Multiple sequence alignment - TraesCS4A01G175500

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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 TraesCS4A01G175500 chr4A 100.000 3430 0 0 986 4415 446608843 446612272 0.000000e+00 6335.0
1 TraesCS4A01G175500 chr4A 100.000 803 0 0 1 803 446607858 446608660 0.000000e+00 1483.0
2 TraesCS4A01G175500 chr4A 96.000 250 6 4 154 403 450333071 450332826 1.910000e-108 403.0
3 TraesCS4A01G175500 chr1B 95.372 3133 100 16 990 4109 173131783 173128683 0.000000e+00 4940.0
4 TraesCS4A01G175500 chr1B 98.406 251 3 1 155 404 664059142 664059392 1.460000e-119 440.0
5 TraesCS4A01G175500 chr1B 97.189 249 4 3 156 404 304518614 304518369 6.830000e-113 418.0
6 TraesCS4A01G175500 chr1B 94.928 138 5 2 4279 4415 173126268 173126132 9.620000e-52 215.0
7 TraesCS4A01G175500 chr1B 92.553 94 3 3 4018 4109 597450204 597450113 9.960000e-27 132.0
8 TraesCS4A01G175500 chr1B 96.552 58 2 0 4134 4191 173127603 173127546 3.630000e-16 97.1
9 TraesCS4A01G175500 chr1B 96.552 58 2 0 4134 4191 173128487 173128430 3.630000e-16 97.1
10 TraesCS4A01G175500 chr4D 94.957 3113 137 10 991 4090 123146653 123143548 0.000000e+00 4861.0
11 TraesCS4A01G175500 chr4D 92.580 283 17 4 4134 4415 123143380 123143101 1.910000e-108 403.0
12 TraesCS4A01G175500 chr4D 95.946 74 3 0 4019 4092 505968141 505968214 2.160000e-23 121.0
13 TraesCS4A01G175500 chr4D 95.588 68 3 0 4021 4088 505921838 505921905 4.670000e-20 110.0
14 TraesCS4A01G175500 chr4B 94.609 3135 151 7 990 4112 187732817 187729689 0.000000e+00 4837.0
15 TraesCS4A01G175500 chr4B 96.838 253 6 2 154 404 249050049 249050301 5.280000e-114 422.0
16 TraesCS4A01G175500 chr4B 91.697 277 16 3 4139 4415 187729547 187729278 1.160000e-100 377.0
17 TraesCS4A01G175500 chr4B 90.583 223 14 3 4193 4415 187729178 187728963 5.590000e-74 289.0
18 TraesCS4A01G175500 chr1A 96.935 2545 61 8 1392 3922 121135464 121132923 0.000000e+00 4252.0
19 TraesCS4A01G175500 chr1A 96.560 407 14 0 990 1396 121136032 121135626 0.000000e+00 675.0
20 TraesCS4A01G175500 chr1A 88.384 198 16 4 3914 4111 121132521 121132331 9.550000e-57 231.0
21 TraesCS4A01G175500 chr1A 94.161 137 8 0 4279 4415 121131897 121131761 4.470000e-50 209.0
22 TraesCS4A01G175500 chr1A 89.726 146 12 3 656 800 439929213 439929356 2.710000e-42 183.0
23 TraesCS4A01G175500 chr1A 91.398 93 6 2 4018 4109 537973601 537973692 4.640000e-25 126.0
24 TraesCS4A01G175500 chr7D 93.393 1665 85 10 1615 3266 590451994 590450342 0.000000e+00 2442.0
25 TraesCS4A01G175500 chr7D 90.141 639 48 5 987 1613 590518600 590517965 0.000000e+00 817.0
26 TraesCS4A01G175500 chr7D 87.156 327 26 4 3261 3571 590447425 590447099 1.510000e-94 357.0
27 TraesCS4A01G175500 chr7D 89.262 149 11 5 656 803 517561176 517561320 9.750000e-42 182.0
28 TraesCS4A01G175500 chr7D 77.593 241 41 9 3858 4092 590446937 590446704 2.770000e-27 134.0
29 TraesCS4A01G175500 chr3B 98.367 245 2 2 160 404 820904401 820904159 3.160000e-116 429.0
30 TraesCS4A01G175500 chr3B 97.959 245 2 1 160 404 820904036 820903795 5.280000e-114 422.0
31 TraesCS4A01G175500 chr3B 97.951 244 2 1 161 404 820904217 820903977 1.900000e-113 420.0
