Multiple sequence alignment - TraesCS7A01G079600

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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 TraesCS7A01G079600 chr7A 100.000 2761 0 0 1 2761 45594751 45591991 0.000000e+00 5099.0
1 TraesCS7A01G079600 chr7A 98.617 2458 34 0 304 2761 45574758 45572301 0.000000e+00 4351.0
2 TraesCS7A01G079600 chr7A 96.957 2530 67 7 233 2761 45603530 45601010 0.000000e+00 4237.0
3 TraesCS7A01G079600 chr7A 87.415 1176 108 24 447 1611 43458471 43457325 0.000000e+00 1315.0
4 TraesCS7A01G079600 chr7A 87.208 899 86 17 717 1611 43439522 43438649 0.000000e+00 996.0
5 TraesCS7A01G079600 chr7A 86.275 867 95 12 1553 2402 45071387 45070528 0.000000e+00 920.0
6 TraesCS7A01G079600 chr7A 85.405 740 83 13 1681 2403 43251496 43250765 0.000000e+00 745.0
7 TraesCS7A01G079600 chr7A 85.339 723 84 11 1687 2403 43417298 43416592 0.000000e+00 728.0
8 TraesCS7A01G079600 chr7A 86.478 673 69 10 1553 2209 45024533 45023867 0.000000e+00 719.0
9 TraesCS7A01G079600 chr7A 85.236 657 68 18 895 1533 45067710 45067065 0.000000e+00 649.0
10 TraesCS7A01G079600 chr7A 85.463 626 80 7 1772 2397 45167270 45166656 2.320000e-180 641.0
11 TraesCS7A01G079600 chr7A 86.096 561 61 6 1220 1775 45185987 45185439 3.060000e-164 588.0
12 TraesCS7A01G079600 chr7A 93.668 379 24 0 323 701 43439979 43439601 3.990000e-158 568.0
13 TraesCS7A01G079600 chr7A 86.753 385 34 10 1500 1883 44942440 44942072 1.980000e-111 412.0
14 TraesCS7A01G079600 chr7A 90.400 250 24 0 889 1138 44884948 44884699 2.050000e-86 329.0
15 TraesCS7A01G079600 chr7A 84.774 243 24 4 792 1024 43260083 43259844 5.950000e-57 231.0
16 TraesCS7A01G079600 chr7A 93.701 127 8 0 323 449 43459851 43459725 1.010000e-44 191.0
17 TraesCS7A01G079600 chr7D 86.131 1644 142 27 790 2403 43384816 43383229 0.000000e+00 1694.0
18 TraesCS7A01G079600 chr7D 85.366 738 77 13 1681 2403 43424958 43424237 0.000000e+00 736.0
19 TraesCS7A01G079600 chr7D 88.556 568 48 9 1046 1611 43430106 43429554 0.000000e+00 673.0
20 TraesCS7A01G079600 chr7D 94.801 327 13 2 317 643 43430681 43430359 8.820000e-140 507.0
21 TraesCS7A01G079600 chr7D 94.595 259 9 2 771 1024 43430357 43430099 1.990000e-106 396.0
22 TraesCS7A01G079600 chr7D 89.024 246 18 4 399 643 43385080 43384843 2.080000e-76 296.0
23 TraesCS7A01G079600 chr7D 93.496 123 7 1 642 764 447766701 447766822 6.070000e-42 182.0
24 TraesCS7A01G079600 chr4A 87.419 771 73 9 1199 1961 651637819 651637065 0.000000e+00 865.0
25 TraesCS7A01G079600 chr4A 85.319 831 87 18 802 1619 651986141 651985333 0.000000e+00 826.0
26 TraesCS7A01G079600 chr4A 86.192 449 34 12 771 1207 651638675 651638243 6.970000e-126 460.0
27 TraesCS7A01G079600 chr4A 92.258 310 23 1 1 309 628156011 628155702 3.260000e-119 438.0
28 TraesCS7A01G079600 chr4A 91.262 309 24 3 1 308 357665496 357665802 4.250000e-113 418.0
29 TraesCS7A01G079600 chr4A 88.923 325 28 8 1706 2026 651837229 651836909 7.170000e-106 394.0
30 TraesCS7A01G079600 chr4A 88.980 245 19 3 399 643 651638913 651638677 2.080000e-76 296.0
31 TraesCS7A01G079600 chr4A 90.370 135 12 1 637 771 618085028 618085161 2.830000e-40 176.0
32 TraesCS7A01G079600 chr5A 95.205 292 13 1 1 291 178557734 178557443 6.970000e-126 460.0
33 TraesCS7A01G079600 chr5A 93.793 290 17 1 1 289 30854112 30853823 4.220000e-118 435.0
34 TraesCS7A01G079600 chr5A 93.000 300 14 5 1 293 388626861 388626562 5.460000e-117 431.0
