Multiple sequence alignment - TraesCS2D01G001300

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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 TraesCS2D01G001300 chr2D 100.000 3032 0 0 1 3032 673159 676190 0.000000e+00 5600
1 TraesCS2D01G001300 chr2D 85.272 1453 156 42 875 2292 648746909 648748338 0.000000e+00 1445
2 TraesCS2D01G001300 chr2D 95.294 85 4 0 114 198 54674328 54674244 5.270000e-28 135
3 TraesCS2D01G001300 chr2B 93.338 1501 61 15 913 2381 10786217 10784724 0.000000e+00 2182
4 TraesCS2D01G001300 chr2B 95.331 257 10 1 2776 3032 10784365 10784111 1.010000e-109 407
5 TraesCS2D01G001300 chr2B 92.748 262 16 3 2412 2672 10784722 10784463 2.850000e-100 375
6 TraesCS2D01G001300 chr2B 93.464 153 10 0 207 359 10786697 10786545 8.460000e-56 228
7 TraesCS2D01G001300 chr2B 92.073 164 4 3 722 876 10786375 10786212 3.930000e-54 222
8 TraesCS2D01G001300 chr2B 97.674 129 3 0 594 722 10786537 10786409 3.930000e-54 222
9 TraesCS2D01G001300 chr2A 86.675 1606 106 46 1325 2882 527722 529267 0.000000e+00 1681
10 TraesCS2D01G001300 chr2A 92.399 671 33 7 722 1374 527031 527701 0.000000e+00 941
11 TraesCS2D01G001300 chr2A 84.174 436 29 20 1 403 526254 526682 1.320000e-103 387
12 TraesCS2D01G001300 chr2A 91.102 236 13 3 494 722 526766 527000 2.270000e-81 313
13 TraesCS2D01G001300 chr2A 97.546 163 4 0 2868 3030 529288 529450 2.300000e-71 279
14 TraesCS2D01G001300 chr5A 86.865 906 79 14 842 1714 219452005 219451107 0.000000e+00 977
15 TraesCS2D01G001300 chr5A 92.632 95 6 1 117 211 432230463 432230370 5.270000e-28 135
16 TraesCS2D01G001300 chr3D 86.475 902 66 26 842 1716 462477404 462476532 0.000000e+00 939
17 TraesCS2D01G001300 chr3D 86.957 115 11 4 106 218 67676210 67676322 3.170000e-25 126
18 TraesCS2D01G001300 chr4D 92.241 116 4 4 1 111 182204443 182204558 3.130000e-35 159
19 TraesCS2D01G001300 chr4D 90.909 110 10 0 210 319 182204565 182204674 6.770000e-32 148
20 TraesCS2D01G001300 chr7D 95.349 86 4 0 113 198 22964253 22964338 1.470000e-28 137
21 TraesCS2D01G001300 chr6B 93.333 90 6 0 109 198 618335040 618334951 1.900000e-27 134
22 TraesCS2D01G001300 chr1D 94.253 87 5 0 112 198 409047048 409047134 1.900000e-27 134
23 TraesCS2D01G001300 chr1A 94.253 87 5 0 115 201 241320009 241319923 1.900000e-27 134
24 TraesCS2D01G001300 chr5D 90.526 95 8 1 105 198 175298823 175298729 1.140000e-24 124


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 TraesCS2D01G001300 chr2D 673159 676190 3031 False 5600.0 5600 100.000000 1 3032 1 chr2D.!!$F1 3031
1 TraesCS2D01G001300 chr2D 648746909 648748338 1429 False 1445.0 1445 85.272000 875 2292 1 chr2D.!!$F2 1417
2 TraesCS2D01G001300 chr2B 10784111 10786697 2586 True 606.0 2182 94.104667 207 3032 6 chr2B.!!$R1 2825
3 TraesCS2D01G001300 chr2A 526254 529450 3196 False 720.2 1681 90.379200 1 3030 5 chr2A.!!$F1 3029
4 TraesCS2D01G001300 chr5A 219451107 219452005 898 True 977.0 977 86.865000 842 1714 1 chr5A.!!$R1 872
5 TraesCS2D01G001300 chr3D 462476532 462477404 872 True 939.0 939 86.475000 842 1716 1 chr3D.!!$R1 874

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
416 481 0.03563 CCTCTGCCAGTAGCTTGCTT 60.036 55.0 0.0 0.0 44.23 3.91 F
418 483 0.03601 TCTGCCAGTAGCTTGCTTCC 60.036 55.0 0.0 0.0 44.23 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2103 0.540923 TCATCCACGGCATCATCACA 59.459 50.0 0.00 0.0 0.00 3.58 R
2077 2347 0.955919 GCGCCTAAGCTTCACAGGTT 60.956 55.0 13.99 0.0 43.37 3.50 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