32 TraesCS4A01G175500 chr3B 97.942 243 2 1 162 404 265849532 265849771 6.830000e-113 418.0
33 TraesCS4A01G175500 chr3B 85.455 110 8 4 426 528 29949708 29949600 1.680000e-19 108.0
34 TraesCS4A01G175500 chr2B 97.541 244 3 1 161 404 69371620 69371860 8.830000e-112 414.0
35 TraesCS4A01G175500 chr2B 86.957 92 9 2 456 545 714256873 714256963 2.810000e-17 100.0
36 TraesCS4A01G175500 chr2B 86.957 92 9 2 456 545 714311870 714311960 2.810000e-17 100.0
37 TraesCS4A01G175500 chr2A 94.862 253 12 1 550 802 1819443 1819694 1.150000e-105 394.0
38 TraesCS4A01G175500 chr2A 88.571 105 10 2 561 664 578037791 578037894 4.640000e-25 126.0
39 TraesCS4A01G175500 chr2A 87.619 105 11 2 561 664 577441918 577442021 2.160000e-23 121.0
40 TraesCS4A01G175500 chr2A 88.043 92 8 2 456 545 577443004 577443094 6.040000e-19 106.0
41 TraesCS4A01G175500 chr2A 88.043 92 8 2 456 545 578035841 578035931 6.040000e-19 106.0
42 TraesCS4A01G175500 chr7B 91.852 270 12 7 543 803 623819234 623818966 6.980000e-98 368.0
43 TraesCS4A01G175500 chr7B 90.957 188 7 7 598 784 707011215 707011037 1.230000e-60 244.0
44 TraesCS4A01G175500 chr7B 94.776 134 4 1 24 154 623819647 623819514 5.790000e-49 206.0
45 TraesCS4A01G175500 chr7B 93.284 134 6 1 24 154 707011942 707011809 1.250000e-45 195.0
46 TraesCS4A01G175500 chr7B 89.922 129 12 1 418 545 707011638 707011510 9.820000e-37 165.0
47 TraesCS4A01G175500 chr7B 92.063 63 3 2 540 601 707011373 707011312 2.190000e-13 87.9
48 TraesCS4A01G175500 chrUn 92.095 253 19 1 1562 1813 261868755 261869007 5.430000e-94 355.0
49 TraesCS4A01G175500 chrUn 90.769 130 10 2 659 787 19790449 19790321 5.870000e-39 172.0
50 TraesCS4A01G175500 chrUn 84.496 129 10 5 426 545 19793105 19792978 7.760000e-23 119.0
51 TraesCS4A01G175500 chr2D 92.095 253 19 1 1562 1813 453710421 453710169 5.430000e-94 355.0
52 TraesCS4A01G175500 chr5D 91.406 256 21 1 1559 1813 119459884 119460139 2.530000e-92 350.0
53 TraesCS4A01G175500 chr5D 91.034 145 8 5 659 803 185254091 185253952 1.620000e-44 191.0
54 TraesCS4A01G175500 chr5D 89.865 148 11 4 656 803 528401088 528401231 2.100000e-43 187.0
55 TraesCS4A01G175500 chr5D 94.048 84 3 2 4010 4092 305712686 305712768 4.640000e-25 126.0
56 TraesCS4A01G175500 chr5D 96.000 75 3 0 4018 4092 539481167 539481241 6.000000e-24 122.0
57 TraesCS4A01G175500 chr5D 90.110 91 7 2 456 545 185256701 185256612 2.790000e-22 117.0
58 TraesCS4A01G175500 chr6D 90.734 259 20 3 1559 1813 285487738 285487996 4.230000e-90 342.0
59 TraesCS4A01G175500 chr5B 89.189 148 11 5 656 803 704108449 704108591 3.510000e-41 180.0
60 TraesCS4A01G175500 chr3A 92.079 101 4 3 4014 4111 703902586 703902685 5.950000e-29 139.0
61 TraesCS4A01G175500 chr3A 92.473 93 5 2 4004 4095 718376636 718376727 9.960000e-27 132.0
62 TraesCS4A01G175500 chr3A 93.333 90 5 1 4004 4093 719333510 719333598 9.960000e-27 132.0
63 TraesCS4A01G175500 chr3A 90.816 98 7 2 3995 4092 719044454 719044359 3.580000e-26 130.0
64 TraesCS4A01G175500 chr3A 89.423 104 8 3 4008 4111 718372550 718372650 1.290000e-25 128.0
65 TraesCS4A01G175500 chr3A 87.500 112 8 4 4003 4112 655646780 655646673 1.670000e-24 124.0
66 TraesCS4A01G175500 chr6B 86.290 124 13 4 561 682 578003265 578003386 9.960000e-27 132.0
