Multiple sequence alignment - TraesCS5B01G327500

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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 TraesCS5B01G327500 chr5B 100.000 3017 0 0 1 3017 511363077 511360061 0.000000e+00 5572.0
1 TraesCS5B01G327500 chr5B 85.500 1000 119 22 1053 2035 511602151 511603141 0.000000e+00 1020.0
2 TraesCS5B01G327500 chr5D 91.057 1845 89 46 606 2417 423513312 423511511 0.000000e+00 2423.0
3 TraesCS5B01G327500 chr5D 84.789 973 138 7 1053 2017 423756765 423757735 0.000000e+00 968.0
4 TraesCS5B01G327500 chr5D 89.247 465 36 7 2554 3017 423511503 423511052 1.210000e-158 569.0
5 TraesCS5B01G327500 chr5D 94.000 50 3 0 2503 2552 541565447 541565398 3.230000e-10 76.8
6 TraesCS5B01G327500 chr5A 92.616 1598 62 24 507 2075 537118754 537117184 0.000000e+00 2246.0
7 TraesCS5B01G327500 chr5A 85.773 977 121 17 1053 2017 537249038 537250008 0.000000e+00 1018.0
8 TraesCS5B01G327500 chr5A 86.567 469 34 12 2558 3017 537113803 537113355 9.720000e-135 490.0
9 TraesCS5B01G327500 chr5A 84.296 433 41 19 63 474 537119180 537118754 6.060000e-107 398.0
10 TraesCS5B01G327500 chr3D 84.000 100 11 4 2465 2561 49831772 49831869 1.150000e-14 91.6
11 TraesCS5B01G327500 chr2D 84.000 100 11 4 2465 2561 288047248 288047345 1.150000e-14 91.6
12 TraesCS5B01G327500 chr2B 83.673 98 12 4 2465 2561 254010564 254010470 4.140000e-14 89.8
13 TraesCS5B01G327500 chr6A 83.000 100 12 4 2465 2561 191526376 191526473 5.360000e-13 86.1
14 TraesCS5B01G327500 chr6A 81.000 100 13 5 2465 2561 121926086 121926182 1.160000e-09 75.0
15 TraesCS5B01G327500 chr3B 83.000 100 12 4 2465 2561 722648245 722648342 5.360000e-13 86.1
16 TraesCS5B01G327500 chr3B 94.286 35 2 0 2421 2455 801414561 801414595 2.000000e-03 54.7
17 TraesCS5B01G327500 chr7A 91.228 57 5 0 2503 2559 67464965 67465021 8.970000e-11 78.7
18 TraesCS5B01G327500 chr6B 82.418 91 14 2 2465 2554 292818520 292818609 8.970000e-11 78.7
19 TraesCS5B01G327500 chr2A 100.000 30 0 0 1229 1258 49068506 49068477 4.200000e-04 56.5


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 TraesCS5B01G327500 chr5B 511360061 511363077 3016 True 5572.000000 5572 100.000000 1 3017 1 chr5B.!!$R1 3016
1 TraesCS5B01G327500 chr5B 511602151 511603141 990 False 1020.000000 1020 85.500000 1053 2035 1 chr5B.!!$F1 982
2 TraesCS5B01G327500 chr5D 423511052 423513312 2260 True 1496.000000 2423 90.152000 606 3017 2 chr5D.!!$R2 2411
3 TraesCS5B01G327500 chr5D 423756765 423757735 970 False 968.000000 968 84.789000 1053 2017 1 chr5D.!!$F1 964
4 TraesCS5B01G327500 chr5A 537113355 537119180 5825 True 1044.666667 2246 87.826333 63 3017 3 chr5A.!!$R1 2954
5 TraesCS5B01G327500 chr5A 537249038 537250008 970 False 1018.000000 1018 85.773000 1053 2017 1 chr5A.!!$F1 964

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
187 188 0.247576 CGATCGCACGTCTAACGACT 60.248 55.0 0.26 0.0 46.05 4.18 F
455 489 0.254178 ACCATCGCTCCTGCAAATCT 59.746 50.0 0.00 0.0 39.64 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1027 1104 0.531974 TTCTTCTTGCCGCTGTCGTT 60.532 50.000 0.0 0.0 0.00 3.85 R
2120 5081 1.070275 CTCTGCTCTGCACACCACA 59.930 57.895 0.0 0.0 33.79 4.17 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
17 18 4.175337 GGCGGGCATGGTCAGCTA 62.175 66.667 0.00 0.00 0.00 3.32
18 19 2.124736 GCGGGCATGGTCAGCTAA 60.125 61.111 0.00 0.00 0.00 3.09
19 20 1.748879 GCGGGCATGGTCAGCTAAA 60.749 57.895 0.00 0.00 0.00 1.85
20 21 1.103398 GCGGGCATGGTCAGCTAAAT 61.103 55.000 0.00 0.00 0.00 1.40
21 22 1.392589 CGGGCATGGTCAGCTAAATT 58.607 50.000 0.00 0.00 0.00 1.82
22 23 1.066002 CGGGCATGGTCAGCTAAATTG 59.934 52.381 0.00 0.00 0.00 2.32
23 24 1.202452 GGGCATGGTCAGCTAAATTGC 60.202 52.381 0.00 0.00 0.00 3.56
24 25 1.753073 GGCATGGTCAGCTAAATTGCT 59.247 47.619 0.00 0.00 45.18 3.91
25 26 2.223665 GGCATGGTCAGCTAAATTGCTC 60.224 50.000 0.00 0.00 41.98 4.26
26 27 2.540361 GCATGGTCAGCTAAATTGCTCG 60.540 50.000 0.00 0.00 41.98 5.03
27 28 2.760634 TGGTCAGCTAAATTGCTCGA 57.239 45.000 0.00 0.00 41.98 4.04
28 29 3.052455 TGGTCAGCTAAATTGCTCGAA 57.948 42.857 0.00 0.00 41.98 3.71
29 30 3.002791 TGGTCAGCTAAATTGCTCGAAG 58.997 45.455 0.00 0.00 41.98 3.79
30 31 2.223135 GGTCAGCTAAATTGCTCGAAGC 60.223 50.000 0.00 0.00 41.98 3.86
31 32 1.660607 TCAGCTAAATTGCTCGAAGCG 59.339 47.619 0.00 0.00 46.26 4.68
32 33 0.375106 AGCTAAATTGCTCGAAGCGC 59.625 50.000 0.00 0.00 46.26 5.92
33 34 0.921214 GCTAAATTGCTCGAAGCGCG 60.921 55.000 0.00 0.00 46.26 6.86
34 35 0.645355 CTAAATTGCTCGAAGCGCGA 59.355 50.000 12.10 4.72 46.26 5.87
41 42 4.944249 TCGAAGCGCGATGATAGG 57.056 55.556 12.10 0.00 45.59 2.57
