090 1.790000e-44 191.0
10 TraesCS3D01G501300 chr3D 89.076 119 11 2 1879 1997 590307152 590307268 3.930000e-31 147.0
11 TraesCS3D01G501300 chr3B 86.298 2715 268 55 378 3024 789175446 789178124 0.000000e+00 2857.0
12 TraesCS3D01G501300 chr3B 86.619 1547 164 21 338 1875 789217302 789218814 0.000000e+00 1670.0
13 TraesCS3D01G501300 chr3B 85.024 1636 158 41 2502 4115 789220097 789221667 0.000000e+00 1583.0
14 TraesCS3D01G501300 chr3B 90.354 1130 83 14 3024 4137 789179173 789180292 0.000000e+00 1459.0
15 TraesCS3D01G501300 chr3B 85.507 897 107 10 989 1875 789226963 789227846 0.000000e+00 915.0
16 TraesCS3D01G501300 chr3B 91.149 644 47 3 3496 4132 789229004 789229644 0.000000e+00 865.0
17 TraesCS3D01G501300 chr3B 82.035 924 118 33 2507 3401 789228051 789228955 0.000000e+00 743.0
18 TraesCS3D01G501300 chr3B 94.006 317 19 0 4135 4451 789180691 789181007 9.500000e-132 481.0
19 TraesCS3D01G501300 chr3B 87.838 296 28 3 4136 4423 789222098 789222393 1.680000e-89 340.0
20 TraesCS3D01G501300 chr3B 86.076 316 29 2 4136 4451 789230068 789230368 4.710000e-85 326.0
21 TraesCS3D01G501300 chr3B 87.324 71 8 1 4696 4765 789230750 789230820 4.050000e-11 80.5
22 TraesCS3D01G501300 chr3A 90.833 2018 159 14 2138 4137 719934634 719936643 0.000000e+00 2678.0
23 TraesCS3D01G501300 chr3A 89.755 1347 79 27 524 1861 719932590 719933886 0.000000e+00 1668.0
24 TraesCS3D01G501300 chr3A 84.997 1653 159 38 2504 4132 719995150 719996737 0.000000e+00 1596.0
25 TraesCS3D01G501300 chr3A 82.982 1422 181 28 859 2255 720228116 720229501 0.000000e+00 1229.0
26 TraesCS3D01G501300 chr3A 83.504 1170 157 16 721 1875 719991528 719992676 0.000000e+00 1059.0
27 TraesCS3D01G501300 chr3A 79.349 1506 229 38 733 2206 720214224 720215679 0.000000e+00 983.0
28 TraesCS3D01G501300 chr3A 91.493 623 46 5 3517 4132 720077497 720078119 0.000000e+00 850.0
29 TraesCS3D01G501300 chr3A 81.341 1104 146 40 2332 3397 720229665 720230746 0.000000e+00 843.0
30 TraesCS3D01G501300 chr3A 90.610 639 53 2 3501 4132 720230804 720231442 0.000000e+00 841.0
31 TraesCS3D01G501300 chr3A 81.044 1034 151 26 859 1875 720075253 720076258 0.000000e+00 782.0
32 TraesCS3D01G501300 chr3A 82.220 928 115 32 2507 3401 720076526 720077436 0.000000e+00 754.0
33 TraesCS3D01G501300 chr3A 80.556 972 113 37 2199 3134 720215842 720216773 0.000000e+00 678.0
34 TraesCS3D01G501300 chr3A 94.637 317 17 0 4135 4451 719937042 719937358 4.390000e-135 492.0
35 TraesCS3D01G501300 chr3A 85.166 391 29 9 84 472 719931977 719932340 1.660000e-99 374.0
36 TraesCS3D01G501300 chr3A 84.416 385 40 13 377 756 720084626 720084257 1.290000e-95 361.0
37 TraesCS3D01G501300 chr3A 86.280 328 33 4 4136 4451 719997161 719997488 3.610000e-91 346.0
38 TraesCS3D01G501300 chr3A 86.709 316 27 1 4136 4451 720231851 720232151 2.180000e-88 337.0
39 TraesCS3D01G501300 chr3A 86.392 316 28 1 4136 4451 720078532 720078832 1.010000e-86 331.0
40 TraesCS3D01G501300 chr3A 88.686 274 17 5 336 607 719991174 719991435 6.090000e-84 322.0
41 TraesCS3D01G501300 chr3A 79.588 485 67 17 3 466 719990743 719991216 7.880000e-83 318.0
42 TraesCS3D01G501300 chr3A 86.170 282 25 6 1879 2147 719933943 719934223 4.780000e-75 292.0
43 TraesCS3D01G501300 chr3A 89.076 119 11 2 349 466 719991143 719991260 3.930000e-31 147.0
44 TraesCS3D01G501300 chr3A 85.417 144 17 2 4691 4830 720232558 720232701 3.930000e-31 147.0
45 TraesCS3D01G501300 chr3A 80.769 208 20 8 1879 2071 720076295 720076497 1.420000e-30 145.0


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 TraesCS3D01G501300 chr3D 590237489 590242366 4877 False 9009.000000 9009 100.000000 1 4878 1 chr3D.!!$F1 4877
1 TraesCS3D01G501300 chr3D 590199650 590205412 5762 False 1269.250000 2346 91.292750 1 4451 4 chr3D.!!$F3 4450
2 TraesCS3D01G501300 chr3D 589000064 589000712 648 True 804.000000 804 89.231000 3495 4135 1 chr3D.!!$R1 640
3 TraesCS3D01G501300 chr3D 590306093 590309691 3598 False 525.750000 848 85.227500 871 4451 4 chr3D.!!$F4 3580
4 TraesCS3D01G501300 chr3B 789175446 789181007 5561 False 1599.000000 2857 90.219333 378 4451 3 chr3B.!!$F1 4073
5 TraesCS3D01G501300 chr3B 789217302 789222393 5091 False 1197.666667 1670 86.493667 338 4423 3 chr3B.!!$F2 4085
6 TraesCS3D01G501300 chr3B 789226963 789230820 3857 False 585.900000 915 86.418200 989 4765 5 chr3B.!!$F3 3776
7 TraesCS3D01G501300 chr3A 719931977 719937358 5381 False 1100.800000 2678 89.312200 84 4451 5 chr3A.!!$F1 4367
8 TraesCS3D01G501300 chr3A 720214224 720216773 2549 False 830.500000 983 79.952500 733 3134 2 chr3A.!!$F4 2401