35 TraesCS7A01G079600 chr5A 88.194 144 15 2 634 776 131187486 131187628 1.310000e-38 171.0
36 TraesCS7A01G079600 chr5A 98.113 53 1 0 2351 2403 257247220 257247272 2.930000e-15 93.5
37 TraesCS7A01G079600 chr1B 93.537 294 18 1 1 293 163076746 163076453 1.170000e-118 436.0
38 TraesCS7A01G079600 chr1B 92.691 301 19 2 1 300 191310837 191310539 5.460000e-117 431.0
39 TraesCS7A01G079600 chr1B 98.113 53 1 0 2351 2403 312328157 312328209 2.930000e-15 93.5
40 TraesCS7A01G079600 chr6A 93.515 293 18 1 1 292 436152703 436152995 4.220000e-118 435.0
41 TraesCS7A01G079600 chr6A 96.296 54 2 0 2350 2403 418855525 418855578 3.790000e-14 89.8
42 TraesCS7A01G079600 chr3B 93.793 290 15 2 1 289 167309657 167309944 1.520000e-117 433.0
43 TraesCS7A01G079600 chr6B 90.000 160 12 4 2405 2562 626486606 626486449 1.300000e-48 204.0
44 TraesCS7A01G079600 chr3A 90.260 154 14 1 2410 2563 35417699 35417851 1.680000e-47 200.0
45 TraesCS7A01G079600 chr3A 90.370 135 12 1 643 777 511600001 511600134 2.830000e-40 176.0
46 TraesCS7A01G079600 chr4B 90.370 135 12 1 637 771 656114139 656114272 2.830000e-40 176.0
47 TraesCS7A01G079600 chr4B 92.000 50 3 1 2351 2400 242292491 242292539 4.930000e-08 69.4
48 TraesCS7A01G079600 chr4B 90.385 52 5 0 2351 2402 590680364 590680313 4.930000e-08 69.4
49 TraesCS7A01G079600 chr4B 93.617 47 2 1 2350 2396 667353260 667353305 4.930000e-08 69.4
50 TraesCS7A01G079600 chr4B 90.385 52 4 1 2351 2402 18429574 18429524 1.770000e-07 67.6
51 TraesCS7A01G079600 chr7B 89.286 140 13 2 641 779 678632356 678632494 1.020000e-39 174.0
52 TraesCS7A01G079600 chr7B 96.226 53 2 0 2349 2401 663650968 663651020 1.360000e-13 87.9
53 TraesCS7A01G079600 chr7B 96.226 53 2 0 2349 2401 663704332 663704384 1.360000e-13 87.9
54 TraesCS7A01G079600 chr1D 86.076 158 15 6 628 783 406733779 406733931 2.200000e-36 163.0
55 TraesCS7A01G079600 chr1D 96.296 54 2 0 2350 2403 203264868 203264921 3.790000e-14 89.8
56 TraesCS7A01G079600 chr1D 96.296 54 2 0 2351 2404 487907246 487907299 3.790000e-14 89.8
57 TraesCS7A01G079600 chr1D 92.453 53 4 0 2351 2403 244830595 244830647 2.950000e-10 76.8
58 TraesCS7A01G079600 chr1D 90.741 54 5 0 2350 2403 96910167 96910114 3.810000e-09 73.1
59 TraesCS7A01G079600 chrUn 96.296 54 2 0 2351 2404 129562235 129562288 3.790000e-14 89.8
60 TraesCS7A01G079600 chr3D 94.737 57 3 0 2348 2404 497817240 497817184 3.790000e-14 89.8
61 TraesCS7A01G079600 chr1A 94.340 53 3 0 2351 2403 580135438 580135490 6.340000e-12 82.4
62 TraesCS7A01G079600 chr1A 92.727 55 4 0 2350 2404 463191496 463191550 2.280000e-11 80.5
63 TraesCS7A01G079600 chr1A 92.727 55 2 2 2350 2403 285955398 285955345 8.200000e-11 78.7
64 TraesCS7A01G079600 chr6D 92.593 54 4 0 2350 2403 151511230 151511177 8.200000e-11 78.7
65 TraesCS7A01G079600 chr6D 92.453 53 4 0 2351 2403 156395833 156395885 2.950000e-10 76.8
66 TraesCS7A01G079600 chr6D 90.566 53 5 0 2351 2403 218059291 218059239 1.370000e-08 71.3
67 TraesCS7A01G079600 chr4D 92.453 53 4 0 2351 2403 391582586 391582638 2.950000e-10 76.8
68 TraesCS7A01G079600 chr4D 95.455 44 2 0 2360 2403 45853316 45853273 1.370000e-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 TraesCS7A01G079600 chr7A 45591991 45594751 2760 True 5099.000000 5099 100.000000 1 2761 1 chr7A.!!$R10 2760
1 TraesCS7A01G079600 chr7A 45572301 45574758 2457 True 4351.000000 4351 98.617000 304 2761 1 chr7A.!!$R9 2457
2 TraesCS7A01G079600 chr7A 45601010 45603530 2520 True 4237.000000 4237 96.957000 233 2761 1 chr7A.!!$R11 2528
