Multiple sequence alignment - TraesCS2D01G462600

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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 TraesCS2D01G462600 chr2D 100.000 3718 0 0 1 3718 568463209 568466926 0.000000e+00 6866.0
1 TraesCS2D01G462600 chr2D 91.432 1669 122 12 1060 2723 568308542 568310194 0.000000e+00 2270.0
2 TraesCS2D01G462600 chr2D 96.684 1327 28 7 1464 2780 568357758 568359078 0.000000e+00 2193.0
3 TraesCS2D01G462600 chr2D 88.023 526 29 12 947 1472 568351800 568352291 3.200000e-165 592.0
4 TraesCS2D01G462600 chr2D 88.662 441 31 1 2283 2723 568423406 568423827 1.530000e-143 520.0
5 TraesCS2D01G462600 chr2D 91.200 375 28 3 2377 2748 568445054 568445426 4.290000e-139 505.0
6 TraesCS2D01G462600 chr2D 89.526 401 30 4 1067 1467 568439853 568440241 7.170000e-137 497.0
7 TraesCS2D01G462600 chr2D 91.786 280 20 2 148 425 215486913 215487191 1.620000e-103 387.0
8 TraesCS2D01G462600 chr2D 90.780 282 18 5 150 423 509897624 509897905 1.630000e-98 370.0
9 TraesCS2D01G462600 chr2D 84.071 113 18 0 1487 1599 23295068 23294956 3.930000e-20 110.0
10 TraesCS2D01G462600 chr2D 95.082 61 3 0 3658 3718 568445682 568445742 3.060000e-16 97.1
11 TraesCS2D01G462600 chr2B 90.588 1668 135 10 1061 2723 680862471 680864121 0.000000e+00 2191.0
12 TraesCS2D01G462600 chr2B 89.346 826 63 16 2774 3576 801188508 801189331 0.000000e+00 1014.0
13 TraesCS2D01G462600 chr2B 93.187 455 12 4 947 1401 681123263 681123698 0.000000e+00 651.0
14 TraesCS2D01G462600 chr2B 85.586 444 29 12 420 837 592770997 592770563 2.050000e-117 433.0
15 TraesCS2D01G462600 chr2B 94.667 150 8 0 1 150 592771140 592770991 2.230000e-57 233.0
16 TraesCS2D01G462600 chr2A 90.846 1300 112 5 1347 2640 707796419 707797717 0.000000e+00 1735.0
17 TraesCS2D01G462600 chr2A 94.250 1113 28 14 838 1949 707957402 707958479 0.000000e+00 1668.0
18 TraesCS2D01G462600 chr2A 95.202 521 25 0 2211 2731 707958479 707958999 0.000000e+00 824.0
19 TraesCS2D01G462600 chr2A 91.349 289 15 2 145 423 455343622 455343910 1.620000e-103 387.0
20 TraesCS2D01G462600 chr7A 81.926 1516 238 26 1211 2703 705547427 705545925 0.000000e+00 1249.0
21 TraesCS2D01G462600 chr3D 89.066 814 61 14 2769 3557 594542544 594543354 0.000000e+00 985.0
22 TraesCS2D01G462600 chr3D 93.418 471 29 2 3103 3573 115643439 115642971 0.000000e+00 697.0
23 TraesCS2D01G462600 chr3D 75.986 558 113 18 2092 2640 48349689 48350234 6.120000e-68 268.0
24 TraesCS2D01G462600 chr3D 74.043 235 48 11 2377 2603 130942863 130943092 2.380000e-12 84.2
25 TraesCS2D01G462600 chr7B 78.457 1504 273 34 1213 2702 730309995 730308529 0.000000e+00 935.0
26 TraesCS2D01G462600 chr7B 77.635 1243 225 35 1485 2700 704824973 704823757 0.000000e+00 706.0
27 TraesCS2D01G462600 chr7B 83.178 642 102 2 2090 2725 704826534 704825893 1.920000e-162 582.0
28 TraesCS2D01G462600 chr7B 90.094 424 30 3 414 837 687062370 687062781 1.170000e-149 540.0
29 TraesCS2D01G462600 chr7B 89.619 289 20 5 148 434 272321193 272320913 3.530000e-95 359.0
30 TraesCS2D01G462600 chr7B 75.705 745 155 21 1204 1935 704664172 704663441 2.120000e-92 350.0
31 TraesCS2D01G462600 chr7B 96.000 150 6 0 1 150 687062233 687062382 1.030000e-60 244.0
32 TraesCS2D01G462600 chr7B 82.609 138 23 1 700 837 740456229 740456093 1.810000e-23 121.0
33 TraesCS2D01G462600 chr6D 92.857 490 28 7 3079 3566 159505170 159504686 0.000000e+00 704.0
34 TraesCS2D01G462600 chr6D 92.308 338 23 2 2772 3106 17972237 17972574 9.340000e-131 477.0
35 TraesCS2D01G462600 chr6D 91.985 262 19 1 166 425 342932222 342931961 2.110000e-97 366.0
36 TraesCS2D01G462600 chr6D 91.923 260 19 1 166 423 297242248 297242507 2.730000e-96 363.0
37 TraesCS2D01G462600 chr6D 91.667 264 16 4 166 423 151119903 151119640 9.820000e-96 361.0
38 TraesCS2D01G462600 chr6D 92.157 255 18 1 171 423 354448003 354448257 3.530000e-95 359.0
39 TraesCS2D01G462600 chr6D 88.963 299 19 5 148 434 147626061 147625765 1.270000e-94 357.0
40 TraesCS2D01G462600 chr6D 89.825 285 19 2 149 423 172341926 172341642 1.270000e-94 357.0
41 TraesCS2D01G462600 chr6D 88.889 297 21 5 149 433 77411943 77411647 4.570000e-94 355.0
42 TraesCS2D01G462600 chr6D 89.199 287 19 3 149 423 345168665 345168379 7.640000e-92 348.0
43 TraesCS2D01G462600 chr6D 90.530 264 21 3 166 426 202566648 202566910 2.750000e-91 346.0
44 TraesCS2D01G462600 chr6D 76.102 590 127 12 2093 2675 143091407 143090825 2.810000e-76 296.0
45 TraesCS2D01G462600 chr7D 91.585 511 39 4 3079 3587 190131493 190130985 0.000000e+00 702.0
46 TraesCS2D01G462600 chr7D 92.449 490 30 6 3079 3566 454092767 454093251 0.000000e+00 693.0
47 TraesCS2D01G462600 chr7D 91.784 499 33 8 3079 3573 438545915 438546409 0.000000e+00 688.0
48 TraesCS2D01G462600 chr7D 81.990 794 138 4 1205 1996 613767334 613766544 0.000000e+00 669.0
49 TraesCS2D01G462600 chr7D 91.404 349 24 6 2757 3103 561873385 561873729 1.210000e-129 473.0
50 TraesCS2D01G462600 chr7D 84.472 483 68 3 2227 2703 613765894 613765413 1.560000e-128 470.0
51 TraesCS2D01G462600 chr7D 90.028 361 32 4 2769 3125 410554887 410554527 7.270000e-127 464.0
52 TraesCS2D01G462600 chr7D 90.747 281 18 3 148 426 276254907 276255181 5.870000e-98 368.0
53 TraesCS2D01G462600 chrUn 92.434 489 33 4 3079 3565 10748600 10749086 0.000000e+00 695.0
54 TraesCS2D01G462600 chrUn 92.434 489 33 4 3079 3565 10764228 10764714 0.000000e+00 695.0
55 TraesCS2D01G462600 chrUn 90.661 257 21 2 171 425 90076531 90076786 4.600000e-89 339.0
56 TraesCS2D01G462600 chrUn 90.204 245 22 1 184 426 334937582 334937826 5.990000e-83 318.0
