Multiple sequence alignment - TraesCS5A01G222300

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 TraesCS5A01G222300 chr5A 100.000 4995 0 0 1 4995 438411557 438406563 0.000000e+00 9225
1 TraesCS5A01G222300 chr5A 91.019 3318 242 14 710 3973 438357743 438354428 0.000000e+00 4425
2 TraesCS5A01G222300 chr5A 83.333 516 37 29 147 652 549422873 549423349 9.930000e-117 431
3 TraesCS5A01G222300 chr5A 87.701 374 27 7 208 562 549404024 549404397 7.730000e-113 418
4 TraesCS5A01G222300 chr5A 88.047 343 35 6 368 708 438411413 438411751 7.790000e-108 401
5 TraesCS5A01G222300 chr5A 92.233 206 14 2 4774 4979 573964481 573964684 1.760000e-74 291
6 TraesCS5A01G222300 chr5A 96.552 145 5 0 1 145 438411046 438411190 1.800000e-59 241
7 TraesCS5A01G222300 chr5A 98.347 121 2 0 25 145 549404317 549404197 3.920000e-51 213
8 TraesCS5A01G222300 chr5A 79.736 227 26 15 342 558 549382383 549382599 4.030000e-31 147
9 TraesCS5A01G222300 chr5B 90.028 3600 266 38 710 4246 395684083 395680514 0.000000e+00 4573
10 TraesCS5A01G222300 chr5B 92.920 1130 62 11 3858 4984 395706960 395705846 0.000000e+00 1628
11 TraesCS5A01G222300 chr5B 92.536 1045 78 0 816 1860 395709752 395708708 0.000000e+00 1498
12 TraesCS5A01G222300 chr5B 87.213 1001 78 9 1856 2839 395708225 395707258 0.000000e+00 1094
13 TraesCS5A01G222300 chr5B 93.729 303 15 1 3060 3358 395707262 395706960 7.630000e-123 451
14 TraesCS5A01G222300 chr5B 85.843 332 25 11 307 631 529229735 529230051 2.880000e-87 333
15 TraesCS5A01G222300 chr5B 82.203 354 34 12 147 494 529365263 529365593 1.370000e-70 278
16 TraesCS5A01G222300 chr5B 84.426 244 25 6 299 530 529384670 529384912 1.400000e-55 228
17 TraesCS5A01G222300 chr5B 94.483 145 8 0 1 145 529229933 529229789 1.810000e-54 224
18 TraesCS5A01G222300 chr5B 93.701 127 7 1 19 145 529365593 529365468 6.600000e-44 189
19 TraesCS5A01G222300 chr5B 88.393 112 8 3 149 260 529194233 529194339 4.060000e-26 130
20 TraesCS5A01G222300 chr5B 90.698 86 8 0 710 795 395710016 395709931 1.140000e-21 115
21 TraesCS5A01G222300 chr5D 89.973 3301 274 20 710 3973 337185972 337182692 0.000000e+00 4209
22 TraesCS5A01G222300 chr5D 94.060 1330 65 3 2538 3855 337216431 337215104 0.000000e+00 2006
23 TraesCS5A01G222300 chr5D 94.961 1151 46 1 710 1860 337218680 337217542 0.000000e+00 1794
24 TraesCS5A01G222300 chr5D 92.052 843 47 6 4150 4990 337207542 337206718 0.000000e+00 1168
25 TraesCS5A01G222300 chr5D 90.122 658 56 3 1856 2505 337217085 337216429 0.000000e+00 846
26 TraesCS5A01G222300 chr5D 95.333 300 13 1 3851 4150 337209677 337209379 4.520000e-130 475
27 TraesCS5A01G222300 chr5D 79.181 562 67 25 170 695 435614770 435615317 1.330000e-90 344
28 TraesCS5A01G222300 chr5D 82.250 400 35 13 182 563 435677335 435677716 3.750000e-81 313
29 TraesCS5A01G222300 chr5D 86.957 138 12 2 10 141 435615125 435614988 3.110000e-32 150
30 TraesCS5A01G222300 chr5D 87.850 107 11 1 1 107 435677673 435677569 1.890000e-24 124
31 TraesCS5A01G222300 chr5D 82.014 139 12 7 4026 4164 337182613 337182488 6.840000e-19 106
32 TraesCS5A01G222300 chr6B 87.432 366 44 2 4405 4769 154304134 154303770 2.150000e-113 420
33 TraesCS5A01G222300 chr6A 81.200 500 92 2 4267 4764 387070473 387070972 7.790000e-108 401
34 TraesCS5A01G222300 chr7B 87.622 307 36 2 4464 4769 71156797 71156492 6.150000e-94 355
35 TraesCS5A01G222300 chr7B 90.476 210 18 2 4770 4979 627032554 627032761 4.930000e-70 276
36 TraesCS5A01G222300 chr3B 94.118 204 9 2 4770 4973 227430931 227430731 1.750000e-79 307
37 TraesCS5A01G222300 chr1A 93.069 202 12 2 4768 4969 530234528 530234329 1.360000e-75 294
38 TraesCS5A01G222300 chr2D 91.748 206 16 1 4770 4975 420566219 420566015 8.180000e-73 285
39 TraesCS5A01G222300 chr2B 91.667 204 16 1 4770 4973 202377045 202376843 1.060000e-71 281
40 TraesCS5A01G222300 chr2B 91.667 204 16 1 4770 4973 202399244 202399042 1.060000e-71 281
41 TraesCS5A01G222300 chr7D 88.172 186 22 0 4584 4769 556244894 556244709 6.510000e-54 222
42 TraesCS5A01G222300 chr4D 73.559 503 116 14 4267 4759 89439608 89440103 5.140000e-40 176


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 TraesCS5A01G222300 chr5A 438406563 438411557 4994 True 9225.000000 9225 100.000000 1 4995 1 chr5A.!!$R2 4994
1 TraesCS5A01G222300 chr5A 438354428 438357743 3315 True 4425.000000 4425 91.019000 710 3973 1 chr5A.!!$R1 3263
2 TraesCS5A01G222300 chr5A 438411046 438411751 705 False 321.000000 401 92.299500 1 708 2 chr5A.!!$F5 707