25 26 8.472007 CCTTAACAAGTCAGACTAGAGGATAT 57.528 38.462 2.64 0.00 0.00 1.63
26 27 8.356657 CCTTAACAAGTCAGACTAGAGGATATG 58.643 40.741 2.64 0.00 0.00 1.78
27 28 5.782893 ACAAGTCAGACTAGAGGATATGC 57.217 43.478 2.64 0.00 0.00 3.14
29 30 5.534654 ACAAGTCAGACTAGAGGATATGCTC 59.465 44.000 15.94 15.94 0.00 4.26
31 32 3.761752 GTCAGACTAGAGGATATGCTCCC 59.238 52.174 19.55 7.78 46.27 4.30
32 33 3.399305 TCAGACTAGAGGATATGCTCCCA 59.601 47.826 19.55 8.09 46.27 4.37
33 34 4.045207 TCAGACTAGAGGATATGCTCCCAT 59.955 45.833 19.55 6.07 46.27 4.00
34 35 4.160065 CAGACTAGAGGATATGCTCCCATG 59.840 50.000 19.55 10.30 46.27 3.66
35 36 4.093011 GACTAGAGGATATGCTCCCATGT 58.907 47.826 19.55 13.05 46.27 3.21
37 38 1.898472 AGAGGATATGCTCCCATGTCG 59.102 52.381 19.55 0.00 46.27 4.35
39 40 2.037772 GAGGATATGCTCCCATGTCGTT 59.962 50.000 12.99 0.00 46.27 3.85
40 41 2.439507 AGGATATGCTCCCATGTCGTTT 59.560 45.455 0.00 0.00 46.27 3.60
41 42 2.549754 GGATATGCTCCCATGTCGTTTG 59.450 50.000 0.00 0.00 39.63 2.93
48 59 2.674852 CTCCCATGTCGTTTGATGACAG 59.325 50.000 8.71 2.40 46.10 3.51
54 65 5.389830 CCATGTCGTTTGATGACAGTTACTG 60.390 44.000 11.21 11.21 46.10 2.74
85 96 9.433153 TGCTTGCAGAATTAGATAGATATTCAG 57.567 33.333 0.00 0.00 32.11 3.02
118 132 9.923143 ACCATGTGTATGTATGTATGTATGTAC 57.077 33.333 0.00 0.00 32.21 2.90
125 143 9.463902 GTATGTATGTATGTATGTACTCCCTCT 57.536 37.037 0.00 0.00 0.00 3.69
129 147 5.138276 TGTATGTATGTACTCCCTCTGTCC 58.862 45.833 0.00 0.00 0.00 4.02
130 148 4.544564 ATGTATGTACTCCCTCTGTCCT 57.455 45.455 0.00 0.00 0.00 3.85
136 154 8.897692 TGTATGTACTCCCTCTGTCCTATAATA 58.102 37.037 0.00 0.00 0.00 0.98
137 155 9.176460 GTATGTACTCCCTCTGTCCTATAATAC 57.824 40.741 0.00 0.00 0.00 1.89
142 160 7.007723 ACTCCCTCTGTCCTATAATACAAGAG 58.992 42.308 0.00 0.00 0.00 2.85
143 161 5.775701 TCCCTCTGTCCTATAATACAAGAGC 59.224 44.000 0.00 0.00 0.00 4.09
144 162 5.336055 CCCTCTGTCCTATAATACAAGAGCG 60.336 48.000 0.00 0.00 0.00 5.03
174 192 3.387397 ACTAGTGTAGTGTCCAAAACGC 58.613 45.455 0.00 0.00 37.69 4.84
180 198 4.689345 GTGTAGTGTCCAAAACGCTCTTAT 59.311 41.667 0.00 0.00 45.69 1.73
198 216 5.021458 TCTTATATTATGGGACGGAGGGAC 58.979 45.833 0.00 0.00 0.00 4.46
200 218 1.424638 ATTATGGGACGGAGGGACTG 58.575 55.000 0.00 0.00 41.55 3.51
201 219 0.337082 TTATGGGACGGAGGGACTGA 59.663 55.000 0.00 0.00 41.55 3.41
202 220 0.106167 TATGGGACGGAGGGACTGAG 60.106 60.000 0.00 0.00 41.55 3.35
203 221 2.760385 GGGACGGAGGGACTGAGG 60.760 72.222 0.00 0.00 41.55 3.86
204 222 2.760385 GGACGGAGGGACTGAGGG 60.760 72.222 0.00 0.00 41.55 4.30
253 275 9.840427 GAAAGAAAACAACATAATGCTAGCTAA 57.160 29.630 17.23 1.22 0.00 3.09
270 298 4.463070 AGCTAAGCTAGGTGTACTACTCC 58.537 47.826 0.00 0.00 36.99 3.85
283 311 6.321690 GGTGTACTACTCCAACTGACATCTAT 59.678 42.308 2.89 0.00 32.30 1.98
299 327 7.567458 TGACATCTATGAATGATGGTTCTGAA 58.433 34.615 8.32 0.00 43.88 3.02
382 414 9.897744 CATACATACAATCAATAAGCGGAAAAT 57.102 29.630 0.00 0.00 0.00 1.82
383 415 9.897744 ATACATACAATCAATAAGCGGAAAATG 57.102 29.630 0.00 0.00 0.00 2.32
403 468 2.700897 TGGTTAGCTAATCCTCCTCTGC 59.299 50.000 14.17 0.00 0.00 4.26
405 470 2.700897 GTTAGCTAATCCTCCTCTGCCA 59.299 50.000 9.88 0.00 0.00 4.92
406 471 1.422531 AGCTAATCCTCCTCTGCCAG 58.577 55.000 0.00 0.00 0.00 4.85
409 474 2.298729 GCTAATCCTCCTCTGCCAGTAG 59.701 54.545 0.00 0.00 0.00 2.57
410 475 1.127343 AATCCTCCTCTGCCAGTAGC 58.873 55.000 0.00 0.00 44.14 3.58