67 TraesCS4A01G175500 chr3D 92.473 93 6 1 4003 4095 589373609 589373518 9.960000e-27 132.0
68 TraesCS4A01G175500 chr3D 91.398 93 6 2 4004 4095 588345396 588345487 4.640000e-25 126.0
69 TraesCS4A01G175500 chr3D 90.526 95 8 1 4019 4113 497869618 497869525 1.670000e-24 124.0
70 TraesCS4A01G175500 chr3D 92.135 89 6 1 4004 4092 588335053 588335140 1.670000e-24 124.0
71 TraesCS4A01G175500 chr3D 92.135 89 6 1 4020 4108 589411004 589411091 1.670000e-24 124.0
72 TraesCS4A01G175500 chr3D 89.320 103 6 3 4015 4112 612302310 612302412 1.670000e-24 124.0
73 TraesCS4A01G175500 chr3D 91.398 93 3 4 4019 4111 570803527 570803440 6.000000e-24 122.0
74 TraesCS4A01G175500 chr7A 85.484 124 14 4 561 682 54671083 54670962 4.640000e-25 126.0
75 TraesCS4A01G175500 chr7A 89.130 92 7 2 456 545 54673033 54672943 1.300000e-20 111.0
76 TraesCS4A01G175500 chr1D 90.625 96 8 1 4018 4112 439868664 439868569 4.640000e-25 126.0
77 TraesCS4A01G175500 chr1D 91.304 92 6 2 4018 4109 315607882 315607971 1.670000e-24 124.0
78 TraesCS4A01G175500 chr1D 96.000 75 3 0 4018 4092 47880388 47880462 6.000000e-24 122.0
79 TraesCS4A01G175500 chr1D 96.000 75 3 0 4018 4092 432396620 432396546 6.000000e-24 122.0
80 TraesCS4A01G175500 chr1D 94.667 75 4 0 4018 4092 433679605 433679679 2.790000e-22 117.0
81 TraesCS4A01G175500 chr1D 89.247 93 8 2 4019 4111 381067956 381067866 1.000000e-21 115.0
82 TraesCS4A01G175500 chr1D 97.015 67 2 0 4018 4084 315609616 315609682 3.610000e-21 113.0


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 TraesCS4A01G175500 chr4A 446607858 446612272 4414 False 3909.000000 6335 100.000000 1 4415 2 chr4A.!!$F1 4414
1 TraesCS4A01G175500 chr1B 173126132 173131783 5651 True 1337.300000 4940 95.851000 990 4415 4 chr1B.!!$R3 3425
2 TraesCS4A01G175500 chr4D 123143101 123146653 3552 True 2632.000000 4861 93.768500 991 4415 2 chr4D.!!$R1 3424
3 TraesCS4A01G175500 chr4B 187728963 187732817 3854 True 1834.333333 4837 92.296333 990 4415 3 chr4B.!!$R1 3425
4 TraesCS4A01G175500 chr1A 121131761 121136032 4271 True 1341.750000 4252 94.010000 990 4415 4 chr1A.!!$R1 3425
5 TraesCS4A01G175500 chr7D 590446704 590451994 5290 True 977.666667 2442 86.047333 1615 4092 3 chr7D.!!$R2 2477
6 TraesCS4A01G175500 chr7D 590517965 590518600 635 True 817.000000 817 90.141000 987 1613 1 chr7D.!!$R1 626
7 TraesCS4A01G175500 chr3B 820903795 820904401 606 True 423.666667 429 98.092333 160 404 3 chr3B.!!$R2 244
8 TraesCS4A01G175500 chr7B 623818966 623819647 681 True 287.000000 368 93.314000 24 803 2 chr7B.!!$R1 779


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
475 663 0.040058 TCCATTGCAATCCAGCAGGT 59.960 50.000 9.53 0.0 46.54 4.00 F
481 669 0.543749 GCAATCCAGCAGGTAGAGGT 59.456 55.000 0.00 0.0 35.89 3.85 F
1212 1557 0.731514 GACGAATCAACGACGAGCCA 60.732 55.000 0.00 0.0 37.03 4.75 F
2629 3160 2.250031 AGAGGCTCTAGATGCAGATGG 58.750 52.381 17.09 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2377 3.505836 GCATCTAGCAAAACAAAGAGCC 58.494 45.455 0.00 0.0 44.79 4.70 R
2498 3029 2.089201 CTTGCATCACCATCTTCAGCA 58.911 47.619 0.00 0.0 0.00 4.41 R
2871 3404 0.169009 GTGTGCTCTTTCCGGCATTC 59.831 55.000 0.00 0.0 40.66 2.67 R
