Multiple sequence alignment - TraesCS5D01G245700

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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 TraesCS5D01G245700 chr5D 100.000 3301 0 0 1 3301 353952833 353956133 0.000000e+00 6096.0
1 TraesCS5D01G245700 chr5D 89.109 1616 106 26 574 2143 388411377 388412968 0.000000e+00 1945.0
2 TraesCS5D01G245700 chr5D 89.483 1179 75 15 1015 2160 388380759 388381921 0.000000e+00 1445.0
3 TraesCS5D01G245700 chr5D 85.366 1353 107 27 748 2061 386958188 386959488 0.000000e+00 1317.0
4 TraesCS5D01G245700 chr5D 84.102 1409 105 41 795 2161 388591735 388593066 0.000000e+00 1251.0
5 TraesCS5D01G245700 chr5D 84.337 1328 130 23 774 2058 370777320 370778612 0.000000e+00 1229.0
6 TraesCS5D01G245700 chr5D 86.504 615 50 10 2691 3301 388382440 388383025 0.000000e+00 645.0
7 TraesCS5D01G245700 chr5D 92.857 350 19 6 2185 2532 388595966 388596311 1.370000e-138 503.0
8 TraesCS5D01G245700 chr5D 85.430 453 27 17 2691 3139 388596305 388596722 5.060000e-118 435.0
9 TraesCS5D01G245700 chr5D 84.100 478 38 18 2691 3167 353968308 353968748 8.470000e-116 427.0
10 TraesCS5D01G245700 chr5D 84.783 276 22 8 2191 2459 388382155 388382417 3.270000e-65 259.0
11 TraesCS5D01G245700 chr5D 93.396 106 3 2 2414 2519 353968204 353968305 1.590000e-33 154.0
12 TraesCS5D01G245700 chr5D 87.931 116 10 3 2180 2293 386959632 386959745 2.070000e-27 134.0
13 TraesCS5D01G245700 chr5D 86.301 73 7 3 929 999 300955683 300955754 3.530000e-10 76.8
14 TraesCS5D01G245700 chr5D 97.561 41 1 0 393 433 388411161 388411201 1.640000e-08 71.3
15 TraesCS5D01G245700 chr5D 88.333 60 5 1 748 807 388591662 388591719 1.640000e-08 71.3
16 TraesCS5D01G245700 chr5D 100.000 32 0 0 2995 3026 353957276 353957245 3.560000e-05 60.2
17 TraesCS5D01G245700 chr5A 89.383 1215 76 20 827 2014 491583822 491585010 0.000000e+00 1480.0
18 TraesCS5D01G245700 chr5A 82.210 1602 139 56 752 2293 489677179 489678694 0.000000e+00 1245.0
19 TraesCS5D01G245700 chr5A 83.199 1369 114 43 752 2060 489661251 489662563 0.000000e+00 1147.0
20 TraesCS5D01G245700 chr5A 82.663 1044 112 33 1284 2293 489763905 489764913 0.000000e+00 861.0
21 TraesCS5D01G245700 chr5A 89.005 573 30 9 1525 2064 491569379 491569951 0.000000e+00 678.0
22 TraesCS5D01G245700 chr5A 87.055 618 41 17 2691 3301 491570427 491571012 0.000000e+00 662.0
23 TraesCS5D01G245700 chr5A 85.811 592 42 21 26 596 491583024 491583594 1.020000e-164 590.0
24 TraesCS5D01G245700 chr5A 84.768 453 30 17 2691 3139 491585767 491586184 5.090000e-113 418.0
25 TraesCS5D01G245700 chr5A 93.373 166 8 3 2369 2532 491585609 491585773 3.290000e-60 243.0
26 TraesCS5D01G245700 chr5A 82.993 294 22 11 2180 2459 491570125 491570404 1.180000e-59 241.0
27 TraesCS5D01G245700 chr5A 97.222 36 1 0 451 486 491583512 491583547 9.890000e-06 62.1
28 TraesCS5D01G245700 chr5A 100.000 29 0 0 678 706 491583666 491583694 2.000000e-03 54.7
29 TraesCS5D01G245700 chr7B 85.831 1348 122 19 752 2060 456502933 456501616 0.000000e+00 1367.0
30 TraesCS5D01G245700 chr6D 85.683 1369 114 31 752 2060 60557186 60555840 0.000000e+00 1367.0
31 TraesCS5D01G245700 chr6D 86.154 1170 85 20 1011 2143 106951721 106952850 0.000000e+00 1192.0
32 TraesCS5D01G245700 chr6D 92.529 174 8 2 2530 2703 72143436 72143268 9.150000e-61 244.0
33 TraesCS5D01G245700 chr5B 88.534 1160 62 13 1021 2143 467019390 467020515 0.000000e+00 1339.0
34 TraesCS5D01G245700 chr5B 86.304 1139 99 22 867 1982 465053699 465054803 0.000000e+00 1186.0
35 TraesCS5D01G245700 chr5B 85.556 450 29 16 2691 3139 467021230 467021644 3.910000e-119 438.0
36 TraesCS5D01G245700 chr5B 88.000 200 14 6 2341 2532 467021039 467021236 9.220000e-56 228.0
37 TraesCS5D01G245700 chr7D 85.309 1341 134 20 752 2060 437591913 437593222 0.000000e+00 1327.0
38 TraesCS5D01G245700 chr7D 92.398 171 6 3 2529 2697 235502405 235502570 1.530000e-58 237.0
39 TraesCS5D01G245700 chr6A 86.752 1170 87 19 1011 2143 130412805 130413943 0.000000e+00 1240.0
40 TraesCS5D01G245700 chr7A 82.826 821 103 12 752 1560 488029399 488030193 0.000000e+00 701.0
41 TraesCS5D01G245700 chr7A 93.373 166 6 3 2530 2695 206712118 206711958 1.180000e-59 241.0
42 TraesCS5D01G245700 chr4A 86.319 614 52 10 2691 3301 45872500 45873084 9.990000e-180 640.0
43 TraesCS5D01G245700 chr4A 87.265 479 33 5 1005 1482 45871087 45871538 3.770000e-144 521.0
44 TraesCS5D01G245700 chr4A 86.143 433 34 4 1633 2044 45871629 45872056 8.410000e-121 444.0
45 TraesCS5D01G245700 chr4A 85.616 292 17 9 2180 2459 45872199 45872477 1.940000e-72 283.0
46 TraesCS5D01G245700 chr4A 92.814 167 8 1 2530 2696 660522538 660522376 4.260000e-59 239.0
47 TraesCS5D01G245700 chr4B 84.472 483 39 19 2691 3166 31872232 31871779 8.410000e-121 444.0
48 TraesCS5D01G245700 chr2D 94.012 167 6 1 2529 2695 445733833 445733671 1.970000e-62 250.0
49 TraesCS5D01G245700 chr2D 92.899 169 8 1 2530 2698 56541156 56540992 3.290000e-60 243.0
50 TraesCS5D01G245700 chr1D 93.976 166 6 1 2530 2695 427827082 427826921 7.070000e-62 248.0
51 TraesCS5D01G245700 chr2B 92.000 175 10 1 2529 2703 291855169 291854999 3.290000e-60 243.0
52 TraesCS5D01G245700 chr3B 92.814 167 8 1 2529 2695 252358444 252358606 4.260000e-59 239.0


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 TraesCS5D01G245700 chr5D 353952833 353956133 3300 False 6096.000000 6096 100.000000 1 3301 1 chr5D.!!$F2 3300
