Multiple sequence alignment - TraesCS3D01G115300

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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 TraesCS3D01G115300 chr3D 100.000 2483 0 0 1 2483 68832271 68834753 0.000000e+00 4586.0
1 TraesCS3D01G115300 chr3D 86.222 1125 85 39 694 1767 68336122 68335017 0.000000e+00 1155.0
2 TraesCS3D01G115300 chr3D 92.760 732 36 11 835 1559 68430400 68431121 0.000000e+00 1042.0
3 TraesCS3D01G115300 chr3D 86.988 953 72 28 628 1559 68388805 68389726 0.000000e+00 1026.0
4 TraesCS3D01G115300 chr3D 83.392 1132 91 38 841 1914 68325729 68324637 0.000000e+00 959.0
5 TraesCS3D01G115300 chr3D 82.586 580 79 16 1 565 522162533 522163105 2.220000e-135 492.0
6 TraesCS3D01G115300 chr3D 82.441 467 61 16 114 570 579260455 579260000 2.990000e-104 388.0
7 TraesCS3D01G115300 chr3D 84.881 377 35 16 1987 2346 68431672 68432043 6.530000e-96 361.0
8 TraesCS3D01G115300 chr3D 85.714 315 17 10 2120 2432 68390264 68390552 8.630000e-80 307.0
9 TraesCS3D01G115300 chr3D 81.701 388 28 13 1558 1911 68431190 68431568 1.450000e-72 283.0
10 TraesCS3D01G115300 chr3D 94.521 146 7 1 1925 2069 68390108 68390253 8.940000e-55 224.0
11 TraesCS3D01G115300 chr3D 88.830 188 12 5 1588 1767 68389821 68390007 3.210000e-54 222.0
12 TraesCS3D01G115300 chr3D 90.164 122 8 3 1794 1911 68390005 68390126 3.310000e-34 156.0
13 TraesCS3D01G115300 chr3D 96.364 55 2 0 1927 1981 68431552 68431606 9.460000e-15 91.6
14 TraesCS3D01G115300 chr3D 97.143 35 1 0 1932 1966 68334942 68334908 2.670000e-05 60.2
15 TraesCS3D01G115300 chr3B 86.457 1019 66 34 835 1807 112497297 112496305 0.000000e+00 1051.0
16 TraesCS3D01G115300 chr3B 86.590 962 86 18 639 1565 113299630 113298677 0.000000e+00 1022.0
17 TraesCS3D01G115300 chr3B 91.633 741 37 8 835 1559 112948541 112947810 0.000000e+00 1002.0
18 TraesCS3D01G115300 chr3B 87.662 851 62 22 658 1474 113483150 113483991 0.000000e+00 950.0
19 TraesCS3D01G115300 chr3B 90.096 727 54 7 835 1549 112465799 112465079 0.000000e+00 928.0
20 TraesCS3D01G115300 chr3B 87.943 564 53 11 1927 2482 112835027 112834471 0.000000e+00 651.0
21 TraesCS3D01G115300 chr3B 91.589 428 29 4 1964 2390 112496303 112495882 3.560000e-163 584.0
22 TraesCS3D01G115300 chr3B 90.261 421 31 8 1929 2346 113298149 113297736 2.170000e-150 542.0
23 TraesCS3D01G115300 chr3B 83.611 360 54 4 66 422 349933034 349932677 1.420000e-87 333.0
24 TraesCS3D01G115300 chr3B 81.701 388 27 15 1558 1911 112835388 112835011 1.450000e-72 283.0
25 TraesCS3D01G115300 chr3B 87.586 145 13 3 1770 1911 113298277 113298135 1.980000e-36 163.0
26 TraesCS3D01G115300 chr3B 81.140 228 13 14 1558 1766 113298614 113298398 3.310000e-34 156.0
27 TraesCS3D01G115300 chr3B 97.059 68 2 0 567 634 256253743 256253810 5.610000e-22 115.0
28 TraesCS3D01G115300 chr3B 97.297 37 1 0 1927 1963 113487750 113487786 2.060000e-06 63.9
29 TraesCS3D01G115300 chr3A 89.696 854 45 13 739 1558 80412828 80413672 0.000000e+00 1050.0
30 TraesCS3D01G115300 chr3A 79.670 364 33 12 1588 1911 80410172 80409810 8.940000e-55 224.0
31 TraesCS3D01G115300 chr3A 83.069 189 24 5 381 564 435461481 435461666 5.490000e-37 165.0
32 TraesCS3D01G115300 chr5D 83.305 593 71 20 3 575 130459392 130459976 2.830000e-144 521.0
33 TraesCS3D01G115300 chr5D 94.203 69 4 0 566 634 406165534 406165466 3.380000e-19 106.0
34 TraesCS3D01G115300 chr4B 83.601 561 71 15 2 549 548765966 548766518 7.920000e-140 507.0
35 TraesCS3D01G115300 chr4B 89.024 82 8 1 566 647 575629372 575629292 1.570000e-17 100.0
36 TraesCS3D01G115300 chr4D 82.639 576 83 12 1 564 441900051 441900621 6.170000e-136 494.0
37 TraesCS3D01G115300 chr2D 83.752 517 70 9 42 553 598371207 598371714 6.210000e-131 477.0
38 TraesCS3D01G115300 chr2D 95.775 71 3 0 568 638 112543842 112543912 5.610000e-22 115.0
39 TraesCS3D01G115300 chr7A 79.304 575 97 18 1 562 724610204 724609639 1.390000e-102 383.0
40 TraesCS3D01G115300 chr6A 78.764 518 92 14 46 553 477509218 477509727 5.120000e-87 331.0
41 TraesCS3D01G115300 chr2B 92.405 79 5 1 568 645 743698013 743698091 7.260000e-21 111.0
42 TraesCS3D01G115300 chr2B 95.522 67 3 0 565 631 781810124 781810190 9.390000e-20 108.0
43 TraesCS3D01G115300 chr1D 96.923 65 2 0 568 632 37526988 37527052 2.610000e-20 110.0
44 TraesCS3D01G115300 chr6D 94.286 70 4 0 566 635 345760497 345760566 9.390000e-20 108.0
45 TraesCS3D01G115300 chrUn 95.455 66 3 0 566 631 23574904 23574969 3.380000e-19 106.0
46 TraesCS3D01G115300 chr7B 88.172 93 6 3 1770 1857 603660214 603660306 3.380000e-19 106.0
