Multiple sequence alignment - TraesCS1A01G079900

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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 TraesCS1A01G079900 chr1A 100.000 2312 0 0 1 2312 62795483 62793172 0.000000e+00 4270.0
1 TraesCS1A01G079900 chr1A 85.878 1225 109 40 713 1894 490418032 490419235 0.000000e+00 1245.0
2 TraesCS1A01G079900 chr1A 87.602 976 82 19 688 1633 490759742 490760708 0.000000e+00 1096.0
3 TraesCS1A01G079900 chr1A 90.942 552 40 10 774 1319 487568502 487569049 0.000000e+00 734.0
4 TraesCS1A01G079900 chr1A 84.861 469 33 15 1878 2312 490419423 490419887 2.730000e-119 438.0
5 TraesCS1A01G079900 chr1A 89.213 343 24 6 1886 2220 490778341 490778678 1.280000e-112 416.0
6 TraesCS1A01G079900 chr1A 90.254 236 12 5 1630 1861 490777848 490778076 4.830000e-77 298.0
7 TraesCS1A01G079900 chr1A 85.470 117 12 5 502 614 490417462 490417577 1.450000e-22 117.0
8 TraesCS1A01G079900 chr1B 91.449 1649 60 29 718 2312 104481778 104480157 0.000000e+00 2189.0
9 TraesCS1A01G079900 chr1B 85.233 1158 101 42 630 1740 527287935 527289069 0.000000e+00 1127.0
10 TraesCS1A01G079900 chr1B 86.767 665 64 16 793 1444 608335832 608335179 0.000000e+00 719.0
11 TraesCS1A01G079900 chr1B 88.425 527 47 10 793 1313 608042961 608042443 7.010000e-175 623.0
12 TraesCS1A01G079900 chr1B 83.357 703 74 18 772 1444 610893040 610893729 5.460000e-171 610.0
13 TraesCS1A01G079900 chr1B 86.436 376 42 7 1623 1994 521767559 521767929 9.950000e-109 403.0
14 TraesCS1A01G079900 chr1B 83.820 445 35 18 1902 2312 527289882 527290323 2.790000e-104 388.0
15 TraesCS1A01G079900 chr1B 94.608 204 11 0 408 611 104483289 104483086 1.330000e-82 316.0
16 TraesCS1A01G079900 chr1B 93.000 100 7 0 1805 1904 527289071 527289170 1.850000e-31 147.0
17 TraesCS1A01G079900 chr1D 93.027 1133 41 15 689 1792 63682395 63681272 0.000000e+00 1620.0
18 TraesCS1A01G079900 chr1D 85.634 710 70 25 790 1477 388603426 388604125 0.000000e+00 717.0
19 TraesCS1A01G079900 chr1D 89.474 551 50 8 774 1319 388024387 388024934 0.000000e+00 689.0
20 TraesCS1A01G079900 chr1D 88.433 536 45 10 95 619 63682952 63682423 4.190000e-177 630.0
21 TraesCS1A01G079900 chr1D 85.000 640 48 21 1326 1927 394490842 394490213 7.060000e-170 606.0
22 TraesCS1A01G079900 chr1D 80.791 354 31 22 84 403 267202013 267201663 2.300000e-60 243.0
23 TraesCS1A01G079900 chr1D 94.161 137 8 0 2083 2219 394490181 394490045 2.330000e-50 209.0
24 TraesCS1A01G079900 chr1D 97.368 38 1 0 633 670 63682435 63682398 5.330000e-07 65.8
25 TraesCS1A01G079900 chr6B 84.732 1251 112 47 502 1707 679983919 679982703 0.000000e+00 1179.0
26 TraesCS1A01G079900 chr6B 86.822 387 30 9 1777 2145 679982685 679982302 1.650000e-111 412.0
27 TraesCS1A01G079900 chr5B 86.997 323 30 9 85 400 470198299 470198616 1.020000e-93 353.0
28 TraesCS1A01G079900 chr7A 84.438 347 38 8 69 402 653468054 653468397 6.160000e-86 327.0
29 TraesCS1A01G079900 chr7A 98.571 70 1 0 1 70 34184706 34184637 8.670000e-25 124.0
30 TraesCS1A01G079900 chr7A 88.172 93 10 1 1 92 694568575 694568667 2.430000e-20 110.0
31 TraesCS1A01G079900 chr7D 85.669 314 31 12 95 400 503976501 503976194 3.710000e-83 318.0
32 TraesCS1A01G079900 chr7D 80.833 360 41 9 69 403 255305912 255305556 8.200000e-65 257.0