1 TraesCS5D01G245700 chr5D 370777320 370778612 1292 False 1229.000000 1229 84.337000 774 2058 1 chr5D.!!$F3 1284
2 TraesCS5D01G245700 chr5D 388411161 388412968 1807 False 1008.150000 1945 93.335000 393 2143 2 chr5D.!!$F7 1750
3 TraesCS5D01G245700 chr5D 388380759 388383025 2266 False 783.000000 1445 86.923333 1015 3301 3 chr5D.!!$F6 2286
4 TraesCS5D01G245700 chr5D 386958188 386959745 1557 False 725.500000 1317 86.648500 748 2293 2 chr5D.!!$F5 1545
5 TraesCS5D01G245700 chr5D 388591662 388596722 5060 False 565.075000 1251 87.680500 748 3139 4 chr5D.!!$F8 2391
6 TraesCS5D01G245700 chr5D 353968204 353968748 544 False 290.500000 427 88.748000 2414 3167 2 chr5D.!!$F4 753
7 TraesCS5D01G245700 chr5A 489677179 489678694 1515 False 1245.000000 1245 82.210000 752 2293 1 chr5A.!!$F2 1541
8 TraesCS5D01G245700 chr5A 489661251 489662563 1312 False 1147.000000 1147 83.199000 752 2060 1 chr5A.!!$F1 1308
9 TraesCS5D01G245700 chr5A 489763905 489764913 1008 False 861.000000 861 82.663000 1284 2293 1 chr5A.!!$F3 1009
10 TraesCS5D01G245700 chr5A 491569379 491571012 1633 False 527.000000 678 86.351000 1525 3301 3 chr5A.!!$F4 1776
11 TraesCS5D01G245700 chr5A 491583024 491586184 3160 False 474.633333 1480 91.759500 26 3139 6 chr5A.!!$F5 3113
12 TraesCS5D01G245700 chr7B 456501616 456502933 1317 True 1367.000000 1367 85.831000 752 2060 1 chr7B.!!$R1 1308
13 TraesCS5D01G245700 chr6D 60555840 60557186 1346 True 1367.000000 1367 85.683000 752 2060 1 chr6D.!!$R1 1308
14 TraesCS5D01G245700 chr6D 106951721 106952850 1129 False 1192.000000 1192 86.154000 1011 2143 1 chr6D.!!$F1 1132
15 TraesCS5D01G245700 chr5B 465053699 465054803 1104 False 1186.000000 1186 86.304000 867 1982 1 chr5B.!!$F1 1115
16 TraesCS5D01G245700 chr5B 467019390 467021644 2254 False 668.333333 1339 87.363333 1021 3139 3 chr5B.!!$F2 2118
17 TraesCS5D01G245700 chr7D 437591913 437593222 1309 False 1327.000000 1327 85.309000 752 2060 1 chr7D.!!$F2 1308
18 TraesCS5D01G245700 chr6A 130412805 130413943 1138 False 1240.000000 1240 86.752000 1011 2143 1 chr6A.!!$F1 1132
19 TraesCS5D01G245700 chr7A 488029399 488030193 794 False 701.000000 701 82.826000 752 1560 1 chr7A.!!$F1 808
20 TraesCS5D01G245700 chr4A 45871087 45873084 1997 False 472.000000 640 86.335750 1005 3301 4 chr4A.!!$F1 2296

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
821 1039 0.390472 GAAGCCTCAACTGACTCGGG 60.39 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 6799 0.107643 TGACACCGCCTGAAACATCA 59.892 50.0 0.0 0.0 0.0 3.07 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
18 19 3.666192 AGCAGCTTGGAAATGAGCT 57.334 47.368 0.00 0.00 38.25 4.09
19 20 1.920610 AGCAGCTTGGAAATGAGCTT 58.079 45.000 0.00 0.00 35.17 3.74
20 21 2.245582 AGCAGCTTGGAAATGAGCTTT 58.754 42.857 0.00 0.00 35.17 3.51
21 22 2.631545 AGCAGCTTGGAAATGAGCTTTT 59.368 40.909 0.00 0.00 35.17 2.27
22 23 2.735134 GCAGCTTGGAAATGAGCTTTTG 59.265 45.455 0.00 0.00 35.17 2.44
68 69 1.740025 GTTAAGCTCTGTGGCACCATC 59.260 52.381 16.26 1.67 34.17 3.51
74 75 2.352127 GCTCTGTGGCACCATCTTTTTC 60.352 50.000 16.26 0.00 0.00 2.29
88 89 1.271656 CTTTTTCCAGAAGCAGGGCAG 59.728 52.381 0.00 0.00 0.00 4.85
96 97 1.303155 AAGCAGGGCAGTGAAGCTC 60.303 57.895 0.00 0.00 33.83 4.09
114 115 7.489113 GTGAAGCTCTGTTGATTTCTTCAAAAA 59.511 33.333 4.34 0.00 45.71 1.94
130 131 4.305769 TCAAAAATTTCACCCGCAATCTG 58.694 39.130 0.00 0.00 0.00 2.90
159 160 2.665165 TGTGGAAAACAGCCATCACTT 58.335 42.857 0.00 0.00 37.81 3.16
160 161 2.361757 TGTGGAAAACAGCCATCACTTG 59.638 45.455 0.00 0.00 37.81 3.16
191 196 1.595311 TACCCCAGCATGACCTGAAT 58.405 50.000 0.00 0.00 39.69 2.57
241 246 1.613630 GCCTTCTCAGGTGGGGAGA 60.614 63.158 0.00 0.00 43.18 3.71
247 252 3.086600 CAGGTGGGGAGAGGAGGC 61.087 72.222 0.00 0.00 0.00 4.70
250 255 3.086600 GTGGGGAGAGGAGGCCAG 61.087 72.222 5.01 0.00 0.00 4.85
251 256 3.284251 TGGGGAGAGGAGGCCAGA 61.284 66.667 5.01 0.00 0.00 3.86
253 258 2.371259 GGGGAGAGGAGGCCAGAAC 61.371 68.421 5.01 0.00 0.00 3.01
254 259 1.306568 GGGAGAGGAGGCCAGAACT 60.307 63.158 5.01 0.00 0.00 3.01
255 260 1.334384 GGGAGAGGAGGCCAGAACTC 61.334 65.000 5.01 8.47 0.00 3.01
259 264 3.003763 GGAGGCCAGAACTCCGGT 61.004 66.667 5.01 0.00 44.50 5.28
260 265 2.593956 GGAGGCCAGAACTCCGGTT 61.594 63.158 5.01 0.00 44.50 4.44
261 266 1.375326 GAGGCCAGAACTCCGGTTT 59.625 57.895 5.01 0.00 35.58 3.27
263 268 0.613777 AGGCCAGAACTCCGGTTTAG 59.386 55.000 5.01 0.00 35.58 1.85
264 269 0.611714 GGCCAGAACTCCGGTTTAGA 59.388 55.000 0.00 0.00 35.58 2.10
265 270 1.405661 GGCCAGAACTCCGGTTTAGAG 60.406 57.143 0.00 0.00 35.58 2.43
266 271 1.549170 GCCAGAACTCCGGTTTAGAGA 59.451 52.381 0.00 0.00 35.58 3.10
267 272 2.028385 GCCAGAACTCCGGTTTAGAGAA 60.028 50.000 0.00 0.00 35.58 2.87
268 273 3.586892 CCAGAACTCCGGTTTAGAGAAC 58.413 50.000 0.00 0.00 35.58 3.01
269 274 3.243336 CAGAACTCCGGTTTAGAGAACG 58.757 50.000 0.00 0.00 35.58 3.95
271 276 0.893447 ACTCCGGTTTAGAGAACGGG 59.107 55.000 0.00 8.65 45.97 5.28
272 277 0.893447 CTCCGGTTTAGAGAACGGGT 59.107 55.000 0.00 0.00 45.97 5.28
273 278 1.274447 CTCCGGTTTAGAGAACGGGTT 59.726 52.381 0.00 0.00 45.97 4.11
274 279 1.001181 TCCGGTTTAGAGAACGGGTTG 59.999 52.381 0.00 0.00 45.97 3.77
275 280 1.270465 CCGGTTTAGAGAACGGGTTGT 60.270 52.381 0.00 0.00 42.48 3.32
276 281 2.064014 CGGTTTAGAGAACGGGTTGTC 58.936 52.381 0.79 0.79 33.55 3.18
277 282 2.420642 GGTTTAGAGAACGGGTTGTCC 58.579 52.381 5.22 0.00 33.82 4.02