3 TraesCS5A01G222300 chr5B 395680514 395684083 3569 True 4573.000000 4573 90.028000 710 4246 1 chr5B.!!$R1 3536
4 TraesCS5A01G222300 chr5B 395705846 395710016 4170 True 957.200000 1628 91.419200 710 4984 5 chr5B.!!$R4 4274
5 TraesCS5A01G222300 chr5D 337182488 337185972 3484 True 2157.500000 4209 85.993500 710 4164 2 chr5D.!!$R3 3454
6 TraesCS5A01G222300 chr5D 337215104 337218680 3576 True 1548.666667 2006 93.047667 710 3855 3 chr5D.!!$R5 3145
7 TraesCS5A01G222300 chr5D 337206718 337209677 2959 True 821.500000 1168 93.692500 3851 4990 2 chr5D.!!$R4 1139
8 TraesCS5A01G222300 chr5D 435614770 435615317 547 False 344.000000 344 79.181000 170 695 1 chr5D.!!$F1 525

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
157 158 0.033504 CGAGTGGTGTGCTACAAGGT 59.966 55.0 0.00 0.00 0.00 3.50 F
275 395 0.108329 TGTTGGCTAGCTAGAACCGC 60.108 55.0 25.15 9.17 0.00 5.68 F
2202 3036 0.106519 ACCTGCAGAACAACCAGCTT 60.107 50.0 17.39 0.00 0.00 3.74 F
2837 3917 0.038166 GTTGGTGCCTGGAAGATCCA 59.962 55.0 0.00 0.00 45.98 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2870 0.320771 CGTTGTTGGACAGGGAGAGG 60.321 60.000 0.00 0.00 0.00 3.69 R
2219 3053 1.928706 GCATTCGGCAAGGCGGTTTA 61.929 55.000 16.03 0.47 43.97 2.01 R
3625 4861 0.320374 ACACATCACCCATCGTCGTT 59.680 50.000 0.00 0.00 0.00 3.85 R
4476 7590 1.001924 CATCGATCACCAGAGGAGTCG 60.002 57.143 0.00 0.00 0.00 4.18 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
31 32 9.054922 TCATTTTGTTGAATTTCCAAAAGGATC 57.945 29.630 16.89 0.00 41.26 3.36
101 102 7.093858 ACCGAGGTTGATTAGATTAGTATAGGC 60.094 40.741 0.00 0.00 0.00 3.93
155 156 2.827604 CCGAGTGGTGTGCTACAAG 58.172 57.895 0.00 0.00 0.00 3.16
157 158 0.033504 CGAGTGGTGTGCTACAAGGT 59.966 55.000 0.00 0.00 0.00 3.50
158 159 1.797025 GAGTGGTGTGCTACAAGGTC 58.203 55.000 0.00 0.00 0.00 3.85
159 160 0.033504 AGTGGTGTGCTACAAGGTCG 59.966 55.000 0.00 0.00 0.00 4.79
160 161 0.249741 GTGGTGTGCTACAAGGTCGT 60.250 55.000 0.00 0.00 0.00 4.34
162 163 0.317479 GGTGTGCTACAAGGTCGTCT 59.683 55.000 0.00 0.00 0.00 4.18
163 164 1.270147 GGTGTGCTACAAGGTCGTCTT 60.270 52.381 0.00 0.00 35.79 3.01
164 165 2.480845 GTGTGCTACAAGGTCGTCTTT 58.519 47.619 0.00 0.00 32.41 2.52
165 166 2.221055 GTGTGCTACAAGGTCGTCTTTG 59.779 50.000 3.13 3.13 36.83 2.77
166 167 2.159014 TGTGCTACAAGGTCGTCTTTGT 60.159 45.455 13.88 13.88 44.12 2.83
167 168 2.870411 GTGCTACAAGGTCGTCTTTGTT 59.130 45.455 14.53 1.31 40.15 2.83
187 272 9.720769 CTTTGTTCTCTTTGGTTATTCTACCTA 57.279 33.333 0.00 0.00 39.04 3.08
189 274 7.618137 TGTTCTCTTTGGTTATTCTACCTACC 58.382 38.462 0.00 0.00 39.04 3.18
195 280 8.534496 TCTTTGGTTATTCTACCTACCTTGTAC 58.466 37.037 0.00 0.00 39.04 2.90
197 282 7.414222 TGGTTATTCTACCTACCTTGTACTG 57.586 40.000 0.00 0.00 39.04 2.74
198 283 6.955851 TGGTTATTCTACCTACCTTGTACTGT 59.044 38.462 0.00 0.00 39.04 3.55
199 284 8.115384 TGGTTATTCTACCTACCTTGTACTGTA 58.885 37.037 0.00 0.00 39.04 2.74
200 285 8.409371 GGTTATTCTACCTACCTTGTACTGTAC 58.591 40.741 10.98 10.98 35.23 2.90
230 346 3.129287 ACGCAAGAAATGAAATGGCTAGG 59.871 43.478 0.00 0.00 43.62 3.02
235 351 6.820152 GCAAGAAATGAAATGGCTAGGAAATT 59.180 34.615 0.00 0.00 0.00 1.82
252 372 5.358160 AGGAAATTCAAAGCCGGAGAATAAG 59.642 40.000 5.05 0.00 32.11 1.73
254 374 5.567138 AATTCAAAGCCGGAGAATAAGTG 57.433 39.130 5.05 0.00 32.11 3.16
255 375 3.695830 TCAAAGCCGGAGAATAAGTGT 57.304 42.857 5.05 0.00 0.00 3.55
256 376 4.015872 TCAAAGCCGGAGAATAAGTGTT 57.984 40.909 5.05 0.00 0.00 3.32
258 378 3.418684 AAGCCGGAGAATAAGTGTTGT 57.581 42.857 5.05 0.00 0.00 3.32
259 379 3.418684 AGCCGGAGAATAAGTGTTGTT 57.581 42.857 5.05 0.00 0.00 2.83
260 380 3.074412 AGCCGGAGAATAAGTGTTGTTG 58.926 45.455 5.05 0.00 0.00 3.33
261 381 2.161609 GCCGGAGAATAAGTGTTGTTGG 59.838 50.000 5.05 0.00 0.00 3.77
263 383 3.074412 CGGAGAATAAGTGTTGTTGGCT 58.926 45.455 0.00 0.00 0.00 4.75
265 385 4.330074 CGGAGAATAAGTGTTGTTGGCTAG 59.670 45.833 0.00 0.00 0.00 3.42
266 386 4.095036 GGAGAATAAGTGTTGTTGGCTAGC 59.905 45.833 6.04 6.04 0.00 3.42
267 387 4.911390 AGAATAAGTGTTGTTGGCTAGCT 58.089 39.130 15.72 0.00 0.00 3.32
268 388 6.049955 AGAATAAGTGTTGTTGGCTAGCTA 57.950 37.500 15.72 5.44 0.00 3.32
271 391 4.351874 AAGTGTTGTTGGCTAGCTAGAA 57.648 40.909 25.15 7.87 0.00 2.10
273 393 2.742589 GTGTTGTTGGCTAGCTAGAACC 59.257 50.000 25.15 16.68 0.00 3.62
274 394 2.000447 GTTGTTGGCTAGCTAGAACCG 59.000 52.381 25.15 0.00 0.00 4.44
275 395 0.108329 TGTTGGCTAGCTAGAACCGC 60.108 55.000 25.15 9.17 0.00 5.68