47 TraesCS3D01G115300 chr2A 81.319 91 14 2 2 89 84365147 84365057 1.230000e-08 71.3


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 TraesCS3D01G115300 chr3D 68832271 68834753 2482 False 4586.00 4586 100.00000 1 2483 1 chr3D.!!$F1 2482
1 TraesCS3D01G115300 chr3D 68324637 68325729 1092 True 959.00 959 83.39200 841 1914 1 chr3D.!!$R1 1073
2 TraesCS3D01G115300 chr3D 68334908 68336122 1214 True 607.60 1155 91.68250 694 1966 2 chr3D.!!$R3 1272
3 TraesCS3D01G115300 chr3D 522162533 522163105 572 False 492.00 492 82.58600 1 565 1 chr3D.!!$F2 564
4 TraesCS3D01G115300 chr3D 68430400 68432043 1643 False 444.40 1042 88.92650 835 2346 4 chr3D.!!$F4 1511
5 TraesCS3D01G115300 chr3D 68388805 68390552 1747 False 387.00 1026 89.24340 628 2432 5 chr3D.!!$F3 1804
6 TraesCS3D01G115300 chr3B 112947810 112948541 731 True 1002.00 1002 91.63300 835 1559 1 chr3B.!!$R2 724
7 TraesCS3D01G115300 chr3B 112465079 112465799 720 True 928.00 928 90.09600 835 1549 1 chr3B.!!$R1 714
8 TraesCS3D01G115300 chr3B 112495882 112497297 1415 True 817.50 1051 89.02300 835 2390 2 chr3B.!!$R4 1555
9 TraesCS3D01G115300 chr3B 113483150 113487786 4636 False 506.95 950 92.47950 658 1963 2 chr3B.!!$F2 1305
10 TraesCS3D01G115300 chr3B 113297736 113299630 1894 True 470.75 1022 86.39425 639 2346 4 chr3B.!!$R6 1707
11 TraesCS3D01G115300 chr3B 112834471 112835388 917 True 467.00 651 84.82200 1558 2482 2 chr3B.!!$R5 924
12 TraesCS3D01G115300 chr3A 80412828 80413672 844 False 1050.00 1050 89.69600 739 1558 1 chr3A.!!$F1 819
13 TraesCS3D01G115300 chr5D 130459392 130459976 584 False 521.00 521 83.30500 3 575 1 chr5D.!!$F1 572
14 TraesCS3D01G115300 chr4B 548765966 548766518 552 False 507.00 507 83.60100 2 549 1 chr4B.!!$F1 547
15 TraesCS3D01G115300 chr4D 441900051 441900621 570 False 494.00 494 82.63900 1 564 1 chr4D.!!$F1 563
16 TraesCS3D01G115300 chr2D 598371207 598371714 507 False 477.00 477 83.75200 42 553 1 chr2D.!!$F2 511
17 TraesCS3D01G115300 chr7A 724609639 724610204 565 True 383.00 383 79.30400 1 562 1 chr7A.!!$R1 561
18 TraesCS3D01G115300 chr6A 477509218 477509727 509 False 331.00 331 78.76400 46 553 1 chr6A.!!$F1 507

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
680 692 0.027586 AAAAATATCTCGGCGTGCGC 59.972 50.0 6.85 8.17 41.06 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 5462 1.003118 CGAAACCAGAGAACATCCCCA 59.997 52.381 0.0 0.0 0.0 4.96 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
37 38 4.873129 GAGATCGCTGCCGCCGAA 62.873 66.667 0.00 0.00 38.31 4.30
54 58 3.569049 AAGTCGACGCCTCCAACGG 62.569 63.158 10.46 0.00 34.00 4.44
93 97 3.822192 CACGTCCTCGATGGCCGA 61.822 66.667 10.51 0.00 39.97 5.54
133 137 3.541713 GAGGCGGCGGAGAGGATT 61.542 66.667 9.78 0.00 0.00 3.01
146 150 2.032620 AGAGGATTATCCGTGAGCGTT 58.967 47.619 5.50 0.00 42.75 4.84
168 173 3.777910 GGACGCCGGAAAGCCCTA 61.778 66.667 5.05 0.00 0.00 3.53
213 223 3.467119 CAAAGCCCGACGACGACG 61.467 66.667 12.66 12.66 42.66 5.12
250 260 1.096416 GACGATGACGAAGGAGGAGT 58.904 55.000 0.00 0.00 42.66 3.85
251 261 1.473278 GACGATGACGAAGGAGGAGTT 59.527 52.381 0.00 0.00 42.66 3.01
253 263 1.646189 GATGACGAAGGAGGAGTTGC 58.354 55.000 0.00 0.00 0.00 4.17
256 266 1.874345 GACGAAGGAGGAGTTGCCGA 61.874 60.000 0.00 0.00 43.43 5.54
294 304 1.891150 ACGAGGTCACCGTGAAGTATT 59.109 47.619 1.88 0.00 38.97 1.89
295 305 3.084039 ACGAGGTCACCGTGAAGTATTA 58.916 45.455 1.88 0.00 38.97 0.98
296 306 3.128242 ACGAGGTCACCGTGAAGTATTAG 59.872 47.826 1.88 0.00 38.97 1.73
308 318 7.015001 ACCGTGAAGTATTAGGATAGTTTAGGG 59.985 40.741 12.26 12.26 42.51 3.53
309 319 7.232127 CCGTGAAGTATTAGGATAGTTTAGGGA 59.768 40.741 9.88 0.00 41.03 4.20
322 332 9.570468 GGATAGTTTAGGGATTTAGTTTTAGGG 57.430 37.037 0.00 0.00 0.00 3.53
337 347 3.421919 TTAGGGTTTTAGTTCACCGGG 57.578 47.619 6.32 0.00 33.34 5.73
366 376 5.880054 ATCGTCCAGTTTTATGTCCAAAG 57.120 39.130 0.00 0.00 0.00 2.77
370 380 6.592607 TCGTCCAGTTTTATGTCCAAAGTATC 59.407 38.462 0.00 0.00 0.00 2.24
391 401 8.047310 AGTATCCTACTTTCAATGAAATCCGTT 58.953 33.333 9.02 0.00 34.86 4.44
403 413 9.173021 TCAATGAAATCCGTTGTGTTTATATCT 57.827 29.630 0.00 0.00 41.41 1.98
410 420 7.709269 TCCGTTGTGTTTATATCTAATCTGC 57.291 36.000 0.00 0.00 0.00 4.26
411 421 7.269316 TCCGTTGTGTTTATATCTAATCTGCA 58.731 34.615 0.00 0.00 0.00 4.41
413 423 7.224753 CCGTTGTGTTTATATCTAATCTGCACT 59.775 37.037 0.00 0.00 0.00 4.40
420 430 9.226345 GTTTATATCTAATCTGCACTTGTTTGC 57.774 33.333 0.00 0.00 43.31 3.68