278 283 2.224354 GGTTTAGAGAACGGGTTGTCCA 60.224 50.000 5.22 0.00 33.82 4.02
279 284 3.064931 GTTTAGAGAACGGGTTGTCCAG 58.935 50.000 5.22 0.00 33.82 3.86
334 339 1.443194 CCAATTGAGTGTGCGCTGC 60.443 57.895 9.73 1.68 0.00 5.25
335 340 1.443194 CAATTGAGTGTGCGCTGCC 60.443 57.895 9.73 0.00 0.00 4.85
356 361 2.268920 GATGCCTCTCGCCCAACA 59.731 61.111 0.00 0.00 36.24 3.33
362 367 1.367471 CTCTCGCCCAACACACTGA 59.633 57.895 0.00 0.00 0.00 3.41
391 396 2.591429 TGCACTGTCGTGGCCTTG 60.591 61.111 3.32 0.00 41.51 3.61
402 407 1.069022 CGTGGCCTTGTCTGAATGTTG 60.069 52.381 3.32 0.00 0.00 3.33
433 441 6.179906 TCTCTGTCAGAAACCTTGAGAATT 57.820 37.500 3.67 0.00 30.24 2.17
487 610 2.132762 TCCGCGTCAGAAAGTTTTCTC 58.867 47.619 4.92 0.00 45.23 2.87
493 616 4.552961 GCGTCAGAAAGTTTTCTCAACTCC 60.553 45.833 4.20 0.00 45.23 3.85
494 617 4.024809 CGTCAGAAAGTTTTCTCAACTCCC 60.025 45.833 4.20 0.00 45.23 4.30
495 618 5.126779 GTCAGAAAGTTTTCTCAACTCCCT 58.873 41.667 4.20 0.00 45.23 4.20
496 619 5.590663 GTCAGAAAGTTTTCTCAACTCCCTT 59.409 40.000 4.20 0.00 45.23 3.95
498 621 5.358160 CAGAAAGTTTTCTCAACTCCCTTGT 59.642 40.000 4.20 0.00 45.23 3.16
499 622 5.590663 AGAAAGTTTTCTCAACTCCCTTGTC 59.409 40.000 1.35 0.00 43.72 3.18
500 623 4.779993 AGTTTTCTCAACTCCCTTGTCT 57.220 40.909 0.00 0.00 0.00 3.41
501 624 5.117406 AGTTTTCTCAACTCCCTTGTCTT 57.883 39.130 0.00 0.00 0.00 3.01
502 625 4.884164 AGTTTTCTCAACTCCCTTGTCTTG 59.116 41.667 0.00 0.00 0.00 3.02
503 626 4.771114 TTTCTCAACTCCCTTGTCTTGA 57.229 40.909 0.00 0.00 0.00 3.02
506 629 4.163427 TCTCAACTCCCTTGTCTTGAGAT 58.837 43.478 5.11 0.00 42.27 2.75
507 630 4.221703 TCTCAACTCCCTTGTCTTGAGATC 59.778 45.833 5.11 0.00 42.27 2.75
508 631 3.261897 TCAACTCCCTTGTCTTGAGATCC 59.738 47.826 0.00 0.00 0.00 3.36
509 632 2.907892 ACTCCCTTGTCTTGAGATCCA 58.092 47.619 0.00 0.00 0.00 3.41
512 635 1.065126 CCCTTGTCTTGAGATCCACCC 60.065 57.143 0.00 0.00 0.00 4.61
513 636 1.912043 CCTTGTCTTGAGATCCACCCT 59.088 52.381 0.00 0.00 0.00 4.34
514 637 3.107601 CCTTGTCTTGAGATCCACCCTA 58.892 50.000 0.00 0.00 0.00 3.53
515 638 3.133721 CCTTGTCTTGAGATCCACCCTAG 59.866 52.174 0.00 0.00 0.00 3.02
519 642 3.383185 GTCTTGAGATCCACCCTAGACAG 59.617 52.174 0.00 0.00 32.79 3.51
520 643 1.781786 TGAGATCCACCCTAGACAGC 58.218 55.000 0.00 0.00 0.00 4.40
521 644 1.044611 GAGATCCACCCTAGACAGCC 58.955 60.000 0.00 0.00 0.00 4.85
522 645 0.639392 AGATCCACCCTAGACAGCCT 59.361 55.000 0.00 0.00 0.00 4.58
523 646 1.044611 GATCCACCCTAGACAGCCTC 58.955 60.000 0.00 0.00 0.00 4.70
524 647 0.639392 ATCCACCCTAGACAGCCTCT 59.361 55.000 0.00 0.00 0.00 3.69
526 649 0.827368 CCACCCTAGACAGCCTCTTC 59.173 60.000 0.00 0.00 0.00 2.87
527 650 1.621072 CCACCCTAGACAGCCTCTTCT 60.621 57.143 0.00 0.00 0.00 2.85
528 651 2.183679 CACCCTAGACAGCCTCTTCTT 58.816 52.381 0.00 0.00 0.00 2.52
530 653 3.769844 CACCCTAGACAGCCTCTTCTTTA 59.230 47.826 0.00 0.00 0.00 1.85
532 655 5.033522 ACCCTAGACAGCCTCTTCTTTAAT 58.966 41.667 0.00 0.00 0.00 1.40
534 657 6.012421 ACCCTAGACAGCCTCTTCTTTAATTT 60.012 38.462 0.00 0.00 0.00 1.82
535 658 7.182206 ACCCTAGACAGCCTCTTCTTTAATTTA 59.818 37.037 0.00 0.00 0.00 1.40
536 659 8.214364 CCCTAGACAGCCTCTTCTTTAATTTAT 58.786 37.037 0.00 0.00 0.00 1.40
537 660 9.267084 CCTAGACAGCCTCTTCTTTAATTTATC 57.733 37.037 0.00 0.00 0.00 1.75
538 661 9.267084 CTAGACAGCCTCTTCTTTAATTTATCC 57.733 37.037 0.00 0.00 0.00 2.59
539 662 7.633789 AGACAGCCTCTTCTTTAATTTATCCA 58.366 34.615 0.00 0.00 0.00 3.41
540 663 7.772757 AGACAGCCTCTTCTTTAATTTATCCAG 59.227 37.037 0.00 0.00 0.00 3.86
541 664 7.633789 ACAGCCTCTTCTTTAATTTATCCAGA 58.366 34.615 0.00 0.00 0.00 3.86
542 665 8.109634 ACAGCCTCTTCTTTAATTTATCCAGAA 58.890 33.333 0.00 0.00 0.00 3.02
543 666 8.960591 CAGCCTCTTCTTTAATTTATCCAGAAA 58.039 33.333 0.00 0.00 0.00 2.52
544 667 9.706529 AGCCTCTTCTTTAATTTATCCAGAAAT 57.293 29.630 0.00 0.00 0.00 2.17
602 735 4.771590 CTGCATTTGGTAGCAAGAAAGA 57.228 40.909 7.51 0.00 40.73 2.52
603 736 4.730657 CTGCATTTGGTAGCAAGAAAGAG 58.269 43.478 7.51 0.00 40.73 2.85
604 737 4.397420 TGCATTTGGTAGCAAGAAAGAGA 58.603 39.130 7.51 0.00 37.90 3.10
605 738 4.456911 TGCATTTGGTAGCAAGAAAGAGAG 59.543 41.667 7.51 0.00 37.90 3.20
606 739 4.142513 GCATTTGGTAGCAAGAAAGAGAGG 60.143 45.833 7.51 0.00 0.00 3.69
607 740 4.974645 TTTGGTAGCAAGAAAGAGAGGA 57.025 40.909 7.51 0.00 0.00 3.71
608 741 3.963428 TGGTAGCAAGAAAGAGAGGAC 57.037 47.619 0.00 0.00 0.00 3.85
609 742 2.231478 TGGTAGCAAGAAAGAGAGGACG 59.769 50.000 0.00 0.00 0.00 4.79
724 877 2.811317 CAGCGAGCAGGACGAACC 60.811 66.667 0.00 0.00 39.35 3.62
745 898 1.851304 GGGGGAAATGAAGACATGCA 58.149 50.000 0.00 0.00 36.79 3.96
746 899 2.391678 GGGGGAAATGAAGACATGCAT 58.608 47.619 0.00 0.00 36.79 3.96
790 944 2.500910 AGCTAAGCTTGAGAGATGCACT 59.499 45.455 9.86 0.00 33.89 4.40
791 945 3.055240 AGCTAAGCTTGAGAGATGCACTT 60.055 43.478 9.86 0.00 33.89 3.16
807 962 1.743394 CACTTACCCAAATCCGAAGCC 59.257 52.381 0.00 0.00 0.00 4.35
809 964 2.289565 CTTACCCAAATCCGAAGCCTC 58.710 52.381 0.00 0.00 0.00 4.70
821 1039 0.390472 GAAGCCTCAACTGACTCGGG 60.390 60.000 0.00 0.00 0.00 5.14
823 1041 2.266055 CCTCAACTGACTCGGGCC 59.734 66.667 0.00 0.00 0.00 5.80
824 1042 2.266055 CTCAACTGACTCGGGCCC 59.734 66.667 13.57 13.57 0.00 5.80
825 1043 2.525629 TCAACTGACTCGGGCCCA 60.526 61.111 24.92 8.28 0.00 5.36
980 1249 4.147449 CACCGCATCCTCTCGCCA 62.147 66.667 0.00 0.00 0.00 5.69
1467 1792 2.564471 GCAGAAGCAGCTGGACAAT 58.436 52.632 17.12 0.00 41.58 2.71