42 43 2.327228 TCGAAGCGCGATGATAGGA 58.673 52.632 12.10 0.00 45.59 2.94
43 44 0.881796 TCGAAGCGCGATGATAGGAT 59.118 50.000 12.10 0.00 45.59 3.24
44 45 0.987715 CGAAGCGCGATGATAGGATG 59.012 55.000 12.10 0.00 44.57 3.51
45 46 1.401539 CGAAGCGCGATGATAGGATGA 60.402 52.381 12.10 0.00 44.57 2.92
46 47 2.257894 GAAGCGCGATGATAGGATGAG 58.742 52.381 12.10 0.00 0.00 2.90
47 48 0.529833 AGCGCGATGATAGGATGAGG 59.470 55.000 12.10 0.00 0.00 3.86
48 49 1.080995 GCGCGATGATAGGATGAGGC 61.081 60.000 12.10 0.00 0.00 4.70
49 50 0.799917 CGCGATGATAGGATGAGGCG 60.800 60.000 0.00 0.00 36.29 5.52
50 51 0.528017 GCGATGATAGGATGAGGCGA 59.472 55.000 0.00 0.00 0.00 5.54
51 52 1.135915 GCGATGATAGGATGAGGCGAT 59.864 52.381 0.00 0.00 0.00 4.58
52 53 2.797792 GCGATGATAGGATGAGGCGATC 60.798 54.545 0.00 0.00 0.00 3.69
53 54 2.687425 CGATGATAGGATGAGGCGATCT 59.313 50.000 0.00 0.00 0.00 2.75
54 55 3.130164 CGATGATAGGATGAGGCGATCTT 59.870 47.826 0.00 0.00 0.00 2.40
55 56 4.681744 GATGATAGGATGAGGCGATCTTC 58.318 47.826 0.00 0.00 0.00 2.87
56 57 3.772387 TGATAGGATGAGGCGATCTTCT 58.228 45.455 0.00 0.00 33.58 2.85
57 58 3.509184 TGATAGGATGAGGCGATCTTCTG 59.491 47.826 0.00 0.00 33.58 3.02
58 59 1.047002 AGGATGAGGCGATCTTCTGG 58.953 55.000 0.00 0.00 33.58 3.86
59 60 0.602372 GGATGAGGCGATCTTCTGGC 60.602 60.000 0.00 0.00 33.58 4.85
60 61 0.392336 GATGAGGCGATCTTCTGGCT 59.608 55.000 0.00 0.00 44.53 4.75
105 106 2.223688 CCGAGAGCTACTGATTGGTCTG 60.224 54.545 0.00 0.00 40.53 3.51
111 112 2.748605 CTACTGATTGGTCTGATCCGC 58.251 52.381 0.00 0.00 0.00 5.54
129 130 8.500753 TGATCCGCTTTATTACTGTACAAAAT 57.499 30.769 0.00 2.79 0.00 1.82
135 136 7.696453 CGCTTTATTACTGTACAAAATTGGAGG 59.304 37.037 8.06 0.00 0.00 4.30
136 137 7.973944 GCTTTATTACTGTACAAAATTGGAGGG 59.026 37.037 8.06 0.00 0.00 4.30
159 160 0.681733 ACAGAGCTCGTGGTTCATGT 59.318 50.000 8.37 1.31 0.00 3.21
185 186 1.581912 GCGATCGCACGTCTAACGA 60.582 57.895 33.89 2.52 45.86 3.85
187 188 0.247576 CGATCGCACGTCTAACGACT 60.248 55.000 0.26 0.00 46.05 4.18
207 208 3.408851 GCCCGTTCGTGTCCGTTC 61.409 66.667 0.00 0.00 35.01 3.95
214 215 2.220133 CGTTCGTGTCCGTTCATTTTCT 59.780 45.455 0.00 0.00 35.01 2.52
216 217 4.209112 GTTCGTGTCCGTTCATTTTCTTC 58.791 43.478 0.00 0.00 35.01 2.87
232 233 3.350219 TCTTCTTGGAGGGGAATTTCG 57.650 47.619 0.00 0.00 0.00 3.46
246 247 5.358725 GGGGAATTTCGGAATGCTAAAACTA 59.641 40.000 0.00 0.00 0.00 2.24
251 252 8.911247 AATTTCGGAATGCTAAAACTATTCAC 57.089 30.769 0.00 0.00 33.57 3.18
258 259 2.536928 GCTAAAACTATTCACTGGCGCG 60.537 50.000 0.00 0.00 0.00 6.86
272 273 2.202623 CGCGAGTCACCTACAGGC 60.203 66.667 0.00 0.00 39.32 4.85
273 274 2.970639 GCGAGTCACCTACAGGCA 59.029 61.111 0.00 0.00 39.32 4.75
274 275 1.153745 GCGAGTCACCTACAGGCAG 60.154 63.158 0.00 0.00 39.32 4.85
275 276 1.153745 CGAGTCACCTACAGGCAGC 60.154 63.158 0.00 0.00 39.32 5.25
276 277 1.219393 GAGTCACCTACAGGCAGCC 59.781 63.158 1.84 1.84 39.32 4.85
291 292 1.339438 GCAGCCTTCACTCATTCTGGA 60.339 52.381 0.00 0.00 0.00 3.86
301 302 0.953471 TCATTCTGGACCGTTTGCCG 60.953 55.000 0.00 0.00 0.00 5.69
335 336 6.464311 GTCGTAACTGTTGAATATTCCGAAC 58.536 40.000 12.90 11.43 0.00 3.95
336 337 6.309737 GTCGTAACTGTTGAATATTCCGAACT 59.690 38.462 12.90 0.00 0.00 3.01
337 338 6.869913 TCGTAACTGTTGAATATTCCGAACTT 59.130 34.615 12.90 5.90 0.00 2.66
338 339 7.062605 TCGTAACTGTTGAATATTCCGAACTTC 59.937 37.037 12.90 0.00 0.00 3.01
339 340 7.063074 CGTAACTGTTGAATATTCCGAACTTCT 59.937 37.037 12.90 3.61 0.00 2.85
340 341 6.727824 ACTGTTGAATATTCCGAACTTCTG 57.272 37.500 12.90 6.53 0.00 3.02
346 375 5.350365 TGAATATTCCGAACTTCTGTTTCGG 59.650 40.000 15.74 15.74 42.52 4.30
350 379 1.128692 CCGAACTTCTGTTTCGGATGC 59.871 52.381 16.68 0.00 43.13 3.91
378 407 5.378292 TGGATATACGAGTTGAGATGCTC 57.622 43.478 0.00 0.00 0.00 4.26
380 409 5.536538 TGGATATACGAGTTGAGATGCTCTT 59.463 40.000 0.00 0.00 0.00 2.85
381 410 6.040955 TGGATATACGAGTTGAGATGCTCTTT 59.959 38.462 0.00 0.00 0.00 2.52
382 411 6.926272 GGATATACGAGTTGAGATGCTCTTTT 59.074 38.462 0.00 0.00 0.00 2.27
383 412 7.095857 GGATATACGAGTTGAGATGCTCTTTTG 60.096 40.741 0.00 0.00 0.00 2.44
384 413 3.733337 ACGAGTTGAGATGCTCTTTTGT 58.267 40.909 0.00 0.00 0.00 2.83
385 414 3.496130 ACGAGTTGAGATGCTCTTTTGTG 59.504 43.478 0.00 0.00 0.00 3.33
386 415 3.666374 CGAGTTGAGATGCTCTTTTGTGC 60.666 47.826 0.00 0.00 39.19 4.57
392 421 2.736197 TGCTCTTTTGTGCATGCCT 58.264 47.368 16.68 0.00 42.99 4.75
393 422 0.315886 TGCTCTTTTGTGCATGCCTG 59.684 50.000 16.68 0.00 42.99 4.85
431 463 2.360350 CTGCCGGGACACATGCTT 60.360 61.111 2.18 0.00 0.00 3.91
442 474 1.999735 ACACATGCTTTCGTACCATCG 59.000 47.619 0.00 0.00 0.00 3.84