442 452 3.465122 CGAATTTCGTCCGGTTGATTT 57.535 42.857 10.61 0.00 34.72 2.17
443 453 4.587211 CGAATTTCGTCCGGTTGATTTA 57.413 40.909 10.61 0.00 34.72 1.40
445 455 5.565695 CGAATTTCGTCCGGTTGATTTAAT 58.434 37.500 10.61 0.00 34.72 1.40
481 491 2.106683 GCGGCTAGCGTTGGATGTT 61.107 57.895 9.00 0.00 35.41 2.71
482 492 0.808453 GCGGCTAGCGTTGGATGTTA 60.808 55.000 9.00 0.00 35.41 2.41
483 493 0.928229 CGGCTAGCGTTGGATGTTAC 59.072 55.000 9.00 0.00 0.00 2.50
484 494 1.296727 GGCTAGCGTTGGATGTTACC 58.703 55.000 9.00 0.00 0.00 2.85
485 495 1.134491 GGCTAGCGTTGGATGTTACCT 60.134 52.381 9.00 0.00 0.00 3.08
486 496 2.202566 GCTAGCGTTGGATGTTACCTC 58.797 52.381 0.00 0.00 0.00 3.85
487 497 2.822764 CTAGCGTTGGATGTTACCTCC 58.177 52.381 0.00 0.00 0.00 4.30
488 498 0.252197 AGCGTTGGATGTTACCTCCC 59.748 55.000 4.29 0.00 31.32 4.30
489 499 1.087771 GCGTTGGATGTTACCTCCCG 61.088 60.000 4.29 3.16 31.32 5.14
490 500 1.087771 CGTTGGATGTTACCTCCCGC 61.088 60.000 4.29 0.00 31.32 6.13
491 501 0.035820 GTTGGATGTTACCTCCCGCA 60.036 55.000 4.29 0.00 31.32 5.69
492 502 0.251916 TTGGATGTTACCTCCCGCAG 59.748 55.000 4.29 0.00 31.32 5.18
493 503 0.907704 TGGATGTTACCTCCCGCAGT 60.908 55.000 4.29 0.00 31.32 4.40
494 504 0.462047 GGATGTTACCTCCCGCAGTG 60.462 60.000 0.00 0.00 0.00 3.66
495 505 0.249398 GATGTTACCTCCCGCAGTGT 59.751 55.000 0.00 0.00 0.00 3.55
496 506 0.249398 ATGTTACCTCCCGCAGTGTC 59.751 55.000 0.00 0.00 0.00 3.67
497 507 1.079336 GTTACCTCCCGCAGTGTCC 60.079 63.158 0.00 0.00 0.00 4.02
498 508 1.534476 TTACCTCCCGCAGTGTCCA 60.534 57.895 0.00 0.00 0.00 4.02
499 509 1.823169 TTACCTCCCGCAGTGTCCAC 61.823 60.000 0.00 0.00 0.00 4.02
500 510 4.742201 CCTCCCGCAGTGTCCACG 62.742 72.222 0.00 0.00 36.20 4.94
501 511 4.742201 CTCCCGCAGTGTCCACGG 62.742 72.222 0.36 0.36 46.50 4.94
505 515 2.734723 CGCAGTGTCCACGGACTG 60.735 66.667 16.88 9.10 44.80 3.51
506 516 2.357517 GCAGTGTCCACGGACTGG 60.358 66.667 16.88 7.67 44.80 4.00
512 522 2.283676 TCCACGGACTGGACCCTC 60.284 66.667 0.00 0.00 44.99 4.30
513 523 3.391382 CCACGGACTGGACCCTCC 61.391 72.222 0.00 0.00 43.95 4.30
514 524 3.391382 CACGGACTGGACCCTCCC 61.391 72.222 0.00 0.00 35.03 4.30
515 525 3.602030 ACGGACTGGACCCTCCCT 61.602 66.667 0.00 0.00 35.03 4.20
516 526 2.760385 CGGACTGGACCCTCCCTC 60.760 72.222 0.00 0.00 35.03 4.30
517 527 2.781406 GGACTGGACCCTCCCTCT 59.219 66.667 0.00 0.00 35.03 3.69
518 528 1.382009 GGACTGGACCCTCCCTCTC 60.382 68.421 0.00 0.00 35.03 3.20
519 529 1.382009 GACTGGACCCTCCCTCTCC 60.382 68.421 0.00 0.00 35.03 3.71
520 530 2.443016 CTGGACCCTCCCTCTCCG 60.443 72.222 0.00 0.00 35.03 4.63
521 531 4.779733 TGGACCCTCCCTCTCCGC 62.780 72.222 0.00 0.00 35.03 5.54
536 546 4.271816 CGCGGACGGATGGGAGAG 62.272 72.222 0.00 0.00 34.97 3.20
537 547 2.833582 GCGGACGGATGGGAGAGA 60.834 66.667 0.00 0.00 0.00 3.10
538 548 2.203771 GCGGACGGATGGGAGAGAT 61.204 63.158 0.00 0.00 0.00 2.75
539 549 1.749334 GCGGACGGATGGGAGAGATT 61.749 60.000 0.00 0.00 0.00 2.40
540 550 0.753262 CGGACGGATGGGAGAGATTT 59.247 55.000 0.00 0.00 0.00 2.17
541 551 1.139058 CGGACGGATGGGAGAGATTTT 59.861 52.381 0.00 0.00 0.00 1.82
542 552 2.420129 CGGACGGATGGGAGAGATTTTT 60.420 50.000 0.00 0.00 0.00 1.94
558 568 2.393271 TTTTTGTGGGTTGCTGTTGG 57.607 45.000 0.00 0.00 0.00 3.77
559 569 1.561643 TTTTGTGGGTTGCTGTTGGA 58.438 45.000 0.00 0.00 0.00 3.53
560 570 1.110442 TTTGTGGGTTGCTGTTGGAG 58.890 50.000 0.00 0.00 0.00 3.86
561 571 0.257328 TTGTGGGTTGCTGTTGGAGA 59.743 50.000 0.00 0.00 0.00 3.71
562 572 0.478072 TGTGGGTTGCTGTTGGAGAT 59.522 50.000 0.00 0.00 0.00 2.75
563 573 0.883833 GTGGGTTGCTGTTGGAGATG 59.116 55.000 0.00 0.00 0.00 2.90
564 574 0.478072 TGGGTTGCTGTTGGAGATGT 59.522 50.000 0.00 0.00 0.00 3.06
565 575 0.883833 GGGTTGCTGTTGGAGATGTG 59.116 55.000 0.00 0.00 0.00 3.21
566 576 0.242017 GGTTGCTGTTGGAGATGTGC 59.758 55.000 0.00 0.00 0.00 4.57
567 577 1.242076 GTTGCTGTTGGAGATGTGCT 58.758 50.000 0.00 0.00 0.00 4.40
568 578 1.610522 GTTGCTGTTGGAGATGTGCTT 59.389 47.619 0.00 0.00 0.00 3.91
569 579 2.813754 GTTGCTGTTGGAGATGTGCTTA 59.186 45.455 0.00 0.00 0.00 3.09
570 580 3.138884 TGCTGTTGGAGATGTGCTTAA 57.861 42.857 0.00 0.00 0.00 1.85
571 581 3.689347 TGCTGTTGGAGATGTGCTTAAT 58.311 40.909 0.00 0.00 0.00 1.40
572 582 4.842574 TGCTGTTGGAGATGTGCTTAATA 58.157 39.130 0.00 0.00 0.00 0.98
573 583 4.635765 TGCTGTTGGAGATGTGCTTAATAC 59.364 41.667 0.00 0.00 0.00 1.89
574 584 4.635765 GCTGTTGGAGATGTGCTTAATACA 59.364 41.667 0.00 0.00 0.00 2.29
575 585 5.123820 GCTGTTGGAGATGTGCTTAATACAA 59.876 40.000 0.00 0.00 0.00 2.41