57 TraesCS2D01G462600 chrUn 89.200 250 25 1 184 431 91443500 91443749 1.000000e-80 311.0
58 TraesCS2D01G462600 chrUn 87.143 280 29 3 148 425 96182204 96182478 1.000000e-80 311.0
59 TraesCS2D01G462600 chrUn 89.873 237 18 4 193 423 24955435 24955199 2.170000e-77 300.0
60 TraesCS2D01G462600 chrUn 86.170 282 25 7 149 427 36485597 36485867 3.630000e-75 292.0
61 TraesCS2D01G462600 chrUn 86.381 257 33 1 166 420 93661424 93661168 2.830000e-71 279.0
62 TraesCS2D01G462600 chrUn 88.341 223 18 3 203 423 5388560 5388344 1.020000e-65 261.0
63 TraesCS2D01G462600 chrUn 87.273 220 24 2 210 425 86353465 86353246 7.970000e-62 248.0
64 TraesCS2D01G462600 chr3B 92.261 491 34 4 3079 3566 571135269 571135758 0.000000e+00 693.0
65 TraesCS2D01G462600 chr5D 91.816 501 34 6 3079 3577 168013940 168013445 0.000000e+00 691.0
66 TraesCS2D01G462600 chr5D 92.658 395 19 2 420 814 543634824 543634440 9.020000e-156 560.0
67 TraesCS2D01G462600 chr5D 92.749 331 21 2 2779 3106 272356444 272356114 3.360000e-130 475.0
68 TraesCS2D01G462600 chr5D 90.378 291 18 2 148 428 108405713 108405423 1.260000e-99 374.0
69 TraesCS2D01G462600 chr5D 97.333 150 4 0 1 150 543634967 543634818 4.770000e-64 255.0
70 TraesCS2D01G462600 chr5A 91.274 424 26 3 414 837 11789377 11789789 5.390000e-158 568.0
71 TraesCS2D01G462600 chr5A 94.000 150 9 0 1 150 11789240 11789389 1.040000e-55 228.0
72 TraesCS2D01G462600 chr5A 89.222 167 11 1 671 837 355175122 355175281 6.300000e-48 202.0
73 TraesCS2D01G462600 chr5B 91.496 341 25 3 2768 3106 12641423 12641761 2.020000e-127 466.0
74 TraesCS2D01G462600 chr5B 91.520 342 23 6 2773 3110 586341856 586341517 2.020000e-127 466.0
75 TraesCS2D01G462600 chr1D 91.691 337 26 2 2772 3107 417194618 417194953 2.020000e-127 466.0
76 TraesCS2D01G462600 chr1D 77.389 743 140 19 1208 1936 337217318 337218046 2.070000e-112 416.0
77 TraesCS2D01G462600 chr1D 92.776 263 17 1 166 426 245785305 245785043 2.710000e-101 379.0
78 TraesCS2D01G462600 chr1D 90.909 286 14 4 149 423 29851688 29851404 1.260000e-99 374.0
79 TraesCS2D01G462600 chr1D 91.103 281 17 3 148 426 121098779 121098505 1.260000e-99 374.0
80 TraesCS2D01G462600 chr4D 86.256 422 29 11 414 835 44037746 44038138 7.380000e-117 431.0
81 TraesCS2D01G462600 chr4D 92.395 263 18 1 166 426 104582971 104583233 1.260000e-99 374.0
82 TraesCS2D01G462600 chr4D 92.278 259 18 1 170 426 131061355 131061613 2.110000e-97 366.0
83 TraesCS2D01G462600 chr4D 90.391 281 19 3 148 426 149660092 149659818 2.730000e-96 363.0
84 TraesCS2D01G462600 chr4D 91.603 262 19 2 166 425 25663279 25663539 3.530000e-95 359.0
85 TraesCS2D01G462600 chr4D 90.036 281 20 3 148 426 235278569 235278295 1.270000e-94 357.0
86 TraesCS2D01G462600 chr4D 90.036 281 20 3 148 426 305422288 305422562 1.270000e-94 357.0
87 TraesCS2D01G462600 chr4D 90.511 274 18 3 148 419 454176272 454176005 4.570000e-94 355.0
88 TraesCS2D01G462600 chr4D 95.333 150 7 0 1 150 44037609 44037758 4.800000e-59 239.0
89 TraesCS2D01G462600 chr4D 92.308 78 5 1 463 539 353521386 353521463 3.930000e-20 110.0
90 TraesCS2D01G462600 chr1A 91.379 290 13 4 148 426 154329637 154329925 1.620000e-103 387.0
91 TraesCS2D01G462600 chr1A 76.431 751 142 25 1208 1936 436421329 436422066 1.260000e-99 374.0
92 TraesCS2D01G462600 chr1A 90.975 277 18 2 149 423 370888997 370889268 2.110000e-97 366.0
93 TraesCS2D01G462600 chr6A 90.975 277 18 2 149 423 55294825 55294554 2.110000e-97 366.0
94 TraesCS2D01G462600 chr6A 90.391 281 19 3 148 426 353765995 353766269 2.730000e-96 363.0
95 TraesCS2D01G462600 chr6A 75.635 591 130 12 2093 2676 188354006 188353423 7.860000e-72 281.0
96 TraesCS2D01G462600 chr6B 76.650 591 124 12 2093 2676 255072456 255071873 7.750000e-82 315.0
97 TraesCS2D01G462600 chr3A 74.370 238 49 11 2384 2612 143023105 143023339 1.420000e-14 91.6


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 TraesCS2D01G462600 chr2D 568463209 568466926 3717 False 6866.00 6866 100.0000 1 3718 1 chr2D.!!$F8 3717
1 TraesCS2D01G462600 chr2D 568308542 568310194 1652 False 2270.00 2270 91.4320 1060 2723 1 chr2D.!!$F3 1663
2 TraesCS2D01G462600 chr2D 568357758 568359078 1320 False 2193.00 2193 96.6840 1464 2780 1 chr2D.!!$F5 1316
3 TraesCS2D01G462600 chr2D 568445054 568445742 688 False 301.05 505 93.1410 2377 3718 2 chr2D.!!$F9 1341
4 TraesCS2D01G462600 chr2B 680862471 680864121 1650 False 2191.00 2191 90.5880 1061 2723 1 chr2B.!!$F1 1662
5 TraesCS2D01G462600 chr2B 801188508 801189331 823 False 1014.00 1014 89.3460 2774 3576 1 chr2B.!!$F3 802
6 TraesCS2D01G462600 chr2B 592770563 592771140 577 True 333.00 433 90.1265 1 837 2 chr2B.!!$R1 836
7 TraesCS2D01G462600 chr2A 707796419 707797717 1298 False 1735.00 1735 90.8460 1347 2640 1 chr2A.!!$F2 1293
8 TraesCS2D01G462600 chr2A 707957402 707958999 1597 False 1246.00 1668 94.7260 838 2731 2 chr2A.!!$F3 1893
9 TraesCS2D01G462600 chr7A 705545925 705547427 1502 True 1249.00 1249 81.9260 1211 2703 1 chr7A.!!$R1 1492
10 TraesCS2D01G462600 chr3D 594542544 594543354 810 False 985.00 985 89.0660 2769 3557 1 chr3D.!!$F3 788
11 TraesCS2D01G462600 chr3D 48349689 48350234 545 False 268.00 268 75.9860 2092 2640 1 chr3D.!!$F1 548
12 TraesCS2D01G462600 chr7B 730308529 730309995 1466 True 935.00 935 78.4570 1213 2702 1 chr7B.!!$R3 1489
13 TraesCS2D01G462600 chr7B 704823757 704826534 2777 True 644.00 706 80.4065 1485 2725 2 chr7B.!!$R5 1240
14 TraesCS2D01G462600 chr7B 687062233 687062781 548 False 392.00 540 93.0470 1 837 2 chr7B.!!$F1 836
15 TraesCS2D01G462600 chr7B 704663441 704664172 731 True 350.00 350 75.7050 1204 1935 1 chr7B.!!$R2 731