3 TraesCS7A01G079600 chr7A 45067065 45071387 4322 True 784.500000 920 85.755500 895 2402 2 chr7A.!!$R14 1507
4 TraesCS7A01G079600 chr7A 43438649 43439979 1330 True 782.000000 996 90.438000 323 1611 2 chr7A.!!$R12 1288
5 TraesCS7A01G079600 chr7A 43457325 43459851 2526 True 753.000000 1315 90.558000 323 1611 2 chr7A.!!$R13 1288
6 TraesCS7A01G079600 chr7A 43250765 43251496 731 True 745.000000 745 85.405000 1681 2403 1 chr7A.!!$R1 722
7 TraesCS7A01G079600 chr7A 43416592 43417298 706 True 728.000000 728 85.339000 1687 2403 1 chr7A.!!$R3 716
8 TraesCS7A01G079600 chr7A 45023867 45024533 666 True 719.000000 719 86.478000 1553 2209 1 chr7A.!!$R6 656
9 TraesCS7A01G079600 chr7A 45166656 45167270 614 True 641.000000 641 85.463000 1772 2397 1 chr7A.!!$R7 625
10 TraesCS7A01G079600 chr7A 45185439 45185987 548 True 588.000000 588 86.096000 1220 1775 1 chr7A.!!$R8 555
11 TraesCS7A01G079600 chr7D 43383229 43385080 1851 True 995.000000 1694 87.577500 399 2403 2 chr7D.!!$R2 2004
12 TraesCS7A01G079600 chr7D 43424237 43424958 721 True 736.000000 736 85.366000 1681 2403 1 chr7D.!!$R1 722
13 TraesCS7A01G079600 chr7D 43429554 43430681 1127 True 525.333333 673 92.650667 317 1611 3 chr7D.!!$R3 1294
14 TraesCS7A01G079600 chr4A 651985333 651986141 808 True 826.000000 826 85.319000 802 1619 1 chr4A.!!$R3 817
15 TraesCS7A01G079600 chr4A 651637065 651638913 1848 True 540.333333 865 87.530333 399 1961 3 chr4A.!!$R4 1562

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
185 186 0.249868 CGAAGCAGGTCAGGTTGTGA 60.250 55.0 0.00 0.0 0.0 3.58 F
1323 4594 0.118346 ACTGTGACCCCCATGGACTA 59.882 55.0 15.22 0.0 38.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 4676 1.525077 GGAAACACACTCGCCCACA 60.525 57.895 0.0 0.0 0.00 4.17 R
2293 5639 1.195900 GACACCTTGCGATTTTGCGTA 59.804 47.619 0.0 0.0 37.81 4.42 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
24 25 4.450082 AACGGTTTTCAAAACTGCTCTT 57.550 36.364 19.93 6.12 0.00 2.85
25 26 5.570234 AACGGTTTTCAAAACTGCTCTTA 57.430 34.783 19.93 0.00 0.00 2.10
26 27 5.570234 ACGGTTTTCAAAACTGCTCTTAA 57.430 34.783 19.93 0.00 0.00 1.85
27 28 5.956642 ACGGTTTTCAAAACTGCTCTTAAA 58.043 33.333 19.93 0.00 0.00 1.52
29 30 5.231357 CGGTTTTCAAAACTGCTCTTAAACC 59.769 40.000 12.74 0.00 39.70 3.27
30 31 5.231357 GGTTTTCAAAACTGCTCTTAAACCG 59.769 40.000 12.74 0.00 35.47 4.44
31 32 3.619233 TCAAAACTGCTCTTAAACCGC 57.381 42.857 0.00 0.00 0.00 5.68
32 33 3.211045 TCAAAACTGCTCTTAAACCGCT 58.789 40.909 0.00 0.00 0.00 5.52
34 35 4.817464 TCAAAACTGCTCTTAAACCGCTTA 59.183 37.500 0.00 0.00 0.00 3.09
35 36 5.472137 TCAAAACTGCTCTTAAACCGCTTAT 59.528 36.000 0.00 0.00 0.00 1.73
36 37 6.651643 TCAAAACTGCTCTTAAACCGCTTATA 59.348 34.615 0.00 0.00 0.00 0.98
38 39 7.625828 AAACTGCTCTTAAACCGCTTATATT 57.374 32.000 0.00 0.00 0.00 1.28
40 41 7.625828 ACTGCTCTTAAACCGCTTATATTTT 57.374 32.000 0.00 0.00 0.00 1.82
41 42 7.472543 ACTGCTCTTAAACCGCTTATATTTTG 58.527 34.615 0.00 0.00 0.00 2.44
42 43 6.262601 TGCTCTTAAACCGCTTATATTTTGC 58.737 36.000 0.00 0.00 0.00 3.68
43 44 5.685954 GCTCTTAAACCGCTTATATTTTGCC 59.314 40.000 0.00 0.00 0.00 4.52
44 45 6.679392 GCTCTTAAACCGCTTATATTTTGCCA 60.679 38.462 0.00 0.00 0.00 4.92
47 48 8.088981 TCTTAAACCGCTTATATTTTGCCAAAA 58.911 29.630 4.87 4.87 34.41 2.44
73 74 9.520515 AAATTAACTTGGTCTTGATACTGATGT 57.479 29.630 0.00 0.00 0.00 3.06
74 75 9.520515 AATTAACTTGGTCTTGATACTGATGTT 57.479 29.630 0.00 0.00 0.00 2.71