33 TraesCS1A01G079900 chr7D 88.108 185 15 4 69 248 566902432 566902614 1.800000e-51 213.0
34 TraesCS1A01G079900 chr7D 88.000 175 12 5 68 234 551831544 551831717 5.040000e-47 198.0
35 TraesCS1A01G079900 chr2D 81.522 368 33 17 69 403 15112602 15112237 1.050000e-68 270.0
36 TraesCS1A01G079900 chr2D 100.000 69 0 0 1 69 592998499 592998431 6.700000e-26 128.0
37 TraesCS1A01G079900 chr2D 97.222 72 2 0 1 72 460287639 460287710 3.120000e-24 122.0
38 TraesCS1A01G079900 chr3D 82.595 316 40 13 98 404 419656477 419656168 4.900000e-67 265.0
39 TraesCS1A01G079900 chr3D 82.069 145 20 3 1597 1740 114880089 114879950 4.040000e-23 119.0
40 TraesCS1A01G079900 chr5D 81.847 314 46 9 96 403 362874217 362873909 1.060000e-63 254.0
41 TraesCS1A01G079900 chr3A 84.211 266 33 6 69 327 26111102 26111365 1.370000e-62 250.0
42 TraesCS1A01G079900 chr6A 79.730 370 37 22 69 404 28945483 28945848 1.380000e-57 233.0
43 TraesCS1A01G079900 chr7B 100.000 68 0 0 2 69 126113824 126113757 2.410000e-25 126.0
44 TraesCS1A01G079900 chr6D 98.571 70 1 0 1 70 40887659 40887590 8.670000e-25 124.0
45 TraesCS1A01G079900 chr4A 98.571 70 1 0 1 70 450392690 450392759 8.670000e-25 124.0
46 TraesCS1A01G079900 chr2B 98.571 70 1 0 1 70 335625861 335625930 8.670000e-25 124.0
47 TraesCS1A01G079900 chr2A 95.000 80 2 2 1 80 701743981 701743904 8.670000e-25 124.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G079900 chr1A 62793172 62795483 2311 True 4270.000000 4270 100.000000 1 2312 1 chr1A.!!$R1 2311
1 TraesCS1A01G079900 chr1A 490759742 490760708 966 False 1096.000000 1096 87.602000 688 1633 1 chr1A.!!$F2 945
2 TraesCS1A01G079900 chr1A 487568502 487569049 547 False 734.000000 734 90.942000 774 1319 1 chr1A.!!$F1 545
3 TraesCS1A01G079900 chr1A 490417462 490419887 2425 False 600.000000 1245 85.403000 502 2312 3 chr1A.!!$F3 1810
4 TraesCS1A01G079900 chr1A 490777848 490778678 830 False 357.000000 416 89.733500 1630 2220 2 chr1A.!!$F4 590
5 TraesCS1A01G079900 chr1B 104480157 104483289 3132 True 1252.500000 2189 93.028500 408 2312 2 chr1B.!!$R3 1904
6 TraesCS1A01G079900 chr1B 608335179 608335832 653 True 719.000000 719 86.767000 793 1444 1 chr1B.!!$R2 651
7 TraesCS1A01G079900 chr1B 608042443 608042961 518 True 623.000000 623 88.425000 793 1313 1 chr1B.!!$R1 520
8 TraesCS1A01G079900 chr1B 610893040 610893729 689 False 610.000000 610 83.357000 772 1444 1 chr1B.!!$F2 672
9 TraesCS1A01G079900 chr1B 527287935 527290323 2388 False 554.000000 1127 87.351000 630 2312 3 chr1B.!!$F3 1682
10 TraesCS1A01G079900 chr1D 63681272 63682952 1680 True 771.933333 1620 92.942667 95 1792 3 chr1D.!!$R2 1697
11 TraesCS1A01G079900 chr1D 388603426 388604125 699 False 717.000000 717 85.634000 790 1477 1 chr1D.!!$F2 687
12 TraesCS1A01G079900 chr1D 388024387 388024934 547 False 689.000000 689 89.474000 774 1319 1 chr1D.!!$F1 545
13 TraesCS1A01G079900 chr1D 394490045 394490842 797 True 407.500000 606 89.580500 1326 2219 2 chr1D.!!$R3 893
14 TraesCS1A01G079900 chr6B 679982302 679983919 1617 True 795.500000 1179 85.777000 502 2145 2 chr6B.!!$R1 1643

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