455 489 0.254178 ACCATCGCTCCTGCAAATCT 59.746 50.000 0.00 0.00 39.64 2.40
461 495 0.654683 GCTCCTGCAAATCTACTGCG 59.345 55.000 0.00 0.00 42.97 5.18
473 507 6.355638 CAAATCTACTGCGTAAATCCGAATC 58.644 40.000 0.00 0.00 0.00 2.52
474 508 3.973657 TCTACTGCGTAAATCCGAATCC 58.026 45.455 0.00 0.00 0.00 3.01
475 509 2.684001 ACTGCGTAAATCCGAATCCA 57.316 45.000 0.00 0.00 0.00 3.41
476 510 2.550978 ACTGCGTAAATCCGAATCCAG 58.449 47.619 0.00 0.00 0.00 3.86
477 511 2.167693 ACTGCGTAAATCCGAATCCAGA 59.832 45.455 0.00 0.00 0.00 3.86
478 512 3.194861 CTGCGTAAATCCGAATCCAGAA 58.805 45.455 0.00 0.00 0.00 3.02
479 513 3.601435 TGCGTAAATCCGAATCCAGAAA 58.399 40.909 0.00 0.00 0.00 2.52
480 514 4.004314 TGCGTAAATCCGAATCCAGAAAA 58.996 39.130 0.00 0.00 0.00 2.29
481 515 4.094294 TGCGTAAATCCGAATCCAGAAAAG 59.906 41.667 0.00 0.00 0.00 2.27
482 516 4.588278 CGTAAATCCGAATCCAGAAAAGC 58.412 43.478 0.00 0.00 0.00 3.51
483 517 4.094294 CGTAAATCCGAATCCAGAAAAGCA 59.906 41.667 0.00 0.00 0.00 3.91
484 518 4.708726 AAATCCGAATCCAGAAAAGCAG 57.291 40.909 0.00 0.00 0.00 4.24
485 519 3.634397 ATCCGAATCCAGAAAAGCAGA 57.366 42.857 0.00 0.00 0.00 4.26
486 520 3.417069 TCCGAATCCAGAAAAGCAGAA 57.583 42.857 0.00 0.00 0.00 3.02
487 521 3.750371 TCCGAATCCAGAAAAGCAGAAA 58.250 40.909 0.00 0.00 0.00 2.52
488 522 4.141287 TCCGAATCCAGAAAAGCAGAAAA 58.859 39.130 0.00 0.00 0.00 2.29
489 523 4.582656 TCCGAATCCAGAAAAGCAGAAAAA 59.417 37.500 0.00 0.00 0.00 1.94
490 524 4.919754 CCGAATCCAGAAAAGCAGAAAAAG 59.080 41.667 0.00 0.00 0.00 2.27
491 525 5.507985 CCGAATCCAGAAAAGCAGAAAAAGT 60.508 40.000 0.00 0.00 0.00 2.66
492 526 5.979517 CGAATCCAGAAAAGCAGAAAAAGTT 59.020 36.000 0.00 0.00 0.00 2.66
493 527 6.074676 CGAATCCAGAAAAGCAGAAAAAGTTG 60.075 38.462 0.00 0.00 0.00 3.16
494 528 5.659440 TCCAGAAAAGCAGAAAAAGTTGT 57.341 34.783 0.00 0.00 0.00 3.32
495 529 6.767524 TCCAGAAAAGCAGAAAAAGTTGTA 57.232 33.333 0.00 0.00 0.00 2.41
496 530 6.560711 TCCAGAAAAGCAGAAAAAGTTGTAC 58.439 36.000 0.00 0.00 0.00 2.90
497 531 5.748630 CCAGAAAAGCAGAAAAAGTTGTACC 59.251 40.000 0.00 0.00 0.00 3.34
498 532 5.748630 CAGAAAAGCAGAAAAAGTTGTACCC 59.251 40.000 0.00 0.00 0.00 3.69
499 533 5.420739 AGAAAAGCAGAAAAAGTTGTACCCA 59.579 36.000 0.00 0.00 0.00 4.51
500 534 5.869649 AAAGCAGAAAAAGTTGTACCCAT 57.130 34.783 0.00 0.00 0.00 4.00
501 535 5.869649 AAGCAGAAAAAGTTGTACCCATT 57.130 34.783 0.00 0.00 0.00 3.16
502 536 6.969993 AAGCAGAAAAAGTTGTACCCATTA 57.030 33.333 0.00 0.00 0.00 1.90
503 537 6.327279 AGCAGAAAAAGTTGTACCCATTAC 57.673 37.500 0.00 0.00 0.00 1.89
504 538 5.243060 AGCAGAAAAAGTTGTACCCATTACC 59.757 40.000 0.00 0.00 0.00 2.85
505 539 5.566032 GCAGAAAAAGTTGTACCCATTACCC 60.566 44.000 0.00 0.00 0.00 3.69
513 547 1.339644 TACCCATTACCCCACGAGCC 61.340 60.000 0.00 0.00 0.00 4.70
534 568 3.821033 CCTTTCGTCCCAAAGTCTTCATT 59.179 43.478 0.00 0.00 32.26 2.57
541 575 4.023707 GTCCCAAAGTCTTCATTGACACAG 60.024 45.833 0.00 0.00 39.27 3.66
543 577 3.316029 CCAAAGTCTTCATTGACACAGCA 59.684 43.478 0.00 0.00 39.27 4.41
555 589 6.539826 TCATTGACACAGCAGAATTATACAGG 59.460 38.462 0.00 0.00 0.00 4.00
568 602 1.704641 ATACAGGCACGAGCTCCATA 58.295 50.000 8.47 0.00 41.70 2.74
573 607 2.684881 CAGGCACGAGCTCCATATTTTT 59.315 45.455 8.47 0.00 41.70 1.94
596 630 0.989164 TCTCGAAATTGTACGCGCTG 59.011 50.000 5.73 1.02 0.00 5.18
616 650 4.498513 GCTGCATATTGATAAGCTGCAACA 60.499 41.667 18.68 0.00 45.17 3.33
657 691 3.722101 CCTAACCCATCCTATCACCCTTT 59.278 47.826 0.00 0.00 0.00 3.11
669 703 6.003950 CCTATCACCCTTTTTCTGAACAAGA 58.996 40.000 15.86 0.00 0.00 3.02
704 738 2.742372 CGTGCTGCCACTACCACC 60.742 66.667 0.00 0.00 39.86 4.61
711 745 1.599797 GCCACTACCACCACCACAC 60.600 63.158 0.00 0.00 0.00 3.82
712 746 1.072505 CCACTACCACCACCACACC 59.927 63.158 0.00 0.00 0.00 4.16
713 747 1.701031 CCACTACCACCACCACACCA 61.701 60.000 0.00 0.00 0.00 4.17
774 808 1.134175 ACACACAAACGCCCAAGAAAG 59.866 47.619 0.00 0.00 0.00 2.62
791 825 2.660258 AAGAACACGCCACGCTTCCT 62.660 55.000 0.00 0.00 0.00 3.36
794 828 4.379243 CACGCCACGCTTCCTCCT 62.379 66.667 0.00 0.00 0.00 3.69
795 829 4.070552 ACGCCACGCTTCCTCCTC 62.071 66.667 0.00 0.00 0.00 3.71
797 831 3.394836 GCCACGCTTCCTCCTCCT 61.395 66.667 0.00 0.00 0.00 3.69
799 833 2.726351 CCACGCTTCCTCCTCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
800 834 2.364448 ACGCTTCCTCCTCCTCCC 60.364 66.667 0.00 0.00 0.00 4.30
802 836 2.370633 GCTTCCTCCTCCTCCCCT 59.629 66.667 0.00 0.00 0.00 4.79
820 865 2.069465 CTCATCGACCCGAGCTCCAG 62.069 65.000 8.47 1.70 39.91 3.86
1018 1095 1.343884 CCATGTCTTCCTCCTCTCCCT 60.344 57.143 0.00 0.00 0.00 4.20