277 397 0.175760 TTGGCTAGCTAGAACCGCTG 59.824 55.000 25.15 0.00 38.38 5.18
279 399 1.068250 GCTAGCTAGAACCGCTGGG 59.932 63.158 25.15 0.00 38.38 4.45
288 408 3.706373 ACCGCTGGGTCGCTGATT 61.706 61.111 0.00 0.00 46.01 2.57
289 409 3.197790 CCGCTGGGTCGCTGATTG 61.198 66.667 0.00 0.00 0.00 2.67
290 410 2.434884 CGCTGGGTCGCTGATTGT 60.435 61.111 0.00 0.00 0.00 2.71
291 411 2.034879 CGCTGGGTCGCTGATTGTT 61.035 57.895 0.00 0.00 0.00 2.83
292 412 1.503542 GCTGGGTCGCTGATTGTTG 59.496 57.895 0.00 0.00 0.00 3.33
293 413 1.503542 CTGGGTCGCTGATTGTTGC 59.496 57.895 0.00 0.00 0.00 4.17
294 414 0.957395 CTGGGTCGCTGATTGTTGCT 60.957 55.000 0.00 0.00 0.00 3.91
295 415 0.955428 TGGGTCGCTGATTGTTGCTC 60.955 55.000 0.00 0.00 0.00 4.26
296 416 1.648467 GGGTCGCTGATTGTTGCTCC 61.648 60.000 0.00 0.00 0.00 4.70
297 417 1.648467 GGTCGCTGATTGTTGCTCCC 61.648 60.000 0.00 0.00 0.00 4.30
298 418 1.377202 TCGCTGATTGTTGCTCCCC 60.377 57.895 0.00 0.00 0.00 4.81
299 419 2.753966 CGCTGATTGTTGCTCCCCG 61.754 63.158 0.00 0.00 0.00 5.73
300 420 2.409870 GCTGATTGTTGCTCCCCGG 61.410 63.158 0.00 0.00 0.00 5.73
301 421 2.361104 TGATTGTTGCTCCCCGGC 60.361 61.111 0.00 0.00 0.00 6.13
302 422 3.508840 GATTGTTGCTCCCCGGCG 61.509 66.667 0.00 0.00 34.52 6.46
327 447 3.809423 GGGTTCCGAAGCCGAATC 58.191 61.111 13.45 0.00 39.57 2.52
328 448 1.818363 GGGTTCCGAAGCCGAATCC 60.818 63.158 13.45 0.00 39.57 3.01
329 449 2.171725 GGTTCCGAAGCCGAATCCG 61.172 63.158 0.00 0.00 38.22 4.18
330 450 2.510691 TTCCGAAGCCGAATCCGC 60.511 61.111 0.00 0.00 38.22 5.54
331 451 4.865761 TCCGAAGCCGAATCCGCG 62.866 66.667 0.00 0.00 38.22 6.46
332 452 4.865761 CCGAAGCCGAATCCGCGA 62.866 66.667 8.23 0.00 38.22 5.87
333 453 3.617538 CGAAGCCGAATCCGCGAC 61.618 66.667 8.23 0.00 38.22 5.19
334 454 3.617538 GAAGCCGAATCCGCGACG 61.618 66.667 8.23 7.85 0.00 5.12
335 455 4.430765 AAGCCGAATCCGCGACGT 62.431 61.111 8.23 0.00 0.00 4.34
336 456 4.849329 AGCCGAATCCGCGACGTC 62.849 66.667 8.23 5.18 0.00 4.34
357 477 4.267503 GTCGCCGGTCGGGATCTC 62.268 72.222 16.35 0.00 38.47 2.75
358 478 4.807631 TCGCCGGTCGGGATCTCA 62.808 66.667 16.35 0.00 38.47 3.27
359 479 3.606662 CGCCGGTCGGGATCTCAT 61.607 66.667 11.60 0.00 38.47 2.90
360 480 2.822399 GCCGGTCGGGATCTCATT 59.178 61.111 11.60 0.00 38.47 2.57
361 481 1.301009 GCCGGTCGGGATCTCATTC 60.301 63.158 11.60 0.00 38.47 2.67
362 482 1.749334 GCCGGTCGGGATCTCATTCT 61.749 60.000 11.60 0.00 38.47 2.40
363 483 0.753262 CCGGTCGGGATCTCATTCTT 59.247 55.000 0.74 0.00 38.47 2.52
364 484 1.539065 CCGGTCGGGATCTCATTCTTG 60.539 57.143 0.74 0.00 38.47 3.02
365 485 1.587547 GGTCGGGATCTCATTCTTGC 58.412 55.000 0.00 0.00 0.00 4.01
366 486 1.139853 GGTCGGGATCTCATTCTTGCT 59.860 52.381 0.00 0.00 0.00 3.91
381 501 3.371063 GCTCCACTCGGTCGGTCA 61.371 66.667 0.00 0.00 0.00 4.02
410 530 0.259938 GGATTCTTCCAGCCCACCAT 59.740 55.000 0.00 0.00 42.12 3.55
466 586 3.190118 ACGAAGGTTACGTCAGGACTAAG 59.810 47.826 0.00 0.00 39.87 2.18
480 600 4.816385 CAGGACTAAGACAAAAGTCTTGCA 59.184 41.667 18.28 1.79 41.17 4.08
522 642 0.322816 ATGACCCTGCATTCGCTGTT 60.323 50.000 0.00 0.00 39.64 3.16
538 658 2.668834 GCTGTTAGTCAGTGAGTCGGTC 60.669 54.545 3.04 0.00 45.23 4.79
563 683 4.469945 TCTCTGATTTAACCAACCGATCCT 59.530 41.667 0.00 0.00 0.00 3.24
576 720 5.356751 CCAACCGATCCTTAATTCAATGACA 59.643 40.000 0.00 0.00 0.00 3.58
578 722 7.228507 CCAACCGATCCTTAATTCAATGACATA 59.771 37.037 0.00 0.00 0.00 2.29
579 723 7.730364 ACCGATCCTTAATTCAATGACATAC 57.270 36.000 0.00 0.00 0.00 2.39
580 724 6.423905 ACCGATCCTTAATTCAATGACATACG 59.576 38.462 0.00 0.00 0.00 3.06
581 725 6.645003 CCGATCCTTAATTCAATGACATACGA 59.355 38.462 0.00 0.00 0.00 3.43
582 726 7.331934 CCGATCCTTAATTCAATGACATACGAT 59.668 37.037 0.00 0.00 0.00 3.73
583 727 9.353999 CGATCCTTAATTCAATGACATACGATA 57.646 33.333 0.00 0.00 0.00 2.92
591 735 9.811655 AATTCAATGACATACGATATTTAAGCG 57.188 29.630 0.00 0.00 0.00 4.68
592 736 6.817396 TCAATGACATACGATATTTAAGCGC 58.183 36.000 0.00 0.00 0.00 5.92
593 737 6.645003 TCAATGACATACGATATTTAAGCGCT 59.355 34.615 2.64 2.64 0.00 5.92
594 738 5.822584 TGACATACGATATTTAAGCGCTG 57.177 39.130 12.58 0.00 0.00 5.18
595 739 4.684242 TGACATACGATATTTAAGCGCTGG 59.316 41.667 12.58 0.00 0.00 4.85
596 740 3.432252 ACATACGATATTTAAGCGCTGGC 59.568 43.478 12.58 0.00 40.37 4.85
597 741 1.226746 ACGATATTTAAGCGCTGGCC 58.773 50.000 12.58 0.00 41.24 5.36
598 742 0.163788 CGATATTTAAGCGCTGGCCG 59.836 55.000 12.58 4.39 41.24 6.13