411 476 0.264359 ATCCTCCTCTGCCAGTAGCT 59.736 55.000 0.00 0.00 44.23 3.32
412 477 0.041833 TCCTCCTCTGCCAGTAGCTT 59.958 55.000 0.00 0.00 44.23 3.74
413 478 0.177604 CCTCCTCTGCCAGTAGCTTG 59.822 60.000 0.00 0.00 44.23 4.01
414 479 0.461693 CTCCTCTGCCAGTAGCTTGC 60.462 60.000 0.00 0.00 44.23 4.01
415 480 0.906756 TCCTCTGCCAGTAGCTTGCT 60.907 55.000 0.00 0.00 44.23 3.91
416 481 0.035630 CCTCTGCCAGTAGCTTGCTT 60.036 55.000 0.00 0.00 44.23 3.91
417 482 1.367659 CTCTGCCAGTAGCTTGCTTC 58.632 55.000 0.00 0.00 44.23 3.86
418 483 0.036010 TCTGCCAGTAGCTTGCTTCC 60.036 55.000 0.00 0.00 44.23 3.46
419 484 1.002134 TGCCAGTAGCTTGCTTCCC 60.002 57.895 0.00 0.00 44.23 3.97
420 485 1.301293 GCCAGTAGCTTGCTTCCCT 59.699 57.895 0.00 0.00 38.99 4.20
421 486 0.541863 GCCAGTAGCTTGCTTCCCTA 59.458 55.000 0.00 0.00 38.99 3.53
422 487 1.744114 GCCAGTAGCTTGCTTCCCTAC 60.744 57.143 0.00 0.00 38.99 3.18
423 488 1.834263 CCAGTAGCTTGCTTCCCTACT 59.166 52.381 0.00 0.00 41.67 2.57
424 489 2.159028 CCAGTAGCTTGCTTCCCTACTC 60.159 54.545 0.00 0.00 39.64 2.59
425 490 2.112190 AGTAGCTTGCTTCCCTACTCC 58.888 52.381 0.00 0.00 37.77 3.85
426 491 1.139256 GTAGCTTGCTTCCCTACTCCC 59.861 57.143 0.00 0.00 0.00 4.30
427 492 0.547712 AGCTTGCTTCCCTACTCCCA 60.548 55.000 0.00 0.00 0.00 4.37
428 493 0.107459 GCTTGCTTCCCTACTCCCAG 60.107 60.000 0.00 0.00 0.00 4.45
429 494 0.107459 CTTGCTTCCCTACTCCCAGC 60.107 60.000 0.00 0.00 0.00 4.85
430 495 1.899437 TTGCTTCCCTACTCCCAGCG 61.899 60.000 0.00 0.00 32.85 5.18
431 496 2.058595 GCTTCCCTACTCCCAGCGA 61.059 63.158 0.00 0.00 0.00 4.93
432 497 2.022240 GCTTCCCTACTCCCAGCGAG 62.022 65.000 0.00 0.00 44.95 5.03
439 504 2.179517 CTCCCAGCGAGTCGTGTC 59.820 66.667 15.08 0.00 33.51 3.67
440 505 3.669036 CTCCCAGCGAGTCGTGTCG 62.669 68.421 15.08 5.04 43.08 4.35
446 511 3.742353 CGAGTCGTGTCGCTCTTG 58.258 61.111 3.82 1.84 32.22 3.02
447 512 1.082038 CGAGTCGTGTCGCTCTTGT 60.082 57.895 3.82 0.00 32.22 3.16
448 513 0.165295 CGAGTCGTGTCGCTCTTGTA 59.835 55.000 3.82 0.00 32.22 2.41
449 514 1.604396 GAGTCGTGTCGCTCTTGTAC 58.396 55.000 0.00 0.00 31.32 2.90
450 515 1.197264 GAGTCGTGTCGCTCTTGTACT 59.803 52.381 0.00 0.00 31.32 2.73
451 516 1.069159 AGTCGTGTCGCTCTTGTACTG 60.069 52.381 0.00 0.00 0.00 2.74
452 517 0.240145 TCGTGTCGCTCTTGTACTGG 59.760 55.000 0.00 0.00 0.00 4.00
453 518 0.039437 CGTGTCGCTCTTGTACTGGT 60.039 55.000 0.00 0.00 0.00 4.00
454 519 1.419374 GTGTCGCTCTTGTACTGGTG 58.581 55.000 0.00 0.00 0.00 4.17
455 520 0.317160 TGTCGCTCTTGTACTGGTGG 59.683 55.000 0.00 0.00 0.00 4.61
456 521 0.601558 GTCGCTCTTGTACTGGTGGA 59.398 55.000 0.00 0.00 0.00 4.02
457 522 0.888619 TCGCTCTTGTACTGGTGGAG 59.111 55.000 0.00 0.00 0.00 3.86
458 523 0.603569 CGCTCTTGTACTGGTGGAGT 59.396 55.000 0.00 0.00 38.88 3.85
459 524 1.000955 CGCTCTTGTACTGGTGGAGTT 59.999 52.381 0.00 0.00 35.96 3.01
460 525 2.689646 GCTCTTGTACTGGTGGAGTTC 58.310 52.381 0.00 0.00 35.96 3.01
461 526 2.300437 GCTCTTGTACTGGTGGAGTTCT 59.700 50.000 0.00 0.00 35.96 3.01
462 527 3.615351 GCTCTTGTACTGGTGGAGTTCTC 60.615 52.174 0.00 0.00 35.96 2.87
463 528 3.829601 CTCTTGTACTGGTGGAGTTCTCT 59.170 47.826 0.00 0.00 35.96 3.10
464 529 4.223953 TCTTGTACTGGTGGAGTTCTCTT 58.776 43.478 0.00 0.00 35.96 2.85
465 530 4.281182 TCTTGTACTGGTGGAGTTCTCTTC 59.719 45.833 0.00 0.00 35.96 2.87
466 531 3.845860 TGTACTGGTGGAGTTCTCTTCT 58.154 45.455 0.00 0.00 35.96 2.85
467 532 4.223953 TGTACTGGTGGAGTTCTCTTCTT 58.776 43.478 0.00 0.00 35.96 2.52