1482 1846 2.933260 GGACAATTTCCTTCGAGAGAGC 59.067 50.000 0.00 0.00 41.95 4.09
1484 1848 3.997021 GACAATTTCCTTCGAGAGAGCAA 59.003 43.478 0.00 0.00 43.69 3.91
1517 1881 3.228749 CGCATCATCAACACAAACAGAC 58.771 45.455 0.00 0.00 0.00 3.51
2017 2513 2.033755 AAGCAGCAGCAGAGCTTCG 61.034 57.895 12.42 0.00 44.67 3.79
2080 2576 8.930760 CATCGTTTTCTTTTCTAGAAGTGATCT 58.069 33.333 5.12 0.00 43.52 2.75
2143 2778 5.448438 TGCTGAACGTGATTGAAAATGTAC 58.552 37.500 0.00 0.00 0.00 2.90
2147 2782 7.426456 GCTGAACGTGATTGAAAATGTACTATG 59.574 37.037 0.00 0.00 0.00 2.23
2185 3036 3.229293 TCAACTGATTTGGTTGCCATCA 58.771 40.909 0.00 0.00 42.40 3.07
2186 3037 3.256383 TCAACTGATTTGGTTGCCATCAG 59.744 43.478 14.00 14.00 42.85 2.90
2188 3039 3.087031 ACTGATTTGGTTGCCATCAGAG 58.913 45.455 19.65 5.08 40.91 3.35
2189 3040 3.245016 ACTGATTTGGTTGCCATCAGAGA 60.245 43.478 19.65 0.00 40.91 3.10
2190 3041 3.760151 CTGATTTGGTTGCCATCAGAGAA 59.240 43.478 11.38 0.00 40.91 2.87
2285 6017 9.996554 ACCATATGAAAGTACATGATCGATTAA 57.003 29.630 3.65 0.00 0.00 1.40
2335 6076 4.883300 CGTAGCGCCCGAGACGTC 62.883 72.222 7.70 7.70 0.00 4.34
2419 6446 8.842358 AAAAACAATCTCTTTGGTACGAGATA 57.158 30.769 10.30 0.00 44.04 1.98
2495 6524 6.594159 GTGCATATGTATAGCCCTTTATTCGT 59.406 38.462 4.29 0.00 0.00 3.85
2531 6560 9.591792 ACCGGTTGTTCTTTTATATAGAGTTAC 57.408 33.333 0.00 0.00 0.00 2.50
2532 6561 9.813446 CCGGTTGTTCTTTTATATAGAGTTACT 57.187 33.333 0.00 0.00 0.00 2.24
2539 6568 8.632906 TCTTTTATATAGAGTTACTCCCTCCG 57.367 38.462 8.96 0.00 0.00 4.63
2540 6569 8.223330 TCTTTTATATAGAGTTACTCCCTCCGT 58.777 37.037 8.96 0.00 0.00 4.69
2541 6570 8.773033 TTTTATATAGAGTTACTCCCTCCGTT 57.227 34.615 8.96 0.00 0.00 4.44
2542 6571 7.992754 TTATATAGAGTTACTCCCTCCGTTC 57.007 40.000 8.96 0.00 0.00 3.95
2543 6572 1.849977 AGAGTTACTCCCTCCGTTCC 58.150 55.000 8.96 0.00 0.00 3.62
2544 6573 1.358445 AGAGTTACTCCCTCCGTTCCT 59.642 52.381 8.96 0.00 0.00 3.36
2545 6574 2.579860 AGAGTTACTCCCTCCGTTCCTA 59.420 50.000 8.96 0.00 0.00 2.94
2546 6575 3.011032 AGAGTTACTCCCTCCGTTCCTAA 59.989 47.826 8.96 0.00 0.00 2.69
2547 6576 3.766051 GAGTTACTCCCTCCGTTCCTAAA 59.234 47.826 0.00 0.00 0.00 1.85
2548 6577 4.359996 AGTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
2549 6578 5.522641 AGTTACTCCCTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
2550 6579 6.141790 AGTTACTCCCTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
2551 6580 7.300658 AGTTACTCCCTCCGTTCCTAAATATA 58.699 38.462 0.00 0.00 0.00 0.86
2552 6581 7.954620 AGTTACTCCCTCCGTTCCTAAATATAT 59.045 37.037 0.00 0.00 0.00 0.86
2553 6582 6.607004 ACTCCCTCCGTTCCTAAATATATG 57.393 41.667 0.00 0.00 0.00 1.78
2554 6583 6.082707 ACTCCCTCCGTTCCTAAATATATGT 58.917 40.000 0.00 0.00 0.00 2.29
2555 6584 6.210984 ACTCCCTCCGTTCCTAAATATATGTC 59.789 42.308 0.00 0.00 0.00 3.06
2556 6585 6.320518 TCCCTCCGTTCCTAAATATATGTCT 58.679 40.000 0.00 0.00 0.00 3.41
2557 6586 6.785963 TCCCTCCGTTCCTAAATATATGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
2558 6587 7.291651 TCCCTCCGTTCCTAAATATATGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
2559 6588 7.387948 CCCTCCGTTCCTAAATATATGTCTTTG 59.612 40.741 0.00 0.00 0.00 2.77
2560 6589 7.931948 CCTCCGTTCCTAAATATATGTCTTTGT 59.068 37.037 0.00 0.00 0.00 2.83
2561 6590 9.976511 CTCCGTTCCTAAATATATGTCTTTGTA 57.023 33.333 0.00 0.00 0.00 2.41
2594 6623 9.816354 TCATTATATATGAACCACATACGGATG 57.184 33.333 5.94 5.94 43.12 3.51
2602 6631 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
2603 6632 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
2604 6633 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
2605 6634 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2606 6635 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2607 6636 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2608 6637 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2609 6638 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2610 6639 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2614 6643 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
2615 6644 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
2625 6654 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
2636 6665 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2637 6666 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2638 6667 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2639 6668 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2640 6669 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2641 6670 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2642 6671 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2643 6672 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2644 6673 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2645 6674 5.483811 TCACTCATTTTGCTCCGTATGTAA 58.516 37.500 0.00 0.00 0.00 2.41
2646 6675 6.112734 TCACTCATTTTGCTCCGTATGTAAT 58.887 36.000 0.00 0.00 0.00 1.89
2647 6676 6.257849 TCACTCATTTTGCTCCGTATGTAATC 59.742 38.462 0.00 0.00 0.00 1.75
2648 6677 6.258727 CACTCATTTTGCTCCGTATGTAATCT 59.741 38.462 0.00 0.00 0.00 2.40
2649 6678 7.438160 CACTCATTTTGCTCCGTATGTAATCTA 59.562 37.037 0.00 0.00 0.00 1.98
2650 6679 8.150945 ACTCATTTTGCTCCGTATGTAATCTAT 58.849 33.333 0.00 0.00 0.00 1.98
2651 6680 9.639601 CTCATTTTGCTCCGTATGTAATCTATA 57.360 33.333 0.00 0.00 0.00 1.31
2652 6681 9.639601 TCATTTTGCTCCGTATGTAATCTATAG 57.360 33.333 0.00 0.00 0.00 1.31