991 2297 0.17915 CGCTCGAACCAAGGAGAGAG 60.179 60.0 12.46 9.05 32.65 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 4756 1.693062 ACTTGACCCAATGCAATGCAA 59.307 42.857 13.45 0.0 43.62 4.08 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 6.665992 AAACACAATACTACTCAGAGTCCA 57.334 37.500 6.27 0.00 0.00 4.02
26 27 6.665992 AACACAATACTACTCAGAGTCCAA 57.334 37.500 6.27 0.00 0.00 3.53
27 28 6.026947 ACACAATACTACTCAGAGTCCAAC 57.973 41.667 6.27 0.00 0.00 3.77
28 29 5.775701 ACACAATACTACTCAGAGTCCAACT 59.224 40.000 6.27 0.00 0.00 3.16
29 30 6.096036 CACAATACTACTCAGAGTCCAACTG 58.904 44.000 6.27 3.54 36.80 3.16
30 31 5.775701 ACAATACTACTCAGAGTCCAACTGT 59.224 40.000 6.27 4.17 36.81 3.55
31 32 6.946583 ACAATACTACTCAGAGTCCAACTGTA 59.053 38.462 6.27 3.18 36.81 2.74
32 33 7.450634 ACAATACTACTCAGAGTCCAACTGTAA 59.549 37.037 6.27 0.00 36.81 2.41
33 34 5.708877 ACTACTCAGAGTCCAACTGTAAC 57.291 43.478 6.27 0.00 36.81 2.50
34 35 4.523558 ACTACTCAGAGTCCAACTGTAACC 59.476 45.833 6.27 0.00 36.81 2.85
35 36 3.577919 ACTCAGAGTCCAACTGTAACCT 58.422 45.455 0.00 0.00 36.81 3.50
36 37 4.737578 ACTCAGAGTCCAACTGTAACCTA 58.262 43.478 0.00 0.00 36.81 3.08
37 38 5.334421 ACTCAGAGTCCAACTGTAACCTAT 58.666 41.667 0.00 0.00 36.81 2.57
38 39 5.419471 ACTCAGAGTCCAACTGTAACCTATC 59.581 44.000 0.00 0.00 36.81 2.08
39 40 5.580998 TCAGAGTCCAACTGTAACCTATCT 58.419 41.667 0.00 0.00 36.81 1.98
40 41 6.017192 TCAGAGTCCAACTGTAACCTATCTT 58.983 40.000 0.00 0.00 36.81 2.40
41 42 6.071334 TCAGAGTCCAACTGTAACCTATCTTG 60.071 42.308 0.00 0.00 36.81 3.02
42 43 5.780793 AGAGTCCAACTGTAACCTATCTTGT 59.219 40.000 0.00 0.00 0.00 3.16
43 44 6.952358 AGAGTCCAACTGTAACCTATCTTGTA 59.048 38.462 0.00 0.00 0.00 2.41
44 45 6.932947 AGTCCAACTGTAACCTATCTTGTAC 58.067 40.000 0.00 0.00 0.00 2.90
45 46 6.495872 AGTCCAACTGTAACCTATCTTGTACA 59.504 38.462 0.00 0.00 0.00 2.90
46 47 6.589139 GTCCAACTGTAACCTATCTTGTACAC 59.411 42.308 0.00 0.00 0.00 2.90
47 48 6.268158 TCCAACTGTAACCTATCTTGTACACA 59.732 38.462 0.00 0.00 0.00 3.72
48 49 6.932400 CCAACTGTAACCTATCTTGTACACAA 59.068 38.462 0.00 0.00 0.00 3.33
49 50 7.606456 CCAACTGTAACCTATCTTGTACACAAT 59.394 37.037 0.00 0.00 35.02 2.71
50 51 9.647797 CAACTGTAACCTATCTTGTACACAATA 57.352 33.333 0.00 0.00 35.02 1.90
54 55 9.524106 TGTAACCTATCTTGTACACAATATTCG 57.476 33.333 0.00 0.00 35.02 3.34
55 56 9.740239 GTAACCTATCTTGTACACAATATTCGA 57.260 33.333 0.00 0.00 35.02 3.71
56 57 8.644318 AACCTATCTTGTACACAATATTCGAC 57.356 34.615 0.00 0.00 35.02 4.20
57 58 7.778083 ACCTATCTTGTACACAATATTCGACA 58.222 34.615 0.00 0.00 35.02 4.35
58 59 7.705325 ACCTATCTTGTACACAATATTCGACAC 59.295 37.037 0.00 0.00 35.02 3.67
59 60 7.704899 CCTATCTTGTACACAATATTCGACACA 59.295 37.037 0.00 0.00 35.02 3.72
60 61 7.899178 ATCTTGTACACAATATTCGACACAA 57.101 32.000 0.00 0.00 35.02 3.33
61 62 7.112528 TCTTGTACACAATATTCGACACAAC 57.887 36.000 0.00 0.00 35.02 3.32
62 63 6.926826 TCTTGTACACAATATTCGACACAACT 59.073 34.615 0.00 0.00 35.02 3.16
63 64 6.699895 TGTACACAATATTCGACACAACTC 57.300 37.500 0.00 0.00 0.00 3.01
64 65 6.452242 TGTACACAATATTCGACACAACTCT 58.548 36.000 0.00 0.00 0.00 3.24
65 66 7.595604 TGTACACAATATTCGACACAACTCTA 58.404 34.615 0.00 0.00 0.00 2.43
66 67 8.083462 TGTACACAATATTCGACACAACTCTAA 58.917 33.333 0.00 0.00 0.00 2.10
67 68 7.347508 ACACAATATTCGACACAACTCTAAC 57.652 36.000 0.00 0.00 0.00 2.34