1027 1104 1.413662 CCTCCTCTCCCTCCAATAGCA 60.414 57.143 0.00 0.00 0.00 3.49
2025 2108 4.842091 GCCGCGTGATCCGTACGT 62.842 66.667 15.21 0.00 43.09 3.57
2035 2120 3.505184 CCGTACGTTGCATGGGGC 61.505 66.667 15.21 0.00 45.13 5.80
2036 2121 3.505184 CGTACGTTGCATGGGGCC 61.505 66.667 7.22 0.00 43.89 5.80
2037 2122 2.045340 GTACGTTGCATGGGGCCT 60.045 61.111 0.84 0.00 43.89 5.19
2038 2123 2.045438 TACGTTGCATGGGGCCTG 60.045 61.111 0.84 0.00 43.89 4.85
2055 2140 2.795470 GCCTGCGTGTAGTAATTAGAGC 59.205 50.000 0.00 0.00 0.00 4.09
2056 2141 3.043586 CCTGCGTGTAGTAATTAGAGCG 58.956 50.000 0.00 0.00 0.00 5.03
2090 5051 3.593096 GATTAGAGGGGTTCGTTCGTTT 58.407 45.455 0.00 0.00 0.00 3.60
2108 5069 2.249844 TTGTCCTTCGGGTTGTCTTC 57.750 50.000 0.00 0.00 36.28 2.87
2109 5070 1.420430 TGTCCTTCGGGTTGTCTTCT 58.580 50.000 0.00 0.00 36.28 2.85
2113 5074 2.704065 TCCTTCGGGTTGTCTTCTCTTT 59.296 45.455 0.00 0.00 36.28 2.52
2115 5076 3.498777 CCTTCGGGTTGTCTTCTCTTTTC 59.501 47.826 0.00 0.00 0.00 2.29
2116 5077 2.750948 TCGGGTTGTCTTCTCTTTTCG 58.249 47.619 0.00 0.00 0.00 3.46
2118 5079 2.221055 CGGGTTGTCTTCTCTTTTCGTG 59.779 50.000 0.00 0.00 0.00 4.35
2119 5080 2.548480 GGGTTGTCTTCTCTTTTCGTGG 59.452 50.000 0.00 0.00 0.00 4.94
2120 5081 3.203716 GGTTGTCTTCTCTTTTCGTGGT 58.796 45.455 0.00 0.00 0.00 4.16
2144 5107 1.448189 GTGCAGAGCAGAGCAGAGG 60.448 63.158 0.00 0.00 42.14 3.69
2202 5175 5.457052 CCGGGTGGGGATTATTTACTTACAT 60.457 44.000 0.00 0.00 0.00 2.29
2205 5178 6.264518 GGGTGGGGATTATTTACTTACATGTG 59.735 42.308 9.11 0.00 0.00 3.21
2209 5182 9.707957 TGGGGATTATTTACTTACATGTGAATT 57.292 29.630 9.11 0.00 30.54 2.17
2219 5192 1.885887 ACATGTGAATTTGGGACACCG 59.114 47.619 0.00 0.00 39.29 4.94
2249 5222 1.668751 GGTGTTGATGTTCGTGTGTGT 59.331 47.619 0.00 0.00 0.00 3.72
2250 5223 2.538737 GGTGTTGATGTTCGTGTGTGTG 60.539 50.000 0.00 0.00 0.00 3.82
2251 5224 2.095213 GTGTTGATGTTCGTGTGTGTGT 59.905 45.455 0.00 0.00 0.00 3.72
2349 5328 6.204495 TGATGTGAATTGTTCGTTCATCTCAA 59.796 34.615 15.71 0.00 37.84 3.02
2361 5340 5.692204 TCGTTCATCTCAACAGAGAAAAGTC 59.308 40.000 0.00 0.00 41.44 3.01
2371 5350 5.686159 ACAGAGAAAAGTCTTCATGCAAG 57.314 39.130 0.00 0.00 32.80 4.01
2375 5355 6.648310 CAGAGAAAAGTCTTCATGCAAGTAGA 59.352 38.462 0.00 0.00 32.80 2.59
2391 5374 7.799081 TGCAAGTAGACACTAGTAGGATAGTA 58.201 38.462 1.45 0.00 34.21 1.82
2421 5405 8.754991 TCTAAAAAGAAACCTTGATTACACCA 57.245 30.769 0.00 0.00 0.00 4.17
2429 5424 7.947890 AGAAACCTTGATTACACCATTCCTAAA 59.052 33.333 0.00 0.00 0.00 1.85
2458 5453 7.482169 AATCTTTGTAGATAGTCCACTGTGA 57.518 36.000 9.86 0.00 40.26 3.58
2459 5454 6.911250 TCTTTGTAGATAGTCCACTGTGAA 57.089 37.500 9.86 0.00 0.00 3.18
2460 5455 7.482169 TCTTTGTAGATAGTCCACTGTGAAT 57.518 36.000 9.86 0.00 0.00 2.57
2462 5457 6.850752 TTGTAGATAGTCCACTGTGAATCA 57.149 37.500 9.86 0.00 0.00 2.57
2463 5458 7.423844 TTGTAGATAGTCCACTGTGAATCAT 57.576 36.000 9.86 0.00 0.00 2.45
2464 5459 8.533569 TTGTAGATAGTCCACTGTGAATCATA 57.466 34.615 9.86 0.00 0.00 2.15
2465 5460 8.712228 TGTAGATAGTCCACTGTGAATCATAT 57.288 34.615 9.86 0.60 0.00 1.78
2466 5461 8.579863 TGTAGATAGTCCACTGTGAATCATATG 58.420 37.037 9.86 0.00 0.00 1.78
2467 5462 6.462500 AGATAGTCCACTGTGAATCATATGC 58.538 40.000 9.86 0.00 0.00 3.14
2468 5463 4.492494 AGTCCACTGTGAATCATATGCA 57.508 40.909 9.86 0.00 0.00 3.96
2469 5464 5.045012 AGTCCACTGTGAATCATATGCAT 57.955 39.130 9.86 3.79 0.00 3.96
2470 5465 5.443283 AGTCCACTGTGAATCATATGCATT 58.557 37.500 3.54 0.00 0.00 3.56
2471 5466 5.889853 AGTCCACTGTGAATCATATGCATTT 59.110 36.000 3.54 0.00 0.00 2.32
2472 5467 6.379133 AGTCCACTGTGAATCATATGCATTTT 59.621 34.615 3.54 0.00 0.00 1.82
2473 5468 7.037438 GTCCACTGTGAATCATATGCATTTTT 58.963 34.615 3.54 0.00 0.00 1.94
2475 5470 8.407832 TCCACTGTGAATCATATGCATTTTTAG 58.592 33.333 3.54 0.00 0.00 1.85
2477 5472 9.447040 CACTGTGAATCATATGCATTTTTAGAG 57.553 33.333 3.54 2.20 0.00 2.43
2480 5475 8.959548 TGTGAATCATATGCATTTTTAGAGTGT 58.040 29.630 3.54 0.00 0.00 3.55
2501 5496 7.665080 GTGTAAATCACTCATTTTATTCCGC 57.335 36.000 0.00 0.00 43.13 5.54
2502 5497 7.247728 GTGTAAATCACTCATTTTATTCCGCA 58.752 34.615 0.00 0.00 43.13 5.69
2503 5498 7.915397 GTGTAAATCACTCATTTTATTCCGCAT 59.085 33.333 0.00 0.00 43.13 4.73
2504 5499 7.914871 TGTAAATCACTCATTTTATTCCGCATG 59.085 33.333 0.00 0.00 36.09 4.06
2505 5500 6.455360 AATCACTCATTTTATTCCGCATGT 57.545 33.333 0.00 0.00 0.00 3.21
2506 5501 7.566760 AATCACTCATTTTATTCCGCATGTA 57.433 32.000 0.00 0.00 0.00 2.29
2509 5504 6.257849 TCACTCATTTTATTCCGCATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2512 5507 8.150945 ACTCATTTTATTCCGCATGTAGTCTAT 58.849 33.333 0.00 0.00 0.00 1.98