468 533 4.281182 TGTACTGGTGGAGTTCTCTTCTTC 59.719 45.833 0.00 0.00 35.96 2.87
469 534 3.582164 ACTGGTGGAGTTCTCTTCTTCT 58.418 45.455 0.00 0.00 0.00 2.85
470 535 3.970640 ACTGGTGGAGTTCTCTTCTTCTT 59.029 43.478 0.00 0.00 0.00 2.52
483 548 6.377080 TCTCTTCTTCTTGCCATAGAGGATA 58.623 40.000 0.00 0.00 41.22 2.59
485 550 7.345653 TCTCTTCTTCTTGCCATAGAGGATAAA 59.654 37.037 0.00 0.00 41.22 1.40
487 552 8.497745 TCTTCTTCTTGCCATAGAGGATAAAAT 58.502 33.333 0.00 0.00 41.22 1.82
488 553 8.682936 TTCTTCTTGCCATAGAGGATAAAATC 57.317 34.615 0.00 0.00 41.22 2.17
489 554 8.038862 TCTTCTTGCCATAGAGGATAAAATCT 57.961 34.615 0.00 0.00 41.22 2.40
490 555 8.497745 TCTTCTTGCCATAGAGGATAAAATCTT 58.502 33.333 0.00 0.00 41.22 2.40
492 567 8.682936 TCTTGCCATAGAGGATAAAATCTTTC 57.317 34.615 0.00 0.00 41.22 2.62
496 571 8.157476 TGCCATAGAGGATAAAATCTTTCTACC 58.843 37.037 0.00 0.00 41.22 3.18
512 587 8.740123 TCTTTCTACCATCACTAAACAAACAA 57.260 30.769 0.00 0.00 0.00 2.83
516 591 8.684386 TCTACCATCACTAAACAAACAATTCA 57.316 30.769 0.00 0.00 0.00 2.57
517 592 8.783093 TCTACCATCACTAAACAAACAATTCAG 58.217 33.333 0.00 0.00 0.00 3.02
566 644 6.487668 CACATTTATCATGGGCAGACTTCATA 59.512 38.462 0.00 0.00 0.00 2.15
570 648 7.514784 TTATCATGGGCAGACTTCATAAATG 57.485 36.000 0.00 0.00 0.00 2.32
633 715 9.371136 GATGTTCTGTACAATTTCTCTGTCATA 57.629 33.333 0.00 0.00 40.89 2.15
752 868 5.881923 AATCGAAATTACTACCCTGCCTA 57.118 39.130 0.00 0.00 0.00 3.93
832 954 2.422127 ACGGTTGCACCTTATGTTATGC 59.578 45.455 0.00 0.00 35.66 3.14
839 971 7.763985 GGTTGCACCTTATGTTATGCTTTAATT 59.236 33.333 0.00 0.00 38.90 1.40
942 1076 5.234116 GGCATTGCATTTATTTTAACTCCGG 59.766 40.000 11.39 0.00 0.00 5.14
944 1078 6.975772 GCATTGCATTTATTTTAACTCCGGTA 59.024 34.615 0.00 0.00 0.00 4.02
1089 1224 9.543783 CTGATTAAAACTGGGTTAGGAGTATAC 57.456 37.037 0.00 0.00 0.00 1.47
1144 1279 0.654683 GCAGAGCAATGTAAGGAGCG 59.345 55.000 0.00 0.00 0.00 5.03
1377 1616 4.960469 TGTATCGGGTTCTTCTATCTGGTT 59.040 41.667 0.00 0.00 0.00 3.67
1390 1630 9.658799 TCTTCTATCTGGTTTACTGAAATGAAG 57.341 33.333 0.00 0.00 35.57 3.02
1392 1632 9.436957 TTCTATCTGGTTTACTGAAATGAAGTC 57.563 33.333 0.00 0.00 0.00 3.01
1518 1758 2.485122 CCTTTCATGGCGTTCGGC 59.515 61.111 11.64 11.64 42.51 5.54
1533 1773 4.116961 CGTTCGGCACCTTCATTATTCTA 58.883 43.478 0.00 0.00 0.00 2.10
1695 1946 2.373169 TCAGTTCACAAGAGGGCTGATT 59.627 45.455 0.00 0.00 29.94 2.57
1731 1982 2.178912 TCGTGTTCCTAAAAGGGCTG 57.821 50.000 0.00 0.00 35.59 4.85
1749 2000 2.194212 GCTCTACTCGATGGGCGGA 61.194 63.158 0.00 0.00 41.33 5.54
1851 2103 5.772004 CTCCTATGGGCCTACTCATACTAT 58.228 45.833 4.53 0.00 0.00 2.12
2077 2347 5.043248 GCACTAGAAAAAGAAAAAGCAGCA 58.957 37.500 0.00 0.00 0.00 4.41
2335 2631 3.641648 ACTGGCATTGTTTGAATGTTCG 58.358 40.909 0.00 0.00 0.00 3.95
2336 2632 2.988493 CTGGCATTGTTTGAATGTTCGG 59.012 45.455 0.00 0.00 0.00 4.30
2362 2658 8.328864 GTCAGTGAAAGTATATGGATTTTCGAC 58.671 37.037 0.00 0.00 33.40 4.20
2399 2695 3.055819 GCTCCAGTCTGTCATTTGGTAGA 60.056 47.826 0.00 0.00 32.51 2.59
2518 2818 7.511959 AGAGATTTGGTCTAACAGTTTTTCC 57.488 36.000 0.00 0.00 37.29 3.13
2520 2820 4.904253 TTTGGTCTAACAGTTTTTCCCG 57.096 40.909 0.00 0.00 0.00 5.14
2539 2839 5.823353 TCCCGAAACAAGACAAACAAATAC 58.177 37.500 0.00 0.00 0.00 1.89
2610 2911 5.918576 CAGATTTACGCGTGATAACTATCCA 59.081 40.000 24.59 0.00 31.71 3.41
2669 2971 5.565723 GCATTAGCAACAAGTGAACAAAG 57.434 39.130 0.00 0.00 41.58 2.77
