Multiple sequence alignment - TraesCS7D01G152500

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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 TraesCS7D01G152500 chr7D 100.000 4658 0 0 551 5208 101098406 101093749 0.000000e+00 8602.0
1 TraesCS7D01G152500 chr7D 81.943 1462 197 39 2665 4120 6781363 6782763 0.000000e+00 1175.0
2 TraesCS7D01G152500 chr7D 81.385 1300 234 8 1303 2598 6780073 6781368 0.000000e+00 1053.0
3 TraesCS7D01G152500 chr7D 100.000 241 0 0 1 241 101098956 101098716 3.700000e-121 446.0
4 TraesCS7D01G152500 chr7B 94.541 4598 200 23 638 5208 57636569 57631996 0.000000e+00 7053.0
5 TraesCS7D01G152500 chr7B 79.652 747 132 18 4444 5178 32549249 32549987 2.150000e-143 520.0
6 TraesCS7D01G152500 chr7B 95.714 70 3 0 172 241 57636983 57636914 4.260000e-21 113.0
7 TraesCS7D01G152500 chr7A 95.427 3674 125 11 600 4263 103218119 103214479 0.000000e+00 5814.0
8 TraesCS7D01G152500 chr7A 82.809 1239 207 6 1364 2599 7766074 7767309 0.000000e+00 1103.0
9 TraesCS7D01G152500 chr7A 82.646 582 91 8 4356 4929 103211729 103211150 1.670000e-139 507.0
10 TraesCS7D01G152500 chr7A 88.492 252 27 1 4935 5184 103196605 103196354 2.360000e-78 303.0
11 TraesCS7D01G152500 chr7A 82.043 323 58 0 2665 2987 7767303 7767625 5.140000e-70 276.0
12 TraesCS7D01G152500 chr7A 92.806 139 5 2 104 241 103218280 103218146 4.110000e-46 196.0
13 TraesCS7D01G152500 chr4A 81.296 1481 195 47 2665 4120 733421772 733420349 0.000000e+00 1125.0
14 TraesCS7D01G152500 chr4A 81.472 1236 229 0 1364 2599 733452775 733454010 0.000000e+00 1014.0
15 TraesCS7D01G152500 chr4A 80.551 1306 248 5 1303 2605 733423062 733421760 0.000000e+00 1000.0
16 TraesCS7D01G152500 chr4A 82.833 932 123 25 3067 3984 733454371 733455279 0.000000e+00 800.0
17 TraesCS7D01G152500 chrUn 81.437 1239 230 0 1367 2605 334535599 334534361 0.000000e+00 1014.0
18 TraesCS7D01G152500 chrUn 80.857 1144 219 0 1462 2605 339771814 339770671 0.000000e+00 900.0
19 TraesCS7D01G152500 chrUn 80.931 1138 217 0 1462 2599 339774475 339775612 0.000000e+00 900.0
20 TraesCS7D01G152500 chrUn 80.857 1144 219 0 1462 2605 408507537 408506394 0.000000e+00 900.0
21 TraesCS7D01G152500 chrUn 83.422 935 112 27 3067 3984 339770316 339769408 0.000000e+00 828.0
22 TraesCS7D01G152500 chrUn 83.422 935 112 27 3067 3984 339775973 339776881 0.000000e+00 828.0
23 TraesCS7D01G152500 chrUn 82.924 814 96 27 3188 3984 464059170 464058383 0.000000e+00 693.0
24 TraesCS7D01G152500 chrUn 82.393 727 91 25 3272 3984 467116536 467115833 2.680000e-167 599.0
25 TraesCS7D01G152500 chrUn 75.500 400 69 23 4394 4785 108612429 108612807 8.970000e-38 169.0
26 TraesCS7D01G152500 chr1A 79.070 516 75 19 4665 5148 495282814 495282300 1.810000e-84 324.0
27 TraesCS7D01G152500 chr1A 77.755 490 91 8 4693 5178 479827252 479826777 8.540000e-73 285.0
28 TraesCS7D01G152500 chr1A 77.089 371 60 16 4691 5037 562046266 562045897 1.910000e-44 191.0
29 TraesCS7D01G152500 chr3B 76.220 635 111 25 4576 5178 776175282 776175908 3.050000e-77 300.0
30 TraesCS7D01G152500 chr3B 89.552 67 7 0 2854 2920 43343244 43343178 9.290000e-13 86.1
31 TraesCS7D01G152500 chr1D 76.200 521 80 28 4699 5181 480995630 480995116 8.720000e-58 235.0
32 TraesCS7D01G152500 chr1D 77.674 215 24 12 4903 5094 332469383 332469596 5.510000e-20 110.0
33 TraesCS7D01G152500 chr1D 90.541 74 3 3 4937 5006 269731903 269731830 1.540000e-15 95.3
34 TraesCS7D01G152500 chr1B 74.862 545 87 28 4677 5178 669218748 669218211 8.840000e-48 202.0
35 TraesCS7D01G152500 chr3D 88.816 152 17 0 2851 3002 26104595 26104444 2.480000e-43 187.0
36 TraesCS7D01G152500 chr3D 89.394 66 6 1 2892 2957 549451113 549451177 1.200000e-11 82.4
37 TraesCS7D01G152500 chr6B 82.036 167 30 0 5015 5181 572556919 572556753 5.440000e-30 143.0
38 TraesCS7D01G152500 chr6B 92.308 52 3 1 3819 3869 513136341 513136392 7.230000e-09 73.1