599 743 0.517316 GATATTTAAGCGCTGGCCGG 59.483 55.000 12.58 7.41 41.24 6.13
600 744 1.515521 ATATTTAAGCGCTGGCCGGC 61.516 55.000 27.67 27.67 41.24 6.13
627 771 1.838073 AAGGGACGGGCGATCAAGTT 61.838 55.000 0.00 0.00 0.00 2.66
633 777 1.737793 ACGGGCGATCAAGTTGATTTC 59.262 47.619 19.19 13.23 37.20 2.17
637 781 1.852077 GCGATCAAGTTGATTTCGCCG 60.852 52.381 30.30 23.27 44.48 6.46
647 792 3.310860 ATTTCGCCGGCTCGACCTT 62.311 57.895 26.68 0.00 38.30 3.50
659 804 3.315470 GGCTCGACCTTTAATGGATTTCC 59.685 47.826 14.04 4.99 34.51 3.13
675 820 2.099141 TTCCTCTTCGATTGCAGGTG 57.901 50.000 0.00 0.00 0.00 4.00
708 853 2.777305 GCGTTGCAAGCATTTGTTTTTG 59.223 40.909 0.00 0.00 36.65 2.44
738 883 1.536922 CGTCACCTCATTCTCCATCCG 60.537 57.143 0.00 0.00 0.00 4.18
811 1129 6.809630 TTCTGATCCATCTCTAGTACATCG 57.190 41.667 0.00 0.00 0.00 3.84
812 1130 6.115448 TCTGATCCATCTCTAGTACATCGA 57.885 41.667 0.00 0.00 0.00 3.59
813 1131 6.169800 TCTGATCCATCTCTAGTACATCGAG 58.830 44.000 0.00 0.00 0.00 4.04
814 1132 5.249420 TGATCCATCTCTAGTACATCGAGG 58.751 45.833 0.00 0.00 0.00 4.63
815 1133 4.708576 TCCATCTCTAGTACATCGAGGT 57.291 45.455 8.21 8.21 0.00 3.85
816 1134 4.643463 TCCATCTCTAGTACATCGAGGTC 58.357 47.826 5.75 0.00 0.00 3.85
953 1275 4.424711 GGCTCCCATGGCCGTCAA 62.425 66.667 6.09 0.00 40.19 3.18
987 1327 1.079256 CCTCCTCCTCCACCTCACA 59.921 63.158 0.00 0.00 0.00 3.58
1104 1447 1.298157 CGCTCCTGGCATTGAAACGA 61.298 55.000 0.00 0.00 41.91 3.85
1418 1761 0.614415 CTGTCCCTCTCTGAGCTGGT 60.614 60.000 12.98 0.00 0.00 4.00
1435 1778 2.040412 CTGGTAAGCTTGGGTTTCCTCT 59.960 50.000 9.86 0.00 32.93 3.69
1436 1779 2.445525 TGGTAAGCTTGGGTTTCCTCTT 59.554 45.455 9.86 0.00 32.93 2.85
1496 1839 3.777106 TCTCTTCAAGAACTGCACCAT 57.223 42.857 0.00 0.00 0.00 3.55
1501 1844 5.620206 TCTTCAAGAACTGCACCATTCTAA 58.380 37.500 4.07 0.00 34.01 2.10
1504 1847 4.756642 TCAAGAACTGCACCATTCTAAGTG 59.243 41.667 4.07 0.00 34.01 3.16
1534 1877 1.202486 TCGGCAACAACGATCTATCCC 60.202 52.381 0.00 0.00 35.12 3.85
1608 1951 3.404899 CAACAGGCTAACCGGAAAACTA 58.595 45.455 9.46 0.00 42.76 2.24
1893 2723 0.184692 TGCTCCCACCAAACATGTCA 59.815 50.000 0.00 0.00 0.00 3.58
1964 2794 5.239306 ACATCGGCGAAATGATAAACATCAT 59.761 36.000 15.93 0.00 42.62 2.45
1965 2795 5.094429 TCGGCGAAATGATAAACATCATG 57.906 39.130 7.35 0.00 40.81 3.07
2006 2836 1.534235 AGCTGAACGGGACAGTCCT 60.534 57.895 19.57 0.00 36.57 3.85
2060 2890 0.320771 CTCTCCCTGTCCAACAACGG 60.321 60.000 0.00 0.00 0.00 4.44
2202 3036 0.106519 ACCTGCAGAACAACCAGCTT 60.107 50.000 17.39 0.00 0.00 3.74
2321 3163 5.133221 GGTCTCTGGCACCAACATTATATT 58.867 41.667 0.00 0.00 33.63 1.28
2325 3167 6.767902 TCTCTGGCACCAACATTATATTTCTC 59.232 38.462 0.00 0.00 0.00 2.87
2334 3176 7.888021 ACCAACATTATATTTCTCAACCTGTCA 59.112 33.333 0.00 0.00 0.00 3.58
2421 3263 2.421388 CCTGTCCTGGAACAACTTCACA 60.421 50.000 0.00 0.00 38.70 3.58
2433 3275 1.261480 ACTTCACAGGCACGATCTCT 58.739 50.000 0.00 0.00 0.00 3.10
2505 3347 3.066190 CTCACCGGCGTCCTACCA 61.066 66.667 6.01 0.00 0.00 3.25
2526 3368 0.109226 CGTCCTTCGACCTCCTCAAC 60.109 60.000 0.00 0.00 42.86 3.18
2532 3374 1.213013 CGACCTCCTCAACGACCTG 59.787 63.158 0.00 0.00 0.00 4.00
2547 3389 2.546373 CGACCTGAAAAACCTGGACGTA 60.546 50.000 0.00 0.00 38.03 3.57
2551 3393 3.007635 CTGAAAAACCTGGACGTATCCC 58.992 50.000 0.00 0.00 45.59 3.85
2564 3406 1.553248 CGTATCCCACAACTCCCTGAA 59.447 52.381 0.00 0.00 0.00 3.02
2589 3431 1.003580 GAGATCCCTGCAAACCTGACA 59.996 52.381 0.00 0.00 0.00 3.58
2820 3675 1.741770 GACAATCCTCTGCGCGGTT 60.742 57.895 17.37 0.00 0.00 4.44
2837 3917 0.038166 GTTGGTGCCTGGAAGATCCA 59.962 55.000 0.00 0.00 45.98 3.41
2853 3933 1.289160 TCCAGGATTGGTTAGCTGCT 58.711 50.000 7.57 7.57 45.26 4.24
2854 3934 1.065199 TCCAGGATTGGTTAGCTGCTG 60.065 52.381 13.43 0.00 45.26 4.41
2858 3938 1.167851 GATTGGTTAGCTGCTGTGCA 58.832 50.000 13.43 0.00 36.92 4.57
2904 3984 2.435059 GGAGGCTTGTCGCTGGTC 60.435 66.667 0.00 0.00 39.13 4.02
2913 3993 3.525537 CTTGTCGCTGGTCATGAAGTAT 58.474 45.455 0.00 0.00 0.00 2.12
2932 4012 1.031571 TAAGTACCCGCGGATCACGT 61.032 55.000 30.73 18.38 46.52 4.49
2937 4017 2.182284 CCGCGGATCACGTACCAA 59.818 61.111 24.07 0.00 46.52 3.67
2955 4035 0.468226 AAGAGTTGGTTGAGGCGACA 59.532 50.000 0.00 0.00 0.00 4.35
2956 4036 0.249911 AGAGTTGGTTGAGGCGACAC 60.250 55.000 0.00 0.00 0.00 3.67
2964 4044 0.468226 TTGAGGCGACACAGGAGTTT 59.532 50.000 0.00 0.00 30.79 2.66
2966 4046 1.689813 TGAGGCGACACAGGAGTTTAA 59.310 47.619 0.00 0.00 0.00 1.52