3884 7415 0.388659 TTTGGCGCAAGTTTCAGCAT 59.611 45.000 10.83 0.0 41.68 3.79 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
33 34 7.386573 TCTGTAATTTGTTAACGCTTCTGATCA 59.613 33.333 0.26 0.00 0.00 2.92
41 42 4.679373 AACGCTTCTGATCAGGATATGT 57.321 40.909 22.42 9.65 0.00 2.29
147 151 9.503427 GTGATGCAAATTACCTTGTATTAGTTC 57.497 33.333 0.00 0.00 32.56 3.01
148 152 8.682710 TGATGCAAATTACCTTGTATTAGTTCC 58.317 33.333 0.00 0.00 32.56 3.62
149 153 8.823220 ATGCAAATTACCTTGTATTAGTTCCT 57.177 30.769 0.00 0.00 28.50 3.36
150 154 9.914834 ATGCAAATTACCTTGTATTAGTTCCTA 57.085 29.630 0.00 0.00 28.50 2.94
151 155 9.914834 TGCAAATTACCTTGTATTAGTTCCTAT 57.085 29.630 0.00 0.00 0.00 2.57
204 208 3.434319 CGCTTGCGCAGGGTTCAT 61.434 61.111 21.88 0.00 35.30 2.57
327 514 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
328 515 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
329 516 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
330 517 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
331 518 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
332 519 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
333 520 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
334 521 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
366 553 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
367 554 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
368 555 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
369 556 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
370 557 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
376 563 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
377 564 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
378 565 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
379 566 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
382 569 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
394 581 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
395 582 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
396 583 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
397 584 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
398 585 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
399 586 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
400 587 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
401 588 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
402 589 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
475 663 0.040058 TCCATTGCAATCCAGCAGGT 59.960 50.000 9.53 0.00 46.54 4.00
478 666 2.646930 CATTGCAATCCAGCAGGTAGA 58.353 47.619 9.53 0.00 46.54 2.59
479 667 2.408271 TTGCAATCCAGCAGGTAGAG 57.592 50.000 0.00 0.00 46.54 2.43
481 669 0.543749 GCAATCCAGCAGGTAGAGGT 59.456 55.000 0.00 0.00 35.89 3.85
484 672 3.181450 GCAATCCAGCAGGTAGAGGTTAT 60.181 47.826 0.00 0.00 35.89 1.89
498 686 6.536941 GGTAGAGGTTATGAAGAGAAAAGCAG 59.463 42.308 0.00 0.00 0.00 4.24
499 687 5.495640 AGAGGTTATGAAGAGAAAAGCAGG 58.504 41.667 0.00 0.00 0.00 4.85
510 699 0.980231 AAAAGCAGGGCCAAACACCA 60.980 50.000 6.18 0.00 0.00 4.17
556 890 3.190118 GGTTGCTTCAAATCTGAGTCCAG 59.810 47.826 0.00 0.00 41.74 3.86
643 984 8.084073 TGGTTGCTTTTTATCTTCAGAATTGAG 58.916 33.333 0.00 0.00 34.15 3.02