576 586 6.494893 TGTTGGAGATGTGCTTAATACAAC 57.505 37.500 0.00 0.00 36.97 3.32
577 587 6.237901 TGTTGGAGATGTGCTTAATACAACT 58.762 36.000 0.00 3.47 37.25 3.16
578 588 6.714810 TGTTGGAGATGTGCTTAATACAACTT 59.285 34.615 0.00 0.00 37.25 2.66
579 589 7.230510 TGTTGGAGATGTGCTTAATACAACTTT 59.769 33.333 0.00 0.00 37.25 2.66
580 590 7.144722 TGGAGATGTGCTTAATACAACTTTG 57.855 36.000 4.89 0.00 32.28 2.77
581 591 6.714810 TGGAGATGTGCTTAATACAACTTTGT 59.285 34.615 0.00 0.00 44.86 2.83
582 592 7.880713 TGGAGATGTGCTTAATACAACTTTGTA 59.119 33.333 4.34 4.34 46.55 2.41
583 593 8.175716 GGAGATGTGCTTAATACAACTTTGTAC 58.824 37.037 3.95 0.00 45.47 2.90
584 594 8.848474 AGATGTGCTTAATACAACTTTGTACT 57.152 30.769 3.95 0.00 45.47 2.73
585 595 9.938280 AGATGTGCTTAATACAACTTTGTACTA 57.062 29.630 3.95 0.00 45.47 1.82
619 629 8.974060 ACAAAGTTGAGACACTTATTTTAGGA 57.026 30.769 0.00 0.00 35.87 2.94
620 630 8.837389 ACAAAGTTGAGACACTTATTTTAGGAC 58.163 33.333 0.00 0.00 35.87 3.85
621 631 7.653767 AAGTTGAGACACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
622 632 6.164176 AGTTGAGACACTTATTTTAGGACGG 58.836 40.000 0.00 0.00 0.00 4.79
623 633 5.988310 TGAGACACTTATTTTAGGACGGA 57.012 39.130 0.00 0.00 0.00 4.69
624 634 5.962433 TGAGACACTTATTTTAGGACGGAG 58.038 41.667 0.00 0.00 0.00 4.63
625 635 5.105473 TGAGACACTTATTTTAGGACGGAGG 60.105 44.000 0.00 0.00 0.00 4.30
626 636 4.161754 AGACACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
627 637 4.098894 ACACTTATTTTAGGACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
628 638 4.161754 ACACTTATTTTAGGACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
629 639 4.161754 CACTTATTTTAGGACGGAGGGAGT 59.838 45.833 0.00 0.00 0.00 3.85
630 640 5.361857 CACTTATTTTAGGACGGAGGGAGTA 59.638 44.000 0.00 0.00 0.00 2.59
631 641 5.597594 ACTTATTTTAGGACGGAGGGAGTAG 59.402 44.000 0.00 0.00 0.00 2.57
632 642 3.744940 TTTTAGGACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
633 643 3.744940 TTTAGGACGGAGGGAGTAGAA 57.255 47.619 0.00 0.00 0.00 2.10
637 647 2.024273 AGGACGGAGGGAGTAGAATTCA 60.024 50.000 8.44 0.00 0.00 2.57
656 666 4.908601 TCAGAATAGAAGTCCCTTTGCA 57.091 40.909 0.00 0.00 0.00 4.08
680 692 0.027586 AAAAATATCTCGGCGTGCGC 59.972 50.000 6.85 8.17 41.06 6.09
686 700 2.240612 ATCTCGGCGTGCGCTTTTTC 62.241 55.000 16.21 0.00 41.60 2.29
687 701 3.235292 CTCGGCGTGCGCTTTTTCA 62.235 57.895 16.21 0.00 41.60 2.69
688 702 2.796617 CGGCGTGCGCTTTTTCAG 60.797 61.111 16.21 0.00 41.60 3.02
692 706 0.772341 GCGTGCGCTTTTTCAGAAAG 59.228 50.000 9.73 0.00 38.26 2.62
694 708 2.715268 CGTGCGCTTTTTCAGAAAGAA 58.285 42.857 9.73 0.00 0.00 2.52
696 710 3.178423 CGTGCGCTTTTTCAGAAAGAAAG 59.822 43.478 9.73 3.72 46.24 2.62
697 711 4.351192 GTGCGCTTTTTCAGAAAGAAAGA 58.649 39.130 9.73 0.00 46.24 2.52
701 715 6.178507 GCGCTTTTTCAGAAAGAAAGAAAAC 58.821 36.000 10.40 0.00 46.24 2.43
704 718 7.700656 CGCTTTTTCAGAAAGAAAGAAAACCTA 59.299 33.333 10.40 0.00 46.24 3.08
716 730 8.336801 AGAAAGAAAACCTATCTTTGCGTATT 57.663 30.769 6.27 0.00 44.81 1.89
723 737 9.490379 AAAACCTATCTTTGCGTATTCTATAGG 57.510 33.333 0.00 0.00 40.11 2.57
726 740 8.867097 ACCTATCTTTGCGTATTCTATAGGAAA 58.133 33.333 11.42 0.00 37.67 3.13
785 799 2.027460 CCAAAGCCACCGCACAAC 59.973 61.111 0.00 0.00 37.52 3.32
786 800 2.780094 CCAAAGCCACCGCACAACA 61.780 57.895 0.00 0.00 37.52 3.33
787 801 1.140589 CAAAGCCACCGCACAACAA 59.859 52.632 0.00 0.00 37.52 2.83
788 802 0.249405 CAAAGCCACCGCACAACAAT 60.249 50.000 0.00 0.00 37.52 2.71
789 803 0.463620 AAAGCCACCGCACAACAATT 59.536 45.000 0.00 0.00 37.52 2.32
790 804 0.031994 AAGCCACCGCACAACAATTC 59.968 50.000 0.00 0.00 37.52 2.17
816 837 3.436496 GGTCGAACCTCTAGAACATTCG 58.564 50.000 19.32 19.32 42.63 3.34
857 904 2.749621 CCCCTTTCAGAAGTTTCCATCG 59.250 50.000 0.00 0.00 0.00 3.84
870 917 1.227089 CCATCGCCTTCCAGACTCG 60.227 63.158 0.00 0.00 0.00 4.18
906 966 2.119495 ACATAAACTCCCTCGCCATCT 58.881 47.619 0.00 0.00 0.00 2.90
926 986 0.457035 CATCCCCACCAAAGCATTCG 59.543 55.000 0.00 0.00 0.00 3.34
939 999 5.333263 CCAAAGCATTCGACAAAATTCAACC 60.333 40.000 0.00 0.00 0.00 3.77
947 1007 3.674753 CGACAAAATTCAACCAGCAATCC 59.325 43.478 0.00 0.00 0.00 3.01
948 1008 4.630111 GACAAAATTCAACCAGCAATCCA 58.370 39.130 0.00 0.00 0.00 3.41
949 1009 5.033589 ACAAAATTCAACCAGCAATCCAA 57.966 34.783 0.00 0.00 0.00 3.53
950 1010 4.815846 ACAAAATTCAACCAGCAATCCAAC 59.184 37.500 0.00 0.00 0.00 3.77
951 1011 3.302365 AATTCAACCAGCAATCCAACG 57.698 42.857 0.00 0.00 0.00 4.10