68 69 6.926826 ACACAATATTCGACACAACTCTAACA 59.073 34.615 0.00 0.00 0.00 2.41
69 70 7.116376 ACACAATATTCGACACAACTCTAACAG 59.884 37.037 0.00 0.00 0.00 3.16
70 71 6.090898 ACAATATTCGACACAACTCTAACAGC 59.909 38.462 0.00 0.00 0.00 4.40
71 72 3.446310 TTCGACACAACTCTAACAGCA 57.554 42.857 0.00 0.00 0.00 4.41
72 73 3.660501 TCGACACAACTCTAACAGCAT 57.339 42.857 0.00 0.00 0.00 3.79
73 74 4.776795 TCGACACAACTCTAACAGCATA 57.223 40.909 0.00 0.00 0.00 3.14
74 75 4.733850 TCGACACAACTCTAACAGCATAG 58.266 43.478 0.00 0.00 0.00 2.23
75 76 4.457949 TCGACACAACTCTAACAGCATAGA 59.542 41.667 0.00 0.00 0.00 1.98
76 77 5.125578 TCGACACAACTCTAACAGCATAGAT 59.874 40.000 0.00 0.00 31.75 1.98
77 78 5.230936 CGACACAACTCTAACAGCATAGATG 59.769 44.000 0.00 0.00 31.75 2.90
88 89 2.156542 CATAGATGCCATGCCGACG 58.843 57.895 0.00 0.00 0.00 5.12
89 90 1.669115 ATAGATGCCATGCCGACGC 60.669 57.895 0.00 0.00 0.00 5.19
90 91 3.807631 TAGATGCCATGCCGACGCC 62.808 63.158 0.00 0.00 0.00 5.68
149 150 1.468520 CCGTCGTTTGATGCATTCCTT 59.531 47.619 0.00 0.00 0.00 3.36
160 161 1.076332 GCATTCCTTTGTCTACGCGT 58.924 50.000 19.17 19.17 0.00 6.01
161 162 1.060698 GCATTCCTTTGTCTACGCGTC 59.939 52.381 18.63 1.04 0.00 5.19
165 166 1.342174 TCCTTTGTCTACGCGTCCTTT 59.658 47.619 18.63 0.00 0.00 3.11
176 178 0.385598 GCGTCCTTTCTTTGAACGCC 60.386 55.000 6.91 0.00 38.91 5.68
201 203 5.917541 ACTTTTCGTGTATGTTTGATCGT 57.082 34.783 0.00 0.00 0.00 3.73
206 208 3.849708 TCGTGTATGTTTGATCGTCGAAG 59.150 43.478 0.00 0.00 0.00 3.79
273 284 9.313118 GGAAAAGACAAGTTTGAATTTATGTGT 57.687 29.630 0.00 0.00 0.00 3.72
279 290 9.944663 GACAAGTTTGAATTTATGTGTGTCTTA 57.055 29.630 0.00 0.00 31.26 2.10
290 301 4.395959 TGTGTGTCTTAAGACCGAAACT 57.604 40.909 28.43 0.00 44.15 2.66
291 302 4.761975 TGTGTGTCTTAAGACCGAAACTT 58.238 39.130 28.43 0.00 44.15 2.66
294 305 3.497262 GTGTCTTAAGACCGAAACTTGGG 59.503 47.826 28.43 0.00 44.15 4.12
295 306 3.072211 GTCTTAAGACCGAAACTTGGGG 58.928 50.000 22.74 0.00 39.07 4.96
296 307 1.810755 CTTAAGACCGAAACTTGGGGC 59.189 52.381 0.00 0.00 33.67 5.80
303 314 4.338710 AAACTTGGGGCGCGGCTA 62.339 61.111 32.30 18.76 0.00 3.93
326 337 4.731853 TGGATCGTCCCCAGGGCA 62.732 66.667 0.00 0.00 35.03 5.36
357 368 2.874751 GCGCATAGGCCAAAACGT 59.125 55.556 5.01 0.00 36.38 3.99
364 375 1.000884 TAGGCCAAAACGTAATCGCG 58.999 50.000 5.01 0.00 41.18 5.87
367 378 1.637478 GCCAAAACGTAATCGCGGGA 61.637 55.000 6.13 4.03 41.18 5.14
398 410 1.200948 GGCAAACAAGTGGAGATGCTC 59.799 52.381 0.00 0.00 34.37 4.26
400 412 2.555757 GCAAACAAGTGGAGATGCTCTT 59.444 45.455 0.00 0.00 0.00 2.85
416 428 3.924686 TGCTCTTAGATCGAACGTTTTCC 59.075 43.478 0.46 0.00 0.00 3.13
437 449 1.485124 TCGCTAGGCTGATCTTTCCA 58.515 50.000 0.00 0.00 0.00 3.53
488 500 1.523758 ACAAATCTGACGTTCCCAGC 58.476 50.000 0.00 0.00 0.00 4.85
541 557 9.709600 GCCGATTTACTTTTCATTTTTCAAAAA 57.290 25.926 0.00 0.00 0.00 1.94
590 606 5.931441 CTAGTCAAGGAAAGTTTGTGGAG 57.069 43.478 0.00 0.00 0.00 3.86
605 621 2.903784 TGTGGAGCTACCTTTGCTTAGA 59.096 45.455 0.00 0.00 41.30 2.10
606 622 3.326588 TGTGGAGCTACCTTTGCTTAGAA 59.673 43.478 0.00 0.00 41.30 2.10
607 623 4.202419 TGTGGAGCTACCTTTGCTTAGAAA 60.202 41.667 0.00 0.00 41.30 2.52
608 624 4.760204 GTGGAGCTACCTTTGCTTAGAAAA 59.240 41.667 0.00 0.00 41.30 2.29