2670 2972 5.043248 GCATTAGCAACAAGTGAACAAAGT 58.957 37.500 0.00 0.00 41.58 2.66
2671 2973 5.051508 GCATTAGCAACAAGTGAACAAAGTG 60.052 40.000 0.00 0.00 41.58 3.16
2672 2974 3.508744 AGCAACAAGTGAACAAAGTGG 57.491 42.857 0.00 0.00 0.00 4.00
2674 2976 3.258123 AGCAACAAGTGAACAAAGTGGTT 59.742 39.130 0.00 0.00 0.00 3.67
2676 2978 5.047660 AGCAACAAGTGAACAAAGTGGTTAA 60.048 36.000 0.00 0.00 0.00 2.01
2682 2984 7.383843 ACAAGTGAACAAAGTGGTTAACAAAAG 59.616 33.333 8.10 0.00 35.02 2.27
2684 2986 7.836842 AGTGAACAAAGTGGTTAACAAAAGAT 58.163 30.769 8.10 0.00 35.02 2.40
2685 2987 8.311109 AGTGAACAAAGTGGTTAACAAAAGATT 58.689 29.630 8.10 0.00 35.02 2.40
2686 2988 8.931775 GTGAACAAAGTGGTTAACAAAAGATTT 58.068 29.630 8.10 0.00 33.16 2.17
2734 3036 1.413118 AAAACACAGCTTTGGAGGGG 58.587 50.000 4.63 0.00 0.00 4.79
2752 3054 4.479158 AGGGGACACAAAAGCAAAATAGA 58.521 39.130 0.00 0.00 0.00 1.98
2760 3062 5.870978 CACAAAAGCAAAATAGATTCCCAGG 59.129 40.000 0.00 0.00 0.00 4.45
2762 3064 6.723977 ACAAAAGCAAAATAGATTCCCAGGTA 59.276 34.615 0.00 0.00 0.00 3.08
2763 3065 6.775594 AAAGCAAAATAGATTCCCAGGTAC 57.224 37.500 0.00 0.00 0.00 3.34
2764 3066 4.793201 AGCAAAATAGATTCCCAGGTACC 58.207 43.478 2.73 2.73 0.00 3.34
2765 3067 4.229582 AGCAAAATAGATTCCCAGGTACCA 59.770 41.667 15.94 0.00 0.00 3.25
2766 3068 4.953579 GCAAAATAGATTCCCAGGTACCAA 59.046 41.667 15.94 0.00 0.00 3.67
2767 3069 5.598417 GCAAAATAGATTCCCAGGTACCAAT 59.402 40.000 15.94 4.66 0.00 3.16
2768 3070 6.098266 GCAAAATAGATTCCCAGGTACCAATT 59.902 38.462 15.94 0.00 0.00 2.32
2769 3071 7.684428 GCAAAATAGATTCCCAGGTACCAATTC 60.684 40.741 15.94 2.14 0.00 2.17
2773 3075 4.540099 AGATTCCCAGGTACCAATTCTCAA 59.460 41.667 15.94 0.00 0.00 3.02
2774 3076 4.301072 TTCCCAGGTACCAATTCTCAAG 57.699 45.455 15.94 0.00 0.00 3.02
2787 3112 4.996788 ATTCTCAAGCATGGATTTCACC 57.003 40.909 0.00 0.00 0.00 4.02
2791 3116 0.527565 AAGCATGGATTTCACCGCAC 59.472 50.000 0.00 0.00 31.56 5.34
2884 3244 5.990386 TCGTATTAAACAGTGCAAAGGTACA 59.010 36.000 0.00 0.00 31.27 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.003003 TCATCAAACGACATGGGAGCA 59.997 47.619 0.00 0.00 0.00 4.26
26 27 1.398390 GTCATCAAACGACATGGGAGC 59.602 52.381 0.00 0.00 33.43 4.70
27 28 2.674852 CTGTCATCAAACGACATGGGAG 59.325 50.000 0.00 0.00 42.27 4.30
29 30 2.426522 ACTGTCATCAAACGACATGGG 58.573 47.619 0.00 0.00 42.27 4.00
31 32 5.405269 TCAGTAACTGTCATCAAACGACATG 59.595 40.000 0.00 0.00 42.27 3.21
32 33 5.405571 GTCAGTAACTGTCATCAAACGACAT 59.594 40.000 0.00 0.00 42.27 3.06
33 34 4.743151 GTCAGTAACTGTCATCAAACGACA 59.257 41.667 0.00 0.00 41.00 4.35
34 35 4.143597 CGTCAGTAACTGTCATCAAACGAC 60.144 45.833 0.00 0.00 32.61 4.34
35 36 3.978855 CGTCAGTAACTGTCATCAAACGA 59.021 43.478 0.00 0.00 32.61 3.85
37 38 4.056050 ACCGTCAGTAACTGTCATCAAAC 58.944 43.478 0.00 0.00 32.61 2.93
39 40 3.649073 CACCGTCAGTAACTGTCATCAA 58.351 45.455 0.00 0.00 32.61 2.57
40 41 2.609491 GCACCGTCAGTAACTGTCATCA 60.609 50.000 0.00 0.00 32.61 3.07
41 42 1.993370 GCACCGTCAGTAACTGTCATC 59.007 52.381 0.00 0.00 32.61 2.92
48 59 0.512952 CTGCAAGCACCGTCAGTAAC 59.487 55.000 0.00 0.00 0.00 2.50
54 65 2.346803 TCTAATTCTGCAAGCACCGTC 58.653 47.619 0.00 0.00 0.00 4.79
118 132 6.071616 GCTCTTGTATTATAGGACAGAGGGAG 60.072 46.154 0.00 0.00 0.00 4.30
119 133 5.775701 GCTCTTGTATTATAGGACAGAGGGA 59.224 44.000 0.00 0.00 0.00 4.20
120 134 5.336055 CGCTCTTGTATTATAGGACAGAGGG 60.336 48.000 0.00 0.00 32.82 4.30