2514 5509 9.990360 TCATTTTATTCCGCATGTAGTCTATAA 57.010 29.630 0.00 0.00 0.00 0.98
2553 5567 4.553678 ACTTATATTCAGGAACGGAGGGA 58.446 43.478 0.00 0.00 31.97 4.20
2554 5568 4.966805 ACTTATATTCAGGAACGGAGGGAA 59.033 41.667 0.00 0.00 31.97 3.97
2555 5569 5.607171 ACTTATATTCAGGAACGGAGGGAAT 59.393 40.000 0.00 0.00 31.97 3.01
2556 5570 6.785963 ACTTATATTCAGGAACGGAGGGAATA 59.214 38.462 0.00 0.00 35.59 1.75
2557 5571 5.746990 ATATTCAGGAACGGAGGGAATAG 57.253 43.478 0.00 0.00 34.88 1.73
2558 5572 2.544844 TCAGGAACGGAGGGAATAGT 57.455 50.000 0.00 0.00 0.00 2.12
2560 5574 4.194678 TCAGGAACGGAGGGAATAGTAT 57.805 45.455 0.00 0.00 0.00 2.12
2561 5575 4.150359 TCAGGAACGGAGGGAATAGTATC 58.850 47.826 0.00 0.00 0.00 2.24
2562 5576 3.258622 CAGGAACGGAGGGAATAGTATCC 59.741 52.174 0.00 0.00 38.86 2.59
2630 5647 3.006217 GCTTTCAGGATGGCTTTCAACTT 59.994 43.478 0.00 0.00 36.16 2.66
2640 5657 0.785979 CTTTCAACTTGCGGCAATGC 59.214 50.000 16.80 0.00 0.00 3.56
2672 5689 4.689345 GCTGTTACCATCGAAGTTACTTGT 59.311 41.667 0.93 0.00 0.00 3.16
2678 5695 5.171476 ACCATCGAAGTTACTTGTGATCAG 58.829 41.667 0.93 2.88 0.00 2.90
2710 5727 2.347452 ACGGTTGAGCATTTATTCGACG 59.653 45.455 0.00 0.00 0.00 5.12
2754 5771 8.103305 ACACTAACATCACATCAGGTCTATTTT 58.897 33.333 0.00 0.00 0.00 1.82
2755 5772 8.950210 CACTAACATCACATCAGGTCTATTTTT 58.050 33.333 0.00 0.00 0.00 1.94
2805 5822 9.796120 TCACAACAGGTCATTTTAAACTTTTAG 57.204 29.630 0.00 0.00 0.00 1.85
2830 5847 6.192682 GCTTTTGCTCGTTTGATTTTTCAAAC 59.807 34.615 17.44 17.44 46.28 2.93
2915 5936 5.239351 TGCATGAAAATACAGCTTGCAATT 58.761 33.333 0.00 0.00 38.98 2.32
3002 6023 1.757682 AAGAAAGTTGGCGGTTGACA 58.242 45.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.697439 TTAGCTGACCATGCCCGCC 62.697 63.158 0.00 0.00 0.00 6.13
1 2 1.103398 ATTTAGCTGACCATGCCCGC 61.103 55.000 0.00 0.00 0.00 6.13
2 3 1.066002 CAATTTAGCTGACCATGCCCG 59.934 52.381 0.00 0.00 0.00 6.13
3 4 1.202452 GCAATTTAGCTGACCATGCCC 60.202 52.381 0.00 0.00 0.00 5.36
4 5 1.753073 AGCAATTTAGCTGACCATGCC 59.247 47.619 0.00 0.00 44.66 4.40
5 6 2.540361 CGAGCAATTTAGCTGACCATGC 60.540 50.000 0.00 0.47 46.75 4.06
6 7 2.938451 TCGAGCAATTTAGCTGACCATG 59.062 45.455 0.00 0.00 46.75 3.66
7 8 3.266510 TCGAGCAATTTAGCTGACCAT 57.733 42.857 0.00 0.00 46.75 3.55
8 9 2.760634 TCGAGCAATTTAGCTGACCA 57.239 45.000 0.00 0.00 46.75 4.02
9 10 2.223135 GCTTCGAGCAATTTAGCTGACC 60.223 50.000 0.00 0.00 46.75 4.02
10 11 2.535732 CGCTTCGAGCAATTTAGCTGAC 60.536 50.000 0.00 0.00 46.75 3.51
11 12 1.660607 CGCTTCGAGCAATTTAGCTGA 59.339 47.619 0.00 0.00 46.75 4.26
12 13 1.853646 GCGCTTCGAGCAATTTAGCTG 60.854 52.381 0.00 0.76 46.75 4.24
14 15 0.921214 CGCGCTTCGAGCAATTTAGC 60.921 55.000 5.56 0.90 42.58 3.09
15 16 0.645355 TCGCGCTTCGAGCAATTTAG 59.355 50.000 5.56 0.00 42.58 1.85
16 17 2.744461 TCGCGCTTCGAGCAATTTA 58.256 47.368 5.56 0.00 42.58 1.40
17 18 3.561429 TCGCGCTTCGAGCAATTT 58.439 50.000 5.56 0.00 42.58 1.82
25 26 0.987715 CATCCTATCATCGCGCTTCG 59.012 55.000 5.56 0.00 40.15 3.79
26 27 2.257894 CTCATCCTATCATCGCGCTTC 58.742 52.381 5.56 0.00 0.00 3.86
27 28 1.067283 CCTCATCCTATCATCGCGCTT 60.067 52.381 5.56 0.00 0.00 4.68
28 29 0.529833 CCTCATCCTATCATCGCGCT 59.470 55.000 5.56 0.00 0.00 5.92
29 30 1.080995 GCCTCATCCTATCATCGCGC 61.081 60.000 0.00 0.00 0.00 6.86
30 31 0.799917 CGCCTCATCCTATCATCGCG 60.800 60.000 0.00 0.00 0.00 5.87
31 32 0.528017 TCGCCTCATCCTATCATCGC 59.472 55.000 0.00 0.00 0.00 4.58
32 33 2.687425 AGATCGCCTCATCCTATCATCG 59.313 50.000 0.00 0.00 0.00 3.84
33 34 4.402155 AGAAGATCGCCTCATCCTATCATC 59.598 45.833 0.00 0.00 0.00 2.92
34 35 4.160065 CAGAAGATCGCCTCATCCTATCAT 59.840 45.833 0.00 0.00 0.00 2.45
35 36 3.509184 CAGAAGATCGCCTCATCCTATCA 59.491 47.826 0.00 0.00 0.00 2.15
36 37 3.119173 CCAGAAGATCGCCTCATCCTATC 60.119 52.174 0.00 0.00 0.00 2.08
37 38 2.830923 CCAGAAGATCGCCTCATCCTAT 59.169 50.000 0.00 0.00 0.00 2.57
38 39 2.242926 CCAGAAGATCGCCTCATCCTA 58.757 52.381 0.00 0.00 0.00 2.94
39 40 1.047002 CCAGAAGATCGCCTCATCCT 58.953 55.000 0.00 0.00 0.00 3.24
40 41 0.602372 GCCAGAAGATCGCCTCATCC 60.602 60.000 0.00 0.00 0.00 3.51
41 42 0.392336 AGCCAGAAGATCGCCTCATC 59.608 55.000 0.00 0.00 0.00 2.92
42 43 0.392336 GAGCCAGAAGATCGCCTCAT 59.608 55.000 0.00 0.00 0.00 2.90
43 44 1.819229 GAGCCAGAAGATCGCCTCA 59.181 57.895 0.00 0.00 0.00 3.86
44 45 1.299773 CGAGCCAGAAGATCGCCTC 60.300 63.158 0.00 0.00 0.00 4.70
45 46 2.811101 CGAGCCAGAAGATCGCCT 59.189 61.111 0.00 0.00 0.00 5.52
48 49 0.460987 AAAGGCGAGCCAGAAGATCG 60.461 55.000 17.18 0.00 38.92 3.69
49 50 1.012841 CAAAGGCGAGCCAGAAGATC 58.987 55.000 17.18 0.00 38.92 2.75