609 625 5.240844 GTGGAGCTACCTTTGCTTAGAAAAA 59.759 40.000 0.00 0.00 41.30 1.94
610 626 5.240844 TGGAGCTACCTTTGCTTAGAAAAAC 59.759 40.000 0.00 0.00 41.30 2.43
611 627 5.240844 GGAGCTACCTTTGCTTAGAAAAACA 59.759 40.000 0.00 0.00 41.30 2.83
612 628 6.238925 GGAGCTACCTTTGCTTAGAAAAACAA 60.239 38.462 0.00 0.00 41.30 2.83
613 629 7.290110 AGCTACCTTTGCTTAGAAAAACAAT 57.710 32.000 0.00 0.00 37.52 2.71
614 630 8.404107 AGCTACCTTTGCTTAGAAAAACAATA 57.596 30.769 0.00 0.00 37.52 1.90
615 631 9.025041 AGCTACCTTTGCTTAGAAAAACAATAT 57.975 29.630 0.00 0.00 37.52 1.28
616 632 9.639601 GCTACCTTTGCTTAGAAAAACAATATT 57.360 29.630 0.00 0.00 0.00 1.28
623 639 8.288689 TGCTTAGAAAAACAATATTCTACCCC 57.711 34.615 0.00 0.00 37.75 4.95
624 640 7.066525 TGCTTAGAAAAACAATATTCTACCCCG 59.933 37.037 0.00 0.00 37.75 5.73
625 641 5.830000 AGAAAAACAATATTCTACCCCGC 57.170 39.130 0.00 0.00 34.24 6.13
626 642 5.258051 AGAAAAACAATATTCTACCCCGCA 58.742 37.500 0.00 0.00 34.24 5.69
627 643 5.712917 AGAAAAACAATATTCTACCCCGCAA 59.287 36.000 0.00 0.00 34.24 4.85
628 644 5.986501 AAAACAATATTCTACCCCGCAAA 57.013 34.783 0.00 0.00 0.00 3.68
672 1717 1.884444 GACGTCACAGACTCCCCTC 59.116 63.158 11.55 0.00 0.00 4.30
673 1718 1.596895 GACGTCACAGACTCCCCTCC 61.597 65.000 11.55 0.00 0.00 4.30
686 1731 2.190578 CCTCCCGTGCCCATTCTC 59.809 66.667 0.00 0.00 0.00 2.87
694 1949 4.421365 GCCCATTCTCAGTTGGCA 57.579 55.556 0.00 0.00 41.76 4.92
708 1963 3.047877 GGCACCACTGGCGTACAC 61.048 66.667 0.00 0.00 32.44 2.90
709 1964 3.047877 GCACCACTGGCGTACACC 61.048 66.667 0.00 0.00 0.00 4.16
710 1965 2.423874 CACCACTGGCGTACACCA 59.576 61.111 1.96 1.96 38.29 4.17
839 2121 0.250467 CCCCGGATCGCAATCTCAAT 60.250 55.000 0.73 0.00 32.12 2.57
841 2123 1.541015 CCCGGATCGCAATCTCAATCA 60.541 52.381 0.73 0.00 32.12 2.57
894 2185 3.670629 CTCCTCCCACCTCTCGCCT 62.671 68.421 0.00 0.00 0.00 5.52
972 2278 4.593864 GACCTCCATCCGCTCGCC 62.594 72.222 0.00 0.00 0.00 5.54
991 2297 0.179150 CGCTCGAACCAAGGAGAGAG 60.179 60.000 12.46 9.05 32.65 3.20
1105 2415 2.982643 ATCACCAAGCCGGCCATCA 61.983 57.895 26.15 2.27 39.03 3.07
1376 2735 5.122396 CGGCTTGTTTAGTTCTCTATTTGCT 59.878 40.000 0.00 0.00 0.00 3.91
1435 2795 3.226346 CATGTGTTGCTGGAAATGGAG 57.774 47.619 0.00 0.00 0.00 3.86
1444 2804 2.005451 CTGGAAATGGAGCTTGTCTCG 58.995 52.381 0.00 0.00 42.82 4.04
1445 2805 1.623311 TGGAAATGGAGCTTGTCTCGA 59.377 47.619 0.00 0.00 42.82 4.04
1494 2856 7.054491 TCTGCTGCATCTCTGTTAATGTATA 57.946 36.000 1.31 0.00 0.00 1.47
1517 2879 2.839486 TGTTCTTTCTCCTGCGATGT 57.161 45.000 0.00 0.00 0.00 3.06
1547 2909 1.508088 CGCTTGGGAGTTGGATTGC 59.492 57.895 0.00 0.00 0.00 3.56
1569 2931 4.809673 CTTTGCCATTCTTTTACCAGGAC 58.190 43.478 0.00 0.00 0.00 3.85
1628 2992 1.024046 TGGCCGAATCACCAACATCG 61.024 55.000 0.00 0.00 31.46 3.84
1774 3177 2.144833 TTTGCCATGCCACTTGCTCG 62.145 55.000 0.00 0.00 42.00 5.03
1825 3228 4.060900 TCAGAAGTGTCACTTGCTCAATC 58.939 43.478 22.83 6.71 38.80 2.67
1835 3238 3.072944 ACTTGCTCAATCTCTGCTGTTC 58.927 45.455 0.00 0.00 0.00 3.18
2079 4685 4.141018 AGGAATGAAAACCAGTTAGGGTGT 60.141 41.667 0.00 0.00 41.32 4.16
2150 4756 8.796475 AGCAATGAAAAATGACAATAGTAGTGT 58.204 29.630 2.26 2.26 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.827701 TGGACTCTGAGTAGTATTGTGTTTAG 58.172 38.462 10.86 0.00 0.00 1.85