121 135 5.241949 ACGCTCTTGTATTATAGGACAGAGG 59.758 44.000 0.00 0.00 0.00 3.69
153 171 3.069158 AGCGTTTTGGACACTACACTAGT 59.931 43.478 0.00 0.00 40.28 2.57
167 185 6.347402 CCGTCCCATAATATAAGAGCGTTTTG 60.347 42.308 0.00 0.00 0.00 2.44
172 190 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
173 191 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
174 192 5.127356 GTCCCTCCGTCCCATAATATAAGAG 59.873 48.000 0.00 0.00 0.00 2.85
180 198 2.178325 TCAGTCCCTCCGTCCCATAATA 59.822 50.000 0.00 0.00 0.00 0.98
198 216 3.386078 TCTGCTGCTAAATACTCCCTCAG 59.614 47.826 0.00 0.00 0.00 3.35
200 218 3.723260 GTCTGCTGCTAAATACTCCCTC 58.277 50.000 0.00 0.00 0.00 4.30
201 219 2.101582 CGTCTGCTGCTAAATACTCCCT 59.898 50.000 0.00 0.00 0.00 4.20
202 220 2.474816 CGTCTGCTGCTAAATACTCCC 58.525 52.381 0.00 0.00 0.00 4.30
203 221 1.861575 GCGTCTGCTGCTAAATACTCC 59.138 52.381 0.00 0.00 38.39 3.85
204 222 2.540515 TGCGTCTGCTGCTAAATACTC 58.459 47.619 0.00 0.00 43.34 2.59
253 275 4.017808 CAGTTGGAGTAGTACACCTAGCT 58.982 47.826 16.49 9.47 29.70 3.32
270 298 7.498239 AGAACCATCATTCATAGATGTCAGTTG 59.502 37.037 0.00 0.00 40.93 3.16
299 327 4.227300 TGAGTTGGTAAAGGATATGCAGGT 59.773 41.667 0.00 0.00 0.00 4.00
301 329 5.882557 AGTTGAGTTGGTAAAGGATATGCAG 59.117 40.000 0.00 0.00 0.00 4.41
366 398 5.594317 AGCTAACCATTTTCCGCTTATTGAT 59.406 36.000 0.00 0.00 0.00 2.57
374 406 3.883489 AGGATTAGCTAACCATTTTCCGC 59.117 43.478 20.32 1.26 0.00 5.54
382 414 2.700897 GCAGAGGAGGATTAGCTAACCA 59.299 50.000 20.32 0.00 0.00 3.67
383 415 2.037902 GGCAGAGGAGGATTAGCTAACC 59.962 54.545 8.70 12.03 0.00 2.85
403 468 1.834263 AGTAGGGAAGCAAGCTACTGG 59.166 52.381 0.00 0.00 30.69 4.00
405 470 2.112190 GGAGTAGGGAAGCAAGCTACT 58.888 52.381 0.00 0.00 34.05 2.57
406 471 1.139256 GGGAGTAGGGAAGCAAGCTAC 59.861 57.143 0.00 0.00 0.00 3.58
409 474 0.107459 CTGGGAGTAGGGAAGCAAGC 60.107 60.000 0.00 0.00 0.00 4.01
410 475 0.107459 GCTGGGAGTAGGGAAGCAAG 60.107 60.000 0.00 0.00 34.01 4.01
411 476 1.899437 CGCTGGGAGTAGGGAAGCAA 61.899 60.000 0.00 0.00 33.41 3.91
412 477 2.359169 CGCTGGGAGTAGGGAAGCA 61.359 63.158 0.00 0.00 33.41 3.91
413 478 2.022240 CTCGCTGGGAGTAGGGAAGC 62.022 65.000 13.10 0.00 38.88 3.86
414 479 2.119886 CTCGCTGGGAGTAGGGAAG 58.880 63.158 13.10 0.00 38.88 3.46
415 480 4.356979 CTCGCTGGGAGTAGGGAA 57.643 61.111 13.10 0.00 38.88 3.97
423 488 3.733960 CGACACGACTCGCTGGGA 61.734 66.667 0.00 0.00 0.00 4.37
429 494 0.165295 TACAAGAGCGACACGACTCG 59.835 55.000 0.00 0.00 36.04 4.18
430 495 1.197264 AGTACAAGAGCGACACGACTC 59.803 52.381 0.00 0.00 33.03 3.36
431 496 1.069159 CAGTACAAGAGCGACACGACT 60.069 52.381 0.00 0.00 0.00 4.18
432 497 1.328439 CAGTACAAGAGCGACACGAC 58.672 55.000 0.00 0.00 0.00 4.34
433 498 0.240145 CCAGTACAAGAGCGACACGA 59.760 55.000 0.00 0.00 0.00 4.35
434 499 0.039437 ACCAGTACAAGAGCGACACG 60.039 55.000 0.00 0.00 0.00 4.49
435 500 1.419374 CACCAGTACAAGAGCGACAC 58.581 55.000 0.00 0.00 0.00 3.67
436 501 0.317160 CCACCAGTACAAGAGCGACA 59.683 55.000 0.00 0.00 0.00 4.35
437 502 0.601558 TCCACCAGTACAAGAGCGAC 59.398 55.000 0.00 0.00 0.00 5.19
438 503 0.888619 CTCCACCAGTACAAGAGCGA 59.111 55.000 0.00 0.00 0.00 4.93
439 504 0.603569 ACTCCACCAGTACAAGAGCG 59.396 55.000 0.00 0.00 31.37 5.03
440 505 2.300437 AGAACTCCACCAGTACAAGAGC 59.700 50.000 0.00 0.00 32.30 4.09
441 506 3.829601 AGAGAACTCCACCAGTACAAGAG 59.170 47.826 0.00 0.00 32.30 2.85
442 507 3.845860 AGAGAACTCCACCAGTACAAGA 58.154 45.455 0.00 0.00 32.30 3.02