50 51 1.028868 GCAAAGGCGAGCCAGAAGAT 61.029 55.000 17.18 0.00 38.92 2.40
51 52 1.672356 GCAAAGGCGAGCCAGAAGA 60.672 57.895 17.18 0.00 38.92 2.87
52 53 2.873288 GCAAAGGCGAGCCAGAAG 59.127 61.111 17.18 4.37 38.92 2.85
105 106 9.221775 CAATTTTGTACAGTAATAAAGCGGATC 57.778 33.333 0.00 0.00 0.00 3.36
111 112 9.238368 TCCCTCCAATTTTGTACAGTAATAAAG 57.762 33.333 0.00 0.47 0.00 1.85
129 130 1.270839 CGAGCTCTGTTTTCCCTCCAA 60.271 52.381 12.85 0.00 0.00 3.53
135 136 1.531578 GAACCACGAGCTCTGTTTTCC 59.468 52.381 12.85 0.00 0.00 3.13
136 137 2.210116 TGAACCACGAGCTCTGTTTTC 58.790 47.619 12.85 14.62 0.00 2.29
159 160 2.379634 CGTGCGATCGCTGTCCAAA 61.380 57.895 37.01 15.56 42.51 3.28
185 186 4.353437 GACACGAACGGGCCGAGT 62.353 66.667 35.78 24.90 33.85 4.18
207 208 6.364568 AAATTCCCCTCCAAGAAGAAAATG 57.635 37.500 0.00 0.00 0.00 2.32
214 215 1.989586 TCCGAAATTCCCCTCCAAGAA 59.010 47.619 0.00 0.00 0.00 2.52
216 217 2.507407 TTCCGAAATTCCCCTCCAAG 57.493 50.000 0.00 0.00 0.00 3.61
232 233 5.582550 GCCAGTGAATAGTTTTAGCATTCC 58.417 41.667 0.00 0.00 0.00 3.01
246 247 1.738099 GTGACTCGCGCCAGTGAAT 60.738 57.895 13.85 0.00 36.32 2.57
258 259 1.219393 GGCTGCCTGTAGGTGACTC 59.781 63.158 12.43 0.00 43.67 3.36
272 273 2.354259 GTCCAGAATGAGTGAAGGCTG 58.646 52.381 0.00 0.00 39.69 4.85
273 274 1.280421 GGTCCAGAATGAGTGAAGGCT 59.720 52.381 0.00 0.00 39.69 4.58
274 275 1.743996 GGTCCAGAATGAGTGAAGGC 58.256 55.000 0.00 0.00 39.69 4.35
275 276 1.276421 ACGGTCCAGAATGAGTGAAGG 59.724 52.381 0.00 0.00 39.69 3.46
276 277 2.751166 ACGGTCCAGAATGAGTGAAG 57.249 50.000 0.00 0.00 39.69 3.02
301 302 0.716926 CAGTTACGACGTGTTTGCGC 60.717 55.000 11.56 0.00 34.88 6.09
335 336 4.201851 CCAACATAGCATCCGAAACAGAAG 60.202 45.833 0.00 0.00 0.00 2.85
336 337 3.689161 CCAACATAGCATCCGAAACAGAA 59.311 43.478 0.00 0.00 0.00 3.02
337 338 3.055458 TCCAACATAGCATCCGAAACAGA 60.055 43.478 0.00 0.00 0.00 3.41
338 339 3.270027 TCCAACATAGCATCCGAAACAG 58.730 45.455 0.00 0.00 0.00 3.16
339 340 3.342377 TCCAACATAGCATCCGAAACA 57.658 42.857 0.00 0.00 0.00 2.83
340 341 6.183360 CGTATATCCAACATAGCATCCGAAAC 60.183 42.308 0.00 0.00 0.00 2.78
346 375 7.090808 TCAACTCGTATATCCAACATAGCATC 58.909 38.462 0.00 0.00 0.00 3.91
350 379 7.274468 GCATCTCAACTCGTATATCCAACATAG 59.726 40.741 0.00 0.00 0.00 2.23
386 415 2.713967 CCCGGGAAAAGCAGGCATG 61.714 63.158 18.48 0.00 0.00 4.06
387 416 2.362889 CCCGGGAAAAGCAGGCAT 60.363 61.111 18.48 0.00 0.00 4.40
390 419 4.366684 AGGCCCGGGAAAAGCAGG 62.367 66.667 29.31 0.00 0.00 4.85
391 420 3.064324 CAGGCCCGGGAAAAGCAG 61.064 66.667 29.31 1.36 0.00 4.24
392 421 3.860930 GACAGGCCCGGGAAAAGCA 62.861 63.158 29.31 0.00 0.00 3.91
393 422 3.062466 GACAGGCCCGGGAAAAGC 61.062 66.667 29.31 8.14 0.00 3.51
394 423 1.377333 GAGACAGGCCCGGGAAAAG 60.377 63.158 29.31 13.19 0.00 2.27
395 424 1.838073 GAGAGACAGGCCCGGGAAAA 61.838 60.000 29.31 0.00 0.00 2.29
396 425 2.203938 AGAGACAGGCCCGGGAAA 60.204 61.111 29.31 0.00 0.00 3.13
397 426 2.683933 GAGAGACAGGCCCGGGAA 60.684 66.667 29.31 0.00 0.00 3.97
398 427 3.673597 AGAGAGACAGGCCCGGGA 61.674 66.667 29.31 0.00 0.00 5.14
431 463 1.141019 GCAGGAGCGATGGTACGAA 59.859 57.895 0.00 0.00 35.09 3.85
442 474 0.654683 CGCAGTAGATTTGCAGGAGC 59.345 55.000 0.00 0.00 41.59 4.70
455 489 3.382227 TCTGGATTCGGATTTACGCAGTA 59.618 43.478 0.00 0.00 45.11 2.74
461 495 5.354234 TCTGCTTTTCTGGATTCGGATTTAC 59.646 40.000 0.00 0.00 0.00 2.01
473 507 5.748630 GGTACAACTTTTTCTGCTTTTCTGG 59.251 40.000 0.00 0.00 0.00 3.86
474 508 5.748630 GGGTACAACTTTTTCTGCTTTTCTG 59.251 40.000 0.00 0.00 0.00 3.02
475 509 5.420739 TGGGTACAACTTTTTCTGCTTTTCT 59.579 36.000 0.00 0.00 0.00 2.52
476 510 5.656480 TGGGTACAACTTTTTCTGCTTTTC 58.344 37.500 0.00 0.00 0.00 2.29
477 511 5.669164 TGGGTACAACTTTTTCTGCTTTT 57.331 34.783 0.00 0.00 0.00 2.27
478 512 5.869649 ATGGGTACAACTTTTTCTGCTTT 57.130 34.783 0.00 0.00 0.00 3.51
479 513 5.869649 AATGGGTACAACTTTTTCTGCTT 57.130 34.783 0.00 0.00 0.00 3.91
480 514 5.243060 GGTAATGGGTACAACTTTTTCTGCT 59.757 40.000 0.00 0.00 34.01 4.24
481 515 5.466819 GGTAATGGGTACAACTTTTTCTGC 58.533 41.667 0.00 0.00 34.01 4.26
482 516 5.047590 GGGGTAATGGGTACAACTTTTTCTG 60.048 44.000 0.00 0.00 34.01 3.02
483 517 5.081728 GGGGTAATGGGTACAACTTTTTCT 58.918 41.667 0.00 0.00 34.01 2.52
484 518 4.833938 TGGGGTAATGGGTACAACTTTTTC 59.166 41.667 0.00 0.00 34.01 2.29
485 519 4.589798 GTGGGGTAATGGGTACAACTTTTT 59.410 41.667 0.00 0.00 34.01 1.94
486 520 4.154176 GTGGGGTAATGGGTACAACTTTT 58.846 43.478 0.00 0.00 34.01 2.27
487 521 3.770046 GTGGGGTAATGGGTACAACTTT 58.230 45.455 0.00 0.00 34.01 2.66
488 522 2.290450 CGTGGGGTAATGGGTACAACTT 60.290 50.000 0.00 0.00 34.01 2.66