644 985 7.062722 GGTTGCTTTTTATCTTCAGAATTGAGC 59.937 37.037 0.00 0.00 34.15 4.26
711 1052 6.761714 CAGTCGTAGAGGCCACTTTAAATTAT 59.238 38.462 8.39 0.00 36.95 1.28
715 1056 7.436080 TCGTAGAGGCCACTTTAAATTATTACG 59.564 37.037 8.39 8.18 0.00 3.18
768 1109 8.556213 AGCAAAACCTTGTTCTATACGATTAA 57.444 30.769 0.00 0.00 34.79 1.40
787 1129 9.634163 ACGATTAATTTTTGTACTGGGATTTTC 57.366 29.630 0.00 0.00 0.00 2.29
1212 1557 0.731514 GACGAATCAACGACGAGCCA 60.732 55.000 0.00 0.00 37.03 4.75
1519 2037 4.040095 TGTTTGCATCATTGACCATCCAAA 59.960 37.500 0.00 0.00 0.00 3.28
1650 2169 7.542130 GTCAAAATGTTTCTAATAGCCCAAGTG 59.458 37.037 0.00 0.00 0.00 3.16
1834 2355 6.691388 GGTATCATCTTATTTTGTGTTTCGGC 59.309 38.462 0.00 0.00 0.00 5.54
2062 2583 7.833786 AGATTCTGCAGAATTTATGCTTTTCA 58.166 30.769 35.91 10.17 44.14 2.69
2498 3029 3.412386 CTCCAAGACTGGGTTTTCGAAT 58.588 45.455 0.00 0.00 43.71 3.34
2597 3128 6.496743 TGAAGAATTTTGGGAGGATGAAGAT 58.503 36.000 0.00 0.00 0.00 2.40
2629 3160 2.250031 AGAGGCTCTAGATGCAGATGG 58.750 52.381 17.09 0.00 0.00 3.51
2871 3404 2.028925 GGCCTTGTTGGTTTGCCG 59.971 61.111 0.00 0.00 38.35 5.69
2916 3449 3.758172 GCTCTCTCTAGGGCTCGG 58.242 66.667 0.00 0.00 46.53 4.63
3157 3730 1.842007 CCACCATGGGAGCAGCTAT 59.158 57.895 18.09 0.00 32.67 2.97
3350 6845 0.179936 CCTGATCTGAGAGTTGGCCC 59.820 60.000 0.00 0.00 0.00 5.80
3363 6858 1.209747 GTTGGCCCGAGAGACCTTATT 59.790 52.381 0.00 0.00 0.00 1.40
3444 6955 2.093128 GCCCCTCGTTGGAGAAGAATTA 60.093 50.000 0.00 0.00 43.27 1.40
3546 7058 4.063998 TGCGTTGCAGAATAGATCATCT 57.936 40.909 0.00 0.00 33.32 2.90
3548 7060 4.984785 TGCGTTGCAGAATAGATCATCTAC 59.015 41.667 0.00 0.00 30.53 2.59
3676 7195 6.183359 GCGCTATTTCTAGTGTCCGAAATATC 60.183 42.308 0.00 0.00 39.79 1.63
3755 7275 0.603065 GTGAGTTTTGCATGGGACCC 59.397 55.000 2.45 2.45 0.00 4.46
3781 7301 3.947834 ACCAAGAACTTGACTGAAACCTG 59.052 43.478 14.99 0.00 42.93 4.00
3820 7347 4.058124 TGTTTCTCAAAGTCATGGTCTCG 58.942 43.478 0.00 0.00 0.00 4.04
3872 7399 6.407187 CCAGATGCCATGGATTTTGATTGTTA 60.407 38.462 18.40 0.00 40.51 2.41
3873 7400 7.214381 CAGATGCCATGGATTTTGATTGTTAT 58.786 34.615 18.40 0.00 0.00 1.89
3884 7415 8.519526 GGATTTTGATTGTTATTGACTGGTGTA 58.480 33.333 0.00 0.00 0.00 2.90
3957 7895 4.591321 ATTTCAAGAATAGAGGCCACCA 57.409 40.909 5.01 0.00 0.00 4.17
3982 7920 3.558418 TGTCAACTTTTTCCGAGTACAGC 59.442 43.478 0.00 0.00 0.00 4.40
4032 7970 2.102588 TCAAATAAGCCCGTCTAGCTCC 59.897 50.000 0.00 0.00 40.49 4.70
4088 8075 4.309950 GTTCGAGCCCCACGGTGT 62.310 66.667 7.45 0.00 0.00 4.16
4103 8090 1.231221 GGTGTGCGTGTCCATTGTTA 58.769 50.000 0.00 0.00 0.00 2.41
4130 9002 2.296945 AAAGCCAGCCACCCTTGTCA 62.297 55.000 0.00 0.00 0.00 3.58
4132 9004 1.207488 AGCCAGCCACCCTTGTCATA 61.207 55.000 0.00 0.00 0.00 2.15
4167 9221 1.824852 CACCAGGCCATTACTTTTCCC 59.175 52.381 5.01 0.00 0.00 3.97
4234 10167 7.798710 ATATACTGTATATGCCACCAGTTCT 57.201 36.000 17.28 0.00 38.91 3.01
4241 10174 1.656587 TGCCACCAGTTCTATGGAGT 58.343 50.000 0.00 0.00 43.57 3.85
4242 10175 2.827755 TGCCACCAGTTCTATGGAGTA 58.172 47.619 0.00 0.00 43.57 2.59
4249 10182 4.158025 ACCAGTTCTATGGAGTACAGTTCG 59.842 45.833 0.00 0.00 43.57 3.95