443 508 4.282195 AGAAGAGAACTCCACCAGTACAAG 59.718 45.833 0.00 0.00 32.30 3.16
444 509 4.223953 AGAAGAGAACTCCACCAGTACAA 58.776 43.478 0.00 0.00 32.30 2.41
445 510 3.845860 AGAAGAGAACTCCACCAGTACA 58.154 45.455 0.00 0.00 32.30 2.90
446 511 4.525100 AGAAGAAGAGAACTCCACCAGTAC 59.475 45.833 0.00 0.00 32.30 2.73
447 512 4.742012 AGAAGAAGAGAACTCCACCAGTA 58.258 43.478 0.00 0.00 32.30 2.74
448 513 3.582164 AGAAGAAGAGAACTCCACCAGT 58.418 45.455 0.00 0.00 36.64 4.00
449 514 4.314121 CAAGAAGAAGAGAACTCCACCAG 58.686 47.826 0.00 0.00 0.00 4.00
450 515 3.495100 GCAAGAAGAAGAGAACTCCACCA 60.495 47.826 0.00 0.00 0.00 4.17
451 516 3.070748 GCAAGAAGAAGAGAACTCCACC 58.929 50.000 0.00 0.00 0.00 4.61
452 517 3.070748 GGCAAGAAGAAGAGAACTCCAC 58.929 50.000 0.00 0.00 0.00 4.02
453 518 2.705658 TGGCAAGAAGAAGAGAACTCCA 59.294 45.455 0.00 0.00 0.00 3.86
454 519 3.409026 TGGCAAGAAGAAGAGAACTCC 57.591 47.619 0.00 0.00 0.00 3.85
455 520 5.971763 TCTATGGCAAGAAGAAGAGAACTC 58.028 41.667 0.00 0.00 0.00 3.01
456 521 5.104982 CCTCTATGGCAAGAAGAAGAGAACT 60.105 44.000 0.00 0.00 33.82 3.01
457 522 5.105146 TCCTCTATGGCAAGAAGAAGAGAAC 60.105 44.000 0.00 0.00 33.82 3.01
458 523 5.026121 TCCTCTATGGCAAGAAGAAGAGAA 58.974 41.667 0.00 0.00 33.82 2.87
459 524 4.614475 TCCTCTATGGCAAGAAGAAGAGA 58.386 43.478 0.00 0.00 33.82 3.10
460 525 5.549742 ATCCTCTATGGCAAGAAGAAGAG 57.450 43.478 0.00 0.00 35.26 2.85
461 526 7.437713 TTTATCCTCTATGGCAAGAAGAAGA 57.562 36.000 0.00 0.00 35.26 2.87
462 527 8.688747 ATTTTATCCTCTATGGCAAGAAGAAG 57.311 34.615 0.00 0.00 35.26 2.85
463 528 8.497745 AGATTTTATCCTCTATGGCAAGAAGAA 58.502 33.333 0.00 0.00 35.26 2.52
464 529 8.038862 AGATTTTATCCTCTATGGCAAGAAGA 57.961 34.615 0.00 0.00 35.26 2.87
465 530 8.688747 AAGATTTTATCCTCTATGGCAAGAAG 57.311 34.615 0.00 0.00 35.26 2.85
466 531 9.125026 GAAAGATTTTATCCTCTATGGCAAGAA 57.875 33.333 0.00 0.00 35.26 2.52
467 532 8.497745 AGAAAGATTTTATCCTCTATGGCAAGA 58.502 33.333 0.00 0.00 35.26 3.02
468 533 8.688747 AGAAAGATTTTATCCTCTATGGCAAG 57.311 34.615 0.00 0.00 35.26 4.01
469 534 9.561069 GTAGAAAGATTTTATCCTCTATGGCAA 57.439 33.333 0.00 0.00 35.26 4.52
470 535 8.157476 GGTAGAAAGATTTTATCCTCTATGGCA 58.843 37.037 0.00 0.00 35.26 4.92
485 550 9.349713 TGTTTGTTTAGTGATGGTAGAAAGATT 57.650 29.630 0.00 0.00 0.00 2.40
487 552 8.740123 TTGTTTGTTTAGTGATGGTAGAAAGA 57.260 30.769 0.00 0.00 0.00 2.52
488 553 9.965824 AATTGTTTGTTTAGTGATGGTAGAAAG 57.034 29.630 0.00 0.00 0.00 2.62
489 554 9.959749 GAATTGTTTGTTTAGTGATGGTAGAAA 57.040 29.630 0.00 0.00 0.00 2.52
490 555 9.126151 TGAATTGTTTGTTTAGTGATGGTAGAA 57.874 29.630 0.00 0.00 0.00 2.10
492 567 8.023128 CCTGAATTGTTTGTTTAGTGATGGTAG 58.977 37.037 0.00 0.00 0.00 3.18
496 571 6.642131 CACCCTGAATTGTTTGTTTAGTGATG 59.358 38.462 0.00 0.00 0.00 3.07
500 575 4.404073 TGCACCCTGAATTGTTTGTTTAGT 59.596 37.500 0.00 0.00 0.00 2.24
512 587 1.615392 GCAGAAACTTGCACCCTGAAT 59.385 47.619 0.00 0.00 43.53 2.57
752 868 8.261522 GGAACAGAGTTTATCTTGGATACTTCT 58.738 37.037 0.00 0.00 35.47 2.85
942 1076 4.157656 TCATACATGGCTGCAAAAAGGTAC 59.842 41.667 0.50 0.00 0.00 3.34
944 1078 3.164268 TCATACATGGCTGCAAAAAGGT 58.836 40.909 0.50 0.00 0.00 3.50
1053 1188 3.372206 CAGTTTTAATCAGACCCGAGCTG 59.628 47.826 0.00 0.00 34.71 4.24
1089 1224 2.893398 CCGAGGAACTTCTCCCCG 59.107 66.667 0.00 0.00 46.81 5.73
1144 1279 2.447443 GGGGATCAAGGTTCTTTGGAC 58.553 52.381 0.00 0.00 0.00 4.02
1377 1616 7.147312 CCATTGCAAAGACTTCATTTCAGTAA 58.853 34.615 1.71 0.00 0.00 2.24