16 TraesCS2D01G462600 chr6D 143090825 143091407 582 True 296.00 296 76.1020 2093 2675 1 chr6D.!!$R2 582
17 TraesCS2D01G462600 chr7D 190130985 190131493 508 True 702.00 702 91.5850 3079 3587 1 chr7D.!!$R1 508
18 TraesCS2D01G462600 chr7D 613765413 613767334 1921 True 569.50 669 83.2310 1205 2703 2 chr7D.!!$R3 1498
19 TraesCS2D01G462600 chr5D 543634440 543634967 527 True 407.50 560 94.9955 1 814 2 chr5D.!!$R4 813
20 TraesCS2D01G462600 chr5A 11789240 11789789 549 False 398.00 568 92.6370 1 837 2 chr5A.!!$F2 836
21 TraesCS2D01G462600 chr1D 337217318 337218046 728 False 416.00 416 77.3890 1208 1936 1 chr1D.!!$F1 728
22 TraesCS2D01G462600 chr4D 44037609 44038138 529 False 335.00 431 90.7945 1 835 2 chr4D.!!$F6 834
23 TraesCS2D01G462600 chr1A 436421329 436422066 737 False 374.00 374 76.4310 1208 1936 1 chr1A.!!$F3 728
24 TraesCS2D01G462600 chr6A 188353423 188354006 583 True 281.00 281 75.6350 2093 2676 1 chr6A.!!$R2 583
25 TraesCS2D01G462600 chr6B 255071873 255072456 583 True 315.00 315 76.6500 2093 2676 1 chr6B.!!$R1 583

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
787 815 0.179132 TGCATCCACATGATTTGCGC 60.179 50.0 0.0 0.0 30.57 6.09 F
1098 1126 0.243907 TGGAGTCGTTGCAGCTCTAC 59.756 55.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2197 1.471676 GGCGAACATGTCCTGTAGGAG 60.472 57.143 0.0 0.0 46.49 3.69 R
2813 3370 1.679153 TGAAGGCGTATGAGCGATGTA 59.321 47.619 0.0 0.0 38.18 2.29 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
144 145 4.104086 TCACTATGAATGAAGTGGGAGGT 58.896 43.478 2.91 0.00 42.72 3.85
145 146 4.162320 TCACTATGAATGAAGTGGGAGGTC 59.838 45.833 2.91 0.00 42.72 3.85
146 147 2.698855 ATGAATGAAGTGGGAGGTCG 57.301 50.000 0.00 0.00 0.00 4.79
147 148 1.639722 TGAATGAAGTGGGAGGTCGA 58.360 50.000 0.00 0.00 0.00 4.20
148 149 1.974957 TGAATGAAGTGGGAGGTCGAA 59.025 47.619 0.00 0.00 0.00 3.71
149 150 2.028112 TGAATGAAGTGGGAGGTCGAAG 60.028 50.000 0.00 0.00 0.00 3.79
150 151 1.938585 ATGAAGTGGGAGGTCGAAGA 58.061 50.000 0.00 0.00 0.00 2.87
163 164 2.672961 TCGAAGACTAGCCACAATGG 57.327 50.000 0.00 0.00 41.55 3.16
164 165 1.207089 TCGAAGACTAGCCACAATGGG 59.793 52.381 0.00 0.00 38.19 4.00
175 176 4.748277 GCCACAATGGGTAGTCTAGTAA 57.252 45.455 0.00 0.00 38.19 2.24
177 178 4.081309 GCCACAATGGGTAGTCTAGTAACA 60.081 45.833 0.00 0.00 38.19 2.41
178 179 5.396436 GCCACAATGGGTAGTCTAGTAACAT 60.396 44.000 0.00 0.00 38.19 2.71
180 181 5.523916 CACAATGGGTAGTCTAGTAACATGC 59.476 44.000 0.00 0.00 0.00 4.06
181 182 5.188948 ACAATGGGTAGTCTAGTAACATGCA 59.811 40.000 0.00 0.00 0.00 3.96
182 183 6.126768 ACAATGGGTAGTCTAGTAACATGCAT 60.127 38.462 0.00 0.00 0.00 3.96
183 184 7.070696 ACAATGGGTAGTCTAGTAACATGCATA 59.929 37.037 0.00 0.00 0.00 3.14
184 185 7.798710 ATGGGTAGTCTAGTAACATGCATAT 57.201 36.000 0.00 0.00 0.00 1.78
185 186 6.993079 TGGGTAGTCTAGTAACATGCATATG 58.007 40.000 0.00 0.00 40.24 1.78
218 219 9.850198 GTCTATATTACTACCTCTATAGTGGGG 57.150 40.741 21.82 16.35 36.09 4.96
219 220 9.809705 TCTATATTACTACCTCTATAGTGGGGA 57.190 37.037 21.82 11.28 36.09 4.81
221 222 6.800223 ATTACTACCTCTATAGTGGGGAGT 57.200 41.667 24.72 24.72 36.09 3.85
222 223 7.901804 ATTACTACCTCTATAGTGGGGAGTA 57.098 40.000 23.32 23.32 36.09 2.59
223 224 7.712142 TTACTACCTCTATAGTGGGGAGTAA 57.288 40.000 28.26 28.26 38.03 2.24
225 226 3.830121 ACCTCTATAGTGGGGAGTAACG 58.170 50.000 21.82 0.00 33.22 3.18
226 227 3.203934 ACCTCTATAGTGGGGAGTAACGT 59.796 47.826 21.82 0.00 33.22 3.99
227 228 4.413520 ACCTCTATAGTGGGGAGTAACGTA 59.586 45.833 21.82 0.00 33.22 3.57
228 229 5.074239 ACCTCTATAGTGGGGAGTAACGTAT 59.926 44.000 21.82 0.00 33.22 3.06
229 230 6.273260 ACCTCTATAGTGGGGAGTAACGTATA 59.727 42.308 21.82 0.00 33.22 1.47
230 231 7.037008 ACCTCTATAGTGGGGAGTAACGTATAT 60.037 40.741 21.82 0.00 33.22 0.86
232 233 7.693132 TCTATAGTGGGGAGTAACGTATATGT 58.307 38.462 0.00 0.00 0.00 2.29
234 235 3.640029 AGTGGGGAGTAACGTATATGTGG 59.360 47.826 0.00 0.00 0.00 4.17
235 236 3.385755 GTGGGGAGTAACGTATATGTGGT 59.614 47.826 0.00 0.00 0.00 4.16
236 237 4.584325 GTGGGGAGTAACGTATATGTGGTA 59.416 45.833 0.00 0.00 0.00 3.25
237 238 5.068987 GTGGGGAGTAACGTATATGTGGTAA 59.931 44.000 0.00 0.00 0.00 2.85
254 255 5.528043 TGGTAACATGCAACACTTCATTT 57.472 34.783 0.00 0.00 46.17 2.32
256 257 7.225784 TGGTAACATGCAACACTTCATTTAT 57.774 32.000 0.00 0.00 46.17 1.40
257 258 7.665690 TGGTAACATGCAACACTTCATTTATT 58.334 30.769 0.00 0.00 46.17 1.40
258 259 7.598118 TGGTAACATGCAACACTTCATTTATTG 59.402 33.333 0.00 0.00 46.17 1.90
259 260 7.063308 GGTAACATGCAACACTTCATTTATTGG 59.937 37.037 0.00 0.00 0.00 3.16
260 261 5.481105 ACATGCAACACTTCATTTATTGGG 58.519 37.500 0.00 0.00 0.00 4.12
261 262 3.924144 TGCAACACTTCATTTATTGGGC 58.076 40.909 0.00 0.00 0.00 5.36
263 264 4.769488 TGCAACACTTCATTTATTGGGCTA 59.231 37.500 0.00 0.00 0.00 3.93
264 265 5.421693 TGCAACACTTCATTTATTGGGCTAT 59.578 36.000 0.00 0.00 0.00 2.97
265 266 6.605194 TGCAACACTTCATTTATTGGGCTATA 59.395 34.615 0.00 0.00 0.00 1.31
266 267 7.141363 GCAACACTTCATTTATTGGGCTATAG 58.859 38.462 0.00 0.00 0.00 1.31
269 270 7.806180 ACACTTCATTTATTGGGCTATAGACT 58.194 34.615 5.35 0.00 0.00 3.24
270 271 7.934120 ACACTTCATTTATTGGGCTATAGACTC 59.066 37.037 5.35 0.00 0.00 3.36
271 272 7.933577 CACTTCATTTATTGGGCTATAGACTCA 59.066 37.037 5.35 0.00 0.00 3.41
272 273 8.664079 ACTTCATTTATTGGGCTATAGACTCAT 58.336 33.333 5.35 0.50 0.00 2.90
273 274 9.160496 CTTCATTTATTGGGCTATAGACTCATC 57.840 37.037 5.35 0.00 0.00 2.92
274 275 8.441311 TCATTTATTGGGCTATAGACTCATCT 57.559 34.615 5.35 0.00 39.15 2.90
275 276 8.884323 TCATTTATTGGGCTATAGACTCATCTT 58.116 33.333 5.35 0.00 36.29 2.40