2967 4047 2.301870 TGAGGCGACACAGGAGTTTAAT 59.698 45.455 0.00 0.00 0.00 1.40
3077 4157 1.479709 CTCCAGTCAGGGAACTCGAT 58.520 55.000 0.00 0.00 40.21 3.59
3092 4172 0.897621 TCGATCAAGAGCTTCAGCCA 59.102 50.000 0.00 0.00 43.38 4.75
3147 4227 0.249615 ACCTCATGCGGATCATCACG 60.250 55.000 9.17 0.00 31.79 4.35
3516 4745 0.951558 CAGGTAAACCACACACTGCC 59.048 55.000 1.26 0.00 38.89 4.85
3517 4746 0.548989 AGGTAAACCACACACTGCCA 59.451 50.000 1.26 0.00 38.89 4.92
3625 4861 3.766691 GGCTACGGCTCGAACCCA 61.767 66.667 0.00 0.00 38.73 4.51
3882 5118 0.908198 ATTCTCTGCACCCAGGAGAC 59.092 55.000 2.30 0.00 40.06 3.36
3987 5260 7.115520 CGCTACATTCGAAGATATTGATGACTT 59.884 37.037 3.35 0.00 35.04 3.01
4056 5329 3.484649 GGATACGTTGTGTATGCGTAGTG 59.515 47.826 0.00 0.00 43.87 2.74
4061 5334 2.921754 GTTGTGTATGCGTAGTGAGGAC 59.078 50.000 0.00 0.00 0.00 3.85
4068 5341 4.737855 ATGCGTAGTGAGGACTTTATGT 57.262 40.909 0.00 0.00 33.21 2.29
4080 5353 4.039973 AGGACTTTATGTGGTTCTGAACGA 59.960 41.667 13.89 7.79 0.00 3.85
4178 7291 6.187682 AGCTTTGTACATAGGCTTGGTTATT 58.812 36.000 14.16 0.00 0.00 1.40
4179 7292 7.343357 AGCTTTGTACATAGGCTTGGTTATTA 58.657 34.615 14.16 0.00 0.00 0.98
4298 7411 3.771160 CCCTTGCGGCGACTAGGT 61.771 66.667 12.98 0.00 0.00 3.08
4314 7427 0.328592 AGGTCTAGGCGACTCTGACA 59.671 55.000 21.09 0.00 42.36 3.58
4319 7432 4.427661 GGCGACTCTGACAGCGCT 62.428 66.667 20.36 2.64 43.21 5.92
4439 7553 2.203070 ATCGGGCGCAGATGGAAC 60.203 61.111 10.83 0.00 0.00 3.62
4440 7554 3.757248 ATCGGGCGCAGATGGAACC 62.757 63.158 10.83 0.00 0.00 3.62
4466 7580 0.382158 CGGCAAGCTCGACATCTCTA 59.618 55.000 0.00 0.00 0.00 2.43
4476 7590 2.952978 TCGACATCTCTAAAGAGGAGGC 59.047 50.000 7.14 1.94 42.30 4.70
4549 7663 2.436115 GCGGGCAAGGTCCTGTAC 60.436 66.667 0.00 0.00 34.92 2.90
4550 7664 3.065306 CGGGCAAGGTCCTGTACA 58.935 61.111 0.00 0.00 0.00 2.90
4634 7748 2.035321 GGCTTGGTTTTTCGTCCATTGA 59.965 45.455 0.00 0.00 33.50 2.57
4649 7763 3.330405 TCCATTGAGGGAGAACATGTTCA 59.670 43.478 33.92 15.36 38.90 3.18
4651 7765 5.191522 TCCATTGAGGGAGAACATGTTCATA 59.808 40.000 33.92 14.46 38.90 2.15
4653 7767 5.762179 TTGAGGGAGAACATGTTCATAGT 57.238 39.130 33.92 17.83 41.84 2.12
4682 7796 4.547671 TGAATCTAAGAGAGACCGGGATT 58.452 43.478 6.32 0.94 36.87 3.01
4684 7798 3.664551 TCTAAGAGAGACCGGGATTGA 57.335 47.619 6.32 0.00 0.00 2.57
4759 7873 1.913778 TTGAATCACACATGCAGCCT 58.086 45.000 0.00 0.00 0.00 4.58
4764 7878 2.360350 ACACATGCAGCCTTCGGG 60.360 61.111 0.00 0.00 38.37 5.14
4862 7978 5.777850 GGTTGGTTACCATGTTTACTTGT 57.222 39.130 4.38 0.00 46.92 3.16
4883 7999 3.938963 GTCAACCTCACAAGAAGTTGTCA 59.061 43.478 6.80 0.00 43.88 3.58
4908 8024 9.733219 CAAATTTTTGGCAACTTTTGATATTGT 57.267 25.926 17.33 0.00 34.59 2.71
4984 8100 6.583912 TTATCGTCTCAAATTTGATCGGTC 57.416 37.500 28.49 14.90 36.46 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.970003 CAGGACTAAAACAAAAGTCTTGCG 59.030 41.667 2.30 0.00 41.17 4.85
45 46 3.569701 ACGAAGGTTACGTCAGGACTAAA 59.430 43.478 0.00 0.00 39.87 1.85
101 102 0.394899 GGATTCTTCCAGCCCACCAG 60.395 60.000 0.00 0.00 42.12 4.00
130 131 3.667282 ACACCACTCGGTCGGTCG 61.667 66.667 0.00 0.00 44.71 4.79
145 146 2.159014 ACAAAGACGACCTTGTAGCACA 60.159 45.455 0.00 0.00 34.79 4.57
147 148 2.902705 ACAAAGACGACCTTGTAGCA 57.097 45.000 0.00 0.00 34.79 3.49
148 149 3.391049 AGAACAAAGACGACCTTGTAGC 58.609 45.455 2.39 0.00 34.79 3.58
149 150 4.872664 AGAGAACAAAGACGACCTTGTAG 58.127 43.478 2.39 0.00 34.79 2.74
150 151 4.931661 AGAGAACAAAGACGACCTTGTA 57.068 40.909 2.39 0.00 34.79 2.41
152 153 4.260784 CCAAAGAGAACAAAGACGACCTTG 60.261 45.833 0.00 0.00 34.79 3.61
153 154 3.877508 CCAAAGAGAACAAAGACGACCTT 59.122 43.478 0.00 0.00 36.47 3.50
154 155 3.118371 ACCAAAGAGAACAAAGACGACCT 60.118 43.478 0.00 0.00 0.00 3.85
155 156 3.203716 ACCAAAGAGAACAAAGACGACC 58.796 45.455 0.00 0.00 0.00 4.79
157 158 6.990349 AGAATAACCAAAGAGAACAAAGACGA 59.010 34.615 0.00 0.00 0.00 4.20
158 159 7.190920 AGAATAACCAAAGAGAACAAAGACG 57.809 36.000 0.00 0.00 0.00 4.18
159 160 8.504815 GGTAGAATAACCAAAGAGAACAAAGAC 58.495 37.037 0.00 0.00 39.50 3.01
160 161 8.437575 AGGTAGAATAACCAAAGAGAACAAAGA 58.562 33.333 0.00 0.00 42.40 2.52
162 163 9.498176 GTAGGTAGAATAACCAAAGAGAACAAA 57.502 33.333 0.00 0.00 42.40 2.83
163 164 8.098912 GGTAGGTAGAATAACCAAAGAGAACAA 58.901 37.037 0.00 0.00 42.40 2.83
164 165 7.456902 AGGTAGGTAGAATAACCAAAGAGAACA 59.543 37.037 0.00 0.00 42.40 3.18
165 166 7.849160 AGGTAGGTAGAATAACCAAAGAGAAC 58.151 38.462 0.00 0.00 42.40 3.01