952 1012 0.313672 TTCAACCAGCAATCCAACGC 59.686 50.000 0.00 0.00 0.00 4.84
953 1013 0.821301 TCAACCAGCAATCCAACGCA 60.821 50.000 0.00 0.00 0.00 5.24
954 1014 0.031857 CAACCAGCAATCCAACGCAA 59.968 50.000 0.00 0.00 0.00 4.85
956 1016 0.537143 ACCAGCAATCCAACGCAAGA 60.537 50.000 0.00 0.00 43.62 3.02
957 1017 0.109597 CCAGCAATCCAACGCAAGAC 60.110 55.000 0.00 0.00 43.62 3.01
1299 1468 0.340208 GGAGGGAGGAGAAGGAGGAA 59.660 60.000 0.00 0.00 0.00 3.36
1566 5436 4.398988 TGTGATGAGTAATGGATGGTTTGC 59.601 41.667 0.00 0.00 0.00 3.68
1590 5460 4.833380 TGTTTCGTTAATGGAAATGGGGAA 59.167 37.500 7.61 0.00 35.97 3.97
1591 5461 5.482175 TGTTTCGTTAATGGAAATGGGGAAT 59.518 36.000 7.61 0.00 35.97 3.01
1592 5462 6.014156 TGTTTCGTTAATGGAAATGGGGAATT 60.014 34.615 7.61 0.00 35.97 2.17
1593 5463 5.590530 TCGTTAATGGAAATGGGGAATTG 57.409 39.130 0.00 0.00 0.00 2.32
1594 5464 4.404073 TCGTTAATGGAAATGGGGAATTGG 59.596 41.667 0.00 0.00 0.00 3.16
1595 5465 4.442753 CGTTAATGGAAATGGGGAATTGGG 60.443 45.833 0.00 0.00 0.00 4.12
1596 5466 2.195153 ATGGAAATGGGGAATTGGGG 57.805 50.000 0.00 0.00 0.00 4.96
1597 5467 1.096857 TGGAAATGGGGAATTGGGGA 58.903 50.000 0.00 0.00 0.00 4.81
1605 5475 1.570979 GGGGAATTGGGGATGTTCTCT 59.429 52.381 0.00 0.00 0.00 3.10
1608 5478 2.024941 GGAATTGGGGATGTTCTCTGGT 60.025 50.000 0.00 0.00 0.00 4.00
1637 5515 6.425504 CCTGAATAAAACATGCGATTCTCTC 58.574 40.000 0.00 0.00 31.03 3.20
1678 5576 3.992943 AATCCAAGATACCCGTGTTCA 57.007 42.857 0.00 0.00 0.00 3.18
1692 5591 4.976116 CCCGTGTTCAGAAAATTCAGAAAC 59.024 41.667 3.01 4.13 35.03 2.78
1693 5592 5.449862 CCCGTGTTCAGAAAATTCAGAAACA 60.450 40.000 3.01 4.03 35.03 2.83
1698 5597 9.515020 GTGTTCAGAAAATTCAGAAACATGTAA 57.485 29.630 0.00 0.00 35.03 2.41
1722 5629 5.946377 ATTCAGGAAAACTGGATAAGACCAC 59.054 40.000 0.00 0.00 43.85 4.16
1767 5818 2.737252 GGTGGAAAACGAACTAGCTCTG 59.263 50.000 0.00 0.00 0.00 3.35
1768 5819 3.554337 GGTGGAAAACGAACTAGCTCTGA 60.554 47.826 0.00 0.00 0.00 3.27
1818 5913 6.647481 TCTTGCATTTTCATCTTGACAAATGG 59.353 34.615 17.11 8.56 36.51 3.16
1888 5986 5.675778 CAGAAATGTTATTCTGCTTTGCG 57.324 39.130 4.31 0.00 46.88 4.85
1897 5996 3.773860 TTCTGCTTTGCGTGAAAGAAA 57.226 38.095 11.80 2.31 43.50 2.52
1898 5997 3.065019 TCTGCTTTGCGTGAAAGAAAC 57.935 42.857 11.80 0.00 43.50 2.78
1899 5998 2.421775 TCTGCTTTGCGTGAAAGAAACA 59.578 40.909 11.80 2.13 43.50 2.83
1900 5999 3.066621 TCTGCTTTGCGTGAAAGAAACAT 59.933 39.130 11.80 0.00 43.50 2.71
1901 6000 3.114809 TGCTTTGCGTGAAAGAAACATG 58.885 40.909 11.80 0.00 43.50 3.21
1902 6001 3.115554 GCTTTGCGTGAAAGAAACATGT 58.884 40.909 11.80 0.00 43.50 3.21
1903 6002 3.061006 GCTTTGCGTGAAAGAAACATGTG 60.061 43.478 0.00 0.00 43.50 3.21
1904 6003 4.350346 CTTTGCGTGAAAGAAACATGTGA 58.650 39.130 0.00 0.00 43.50 3.58
1905 6004 3.332761 TGCGTGAAAGAAACATGTGAC 57.667 42.857 0.00 0.00 0.00 3.67
1906 6005 2.680339 TGCGTGAAAGAAACATGTGACA 59.320 40.909 0.00 0.00 0.00 3.58
1907 6006 3.127721 TGCGTGAAAGAAACATGTGACAA 59.872 39.130 0.00 0.00 0.00 3.18
1908 6007 4.202000 TGCGTGAAAGAAACATGTGACAAT 60.202 37.500 0.00 0.00 0.00 2.71
1909 6008 4.379793 GCGTGAAAGAAACATGTGACAATC 59.620 41.667 0.00 0.00 0.00 2.67
1910 6009 5.751680 CGTGAAAGAAACATGTGACAATCT 58.248 37.500 0.00 0.00 0.00 2.40
1911 6010 6.201517 CGTGAAAGAAACATGTGACAATCTT 58.798 36.000 0.00 2.40 0.00 2.40
1912 6011 6.692681 CGTGAAAGAAACATGTGACAATCTTT 59.307 34.615 16.85 16.85 39.19 2.52
1913 6012 7.220683 CGTGAAAGAAACATGTGACAATCTTTT 59.779 33.333 17.45 3.31 37.28 2.27
1914 6013 8.872845 GTGAAAGAAACATGTGACAATCTTTTT 58.127 29.630 17.45 3.48 37.28 1.94
2084 6244 4.566907 GGGGGCTAAAAGAGTGATGTGTTA 60.567 45.833 0.00 0.00 0.00 2.41
2160 6321 3.181465 GGGTGTGAGTACATATGTGGGAG 60.181 52.174 18.81 0.00 39.39 4.30
2172 6333 5.891551 ACATATGTGGGAGGTAATTCCAAAC 59.108 40.000 7.78 0.00 39.09 2.93
2178 6339 5.756347 GTGGGAGGTAATTCCAAACAAAAAC 59.244 40.000 0.00 0.00 39.09 2.43
2180 6344 6.100424 TGGGAGGTAATTCCAAACAAAAACAT 59.900 34.615 0.00 0.00 39.09 2.71
2330 6509 9.927668 ATTGTTGATCTTTTTCACCGAAAATAT 57.072 25.926 2.95 1.25 40.50 1.28
2331 6510 9.757227 TTGTTGATCTTTTTCACCGAAAATATT 57.243 25.926 2.95 0.00 40.50 1.28
2355 6534 3.004315 TGAAAGTCATTTCCCGTGAAAGC 59.996 43.478 0.00 0.00 43.39 3.51
2413 6593 4.168101 AGAGTAGGACATTTTGGAGACCA 58.832 43.478 0.00 0.00 0.00 4.02
2432 6612 5.053978 ACCAAATCCAATAGAGGCCTTAG 57.946 43.478 6.77 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.049433 CGTTGGAGGCGTCGACTT 60.049 61.111 14.70 0.00 0.00 3.01
37 38 4.052229 CCGTTGGAGGCGTCGACT 62.052 66.667 14.70 0.00 0.00 4.18