76 77 6.114187 ACTTGGTCTTGATACTGATGTTCA 57.886 37.500 0.00 0.00 0.00 3.18
77 78 6.715280 ACTTGGTCTTGATACTGATGTTCAT 58.285 36.000 0.00 0.00 0.00 2.57
78 79 7.851228 ACTTGGTCTTGATACTGATGTTCATA 58.149 34.615 0.00 0.00 0.00 2.15
79 80 7.984050 ACTTGGTCTTGATACTGATGTTCATAG 59.016 37.037 0.00 0.00 0.00 2.23
80 81 6.283694 TGGTCTTGATACTGATGTTCATAGC 58.716 40.000 0.00 0.00 0.00 2.97
83 84 7.497249 GGTCTTGATACTGATGTTCATAGCTTT 59.503 37.037 0.00 0.00 0.00 3.51
84 85 8.547069 GTCTTGATACTGATGTTCATAGCTTTC 58.453 37.037 0.00 0.00 0.00 2.62
85 86 7.712639 TCTTGATACTGATGTTCATAGCTTTCC 59.287 37.037 0.00 0.00 0.00 3.13
86 87 6.888105 TGATACTGATGTTCATAGCTTTCCA 58.112 36.000 0.00 0.00 0.00 3.53
88 89 5.886960 ACTGATGTTCATAGCTTTCCAAC 57.113 39.130 0.00 0.00 0.00 3.77
89 90 4.393062 ACTGATGTTCATAGCTTTCCAACG 59.607 41.667 0.00 0.00 0.00 4.10
90 91 3.689161 TGATGTTCATAGCTTTCCAACGG 59.311 43.478 0.00 0.00 0.00 4.44
91 92 3.134574 TGTTCATAGCTTTCCAACGGT 57.865 42.857 0.00 0.00 0.00 4.83
93 94 4.839121 TGTTCATAGCTTTCCAACGGTAT 58.161 39.130 0.00 0.00 0.00 2.73
97 98 5.466819 TCATAGCTTTCCAACGGTATATCG 58.533 41.667 3.25 3.25 0.00 2.92
98 99 2.480845 AGCTTTCCAACGGTATATCGC 58.519 47.619 5.03 0.00 0.00 4.58
100 101 2.610374 GCTTTCCAACGGTATATCGCAA 59.390 45.455 5.03 0.00 0.00 4.85
101 102 3.303132 GCTTTCCAACGGTATATCGCAAG 60.303 47.826 5.03 1.93 0.00 4.01
102 103 1.860676 TCCAACGGTATATCGCAAGC 58.139 50.000 5.03 0.00 37.18 4.01
103 104 0.865769 CCAACGGTATATCGCAAGCC 59.134 55.000 5.03 0.00 37.18 4.35
104 105 0.865769 CAACGGTATATCGCAAGCCC 59.134 55.000 5.03 0.00 37.18 5.19
105 106 0.250166 AACGGTATATCGCAAGCCCC 60.250 55.000 5.03 0.00 37.18 5.80
106 107 1.736645 CGGTATATCGCAAGCCCCG 60.737 63.158 0.00 0.00 37.18 5.73
108 109 0.250166 GGTATATCGCAAGCCCCGTT 60.250 55.000 0.00 0.00 37.18 4.44
110 111 1.263217 GTATATCGCAAGCCCCGTTTG 59.737 52.381 0.00 0.00 37.18 2.93
111 112 1.101049 ATATCGCAAGCCCCGTTTGG 61.101 55.000 0.00 0.00 37.18 3.28
121 122 4.671406 CCGTTTGGGCAATGTTGG 57.329 55.556 0.00 0.00 0.00 3.77
128 129 3.365535 GGCAATGTTGGCGGAAGT 58.634 55.556 3.47 0.00 43.97 3.01
132 133 1.269517 GCAATGTTGGCGGAAGTTCAA 60.270 47.619 5.01 0.00 0.00 2.69
133 134 2.393764 CAATGTTGGCGGAAGTTCAAC 58.606 47.619 5.01 1.88 42.87 3.18
134 135 0.958822 ATGTTGGCGGAAGTTCAACC 59.041 50.000 5.01 5.86 42.35 3.77
136 137 1.141254 TGTTGGCGGAAGTTCAACCTA 59.859 47.619 12.98 4.67 42.35 3.08
137 138 1.804748 GTTGGCGGAAGTTCAACCTAG 59.195 52.381 12.98 0.00 39.56 3.02
140 141 2.074576 GGCGGAAGTTCAACCTAGTTC 58.925 52.381 5.01 0.00 0.00 3.01
141 142 2.549349 GGCGGAAGTTCAACCTAGTTCA 60.549 50.000 5.01 0.00 0.00 3.18
144 145 4.124238 CGGAAGTTCAACCTAGTTCACAA 58.876 43.478 5.01 0.00 0.00 3.33
145 146 4.211374 CGGAAGTTCAACCTAGTTCACAAG 59.789 45.833 5.01 0.00 0.00 3.16
146 147 4.515567 GGAAGTTCAACCTAGTTCACAAGG 59.484 45.833 5.01 0.00 38.93 3.61
147 148 5.365619 GAAGTTCAACCTAGTTCACAAGGA 58.634 41.667 0.00 0.00 36.66 3.36
148 149 5.367945 AGTTCAACCTAGTTCACAAGGAA 57.632 39.130 0.00 0.00 36.66 3.36
149 150 5.368989 AGTTCAACCTAGTTCACAAGGAAG 58.631 41.667 0.00 0.00 35.82 3.46
150 151 5.104485 AGTTCAACCTAGTTCACAAGGAAGT 60.104 40.000 0.00 0.00 41.93 3.01
152 153 5.365619 TCAACCTAGTTCACAAGGAAGTTC 58.634 41.667 0.00 0.00 39.80 3.01
154 155 5.367945 ACCTAGTTCACAAGGAAGTTCAA 57.632 39.130 5.01 0.00 39.80 2.69
155 156 5.123936 ACCTAGTTCACAAGGAAGTTCAAC 58.876 41.667 5.01 0.00 39.80 3.18