1518 1758 4.712476 AGCCTGCTAGAATAATGAAGGTG 58.288 43.478 0.00 0.00 0.00 4.00
1533 1773 1.197430 AGCCTAGTGTGAAGCCTGCT 61.197 55.000 0.00 0.00 0.00 4.24
1695 1946 1.121407 CGATCTGTAGGCCCCATCCA 61.121 60.000 0.00 0.00 0.00 3.41
1731 1982 2.136196 CTCCGCCCATCGAGTAGAGC 62.136 65.000 0.00 0.00 41.67 4.09
1776 2027 2.762875 AGGTACCCGCTGTAGGCC 60.763 66.667 8.74 0.00 37.74 5.19
1851 2103 0.540923 TCATCCACGGCATCATCACA 59.459 50.000 0.00 0.00 0.00 3.58
2077 2347 0.955919 GCGCCTAAGCTTCACAGGTT 60.956 55.000 13.99 0.00 43.37 3.50
2149 2419 4.934602 ACAAAACCCTGTCAACAAAACATG 59.065 37.500 0.00 0.00 0.00 3.21
2335 2631 7.494625 TCGAAAATCCATATACTTTCACTGACC 59.505 37.037 0.00 0.00 0.00 4.02
2336 2632 8.328864 GTCGAAAATCCATATACTTTCACTGAC 58.671 37.037 0.00 0.00 0.00 3.51
2362 2658 3.119316 ACTGGAGCTGACTGTCTTTATCG 60.119 47.826 9.51 0.00 0.00 2.92
2518 2818 5.267776 ACGTATTTGTTTGTCTTGTTTCGG 58.732 37.500 0.00 0.00 0.00 4.30
2565 2866 5.945784 TCTGGATACTTGACCAAAAATCCTG 59.054 40.000 17.06 16.42 34.87 3.86
2566 2867 6.139679 TCTGGATACTTGACCAAAAATCCT 57.860 37.500 17.06 0.00 34.87 3.24
2578 2879 4.109766 TCACGCGTAAATCTGGATACTTG 58.890 43.478 13.44 0.00 37.61 3.16
2623 2924 2.306847 TCATACATAGCCAGCGTCTCA 58.693 47.619 0.00 0.00 0.00 3.27
2624 2925 3.371102 TTCATACATAGCCAGCGTCTC 57.629 47.619 0.00 0.00 0.00 3.36
2625 2926 3.819564 TTTCATACATAGCCAGCGTCT 57.180 42.857 0.00 0.00 0.00 4.18
2626 2927 3.364366 GCATTTCATACATAGCCAGCGTC 60.364 47.826 0.00 0.00 0.00 5.19
2627 2928 2.549754 GCATTTCATACATAGCCAGCGT 59.450 45.455 0.00 0.00 0.00 5.07
2628 2929 2.549329 TGCATTTCATACATAGCCAGCG 59.451 45.455 0.00 0.00 0.00 5.18
2629 2930 4.778534 ATGCATTTCATACATAGCCAGC 57.221 40.909 0.00 0.00 32.59 4.85
2670 2972 9.703892 CCATCAACATAAATCTTTTGTTAACCA 57.296 29.630 2.48 0.00 32.57 3.67
2671 2973 9.921637 TCCATCAACATAAATCTTTTGTTAACC 57.078 29.630 2.48 0.00 32.57 2.85
2688 2990 7.608376 TGGTCGTTTAGAATTTATCCATCAACA 59.392 33.333 0.00 0.00 0.00 3.33
2689 2991 7.981142 TGGTCGTTTAGAATTTATCCATCAAC 58.019 34.615 0.00 0.00 0.00 3.18
2692 2994 9.849166 TTTTTGGTCGTTTAGAATTTATCCATC 57.151 29.630 0.00 0.00 0.00 3.51
2706 3008 3.586100 AAGCTGTGTTTTTGGTCGTTT 57.414 38.095 0.00 0.00 0.00 3.60
2734 3036 6.454795 TGGGAATCTATTTTGCTTTTGTGTC 58.545 36.000 0.00 0.00 0.00 3.67
2752 3054 4.860022 CTTGAGAATTGGTACCTGGGAAT 58.140 43.478 14.36 1.06 0.00 3.01
2760 3062 5.841957 AATCCATGCTTGAGAATTGGTAC 57.158 39.130 0.22 0.00 0.00 3.34
2762 3064 4.773674 TGAAATCCATGCTTGAGAATTGGT 59.226 37.500 0.22 0.00 0.00 3.67
2763 3065 5.107133 GTGAAATCCATGCTTGAGAATTGG 58.893 41.667 0.22 0.00 0.00 3.16
2764 3066 5.107133 GGTGAAATCCATGCTTGAGAATTG 58.893 41.667 0.22 0.00 0.00 2.32
2765 3067 4.142315 CGGTGAAATCCATGCTTGAGAATT 60.142 41.667 0.22 0.00 0.00 2.17
2766 3068 3.379372 CGGTGAAATCCATGCTTGAGAAT 59.621 43.478 0.22 0.00 0.00 2.40
2767 3069 2.749076 CGGTGAAATCCATGCTTGAGAA 59.251 45.455 0.22 0.00 0.00 2.87
2768 3070 2.358957 CGGTGAAATCCATGCTTGAGA 58.641 47.619 0.22 0.00 0.00 3.27
2769 3071 1.202222 GCGGTGAAATCCATGCTTGAG 60.202 52.381 0.22 0.00 0.00 3.02
2773 3075 1.647545 CGTGCGGTGAAATCCATGCT 61.648 55.000 0.00 0.00 32.39 3.79
2774 3076 1.226379 CGTGCGGTGAAATCCATGC 60.226 57.895 0.00 0.00 0.00 4.06
2800 3125 0.527565 ACGAATGGCTGTTGGAATGC 59.472 50.000 0.00 0.00 0.00 3.56
2884 3244 2.829720 TGCTCTTGTACCCATAGTCGTT 59.170 45.455 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.