133 137 1.357690 CGCCTAACGCTCACGGATA 59.642 57.895 0.00 0.00 46.04 2.59
153 157 4.091939 GGTAGGGCTTTCCGGCGT 62.092 66.667 6.01 0.00 41.52 5.68
233 243 1.914634 CAACTCCTCCTTCGTCATCG 58.085 55.000 0.00 0.00 38.55 3.84
241 251 1.831652 CTGGTCGGCAACTCCTCCTT 61.832 60.000 0.00 0.00 0.00 3.36
265 275 1.090052 GGTGACCTCGTAGCCAATGC 61.090 60.000 0.00 0.00 37.95 3.56
270 280 1.870055 TTCACGGTGACCTCGTAGCC 61.870 60.000 10.97 0.00 38.94 3.93
296 306 9.570468 CCCTAAAACTAAATCCCTAAACTATCC 57.430 37.037 0.00 0.00 0.00 2.59
308 318 9.903682 GGTGAACTAAAACCCTAAAACTAAATC 57.096 33.333 0.00 0.00 0.00 2.17
309 319 8.570488 CGGTGAACTAAAACCCTAAAACTAAAT 58.430 33.333 0.00 0.00 32.44 1.40
313 323 4.823442 CCGGTGAACTAAAACCCTAAAACT 59.177 41.667 0.00 0.00 32.44 2.66
318 328 1.003464 GCCCGGTGAACTAAAACCCTA 59.997 52.381 0.00 0.00 32.44 3.53
322 332 1.228533 TTCGCCCGGTGAACTAAAAC 58.771 50.000 9.45 0.00 0.00 2.43
366 376 7.787725 ACGGATTTCATTGAAAGTAGGATAC 57.212 36.000 16.34 0.05 43.47 2.24
370 380 6.086222 CACAACGGATTTCATTGAAAGTAGG 58.914 40.000 16.34 8.69 34.92 3.18
391 401 9.448438 AACAAGTGCAGATTAGATATAAACACA 57.552 29.630 0.00 0.00 0.00 3.72
409 419 2.097925 CGAAATTCGTGCAAACAAGTGC 60.098 45.455 7.29 0.00 45.15 4.40
410 420 3.734335 CGAAATTCGTGCAAACAAGTG 57.266 42.857 7.29 0.00 34.72 3.16
433 443 9.367717 CATTTTCACAACAAATTAAATCAACCG 57.632 29.630 0.00 0.00 0.00 4.44
442 452 6.090088 GCCGCATACATTTTCACAACAAATTA 59.910 34.615 0.00 0.00 0.00 1.40
443 453 5.107143 GCCGCATACATTTTCACAACAAATT 60.107 36.000 0.00 0.00 0.00 1.82
445 455 3.738282 GCCGCATACATTTTCACAACAAA 59.262 39.130 0.00 0.00 0.00 2.83
481 491 2.118732 TGGACACTGCGGGAGGTA 59.881 61.111 0.51 0.00 0.00 3.08
482 492 3.626924 GTGGACACTGCGGGAGGT 61.627 66.667 0.51 0.00 0.00 3.85
483 493 4.742201 CGTGGACACTGCGGGAGG 62.742 72.222 0.51 0.00 0.00 4.30
484 494 4.742201 CCGTGGACACTGCGGGAG 62.742 72.222 0.00 0.00 41.60 4.30
487 497 3.991051 AGTCCGTGGACACTGCGG 61.991 66.667 20.51 0.00 46.76 5.69
488 498 2.734723 CAGTCCGTGGACACTGCG 60.735 66.667 20.51 0.70 46.76 5.18
497 507 3.391382 GGGAGGGTCCAGTCCGTG 61.391 72.222 3.90 0.00 38.64 4.94
498 508 3.602030 AGGGAGGGTCCAGTCCGT 61.602 66.667 3.90 1.92 38.64 4.69
499 509 2.760385 GAGGGAGGGTCCAGTCCG 60.760 72.222 3.90 0.00 38.64 4.79
500 510 1.382009 GAGAGGGAGGGTCCAGTCC 60.382 68.421 1.41 1.41 38.64 3.85
501 511 1.382009 GGAGAGGGAGGGTCCAGTC 60.382 68.421 0.00 0.00 38.64 3.51
502 512 2.781406 GGAGAGGGAGGGTCCAGT 59.219 66.667 0.00 0.00 38.64 4.00
503 513 2.443016 CGGAGAGGGAGGGTCCAG 60.443 72.222 0.00 0.00 38.64 3.86
504 514 4.779733 GCGGAGAGGGAGGGTCCA 62.780 72.222 0.00 0.00 38.64 4.02
519 529 4.271816 CTCTCCCATCCGTCCGCG 62.272 72.222 0.00 0.00 37.95 6.46
520 530 1.749334 AATCTCTCCCATCCGTCCGC 61.749 60.000 0.00 0.00 0.00 5.54
521 531 0.753262 AAATCTCTCCCATCCGTCCG 59.247 55.000 0.00 0.00 0.00 4.79
522 532 3.283259 AAAAATCTCTCCCATCCGTCC 57.717 47.619 0.00 0.00 0.00 4.79
539 549 1.902508 TCCAACAGCAACCCACAAAAA 59.097 42.857 0.00 0.00 0.00 1.94
540 550 1.480137 CTCCAACAGCAACCCACAAAA 59.520 47.619 0.00 0.00 0.00 2.44
541 551 1.110442 CTCCAACAGCAACCCACAAA 58.890 50.000 0.00 0.00 0.00 2.83
542 552 0.257328 TCTCCAACAGCAACCCACAA 59.743 50.000 0.00 0.00 0.00 3.33
543 553 0.478072 ATCTCCAACAGCAACCCACA 59.522 50.000 0.00 0.00 0.00 4.17
544 554 0.883833 CATCTCCAACAGCAACCCAC 59.116 55.000 0.00 0.00 0.00 4.61
545 555 0.478072 ACATCTCCAACAGCAACCCA 59.522 50.000 0.00 0.00 0.00 4.51
546 556 0.883833 CACATCTCCAACAGCAACCC 59.116 55.000 0.00 0.00 0.00 4.11
547 557 0.242017 GCACATCTCCAACAGCAACC 59.758 55.000 0.00 0.00 0.00 3.77
548 558 1.242076 AGCACATCTCCAACAGCAAC 58.758 50.000 0.00 0.00 0.00 4.17
549 559 1.985473 AAGCACATCTCCAACAGCAA 58.015 45.000 0.00 0.00 0.00 3.91
550 560 2.857186 TAAGCACATCTCCAACAGCA 57.143 45.000 0.00 0.00 0.00 4.41
551 561 4.635765 TGTATTAAGCACATCTCCAACAGC 59.364 41.667 0.00 0.00 0.00 4.40
552 562 6.372659 AGTTGTATTAAGCACATCTCCAACAG 59.627 38.462 0.00 0.00 33.83 3.16
553 563 6.237901 AGTTGTATTAAGCACATCTCCAACA 58.762 36.000 0.00 0.00 33.83 3.33
554 564 6.743575 AGTTGTATTAAGCACATCTCCAAC 57.256 37.500 0.00 0.00 0.00 3.77
555 565 7.230510 ACAAAGTTGTATTAAGCACATCTCCAA 59.769 33.333 0.00 0.00 40.16 3.53
556 566 6.714810 ACAAAGTTGTATTAAGCACATCTCCA 59.285 34.615 0.00 0.00 40.16 3.86
557 567 7.145932 ACAAAGTTGTATTAAGCACATCTCC 57.854 36.000 0.00 0.00 40.16 3.71
558 568 8.936864 AGTACAAAGTTGTATTAAGCACATCTC 58.063 33.333 7.14 0.00 44.59 2.75