9 TraesCS3D01G501300 chr3A 720228116 720232701 4585 False 679.400000 1229 85.411800 859 4830 5 chr3A.!!$F5 3971
10 TraesCS3D01G501300 chr3A 719990743 719997488 6745 False 631.333333 1596 85.355167 3 4451 6 chr3A.!!$F2 4448
11 TraesCS3D01G501300 chr3A 720075253 720078832 3579 False 572.400000 850 84.383600 859 4451 5 chr3A.!!$F3 3592

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
82 94 0.690744 CCCCATTTTCCCCCATGGTC 60.691 60.0 11.73 0.0 38.72 4.02 F
1571 2037 0.101399 ACCTCGCGCTTAGATGTCAG 59.899 55.0 5.56 0.0 0.00 3.51 F
1928 2452 0.322456 CGGCAGATCCTTGGTTGGAA 60.322 55.0 0.00 0.0 39.85 3.53 F
2590 6376 1.895280 GCGCTCTGGATTATCGCTGC 61.895 60.0 0.00 0.0 42.19 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2452 0.252375 ATTGAAGCCAGGGTGCCATT 60.252 50.0 0.00 0.0 0.00 3.16 R
2590 6376 0.108186 TGACAGTAATGGAGCTGCCG 60.108 55.0 1.53 0.0 40.66 5.69 R
2924 6725 0.899720 TTACCTTGTAGACAGGGCCG 59.100 55.0 10.54 0.0 45.96 6.13 R
4167 9520 0.096976 CGACATTCGACATGGTTGGC 59.903 55.0 0.00 0.0 43.74 4.52 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 3.786656 GGTGGTAAACCCGGTATCC 57.213 57.895 0.00 0.00 44.02 2.59
61 73 3.561960 GGTGGTAAACCCGGTATCCTTTT 60.562 47.826 0.00 0.00 44.02 2.27
66 78 1.284111 ACCCGGTATCCTTTTCCCCC 61.284 60.000 0.00 0.00 0.00 5.40
67 79 1.283381 CCCGGTATCCTTTTCCCCCA 61.283 60.000 0.00 0.00 0.00 4.96
72 84 3.383505 CGGTATCCTTTTCCCCCATTTTC 59.616 47.826 0.00 0.00 0.00 2.29
75 87 1.203376 TCCTTTTCCCCCATTTTCCCC 60.203 52.381 0.00 0.00 0.00 4.81
82 94 0.690744 CCCCATTTTCCCCCATGGTC 60.691 60.000 11.73 0.00 38.72 4.02
121 133 2.798283 CAATGCAAAGCTTTGTGGTCTG 59.202 45.455 33.47 21.43 38.38 3.51
131 143 2.032965 TTGTGGTCTGTAAGCCCCTA 57.967 50.000 0.00 0.00 30.41 3.53
132 144 2.263895 TGTGGTCTGTAAGCCCCTAT 57.736 50.000 0.00 0.00 30.41 2.57
133 145 2.116238 TGTGGTCTGTAAGCCCCTATC 58.884 52.381 0.00 0.00 30.41 2.08
134 146 1.416772 GTGGTCTGTAAGCCCCTATCC 59.583 57.143 0.00 0.00 30.41 2.59
149 161 3.593328 CCCTATCCATCCATAACCCACAT 59.407 47.826 0.00 0.00 0.00 3.21
178 195 3.119319 TCTGCAGTCCCAACCCATAATA 58.881 45.455 14.67 0.00 0.00 0.98
179 196 3.525609 TCTGCAGTCCCAACCCATAATAA 59.474 43.478 14.67 0.00 0.00 1.40
180 197 4.167892 TCTGCAGTCCCAACCCATAATAAT 59.832 41.667 14.67 0.00 0.00 1.28
181 198 4.877773 TGCAGTCCCAACCCATAATAATT 58.122 39.130 0.00 0.00 0.00 1.40
182 199 4.892934 TGCAGTCCCAACCCATAATAATTC 59.107 41.667 0.00 0.00 0.00 2.17
183 200 4.892934 GCAGTCCCAACCCATAATAATTCA 59.107 41.667 0.00 0.00 0.00 2.57
184 201 5.010012 GCAGTCCCAACCCATAATAATTCAG 59.990 44.000 0.00 0.00 0.00 3.02
185 202 6.129179 CAGTCCCAACCCATAATAATTCAGT 58.871 40.000 0.00 0.00 0.00 3.41
186 203 7.287061 CAGTCCCAACCCATAATAATTCAGTA 58.713 38.462 0.00 0.00 0.00 2.74
187 204 7.228706 CAGTCCCAACCCATAATAATTCAGTAC 59.771 40.741 0.00 0.00 0.00 2.73
188 205 6.489022 GTCCCAACCCATAATAATTCAGTACC 59.511 42.308 0.00 0.00 0.00 3.34
189 206 5.773176 CCCAACCCATAATAATTCAGTACCC 59.227 44.000 0.00 0.00 0.00 3.69
190 207 5.773176 CCAACCCATAATAATTCAGTACCCC 59.227 44.000 0.00 0.00 0.00 4.95
191 208 6.411554 CCAACCCATAATAATTCAGTACCCCT 60.412 42.308 0.00 0.00 0.00 4.79
192 209 7.202242 CCAACCCATAATAATTCAGTACCCCTA 60.202 40.741 0.00 0.00 0.00 3.53
193 210 7.569599 ACCCATAATAATTCAGTACCCCTAG 57.430 40.000 0.00 0.00 0.00 3.02
194 211 7.318401 ACCCATAATAATTCAGTACCCCTAGA 58.682 38.462 0.00 0.00 0.00 2.43
267 308 4.854399 TGAATTTTGCTCACGGTAAACAG 58.146 39.130 0.00 0.00 29.68 3.16
290 331 6.872020 CAGCATGTTGAATTGAGAATTTTCCT 59.128 34.615 2.97 0.00 0.00 3.36
296 351 4.021192 TGAATTGAGAATTTTCCTGTGCCC 60.021 41.667 0.00 0.00 0.00 5.36
314 369 5.941058 TGTGCCCGTCAAAATAAAGAGATAA 59.059 36.000 0.00 0.00 0.00 1.75
315 370 6.128117 TGTGCCCGTCAAAATAAAGAGATAAC 60.128 38.462 0.00 0.00 0.00 1.89
316 371 5.941058 TGCCCGTCAAAATAAAGAGATAACA 59.059 36.000 0.00 0.00 0.00 2.41
317 372 6.601613 TGCCCGTCAAAATAAAGAGATAACAT 59.398 34.615 0.00 0.00 0.00 2.71
318 373 7.122055 TGCCCGTCAAAATAAAGAGATAACATT 59.878 33.333 0.00 0.00 0.00 2.71
319 374 7.432252 GCCCGTCAAAATAAAGAGATAACATTG 59.568 37.037 0.00 0.00 0.00 2.82
320 375 8.673711 CCCGTCAAAATAAAGAGATAACATTGA 58.326 33.333 0.00 0.00 0.00 2.57
370 425 2.835156 AGACCTCCTAAACTTCCAGCTC 59.165 50.000 0.00 0.00 0.00 4.09
394 499 7.004086 TCAATCCTGTTTTGACTTGGAATAGT 58.996 34.615 0.00 0.00 0.00 2.12
488 639 6.519382 TGATATCTGAATGGCTACTTGTGAG 58.481 40.000 3.98 0.00 0.00 3.51
561 931 4.457810 CACACACTTCTTTGATGCTTACG 58.542 43.478 0.00 0.00 0.00 3.18
583 953 1.869342 GCCTTCAATTTTGCAGCGTGT 60.869 47.619 0.00 0.00 0.00 4.49