166 167 8.319146 CAAGGTAGGTAGAATAACCAAAGAGAA 58.681 37.037 0.00 0.00 42.40 2.87
167 168 7.456902 ACAAGGTAGGTAGAATAACCAAAGAGA 59.543 37.037 0.00 0.00 42.40 3.10
213 329 7.722949 TGAATTTCCTAGCCATTTCATTTCT 57.277 32.000 0.00 0.00 0.00 2.52
218 334 5.723295 GCTTTGAATTTCCTAGCCATTTCA 58.277 37.500 8.06 0.00 0.00 2.69
230 346 6.030228 CACTTATTCTCCGGCTTTGAATTTC 58.970 40.000 13.84 0.00 33.24 2.17
235 351 3.695830 ACACTTATTCTCCGGCTTTGA 57.304 42.857 0.00 0.00 0.00 2.69
252 372 2.742589 GGTTCTAGCTAGCCAACAACAC 59.257 50.000 20.79 9.72 0.00 3.32
254 374 2.000447 CGGTTCTAGCTAGCCAACAAC 59.000 52.381 20.79 16.52 0.00 3.32
255 375 1.674817 GCGGTTCTAGCTAGCCAACAA 60.675 52.381 20.79 7.48 0.00 2.83
256 376 0.108329 GCGGTTCTAGCTAGCCAACA 60.108 55.000 20.79 2.01 0.00 3.33
258 378 0.175760 CAGCGGTTCTAGCTAGCCAA 59.824 55.000 16.35 3.25 44.06 4.52
259 379 1.676678 CCAGCGGTTCTAGCTAGCCA 61.677 60.000 16.35 0.00 44.06 4.75
260 380 1.068250 CCAGCGGTTCTAGCTAGCC 59.932 63.158 16.35 11.26 44.06 3.93
261 381 1.068250 CCCAGCGGTTCTAGCTAGC 59.932 63.158 16.35 6.62 44.06 3.42
263 383 1.381928 CGACCCAGCGGTTCTAGCTA 61.382 60.000 0.00 0.00 44.88 3.32
265 385 2.202756 CGACCCAGCGGTTCTAGC 60.203 66.667 0.00 0.00 44.88 3.42
266 386 2.202756 GCGACCCAGCGGTTCTAG 60.203 66.667 0.00 0.00 44.88 2.43
267 387 2.678934 AGCGACCCAGCGGTTCTA 60.679 61.111 0.00 0.00 44.88 2.10
268 388 4.379243 CAGCGACCCAGCGGTTCT 62.379 66.667 0.00 0.00 44.88 3.01
273 393 2.034879 AACAATCAGCGACCCAGCG 61.035 57.895 0.00 0.00 43.00 5.18
274 394 1.503542 CAACAATCAGCGACCCAGC 59.496 57.895 0.00 0.00 37.41 4.85
275 395 0.957395 AGCAACAATCAGCGACCCAG 60.957 55.000 0.00 0.00 35.48 4.45
277 397 1.648467 GGAGCAACAATCAGCGACCC 61.648 60.000 0.00 0.00 35.48 4.46
279 399 1.648467 GGGGAGCAACAATCAGCGAC 61.648 60.000 0.00 0.00 35.48 5.19
280 400 1.377202 GGGGAGCAACAATCAGCGA 60.377 57.895 0.00 0.00 35.48 4.93
282 402 2.409870 CCGGGGAGCAACAATCAGC 61.410 63.158 0.00 0.00 0.00 4.26
283 403 2.409870 GCCGGGGAGCAACAATCAG 61.410 63.158 2.18 0.00 0.00 2.90
284 404 2.361104 GCCGGGGAGCAACAATCA 60.361 61.111 2.18 0.00 0.00 2.57
285 405 3.508840 CGCCGGGGAGCAACAATC 61.509 66.667 14.46 0.00 0.00 2.67
310 430 1.818363 GGATTCGGCTTCGGAACCC 60.818 63.158 0.00 0.00 34.13 4.11
311 431 2.171725 CGGATTCGGCTTCGGAACC 61.172 63.158 0.00 0.00 34.13 3.62
312 432 2.810012 GCGGATTCGGCTTCGGAAC 61.810 63.158 8.81 0.00 36.79 3.62
313 433 2.510691 GCGGATTCGGCTTCGGAA 60.511 61.111 8.81 0.00 36.79 4.30
314 434 4.865761 CGCGGATTCGGCTTCGGA 62.866 66.667 13.47 0.00 36.79 4.55
315 435 4.865761 TCGCGGATTCGGCTTCGG 62.866 66.667 6.13 0.00 36.79 4.30
316 436 3.617538 GTCGCGGATTCGGCTTCG 61.618 66.667 6.13 0.00 36.79 3.79
317 437 3.617538 CGTCGCGGATTCGGCTTC 61.618 66.667 6.13 6.17 36.79 3.86
318 438 4.430765 ACGTCGCGGATTCGGCTT 62.431 61.111 6.13 0.00 36.79 4.35
319 439 4.849329 GACGTCGCGGATTCGGCT 62.849 66.667 6.13 0.00 36.79 5.52
340 460 4.267503 GAGATCCCGACCGGCGAC 62.268 72.222 17.96 0.46 44.57 5.19
341 461 4.807631 TGAGATCCCGACCGGCGA 62.808 66.667 17.96 2.71 44.57 5.54
342 462 3.151958 AATGAGATCCCGACCGGCG 62.152 63.158 0.00 6.30 40.47 6.46
343 463 1.301009 GAATGAGATCCCGACCGGC 60.301 63.158 0.00 0.00 0.00 6.13
344 464 0.753262 AAGAATGAGATCCCGACCGG 59.247 55.000 0.00 0.00 0.00 5.28
345 465 1.858091 CAAGAATGAGATCCCGACCG 58.142 55.000 0.00 0.00 0.00 4.79
346 466 1.139853 AGCAAGAATGAGATCCCGACC 59.860 52.381 0.00 0.00 0.00 4.79
347 467 2.478831 GAGCAAGAATGAGATCCCGAC 58.521 52.381 0.00 0.00 0.00 4.79
348 468 1.414181 GGAGCAAGAATGAGATCCCGA 59.586 52.381 0.00 0.00 0.00 5.14
349 469 1.139654 TGGAGCAAGAATGAGATCCCG 59.860 52.381 0.00 0.00 0.00 5.14
350 470 2.172293 AGTGGAGCAAGAATGAGATCCC 59.828 50.000 0.00 0.00 0.00 3.85
351 471 3.465871 GAGTGGAGCAAGAATGAGATCC 58.534 50.000 0.00 0.00 0.00 3.36
352 472 3.122297 CGAGTGGAGCAAGAATGAGATC 58.878 50.000 0.00 0.00 0.00 2.75
353 473 2.158986 CCGAGTGGAGCAAGAATGAGAT 60.159 50.000 0.00 0.00 37.49 2.75
354 474 1.205655 CCGAGTGGAGCAAGAATGAGA 59.794 52.381 0.00 0.00 37.49 3.27
355 475 1.066573 ACCGAGTGGAGCAAGAATGAG 60.067 52.381 0.00 0.00 39.21 2.90
356 476 0.976641 ACCGAGTGGAGCAAGAATGA 59.023 50.000 0.00 0.00 39.21 2.57
357 477 1.363744 GACCGAGTGGAGCAAGAATG 58.636 55.000 0.00 0.00 39.21 2.67
358 478 0.108615 CGACCGAGTGGAGCAAGAAT 60.109 55.000 0.00 0.00 39.21 2.40
359 479 1.289066 CGACCGAGTGGAGCAAGAA 59.711 57.895 0.00 0.00 39.21 2.52