489 523 1.279846 CGTGGGGTAATGGGTACAACT 59.720 52.381 0.00 0.00 34.01 3.16
490 524 1.278699 TCGTGGGGTAATGGGTACAAC 59.721 52.381 0.00 0.00 34.01 3.32
491 525 1.555992 CTCGTGGGGTAATGGGTACAA 59.444 52.381 0.00 0.00 34.01 2.41
492 526 1.196911 CTCGTGGGGTAATGGGTACA 58.803 55.000 0.00 0.00 34.01 2.90
493 527 0.179065 GCTCGTGGGGTAATGGGTAC 60.179 60.000 0.00 0.00 0.00 3.34
494 528 1.339644 GGCTCGTGGGGTAATGGGTA 61.340 60.000 0.00 0.00 0.00 3.69
495 529 2.676265 GGCTCGTGGGGTAATGGGT 61.676 63.158 0.00 0.00 0.00 4.51
496 530 1.921869 AAGGCTCGTGGGGTAATGGG 61.922 60.000 0.00 0.00 0.00 4.00
497 531 0.034477 AAAGGCTCGTGGGGTAATGG 60.034 55.000 0.00 0.00 0.00 3.16
498 532 1.379527 GAAAGGCTCGTGGGGTAATG 58.620 55.000 0.00 0.00 0.00 1.90
499 533 0.107848 CGAAAGGCTCGTGGGGTAAT 60.108 55.000 0.00 0.00 42.89 1.89
500 534 1.294138 CGAAAGGCTCGTGGGGTAA 59.706 57.895 0.00 0.00 42.89 2.85
501 535 2.975536 CGAAAGGCTCGTGGGGTA 59.024 61.111 0.00 0.00 42.89 3.69
513 547 4.515191 TCAATGAAGACTTTGGGACGAAAG 59.485 41.667 5.44 5.44 38.65 2.62
534 568 4.191544 GCCTGTATAATTCTGCTGTGTCA 58.808 43.478 0.00 0.00 0.00 3.58
541 575 2.221981 GCTCGTGCCTGTATAATTCTGC 59.778 50.000 0.00 0.00 0.00 4.26
543 577 3.243907 GGAGCTCGTGCCTGTATAATTCT 60.244 47.826 7.83 0.00 40.80 2.40
573 607 3.059461 AGCGCGTACAATTTCGAGAAAAA 60.059 39.130 8.43 0.00 33.56 1.94
574 608 2.477375 AGCGCGTACAATTTCGAGAAAA 59.523 40.909 8.43 0.00 33.56 2.29
575 609 2.063266 AGCGCGTACAATTTCGAGAAA 58.937 42.857 8.43 0.40 34.46 2.52
592 626 2.224784 TGCAGCTTATCAATATGCAGCG 59.775 45.455 15.52 5.04 43.77 5.18
596 630 6.685828 CGATATGTTGCAGCTTATCAATATGC 59.314 38.462 25.60 7.64 37.40 3.14
616 650 1.364171 GCCACGAGGACAGCGATAT 59.636 57.895 1.86 0.00 36.89 1.63
669 703 4.943705 AGCACGGACAATGTGATCTATTTT 59.056 37.500 0.00 0.00 39.73 1.82
675 709 0.097674 GCAGCACGGACAATGTGATC 59.902 55.000 0.00 0.00 39.73 2.92
680 714 0.673333 TAGTGGCAGCACGGACAATG 60.673 55.000 0.00 0.00 0.00 2.82
704 738 2.518349 GGTGGGTGTGGTGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
711 745 1.074248 GTTAGGTGGGTGGGTGTGG 59.926 63.158 0.00 0.00 0.00 4.17
712 746 1.302192 CGTTAGGTGGGTGGGTGTG 60.302 63.158 0.00 0.00 0.00 3.82
713 747 3.153825 CGTTAGGTGGGTGGGTGT 58.846 61.111 0.00 0.00 0.00 4.16
774 808 2.665185 AGGAAGCGTGGCGTGTTC 60.665 61.111 0.00 0.00 0.00 3.18
791 825 1.230497 GTCGATGAGGGGAGGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
794 828 2.282446 GGGTCGATGAGGGGAGGA 59.718 66.667 0.00 0.00 0.00 3.71
795 829 3.227276 CGGGTCGATGAGGGGAGG 61.227 72.222 0.00 0.00 0.00 4.30
797 831 2.123854 CTCGGGTCGATGAGGGGA 60.124 66.667 0.00 0.00 34.61 4.81
799 833 2.835431 AGCTCGGGTCGATGAGGG 60.835 66.667 12.37 0.00 34.61 4.30
800 834 2.725008 GAGCTCGGGTCGATGAGG 59.275 66.667 0.00 0.00 34.61 3.86
802 836 2.044352 TGGAGCTCGGGTCGATGA 60.044 61.111 7.83 0.00 34.61 2.92
820 865 5.105797 TGTGGAGATGTATGGTTGATTTTGC 60.106 40.000 0.00 0.00 0.00 3.68
875 922 4.582701 TTAATGGCGCCAAAATATCAGG 57.417 40.909 36.33 0.00 0.00 3.86
954 1016 2.276116 GCTCTGACCTGGACGTGGA 61.276 63.158 0.00 0.00 0.00 4.02
1018 1095 0.739462 CCGCTGTCGTTGCTATTGGA 60.739 55.000 0.00 0.00 0.00 3.53
1027 1104 0.531974 TTCTTCTTGCCGCTGTCGTT 60.532 50.000 0.00 0.00 0.00 3.85
1105 1182 4.704833 GGCCAGCTTCTGCGTGGA 62.705 66.667 0.00 0.00 45.42 4.02
2017 2100 2.266372 CCCCATGCAACGTACGGA 59.734 61.111 21.06 0.33 0.00 4.69
2018 2101 3.505184 GCCCCATGCAACGTACGG 61.505 66.667 21.06 3.45 40.77 4.02
2020 2103 2.045340 AGGCCCCATGCAACGTAC 60.045 61.111 0.00 0.00 43.89 3.67
2021 2104 2.045438 CAGGCCCCATGCAACGTA 60.045 61.111 0.00 0.00 43.89 3.57
2035 2120 3.043586 CGCTCTAATTACTACACGCAGG 58.956 50.000 0.00 0.00 0.00 4.85
2036 2121 3.043586 CCGCTCTAATTACTACACGCAG 58.956 50.000 0.00 0.00 0.00 5.18
2037 2122 2.424601 ACCGCTCTAATTACTACACGCA 59.575 45.455 0.00 0.00 0.00 5.24
2038 2123 2.787680 CACCGCTCTAATTACTACACGC 59.212 50.000 0.00 0.00 0.00 5.34
2039 2124 3.369385 CCACCGCTCTAATTACTACACG 58.631 50.000 0.00 0.00 0.00 4.49
2108 5069 1.330521 CACACCACACCACGAAAAGAG 59.669 52.381 0.00 0.00 0.00 2.85
2109 5070 1.374560 CACACCACACCACGAAAAGA 58.625 50.000 0.00 0.00 0.00 2.52
2113 5074 1.817520 CTGCACACCACACCACGAA 60.818 57.895 0.00 0.00 0.00 3.85
2115 5076 2.203001 TCTGCACACCACACCACG 60.203 61.111 0.00 0.00 0.00 4.94
2116 5077 2.546494 GCTCTGCACACCACACCAC 61.546 63.158 0.00 0.00 0.00 4.16
2118 5079 2.203195 TGCTCTGCACACCACACC 60.203 61.111 0.00 0.00 31.71 4.16
2119 5080 1.226686 CTCTGCTCTGCACACCACAC 61.227 60.000 0.00 0.00 33.79 3.82
2120 5081 1.070275 CTCTGCTCTGCACACCACA 59.930 57.895 0.00 0.00 33.79 4.17