4256 10189 7.634671 TCTATGGAGTACAGTTCGTGATTTA 57.365 36.000 0.00 0.00 0.00 1.40
4257 10190 8.058667 TCTATGGAGTACAGTTCGTGATTTAA 57.941 34.615 0.00 0.00 0.00 1.52
4350 10596 6.826231 TGAAGTCTGAACAAAATGAACCTACA 59.174 34.615 0.00 0.00 0.00 2.74
4352 10598 6.357367 AGTCTGAACAAAATGAACCTACACT 58.643 36.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.145323 AGCGTTAACAAATTACAGAAGCAAAT 58.855 30.769 6.39 0.00 0.00 2.32
1 2 6.500041 AGCGTTAACAAATTACAGAAGCAAA 58.500 32.000 6.39 0.00 0.00 3.68
3 4 5.682943 AGCGTTAACAAATTACAGAAGCA 57.317 34.783 6.39 0.00 0.00 3.91
5 6 7.572759 TCAGAAGCGTTAACAAATTACAGAAG 58.427 34.615 6.39 0.00 0.00 2.85
6 7 7.485418 TCAGAAGCGTTAACAAATTACAGAA 57.515 32.000 6.39 0.00 0.00 3.02
7 8 7.386573 TGATCAGAAGCGTTAACAAATTACAGA 59.613 33.333 6.39 0.00 0.00 3.41
8 9 7.518161 TGATCAGAAGCGTTAACAAATTACAG 58.482 34.615 6.39 0.00 0.00 2.74
9 10 7.360861 CCTGATCAGAAGCGTTAACAAATTACA 60.361 37.037 24.62 0.00 0.00 2.41
10 11 6.961554 CCTGATCAGAAGCGTTAACAAATTAC 59.038 38.462 24.62 0.00 0.00 1.89
11 12 6.876789 TCCTGATCAGAAGCGTTAACAAATTA 59.123 34.615 24.62 0.00 0.00 1.40
12 13 5.705441 TCCTGATCAGAAGCGTTAACAAATT 59.295 36.000 24.62 0.00 0.00 1.82
13 14 5.245531 TCCTGATCAGAAGCGTTAACAAAT 58.754 37.500 24.62 0.00 0.00 2.32
14 15 4.637276 TCCTGATCAGAAGCGTTAACAAA 58.363 39.130 24.62 0.00 0.00 2.83
15 16 4.265904 TCCTGATCAGAAGCGTTAACAA 57.734 40.909 24.62 0.00 0.00 2.83
16 17 3.953712 TCCTGATCAGAAGCGTTAACA 57.046 42.857 24.62 0.00 0.00 2.41
17 18 5.986135 ACATATCCTGATCAGAAGCGTTAAC 59.014 40.000 24.62 0.00 0.00 2.01
18 19 6.040955 AGACATATCCTGATCAGAAGCGTTAA 59.959 38.462 24.62 1.11 0.00 2.01
19 20 5.536538 AGACATATCCTGATCAGAAGCGTTA 59.463 40.000 24.62 7.06 0.00 3.18
20 21 4.343526 AGACATATCCTGATCAGAAGCGTT 59.656 41.667 24.62 3.98 0.00 4.84
21 22 3.894427 AGACATATCCTGATCAGAAGCGT 59.106 43.478 24.62 13.40 0.00 5.07
22 23 4.517952 AGACATATCCTGATCAGAAGCG 57.482 45.455 24.62 7.33 0.00 4.68
41 42 7.174253 GTGGGACTGTGACATTTACAAAATAGA 59.826 37.037 0.00 0.00 0.00 1.98
58 59 6.891361 TGAATTCATGATAATTGTGGGACTGT 59.109 34.615 3.38 0.00 0.00 3.55
158 162 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
204 208 1.057851 AAAGTGGTCGGACCCTTCCA 61.058 55.000 23.81 2.25 43.00 3.53
326 513 4.464947 CTTTTATAGAAGGGGAGCCTTGG 58.535 47.826 0.00 0.00 0.00 3.61
327 514 4.464947 CCTTTTATAGAAGGGGAGCCTTG 58.535 47.826 13.22 0.00 42.04 3.61
328 515 4.797912 CCTTTTATAGAAGGGGAGCCTT 57.202 45.455 13.22 0.00 42.04 4.35
336 523 3.954258 CCAGGTTGCCCTTTTATAGAAGG 59.046 47.826 13.94 13.94 44.74 3.46
337 524 4.399303 CACCAGGTTGCCCTTTTATAGAAG 59.601 45.833 0.00 0.00 39.89 2.85
338 525 4.340617 CACCAGGTTGCCCTTTTATAGAA 58.659 43.478 0.00 0.00 39.89 2.10
339 526 3.876156 GCACCAGGTTGCCCTTTTATAGA 60.876 47.826 0.00 0.00 39.89 1.98
340 527 2.427095 GCACCAGGTTGCCCTTTTATAG 59.573 50.000 0.00 0.00 39.89 1.31
341 528 2.225142 TGCACCAGGTTGCCCTTTTATA 60.225 45.455 10.46 0.00 42.25 0.98
342 529 1.266178 GCACCAGGTTGCCCTTTTAT 58.734 50.000 0.00 0.00 39.89 1.40
343 530 0.105964 TGCACCAGGTTGCCCTTTTA 60.106 50.000 10.46 0.00 42.25 1.52
344 531 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
345 532 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