276 277 8.944029 CATTTATTGGGCTATAGACTCATCTTG 58.056 37.037 5.35 0.00 36.29 3.02
278 279 2.634940 TGGGCTATAGACTCATCTTGCC 59.365 50.000 5.35 0.00 40.72 4.52
279 280 2.903135 GGGCTATAGACTCATCTTGCCT 59.097 50.000 5.35 0.00 40.98 4.75
280 281 3.326297 GGGCTATAGACTCATCTTGCCTT 59.674 47.826 5.35 0.00 40.98 4.35
281 282 4.528596 GGGCTATAGACTCATCTTGCCTTA 59.471 45.833 5.35 0.00 40.98 2.69
282 283 5.012148 GGGCTATAGACTCATCTTGCCTTAA 59.988 44.000 5.35 0.00 40.98 1.85
283 284 6.296145 GGGCTATAGACTCATCTTGCCTTAAT 60.296 42.308 5.35 0.00 40.98 1.40
285 286 8.482128 GGCTATAGACTCATCTTGCCTTAATAT 58.518 37.037 3.21 0.00 39.50 1.28
286 287 9.311916 GCTATAGACTCATCTTGCCTTAATATG 57.688 37.037 3.21 0.00 36.29 1.78
289 290 6.893583 AGACTCATCTTGCCTTAATATGTGT 58.106 36.000 0.00 0.00 34.39 3.72
291 292 6.653020 ACTCATCTTGCCTTAATATGTGTGA 58.347 36.000 0.00 0.00 32.09 3.58
292 293 7.285566 ACTCATCTTGCCTTAATATGTGTGAT 58.714 34.615 0.00 0.00 32.09 3.06
293 294 7.228108 ACTCATCTTGCCTTAATATGTGTGATG 59.772 37.037 0.00 0.00 32.09 3.07
295 296 7.557358 TCATCTTGCCTTAATATGTGTGATGTT 59.443 33.333 0.00 0.00 32.21 2.71
296 297 8.839343 CATCTTGCCTTAATATGTGTGATGTTA 58.161 33.333 0.00 0.00 0.00 2.41
297 298 8.208718 TCTTGCCTTAATATGTGTGATGTTAC 57.791 34.615 0.00 0.00 0.00 2.50
298 299 8.046708 TCTTGCCTTAATATGTGTGATGTTACT 58.953 33.333 0.00 0.00 0.00 2.24
299 300 8.574251 TTGCCTTAATATGTGTGATGTTACTT 57.426 30.769 0.00 0.00 0.00 2.24
301 302 9.104965 TGCCTTAATATGTGTGATGTTACTTAC 57.895 33.333 0.00 0.00 0.00 2.34
302 303 9.326413 GCCTTAATATGTGTGATGTTACTTACT 57.674 33.333 0.00 0.00 0.00 2.24
333 334 9.569167 GTAAAAAGCTATGTTACCATTTTCCTC 57.431 33.333 0.00 0.00 32.29 3.71
334 335 7.775053 AAAAGCTATGTTACCATTTTCCTCA 57.225 32.000 0.00 0.00 32.29 3.86
335 336 6.759497 AAGCTATGTTACCATTTTCCTCAC 57.241 37.500 0.00 0.00 32.29 3.51
336 337 6.067217 AGCTATGTTACCATTTTCCTCACT 57.933 37.500 0.00 0.00 32.29 3.41
337 338 6.485171 AGCTATGTTACCATTTTCCTCACTT 58.515 36.000 0.00 0.00 32.29 3.16
338 339 6.948309 AGCTATGTTACCATTTTCCTCACTTT 59.052 34.615 0.00 0.00 32.29 2.66
340 341 7.121315 GCTATGTTACCATTTTCCTCACTTTCT 59.879 37.037 0.00 0.00 32.29 2.52
341 342 7.839680 ATGTTACCATTTTCCTCACTTTCTT 57.160 32.000 0.00 0.00 0.00 2.52
343 344 6.831353 TGTTACCATTTTCCTCACTTTCTTCA 59.169 34.615 0.00 0.00 0.00 3.02
344 345 7.505585 TGTTACCATTTTCCTCACTTTCTTCAT 59.494 33.333 0.00 0.00 0.00 2.57
345 346 6.983906 ACCATTTTCCTCACTTTCTTCATT 57.016 33.333 0.00 0.00 0.00 2.57
346 347 7.365497 ACCATTTTCCTCACTTTCTTCATTT 57.635 32.000 0.00 0.00 0.00 2.32
347 348 8.477419 ACCATTTTCCTCACTTTCTTCATTTA 57.523 30.769 0.00 0.00 0.00 1.40
348 349 9.093458 ACCATTTTCCTCACTTTCTTCATTTAT 57.907 29.630 0.00 0.00 0.00 1.40
349 350 9.933723 CCATTTTCCTCACTTTCTTCATTTATT 57.066 29.630 0.00 0.00 0.00 1.40
355 356 8.299570 TCCTCACTTTCTTCATTTATTTCTTGC 58.700 33.333 0.00 0.00 0.00 4.01
357 358 7.950512 TCACTTTCTTCATTTATTTCTTGCCA 58.049 30.769 0.00 0.00 0.00 4.92
358 359 7.867403 TCACTTTCTTCATTTATTTCTTGCCAC 59.133 33.333 0.00 0.00 0.00 5.01
359 360 7.652909 CACTTTCTTCATTTATTTCTTGCCACA 59.347 33.333 0.00 0.00 0.00 4.17
360 361 8.370182 ACTTTCTTCATTTATTTCTTGCCACAT 58.630 29.630 0.00 0.00 0.00 3.21
361 362 8.761575 TTTCTTCATTTATTTCTTGCCACATC 57.238 30.769 0.00 0.00 0.00 3.06
363 364 8.070034 TCTTCATTTATTTCTTGCCACATCAT 57.930 30.769 0.00 0.00 0.00 2.45
364 365 8.192774 TCTTCATTTATTTCTTGCCACATCATC 58.807 33.333 0.00 0.00 0.00 2.92
366 367 8.750515 TCATTTATTTCTTGCCACATCATCTA 57.249 30.769 0.00 0.00 0.00 1.98
367 368 9.358406 TCATTTATTTCTTGCCACATCATCTAT 57.642 29.630 0.00 0.00 0.00 1.98
368 369 9.976511 CATTTATTTCTTGCCACATCATCTATT 57.023 29.630 0.00 0.00 0.00 1.73
374 375 8.985315 TTCTTGCCACATCATCTATTTTATCT 57.015 30.769 0.00 0.00 0.00 1.98
376 377 9.716531 TCTTGCCACATCATCTATTTTATCTAG 57.283 33.333 0.00 0.00 0.00 2.43
377 378 9.716531 CTTGCCACATCATCTATTTTATCTAGA 57.283 33.333 0.00 0.00 0.00 2.43
408 409 7.592885 TGATGTTACTACCTATGTTACTCCC 57.407 40.000 0.00 0.00 0.00 4.30
409 410 7.127405 TGATGTTACTACCTATGTTACTCCCA 58.873 38.462 0.00 0.00 0.00 4.37
410 411 6.780457 TGTTACTACCTATGTTACTCCCAC 57.220 41.667 0.00 0.00 0.00 4.61
411 412 6.496743 TGTTACTACCTATGTTACTCCCACT 58.503 40.000 0.00 0.00 0.00 4.00
412 413 7.642186 TGTTACTACCTATGTTACTCCCACTA 58.358 38.462 0.00 0.00 0.00 2.74
413 414 8.284435 TGTTACTACCTATGTTACTCCCACTAT 58.716 37.037 0.00 0.00 0.00 2.12
414 415 8.574737 GTTACTACCTATGTTACTCCCACTATG 58.425 40.741 0.00 0.00 0.00 2.23
459 460 9.725019 TTCAGTCTTATGTTATTCTGTGTTCAT 57.275 29.630 0.00 0.00 0.00 2.57
602 603 2.645163 CTTGCTATGCTCGACGACTAG 58.355 52.381 0.00 0.00 0.00 2.57
610 611 1.903775 GCTCGACGACTAGACGTTTTC 59.096 52.381 20.56 8.08 46.52 2.29
622 649 1.065551 GACGTTTTCCTGCTGCACTTT 59.934 47.619 0.00 0.00 0.00 2.66
687 715 5.994668 TGTTGTATATGAGTGAACACTGCAA 59.005 36.000 12.29 2.04 42.66 4.08
688 716 6.654582 TGTTGTATATGAGTGAACACTGCAAT 59.345 34.615 12.29 6.04 42.66 3.56
690 718 6.405538 TGTATATGAGTGAACACTGCAATGA 58.594 36.000 12.29 2.35 42.66 2.57
691 719 7.049754 TGTATATGAGTGAACACTGCAATGAT 58.950 34.615 12.29 0.00 42.66 2.45
692 720 4.959596 ATGAGTGAACACTGCAATGATC 57.040 40.909 12.29 0.00 42.66 2.92
693 721 4.011966 TGAGTGAACACTGCAATGATCT 57.988 40.909 12.29 0.00 42.66 2.75
696 724 6.877236 TGAGTGAACACTGCAATGATCTATA 58.123 36.000 12.29 0.00 42.66 1.31
786 814 2.502213 ATGCATCCACATGATTTGCG 57.498 45.000 0.00 0.00 30.57 4.85
787 815 0.179132 TGCATCCACATGATTTGCGC 60.179 50.000 0.00 0.00 30.57 6.09