1 2 7.770366 TGGACTCTGAGTAGTATTGTGTTTA 57.230 36.000 10.86 0.00 0.00 2.01
2 3 6.665992 TGGACTCTGAGTAGTATTGTGTTT 57.334 37.500 10.86 0.00 0.00 2.83
3 4 6.267928 AGTTGGACTCTGAGTAGTATTGTGTT 59.732 38.462 10.86 0.00 0.00 3.32
4 5 5.775701 AGTTGGACTCTGAGTAGTATTGTGT 59.224 40.000 10.86 0.00 0.00 3.72
5 6 6.096036 CAGTTGGACTCTGAGTAGTATTGTG 58.904 44.000 10.86 0.00 35.20 3.33
6 7 5.775701 ACAGTTGGACTCTGAGTAGTATTGT 59.224 40.000 10.86 10.02 36.81 2.71
7 8 6.274157 ACAGTTGGACTCTGAGTAGTATTG 57.726 41.667 10.86 9.43 36.81 1.90
8 9 7.093858 GGTTACAGTTGGACTCTGAGTAGTATT 60.094 40.741 10.86 0.00 36.81 1.89
9 10 6.377712 GGTTACAGTTGGACTCTGAGTAGTAT 59.622 42.308 10.86 0.00 36.81 2.12
10 11 5.709164 GGTTACAGTTGGACTCTGAGTAGTA 59.291 44.000 10.86 4.80 36.81 1.82
11 12 4.523558 GGTTACAGTTGGACTCTGAGTAGT 59.476 45.833 10.86 5.68 36.81 2.73
12 13 4.767928 AGGTTACAGTTGGACTCTGAGTAG 59.232 45.833 10.86 0.00 36.81 2.57
13 14 4.737578 AGGTTACAGTTGGACTCTGAGTA 58.262 43.478 10.86 0.00 36.81 2.59
14 15 3.577919 AGGTTACAGTTGGACTCTGAGT 58.422 45.455 10.66 10.66 36.81 3.41
15 16 5.654650 AGATAGGTTACAGTTGGACTCTGAG 59.345 44.000 2.45 2.45 36.81 3.35
16 17 5.580998 AGATAGGTTACAGTTGGACTCTGA 58.419 41.667 0.00 0.00 36.81 3.27
17 18 5.923733 AGATAGGTTACAGTTGGACTCTG 57.076 43.478 0.00 0.00 38.68 3.35
18 19 5.780793 ACAAGATAGGTTACAGTTGGACTCT 59.219 40.000 0.00 0.00 0.00 3.24
19 20 6.038997 ACAAGATAGGTTACAGTTGGACTC 57.961 41.667 0.00 0.00 0.00 3.36
20 21 6.495872 TGTACAAGATAGGTTACAGTTGGACT 59.504 38.462 0.00 0.00 31.25 3.85
21 22 6.589139 GTGTACAAGATAGGTTACAGTTGGAC 59.411 42.308 0.00 0.00 30.70 4.02
22 23 6.268158 TGTGTACAAGATAGGTTACAGTTGGA 59.732 38.462 0.00 0.00 0.00 3.53
23 24 6.460781 TGTGTACAAGATAGGTTACAGTTGG 58.539 40.000 0.00 0.00 0.00 3.77
24 25 7.956420 TTGTGTACAAGATAGGTTACAGTTG 57.044 36.000 0.00 0.00 0.00 3.16
28 29 9.524106 CGAATATTGTGTACAAGATAGGTTACA 57.476 33.333 0.00 0.00 36.85 2.41
29 30 9.740239 TCGAATATTGTGTACAAGATAGGTTAC 57.260 33.333 0.00 0.00 36.85 2.50
30 31 9.740239 GTCGAATATTGTGTACAAGATAGGTTA 57.260 33.333 0.00 0.00 36.85 2.85
31 32 8.255206 TGTCGAATATTGTGTACAAGATAGGTT 58.745 33.333 0.00 0.00 36.85 3.50
32 33 7.705325 GTGTCGAATATTGTGTACAAGATAGGT 59.295 37.037 0.00 0.00 36.85 3.08
33 34 7.704899 TGTGTCGAATATTGTGTACAAGATAGG 59.295 37.037 0.00 2.00 36.85 2.57
34 35 8.628882 TGTGTCGAATATTGTGTACAAGATAG 57.371 34.615 0.00 4.09 36.85 2.08
35 36 8.865978 GTTGTGTCGAATATTGTGTACAAGATA 58.134 33.333 0.00 0.00 36.85 1.98
36 37 7.602644 AGTTGTGTCGAATATTGTGTACAAGAT 59.397 33.333 0.00 1.49 39.22 2.40
37 38 6.926826 AGTTGTGTCGAATATTGTGTACAAGA 59.073 34.615 0.00 0.00 39.47 3.02
38 39 7.116376 AGAGTTGTGTCGAATATTGTGTACAAG 59.884 37.037 0.00 0.00 39.47 3.16
39 40 6.926826 AGAGTTGTGTCGAATATTGTGTACAA 59.073 34.615 0.00 0.00 40.51 2.41
40 41 6.452242 AGAGTTGTGTCGAATATTGTGTACA 58.548 36.000 0.00 0.00 0.00 2.90
41 42 6.946229 AGAGTTGTGTCGAATATTGTGTAC 57.054 37.500 0.00 0.00 0.00 2.90
42 43 8.083462 TGTTAGAGTTGTGTCGAATATTGTGTA 58.917 33.333 0.00 0.00 0.00 2.90
43 44 6.926826 TGTTAGAGTTGTGTCGAATATTGTGT 59.073 34.615 0.00 0.00 0.00 3.72
44 45 7.346208 TGTTAGAGTTGTGTCGAATATTGTG 57.654 36.000 0.00 0.00 0.00 3.33
45 46 6.090898 GCTGTTAGAGTTGTGTCGAATATTGT 59.909 38.462 0.00 0.00 0.00 2.71