346 533 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
347 534 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
348 535 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
349 536 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
350 537 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
351 538 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
352 539 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
377 564 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
378 565 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
379 566 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
380 567 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
381 568 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
382 569 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
383 570 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
384 571 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
385 572 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
386 573 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
395 582 2.288886 GCATTACAGATAGGGTCGGACC 60.289 54.545 19.06 19.06 37.60 4.46
396 583 2.364324 TGCATTACAGATAGGGTCGGAC 59.636 50.000 0.00 0.00 0.00 4.79
397 584 2.673258 TGCATTACAGATAGGGTCGGA 58.327 47.619 0.00 0.00 0.00 4.55
398 585 3.469008 TTGCATTACAGATAGGGTCGG 57.531 47.619 0.00 0.00 0.00 4.79
399 586 7.672983 AAATATTGCATTACAGATAGGGTCG 57.327 36.000 0.00 0.00 0.00 4.79
442 630 9.415544 GGATTGCAATGGAGAATTAACATAATC 57.584 33.333 18.59 0.00 0.00 1.75
444 632 8.303780 TGGATTGCAATGGAGAATTAACATAA 57.696 30.769 18.59 0.00 0.00 1.90
451 639 3.101437 TGCTGGATTGCAATGGAGAATT 58.899 40.909 18.59 0.00 40.29 2.17
455 643 0.744874 CCTGCTGGATTGCAATGGAG 59.255 55.000 18.59 12.84 42.83 3.86
462 650 0.543749 ACCTCTACCTGCTGGATTGC 59.456 55.000 17.64 0.00 37.04 3.56
475 663 6.352222 CCCTGCTTTTCTCTTCATAACCTCTA 60.352 42.308 0.00 0.00 0.00 2.43
478 666 4.593956 CCCTGCTTTTCTCTTCATAACCT 58.406 43.478 0.00 0.00 0.00 3.50
479 667 3.129462 GCCCTGCTTTTCTCTTCATAACC 59.871 47.826 0.00 0.00 0.00 2.85
481 669 3.245229 TGGCCCTGCTTTTCTCTTCATAA 60.245 43.478 0.00 0.00 0.00 1.90
484 672 0.478072 TGGCCCTGCTTTTCTCTTCA 59.522 50.000 0.00 0.00 0.00 3.02
498 686 5.669164 TTAATCTTAATGGTGTTTGGCCC 57.331 39.130 0.00 0.00 0.00 5.80
499 687 5.523552 GCATTAATCTTAATGGTGTTTGGCC 59.476 40.000 19.19 0.00 46.27 5.36
534 724 3.149196 TGGACTCAGATTTGAAGCAACC 58.851 45.455 0.00 0.00 31.69 3.77
545 735 1.899814 TGCGGTTAACTGGACTCAGAT 59.100 47.619 16.13 0.00 43.49 2.90
547 737 2.069273 CTTGCGGTTAACTGGACTCAG 58.931 52.381 16.13 4.31 46.10 3.35
548 738 1.414919 ACTTGCGGTTAACTGGACTCA 59.585 47.619 16.13 2.68 0.00 3.41
556 890 7.578852 AGTAGAAAAACATACTTGCGGTTAAC 58.421 34.615 0.00 0.00 0.00 2.01
601 942 9.586435 AAAAGCAACCAAGATATAACTTAATGC 57.414 29.630 13.85 13.85 34.85 3.56
737 1078 7.744715 CGTATAGAACAAGGTTTTGCTTAAGTG 59.255 37.037 4.02 0.00 37.85 3.16
985 1327 3.265791 GCAACATCTTCACTACTCAGGG 58.734 50.000 0.00 0.00 0.00 4.45
986 1328 2.926200 CGCAACATCTTCACTACTCAGG 59.074 50.000 0.00 0.00 0.00 3.86
987 1329 2.926200 CCGCAACATCTTCACTACTCAG 59.074 50.000 0.00 0.00 0.00 3.35
988 1330 2.930887 GCCGCAACATCTTCACTACTCA 60.931 50.000 0.00 0.00 0.00 3.41