788 816 1.204228 GCATCCACATGATTTGCGCG 61.204 55.000 0.00 0.00 30.57 6.86
789 817 1.064621 ATCCACATGATTTGCGCGC 59.935 52.632 27.26 27.26 0.00 6.86
790 818 1.655885 ATCCACATGATTTGCGCGCA 61.656 50.000 33.09 33.09 0.00 6.09
793 821 1.154169 ACATGATTTGCGCGCACAG 60.154 52.632 36.72 21.97 0.00 3.66
794 822 1.870458 CATGATTTGCGCGCACAGG 60.870 57.895 36.72 25.99 0.00 4.00
795 823 2.039974 ATGATTTGCGCGCACAGGA 61.040 52.632 36.72 17.67 0.00 3.86
796 824 2.202349 GATTTGCGCGCACAGGAC 60.202 61.111 36.72 18.64 0.00 3.85
797 825 3.982424 GATTTGCGCGCACAGGACG 62.982 63.158 36.72 0.00 0.00 4.79
805 833 3.695606 GCACAGGACGGCAGAGGA 61.696 66.667 0.00 0.00 0.00 3.71
806 834 2.575993 CACAGGACGGCAGAGGAG 59.424 66.667 0.00 0.00 0.00 3.69
807 835 2.681778 ACAGGACGGCAGAGGAGG 60.682 66.667 0.00 0.00 0.00 4.30
808 836 4.154347 CAGGACGGCAGAGGAGGC 62.154 72.222 0.00 0.00 0.00 4.70
858 886 2.286872 AGAATGCAAAGCCTCAGATCG 58.713 47.619 0.00 0.00 0.00 3.69
859 887 2.093288 AGAATGCAAAGCCTCAGATCGA 60.093 45.455 0.00 0.00 0.00 3.59
860 888 1.661341 ATGCAAAGCCTCAGATCGAC 58.339 50.000 0.00 0.00 0.00 4.20
862 890 1.285578 GCAAAGCCTCAGATCGACTC 58.714 55.000 0.00 0.00 0.00 3.36
863 891 1.554392 CAAAGCCTCAGATCGACTCG 58.446 55.000 0.00 0.00 0.00 4.18
864 892 1.133216 CAAAGCCTCAGATCGACTCGA 59.867 52.381 3.06 3.06 41.13 4.04
961 989 8.909923 ACCTATTACTATACAATGGTTTTTGGC 58.090 33.333 0.00 0.00 0.00 4.52
962 990 9.131791 CCTATTACTATACAATGGTTTTTGGCT 57.868 33.333 0.00 0.00 0.00 4.75
978 1006 1.268778 GGCTTTGTTTCAAGCGACGC 61.269 55.000 13.03 13.03 42.67 5.19
997 1025 2.021457 GCCATTATTGTAAGCGTGGGT 58.979 47.619 0.00 0.00 0.00 4.51
1004 1032 2.125310 TAAGCGTGGGTGGATGCG 60.125 61.111 0.00 0.00 32.75 4.73
1097 1125 1.134995 CATGGAGTCGTTGCAGCTCTA 60.135 52.381 0.00 0.00 0.00 2.43
1098 1126 0.243907 TGGAGTCGTTGCAGCTCTAC 59.756 55.000 0.00 0.00 0.00 2.59
1099 1127 0.458716 GGAGTCGTTGCAGCTCTACC 60.459 60.000 0.00 0.00 0.00 3.18
1100 1128 0.243907 GAGTCGTTGCAGCTCTACCA 59.756 55.000 0.00 0.00 0.00 3.25
1101 1129 0.244994 AGTCGTTGCAGCTCTACCAG 59.755 55.000 0.00 0.00 0.00 4.00
1117 1145 0.324738 CCAGTACCAGCTCCTCCTCA 60.325 60.000 0.00 0.00 0.00 3.86
1143 1171 1.299976 GGCCATTGTCGTCCCTCTT 59.700 57.895 0.00 0.00 0.00 2.85
1436 1466 3.274586 CCGCATGATCCGCCTGTG 61.275 66.667 0.00 0.00 0.00 3.66
1479 1509 1.378882 TAGTCTTCGCGCCGTATGGT 61.379 55.000 0.00 0.00 37.67 3.55
2028 2131 1.208052 CCTCACTCACGGAATCCACAT 59.792 52.381 0.00 0.00 0.00 3.21
2043 2146 6.603201 GGAATCCACATAACTTCTTCCATCAA 59.397 38.462 0.00 0.00 32.73 2.57
2085 2197 3.066380 TCATGCATGTATCGTGCCATAC 58.934 45.455 25.43 0.00 44.81 2.39
2483 3035 2.046217 GTCGACTTCAAGGGGGCC 60.046 66.667 8.70 0.00 0.00 5.80
2763 3320 7.281774 CACATATGGTATTCCCTCTCATAATGC 59.718 40.741 7.80 0.00 0.00 3.56
2770 3327 5.378230 TTCCCTCTCATAATGCAAGACAT 57.622 39.130 0.00 0.00 42.30 3.06
2797 3354 6.740411 TTTATACGAAAAACTAACGCCCAT 57.260 33.333 0.00 0.00 0.00 4.00
2813 3370 1.231958 CCATACGTGTGGGCGTTTGT 61.232 55.000 22.66 0.00 43.04 2.83
2837 3394 1.341209 TCGCTCATACGCCTTCATCAT 59.659 47.619 0.00 0.00 0.00 2.45
2872 3429 5.293324 GCCACGTATAAACAGATGACATCAA 59.707 40.000 17.57 0.00 0.00 2.57
2893 3450 7.969536 TCAACAGAAATGTTTTTGGTTTTCA 57.030 28.000 1.82 0.00 31.94 2.69
2964 3521 5.106869 CGTTTTCACCATTAAATCCGTCTCA 60.107 40.000 0.00 0.00 0.00 3.27
3015 3572 8.210026 TGTTGATATGTTTCGACGAAATTTTG 57.790 30.769 24.48 3.73 33.97 2.44
3019 3577 7.858382 TGATATGTTTCGACGAAATTTTGTTGT 59.142 29.630 24.48 7.96 33.97 3.32
3046 3604 5.789643 AAGTTGCCATGATGTTTACACTT 57.210 34.783 0.00 0.00 0.00 3.16
3054 3612 6.570378 GCCATGATGTTTACACTTTAGTTGCT 60.570 38.462 0.00 0.00 0.00 3.91
3101 3682 8.028938 GTCATGTGGCAATTTTAGTTTGTAGAT 58.971 33.333 0.00 0.00 0.00 1.98
3282 3863 5.301551 TCATGGCAACTTCAGTGTAAACATT 59.698 36.000 0.00 0.00 37.61 2.71
3321 3902 5.576774 GCAATAGACATGGCAACTTTTAACC 59.423 40.000 0.00 0.00 30.66 2.85
3393 3974 3.153676 TCGTCGCGAGGAATTTAATGA 57.846 42.857 27.50 2.68 0.00 2.57
3413 3994 7.395190 AATGATGAAAACGGATCTTCAATCA 57.605 32.000 0.00 5.21 35.44 2.57
3525 4106 2.059190 TTATAGGGCGTGTGGGCGA 61.059 57.895 0.00 0.00 43.46 5.54
3535 4116 2.032681 GTGGGCGAGTTTGGCTCT 59.967 61.111 0.00 0.00 41.98 4.09
3578 4159 9.698617 GTTAGCGTTGTCCTTTTTATATTAGTG 57.301 33.333 0.00 0.00 0.00 2.74
3625 4206 4.154176 TGAAGGGTGTAGTACAGTAGCAA 58.846 43.478 2.39 0.00 0.00 3.91
3629 4210 3.427233 GGGTGTAGTACAGTAGCAAGTCG 60.427 52.174 2.39 0.00 0.00 4.18
3633 4223 1.817447 AGTACAGTAGCAAGTCGGGAC 59.183 52.381 0.00 0.00 0.00 4.46
3637 4227 1.204704 CAGTAGCAAGTCGGGACATGA 59.795 52.381 8.12 0.00 32.25 3.07
3642 4232 0.038618 CAAGTCGGGACATGACGTGA 60.039 55.000 0.00 0.00 44.98 4.35
3650 4240 3.930229 CGGGACATGACGTGATTTTTCTA 59.070 43.478 0.00 0.00 0.00 2.10
3652 4242 5.751509 CGGGACATGACGTGATTTTTCTATA 59.248 40.000 0.00 0.00 0.00 1.31
3654 4244 7.042051 CGGGACATGACGTGATTTTTCTATATT 60.042 37.037 0.00 0.00 0.00 1.28
3656 4246 9.438291 GGACATGACGTGATTTTTCTATATTTG 57.562 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.148563 GCATTCTGCAGAGAAGCATATG 57.851 45.455 23.71 19.61 44.68 1.78
57 58 8.422566 ACTAATTAAGAGTACCCTATGAACAGC 58.577 37.037 0.00 0.00 0.00 4.40
144 145 1.207089 CCCATTGTGGCTAGTCTTCGA 59.793 52.381 0.00 0.00 35.79 3.71
145 146 1.066143 ACCCATTGTGGCTAGTCTTCG 60.066 52.381 0.00 0.00 35.79 3.79
146 147 2.789409 ACCCATTGTGGCTAGTCTTC 57.211 50.000 0.00 0.00 35.79 2.87
147 148 3.182152 ACTACCCATTGTGGCTAGTCTT 58.818 45.455 0.00 0.00 35.79 3.01
148 149 2.766828 GACTACCCATTGTGGCTAGTCT 59.233 50.000 18.00 0.00 36.78 3.24