584 954 1.788308 CCTTCAATTTTGCAGCGTGTG 59.212 47.619 0.00 0.00 0.00 3.82
587 957 4.475028 CTTCAATTTTGCAGCGTGTGATA 58.525 39.130 0.00 0.00 0.00 2.15
589 959 4.661125 TCAATTTTGCAGCGTGTGATATC 58.339 39.130 0.00 0.00 0.00 1.63
590 960 4.395854 TCAATTTTGCAGCGTGTGATATCT 59.604 37.500 3.98 0.00 0.00 1.98
591 961 5.584251 TCAATTTTGCAGCGTGTGATATCTA 59.416 36.000 3.98 0.00 0.00 1.98
623 993 1.093159 CCAGAGCTGCTCAAATGGAC 58.907 55.000 29.49 2.47 32.06 4.02
638 1008 1.599797 GGACGGTGGTGTTCCCTTG 60.600 63.158 0.00 0.00 0.00 3.61
1158 1606 2.022718 ACCTCAAGCTCCTCTCAACT 57.977 50.000 0.00 0.00 0.00 3.16
1160 1608 3.511477 ACCTCAAGCTCCTCTCAACTAA 58.489 45.455 0.00 0.00 0.00 2.24
1182 1630 1.667830 CCCGAAGAAAGCAGCGTCA 60.668 57.895 2.40 0.00 0.00 4.35
1197 1654 1.308998 CGTCAAGCACCAACCTCTTT 58.691 50.000 0.00 0.00 0.00 2.52
1316 1773 3.322466 CTTCCAGGACGGGCAGGT 61.322 66.667 0.00 0.00 34.36 4.00
1418 1875 1.866237 CCACCACCGTCAATGAACG 59.134 57.895 0.00 0.00 42.24 3.95
1453 1919 1.202498 TGAGCATCGAGAGCTTGATGG 60.202 52.381 22.75 9.87 46.62 3.51
1489 1955 2.650116 GCCGACTCCTTCAGGCTCA 61.650 63.158 0.00 0.00 45.67 4.26
1566 2032 1.676746 TCACTACCTCGCGCTTAGAT 58.323 50.000 5.56 0.00 0.00 1.98
1567 2033 1.333931 TCACTACCTCGCGCTTAGATG 59.666 52.381 5.56 0.00 0.00 2.90
1568 2034 1.065701 CACTACCTCGCGCTTAGATGT 59.934 52.381 5.56 1.20 0.00 3.06
1569 2035 1.334243 ACTACCTCGCGCTTAGATGTC 59.666 52.381 5.56 0.00 0.00 3.06
1570 2036 1.333931 CTACCTCGCGCTTAGATGTCA 59.666 52.381 5.56 0.00 0.00 3.58
1571 2037 0.101399 ACCTCGCGCTTAGATGTCAG 59.899 55.000 5.56 0.00 0.00 3.51
1635 2101 2.105128 GACCTGACCGCCGATGAG 59.895 66.667 0.00 0.00 0.00 2.90
1757 2223 6.889198 ACGAGATATTTCCATTCTTCCAAGA 58.111 36.000 0.00 0.00 0.00 3.02
1785 2251 4.754618 CCCATGCTGCGTATTATCAACTTA 59.245 41.667 0.00 0.00 0.00 2.24
1789 2255 4.270084 TGCTGCGTATTATCAACTTAGCAC 59.730 41.667 0.00 0.00 32.30 4.40
1800 2266 3.135712 TCAACTTAGCACCTGAAGTTCCA 59.864 43.478 0.00 0.00 42.57 3.53
1811 2277 2.738846 CTGAAGTTCCACCGATCAACAG 59.261 50.000 0.00 0.00 0.00 3.16
1898 2422 6.329496 CGGCACTTCATGGTATGTAAAATTT 58.671 36.000 0.00 0.00 0.00 1.82
1928 2452 0.322456 CGGCAGATCCTTGGTTGGAA 60.322 55.000 0.00 0.00 39.85 3.53
1955 2486 3.313526 CACCCTGGCTTCAATTAGATTCG 59.686 47.826 0.00 0.00 0.00 3.34
1978 2511 8.780846 TCGTTAATTTAGGTAACATGTCACAT 57.219 30.769 0.59 0.00 41.41 3.21
2211 4406 4.982295 GCAATGTCCACTTACAAGGAAAAC 59.018 41.667 0.00 0.00 35.29 2.43
2262 4790 7.847487 TGATAATTAGCTTGTTACGTATGTGC 58.153 34.615 1.93 0.00 0.00 4.57
2292 4820 7.658179 TTTTTAGACAAGTAGACATGAGCTG 57.342 36.000 0.00 0.00 0.00 4.24
2300 4828 7.038659 ACAAGTAGACATGAGCTGAAGAATAC 58.961 38.462 0.00 0.00 0.00 1.89
2399 5773 3.510388 TGCTAGAGTCAGAATGGTTCG 57.490 47.619 0.00 0.00 36.16 3.95
2445 5826 2.131972 TCAATTGGTGAAGTGTCGTCG 58.868 47.619 5.42 0.00 31.51 5.12
2446 5827 2.131972 CAATTGGTGAAGTGTCGTCGA 58.868 47.619 0.00 0.00 0.00 4.20
2447 5828 2.519377 ATTGGTGAAGTGTCGTCGAA 57.481 45.000 0.00 0.00 0.00 3.71
2462 5843 5.092105 GTCGTCGAATGAGATGATCCATAG 58.908 45.833 0.00 0.00 38.30 2.23
2465 5846 3.834231 TCGAATGAGATGATCCATAGCCA 59.166 43.478 0.00 0.00 0.00 4.75
2467 5848 4.630505 CGAATGAGATGATCCATAGCCAAG 59.369 45.833 0.00 0.00 0.00 3.61
2477 5858 5.824624 TGATCCATAGCCAAGAACTGATTTC 59.175 40.000 0.00 0.00 33.95 2.17
2479 5860 6.560003 TCCATAGCCAAGAACTGATTTCTA 57.440 37.500 0.00 0.00 44.41 2.10
2558 6344 5.067283 ACTTTGTGTTTTTCTAGGACGCAAT 59.933 36.000 12.64 2.16 41.62 3.56
2590 6376 1.895280 GCGCTCTGGATTATCGCTGC 61.895 60.000 0.00 0.00 42.19 5.25
2623 6409 6.968904 CCATTACTGTCAATATTTCTGTGTGC 59.031 38.462 8.93 0.00 0.00 4.57
2628 6414 6.540189 ACTGTCAATATTTCTGTGTGCTATCC 59.460 38.462 0.00 0.00 0.00 2.59
2645 6431 7.831690 TGTGCTATCCTTTTTGTTGTATGGATA 59.168 33.333 0.00 0.00 36.02 2.59
2694 6481 3.937814 TCACGATTACAACATGCCTCTT 58.062 40.909 0.00 0.00 0.00 2.85
2809 6610 2.035961 CGAATAGGCCGGAAGAAGATGA 59.964 50.000 5.05 0.00 0.00 2.92
2850 6651 6.462347 GGAAGAGAAGAGTTCAGAGTTCACTT 60.462 42.308 0.00 0.00 34.03 3.16
2886 6687 3.803778 TGAGATATTGCATGCTACACACG 59.196 43.478 20.33 0.00 0.00 4.49
2924 6725 1.886542 CTACTTGGGCAAGGTGGTTTC 59.113 52.381 0.00 0.00 42.53 2.78
3162 8045 8.579863 CAGTTATCATATCACTCATCCTGTACA 58.420 37.037 0.00 0.00 0.00 2.90
3216 8101 5.666969 TGCTTTCCATTATATTTCGACGG 57.333 39.130 0.00 0.00 0.00 4.79
3226 8111 2.240493 ATTTCGACGGCCTAGAATGG 57.760 50.000 0.00 0.00 0.00 3.16
3347 8237 4.991153 AGTAACCTAACGTAGCCCTAAC 57.009 45.455 0.00 0.00 0.00 2.34