2653 6682 9.424319 CATTTTGCTCCGTATGTAATCTATAGT 57.576 33.333 0.00 0.00 0.00 2.12
2654 6683 8.812147 TTTTGCTCCGTATGTAATCTATAGTG 57.188 34.615 0.00 0.00 0.00 2.74
2655 6684 7.754851 TTGCTCCGTATGTAATCTATAGTGA 57.245 36.000 0.00 0.00 0.00 3.41
2656 6685 7.754851 TGCTCCGTATGTAATCTATAGTGAA 57.245 36.000 0.00 0.00 0.00 3.18
2657 6686 8.173542 TGCTCCGTATGTAATCTATAGTGAAA 57.826 34.615 0.00 0.00 0.00 2.69
2658 6687 8.803235 TGCTCCGTATGTAATCTATAGTGAAAT 58.197 33.333 0.00 0.00 0.00 2.17
2659 6688 9.291664 GCTCCGTATGTAATCTATAGTGAAATC 57.708 37.037 0.00 0.00 0.00 2.17
2672 6701 9.702253 TCTATAGTGAAATCTCTACAAAGACCT 57.298 33.333 0.00 0.00 0.00 3.85
2726 6755 0.107643 TGCGGTGGTCAGTCAAATCA 59.892 50.000 0.00 0.00 0.00 2.57
2763 6798 5.681437 GCTTCTTGGTAACTACGGATGATGA 60.681 44.000 0.00 0.00 37.61 2.92
2764 6799 6.479972 TTCTTGGTAACTACGGATGATGAT 57.520 37.500 0.00 0.00 37.61 2.45
2765 6800 5.842907 TCTTGGTAACTACGGATGATGATG 58.157 41.667 0.00 0.00 37.61 3.07
2766 6801 5.596772 TCTTGGTAACTACGGATGATGATGA 59.403 40.000 0.00 0.00 37.61 2.92
2767 6802 6.267699 TCTTGGTAACTACGGATGATGATGAT 59.732 38.462 0.00 0.00 37.61 2.45
2768 6803 5.783111 TGGTAACTACGGATGATGATGATG 58.217 41.667 0.00 0.00 37.61 3.07
2841 6876 2.293122 CTCTCTTCCTCGTATCAGGCTG 59.707 54.545 8.58 8.58 32.91 4.85
2864 6902 4.056125 CTCTGCGTGGAGTCGGCA 62.056 66.667 0.00 2.74 0.00 5.69
2890 6928 0.036010 CGGGTGTGCCAAGAAGAGAT 60.036 55.000 0.00 0.00 36.17 2.75
2893 6931 1.280421 GGTGTGCCAAGAAGAGATCCT 59.720 52.381 0.00 0.00 34.09 3.24
2930 6968 1.377333 GGTAGTTGCCTCCCACTGC 60.377 63.158 0.00 0.00 0.00 4.40
2931 6969 1.374947 GTAGTTGCCTCCCACTGCA 59.625 57.895 0.00 0.00 35.27 4.41
2947 6985 2.026542 ACTGCAAGAATCTCCAGCATCA 60.027 45.455 9.78 0.00 37.43 3.07
2979 7017 2.375174 TGGCTTTATCTGGTTGGTCAGT 59.625 45.455 0.00 0.00 36.25 3.41
2993 7031 4.462508 TGGTCAGTCAGAGAAGCATTAG 57.537 45.455 0.00 0.00 0.00 1.73
2994 7032 4.089361 TGGTCAGTCAGAGAAGCATTAGA 58.911 43.478 0.00 0.00 0.00 2.10
2997 7035 5.752955 GGTCAGTCAGAGAAGCATTAGAATC 59.247 44.000 0.00 0.00 0.00 2.52
2999 7037 7.201866 GGTCAGTCAGAGAAGCATTAGAATCTA 60.202 40.741 0.00 0.00 0.00 1.98
3000 7038 8.359642 GTCAGTCAGAGAAGCATTAGAATCTAT 58.640 37.037 0.00 0.00 0.00 1.98
3001 7039 8.358895 TCAGTCAGAGAAGCATTAGAATCTATG 58.641 37.037 0.00 0.00 33.57 2.23
3002 7040 8.143193 CAGTCAGAGAAGCATTAGAATCTATGT 58.857 37.037 0.00 0.00 33.89 2.29
3003 7041 8.359642 AGTCAGAGAAGCATTAGAATCTATGTC 58.640 37.037 0.00 0.00 33.89 3.06
3004 7042 7.598493 GTCAGAGAAGCATTAGAATCTATGTCC 59.402 40.741 0.00 0.00 33.89 4.02
3005 7043 7.288621 TCAGAGAAGCATTAGAATCTATGTCCA 59.711 37.037 0.00 0.00 33.89 4.02
3006 7044 7.930325 CAGAGAAGCATTAGAATCTATGTCCAA 59.070 37.037 0.00 0.00 0.00 3.53
3007 7045 8.489489 AGAGAAGCATTAGAATCTATGTCCAAA 58.511 33.333 0.00 0.00 0.00 3.28
3008 7046 9.282569 GAGAAGCATTAGAATCTATGTCCAAAT 57.717 33.333 0.00 0.00 0.00 2.32
3009 7047 9.064706 AGAAGCATTAGAATCTATGTCCAAATG 57.935 33.333 0.00 0.00 0.00 2.32
3010 7048 8.757982 AAGCATTAGAATCTATGTCCAAATGT 57.242 30.769 0.00 0.00 0.00 2.71
3011 7049 8.757982 AGCATTAGAATCTATGTCCAAATGTT 57.242 30.769 0.00 0.00 0.00 2.71
3012 7050 8.844244 AGCATTAGAATCTATGTCCAAATGTTC 58.156 33.333 0.00 0.00 0.00 3.18
3013 7051 8.623903 GCATTAGAATCTATGTCCAAATGTTCA 58.376 33.333 0.00 0.00 0.00 3.18
3025 7063 9.803507 ATGTCCAAATGTTCATATCTGATATGT 57.196 29.630 27.91 12.96 42.49 2.29
3034 7072 5.005740 TCATATCTGATATGTTTGGCTGGC 58.994 41.667 27.91 0.00 42.49 4.85
3097 7135 9.177608 TCAAAAGTGCAGCATTAGAACTTATAT 57.822 29.630 0.00 0.00 31.09 0.86
3253 7297 2.923020 GAGCACGCAACCAAAAATATGG 59.077 45.455 0.00 0.00 46.38 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.666192 AGCTCATTTCCAAGCTGCT 57.334 47.368 0.00 0.00 46.78 4.24
4 5 2.758009 TGCAAAAGCTCATTTCCAAGC 58.242 42.857 0.00 0.00 38.84 4.01
5 6 4.992319 TGATTGCAAAAGCTCATTTCCAAG 59.008 37.500 1.71 0.00 30.40 3.61
6 7 4.958509 TGATTGCAAAAGCTCATTTCCAA 58.041 34.783 1.71 0.00 31.02 3.53
7 8 4.561938 CCTGATTGCAAAAGCTCATTTCCA 60.562 41.667 1.71 0.00 0.00 3.53
8 9 3.930848 CCTGATTGCAAAAGCTCATTTCC 59.069 43.478 1.71 0.00 0.00 3.13
9 10 3.370061 GCCTGATTGCAAAAGCTCATTTC 59.630 43.478 1.71 0.00 0.00 2.17
10 11 3.007614 AGCCTGATTGCAAAAGCTCATTT 59.992 39.130 1.71 0.00 0.00 2.32
11 12 2.565834 AGCCTGATTGCAAAAGCTCATT 59.434 40.909 1.71 0.00 0.00 2.57
12 13 2.094182 CAGCCTGATTGCAAAAGCTCAT 60.094 45.455 1.71 0.00 0.00 2.90
13 14 1.271379 CAGCCTGATTGCAAAAGCTCA 59.729 47.619 1.71 1.18 0.00 4.26
14 15 1.542915 TCAGCCTGATTGCAAAAGCTC 59.457 47.619 1.71 0.00 0.00 4.09
15 16 1.624336 TCAGCCTGATTGCAAAAGCT 58.376 45.000 1.71 6.64 0.00 3.74
16 17 2.537401 GATCAGCCTGATTGCAAAAGC 58.463 47.619 8.93 4.14 37.20 3.51
17 18 2.479049 CCGATCAGCCTGATTGCAAAAG 60.479 50.000 15.40 4.23 37.20 2.27
18 19 1.473677 CCGATCAGCCTGATTGCAAAA 59.526 47.619 15.40 0.00 37.20 2.44
19 20 1.097232 CCGATCAGCCTGATTGCAAA 58.903 50.000 15.40 0.00 37.20 3.68
20 21 1.378882 GCCGATCAGCCTGATTGCAA 61.379 55.000 19.37 0.00 37.20 4.08
21 22 1.820906 GCCGATCAGCCTGATTGCA 60.821 57.895 19.37 0.00 37.20 4.08
22 23 3.028969 GCCGATCAGCCTGATTGC 58.971 61.111 15.40 13.83 37.20 3.56
68 69 1.271656 CTGCCCTGCTTCTGGAAAAAG 59.728 52.381 0.00 0.00 0.00 2.27
74 75 0.959372 CTTCACTGCCCTGCTTCTGG 60.959 60.000 0.00 0.00 0.00 3.86
88 89 5.679734 TGAAGAAATCAACAGAGCTTCAC 57.320 39.130 0.00 0.00 37.43 3.18