559 569 8.848474 AGTACAAAGTTGTATTAAGCACATCT 57.152 30.769 7.14 0.00 44.59 2.90
594 604 8.837389 GTCCTAAAATAAGTGTCTCAACTTTGT 58.163 33.333 0.00 0.00 40.77 2.83
595 605 8.009974 CGTCCTAAAATAAGTGTCTCAACTTTG 58.990 37.037 0.00 0.00 40.77 2.77
596 606 7.172703 CCGTCCTAAAATAAGTGTCTCAACTTT 59.827 37.037 0.00 0.00 40.77 2.66
597 607 6.649557 CCGTCCTAAAATAAGTGTCTCAACTT 59.350 38.462 0.00 0.00 42.89 2.66
598 608 6.014840 TCCGTCCTAAAATAAGTGTCTCAACT 60.015 38.462 0.00 0.00 0.00 3.16
599 609 6.161381 TCCGTCCTAAAATAAGTGTCTCAAC 58.839 40.000 0.00 0.00 0.00 3.18
600 610 6.349243 TCCGTCCTAAAATAAGTGTCTCAA 57.651 37.500 0.00 0.00 0.00 3.02
601 611 5.105473 CCTCCGTCCTAAAATAAGTGTCTCA 60.105 44.000 0.00 0.00 0.00 3.27
602 612 5.349809 CCTCCGTCCTAAAATAAGTGTCTC 58.650 45.833 0.00 0.00 0.00 3.36
603 613 4.161754 CCCTCCGTCCTAAAATAAGTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
604 614 4.161001 TCCCTCCGTCCTAAAATAAGTGTC 59.839 45.833 0.00 0.00 0.00 3.67
605 615 4.098894 TCCCTCCGTCCTAAAATAAGTGT 58.901 43.478 0.00 0.00 0.00 3.55
606 616 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
607 617 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
608 618 5.832060 TCTACTCCCTCCGTCCTAAAATAAG 59.168 44.000 0.00 0.00 0.00 1.73
609 619 5.769835 TCTACTCCCTCCGTCCTAAAATAA 58.230 41.667 0.00 0.00 0.00 1.40
610 620 5.393068 TCTACTCCCTCCGTCCTAAAATA 57.607 43.478 0.00 0.00 0.00 1.40
611 621 4.261411 TCTACTCCCTCCGTCCTAAAAT 57.739 45.455 0.00 0.00 0.00 1.82
612 622 3.744940 TCTACTCCCTCCGTCCTAAAA 57.255 47.619 0.00 0.00 0.00 1.52
613 623 3.744940 TTCTACTCCCTCCGTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
614 624 3.967467 ATTCTACTCCCTCCGTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
615 625 3.203710 TGAATTCTACTCCCTCCGTCCTA 59.796 47.826 7.05 0.00 0.00 2.94
616 626 2.024273 TGAATTCTACTCCCTCCGTCCT 60.024 50.000 7.05 0.00 0.00 3.85
617 627 2.362717 CTGAATTCTACTCCCTCCGTCC 59.637 54.545 7.05 0.00 0.00 4.79
618 628 3.288964 TCTGAATTCTACTCCCTCCGTC 58.711 50.000 7.05 0.00 0.00 4.79
619 629 3.383698 TCTGAATTCTACTCCCTCCGT 57.616 47.619 7.05 0.00 0.00 4.69
620 630 4.946478 ATTCTGAATTCTACTCCCTCCG 57.054 45.455 7.05 0.00 0.00 4.63
621 631 7.289084 ACTTCTATTCTGAATTCTACTCCCTCC 59.711 40.741 8.38 0.00 0.00 4.30
622 632 8.245195 ACTTCTATTCTGAATTCTACTCCCTC 57.755 38.462 8.38 0.00 0.00 4.30
623 633 7.289084 GGACTTCTATTCTGAATTCTACTCCCT 59.711 40.741 8.38 0.00 0.00 4.20
624 634 7.438564 GGACTTCTATTCTGAATTCTACTCCC 58.561 42.308 8.38 0.00 0.00 4.30
625 635 7.289084 AGGGACTTCTATTCTGAATTCTACTCC 59.711 40.741 8.38 7.64 27.25 3.85
626 636 8.245195 AGGGACTTCTATTCTGAATTCTACTC 57.755 38.462 8.38 0.00 27.25 2.59
666 676 1.017177 AAAAAGCGCACGCCGAGATA 61.017 50.000 11.47 0.00 43.17 1.98
675 685 4.351192 TCTTTCTTTCTGAAAAAGCGCAC 58.649 39.130 11.47 0.00 43.25 5.34
679 691 7.834068 AGGTTTTCTTTCTTTCTGAAAAAGC 57.166 32.000 4.18 3.88 43.25 3.51
686 700 7.324616 CGCAAAGATAGGTTTTCTTTCTTTCTG 59.675 37.037 7.95 2.77 44.67 3.02
687 701 7.013369 ACGCAAAGATAGGTTTTCTTTCTTTCT 59.987 33.333 7.95 0.00 44.67 2.52
688 702 7.139392 ACGCAAAGATAGGTTTTCTTTCTTTC 58.861 34.615 7.95 4.63 44.67 2.62
692 706 8.451748 AGAATACGCAAAGATAGGTTTTCTTTC 58.548 33.333 0.00 0.00 40.53 2.62
694 708 7.923414 AGAATACGCAAAGATAGGTTTTCTT 57.077 32.000 0.00 0.00 34.95 2.52
697 711 9.490379 CCTATAGAATACGCAAAGATAGGTTTT 57.510 33.333 0.00 0.00 32.97 2.43
701 715 9.706691 TTTTCCTATAGAATACGCAAAGATAGG 57.293 33.333 0.00 0.00 37.06 2.57
737 751 1.449246 ATTCGTGGCAGCAGAGAGC 60.449 57.895 0.00 0.00 46.19 4.09
775 789 0.309302 TTCGGAATTGTTGTGCGGTG 59.691 50.000 0.00 0.00 0.00 4.94
816 837 1.447838 TCTTTCGACCGCTGATGGC 60.448 57.895 0.00 0.00 37.64 4.40
832 853 2.108425 GGAAACTTCTGAAAGGGGGTCT 59.892 50.000 0.00 0.00 36.78 3.85
837 884 2.162408 GCGATGGAAACTTCTGAAAGGG 59.838 50.000 0.00 0.00 36.78 3.95
870 917 4.840005 GTAGGTGGCTGGAGCGGC 62.840 72.222 0.00 0.00 43.26 6.53
878 932 2.772515 GAGGGAGTTTATGTAGGTGGCT 59.227 50.000 0.00 0.00 0.00 4.75
881 935 2.483188 GGCGAGGGAGTTTATGTAGGTG 60.483 54.545 0.00 0.00 0.00 4.00
906 966 1.851304 GAATGCTTTGGTGGGGATGA 58.149 50.000 0.00 0.00 0.00 2.92
926 986 4.630111 TGGATTGCTGGTTGAATTTTGTC 58.370 39.130 0.00 0.00 0.00 3.18
939 999 0.109597 GGTCTTGCGTTGGATTGCTG 60.110 55.000 0.00 0.00 0.00 4.41
947 1007 1.841663 CTCGGGTTGGTCTTGCGTTG 61.842 60.000 0.00 0.00 0.00 4.10
948 1008 1.597027 CTCGGGTTGGTCTTGCGTT 60.597 57.895 0.00 0.00 0.00 4.84
949 1009 2.030562 CTCGGGTTGGTCTTGCGT 59.969 61.111 0.00 0.00 0.00 5.24