3413 8305 1.216064 TGCCCTATTCAGCAGTGGAT 58.784 50.000 0.00 0.00 33.08 3.41
3416 8308 2.579873 CCCTATTCAGCAGTGGATTGG 58.420 52.381 0.00 0.00 35.01 3.16
3421 8313 2.957402 TCAGCAGTGGATTGGAACTT 57.043 45.000 0.00 0.00 0.00 2.66
3444 8336 8.734386 ACTTTGAAGGAAATAGAAGTAATGCAG 58.266 33.333 0.00 0.00 0.00 4.41
3459 8351 9.241317 GAAGTAATGCAGTGAAATGGAATATTG 57.759 33.333 0.00 0.00 0.00 1.90
3460 8352 7.719483 AGTAATGCAGTGAAATGGAATATTGG 58.281 34.615 0.00 0.00 0.00 3.16
3468 8360 2.330661 ATGGAATATTGGGGCCATGG 57.669 50.000 7.63 7.63 39.54 3.66
3471 8363 2.999634 TGGAATATTGGGGCCATGGATA 59.000 45.455 18.40 4.03 0.00 2.59
3472 8364 3.601998 TGGAATATTGGGGCCATGGATAT 59.398 43.478 18.40 6.49 0.00 1.63
3474 8366 4.572654 GGAATATTGGGGCCATGGATATGT 60.573 45.833 18.40 0.00 32.21 2.29
3475 8367 2.314071 ATTGGGGCCATGGATATGTG 57.686 50.000 18.40 0.00 32.21 3.21
3478 8370 1.355381 TGGGGCCATGGATATGTGATC 59.645 52.381 18.40 0.00 32.21 2.92
3484 8382 3.008813 GCCATGGATATGTGATCCTGACT 59.991 47.826 18.40 0.00 38.95 3.41
3493 8391 3.554934 TGTGATCCTGACTTGCTGTTTT 58.445 40.909 0.00 0.00 0.00 2.43
3520 8421 4.461081 TGTATCCCAAAAGTCATTTTCCCG 59.539 41.667 0.00 0.00 36.47 5.14
3533 8434 0.679640 TTTCCCGTGGATGGCATGTC 60.680 55.000 3.81 0.00 0.00 3.06
3556 8457 8.298854 TGTCATCCATTTTCTGTAATTTCAGTG 58.701 33.333 11.33 3.36 36.85 3.66
3572 8475 8.773033 AATTTCAGTGAAATATAATGCCTCCT 57.227 30.769 27.15 8.07 40.77 3.69
3591 8494 6.001460 CCTCCTGTTTTGTACATACTTCCAA 58.999 40.000 0.00 0.00 35.85 3.53
3601 8504 4.222124 ACATACTTCCAAGGCCAGTTAG 57.778 45.455 5.01 0.00 0.00 2.34
3638 8541 2.038659 TGCAGTTAAAAGGCTTGCCTT 58.961 42.857 20.03 20.03 0.00 4.35
3639 8542 2.224018 TGCAGTTAAAAGGCTTGCCTTG 60.224 45.455 25.29 14.56 0.00 3.61
3644 8547 2.643995 AAAAGGCTTGCCTTGCATTT 57.356 40.000 25.29 14.05 44.53 2.32
3876 8786 6.922247 ATAAAATGCACTCTCTCAGATGTG 57.078 37.500 0.00 4.15 31.25 3.21
3967 8877 1.739562 CTCCACAAGCACTCTCGGC 60.740 63.158 0.00 0.00 0.00 5.54
4020 8930 4.597507 AGTAACATTCTCTTGGACCAGGAA 59.402 41.667 7.81 8.16 0.00 3.36
4122 9032 4.982916 GTGGGAACATAGTAAGCGTATGAG 59.017 45.833 5.71 0.00 46.14 2.90
4211 9564 3.301642 GCAATGTTAAACAGCGAGAATGC 59.698 43.478 0.00 0.00 0.00 3.56
4252 9605 3.391296 ACATCCGGCATACTTCAACCTAT 59.609 43.478 0.00 0.00 0.00 2.57
4262 9615 7.324178 GCATACTTCAACCTATGGGTATCTAG 58.676 42.308 0.00 0.00 46.67 2.43
4327 9680 6.073765 CGTAACCATCTGCAGTAATAATGACC 60.074 42.308 14.67 0.00 0.00 4.02
4451 9824 6.270156 AGTAAACTAGAGCAGACCAAGTAC 57.730 41.667 0.00 0.00 0.00 2.73
4455 9947 7.425224 AAACTAGAGCAGACCAAGTACATAT 57.575 36.000 0.00 0.00 0.00 1.78
4461 9953 7.796054 AGAGCAGACCAAGTACATATTGTATT 58.204 34.615 0.00 0.00 35.05 1.89
4476 9968 9.874205 ACATATTGTATTTAGCTTTTGTGCATT 57.126 25.926 0.00 0.00 34.99 3.56
4491 9983 3.763097 TGCATTCGCACTATCCTTTTG 57.237 42.857 0.00 0.00 45.36 2.44
4492 9984 2.423185 TGCATTCGCACTATCCTTTTGG 59.577 45.455 0.00 0.00 45.36 3.28
4503 9995 1.903404 CCTTTTGGACTGGCGGCTT 60.903 57.895 11.43 0.00 44.07 4.35
4520 10012 3.569250 GCTTCTGCCGTTGGATTTAAA 57.431 42.857 0.00 0.00 0.00 1.52
4521 10013 4.110036 GCTTCTGCCGTTGGATTTAAAT 57.890 40.909 0.00 0.00 0.00 1.40
4522 10014 3.859386 GCTTCTGCCGTTGGATTTAAATG 59.141 43.478 5.17 0.00 0.00 2.32
4543 10035 7.601705 AATGAGGAAGACTTGAAATCCAAAA 57.398 32.000 0.00 0.00 33.76 2.44
4560 10135 7.787623 ATCCAAAAGATTTCAATCCTCAAGT 57.212 32.000 0.00 0.00 36.04 3.16
4563 10138 7.031975 CCAAAAGATTTCAATCCTCAAGTAGC 58.968 38.462 0.00 0.00 36.04 3.58
4571 10146 5.363101 TCAATCCTCAAGTAGCTGCATTAG 58.637 41.667 4.12 0.00 0.00 1.73
4589 10170 5.049818 GCATTAGCTGAACCTGCTTAGTATG 60.050 44.000 0.00 5.21 39.30 2.39
4598 10179 3.691118 ACCTGCTTAGTATGTGTTGCATG 59.309 43.478 0.00 0.00 38.47 4.06
4603 10184 7.388776 CCTGCTTAGTATGTGTTGCATGTATAT 59.611 37.037 0.00 0.00 38.47 0.86
4623 10204 4.525912 ATGCACCTTTGATGTTTTCCTC 57.474 40.909 0.00 0.00 0.00 3.71
4627 10208 5.115480 GCACCTTTGATGTTTTCCTCAAAA 58.885 37.500 0.00 0.00 41.35 2.44
4642 10223 8.755696 TTTCCTCAAAATTAATTCCATTGACG 57.244 30.769 8.92 6.69 0.00 4.35
4643 10224 7.461182 TCCTCAAAATTAATTCCATTGACGT 57.539 32.000 8.92 0.00 0.00 4.34
4644 10225 7.312154 TCCTCAAAATTAATTCCATTGACGTG 58.688 34.615 8.92 2.54 0.00 4.49
4645 10226 6.034898 CCTCAAAATTAATTCCATTGACGTGC 59.965 38.462 8.92 0.00 0.00 5.34
4646 10227 6.450545 TCAAAATTAATTCCATTGACGTGCA 58.549 32.000 8.92 0.00 0.00 4.57
4647 10228 6.925718 TCAAAATTAATTCCATTGACGTGCAA 59.074 30.769 8.92 0.00 41.53 4.08
4648 10229 6.949578 AAATTAATTCCATTGACGTGCAAG 57.050 33.333 0.10 0.00 40.42 4.01