114 115 5.418840 AGTTTTATCAGATTGCGGGTGAAAT 59.581 36.000 0.00 0.00 0.00 2.17
130 131 5.596845 TGGCTGTTTTCCACAAGTTTTATC 58.403 37.500 0.00 0.00 33.87 1.75
159 160 2.037251 GCTGGGGTATAATTCGAGAGCA 59.963 50.000 0.00 0.00 0.00 4.26
160 161 2.037251 TGCTGGGGTATAATTCGAGAGC 59.963 50.000 0.00 0.00 0.00 4.09
198 203 3.399046 CCAGACGGGTTCATGGGA 58.601 61.111 0.00 0.00 0.00 4.37
241 246 2.685380 CCGGAGTTCTGGCCTCCT 60.685 66.667 3.32 0.00 45.29 3.69
250 255 2.603953 CCGTTCTCTAAACCGGAGTTC 58.396 52.381 9.46 0.00 43.01 3.01
251 256 1.274447 CCCGTTCTCTAAACCGGAGTT 59.726 52.381 9.46 4.11 43.01 3.01
253 258 0.893447 ACCCGTTCTCTAAACCGGAG 59.107 55.000 9.46 0.00 43.01 4.63
254 259 1.001181 CAACCCGTTCTCTAAACCGGA 59.999 52.381 9.46 0.00 43.01 5.14
255 260 1.270465 ACAACCCGTTCTCTAAACCGG 60.270 52.381 0.00 0.00 40.12 5.28
257 262 2.224354 TGGACAACCCGTTCTCTAAACC 60.224 50.000 0.00 0.00 37.93 3.27
259 264 2.038033 CCTGGACAACCCGTTCTCTAAA 59.962 50.000 0.00 0.00 37.93 1.85
260 265 1.621814 CCTGGACAACCCGTTCTCTAA 59.378 52.381 0.00 0.00 37.93 2.10
261 266 1.263356 CCTGGACAACCCGTTCTCTA 58.737 55.000 0.00 0.00 37.93 2.43
263 268 1.671379 GCCTGGACAACCCGTTCTC 60.671 63.158 0.00 0.00 37.93 2.87
264 269 2.430367 GCCTGGACAACCCGTTCT 59.570 61.111 0.00 0.00 37.93 3.01
265 270 2.671963 GGCCTGGACAACCCGTTC 60.672 66.667 0.00 0.00 37.93 3.95
266 271 4.280019 GGGCCTGGACAACCCGTT 62.280 66.667 0.00 0.00 37.93 4.44
270 275 3.808218 TTGCAGGGCCTGGACAACC 62.808 63.158 33.43 16.78 30.08 3.77
271 276 1.187567 ATTTGCAGGGCCTGGACAAC 61.188 55.000 33.43 17.51 30.08 3.32
272 277 0.471591 AATTTGCAGGGCCTGGACAA 60.472 50.000 33.43 25.56 30.08 3.18
273 278 0.407528 TAATTTGCAGGGCCTGGACA 59.592 50.000 33.43 25.39 30.08 4.02
274 279 1.204704 GTTAATTTGCAGGGCCTGGAC 59.795 52.381 33.43 18.98 30.08 4.02
275 280 1.555967 GTTAATTTGCAGGGCCTGGA 58.444 50.000 33.43 29.61 31.21 3.86
276 281 0.536724 GGTTAATTTGCAGGGCCTGG 59.463 55.000 33.43 16.27 31.21 4.45
277 282 0.173255 CGGTTAATTTGCAGGGCCTG 59.827 55.000 29.44 29.44 34.12 4.85
278 283 0.039035 TCGGTTAATTTGCAGGGCCT 59.961 50.000 0.00 0.00 0.00 5.19
279 284 1.111277 ATCGGTTAATTTGCAGGGCC 58.889 50.000 0.00 0.00 0.00 5.80
356 361 2.877786 TGCACGATCATTTTGTCAGTGT 59.122 40.909 0.00 0.00 0.00 3.55
362 367 2.096268 CGACAGTGCACGATCATTTTGT 60.096 45.455 19.37 12.62 0.00 2.83
391 396 6.926272 ACAGAGAAGTAACTCAACATTCAGAC 59.074 38.462 0.00 0.00 39.14 3.51
402 407 6.091718 AGGTTTCTGACAGAGAAGTAACTC 57.908 41.667 13.84 6.96 41.86 3.01
433 441 9.273016 CTGAGGAAGAACTAAAACTGAACATTA 57.727 33.333 0.00 0.00 0.00 1.90
487 610 3.008375 TGGATCTCAAGACAAGGGAGTTG 59.992 47.826 0.00 0.00 42.48 3.16
493 616 1.912043 AGGGTGGATCTCAAGACAAGG 59.088 52.381 0.00 0.00 0.00 3.61
494 617 4.026744 TCTAGGGTGGATCTCAAGACAAG 58.973 47.826 0.00 0.00 0.00 3.16
495 618 3.769844 GTCTAGGGTGGATCTCAAGACAA 59.230 47.826 0.00 0.00 33.69 3.18
496 619 3.245622 TGTCTAGGGTGGATCTCAAGACA 60.246 47.826 10.13 10.13 39.48 3.41
498 621 3.636679 CTGTCTAGGGTGGATCTCAAGA 58.363 50.000 0.00 0.00 0.00 3.02
499 622 2.102252 GCTGTCTAGGGTGGATCTCAAG 59.898 54.545 0.00 0.00 0.00 3.02
500 623 2.111384 GCTGTCTAGGGTGGATCTCAA 58.889 52.381 0.00 0.00 0.00 3.02
501 624 1.689575 GGCTGTCTAGGGTGGATCTCA 60.690 57.143 0.00 0.00 0.00 3.27
502 625 1.044611 GGCTGTCTAGGGTGGATCTC 58.955 60.000 0.00 0.00 0.00 2.75
503 626 0.639392 AGGCTGTCTAGGGTGGATCT 59.361 55.000 0.00 0.00 0.00 2.75
506 629 0.413832 AAGAGGCTGTCTAGGGTGGA 59.586 55.000 0.00 0.00 32.65 4.02
507 630 0.827368 GAAGAGGCTGTCTAGGGTGG 59.173 60.000 0.00 0.00 32.65 4.61
508 631 1.859302 AGAAGAGGCTGTCTAGGGTG 58.141 55.000 0.00 0.00 32.65 4.61
509 632 2.632763 AAGAAGAGGCTGTCTAGGGT 57.367 50.000 0.00 0.00 32.65 4.34
512 635 9.267084 GGATAAATTAAAGAAGAGGCTGTCTAG 57.733 37.037 0.00 0.00 32.65 2.43
513 636 8.768397 TGGATAAATTAAAGAAGAGGCTGTCTA 58.232 33.333 0.00 0.00 32.65 2.59
514 637 7.633789 TGGATAAATTAAAGAAGAGGCTGTCT 58.366 34.615 0.00 0.00 36.94 3.41
515 638 7.770897 TCTGGATAAATTAAAGAAGAGGCTGTC 59.229 37.037 0.00 0.00 0.00 3.51
534 657 9.231297 AGATTTCGTTTTGAGAATTTCTGGATA 57.769 29.630 3.03 0.00 0.00 2.59
535 658 8.025445 CAGATTTCGTTTTGAGAATTTCTGGAT 58.975 33.333 3.03 0.00 36.11 3.41
536 659 7.362662 CAGATTTCGTTTTGAGAATTTCTGGA 58.637 34.615 3.03 0.00 36.11 3.86
537 660 6.583806 CCAGATTTCGTTTTGAGAATTTCTGG 59.416 38.462 3.03 16.68 43.63 3.86
538 661 6.088616 GCCAGATTTCGTTTTGAGAATTTCTG 59.911 38.462 3.03 10.11 37.63 3.02
539 662 6.152379 GCCAGATTTCGTTTTGAGAATTTCT 58.848 36.000 0.00 0.00 0.00 2.52
540 663 5.059710 CGCCAGATTTCGTTTTGAGAATTTC 59.940 40.000 0.00 0.00 0.00 2.17
541 664 4.917415 CGCCAGATTTCGTTTTGAGAATTT 59.083 37.500 0.00 0.00 0.00 1.82
542 665 4.023193 ACGCCAGATTTCGTTTTGAGAATT 60.023 37.500 0.00 0.00 35.09 2.17
543 666 3.502211 ACGCCAGATTTCGTTTTGAGAAT 59.498 39.130 0.00 0.00 35.09 2.40
544 667 2.875933 ACGCCAGATTTCGTTTTGAGAA 59.124 40.909 0.00 0.00 35.09 2.87
545 668 2.223144 CACGCCAGATTTCGTTTTGAGA 59.777 45.455 0.00 0.00 36.73 3.27
546 669 2.574322 CACGCCAGATTTCGTTTTGAG 58.426 47.619 0.00 0.00 36.73 3.02
553 686 1.299541 ATTAGGCACGCCAGATTTCG 58.700 50.000 11.35 0.00 38.92 3.46
599 732 4.163441 TCTCAGATCATCGTCCTCTCTT 57.837 45.455 0.00 0.00 0.00 2.85
602 735 4.468713 TCATTCTCAGATCATCGTCCTCT 58.531 43.478 0.00 0.00 0.00 3.69
603 736 4.844998 TCATTCTCAGATCATCGTCCTC 57.155 45.455 0.00 0.00 0.00 3.71