149 150 2.766828 AGACTACCCATTGTGGCTAGTC 59.233 50.000 17.75 17.75 38.24 2.59
150 151 2.834113 AGACTACCCATTGTGGCTAGT 58.166 47.619 4.13 4.13 35.79 2.57
152 153 3.990369 ACTAGACTACCCATTGTGGCTA 58.010 45.455 0.00 0.00 35.79 3.93
153 154 2.834113 ACTAGACTACCCATTGTGGCT 58.166 47.619 0.00 0.00 35.79 4.75
154 155 4.081309 TGTTACTAGACTACCCATTGTGGC 60.081 45.833 0.00 0.00 35.79 5.01
155 156 5.670792 TGTTACTAGACTACCCATTGTGG 57.329 43.478 0.00 0.00 37.25 4.17
157 158 5.188948 TGCATGTTACTAGACTACCCATTGT 59.811 40.000 0.00 0.00 0.00 2.71
158 159 5.670485 TGCATGTTACTAGACTACCCATTG 58.330 41.667 0.00 0.00 0.00 2.82
160 161 7.235606 ACATATGCATGTTACTAGACTACCCAT 59.764 37.037 10.16 0.00 42.98 4.00
161 162 6.553476 ACATATGCATGTTACTAGACTACCCA 59.447 38.462 10.16 0.00 42.98 4.51
162 163 6.994221 ACATATGCATGTTACTAGACTACCC 58.006 40.000 10.16 0.00 42.98 3.69
192 193 9.850198 CCCCACTATAGAGGTAGTAATATAGAC 57.150 40.741 14.29 0.00 33.29 2.59
193 194 9.809705 TCCCCACTATAGAGGTAGTAATATAGA 57.190 37.037 14.29 0.00 33.29 1.98
196 197 8.479601 ACTCCCCACTATAGAGGTAGTAATAT 57.520 38.462 14.29 0.00 33.29 1.28
197 198 7.901804 ACTCCCCACTATAGAGGTAGTAATA 57.098 40.000 14.29 0.00 33.29 0.98
198 199 6.800223 ACTCCCCACTATAGAGGTAGTAAT 57.200 41.667 14.29 0.00 33.29 1.89
199 200 7.521669 GTTACTCCCCACTATAGAGGTAGTAA 58.478 42.308 23.15 23.15 33.91 2.24
200 201 6.239714 CGTTACTCCCCACTATAGAGGTAGTA 60.240 46.154 17.42 17.42 33.29 1.82
201 202 5.455899 CGTTACTCCCCACTATAGAGGTAGT 60.456 48.000 18.82 18.82 35.34 2.73
202 203 5.002516 CGTTACTCCCCACTATAGAGGTAG 58.997 50.000 14.29 12.87 31.70 3.18
203 204 4.413520 ACGTTACTCCCCACTATAGAGGTA 59.586 45.833 14.29 2.62 31.70 3.08
207 208 7.609146 CACATATACGTTACTCCCCACTATAGA 59.391 40.741 6.78 0.00 0.00 1.98
208 209 7.148120 CCACATATACGTTACTCCCCACTATAG 60.148 44.444 0.00 0.00 0.00 1.31
209 210 6.660521 CCACATATACGTTACTCCCCACTATA 59.339 42.308 0.00 0.00 0.00 1.31
210 211 5.479375 CCACATATACGTTACTCCCCACTAT 59.521 44.000 0.00 0.00 0.00 2.12
211 212 4.828939 CCACATATACGTTACTCCCCACTA 59.171 45.833 0.00 0.00 0.00 2.74
212 213 3.640029 CCACATATACGTTACTCCCCACT 59.360 47.826 0.00 0.00 0.00 4.00
213 214 3.385755 ACCACATATACGTTACTCCCCAC 59.614 47.826 0.00 0.00 0.00 4.61
214 215 3.645434 ACCACATATACGTTACTCCCCA 58.355 45.455 0.00 0.00 0.00 4.96
215 216 5.068987 TGTTACCACATATACGTTACTCCCC 59.931 44.000 0.00 0.00 0.00 4.81
216 217 6.147864 TGTTACCACATATACGTTACTCCC 57.852 41.667 0.00 0.00 0.00 4.30
218 219 6.698329 TGCATGTTACCACATATACGTTACTC 59.302 38.462 0.00 0.00 42.14 2.59
219 220 6.575267 TGCATGTTACCACATATACGTTACT 58.425 36.000 0.00 0.00 42.14 2.24
221 222 6.817140 TGTTGCATGTTACCACATATACGTTA 59.183 34.615 0.00 0.00 42.14 3.18
222 223 5.644206 TGTTGCATGTTACCACATATACGTT 59.356 36.000 0.00 0.00 42.14 3.99
223 224 5.064198 GTGTTGCATGTTACCACATATACGT 59.936 40.000 0.00 0.00 42.14 3.57
225 226 6.677781 AGTGTTGCATGTTACCACATATAC 57.322 37.500 0.00 0.00 42.14 1.47
226 227 6.881602 TGAAGTGTTGCATGTTACCACATATA 59.118 34.615 0.00 0.00 42.14 0.86
227 228 5.709631 TGAAGTGTTGCATGTTACCACATAT 59.290 36.000 0.00 0.00 42.14 1.78
228 229 5.066593 TGAAGTGTTGCATGTTACCACATA 58.933 37.500 0.00 0.00 42.14 2.29
229 230 3.888323 TGAAGTGTTGCATGTTACCACAT 59.112 39.130 0.00 0.00 45.18 3.21
230 231 3.282885 TGAAGTGTTGCATGTTACCACA 58.717 40.909 0.00 0.00 37.31 4.17
232 233 5.528043 AAATGAAGTGTTGCATGTTACCA 57.472 34.783 0.00 0.00 0.00 3.25
234 235 7.063308 CCCAATAAATGAAGTGTTGCATGTTAC 59.937 37.037 0.00 0.00 0.00 2.50
235 236 7.095910 CCCAATAAATGAAGTGTTGCATGTTA 58.904 34.615 0.00 0.00 0.00 2.41
236 237 5.933463 CCCAATAAATGAAGTGTTGCATGTT 59.067 36.000 0.00 0.00 0.00 2.71
237 238 5.481105 CCCAATAAATGAAGTGTTGCATGT 58.519 37.500 0.00 0.00 0.00 3.21
239 240 4.223477 AGCCCAATAAATGAAGTGTTGCAT 59.777 37.500 0.00 0.00 0.00 3.96
240 241 3.577848 AGCCCAATAAATGAAGTGTTGCA 59.422 39.130 0.00 0.00 0.00 4.08
242 243 8.345565 GTCTATAGCCCAATAAATGAAGTGTTG 58.654 37.037 0.00 0.00 0.00 3.33
243 244 8.275040 AGTCTATAGCCCAATAAATGAAGTGTT 58.725 33.333 0.00 0.00 0.00 3.32
244 245 7.806180 AGTCTATAGCCCAATAAATGAAGTGT 58.194 34.615 0.00 0.00 0.00 3.55
245 246 7.933577 TGAGTCTATAGCCCAATAAATGAAGTG 59.066 37.037 0.00 0.00 0.00 3.16
248 249 8.884323 AGATGAGTCTATAGCCCAATAAATGAA 58.116 33.333 0.00 0.00 31.36 2.57
249 250 8.441311 AGATGAGTCTATAGCCCAATAAATGA 57.559 34.615 0.00 0.00 31.36 2.57
250 251 8.944029 CAAGATGAGTCTATAGCCCAATAAATG 58.056 37.037 0.00 0.00 33.30 2.32
251 252 7.609532 GCAAGATGAGTCTATAGCCCAATAAAT 59.390 37.037 0.00 0.00 33.30 1.40
252 253 6.936900 GCAAGATGAGTCTATAGCCCAATAAA 59.063 38.462 0.00 0.00 33.30 1.40
253 254 6.467677 GCAAGATGAGTCTATAGCCCAATAA 58.532 40.000 0.00 0.00 33.30 1.40
254 255 5.046304 GGCAAGATGAGTCTATAGCCCAATA 60.046 44.000 0.00 0.00 39.34 1.90
256 257 3.071602 GGCAAGATGAGTCTATAGCCCAA 59.928 47.826 0.00 0.00 39.34 4.12
257 258 2.634940 GGCAAGATGAGTCTATAGCCCA 59.365 50.000 0.00 0.00 39.34 5.36
258 259 2.903135 AGGCAAGATGAGTCTATAGCCC 59.097 50.000 0.00 0.00 42.97 5.19
259 260 4.615588 AAGGCAAGATGAGTCTATAGCC 57.384 45.455 0.00 0.00 42.62 3.93
260 261 9.311916 CATATTAAGGCAAGATGAGTCTATAGC 57.688 37.037 0.00 0.00 37.95 2.97
263 264 8.654997 ACACATATTAAGGCAAGATGAGTCTAT 58.345 33.333 0.00 0.00 35.57 1.98
264 265 7.928167 CACACATATTAAGGCAAGATGAGTCTA 59.072 37.037 0.00 0.00 37.50 2.59
265 266 6.765036 CACACATATTAAGGCAAGATGAGTCT 59.235 38.462 0.00 0.00 37.50 3.24
266 267 6.763135 TCACACATATTAAGGCAAGATGAGTC 59.237 38.462 0.00 0.00 37.50 3.36
269 270 7.056006 ACATCACACATATTAAGGCAAGATGA 58.944 34.615 0.00 0.00 37.95 2.92