4649 10230 4.433186 TTAATTCCATTGACGTGCAAGG 57.567 40.909 4.26 0.00 40.42 3.61
4650 10231 0.527565 ATTCCATTGACGTGCAAGGC 59.472 50.000 4.26 0.23 40.42 4.35
4651 10232 0.537143 TTCCATTGACGTGCAAGGCT 60.537 50.000 7.12 0.00 40.42 4.58
4652 10233 0.323302 TCCATTGACGTGCAAGGCTA 59.677 50.000 7.12 0.00 40.42 3.93
4653 10234 1.164411 CCATTGACGTGCAAGGCTAA 58.836 50.000 7.12 0.00 40.42 3.09
4654 10235 1.135689 CCATTGACGTGCAAGGCTAAC 60.136 52.381 7.12 0.00 40.42 2.34
4655 10236 1.806542 CATTGACGTGCAAGGCTAACT 59.193 47.619 7.12 0.00 40.42 2.24
4656 10237 2.823924 TTGACGTGCAAGGCTAACTA 57.176 45.000 7.12 0.00 31.55 2.24
4657 10238 2.363788 TGACGTGCAAGGCTAACTAG 57.636 50.000 7.12 0.00 0.00 2.57
4658 10239 1.890489 TGACGTGCAAGGCTAACTAGA 59.110 47.619 7.12 0.00 0.00 2.43
4659 10240 2.297880 TGACGTGCAAGGCTAACTAGAA 59.702 45.455 7.12 0.00 0.00 2.10
4660 10241 3.056107 TGACGTGCAAGGCTAACTAGAAT 60.056 43.478 7.12 0.00 0.00 2.40
4661 10242 4.158949 TGACGTGCAAGGCTAACTAGAATA 59.841 41.667 7.12 0.00 0.00 1.75
4662 10243 5.163447 TGACGTGCAAGGCTAACTAGAATAT 60.163 40.000 7.12 0.00 0.00 1.28
4663 10244 5.671493 ACGTGCAAGGCTAACTAGAATATT 58.329 37.500 4.26 0.00 0.00 1.28
4664 10245 5.523916 ACGTGCAAGGCTAACTAGAATATTG 59.476 40.000 4.26 0.00 0.00 1.90
4665 10246 5.753438 CGTGCAAGGCTAACTAGAATATTGA 59.247 40.000 0.00 0.00 0.00 2.57
4666 10247 6.425114 CGTGCAAGGCTAACTAGAATATTGAT 59.575 38.462 0.00 0.00 0.00 2.57
4667 10248 7.598869 CGTGCAAGGCTAACTAGAATATTGATA 59.401 37.037 0.00 0.00 0.00 2.15
4668 10249 9.442047 GTGCAAGGCTAACTAGAATATTGATAT 57.558 33.333 0.00 0.00 0.00 1.63
4669 10250 9.440773 TGCAAGGCTAACTAGAATATTGATATG 57.559 33.333 0.00 0.00 0.00 1.78
4670 10251 8.394121 GCAAGGCTAACTAGAATATTGATATGC 58.606 37.037 0.00 0.00 0.00 3.14
4671 10252 9.664332 CAAGGCTAACTAGAATATTGATATGCT 57.336 33.333 0.00 0.00 33.26 3.79
4679 10260 9.875691 ACTAGAATATTGATATGCTTATTCGCA 57.124 29.630 0.00 0.00 45.10 5.10
4745 10351 5.918011 TGTTACAAAATGAAGCATTTCCGTC 59.082 36.000 5.92 0.00 42.32 4.79
4758 10365 2.631160 TTCCGTCAGTTGTCATGGTT 57.369 45.000 0.00 0.00 0.00 3.67
4775 10385 2.092323 GGTTAGGCCAACATGGAGTTC 58.908 52.381 5.01 0.00 40.96 3.01
4785 10395 4.301628 CAACATGGAGTTCTTCCTTTTGC 58.698 43.478 0.00 0.00 46.92 3.68
4786 10396 3.565307 ACATGGAGTTCTTCCTTTTGCA 58.435 40.909 0.00 0.00 46.92 4.08
4792 10402 5.654650 TGGAGTTCTTCCTTTTGCAGTTTAA 59.345 36.000 0.00 0.00 46.92 1.52
4794 10404 6.405397 GGAGTTCTTCCTTTTGCAGTTTAACA 60.405 38.462 0.00 0.00 43.16 2.41
4799 10409 4.619973 TCCTTTTGCAGTTTAACATGCTG 58.380 39.130 16.08 0.00 42.98 4.41
4801 10411 5.049167 CCTTTTGCAGTTTAACATGCTGAA 58.951 37.500 16.08 10.48 42.98 3.02
4813 10423 9.109393 GTTTAACATGCTGAAGATGGATAAGTA 57.891 33.333 0.00 0.00 0.00 2.24
4817 10427 6.933521 ACATGCTGAAGATGGATAAGTACATC 59.066 38.462 0.00 0.00 44.67 3.06
4818 10428 6.484364 TGCTGAAGATGGATAAGTACATCA 57.516 37.500 7.32 0.00 46.41 3.07
4821 10431 6.203723 GCTGAAGATGGATAAGTACATCAACC 59.796 42.308 7.32 0.00 46.41 3.77
4830 10440 8.698210 TGGATAAGTACATCAACCGTATTACTT 58.302 33.333 0.00 0.00 34.82 2.24
4835 10445 8.361592 AGTACATCAACCGTATTACTTATTGC 57.638 34.615 0.00 0.00 0.00 3.56
4836 10446 8.202137 AGTACATCAACCGTATTACTTATTGCT 58.798 33.333 0.00 0.00 0.00 3.91
4837 10447 9.467258 GTACATCAACCGTATTACTTATTGCTA 57.533 33.333 0.00 0.00 0.00 3.49
4838 10448 8.951787 ACATCAACCGTATTACTTATTGCTAA 57.048 30.769 0.00 0.00 0.00 3.09
4839 10449 9.386010 ACATCAACCGTATTACTTATTGCTAAA 57.614 29.630 0.00 0.00 0.00 1.85
4869 10479 9.077885 TCTTGATTTAAACTTTATCTGGCAAGT 57.922 29.630 0.00 0.00 34.58 3.16
4870 10480 9.696917 CTTGATTTAAACTTTATCTGGCAAGTT 57.303 29.630 0.00 0.00 43.61 2.66
4876 10486 5.959618 ACTTTATCTGGCAAGTTTGTACC 57.040 39.130 0.00 0.00 28.27 3.34
4877 10487 5.631119 ACTTTATCTGGCAAGTTTGTACCT 58.369 37.500 0.00 0.00 28.27 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.282021 GGGAAAAGGATACCGGGTTTAC 58.718 50.000 4.31 0.00 37.17 2.01
55 56 1.203376 GGGGAAAATGGGGGAAAAGGA 60.203 52.381 0.00 0.00 0.00 3.36
56 57 1.285280 GGGGAAAATGGGGGAAAAGG 58.715 55.000 0.00 0.00 0.00 3.11
57 58 1.285280 GGGGGAAAATGGGGGAAAAG 58.715 55.000 0.00 0.00 0.00 2.27
61 73 1.709082 CATGGGGGAAAATGGGGGA 59.291 57.895 0.00 0.00 0.00 4.81
66 78 3.954258 GTCTTAGACCATGGGGGAAAATG 59.046 47.826 18.09 0.00 41.15 2.32
67 79 3.596046 TGTCTTAGACCATGGGGGAAAAT 59.404 43.478 18.09 0.00 41.15 1.82
72 84 1.584724 ACTGTCTTAGACCATGGGGG 58.415 55.000 18.09 1.08 44.81 5.40
75 87 5.413309 AGAGAAACTGTCTTAGACCATGG 57.587 43.478 11.19 11.19 36.41 3.66