156 157 4.211374 CCTAGTTCACAAGGAAGTTCAACG 59.789 45.833 5.01 0.00 39.80 4.10
160 161 4.395959 TCACAAGGAAGTTCAACGTACT 57.604 40.909 5.01 0.00 0.00 2.73
162 163 5.284079 TCACAAGGAAGTTCAACGTACTAC 58.716 41.667 5.01 0.00 0.00 2.73
163 164 5.068198 TCACAAGGAAGTTCAACGTACTACT 59.932 40.000 5.01 0.00 0.00 2.57
164 165 6.262944 TCACAAGGAAGTTCAACGTACTACTA 59.737 38.462 5.01 0.00 0.00 1.82
166 167 5.307926 AGGAAGTTCAACGTACTACTAGC 57.692 43.478 5.01 0.00 0.00 3.42
167 168 4.094212 GGAAGTTCAACGTACTACTAGCG 58.906 47.826 5.01 0.00 0.00 4.26
168 169 4.142816 GGAAGTTCAACGTACTACTAGCGA 60.143 45.833 5.01 0.00 0.00 4.93
170 171 4.967437 AGTTCAACGTACTACTAGCGAAG 58.033 43.478 0.00 0.00 0.00 3.79
183 184 4.779475 CGAAGCAGGTCAGGTTGT 57.221 55.556 0.00 0.00 0.00 3.32
185 186 0.249868 CGAAGCAGGTCAGGTTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
187 188 2.079925 GAAGCAGGTCAGGTTGTGATC 58.920 52.381 0.00 0.00 37.56 2.92
188 189 1.059098 AGCAGGTCAGGTTGTGATCA 58.941 50.000 0.00 0.00 39.00 2.92
189 190 1.002888 AGCAGGTCAGGTTGTGATCAG 59.997 52.381 0.00 0.00 39.00 2.90
190 191 1.002430 GCAGGTCAGGTTGTGATCAGA 59.998 52.381 0.00 0.00 39.00 3.27
191 192 2.550855 GCAGGTCAGGTTGTGATCAGAA 60.551 50.000 0.23 0.23 39.00 3.02
192 193 3.871463 GCAGGTCAGGTTGTGATCAGAAT 60.871 47.826 8.72 0.00 39.00 2.40
193 194 4.623886 GCAGGTCAGGTTGTGATCAGAATA 60.624 45.833 8.72 0.00 39.00 1.75
194 195 5.678583 CAGGTCAGGTTGTGATCAGAATAT 58.321 41.667 8.72 0.00 39.00 1.28
195 196 6.118170 CAGGTCAGGTTGTGATCAGAATATT 58.882 40.000 8.72 0.00 39.00 1.28
196 197 7.275183 CAGGTCAGGTTGTGATCAGAATATTA 58.725 38.462 8.72 0.00 39.00 0.98
197 198 7.935755 CAGGTCAGGTTGTGATCAGAATATTAT 59.064 37.037 8.72 0.00 39.00 1.28
199 200 8.778358 GGTCAGGTTGTGATCAGAATATTATTC 58.222 37.037 8.72 8.14 36.15 1.75
200 201 9.553064 GTCAGGTTGTGATCAGAATATTATTCT 57.447 33.333 8.72 12.26 37.56 2.40
201 202 9.770097 TCAGGTTGTGATCAGAATATTATTCTC 57.230 33.333 14.67 6.58 0.00 2.87
202 203 9.551734 CAGGTTGTGATCAGAATATTATTCTCA 57.448 33.333 14.67 4.33 0.00 3.27
206 207 9.730705 TTGTGATCAGAATATTATTCTCATCCC 57.269 33.333 20.89 13.81 26.74 3.85
207 208 8.037166 TGTGATCAGAATATTATTCTCATCCCG 58.963 37.037 20.89 9.25 26.74 5.14
208 209 8.037758 GTGATCAGAATATTATTCTCATCCCGT 58.962 37.037 20.89 0.00 26.74 5.28
209 210 8.037166 TGATCAGAATATTATTCTCATCCCGTG 58.963 37.037 20.89 8.82 26.74 4.94
212 213 8.253810 TCAGAATATTATTCTCATCCCGTGATC 58.746 37.037 14.67 0.00 35.97 2.92
215 216 7.724490 ATATTATTCTCATCCCGTGATCAGA 57.276 36.000 0.00 0.00 35.97 3.27
217 218 4.970860 ATTCTCATCCCGTGATCAGAAT 57.029 40.909 1.27 1.27 41.57 2.40
219 220 5.459536 TTCTCATCCCGTGATCAGAATAG 57.540 43.478 0.00 0.00 33.71 1.73
220 221 4.474394 TCTCATCCCGTGATCAGAATAGT 58.526 43.478 0.00 0.00 35.97 2.12
221 222 4.279420 TCTCATCCCGTGATCAGAATAGTG 59.721 45.833 0.00 0.00 35.97 2.74
222 223 3.960755 TCATCCCGTGATCAGAATAGTGT 59.039 43.478 0.00 0.00 0.00 3.55
223 224 4.405680 TCATCCCGTGATCAGAATAGTGTT 59.594 41.667 0.00 0.00 0.00 3.32
225 226 4.503910 TCCCGTGATCAGAATAGTGTTTG 58.496 43.478 0.00 0.00 0.00 2.93
226 227 4.020573 TCCCGTGATCAGAATAGTGTTTGT 60.021 41.667 0.00 0.00 0.00 2.83
227 228 4.093408 CCCGTGATCAGAATAGTGTTTGTG 59.907 45.833 0.00 0.00 0.00 3.33
228 229 4.690748 CCGTGATCAGAATAGTGTTTGTGT 59.309 41.667 0.00 0.00 0.00 3.72
229 230 5.867174 CCGTGATCAGAATAGTGTTTGTGTA 59.133 40.000 0.00 0.00 0.00 2.90
231 232 7.394099 CGTGATCAGAATAGTGTTTGTGTATG 58.606 38.462 0.00 0.00 0.00 2.39