1176 1521 1.149148 GTCGGAACAAGCTTGAGGAC 58.851 55.000 32.50 24.56 0.00 3.85
1212 1557 2.802719 ACAACGGGTATTCAATGCCTT 58.197 42.857 4.31 0.00 35.15 4.35
1519 2037 4.814234 CCGTTGCACCATAGTAACATACAT 59.186 41.667 0.00 0.00 34.33 2.29
1834 2355 7.964624 AGCCCATGACATCTATATATCTCATG 58.035 38.462 8.50 8.50 36.37 3.07
1856 2377 3.505836 GCATCTAGCAAAACAAAGAGCC 58.494 45.455 0.00 0.00 44.79 4.70
2498 3029 2.089201 CTTGCATCACCATCTTCAGCA 58.911 47.619 0.00 0.00 0.00 4.41
2597 3128 0.681564 GAGCCTCTTCCTCCGTCTCA 60.682 60.000 0.00 0.00 0.00 3.27
2629 3160 2.472029 TGTCATCTTCTTCCCTCTCCC 58.528 52.381 0.00 0.00 0.00 4.30
2871 3404 0.169009 GTGTGCTCTTTCCGGCATTC 59.831 55.000 0.00 0.00 40.66 2.67
2916 3449 0.387878 CATAGTCAGCGATCTCCGGC 60.388 60.000 0.00 0.00 39.04 6.13
3350 6845 3.648009 GAGGCATCAATAAGGTCTCTCG 58.352 50.000 0.00 0.00 0.00 4.04
3363 6858 2.649245 CTTGCGGATCCGAGGCATCA 62.649 60.000 37.64 21.09 42.83 3.07
3527 7039 6.212235 ACAGTAGATGATCTATTCTGCAACG 58.788 40.000 15.87 0.00 30.52 4.10
3577 7095 6.170846 AGCATACATACTGGTAACCCTTAC 57.829 41.667 0.00 0.00 35.39 2.34
3585 7103 5.950544 AGACCAAAGCATACATACTGGTA 57.049 39.130 0.00 0.00 37.30 3.25
3652 7170 7.266939 GATATTTCGGACACTAGAAATAGCG 57.733 40.000 13.62 0.00 46.16 4.26
3705 7225 7.385752 ACACTGTCCTAAATGCAAATCAAATTG 59.614 33.333 0.00 0.00 0.00 2.32
3755 7275 5.506317 GGTTTCAGTCAAGTTCTTGGTGATG 60.506 44.000 11.82 6.74 0.00 3.07
3781 7301 3.891056 AACAAAGCAAAGTACGCCTAC 57.109 42.857 0.00 0.00 0.00 3.18
3820 7347 1.664965 GACGTCAGTGCACCTCCAC 60.665 63.158 14.63 4.11 35.98 4.02
3865 7392 6.316140 TCAGCATACACCAGTCAATAACAATC 59.684 38.462 0.00 0.00 0.00 2.67
3872 7399 4.655963 AGTTTCAGCATACACCAGTCAAT 58.344 39.130 0.00 0.00 0.00 2.57
3873 7400 4.085357 AGTTTCAGCATACACCAGTCAA 57.915 40.909 0.00 0.00 0.00 3.18
3884 7415 0.388659 TTTGGCGCAAGTTTCAGCAT 59.611 45.000 10.83 0.00 41.68 3.79
3957 7895 5.607477 TGTACTCGGAAAAAGTTGACAGAT 58.393 37.500 0.00 0.00 0.00 2.90
4010 7948 3.244249 GGAGCTAGACGGGCTTATTTGAT 60.244 47.826 0.00 0.00 40.40 2.57
4032 7970 2.740714 GCCTTGCGCTCTACCAACG 61.741 63.158 9.73 0.00 0.00 4.10
4113 8107 1.207488 TATGACAAGGGTGGCTGGCT 61.207 55.000 2.00 0.00 31.93 4.75
4114 8108 1.032114 GTATGACAAGGGTGGCTGGC 61.032 60.000 0.00 0.00 31.93 4.85
4116 8110 1.003580 ACTGTATGACAAGGGTGGCTG 59.996 52.381 0.00 0.00 31.93 4.85
4117 8111 1.362224 ACTGTATGACAAGGGTGGCT 58.638 50.000 0.00 0.00 31.93 4.75
4118 8112 2.200373 AACTGTATGACAAGGGTGGC 57.800 50.000 0.00 0.00 0.00 5.01
4167 9221 2.509052 TGGACAGTTGAGAGTTGACG 57.491 50.000 0.00 0.00 0.00 4.35
4225 10158 5.407407 AACTGTACTCCATAGAACTGGTG 57.593 43.478 0.00 0.00 37.57 4.17
4234 10167 9.491675 TTTTTAAATCACGAACTGTACTCCATA 57.508 29.630 0.00 0.00 0.00 2.74
4322 10568 8.103948 AGGTTCATTTTGTTCAGACTTCATAG 57.896 34.615 0.00 0.00 0.00 2.23
4326 10572 7.012421 AGTGTAGGTTCATTTTGTTCAGACTTC 59.988 37.037 0.00 0.00 0.00 3.01
4350 10596 3.003689 CAGAAATGACAACGCTTCCAAGT 59.996 43.478 0.00 0.00 0.00 3.16
4352 10598 3.210227 TCAGAAATGACAACGCTTCCAA 58.790 40.909 0.00 0.00 0.00 3.53



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

AutoCloner maintained by Alex Coulton.