270 271 7.268199 ACATCACACATATTAAGGCAAGATG 57.732 36.000 0.00 0.00 40.88 2.90
271 272 7.886629 AACATCACACATATTAAGGCAAGAT 57.113 32.000 0.00 0.00 0.00 2.40
272 273 8.046708 AGTAACATCACACATATTAAGGCAAGA 58.953 33.333 0.00 0.00 0.00 3.02
273 274 8.213518 AGTAACATCACACATATTAAGGCAAG 57.786 34.615 0.00 0.00 0.00 4.01
274 275 8.574251 AAGTAACATCACACATATTAAGGCAA 57.426 30.769 0.00 0.00 0.00 4.52
275 276 9.104965 GTAAGTAACATCACACATATTAAGGCA 57.895 33.333 0.00 0.00 0.00 4.75
276 277 9.326413 AGTAAGTAACATCACACATATTAAGGC 57.674 33.333 0.00 0.00 0.00 4.35
320 321 8.477419 AATGAAGAAAGTGAGGAAAATGGTAA 57.523 30.769 0.00 0.00 0.00 2.85
321 322 8.477419 AAATGAAGAAAGTGAGGAAAATGGTA 57.523 30.769 0.00 0.00 0.00 3.25
322 323 6.983906 AATGAAGAAAGTGAGGAAAATGGT 57.016 33.333 0.00 0.00 0.00 3.55
329 330 8.299570 GCAAGAAATAAATGAAGAAAGTGAGGA 58.700 33.333 0.00 0.00 0.00 3.71
330 331 7.543520 GGCAAGAAATAAATGAAGAAAGTGAGG 59.456 37.037 0.00 0.00 0.00 3.86
333 334 7.652909 TGTGGCAAGAAATAAATGAAGAAAGTG 59.347 33.333 0.00 0.00 0.00 3.16
334 335 7.725251 TGTGGCAAGAAATAAATGAAGAAAGT 58.275 30.769 0.00 0.00 0.00 2.66
335 336 8.767478 ATGTGGCAAGAAATAAATGAAGAAAG 57.233 30.769 0.00 0.00 0.00 2.62
336 337 8.366401 TGATGTGGCAAGAAATAAATGAAGAAA 58.634 29.630 0.00 0.00 0.00 2.52
337 338 7.894708 TGATGTGGCAAGAAATAAATGAAGAA 58.105 30.769 0.00 0.00 0.00 2.52
338 339 7.465353 TGATGTGGCAAGAAATAAATGAAGA 57.535 32.000 0.00 0.00 0.00 2.87
340 341 8.070034 AGATGATGTGGCAAGAAATAAATGAA 57.930 30.769 0.00 0.00 0.00 2.57
341 342 7.649533 AGATGATGTGGCAAGAAATAAATGA 57.350 32.000 0.00 0.00 0.00 2.57
348 349 9.412460 AGATAAAATAGATGATGTGGCAAGAAA 57.588 29.630 0.00 0.00 0.00 2.52
349 350 8.985315 AGATAAAATAGATGATGTGGCAAGAA 57.015 30.769 0.00 0.00 0.00 2.52
351 352 9.716531 TCTAGATAAAATAGATGATGTGGCAAG 57.283 33.333 0.00 0.00 0.00 4.01
382 383 9.305555 GGGAGTAACATAGGTAGTAACATCATA 57.694 37.037 0.00 0.00 0.00 2.15
383 384 7.787904 TGGGAGTAACATAGGTAGTAACATCAT 59.212 37.037 0.00 0.00 0.00 2.45
384 385 7.069085 GTGGGAGTAACATAGGTAGTAACATCA 59.931 40.741 0.00 0.00 0.00 3.07
386 387 7.130775 AGTGGGAGTAACATAGGTAGTAACAT 58.869 38.462 0.00 0.00 0.00 2.71
387 388 6.496743 AGTGGGAGTAACATAGGTAGTAACA 58.503 40.000 0.00 0.00 0.00 2.41
388 389 8.574737 CATAGTGGGAGTAACATAGGTAGTAAC 58.425 40.741 0.00 0.00 0.00 2.50
391 392 6.075984 CCATAGTGGGAGTAACATAGGTAGT 58.924 44.000 0.00 0.00 32.67 2.73
392 393 6.591750 CCATAGTGGGAGTAACATAGGTAG 57.408 45.833 0.00 0.00 32.67 3.18
407 408 5.535406 CACTACCTTAGACTACCCATAGTGG 59.465 48.000 11.31 0.00 41.98 4.00
408 409 5.009811 GCACTACCTTAGACTACCCATAGTG 59.990 48.000 13.32 13.32 41.98 2.74
409 410 5.103601 AGCACTACCTTAGACTACCCATAGT 60.104 44.000 0.00 0.00 44.74 2.12
410 411 5.386924 AGCACTACCTTAGACTACCCATAG 58.613 45.833 0.00 0.00 34.25 2.23
411 412 5.399052 AGCACTACCTTAGACTACCCATA 57.601 43.478 0.00 0.00 0.00 2.74
412 413 4.267341 AGCACTACCTTAGACTACCCAT 57.733 45.455 0.00 0.00 0.00 4.00
413 414 3.752359 AGCACTACCTTAGACTACCCA 57.248 47.619 0.00 0.00 0.00 4.51
414 415 4.021916 TGAAGCACTACCTTAGACTACCC 58.978 47.826 0.00 0.00 0.00 3.69
416 417 5.648960 AGACTGAAGCACTACCTTAGACTAC 59.351 44.000 0.00 0.00 0.00 2.73
417 418 5.817784 AGACTGAAGCACTACCTTAGACTA 58.182 41.667 0.00 0.00 0.00 2.59
418 419 4.668636 AGACTGAAGCACTACCTTAGACT 58.331 43.478 0.00 0.00 0.00 3.24
459 460 6.484977 TGTTAAGCATCACACAGAACACATAA 59.515 34.615 0.00 0.00 0.00 1.90
461 462 4.821260 TGTTAAGCATCACACAGAACACAT 59.179 37.500 0.00 0.00 0.00 3.21
576 577 3.252458 TCGTCGAGCATAGCAAGCTAATA 59.748 43.478 5.81 0.00 43.58 0.98
577 578 2.034685 TCGTCGAGCATAGCAAGCTAAT 59.965 45.455 5.81 0.00 43.58 1.73
602 603 0.663153 AAGTGCAGCAGGAAAACGTC 59.337 50.000 0.00 0.00 0.00 4.34
610 611 8.931385 AATATAAATAACAAAAGTGCAGCAGG 57.069 30.769 0.00 0.00 0.00 4.85
643 670 2.987149 CACAGACGATCGCTAGTTGTTT 59.013 45.455 16.60 0.00 0.00 2.83
696 724 8.396272 ACAAGTGCACTTAACTGAAATAGATT 57.604 30.769 30.67 0.87 34.28 2.40
769 797 1.204228 CGCGCAAATCATGTGGATGC 61.204 55.000 8.75 0.00 40.01 3.91
788 816 3.655810 CTCCTCTGCCGTCCTGTGC 62.656 68.421 0.00 0.00 0.00 4.57
789 817 2.575993 CTCCTCTGCCGTCCTGTG 59.424 66.667 0.00 0.00 0.00 3.66
790 818 2.681778 CCTCCTCTGCCGTCCTGT 60.682 66.667 0.00 0.00 0.00 4.00
821 849 3.376935 CTCACTAGTGGCTGGGGCG 62.377 68.421 22.48 0.00 39.81 6.13
822 850 1.553690 TTCTCACTAGTGGCTGGGGC 61.554 60.000 22.48 0.00 37.82 5.80
823 851 1.134280 CATTCTCACTAGTGGCTGGGG 60.134 57.143 22.48 5.18 0.00 4.96
824 852 1.745141 GCATTCTCACTAGTGGCTGGG 60.745 57.143 22.48 10.94 0.00 4.45
825 853 1.065926 TGCATTCTCACTAGTGGCTGG 60.066 52.381 22.48 10.57 0.00 4.85
826 854 2.391616 TGCATTCTCACTAGTGGCTG 57.608 50.000 22.48 14.65 0.00 4.85
828 856 2.159462 GCTTTGCATTCTCACTAGTGGC 60.159 50.000 22.48 16.98 0.00 5.01
832 860 3.603532 TGAGGCTTTGCATTCTCACTAG 58.396 45.455 0.00 0.00 32.10 2.57
833 861 3.261643 TCTGAGGCTTTGCATTCTCACTA 59.738 43.478 0.00 0.00 33.36 2.74
834 862 2.039480 TCTGAGGCTTTGCATTCTCACT 59.961 45.455 0.00 0.00 33.36 3.41
835 863 2.430465 TCTGAGGCTTTGCATTCTCAC 58.570 47.619 0.00 0.00 33.36 3.51
836 864 2.865119 TCTGAGGCTTTGCATTCTCA 57.135 45.000 0.00 0.00 35.32 3.27
896 924 4.437794 CGTATCCTCGCACACTTACAGTTA 60.438 45.833 0.00 0.00 0.00 2.24
897 925 3.672511 CGTATCCTCGCACACTTACAGTT 60.673 47.826 0.00 0.00 0.00 3.16
898 926 2.159421 CGTATCCTCGCACACTTACAGT 60.159 50.000 0.00 0.00 0.00 3.55
900 928 1.133598 CCGTATCCTCGCACACTTACA 59.866 52.381 0.00 0.00 0.00 2.41
918 946 0.307760 GGTGTCTTTGTGCTTGTCCG 59.692 55.000 0.00 0.00 0.00 4.79