232 233 7.063426 CGTGATCAGAATAGTGTTTGTGTATGT 59.937 37.037 0.00 0.00 0.00 2.29
233 234 9.366216 GTGATCAGAATAGTGTTTGTGTATGTA 57.634 33.333 0.00 0.00 0.00 2.29
392 398 0.961019 TTGCATCCTGAACAGTTGGC 59.039 50.000 0.00 2.37 0.00 4.52
1287 4558 0.823356 AAGGCAGTGACGGCAAATGT 60.823 50.000 10.32 0.00 0.00 2.71
1323 4594 0.118346 ACTGTGACCCCCATGGACTA 59.882 55.000 15.22 0.00 38.00 2.59
1517 4790 1.965643 TGCTGCATGCTTCTTTTTCCT 59.034 42.857 20.33 0.00 43.37 3.36
2293 5639 7.547370 GTCACTAGATTCAGTTGCTTGTAATCT 59.453 37.037 0.00 0.00 39.54 2.40
2503 5850 0.614812 ATGGGCCATGCAGGAAAAAC 59.385 50.000 20.49 0.00 41.22 2.43
2542 5889 1.304381 TGGCCTGCCCAGTCATTTC 60.304 57.895 3.32 0.00 39.18 2.17
2592 5939 5.482908 GTTCAAGTCCTAGACATGACACAT 58.517 41.667 0.00 0.00 39.45 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.234752 AGAGCAGTTTTGAAAACCGTTTTT 58.765 33.333 16.45 0.00 37.65 1.94
2 3 4.450082 AGAGCAGTTTTGAAAACCGTTT 57.550 36.364 16.45 1.37 0.00 3.60
4 5 5.570234 TTAAGAGCAGTTTTGAAAACCGT 57.430 34.783 16.45 2.33 0.00 4.83
5 6 5.231357 GGTTTAAGAGCAGTTTTGAAAACCG 59.769 40.000 16.45 8.33 36.39 4.44
6 7 5.231357 CGGTTTAAGAGCAGTTTTGAAAACC 59.769 40.000 16.45 3.34 40.62 3.27
8 9 4.801516 GCGGTTTAAGAGCAGTTTTGAAAA 59.198 37.500 0.00 0.00 0.00 2.29
9 10 4.097286 AGCGGTTTAAGAGCAGTTTTGAAA 59.903 37.500 0.00 0.00 0.00 2.69
11 12 3.211045 AGCGGTTTAAGAGCAGTTTTGA 58.789 40.909 0.00 0.00 0.00 2.69
12 13 3.626028 AGCGGTTTAAGAGCAGTTTTG 57.374 42.857 0.00 0.00 0.00 2.44
13 14 5.959618 ATAAGCGGTTTAAGAGCAGTTTT 57.040 34.783 4.64 0.00 0.00 2.43
15 16 7.625828 AAATATAAGCGGTTTAAGAGCAGTT 57.374 32.000 4.64 0.00 0.00 3.16
17 18 6.414987 GCAAAATATAAGCGGTTTAAGAGCAG 59.585 38.462 4.64 0.00 0.00 4.24
20 21 6.791303 TGGCAAAATATAAGCGGTTTAAGAG 58.209 36.000 4.64 0.00 0.00 2.85
21 22 6.761099 TGGCAAAATATAAGCGGTTTAAGA 57.239 33.333 4.64 0.00 0.00 2.10
47 48 9.520515 ACATCAGTATCAAGACCAAGTTAATTT 57.479 29.630 0.00 0.00 0.00 1.82
49 50 9.167311 GAACATCAGTATCAAGACCAAGTTAAT 57.833 33.333 0.00 0.00 0.00 1.40
51 52 7.676004 TGAACATCAGTATCAAGACCAAGTTA 58.324 34.615 0.00 0.00 0.00 2.24
52 53 6.533730 TGAACATCAGTATCAAGACCAAGTT 58.466 36.000 0.00 0.00 0.00 2.66
53 54 6.114187 TGAACATCAGTATCAAGACCAAGT 57.886 37.500 0.00 0.00 0.00 3.16
54 55 7.042187 GCTATGAACATCAGTATCAAGACCAAG 60.042 40.741 0.00 0.00 0.00 3.61
57 58 6.520272 AGCTATGAACATCAGTATCAAGACC 58.480 40.000 0.00 0.00 0.00 3.85
58 59 8.430801 AAAGCTATGAACATCAGTATCAAGAC 57.569 34.615 0.00 0.00 0.00 3.01
60 61 7.496920 TGGAAAGCTATGAACATCAGTATCAAG 59.503 37.037 0.00 0.00 0.00 3.02
62 63 6.888105 TGGAAAGCTATGAACATCAGTATCA 58.112 36.000 0.00 0.00 0.00 2.15
63 64 7.517417 CGTTGGAAAGCTATGAACATCAGTATC 60.517 40.741 0.00 0.00 0.00 2.24
66 67 4.393062 CGTTGGAAAGCTATGAACATCAGT 59.607 41.667 0.00 0.00 0.00 3.41
67 68 4.201851 CCGTTGGAAAGCTATGAACATCAG 60.202 45.833 0.00 0.00 0.00 2.90
68 69 3.689161 CCGTTGGAAAGCTATGAACATCA 59.311 43.478 0.00 0.00 0.00 3.07
69 70 3.689649 ACCGTTGGAAAGCTATGAACATC 59.310 43.478 0.00 0.00 0.00 3.06
70 71 3.686016 ACCGTTGGAAAGCTATGAACAT 58.314 40.909 0.00 0.00 0.00 2.71
71 72 3.134574 ACCGTTGGAAAGCTATGAACA 57.865 42.857 0.00 0.00 0.00 3.18
72 73 6.128902 CGATATACCGTTGGAAAGCTATGAAC 60.129 42.308 0.00 0.00 0.00 3.18
73 74 5.924254 CGATATACCGTTGGAAAGCTATGAA 59.076 40.000 0.00 0.00 0.00 2.57
74 75 5.466819 CGATATACCGTTGGAAAGCTATGA 58.533 41.667 0.00 0.00 0.00 2.15
76 77 4.243270 GCGATATACCGTTGGAAAGCTAT 58.757 43.478 0.00 0.00 0.00 2.97