82 94 5.049198 TGCATTGCAAGAGAAACTGTCTTAG 60.049 40.000 9.33 0.00 33.70 2.18
121 133 4.324331 GGTTATGGATGGATAGGGGCTTAC 60.324 50.000 0.00 0.00 0.00 2.34
131 143 2.491455 GGCATGTGGGTTATGGATGGAT 60.491 50.000 0.00 0.00 0.00 3.41
132 144 1.133513 GGCATGTGGGTTATGGATGGA 60.134 52.381 0.00 0.00 0.00 3.41
133 145 1.331214 GGCATGTGGGTTATGGATGG 58.669 55.000 0.00 0.00 0.00 3.51
134 146 1.331214 GGGCATGTGGGTTATGGATG 58.669 55.000 0.00 0.00 0.00 3.51
149 161 2.072487 GGGACTGCAGATAGGGGCA 61.072 63.158 23.35 0.00 38.52 5.36
267 308 6.647895 ACAGGAAAATTCTCAATTCAACATGC 59.352 34.615 0.00 0.00 0.00 4.06
290 331 3.745799 TCTCTTTATTTTGACGGGCACA 58.254 40.909 0.00 0.00 0.00 4.57
314 369 2.288152 ACGCGCTTGGAAAATTCAATGT 60.288 40.909 5.73 0.00 0.00 2.71
315 370 2.327568 ACGCGCTTGGAAAATTCAATG 58.672 42.857 5.73 0.00 0.00 2.82
316 371 2.723124 ACGCGCTTGGAAAATTCAAT 57.277 40.000 5.73 0.00 0.00 2.57
317 372 2.500509 AACGCGCTTGGAAAATTCAA 57.499 40.000 5.73 0.00 0.00 2.69
318 373 2.500509 AAACGCGCTTGGAAAATTCA 57.499 40.000 5.73 0.00 0.00 2.57
319 374 2.792116 TCAAAACGCGCTTGGAAAATTC 59.208 40.909 18.26 0.00 0.00 2.17
320 375 2.538037 GTCAAAACGCGCTTGGAAAATT 59.462 40.909 18.26 0.00 0.00 1.82
321 376 2.124122 GTCAAAACGCGCTTGGAAAAT 58.876 42.857 18.26 0.00 0.00 1.82
322 377 1.133407 AGTCAAAACGCGCTTGGAAAA 59.867 42.857 18.26 0.31 0.00 2.29
323 378 0.736053 AGTCAAAACGCGCTTGGAAA 59.264 45.000 18.26 0.62 0.00 3.13
324 379 0.736053 AAGTCAAAACGCGCTTGGAA 59.264 45.000 18.26 1.25 0.00 3.53
325 380 0.028770 CAAGTCAAAACGCGCTTGGA 59.971 50.000 18.26 8.37 35.87 3.53
370 425 7.175641 AGACTATTCCAAGTCAAAACAGGATTG 59.824 37.037 6.76 0.00 46.89 2.67
394 499 4.505039 GGTTAAGCTGGGAGTTCAGAAAGA 60.505 45.833 0.00 0.00 36.93 2.52
488 639 5.413833 TGCTCCAAATCTCAAAGTTCAGATC 59.586 40.000 0.00 0.00 0.00 2.75
561 931 0.785979 CGCTGCAAAATTGAAGGCAC 59.214 50.000 0.00 0.00 34.24 5.01
583 953 6.611236 TCTGGTGACCATGTTCTTAGATATCA 59.389 38.462 4.03 0.00 30.82 2.15
584 954 7.055667 TCTGGTGACCATGTTCTTAGATATC 57.944 40.000 4.03 0.00 30.82 1.63
587 957 4.383552 GCTCTGGTGACCATGTTCTTAGAT 60.384 45.833 4.03 0.00 30.82 1.98
589 959 3.055530 AGCTCTGGTGACCATGTTCTTAG 60.056 47.826 4.03 0.00 30.82 2.18
590 960 2.906389 AGCTCTGGTGACCATGTTCTTA 59.094 45.455 4.03 0.00 30.82 2.10
591 961 1.701847 AGCTCTGGTGACCATGTTCTT 59.298 47.619 4.03 0.00 30.82 2.52
623 993 2.983592 GGCAAGGGAACACCACCG 60.984 66.667 0.00 0.00 43.89 4.94
638 1008 4.558496 GAGCTGATAGTCAGATACACAGGC 60.558 50.000 10.94 0.00 44.01 4.85
708 1091 5.647225 AGAATCTTCAGAATTCAGAACCTGC 59.353 40.000 9.04 0.00 0.00 4.85
770 1165 4.647564 ACACAGAGGAGAAATGTCCATT 57.352 40.909 0.00 0.00 39.34 3.16
946 1353 8.175716 ACGAAACTGAAGAGTTCTAAAAACAAG 58.824 33.333 0.00 0.00 41.87 3.16
949 1356 8.173130 TGAACGAAACTGAAGAGTTCTAAAAAC 58.827 33.333 7.90 0.00 41.87 2.43
994 1427 1.567649 ACAAGGCAGATCCATGGATGT 59.432 47.619 32.05 25.22 37.85 3.06
1158 1606 1.338769 GCTGCTTTCTTCGGGAGGTTA 60.339 52.381 0.00 0.00 0.00 2.85
1160 1608 1.003233 GCTGCTTTCTTCGGGAGGT 60.003 57.895 0.00 0.00 0.00 3.85
1182 1630 0.396974 TGGCAAAGAGGTTGGTGCTT 60.397 50.000 0.00 0.00 37.73 3.91
1316 1773 1.277326 CTTATAGTTCGCGCAGTGCA 58.723 50.000 16.83 0.00 46.97 4.57
1360 1817 1.674962 GAACCTGAGCATGCAAGGATC 59.325 52.381 34.01 29.02 31.22 3.36
1453 1919 1.996191 GGCTCTTGTCGAGATGTTCAC 59.004 52.381 0.00 0.00 42.62 3.18
1545 2011 2.022195 TCTAAGCGCGAGGTAGTGAAT 58.978 47.619 12.10 0.00 43.76 2.57
1571 2037 1.811679 GTAGGCAAGGAGCTGACGC 60.812 63.158 0.00 0.00 44.79 5.19
1635 2101 2.017783 CTGCAAACATGCCGTGCAC 61.018 57.895 6.82 6.82 43.09 4.57
1785 2251 1.071471 CGGTGGAACTTCAGGTGCT 59.929 57.895 0.00 0.00 36.74 4.40
1789 2255 2.076863 GTTGATCGGTGGAACTTCAGG 58.923 52.381 0.00 0.00 36.74 3.86
1800 2266 1.308069 GCATGGTGCTGTTGATCGGT 61.308 55.000 0.00 0.00 40.96 4.69
1811 2277 0.740737 GGTAATCAGTGGCATGGTGC 59.259 55.000 0.00 0.00 44.08 5.01
1851 2335 4.664677 ACCGGCGACTGTGACTGC 62.665 66.667 9.30 0.00 0.00 4.40
1875 2365 7.816995 TGAAAATTTTACATACCATGAAGTGCC 59.183 33.333 2.75 0.00 0.00 5.01
1898 2422 0.469917 GATCTGCCGGGAAGGATGAA 59.530 55.000 2.18 0.00 45.00 2.57
1928 2452 0.252375 ATTGAAGCCAGGGTGCCATT 60.252 50.000 0.00 0.00 0.00 3.16
2139 4164 9.717942 GCCATGAAAGATAATCTACTGTAGAAT 57.282 33.333 20.40 15.07 38.50 2.40
2236 4432 8.332464 GCACATACGTAACAAGCTAATTATCAA 58.668 33.333 0.00 0.00 0.00 2.57
2262 4790 9.371136 TCATGTCTACTTGTCTAAAAATGCTAG 57.629 33.333 0.00 0.00 0.00 3.42
2440 5821 4.379918 GCTATGGATCATCTCATTCGACGA 60.380 45.833 0.00 0.00 0.00 4.20