360 480 2.636412 CCGACCGAGTGGAGCAAGA 61.636 63.158 0.00 0.00 39.21 3.02
361 481 2.125912 CCGACCGAGTGGAGCAAG 60.126 66.667 0.00 0.00 39.21 4.01
362 482 2.915659 ACCGACCGAGTGGAGCAA 60.916 61.111 0.00 0.00 39.21 3.91
363 483 3.371063 GACCGACCGAGTGGAGCA 61.371 66.667 0.00 0.00 39.21 4.26
364 484 2.615262 GATGACCGACCGAGTGGAGC 62.615 65.000 0.00 0.00 39.21 4.70
365 485 1.313091 TGATGACCGACCGAGTGGAG 61.313 60.000 0.00 0.00 39.21 3.86
366 486 0.896479 TTGATGACCGACCGAGTGGA 60.896 55.000 0.00 0.00 39.21 4.02
410 530 8.168725 ACCGAGGTTGATTAGATTAGTATAGGA 58.831 37.037 0.00 0.00 0.00 2.94
480 600 7.930865 TCATTTTGTCGAATTTCCAAAAGGATT 59.069 29.630 16.59 0.85 41.26 3.01
497 617 2.867429 CGAATGCAGGGTCATTTTGTC 58.133 47.619 0.00 0.00 36.85 3.18
522 642 1.001746 AGACGACCGACTCACTGACTA 59.998 52.381 0.00 0.00 0.00 2.59
538 658 3.581755 TCGGTTGGTTAAATCAGAGACG 58.418 45.455 0.00 0.00 0.00 4.18
576 720 3.000727 GGCCAGCGCTTAAATATCGTAT 58.999 45.455 7.50 0.00 34.44 3.06
578 722 1.226746 GGCCAGCGCTTAAATATCGT 58.773 50.000 7.50 0.00 34.44 3.73
579 723 0.163788 CGGCCAGCGCTTAAATATCG 59.836 55.000 7.50 1.11 34.44 2.92
580 724 0.517316 CCGGCCAGCGCTTAAATATC 59.483 55.000 7.50 0.00 34.44 1.63
581 725 1.515521 GCCGGCCAGCGCTTAAATAT 61.516 55.000 18.11 0.00 34.44 1.28
582 726 2.184167 GCCGGCCAGCGCTTAAATA 61.184 57.895 18.11 0.00 34.44 1.40
583 727 3.518068 GCCGGCCAGCGCTTAAAT 61.518 61.111 18.11 0.00 34.44 1.40
597 741 4.785453 GTCCCTTCTGGCTGGCCG 62.785 72.222 7.14 2.52 39.42 6.13
598 742 4.785453 CGTCCCTTCTGGCTGGCC 62.785 72.222 4.43 4.43 0.00 5.36
599 743 4.785453 CCGTCCCTTCTGGCTGGC 62.785 72.222 0.00 0.00 0.00 4.85
600 744 4.101448 CCCGTCCCTTCTGGCTGG 62.101 72.222 0.00 0.00 0.00 4.85
601 745 4.785453 GCCCGTCCCTTCTGGCTG 62.785 72.222 0.00 0.00 40.77 4.85
604 748 3.447025 GATCGCCCGTCCCTTCTGG 62.447 68.421 0.00 0.00 0.00 3.86
627 771 2.508439 GTCGAGCCGGCGAAATCA 60.508 61.111 23.20 0.00 42.55 2.57
633 777 1.520787 ATTAAAGGTCGAGCCGGCG 60.521 57.895 23.20 8.11 43.70 6.46
637 781 3.315470 GGAAATCCATTAAAGGTCGAGCC 59.685 47.826 11.73 3.31 35.64 4.70
647 792 5.885352 TGCAATCGAAGAGGAAATCCATTAA 59.115 36.000 1.67 0.00 43.63 1.40
659 804 2.093216 GCCACCTGCAATCGAAGAG 58.907 57.895 0.00 0.00 39.56 2.85
738 883 1.320507 GACTGGGGACGAGGATAGAC 58.679 60.000 0.00 0.00 0.00 2.59
791 936 5.221945 ACCTCGATGTACTAGAGATGGATCA 60.222 44.000 12.24 0.00 34.13 2.92
813 1131 3.251487 GTGACTTCTCTATAGGCTCGACC 59.749 52.174 0.00 0.00 39.61 4.79
814 1132 3.251487 GGTGACTTCTCTATAGGCTCGAC 59.749 52.174 0.00 0.00 0.00 4.20
815 1133 3.478509 GGTGACTTCTCTATAGGCTCGA 58.521 50.000 0.00 0.00 0.00 4.04
816 1134 2.224549 CGGTGACTTCTCTATAGGCTCG 59.775 54.545 0.00 0.00 0.00 5.03
833 1151 2.279517 GCGGTAGCATCTCCGGTG 60.280 66.667 0.00 0.00 45.85 4.94
953 1275 4.537433 GGAGAATGGCCGCGAGCT 62.537 66.667 8.23 0.00 43.05 4.09
1071 1414 2.925170 AGCGTGGCCTTCTCCTGT 60.925 61.111 3.32 0.00 0.00 4.00
1095 1438 2.386661 AGGTGAGCGATCGTTTCAAT 57.613 45.000 20.70 12.70 0.00 2.57
1104 1447 2.125512 GACGGCAAGGTGAGCGAT 60.126 61.111 0.00 0.00 0.00 4.58
1157 1500 3.381983 TGAGGCCGCAGACATCGT 61.382 61.111 4.49 0.00 0.00 3.73
1400 1743 0.704664 TACCAGCTCAGAGAGGGACA 59.295 55.000 13.30 0.49 0.00 4.02
1418 1761 2.986728 AGGAAGAGGAAACCCAAGCTTA 59.013 45.455 0.00 0.00 0.00 3.09
1496 1839 2.030540 CCGAAGTCGACCACACTTAGAA 60.031 50.000 13.01 0.00 43.02 2.10
1501 1844 2.023414 TTGCCGAAGTCGACCACACT 62.023 55.000 13.01 0.00 43.02 3.55
1504 1847 1.155424 TTGTTGCCGAAGTCGACCAC 61.155 55.000 13.01 5.71 43.02 4.16
1534 1877 1.227380 CTTCCAGGGGAATCTCGCG 60.227 63.158 0.00 0.00 41.23 5.87
1570 1913 4.040461 CCTGTTGGAGTAGAGGTTGAGAAA 59.960 45.833 0.00 0.00 34.57 2.52
1572 1915 3.165875 CCTGTTGGAGTAGAGGTTGAGA 58.834 50.000 0.00 0.00 34.57 3.27
1608 1951 1.078426 GTTAGCGAGCCACCATGGT 60.078 57.895 13.00 13.00 40.46 3.55
1893 2723 0.764369 TGAGCTCCAGGTTGAGGTGT 60.764 55.000 12.15 0.00 42.81 4.16
1964 2794 1.348696 TGCTTGAGAGGTTCATCAGCA 59.651 47.619 0.71 0.71 43.78 4.41
1965 2795 2.105006 TGCTTGAGAGGTTCATCAGC 57.895 50.000 0.00 0.00 39.21 4.26
2006 2836 3.974835 AACGCGCAGATGGATGCCA 62.975 57.895 5.73 0.00 43.49 4.92
2040 2870 0.320771 CGTTGTTGGACAGGGAGAGG 60.321 60.000 0.00 0.00 0.00 3.69
2219 3053 1.928706 GCATTCGGCAAGGCGGTTTA 61.929 55.000 16.03 0.47 43.97 2.01
2241 3075 2.669569 TCAAGGTGGAGCAAGCGC 60.670 61.111 0.00 0.00 38.99 5.92
2293 3135 1.003118 GTTGGTGCCAGAGACCATGTA 59.997 52.381 0.00 0.00 43.13 2.29