925 953 8.712285 TTGTATAGTAATAGGTGTCTTTGTGC 57.288 34.615 0.00 0.00 0.00 4.57
961 989 0.028770 TGGCGTCGCTTGAAACAAAG 59.971 50.000 18.11 0.00 0.00 2.77
962 990 0.665835 ATGGCGTCGCTTGAAACAAA 59.334 45.000 18.11 0.00 0.00 2.83
963 991 0.665835 AATGGCGTCGCTTGAAACAA 59.334 45.000 18.11 0.00 0.00 2.83
978 1006 2.357637 CCACCCACGCTTACAATAATGG 59.642 50.000 0.00 0.00 0.00 3.16
1010 1038 1.212455 CTGACGCGCCGTATGCATAA 61.212 55.000 8.28 0.00 41.37 1.90
1012 1040 2.961721 CTGACGCGCCGTATGCAT 60.962 61.111 5.73 3.79 41.37 3.96
1013 1041 4.429212 ACTGACGCGCCGTATGCA 62.429 61.111 5.73 0.00 41.37 3.96
1016 1044 2.202570 GACACTGACGCGCCGTAT 60.203 61.111 5.73 0.00 41.37 3.06
1017 1045 3.662153 TGACACTGACGCGCCGTA 61.662 61.111 5.73 0.00 41.37 4.02
1020 1048 3.106407 GAGTGACACTGACGCGCC 61.106 66.667 14.14 0.00 0.00 6.53
1022 1050 0.317854 TTCAGAGTGACACTGACGCG 60.318 55.000 14.14 3.53 42.84 6.01
1023 1051 1.132588 GTTCAGAGTGACACTGACGC 58.867 55.000 14.14 5.32 42.84 5.19
1097 1125 0.324830 GAGGAGGAGCTGGTACTGGT 60.325 60.000 0.00 0.00 41.58 4.00
1098 1126 0.324738 TGAGGAGGAGCTGGTACTGG 60.325 60.000 0.00 0.00 0.00 4.00
1099 1127 0.820871 GTGAGGAGGAGCTGGTACTG 59.179 60.000 0.00 0.00 0.00 2.74
1100 1128 0.707616 AGTGAGGAGGAGCTGGTACT 59.292 55.000 0.00 0.00 0.00 2.73
1101 1129 1.107945 GAGTGAGGAGGAGCTGGTAC 58.892 60.000 0.00 0.00 0.00 3.34
1117 1145 1.194781 ACGACAATGGCCAGGAGAGT 61.195 55.000 13.05 5.81 0.00 3.24
1143 1171 2.202878 GCGCGGTTGAGGCATAGA 60.203 61.111 8.83 0.00 0.00 1.98
1479 1509 1.375908 GATCTGCCGCCACTTGTCA 60.376 57.895 0.00 0.00 0.00 3.58
1531 1609 4.070552 GAAGGACTGGACGCGCCT 62.071 66.667 18.14 7.89 37.63 5.52
2028 2131 8.648698 TTTTCATGGATTGATGGAAGAAGTTA 57.351 30.769 0.00 0.00 33.34 2.24
2085 2197 1.471676 GGCGAACATGTCCTGTAGGAG 60.472 57.143 0.00 0.00 46.49 3.69
2483 3035 4.088421 GGCGTGTACTCCATGTCG 57.912 61.111 0.00 0.00 32.30 4.35
2613 3165 2.125350 GTCGAGCTCCTTGGCCTG 60.125 66.667 8.47 0.00 0.00 4.85
2772 3329 6.963796 TGGGCGTTAGTTTTTCGTATAAAAA 58.036 32.000 0.00 0.00 0.00 1.94
2773 3330 6.551385 TGGGCGTTAGTTTTTCGTATAAAA 57.449 33.333 0.00 0.00 0.00 1.52
2774 3331 6.740411 ATGGGCGTTAGTTTTTCGTATAAA 57.260 33.333 0.00 0.00 0.00 1.40
2775 3332 6.019961 CGTATGGGCGTTAGTTTTTCGTATAA 60.020 38.462 0.00 0.00 0.00 0.98
2776 3333 5.458452 CGTATGGGCGTTAGTTTTTCGTATA 59.542 40.000 0.00 0.00 0.00 1.47
2777 3334 4.268405 CGTATGGGCGTTAGTTTTTCGTAT 59.732 41.667 0.00 0.00 0.00 3.06
2778 3335 3.611986 CGTATGGGCGTTAGTTTTTCGTA 59.388 43.478 0.00 0.00 0.00 3.43
2779 3336 2.412770 CGTATGGGCGTTAGTTTTTCGT 59.587 45.455 0.00 0.00 0.00 3.85
2780 3337 2.412770 ACGTATGGGCGTTAGTTTTTCG 59.587 45.455 0.00 0.00 43.04 3.46
2813 3370 1.679153 TGAAGGCGTATGAGCGATGTA 59.321 47.619 0.00 0.00 38.18 2.29
2821 3378 3.384467 TGAGTGATGATGAAGGCGTATGA 59.616 43.478 0.00 0.00 0.00 2.15
2824 3381 4.406648 AATGAGTGATGATGAAGGCGTA 57.593 40.909 0.00 0.00 0.00 4.42
2837 3394 5.470437 TGTTTATACGTGGCAAAATGAGTGA 59.530 36.000 0.00 0.00 0.00 3.41
2872 3429 6.172630 AGCTGAAAACCAAAAACATTTCTGT 58.827 32.000 0.00 0.00 37.12 3.41
2880 3437 9.619316 AACAATTTTAAGCTGAAAACCAAAAAC 57.381 25.926 11.32 0.00 31.35 2.43
2964 3521 5.480205 GGGTCTAGTTTTGAAGATCTCGTT 58.520 41.667 0.00 0.00 0.00 3.85
3015 3572 3.451141 TCATGGCAACTTTTGGACAAC 57.549 42.857 0.00 0.00 37.61 3.32
3019 3577 4.686191 AAACATCATGGCAACTTTTGGA 57.314 36.364 0.00 0.00 37.61 3.53
3057 3615 7.417612 CACATGACAACTTTAGTTTAAGCACT 58.582 34.615 0.00 0.00 35.83 4.40
3131 3712 6.757947 GCCATGATACATGCACTTAAAATTGT 59.242 34.615 0.00 0.00 0.00 2.71
3254 3835 7.826744 TGTTTACACTGAAGTTGCCATGATATA 59.173 33.333 0.00 0.00 0.00 0.86
3282 3863 5.593502 TGTCTATTGCACATGAATTGCCATA 59.406 36.000 0.00 0.07 39.39 2.74
3393 3974 7.636150 AATCTGATTGAAGATCCGTTTTCAT 57.364 32.000 1.31 0.00 35.83 2.57
3493 4074 3.129988 GCCCTATAACACACAGACTACGT 59.870 47.826 0.00 0.00 0.00 3.57
3525 4106 0.532862 CGTGTGGTGAGAGCCAAACT 60.533 55.000 4.20 0.00 43.04 2.66
3589 4170 9.975218 ACTACACCCTTCATATAAGATTGTTTT 57.025 29.630 0.00 0.00 0.00 2.43
3592 4173 9.209048 TGTACTACACCCTTCATATAAGATTGT 57.791 33.333 0.00 0.00 0.00 2.71
3593 4174 9.698309 CTGTACTACACCCTTCATATAAGATTG 57.302 37.037 0.00 0.00 0.00 2.67
3594 4175 9.435570 ACTGTACTACACCCTTCATATAAGATT 57.564 33.333 0.00 0.00 0.00 2.40
3596 4177 9.570468 CTACTGTACTACACCCTTCATATAAGA 57.430 37.037 0.00 0.00 0.00 2.10
3599 4180 7.292319 TGCTACTGTACTACACCCTTCATATA 58.708 38.462 0.00 0.00 0.00 0.86
3602 4183 4.350245 TGCTACTGTACTACACCCTTCAT 58.650 43.478 0.00 0.00 0.00 2.57
3603 4184 3.770046 TGCTACTGTACTACACCCTTCA 58.230 45.455 0.00 0.00 0.00 3.02
3604 4185 4.220163 ACTTGCTACTGTACTACACCCTTC 59.780 45.833 0.00 0.00 0.00 3.46
3605 4186 4.158015 ACTTGCTACTGTACTACACCCTT 58.842 43.478 0.00 0.00 0.00 3.95
3609 4190 3.427233 CCCGACTTGCTACTGTACTACAC 60.427 52.174 0.00 0.00 0.00 2.90
3610 4191 2.751259 CCCGACTTGCTACTGTACTACA 59.249 50.000 0.00 0.00 0.00 2.74
3614 4195 1.542915 TGTCCCGACTTGCTACTGTAC 59.457 52.381 0.00 0.00 0.00 2.90
3617 4198 1.204704 TCATGTCCCGACTTGCTACTG 59.795 52.381 5.98 0.00 36.69 2.74
3625 4206 0.895530 AATCACGTCATGTCCCGACT 59.104 50.000 8.68 0.00 0.00 4.18
3629 4210 7.730364 ATATAGAAAAATCACGTCATGTCCC 57.270 36.000 0.00 0.00 0.00 4.46
3633 4223 9.986833 TCACAAATATAGAAAAATCACGTCATG 57.013 29.630 0.00 0.00 0.00 3.07
3650 4240 9.793252 GTGAAATAAGAGCATGTTCACAAATAT 57.207 29.630 12.41 0.32 44.72 1.28
3656 4246 8.524870 AAATTGTGAAATAAGAGCATGTTCAC 57.475 30.769 12.41 12.98 45.28 3.18


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

AutoCloner maintained by Alex Coulton.