46 47 6.090763 TGCTGTTAGAGTTGTGTCGAATATTG 59.909 38.462 0.00 0.00 0.00 1.90
47 48 6.163476 TGCTGTTAGAGTTGTGTCGAATATT 58.837 36.000 0.00 0.00 0.00 1.28
48 49 5.720202 TGCTGTTAGAGTTGTGTCGAATAT 58.280 37.500 0.00 0.00 0.00 1.28
49 50 5.128992 TGCTGTTAGAGTTGTGTCGAATA 57.871 39.130 0.00 0.00 0.00 1.75
50 51 3.990092 TGCTGTTAGAGTTGTGTCGAAT 58.010 40.909 0.00 0.00 0.00 3.34
51 52 3.446310 TGCTGTTAGAGTTGTGTCGAA 57.554 42.857 0.00 0.00 0.00 3.71
52 53 3.660501 ATGCTGTTAGAGTTGTGTCGA 57.339 42.857 0.00 0.00 0.00 4.20
53 54 4.733850 TCTATGCTGTTAGAGTTGTGTCG 58.266 43.478 0.00 0.00 0.00 4.35
54 55 6.580963 CATCTATGCTGTTAGAGTTGTGTC 57.419 41.667 0.00 0.00 31.96 3.67
70 71 1.904852 GCGTCGGCATGGCATCTATG 61.905 60.000 20.37 7.77 39.62 2.23
71 72 1.669115 GCGTCGGCATGGCATCTAT 60.669 57.895 20.37 0.00 39.62 1.98
72 73 2.280119 GCGTCGGCATGGCATCTA 60.280 61.111 20.37 0.00 39.62 1.98
124 125 2.750888 GCATCAAACGACGGGCTCC 61.751 63.158 0.00 0.00 0.00 4.70
149 150 2.798283 CAAAGAAAGGACGCGTAGACAA 59.202 45.455 13.97 0.00 0.00 3.18
160 161 1.600485 GTTCGGCGTTCAAAGAAAGGA 59.400 47.619 6.85 0.00 0.00 3.36
161 162 1.602377 AGTTCGGCGTTCAAAGAAAGG 59.398 47.619 6.85 0.00 0.00 3.11
165 166 3.328237 GAAAAGTTCGGCGTTCAAAGA 57.672 42.857 6.85 0.00 0.00 2.52
193 195 1.144969 GCCACACTTCGACGATCAAA 58.855 50.000 0.00 0.00 0.00 2.69
201 203 1.446099 GCGATCTGCCACACTTCGA 60.446 57.895 0.00 0.00 37.76 3.71
243 254 6.385649 AATTCAAACTTGTCTTTTCCGCTA 57.614 33.333 0.00 0.00 0.00 4.26
247 258 9.313118 ACACATAAATTCAAACTTGTCTTTTCC 57.687 29.630 0.00 0.00 0.00 3.13
273 284 3.495453 CCCCAAGTTTCGGTCTTAAGACA 60.495 47.826 31.30 13.77 46.47 3.41
279 290 1.599797 CGCCCCAAGTTTCGGTCTT 60.600 57.895 0.00 0.00 0.00 3.01
280 291 2.032071 CGCCCCAAGTTTCGGTCT 59.968 61.111 0.00 0.00 0.00 3.85
296 307 3.214250 GATCCAGTCCCTAGCCGCG 62.214 68.421 0.00 0.00 0.00 6.46
340 351 0.448593 TTACGTTTTGGCCTATGCGC 59.551 50.000 3.32 0.00 38.85 6.09
342 353 2.853281 GCGATTACGTTTTGGCCTATGC 60.853 50.000 3.32 0.00 41.98 3.14
398 410 4.490479 GCGAAGGAAAACGTTCGATCTAAG 60.490 45.833 22.47 0.00 46.78 2.18
400 412 2.919229 GCGAAGGAAAACGTTCGATCTA 59.081 45.455 22.47 0.00 46.78 1.98
416 428 2.159043 TGGAAAGATCAGCCTAGCGAAG 60.159 50.000 0.00 0.00 0.00 3.79
488 500 5.010516 TGCAATTTTTATGGACCCGGATATG 59.989 40.000 0.73 0.00 0.00 1.78
541 557 6.954352 ACCTAGTTCTAGGGACAAAAGAAT 57.046 37.500 24.22 2.69 41.51 2.40
581 597 2.230660 AGCAAAGGTAGCTCCACAAAC 58.769 47.619 0.00 0.00 38.01 2.93
590 606 9.639601 AATATTGTTTTTCTAAGCAAAGGTAGC 57.360 29.630 0.00 0.00 37.87 3.58
605 621 5.986501 TTGCGGGGTAGAATATTGTTTTT 57.013 34.783 0.00 0.00 0.00 1.94
606 622 5.986501 TTTGCGGGGTAGAATATTGTTTT 57.013 34.783 0.00 0.00 0.00 2.43
607 623 5.712917 TCTTTTGCGGGGTAGAATATTGTTT 59.287 36.000 0.00 0.00 0.00 2.83
608 624 5.258051 TCTTTTGCGGGGTAGAATATTGTT 58.742 37.500 0.00 0.00 0.00 2.83
609 625 4.850680 TCTTTTGCGGGGTAGAATATTGT 58.149 39.130 0.00 0.00 0.00 2.71
610 626 5.828299 TTCTTTTGCGGGGTAGAATATTG 57.172 39.130 0.00 0.00 0.00 1.90
611 627 6.844097 TTTTCTTTTGCGGGGTAGAATATT 57.156 33.333 0.00 0.00 0.00 1.28
612 628 6.209788 TGTTTTTCTTTTGCGGGGTAGAATAT 59.790 34.615 0.00 0.00 0.00 1.28
613 629 5.535406 TGTTTTTCTTTTGCGGGGTAGAATA 59.465 36.000 0.00 0.00 0.00 1.75