604 737 4.588106 ACATCATTCTCAGATCATCGTCCT 59.412 41.667 0.00 0.00 0.00 3.85
605 738 4.880759 ACATCATTCTCAGATCATCGTCC 58.119 43.478 0.00 0.00 0.00 4.79
606 739 5.981915 TCAACATCATTCTCAGATCATCGTC 59.018 40.000 0.00 0.00 0.00 4.20
607 740 5.910614 TCAACATCATTCTCAGATCATCGT 58.089 37.500 0.00 0.00 0.00 3.73
608 741 6.618805 GCATCAACATCATTCTCAGATCATCG 60.619 42.308 0.00 0.00 0.00 3.84
609 742 6.428465 AGCATCAACATCATTCTCAGATCATC 59.572 38.462 0.00 0.00 0.00 2.92
729 882 4.049186 GCATGATGCATGTCTTCATTTCC 58.951 43.478 13.36 0.00 44.26 3.13
743 896 2.027024 CACGGCCATGCATGATGC 59.973 61.111 28.31 21.94 45.29 3.91
744 897 2.122797 ACCACGGCCATGCATGATG 61.123 57.895 28.31 17.95 0.00 3.07
745 898 2.122797 CACCACGGCCATGCATGAT 61.123 57.895 28.31 7.54 0.00 2.45
746 899 2.751036 CACCACGGCCATGCATGA 60.751 61.111 28.31 0.00 0.00 3.07
783 937 2.639065 TCGGATTTGGGTAAGTGCATC 58.361 47.619 0.00 0.00 0.00 3.91
784 938 2.799126 TCGGATTTGGGTAAGTGCAT 57.201 45.000 0.00 0.00 0.00 3.96
790 944 1.631388 TGAGGCTTCGGATTTGGGTAA 59.369 47.619 0.00 0.00 0.00 2.85
791 945 1.281419 TGAGGCTTCGGATTTGGGTA 58.719 50.000 0.00 0.00 0.00 3.69
807 962 1.903877 ATGGGCCCGAGTCAGTTGAG 61.904 60.000 19.37 0.00 0.00 3.02
809 964 1.746615 CATGGGCCCGAGTCAGTTG 60.747 63.158 19.37 0.33 0.00 3.16
821 1039 1.035139 AGAAATCGGAATGCATGGGC 58.965 50.000 0.00 0.00 41.68 5.36
823 1041 3.699067 GTGAAGAAATCGGAATGCATGG 58.301 45.455 0.00 0.00 0.00 3.66
824 1042 3.357021 CGTGAAGAAATCGGAATGCATG 58.643 45.455 0.00 0.00 0.00 4.06
825 1043 2.355756 CCGTGAAGAAATCGGAATGCAT 59.644 45.455 0.00 0.00 46.05 3.96
980 1249 1.614525 GGGGGTAAGGTCCGGAAGT 60.615 63.158 5.23 0.00 0.00 3.01
1467 1792 4.499183 GATTCTTGCTCTCTCGAAGGAAA 58.501 43.478 0.00 0.00 0.00 3.13
1482 1846 4.162640 TGCGTCGACGGATTCTTG 57.837 55.556 36.13 9.21 40.23 3.02
1517 1881 2.066393 TCCTCCTCTTGGGCCATCG 61.066 63.158 7.26 1.25 34.39 3.84
1611 2002 1.064208 CAGATGTCCACGTACTCCTCG 59.936 57.143 0.00 0.00 0.00 4.63
1845 2287 2.493973 GTCTCGAGCAGCTCCTGG 59.506 66.667 17.16 7.16 31.21 4.45
2017 2513 5.663556 TCTCCCCTTCCTCTAAATCTTCTTC 59.336 44.000 0.00 0.00 0.00 2.87
2080 2576 1.203994 AGCTTTCTTACTAGCCGCGAA 59.796 47.619 8.23 0.00 38.14 4.70
2084 2580 3.585862 TCACAAGCTTTCTTACTAGCCG 58.414 45.455 0.00 0.00 38.14 5.52
2160 2948 4.440880 TGGCAACCAAATCAGTTGAAAAG 58.559 39.130 7.77 0.00 46.03 2.27
2285 6017 1.167851 CCACAATCATGCACTCCGTT 58.832 50.000 0.00 0.00 0.00 4.44
2339 6359 3.634397 TGATGAGGTTTAGGCCAAGAG 57.366 47.619 5.01 0.00 0.00 2.85
2419 6446 5.270853 GTTGATTTGTTGCGTTCTTACTGT 58.729 37.500 0.00 0.00 0.00 3.55
2495 6524 6.642707 AAAGAACAACCGGTAATGATGAAA 57.357 33.333 8.00 0.00 0.00 2.69
2529 6558 7.243824 ACATATATTTAGGAACGGAGGGAGTA 58.756 38.462 0.00 0.00 0.00 2.59
2530 6559 6.082707 ACATATATTTAGGAACGGAGGGAGT 58.917 40.000 0.00 0.00 0.00 3.85
2531 6560 6.437793 AGACATATATTTAGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
2532 6561 6.320518 AGACATATATTTAGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
2533 6562 6.607004 AGACATATATTTAGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
2534 6563 7.931948 ACAAAGACATATATTTAGGAACGGAGG 59.068 37.037 0.00 0.00 0.00 4.30
2535 6564 8.888579 ACAAAGACATATATTTAGGAACGGAG 57.111 34.615 0.00 0.00 0.00 4.63
2568 6597 9.816354 CATCCGTATGTGGTTCATATATAATGA 57.184 33.333 0.00 0.00 40.54 2.57
2569 6598 9.599866 ACATCCGTATGTGGTTCATATATAATG 57.400 33.333 0.00 0.00 44.79 1.90
2576 6605 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
2577 6606 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
2578 6607 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
2579 6608 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
2580 6609 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
2581 6610 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
2582 6611 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
2583 6612 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
2588 6617 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
2589 6618 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
2599 6628 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
2600 6629 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
2601 6630 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
2614 6643 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2615 6644 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2616 6645 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2617 6646 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2618 6647 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2619 6648 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2620 6649 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2621 6650 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2622 6651 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2623 6652 5.794687 TTACATACGGAGCAAAATGAGTG 57.205 39.130 0.00 0.00 0.00 3.51
2624 6653 6.349300 AGATTACATACGGAGCAAAATGAGT 58.651 36.000 0.00 0.00 0.00 3.41
2625 6654 6.851222 AGATTACATACGGAGCAAAATGAG 57.149 37.500 0.00 0.00 0.00 2.90
2626 6655 9.639601 CTATAGATTACATACGGAGCAAAATGA 57.360 33.333 0.00 0.00 0.00 2.57
2627 6656 9.424319 ACTATAGATTACATACGGAGCAAAATG 57.576 33.333 6.78 0.00 0.00 2.32
2628 6657 9.424319 CACTATAGATTACATACGGAGCAAAAT 57.576 33.333 6.78 0.00 0.00 1.82
2629 6658 8.635328 TCACTATAGATTACATACGGAGCAAAA 58.365 33.333 6.78 0.00 0.00 2.44