950 1010 2.742372 CCTCGGGTTGGTCTTGCG 60.742 66.667 0.00 0.00 0.00 4.85
951 1011 1.376037 CTCCTCGGGTTGGTCTTGC 60.376 63.158 0.00 0.00 0.00 4.01
952 1012 0.905357 ATCTCCTCGGGTTGGTCTTG 59.095 55.000 0.00 0.00 0.00 3.02
953 1013 1.196012 GATCTCCTCGGGTTGGTCTT 58.804 55.000 0.00 0.00 0.00 3.01
954 1014 1.038130 CGATCTCCTCGGGTTGGTCT 61.038 60.000 0.00 0.00 43.82 3.85
955 1015 1.437986 CGATCTCCTCGGGTTGGTC 59.562 63.158 0.00 0.00 43.82 4.02
956 1016 3.617368 CGATCTCCTCGGGTTGGT 58.383 61.111 0.00 0.00 43.82 3.67
1299 1468 0.464373 CCATCCGCATGTACTTGGCT 60.464 55.000 10.47 0.00 0.00 4.75
1332 1737 0.519999 CGAACTTGCGCATCAGCTTC 60.520 55.000 12.75 11.73 39.10 3.86
1446 1851 1.004745 TGGATGGTCTTGGGCTTCTTC 59.995 52.381 0.00 0.00 0.00 2.87
1503 5212 1.272781 CACTCTGCTTCGATTCGACC 58.727 55.000 8.55 3.71 34.89 4.79
1566 5436 4.461081 TCCCCATTTCCATTAACGAAACAG 59.539 41.667 0.00 0.29 32.30 3.16
1590 5460 3.701664 GAAACCAGAGAACATCCCCAAT 58.298 45.455 0.00 0.00 0.00 3.16
1591 5461 2.552155 CGAAACCAGAGAACATCCCCAA 60.552 50.000 0.00 0.00 0.00 4.12
1592 5462 1.003118 CGAAACCAGAGAACATCCCCA 59.997 52.381 0.00 0.00 0.00 4.96
1593 5463 1.739067 CGAAACCAGAGAACATCCCC 58.261 55.000 0.00 0.00 0.00 4.81
1594 5464 1.087501 GCGAAACCAGAGAACATCCC 58.912 55.000 0.00 0.00 0.00 3.85
1595 5465 1.087501 GGCGAAACCAGAGAACATCC 58.912 55.000 0.00 0.00 38.86 3.51
1596 5466 1.734465 CAGGCGAAACCAGAGAACATC 59.266 52.381 0.00 0.00 43.14 3.06
1597 5467 1.347707 TCAGGCGAAACCAGAGAACAT 59.652 47.619 0.00 0.00 43.14 2.71
1605 5475 4.804108 CATGTTTTATTCAGGCGAAACCA 58.196 39.130 0.00 0.00 43.14 3.67
1637 5515 2.627863 TTCAATCGAAAATGTGGCCG 57.372 45.000 0.00 0.00 0.00 6.13
1668 5546 3.815809 TCTGAATTTTCTGAACACGGGT 58.184 40.909 0.00 0.00 33.11 5.28
1678 5576 9.918630 CCTGAATTACATGTTTCTGAATTTTCT 57.081 29.630 2.30 0.00 0.00 2.52
1692 5591 9.177608 TCTTATCCAGTTTTCCTGAATTACATG 57.822 33.333 0.00 0.00 44.49 3.21
1693 5592 9.178758 GTCTTATCCAGTTTTCCTGAATTACAT 57.821 33.333 0.00 0.00 44.49 2.29
1698 5597 5.946377 GTGGTCTTATCCAGTTTTCCTGAAT 59.054 40.000 0.00 0.00 44.49 2.57
1701 5600 4.651778 TGTGGTCTTATCCAGTTTTCCTG 58.348 43.478 0.00 0.00 38.23 3.86
1722 5629 7.818930 ACCTAATTTTTGCTATTCCACATGTTG 59.181 33.333 0.00 0.00 0.00 3.33
1741 5649 5.557866 AGCTAGTTCGTTTTCCACCTAATT 58.442 37.500 0.00 0.00 0.00 1.40
1767 5818 3.084786 CAGGATTTTTCTCCCTGGTGTC 58.915 50.000 0.00 0.00 42.75 3.67
1768 5819 3.160679 CAGGATTTTTCTCCCTGGTGT 57.839 47.619 0.00 0.00 42.75 4.16
1818 5913 2.717639 TTTCTATCTTCCCAGGCAGC 57.282 50.000 0.00 0.00 0.00 5.25
1888 5986 7.992180 AAAGATTGTCACATGTTTCTTTCAC 57.008 32.000 0.00 0.00 29.87 3.18
1916 6015 4.198530 TCTCACATGTTTCTTGTGCAAGA 58.801 39.130 10.26 10.26 44.94 3.02
1917 6016 4.556942 TCTCACATGTTTCTTGTGCAAG 57.443 40.909 0.00 5.63 43.29 4.01
1918 6017 4.979943 TTCTCACATGTTTCTTGTGCAA 57.020 36.364 0.00 4.44 43.29 4.08
1919 6018 4.823442 AGATTCTCACATGTTTCTTGTGCA 59.177 37.500 0.00 0.00 43.29 4.57
1920 6019 5.368256 AGATTCTCACATGTTTCTTGTGC 57.632 39.130 0.00 0.00 43.29 4.57
1921 6020 5.471116 TGGAGATTCTCACATGTTTCTTGTG 59.529 40.000 15.36 8.73 44.62 3.33
1922 6021 5.624159 TGGAGATTCTCACATGTTTCTTGT 58.376 37.500 15.36 0.00 31.08 3.16
1923 6022 6.564709 TTGGAGATTCTCACATGTTTCTTG 57.435 37.500 15.36 0.00 31.08 3.02
1924 6023 7.771927 ATTTGGAGATTCTCACATGTTTCTT 57.228 32.000 15.36 0.00 31.08 2.52
1925 6024 7.361542 CGAATTTGGAGATTCTCACATGTTTCT 60.362 37.037 15.36 0.00 34.58 2.52
1926 6025 6.744537 CGAATTTGGAGATTCTCACATGTTTC 59.255 38.462 15.36 8.85 34.58 2.78
1927 6026 6.430925 TCGAATTTGGAGATTCTCACATGTTT 59.569 34.615 15.36 1.66 34.58 2.83
1928 6027 5.939883 TCGAATTTGGAGATTCTCACATGTT 59.060 36.000 15.36 8.42 34.58 2.71
1974 6073 8.916654 CATAATACACTGAATCGGTTATCTCAC 58.083 37.037 0.00 0.00 0.00 3.51
2084 6244 9.013229 TGTCAAGATAAAGAAGTTTGTGCATAT 57.987 29.630 0.00 0.00 0.00 1.78
2096 6256 6.837312 TCCCAAGTTCTGTCAAGATAAAGAA 58.163 36.000 0.00 0.00 30.72 2.52
2106 6267 2.238521 GGCATTTCCCAAGTTCTGTCA 58.761 47.619 0.00 0.00 0.00 3.58
2323 6502 7.812669 ACGGGAAATGACTTTCACAATATTTTC 59.187 33.333 1.72 0.00 43.70 2.29
2330 6509 3.546724 TCACGGGAAATGACTTTCACAA 58.453 40.909 0.00 0.00 43.70 3.33
2331 6510 3.201353 TCACGGGAAATGACTTTCACA 57.799 42.857 0.00 0.00 43.70 3.58
2355 6534 9.050601 TGTATAAAAACTTTGGCCAAGAAATTG 57.949 29.630 19.48 8.44 36.21 2.32
2413 6593 9.541884 TTTTTAACTAAGGCCTCTATTGGATTT 57.458 29.630 5.23 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.