614 630 4.342665 TGTTTTTCTTTTGCGGGGTAGAAT 59.657 37.500 0.00 0.00 0.00 2.40
615 631 3.700038 TGTTTTTCTTTTGCGGGGTAGAA 59.300 39.130 0.00 0.00 0.00 2.10
616 632 3.288964 TGTTTTTCTTTTGCGGGGTAGA 58.711 40.909 0.00 0.00 0.00 2.59
617 633 3.719173 TGTTTTTCTTTTGCGGGGTAG 57.281 42.857 0.00 0.00 0.00 3.18
618 634 4.674281 ATTGTTTTTCTTTTGCGGGGTA 57.326 36.364 0.00 0.00 0.00 3.69
619 635 3.552132 ATTGTTTTTCTTTTGCGGGGT 57.448 38.095 0.00 0.00 0.00 4.95
620 636 5.931724 AGAATATTGTTTTTCTTTTGCGGGG 59.068 36.000 0.00 0.00 0.00 5.73
621 637 6.128580 CCAGAATATTGTTTTTCTTTTGCGGG 60.129 38.462 0.00 0.00 29.85 6.13
622 638 6.423604 ACCAGAATATTGTTTTTCTTTTGCGG 59.576 34.615 0.00 0.00 29.85 5.69
623 639 7.406799 ACCAGAATATTGTTTTTCTTTTGCG 57.593 32.000 0.00 0.00 29.85 4.85
672 1717 1.002134 AACTGAGAATGGGCACGGG 60.002 57.895 0.00 0.00 0.00 5.28
673 1718 1.308069 CCAACTGAGAATGGGCACGG 61.308 60.000 1.90 0.00 32.87 4.94
680 1725 1.538512 CAGTGGTGCCAACTGAGAATG 59.461 52.381 12.34 0.00 33.65 2.67
681 1726 1.546323 CCAGTGGTGCCAACTGAGAAT 60.546 52.381 16.69 0.00 33.65 2.40
683 1728 1.451504 CCAGTGGTGCCAACTGAGA 59.548 57.895 16.69 0.00 33.65 3.27
686 1731 3.663176 CGCCAGTGGTGCCAACTG 61.663 66.667 10.38 11.33 0.00 3.16
708 1963 0.109597 GATGTTTTCGTGCTGGCTGG 60.110 55.000 0.00 0.00 0.00 4.85
709 1964 0.453282 CGATGTTTTCGTGCTGGCTG 60.453 55.000 0.00 0.00 43.01 4.85
710 1965 1.868997 CGATGTTTTCGTGCTGGCT 59.131 52.632 0.00 0.00 43.01 4.75
711 1966 4.440214 CGATGTTTTCGTGCTGGC 57.560 55.556 0.00 0.00 43.01 4.85
762 2022 3.023949 ATCGCTGGGTCAGAGGTGC 62.024 63.158 0.00 0.00 32.33 5.01
894 2185 3.270169 GTGGGGAGGGGATTTTTAAGGTA 59.730 47.826 0.00 0.00 0.00 3.08
972 2278 0.179150 CTCTCTCCTTGGTTCGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
1376 2735 3.504906 ACGATTCAGTTCGAACTACAGGA 59.495 43.478 29.28 19.40 41.62 3.86
1435 2795 1.859080 ACGTTGTTTCTCGAGACAAGC 59.141 47.619 16.36 4.17 36.52 4.01
1444 2804 5.659048 AAATCAGAGACACGTTGTTTCTC 57.341 39.130 5.23 5.23 39.46 2.87
1445 2805 5.354234 ACAAAATCAGAGACACGTTGTTTCT 59.646 36.000 5.69 5.69 41.78 2.52
1494 2856 3.194005 TCGCAGGAGAAAGAACAAACT 57.806 42.857 0.00 0.00 0.00 2.66
1517 2879 0.031857 CCCAAGCGCACACAATTTCA 59.968 50.000 11.47 0.00 0.00 2.69
1547 2909 4.280677 TGTCCTGGTAAAAGAATGGCAAAG 59.719 41.667 0.00 0.00 0.00 2.77
1569 2931 0.815734 AAGTACGATCCGTCAGGGTG 59.184 55.000 0.00 0.00 41.54 4.61
1628 2992 5.938322 TCAAATAGCAGAAACGGATCAAAC 58.062 37.500 0.00 0.00 0.00 2.93
1689 3055 7.380870 TCAATTACACACATTGTTGCAACATAC 59.619 33.333 31.48 6.17 39.91 2.39
2009 4604 8.811017 TGAAGTAAGAACTGATCTGATCTTTCT 58.189 33.333 23.60 21.01 38.79 2.52
2034 4637 8.887036 TCCTGCTATAATACAGTAAACACATG 57.113 34.615 0.00 0.00 31.76 3.21
2067 4670 2.403252 GGTCATCACACCCTAACTGG 57.597 55.000 0.00 0.00 0.00 4.00
2079 4685 3.026707 TCTAGGATTGACGGGTCATCA 57.973 47.619 1.83 0.00 39.64 3.07
2090 4696 7.353414 TCACTTCTGTAGGATTCTAGGATTG 57.647 40.000 0.00 0.00 0.00 2.67
2150 4756 1.693062 ACTTGACCCAATGCAATGCAA 59.307 42.857 13.45 0.00 43.62 4.08
2192 4799 4.694509 CCTTCATCTGAACTGTTCTTGAGG 59.305 45.833 20.18 17.97 0.00 3.86
2248 4883 5.241506 TCAACTTGGATAAACTTGCTCCTTG 59.758 40.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.