77 78 3.068448 TGCGATATACCGTTGGAAAGCTA 59.932 43.478 0.00 0.00 0.00 3.32
78 79 2.159014 TGCGATATACCGTTGGAAAGCT 60.159 45.455 0.00 0.00 0.00 3.74
79 80 2.206750 TGCGATATACCGTTGGAAAGC 58.793 47.619 0.00 0.00 0.00 3.51
80 81 3.303132 GCTTGCGATATACCGTTGGAAAG 60.303 47.826 0.00 0.00 0.00 2.62
83 84 1.539496 GGCTTGCGATATACCGTTGGA 60.539 52.381 0.00 0.00 0.00 3.53
84 85 0.865769 GGCTTGCGATATACCGTTGG 59.134 55.000 0.00 0.00 0.00 3.77
85 86 0.865769 GGGCTTGCGATATACCGTTG 59.134 55.000 0.00 0.00 0.00 4.10
86 87 0.250166 GGGGCTTGCGATATACCGTT 60.250 55.000 0.00 0.00 0.00 4.44
88 89 1.736645 CGGGGCTTGCGATATACCG 60.737 63.158 0.00 0.00 0.00 4.02
89 90 0.250166 AACGGGGCTTGCGATATACC 60.250 55.000 0.00 0.00 0.00 2.73
90 91 1.263217 CAAACGGGGCTTGCGATATAC 59.737 52.381 0.00 0.00 0.00 1.47
91 92 1.588674 CAAACGGGGCTTGCGATATA 58.411 50.000 0.00 0.00 0.00 0.86
93 94 1.747367 CCAAACGGGGCTTGCGATA 60.747 57.895 0.00 0.00 0.00 2.92
104 105 1.667510 GCCAACATTGCCCAAACGG 60.668 57.895 0.00 0.00 0.00 4.44
105 106 2.021039 CGCCAACATTGCCCAAACG 61.021 57.895 0.00 0.00 0.00 3.60
106 107 1.667510 CCGCCAACATTGCCCAAAC 60.668 57.895 0.00 0.00 0.00 2.93
108 109 1.814772 CTTCCGCCAACATTGCCCAA 61.815 55.000 0.00 0.00 0.00 4.12
110 111 1.815817 AACTTCCGCCAACATTGCCC 61.816 55.000 0.00 0.00 0.00 5.36
111 112 0.388520 GAACTTCCGCCAACATTGCC 60.389 55.000 0.00 0.00 0.00 4.52
112 113 0.313672 TGAACTTCCGCCAACATTGC 59.686 50.000 0.00 0.00 0.00 3.56
113 114 2.393764 GTTGAACTTCCGCCAACATTG 58.606 47.619 0.00 0.00 39.74 2.82
115 116 0.958822 GGTTGAACTTCCGCCAACAT 59.041 50.000 0.00 0.00 41.22 2.71
116 117 0.106918 AGGTTGAACTTCCGCCAACA 60.107 50.000 0.00 0.00 41.22 3.33
117 118 1.804748 CTAGGTTGAACTTCCGCCAAC 59.195 52.381 0.00 0.00 39.38 3.77
121 122 2.479275 GTGAACTAGGTTGAACTTCCGC 59.521 50.000 0.00 0.00 0.00 5.54
122 123 3.724374 TGTGAACTAGGTTGAACTTCCG 58.276 45.455 0.00 0.00 0.00 4.30
123 124 4.515567 CCTTGTGAACTAGGTTGAACTTCC 59.484 45.833 3.11 0.00 34.77 3.46
124 125 5.365619 TCCTTGTGAACTAGGTTGAACTTC 58.634 41.667 10.17 0.00 39.42 3.01
127 128 5.123936 ACTTCCTTGTGAACTAGGTTGAAC 58.876 41.667 10.17 0.00 39.42 3.18
128 129 5.367945 ACTTCCTTGTGAACTAGGTTGAA 57.632 39.130 10.17 0.00 39.42 2.69
132 133 5.123936 GTTGAACTTCCTTGTGAACTAGGT 58.876 41.667 10.17 0.00 39.42 3.08
133 134 4.211374 CGTTGAACTTCCTTGTGAACTAGG 59.789 45.833 4.74 4.74 39.70 3.02
134 135 4.809426 ACGTTGAACTTCCTTGTGAACTAG 59.191 41.667 0.00 0.00 0.00 2.57
136 137 3.606687 ACGTTGAACTTCCTTGTGAACT 58.393 40.909 0.00 0.00 0.00 3.01
137 138 4.569564 AGTACGTTGAACTTCCTTGTGAAC 59.430 41.667 0.00 0.00 0.00 3.18
140 141 5.287226 AGTAGTACGTTGAACTTCCTTGTG 58.713 41.667 0.00 0.00 0.00 3.33
141 142 5.526506 AGTAGTACGTTGAACTTCCTTGT 57.473 39.130 0.00 0.00 0.00 3.16
144 145 4.142730 CGCTAGTAGTACGTTGAACTTCCT 60.143 45.833 0.00 0.00 0.00 3.36
145 146 4.094212 CGCTAGTAGTACGTTGAACTTCC 58.906 47.826 0.00 0.00 0.00 3.46
146 147 4.962693 TCGCTAGTAGTACGTTGAACTTC 58.037 43.478 0.00 0.00 0.00 3.01
147 148 5.362556 TTCGCTAGTAGTACGTTGAACTT 57.637 39.130 0.00 0.00 0.00 2.66
148 149 4.671250 GCTTCGCTAGTAGTACGTTGAACT 60.671 45.833 0.00 0.00 0.00 3.01
149 150 3.541523 GCTTCGCTAGTAGTACGTTGAAC 59.458 47.826 0.00 0.00 0.00 3.18
150 151 3.189080 TGCTTCGCTAGTAGTACGTTGAA 59.811 43.478 0.00 0.00 0.00 2.69
152 153 3.099362 CTGCTTCGCTAGTAGTACGTTG 58.901 50.000 0.00 0.00 32.46 4.10