2442 5823 4.180057 GGCTATGGATCATCTCATTCGAC 58.820 47.826 0.00 0.00 0.00 4.20
2443 5824 3.834231 TGGCTATGGATCATCTCATTCGA 59.166 43.478 0.00 0.00 0.00 3.71
2444 5825 4.198028 TGGCTATGGATCATCTCATTCG 57.802 45.455 0.00 0.00 0.00 3.34
2445 5826 5.802465 TCTTGGCTATGGATCATCTCATTC 58.198 41.667 0.00 0.00 0.00 2.67
2446 5827 5.837770 TCTTGGCTATGGATCATCTCATT 57.162 39.130 0.00 0.00 0.00 2.57
2447 5828 5.310068 AGTTCTTGGCTATGGATCATCTCAT 59.690 40.000 0.00 0.00 0.00 2.90
2462 5843 7.094634 TGAGACAATTAGAAATCAGTTCTTGGC 60.095 37.037 0.00 0.00 44.64 4.52
2465 5846 9.730705 TGATGAGACAATTAGAAATCAGTTCTT 57.269 29.630 0.00 0.00 44.64 2.52
2467 5848 9.160496 AGTGATGAGACAATTAGAAATCAGTTC 57.840 33.333 0.00 0.00 36.38 3.01
2479 5860 8.950210 ACGAAATGATTTAGTGATGAGACAATT 58.050 29.630 2.85 0.00 0.00 2.32
2531 6311 5.499047 CGTCCTAGAAAAACACAAAGTCAC 58.501 41.667 0.00 0.00 0.00 3.67
2590 6376 0.108186 TGACAGTAATGGAGCTGCCG 60.108 55.000 1.53 0.00 40.66 5.69
2628 6414 8.717821 TCGTCTTCTTATCCATACAACAAAAAG 58.282 33.333 0.00 0.00 0.00 2.27
2645 6431 6.072119 ACAACAAACCTTTTCTTCGTCTTCTT 60.072 34.615 0.00 0.00 0.00 2.52
2688 6475 8.563123 AATAAGTGGTAGTTTTTCTAAGAGGC 57.437 34.615 0.00 0.00 0.00 4.70
2809 6610 5.644188 TCTCTTCCAATCTCCAAACCAATT 58.356 37.500 0.00 0.00 0.00 2.32
2850 6651 8.791327 TGCAATATCTCAGATAAGTCAAACAA 57.209 30.769 0.00 0.00 0.00 2.83
2886 6687 6.017026 CCAAGTAGGTTTTCTTTGGAGAAGTC 60.017 42.308 0.00 0.00 42.55 3.01
2924 6725 0.899720 TTACCTTGTAGACAGGGCCG 59.100 55.000 10.54 0.00 45.96 6.13
3000 6804 8.773033 ATATAAGGATGTTTTCTTGGCAATCT 57.227 30.769 0.00 0.00 0.00 2.40
3064 7929 6.910536 ACTAGGAAAACATAGCAAGATTCG 57.089 37.500 0.00 0.00 0.00 3.34
3095 7961 9.457436 GGAACTTACATTATTTTCCAAGGTAGA 57.543 33.333 0.00 0.00 36.51 2.59
3113 7983 4.335594 GCCATTGTGGATACTGGAACTTAC 59.664 45.833 0.00 0.00 40.96 2.34
3162 8045 3.697542 ACCTTTTTCACCGTAGTTTGCTT 59.302 39.130 0.00 0.00 0.00 3.91
3317 8205 6.419116 GGCTACGTTAGGTTACTTATGCTAAC 59.581 42.308 0.00 0.00 0.00 2.34
3413 8305 9.635404 TTACTTCTATTTCCTTCAAAGTTCCAA 57.365 29.630 0.00 0.00 0.00 3.53
3416 8308 9.561270 GCATTACTTCTATTTCCTTCAAAGTTC 57.439 33.333 0.00 0.00 0.00 3.01
3421 8313 7.882791 TCACTGCATTACTTCTATTTCCTTCAA 59.117 33.333 0.00 0.00 0.00 2.69
3444 8336 3.037549 TGGCCCCAATATTCCATTTCAC 58.962 45.455 0.00 0.00 0.00 3.18
3459 8351 1.341383 GGATCACATATCCATGGCCCC 60.341 57.143 6.96 0.00 38.09 5.80
3460 8352 1.637553 AGGATCACATATCCATGGCCC 59.362 52.381 6.96 0.00 40.61 5.80
3468 8360 4.701765 ACAGCAAGTCAGGATCACATATC 58.298 43.478 0.00 0.00 0.00 1.63
3471 8363 3.430042 AACAGCAAGTCAGGATCACAT 57.570 42.857 0.00 0.00 0.00 3.21
3472 8364 2.936919 AACAGCAAGTCAGGATCACA 57.063 45.000 0.00 0.00 0.00 3.58
3474 8366 3.817084 CAGAAAACAGCAAGTCAGGATCA 59.183 43.478 0.00 0.00 0.00 2.92
3475 8367 3.817647 ACAGAAAACAGCAAGTCAGGATC 59.182 43.478 0.00 0.00 0.00 3.36
3478 8370 2.684881 ACACAGAAAACAGCAAGTCAGG 59.315 45.455 0.00 0.00 0.00 3.86
3484 8382 3.826524 TGGGATACACAGAAAACAGCAA 58.173 40.909 0.00 0.00 39.74 3.91
3493 8391 6.208599 GGAAAATGACTTTTGGGATACACAGA 59.791 38.462 0.00 0.00 34.73 3.41
3533 8434 9.695526 TTTCACTGAAATTACAGAAAATGGATG 57.304 29.630 0.00 0.00 40.63 3.51
3556 8457 8.682710 TGTACAAAACAGGAGGCATTATATTTC 58.317 33.333 0.00 0.00 33.01 2.17
3572 8475 4.521256 GGCCTTGGAAGTATGTACAAAACA 59.479 41.667 0.00 0.00 43.86 2.83
3591 8494 1.065126 GTTCCATCTGCTAACTGGCCT 60.065 52.381 3.32 0.00 0.00 5.19
3601 8504 3.057033 ACTGCAATTTCTGTTCCATCTGC 60.057 43.478 0.00 0.00 0.00 4.26
3638 8541 3.153919 GTGAAACCCTGTCCTAAATGCA 58.846 45.455 0.00 0.00 0.00 3.96
3639 8542 3.153919 TGTGAAACCCTGTCCTAAATGC 58.846 45.455 0.00 0.00 34.36 3.56
3644 8547 4.349636 TGAATTCTGTGAAACCCTGTCCTA 59.650 41.667 7.05 0.00 34.36 2.94
3876 8786 2.119671 CAACCAAAGTTGTTCGGCTC 57.880 50.000 0.00 0.00 46.88 4.70
3903 8813 6.316140 TCCCTTCGATTATCACACATCTTTTG 59.684 38.462 0.00 0.00 0.00 2.44
3945 8855 2.166459 CCGAGAGTGCTTGTGGAGATAA 59.834 50.000 0.00 0.00 0.00 1.75
3967 8877 1.857217 GTCTCTGTGTATGATGCGCAG 59.143 52.381 18.32 16.42 43.54 5.18
4122 9032 5.810525 ACGCACATTAGCTGATTAATTGTC 58.189 37.500 0.00 0.00 0.00 3.18
4132 9042 2.029728 GCTCTTGTACGCACATTAGCTG 59.970 50.000 13.07 0.00 38.67 4.24
4167 9520 0.096976 CGACATTCGACATGGTTGGC 59.903 55.000 0.00 0.00 43.74 4.52
4211 9564 5.994668 GGATGTTTAGGCTCTGGAAGAATAG 59.005 44.000 0.00 0.00 46.34 1.73
4252 9605 4.772624 CGATTCATCTTCCCTAGATACCCA 59.227 45.833 0.00 0.00 41.78 4.51
4262 9615 2.434702 ACACTACCCGATTCATCTTCCC 59.565 50.000 0.00 0.00 0.00 3.97