2321 3163 2.026729 TGGTTGTGTGACAGGTTGAGAA 60.027 45.455 0.00 0.00 0.00 2.87
2325 3167 2.036958 TCTGGTTGTGTGACAGGTTG 57.963 50.000 0.00 0.00 33.19 3.77
2334 3176 2.301296 CTCACCTCTGATCTGGTTGTGT 59.699 50.000 12.86 0.00 33.75 3.72
2421 3263 1.954362 GCTGTGGAGAGATCGTGCCT 61.954 60.000 3.13 0.00 0.00 4.75
2526 3368 0.865769 CGTCCAGGTTTTTCAGGTCG 59.134 55.000 0.00 0.00 0.00 4.79
2547 3389 0.324943 CGTTCAGGGAGTTGTGGGAT 59.675 55.000 0.00 0.00 0.00 3.85
2551 3393 3.217242 CTCCGTTCAGGGAGTTGTG 57.783 57.895 7.31 0.00 46.97 3.33
2564 3406 0.250513 GTTTGCAGGGATCTCTCCGT 59.749 55.000 0.00 0.00 43.11 4.69
2589 3431 1.761784 TGTTTCAGGCTGGTGCATTTT 59.238 42.857 15.73 0.00 41.91 1.82
2654 3497 0.944311 GAAGTCTGCAAAGACGCCGA 60.944 55.000 0.00 0.00 43.15 5.54
2714 3557 3.872603 AGTTGCGCCTCACCACCA 61.873 61.111 4.18 0.00 0.00 4.17
2820 3675 4.248908 TGGATCTTCCAGGCACCA 57.751 55.556 0.00 0.00 42.67 4.17
2837 3917 1.952367 GCACAGCAGCTAACCAATCCT 60.952 52.381 0.00 0.00 0.00 3.24
2853 3933 2.497138 CTGAACATGTCTTCCTGCACA 58.503 47.619 0.00 0.00 0.00 4.57
2854 3934 1.808945 CCTGAACATGTCTTCCTGCAC 59.191 52.381 0.00 0.00 0.00 4.57
2858 3938 0.329596 GCCCCTGAACATGTCTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
2862 3942 1.918293 TCGGCCCCTGAACATGTCT 60.918 57.895 0.00 0.00 0.00 3.41
2894 3974 4.159693 ACTTATACTTCATGACCAGCGACA 59.840 41.667 0.00 0.00 0.00 4.35
2898 3978 5.298347 GGGTACTTATACTTCATGACCAGC 58.702 45.833 0.00 0.00 0.00 4.85
2900 3980 4.202182 GCGGGTACTTATACTTCATGACCA 60.202 45.833 0.00 0.00 0.00 4.02
2904 3984 3.005050 TCCGCGGGTACTTATACTTCATG 59.995 47.826 27.83 0.00 0.00 3.07
2913 3993 1.031571 ACGTGATCCGCGGGTACTTA 61.032 55.000 27.83 4.46 41.96 2.24
2937 4017 0.249911 GTGTCGCCTCAACCAACTCT 60.250 55.000 0.00 0.00 0.00 3.24
2955 4035 2.615493 CCGGTCTGCATTAAACTCCTGT 60.615 50.000 0.00 0.00 0.00 4.00
2956 4036 2.009774 CCGGTCTGCATTAAACTCCTG 58.990 52.381 0.00 0.00 0.00 3.86
2964 4044 3.399046 ACCAGCCGGTCTGCATTA 58.601 55.556 17.35 0.00 44.71 1.90
3031 4111 1.303236 CCTTCACGGCAACCATGGA 60.303 57.895 21.47 0.00 0.00 3.41
3077 4157 0.612229 CTCCTGGCTGAAGCTCTTGA 59.388 55.000 1.74 0.00 41.70 3.02
3092 4172 1.152030 TTCAGGACCTGGCACTCCT 60.152 57.895 21.56 3.51 37.38 3.69
3123 4203 1.326951 TGATCCGCATGAGGTTCCGA 61.327 55.000 19.99 3.84 30.80 4.55
3147 4227 4.175337 TCCGCCAGGCTGCATACC 62.175 66.667 10.54 0.00 37.47 2.73
3297 4381 2.043604 CTGGTGAGTGGTGGTGCAGA 62.044 60.000 0.00 0.00 0.00 4.26
3516 4745 7.693951 CGAGGATAGCTTGTGATTTAACTTTTG 59.306 37.037 0.00 0.00 0.00 2.44
3517 4746 7.390718 ACGAGGATAGCTTGTGATTTAACTTTT 59.609 33.333 0.00 0.00 0.00 2.27
3625 4861 0.320374 ACACATCACCCATCGTCGTT 59.680 50.000 0.00 0.00 0.00 3.85
3987 5260 3.661745 GCTTGCTACCGCTAAGCTA 57.338 52.632 0.00 0.00 42.11 3.32
4056 5329 4.389077 CGTTCAGAACCACATAAAGTCCTC 59.611 45.833 7.76 0.00 0.00 3.71
4061 5334 4.315803 ACCTCGTTCAGAACCACATAAAG 58.684 43.478 7.76 0.00 0.00 1.85
4068 5341 2.496070 CCATCTACCTCGTTCAGAACCA 59.504 50.000 7.76 0.00 0.00 3.67
4080 5353 6.841229 TGTGATATTCAGAAGACCATCTACCT 59.159 38.462 0.00 0.00 0.00 3.08
4214 7327 6.097356 CCGTCACACTAAGCTAATCAGTTAA 58.903 40.000 0.00 0.00 0.00 2.01
4215 7328 5.647589 CCGTCACACTAAGCTAATCAGTTA 58.352 41.667 0.00 0.00 0.00 2.24
4216 7329 4.495422 CCGTCACACTAAGCTAATCAGTT 58.505 43.478 0.00 0.00 0.00 3.16
4217 7330 3.676324 GCCGTCACACTAAGCTAATCAGT 60.676 47.826 0.00 0.00 0.00 3.41
4298 7411 1.369839 CGCTGTCAGAGTCGCCTAGA 61.370 60.000 3.32 0.00 0.00 2.43
4314 7427 1.007502 GATGAGATCTGCGAGCGCT 60.008 57.895 11.27 11.27 42.51 5.92
4347 7460 2.202878 CCATCGTCGCCGGAACAT 60.203 61.111 5.05 0.00 33.95 2.71
4422 7536 2.203070 GTTCCATCTGCGCCCGAT 60.203 61.111 4.18 3.89 0.00 4.18
4476 7590 1.001924 CATCGATCACCAGAGGAGTCG 60.002 57.143 0.00 0.00 0.00 4.18
4549 7663 6.590068 AGTCTGGATGTGGAATAGATTTCTG 58.410 40.000 0.00 0.00 0.00 3.02
4550 7664 6.821616 AGTCTGGATGTGGAATAGATTTCT 57.178 37.500 0.00 0.00 0.00 2.52
4634 7748 4.104086 TCCACTATGAACATGTTCTCCCT 58.896 43.478 32.57 19.42 40.14 4.20
4649 7763 8.691797 GTCTCTCTTAGATTCAAACTCCACTAT 58.308 37.037 0.00 0.00 36.36 2.12
4651 7765 6.071051 GGTCTCTCTTAGATTCAAACTCCACT 60.071 42.308 0.00 0.00 36.36 4.00
4653 7767 5.105716 CGGTCTCTCTTAGATTCAAACTCCA 60.106 44.000 0.00 0.00 36.36 3.86
4764 7878 3.002791 TCAAACCAATCATGCTCGAGTC 58.997 45.455 15.13 7.10 0.00 3.36
4883 7999 9.949174 GACAATATCAAAAGTTGCCAAAAATTT 57.051 25.926 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.