154 155 1.669779 CCTGCTTCGCTAGTAGTACGT 59.330 52.381 0.00 0.00 35.04 3.57
155 156 1.669779 ACCTGCTTCGCTAGTAGTACG 59.330 52.381 0.00 0.00 35.04 3.67
156 157 2.681848 TGACCTGCTTCGCTAGTAGTAC 59.318 50.000 0.00 0.00 35.04 2.73
160 161 1.103803 CCTGACCTGCTTCGCTAGTA 58.896 55.000 0.00 0.00 0.00 1.82
162 163 0.247736 AACCTGACCTGCTTCGCTAG 59.752 55.000 0.00 0.00 0.00 3.42
163 164 0.037326 CAACCTGACCTGCTTCGCTA 60.037 55.000 0.00 0.00 0.00 4.26
164 165 1.302033 CAACCTGACCTGCTTCGCT 60.302 57.895 0.00 0.00 0.00 4.93
166 167 0.249868 TCACAACCTGACCTGCTTCG 60.250 55.000 0.00 0.00 0.00 3.79
167 168 2.079925 GATCACAACCTGACCTGCTTC 58.920 52.381 0.00 0.00 0.00 3.86
168 169 1.421268 TGATCACAACCTGACCTGCTT 59.579 47.619 0.00 0.00 0.00 3.91
170 171 1.002430 TCTGATCACAACCTGACCTGC 59.998 52.381 0.00 0.00 0.00 4.85
171 172 3.407424 TTCTGATCACAACCTGACCTG 57.593 47.619 0.00 0.00 0.00 4.00
172 173 5.965033 ATATTCTGATCACAACCTGACCT 57.035 39.130 0.00 0.00 0.00 3.85
173 174 8.682936 AATAATATTCTGATCACAACCTGACC 57.317 34.615 0.00 0.00 0.00 4.02
174 175 9.553064 AGAATAATATTCTGATCACAACCTGAC 57.447 33.333 14.16 0.00 0.00 3.51
175 176 9.770097 GAGAATAATATTCTGATCACAACCTGA 57.230 33.333 19.15 0.00 0.00 3.86
176 177 9.551734 TGAGAATAATATTCTGATCACAACCTG 57.448 33.333 19.15 0.00 0.00 4.00
181 182 8.037166 CGGGATGAGAATAATATTCTGATCACA 58.963 37.037 30.09 18.64 0.00 3.58
182 183 8.037758 ACGGGATGAGAATAATATTCTGATCAC 58.962 37.037 29.74 27.51 0.00 3.06
183 184 8.037166 CACGGGATGAGAATAATATTCTGATCA 58.963 37.037 29.74 19.10 0.00 2.92
185 186 8.138928 TCACGGGATGAGAATAATATTCTGAT 57.861 34.615 19.15 16.18 31.91 2.90
187 188 8.037166 TGATCACGGGATGAGAATAATATTCTG 58.963 37.037 19.15 7.13 41.91 3.02
188 189 8.138928 TGATCACGGGATGAGAATAATATTCT 57.861 34.615 14.76 14.76 41.91 2.40
189 190 8.253810 TCTGATCACGGGATGAGAATAATATTC 58.746 37.037 14.87 4.89 40.23 1.75
190 191 8.138928 TCTGATCACGGGATGAGAATAATATT 57.861 34.615 14.87 0.00 40.23 1.28
191 192 7.724490 TCTGATCACGGGATGAGAATAATAT 57.276 36.000 14.87 0.00 40.23 1.28
192 193 7.539034 TTCTGATCACGGGATGAGAATAATA 57.461 36.000 23.40 3.46 45.10 0.98
193 194 6.425210 TTCTGATCACGGGATGAGAATAAT 57.575 37.500 23.40 0.00 45.10 1.28
194 195 5.869649 TTCTGATCACGGGATGAGAATAA 57.130 39.130 23.40 4.21 45.10 1.40
199 200 4.038522 ACACTATTCTGATCACGGGATGAG 59.961 45.833 3.97 6.26 41.91 2.90
200 201 3.960755 ACACTATTCTGATCACGGGATGA 59.039 43.478 3.97 0.00 43.13 2.92
201 202 4.327982 ACACTATTCTGATCACGGGATG 57.672 45.455 3.97 0.00 32.67 3.51
202 203 5.118990 CAAACACTATTCTGATCACGGGAT 58.881 41.667 0.00 0.00 36.13 3.85
204 205 4.093408 CACAAACACTATTCTGATCACGGG 59.907 45.833 0.00 0.00 0.00 5.28
205 206 4.690748 ACACAAACACTATTCTGATCACGG 59.309 41.667 0.00 0.00 0.00 4.94
206 207 5.845985 ACACAAACACTATTCTGATCACG 57.154 39.130 0.00 0.00 0.00 4.35
207 208 8.256611 ACATACACAAACACTATTCTGATCAC 57.743 34.615 0.00 0.00 0.00 3.06
392 398 3.186119 ACATTCAAACGTTGGCAAACAG 58.814 40.909 0.00 0.00 35.94 3.16
666 1929 7.660617 ACATCCGTATCTAGACGAATCTAAGAA 59.339 37.037 5.60 0.00 45.82 2.52
707 1971 8.638873 TCTAAATACGGATGTATCAAGTCATGT 58.361 33.333 0.00 0.00 40.42 3.21
1323 4594 2.185310 GATGGTCGGGAGCACCTTGT 62.185 60.000 2.26 0.00 42.02 3.16
1405 4676 1.525077 GGAAACACACTCGCCCACA 60.525 57.895 0.00 0.00 0.00 4.17
2293 5639 1.195900 GACACCTTGCGATTTTGCGTA 59.804 47.619 0.00 0.00 37.81 4.42
2529 5876 2.422597 CTACAACGAAATGACTGGGCA 58.577 47.619 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.