4327 9680 0.177604 GGCTCCTCAGTGATGGTCAG 59.822 60.000 0.00 0.00 0.00 3.51
4455 9947 5.344665 GCGAATGCACAAAAGCTAAATACAA 59.655 36.000 0.00 0.00 42.15 2.41
4475 9967 3.334691 CAGTCCAAAAGGATAGTGCGAA 58.665 45.455 0.00 0.00 0.00 4.70
4476 9968 2.354704 CCAGTCCAAAAGGATAGTGCGA 60.355 50.000 0.00 0.00 0.00 5.10
4482 9974 0.393808 GCCGCCAGTCCAAAAGGATA 60.394 55.000 0.00 0.00 0.00 2.59
4486 9978 0.890996 AGAAGCCGCCAGTCCAAAAG 60.891 55.000 0.00 0.00 0.00 2.27
4503 9995 3.694072 CCTCATTTAAATCCAACGGCAGA 59.306 43.478 0.00 0.00 0.00 4.26
4508 10000 6.743575 AGTCTTCCTCATTTAAATCCAACG 57.256 37.500 0.00 0.00 0.00 4.10
4511 10003 8.704849 TTTCAAGTCTTCCTCATTTAAATCCA 57.295 30.769 0.00 0.00 0.00 3.41
4513 10005 9.794685 GGATTTCAAGTCTTCCTCATTTAAATC 57.205 33.333 0.00 0.00 0.00 2.17
4514 10006 9.312904 TGGATTTCAAGTCTTCCTCATTTAAAT 57.687 29.630 0.00 0.00 0.00 1.40
4520 10012 7.006509 TCTTTTGGATTTCAAGTCTTCCTCAT 58.993 34.615 0.00 0.00 36.62 2.90
4521 10013 6.364701 TCTTTTGGATTTCAAGTCTTCCTCA 58.635 36.000 0.00 0.00 36.62 3.86
4522 10014 6.884280 TCTTTTGGATTTCAAGTCTTCCTC 57.116 37.500 0.00 0.00 36.62 3.71
4543 10035 4.880696 GCAGCTACTTGAGGATTGAAATCT 59.119 41.667 3.21 0.00 35.73 2.40
4563 10138 1.747709 AGCAGGTTCAGCTAATGCAG 58.252 50.000 9.52 0.00 41.32 4.41
4571 10146 3.600388 ACACATACTAAGCAGGTTCAGC 58.400 45.455 0.00 0.00 0.00 4.26
4577 10152 3.691118 ACATGCAACACATACTAAGCAGG 59.309 43.478 0.00 0.00 36.64 4.85
4579 10154 8.086851 CATATACATGCAACACATACTAAGCA 57.913 34.615 0.00 0.00 36.64 3.91
4598 10179 7.100458 AGGAAAACATCAAAGGTGCATATAC 57.900 36.000 0.00 0.00 0.00 1.47
4603 10184 3.295093 TGAGGAAAACATCAAAGGTGCA 58.705 40.909 0.00 0.00 0.00 4.57
4623 10204 6.702972 TGCACGTCAATGGAATTAATTTTG 57.297 33.333 1.43 3.68 32.46 2.44
4627 10208 4.677779 GCCTTGCACGTCAATGGAATTAAT 60.678 41.667 14.26 0.00 32.46 1.40
4637 10218 2.297880 TCTAGTTAGCCTTGCACGTCAA 59.702 45.455 0.00 0.00 0.00 3.18
4638 10219 1.890489 TCTAGTTAGCCTTGCACGTCA 59.110 47.619 0.00 0.00 0.00 4.35
4639 10220 2.649331 TCTAGTTAGCCTTGCACGTC 57.351 50.000 0.00 0.00 0.00 4.34
4640 10221 3.611766 ATTCTAGTTAGCCTTGCACGT 57.388 42.857 0.00 0.00 0.00 4.49
4641 10222 5.753438 TCAATATTCTAGTTAGCCTTGCACG 59.247 40.000 0.00 0.00 0.00 5.34
4642 10223 7.736447 ATCAATATTCTAGTTAGCCTTGCAC 57.264 36.000 0.00 0.00 0.00 4.57
4643 10224 9.440773 CATATCAATATTCTAGTTAGCCTTGCA 57.559 33.333 0.00 0.00 0.00 4.08
4644 10225 8.394121 GCATATCAATATTCTAGTTAGCCTTGC 58.606 37.037 0.00 0.00 0.00 4.01
4645 10226 9.664332 AGCATATCAATATTCTAGTTAGCCTTG 57.336 33.333 0.00 0.00 0.00 3.61
4653 10234 9.875691 TGCGAATAAGCATATCAATATTCTAGT 57.124 29.630 0.00 0.00 42.92 2.57
4684 10265 7.761249 GCTACAAGCATATCAACATTCCTTTTT 59.239 33.333 0.00 0.00 41.89 1.94
4685 10266 7.260603 GCTACAAGCATATCAACATTCCTTTT 58.739 34.615 0.00 0.00 41.89 2.27
4686 10267 6.799512 GCTACAAGCATATCAACATTCCTTT 58.200 36.000 0.00 0.00 41.89 3.11
4687 10268 6.382869 GCTACAAGCATATCAACATTCCTT 57.617 37.500 0.00 0.00 41.89 3.36
4727 10333 4.853924 ACTGACGGAAATGCTTCATTTT 57.146 36.364 6.28 0.00 43.05 1.82
4731 10337 2.548057 GACAACTGACGGAAATGCTTCA 59.452 45.455 0.00 0.00 32.75 3.02
4732 10338 2.548057 TGACAACTGACGGAAATGCTTC 59.452 45.455 0.00 0.00 0.00 3.86
4745 10351 2.198827 TGGCCTAACCATGACAACTG 57.801 50.000 3.32 0.00 46.36 3.16
4758 10365 2.026262 GGAAGAACTCCATGTTGGCCTA 60.026 50.000 3.32 0.00 44.67 3.93
4770 10377 6.560711 TGTTAAACTGCAAAAGGAAGAACTC 58.439 36.000 0.00 0.00 0.00 3.01
4775 10385 5.176223 CAGCATGTTAAACTGCAAAAGGAAG 59.824 40.000 11.77 0.00 40.88 3.46
4785 10395 5.885230 TCCATCTTCAGCATGTTAAACTG 57.115 39.130 0.00 0.00 37.40 3.16
4786 10396 7.831193 ACTTATCCATCTTCAGCATGTTAAACT 59.169 33.333 0.00 0.00 37.40 2.66
4792 10402 6.239217 TGTACTTATCCATCTTCAGCATGT 57.761 37.500 0.00 0.00 37.40 3.21
4794 10404 7.071069 TGATGTACTTATCCATCTTCAGCAT 57.929 36.000 0.00 0.00 38.59 3.79
4799 10409 6.281405 ACGGTTGATGTACTTATCCATCTTC 58.719 40.000 0.00 0.00 38.59 2.87
4801 10411 5.871396 ACGGTTGATGTACTTATCCATCT 57.129 39.130 0.00 0.00 38.59 2.90
4813 10423 8.951787 TTAGCAATAAGTAATACGGTTGATGT 57.048 30.769 8.74 0.00 0.00 3.06
4843 10453 9.077885 ACTTGCCAGATAAAGTTTAAATCAAGA 57.922 29.630 20.59 0.00 32.75 3.02
4844 10454 9.696917 AACTTGCCAGATAAAGTTTAAATCAAG 57.303 29.630 16.31 16.31 42.51 3.02
4853 10463 6.068670 AGGTACAAACTTGCCAGATAAAGTT 58.931 36.000 0.00 0.00 46.03 2.66
4854 10464 5.631119 AGGTACAAACTTGCCAGATAAAGT 58.369 37.500 0.00 0.00 38.25 2.66


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

AutoCloner maintained by Alex Coulton.