2144 5107 1.264045 ACTCTGCTTCTGCTCCCCTC 61.264 60.000 0.00 0.00 40.48 4.30
2202 5175 1.313772 CACGGTGTCCCAAATTCACA 58.686 50.000 0.00 0.00 34.27 3.58
2205 5178 1.834188 ATCCACGGTGTCCCAAATTC 58.166 50.000 7.45 0.00 0.00 2.17
2209 5182 2.619332 CCATTAATCCACGGTGTCCCAA 60.619 50.000 7.45 0.00 0.00 4.12
2219 5192 5.106317 ACGAACATCAACACCATTAATCCAC 60.106 40.000 0.00 0.00 0.00 4.02
2249 5222 4.507691 CCCCCAATCCACTAGTACAAAACA 60.508 45.833 0.00 0.00 0.00 2.83
2250 5223 4.014406 CCCCCAATCCACTAGTACAAAAC 58.986 47.826 0.00 0.00 0.00 2.43
2251 5224 3.658705 ACCCCCAATCCACTAGTACAAAA 59.341 43.478 0.00 0.00 0.00 2.44
2349 5328 5.128919 ACTTGCATGAAGACTTTTCTCTGT 58.871 37.500 6.60 0.00 35.42 3.41
2361 5340 6.095580 TCCTACTAGTGTCTACTTGCATGAAG 59.904 42.308 5.39 0.00 38.36 3.02
2396 5379 8.754991 TGGTGTAATCAAGGTTTCTTTTTAGA 57.245 30.769 0.00 0.00 0.00 2.10
2399 5382 7.931407 GGAATGGTGTAATCAAGGTTTCTTTTT 59.069 33.333 0.00 0.00 0.00 1.94
2404 5388 7.696992 TTAGGAATGGTGTAATCAAGGTTTC 57.303 36.000 0.00 0.00 0.00 2.78
2433 5428 7.907389 TCACAGTGGACTATCTACAAAGATTT 58.093 34.615 0.00 0.00 39.55 2.17
2434 5429 7.482169 TCACAGTGGACTATCTACAAAGATT 57.518 36.000 0.00 0.00 39.55 2.40
2435 5430 7.482169 TTCACAGTGGACTATCTACAAAGAT 57.518 36.000 0.00 0.00 44.80 2.40
2441 5436 7.543868 GCATATGATTCACAGTGGACTATCTAC 59.456 40.741 6.97 0.00 0.00 2.59
2446 5441 5.612725 TGCATATGATTCACAGTGGACTA 57.387 39.130 6.97 0.00 0.00 2.59
2448 5443 5.762825 AATGCATATGATTCACAGTGGAC 57.237 39.130 6.97 0.00 0.00 4.02
2450 5445 8.407832 TCTAAAAATGCATATGATTCACAGTGG 58.592 33.333 6.97 0.00 0.00 4.00
2453 5448 9.447040 CACTCTAAAAATGCATATGATTCACAG 57.553 33.333 6.97 2.78 0.00 3.66
2454 5449 8.959548 ACACTCTAAAAATGCATATGATTCACA 58.040 29.630 6.97 0.00 0.00 3.58
2480 5475 7.995289 ACATGCGGAATAAAATGAGTGATTTA 58.005 30.769 0.00 0.00 32.76 1.40
2481 5476 6.866480 ACATGCGGAATAAAATGAGTGATTT 58.134 32.000 0.00 0.00 35.65 2.17
2482 5477 6.455360 ACATGCGGAATAAAATGAGTGATT 57.545 33.333 0.00 0.00 0.00 2.57
2483 5478 6.767902 ACTACATGCGGAATAAAATGAGTGAT 59.232 34.615 0.00 0.00 0.00 3.06
2484 5479 6.112734 ACTACATGCGGAATAAAATGAGTGA 58.887 36.000 0.00 0.00 0.00 3.41
2485 5480 6.258727 AGACTACATGCGGAATAAAATGAGTG 59.741 38.462 0.00 0.00 0.00 3.51
2486 5481 6.349300 AGACTACATGCGGAATAAAATGAGT 58.651 36.000 0.00 0.00 0.00 3.41
2491 5486 9.990360 TCATTATAGACTACATGCGGAATAAAA 57.010 29.630 0.00 0.00 0.00 1.52
2492 5487 9.990360 TTCATTATAGACTACATGCGGAATAAA 57.010 29.630 0.00 0.00 0.00 1.40
2522 5536 9.158233 CCGTTCCTGAATATAAGTCTTTGTAAA 57.842 33.333 0.00 0.00 0.00 2.01
2523 5537 8.533657 TCCGTTCCTGAATATAAGTCTTTGTAA 58.466 33.333 0.00 0.00 0.00 2.41
2526 5540 6.480320 CCTCCGTTCCTGAATATAAGTCTTTG 59.520 42.308 0.00 0.00 0.00 2.77
2530 5544 4.587684 TCCCTCCGTTCCTGAATATAAGTC 59.412 45.833 0.00 0.00 0.00 3.01
2533 5547 6.785963 ACTATTCCCTCCGTTCCTGAATATAA 59.214 38.462 0.00 0.00 30.12 0.98
2534 5548 6.320518 ACTATTCCCTCCGTTCCTGAATATA 58.679 40.000 0.00 0.00 30.12 0.86
2540 5554 3.258622 GGATACTATTCCCTCCGTTCCTG 59.741 52.174 0.00 0.00 0.00 3.86
2543 5557 3.572604 CGGATACTATTCCCTCCGTTC 57.427 52.381 1.81 0.00 44.30 3.95
2547 5561 2.766828 CCATCCGGATACTATTCCCTCC 59.233 54.545 18.63 0.00 31.61 4.30
2617 5634 1.290009 GCCGCAAGTTGAAAGCCAT 59.710 52.632 7.16 0.00 0.00 4.40
2640 5657 1.679311 TGGTAACAGCAGCAGAGGG 59.321 57.895 0.00 0.00 46.17 4.30
2672 5689 0.739462 CGTAACGCTTGCCCTGATCA 60.739 55.000 0.00 0.00 0.00 2.92
2678 5695 1.908066 CTCAACCGTAACGCTTGCCC 61.908 60.000 0.00 0.00 0.00 5.36
2694 5711 2.093921 TCCACCGTCGAATAAATGCTCA 60.094 45.455 0.00 0.00 0.00 4.26
2710 5727 3.725754 TGGAAAGAAGCTGTCCACC 57.274 52.632 2.19 0.00 42.43 4.61
2766 5783 8.641499 TGACCTGTTGTGATTTTCATTTTTAC 57.359 30.769 0.00 0.00 0.00 2.01
2774 5791 9.313118 AGTTTAAAATGACCTGTTGTGATTTTC 57.687 29.630 5.90 0.00 44.22 2.29
2805 5822 5.388225 TGAAAAATCAAACGAGCAAAAGC 57.612 34.783 0.00 0.00 0.00 3.51
2891 5912 4.459390 TGCAAGCTGTATTTTCATGCAT 57.541 36.364 0.00 0.00 37.40 3.96
2895 5916 5.797051 ACCAATTGCAAGCTGTATTTTCAT 58.203 33.333 4.94 0.00 0.00 2.57
2915 5936 0.618458 CTCCCTTCCCAAATCGACCA 59.382 55.000 0.00 0.00 0.00 4.02
2973 5994 2.552315 GCCAACTTTCTTTCATCGACCA 59.448 45.455 0.00 0.00 0.00 4.02
2974 5995 2.412847 CGCCAACTTTCTTTCATCGACC 60.413 50.000 0.00 0.00 0.00 4.79
2975 5996 2.412847 CCGCCAACTTTCTTTCATCGAC 60.413 50.000 0.00 0.00 0.00 4.20
2976 5997 1.804151 CCGCCAACTTTCTTTCATCGA 59.196 47.619 0.00 0.00 0.00 3.59
2984 6005 1.308998 CTGTCAACCGCCAACTTTCT 58.691 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.