2630 6659 8.173542 TCACTATAGATTACATACGGAGCAAA 57.826 34.615 6.78 0.00 0.00 3.68
2631 6660 7.754851 TCACTATAGATTACATACGGAGCAA 57.245 36.000 6.78 0.00 0.00 3.91
2632 6661 7.754851 TTCACTATAGATTACATACGGAGCA 57.245 36.000 6.78 0.00 0.00 4.26
2633 6662 9.291664 GATTTCACTATAGATTACATACGGAGC 57.708 37.037 6.78 0.00 0.00 4.70
2646 6675 9.702253 AGGTCTTTGTAGAGATTTCACTATAGA 57.298 33.333 6.78 0.00 0.00 1.98
2671 6700 6.718454 TGTACTCCCTCCGTTCCTAAATATAG 59.282 42.308 0.00 0.00 0.00 1.31
2672 6701 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2673 6702 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2674 6703 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2675 6704 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2676 6705 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2677 6706 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2678 6707 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
2679 6708 1.900486 CTTTGTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
2680 6709 1.675116 GCTTTGTACTCCCTCCGTTCC 60.675 57.143 0.00 0.00 0.00 3.62
2681 6710 1.001633 TGCTTTGTACTCCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
2682 6711 1.002087 CTGCTTTGTACTCCCTCCGTT 59.998 52.381 0.00 0.00 0.00 4.44
2683 6712 0.608640 CTGCTTTGTACTCCCTCCGT 59.391 55.000 0.00 0.00 0.00 4.69
2684 6713 0.108138 CCTGCTTTGTACTCCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
2685 6714 1.276622 TCCTGCTTTGTACTCCCTCC 58.723 55.000 0.00 0.00 0.00 4.30
2686 6715 2.769095 AGATCCTGCTTTGTACTCCCTC 59.231 50.000 0.00 0.00 0.00 4.30
2687 6716 2.503356 CAGATCCTGCTTTGTACTCCCT 59.497 50.000 0.00 0.00 0.00 4.20
2688 6717 2.911484 CAGATCCTGCTTTGTACTCCC 58.089 52.381 0.00 0.00 0.00 4.30
2726 6755 2.242043 CAAGAAGCAAAGGGTGGACAT 58.758 47.619 0.00 0.00 0.00 3.06
2763 6798 1.271325 TGACACCGCCTGAAACATCAT 60.271 47.619 0.00 0.00 0.00 2.45
2764 6799 0.107643 TGACACCGCCTGAAACATCA 59.892 50.000 0.00 0.00 0.00 3.07
2765 6800 0.517316 GTGACACCGCCTGAAACATC 59.483 55.000 0.00 0.00 0.00 3.06
2766 6801 1.227999 CGTGACACCGCCTGAAACAT 61.228 55.000 0.00 0.00 0.00 2.71
2767 6802 1.885388 CGTGACACCGCCTGAAACA 60.885 57.895 0.00 0.00 0.00 2.83
2768 6803 2.604174 CCGTGACACCGCCTGAAAC 61.604 63.158 0.00 0.00 0.00 2.78
2841 6876 0.179124 GACTCCACGCAGAGATGTCC 60.179 60.000 9.13 0.00 37.33 4.02
2875 6913 1.280133 CCAGGATCTCTTCTTGGCACA 59.720 52.381 0.00 0.00 43.83 4.57
2890 6928 2.787473 ATGATCAAAACGCTCCAGGA 57.213 45.000 0.00 0.00 0.00 3.86
2893 6931 2.890311 ACCAAATGATCAAAACGCTCCA 59.110 40.909 0.00 0.00 0.00 3.86
2930 6968 1.938577 CGGTGATGCTGGAGATTCTTG 59.061 52.381 0.00 0.00 0.00 3.02
2931 6969 1.745141 GCGGTGATGCTGGAGATTCTT 60.745 52.381 0.00 0.00 0.00 2.52
2947 6985 0.324275 ATAAAGCCACCCATTGCGGT 60.324 50.000 0.00 0.00 36.18 5.68
2979 7017 7.288621 TGGACATAGATTCTAATGCTTCTCTGA 59.711 37.037 0.00 0.00 0.00 3.27
2999 7037 9.803507 ACATATCAGATATGAACATTTGGACAT 57.196 29.630 29.80 6.49 44.19 3.06
3000 7038 9.631257 AACATATCAGATATGAACATTTGGACA 57.369 29.630 29.80 0.00 44.19 4.02
3003 7041 9.687210 CCAAACATATCAGATATGAACATTTGG 57.313 33.333 28.34 28.34 44.19 3.28
3004 7042 9.188588 GCCAAACATATCAGATATGAACATTTG 57.811 33.333 29.80 25.77 44.19 2.32
3005 7043 9.139734 AGCCAAACATATCAGATATGAACATTT 57.860 29.630 29.80 18.96 44.19 2.32
3006 7044 8.573885 CAGCCAAACATATCAGATATGAACATT 58.426 33.333 29.80 17.87 44.19 2.71
3007 7045 7.176165 CCAGCCAAACATATCAGATATGAACAT 59.824 37.037 29.80 14.12 44.19 2.71
3008 7046 6.487668 CCAGCCAAACATATCAGATATGAACA 59.512 38.462 29.80 0.00 44.19 3.18
3009 7047 6.569226 GCCAGCCAAACATATCAGATATGAAC 60.569 42.308 29.80 16.37 44.19 3.18
3010 7048 5.474532 GCCAGCCAAACATATCAGATATGAA 59.525 40.000 29.80 0.00 44.19 2.57
3011 7049 5.005740 GCCAGCCAAACATATCAGATATGA 58.994 41.667 29.80 1.65 44.19 2.15
3012 7050 4.142752 CGCCAGCCAAACATATCAGATATG 60.143 45.833 23.79 23.79 46.26 1.78
3013 7051 4.005650 CGCCAGCCAAACATATCAGATAT 58.994 43.478 0.00 0.00 0.00 1.63
3014 7052 3.181455 ACGCCAGCCAAACATATCAGATA 60.181 43.478 0.00 0.00 0.00 1.98
3015 7053 2.224606 CGCCAGCCAAACATATCAGAT 58.775 47.619 0.00 0.00 0.00 2.90
3016 7054 1.065491 ACGCCAGCCAAACATATCAGA 60.065 47.619 0.00 0.00 0.00 3.27
3017 7055 1.064505 CACGCCAGCCAAACATATCAG 59.935 52.381 0.00 0.00 0.00 2.90
3018 7056 1.093972 CACGCCAGCCAAACATATCA 58.906 50.000 0.00 0.00 0.00 2.15
3019 7057 1.094785 ACACGCCAGCCAAACATATC 58.905 50.000 0.00 0.00 0.00 1.63
3020 7058 1.544724 AACACGCCAGCCAAACATAT 58.455 45.000 0.00 0.00 0.00 1.78
3021 7059 1.000827 CAAACACGCCAGCCAAACATA 60.001 47.619 0.00 0.00 0.00 2.29
3022 7060 0.249405 CAAACACGCCAGCCAAACAT 60.249 50.000 0.00 0.00 0.00 2.71
3025 7063 2.105930 GCAAACACGCCAGCCAAA 59.894 55.556 0.00 0.00 0.00 3.28
3034 7072 1.238439 ACCTTGATGGAGCAAACACG 58.762 50.000 0.00 0.00 39.71 4.49
3097 7135 8.339714 CGTGTCATACTTTGAAAAAGGTTCTTA 58.660 33.333 4.86 0.00 35.70 2.10
3098 7136 7.066525 TCGTGTCATACTTTGAAAAAGGTTCTT 59.933 33.333 4.86 0.00 35.70 2.52
3179 7220 7.681782 GCCAAAATGCTGCACTTCTTGTATATA 60.682 37.037 3.57 0.00 0.00 0.86
3185 7229 1.796459 GCCAAAATGCTGCACTTCTTG 59.204 47.619 3.57 6.20 0.00 3.02
3216 7260 1.768275 TGCTCCAACTGGAAACTGAGA 59.232 47.619 0.00 0.00 44.91 3.27
3217 7261 1.876156 GTGCTCCAACTGGAAACTGAG 59.124 52.381 0.00 0.00 44.91 3.35


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

AutoCloner maintained by Alex Coulton.