39 TraesCS7D01G152500 chr5D 73.661 448 72 20 4747 5149 3504032 3503586 1.180000e-26 132.0
40 TraesCS7D01G152500 chr6D 80.000 160 32 0 5025 5184 431324303 431324144 9.160000e-23 119.0
41 TraesCS7D01G152500 chr6D 92.308 52 3 1 3819 3869 313187463 313187412 7.230000e-09 73.1
42 TraesCS7D01G152500 chr6D 97.368 38 1 0 4574 4611 22270112 22270149 1.210000e-06 65.8
43 TraesCS7D01G152500 chr2A 76.190 273 36 19 4903 5149 662912227 662912496 3.300000e-22 117.0
44 TraesCS7D01G152500 chr2A 87.143 70 7 2 3812 3880 570608621 570608689 1.550000e-10 78.7
45 TraesCS7D01G152500 chr2A 93.878 49 0 2 3815 3860 530381029 530381077 2.600000e-08 71.3
46 TraesCS7D01G152500 chr6A 94.231 52 2 1 3819 3869 450107535 450107484 1.550000e-10 78.7
47 TraesCS7D01G152500 chr2D 93.878 49 0 2 3815 3860 392526363 392526411 2.600000e-08 71.3
48 TraesCS7D01G152500 chr2D 87.931 58 3 4 4556 4611 356733097 356733042 1.210000e-06 65.8
49 TraesCS7D01G152500 chr2B 93.878 49 0 2 3815 3860 464466985 464467033 2.600000e-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 TraesCS7D01G152500 chr7D 101093749 101098956 5207 True 4524.000000 8602 100.0000 1 5208 2 chr7D.!!$R1 5207
1 TraesCS7D01G152500 chr7D 6780073 6782763 2690 False 1114.000000 1175 81.6640 1303 4120 2 chr7D.!!$F1 2817
2 TraesCS7D01G152500 chr7B 57631996 57636983 4987 True 3583.000000 7053 95.1275 172 5208 2 chr7B.!!$R1 5036
3 TraesCS7D01G152500 chr7B 32549249 32549987 738 False 520.000000 520 79.6520 4444 5178 1 chr7B.!!$F1 734
4 TraesCS7D01G152500 chr7A 103211150 103218280 7130 True 2172.333333 5814 90.2930 104 4929 3 chr7A.!!$R2 4825
5 TraesCS7D01G152500 chr7A 7766074 7767625 1551 False 689.500000 1103 82.4260 1364 2987 2 chr7A.!!$F1 1623
6 TraesCS7D01G152500 chr4A 733420349 733423062 2713 True 1062.500000 1125 80.9235 1303 4120 2 chr4A.!!$R1 2817
7 TraesCS7D01G152500 chr4A 733452775 733455279 2504 False 907.000000 1014 82.1525 1364 3984 2 chr4A.!!$F1 2620
8 TraesCS7D01G152500 chrUn 334534361 334535599 1238 True 1014.000000 1014 81.4370 1367 2605 1 chrUn.!!$R1 1238
9 TraesCS7D01G152500 chrUn 408506394 408507537 1143 True 900.000000 900 80.8570 1462 2605 1 chrUn.!!$R2 1143
10 TraesCS7D01G152500 chrUn 339769408 339771814 2406 True 864.000000 900 82.1395 1462 3984 2 chrUn.!!$R5 2522
11 TraesCS7D01G152500 chrUn 339774475 339776881 2406 False 864.000000 900 82.1765 1462 3984 2 chrUn.!!$F2 2522
12 TraesCS7D01G152500 chrUn 464058383 464059170 787 True 693.000000 693 82.9240 3188 3984 1 chrUn.!!$R3 796
13 TraesCS7D01G152500 chrUn 467115833 467116536 703 True 599.000000 599 82.3930 3272 3984 1 chrUn.!!$R4 712
14 TraesCS7D01G152500 chr1A 495282300 495282814 514 True 324.000000 324 79.0700 4665 5148 1 chr1A.!!$R2 483
15 TraesCS7D01G152500 chr3B 776175282 776175908 626 False 300.000000 300 76.2200 4576 5178 1 chr3B.!!$F1 602
16 TraesCS7D01G152500 chr1D 480995116 480995630 514 True 235.000000 235 76.2000 4699 5181 1 chr1D.!!$R2 482
17 TraesCS7D01G152500 chr1B 669218211 669218748 537 True 202.000000 202 74.8620 4677 5178 1 chr1B.!!$R1 501

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
656 939 0.041576 TTAGTCGCGTCCGATCGATG 60.042 55.000 18.66 9.37 46.38 3.84 F
870 1162 0.109919 CTTTAAAACCCCGCGCTGTC 60.110 55.000 5.56 0.00 0.00 3.51 F
900 1192 0.613260 TGCTATCACCAAGCCGTTCT 59.387 50.000 0.00 0.00 39.30 3.01 F
953 1245 0.667453 GCCTCCAGCTACGTACCTAC 59.333 60.000 0.00 0.00 38.99 3.18 F
1611 1903 2.022129 CACGCGTGTCCTGAACCTC 61.022 63.158 30.50 0.00 0.00 3.85 F
3666 3961 0.179004 TCACCGGATTGTTGCAAGGT 60.179 50.000 9.46 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2099 0.093705 GTCGAGTTTGACAGCGATGC 59.906 55.000 0.00 0.0 38.75 3.91 R
2710 3002 0.681733 AGCGACGCCATATTCTCCAT 59.318 50.000 17.79 0.0 0.00 3.41 R
2737 3029 3.671716 AGCCGTTGTAGGAAAAGTTAGG 58.328 45.455 0.00 0.0 0.00 2.69 R
3666 3961 2.185867 GCGATGTAGCCCACGGAA 59.814 61.111 0.00 0.0 0.00 4.30 R
3766 4087 0.662619 CAACCACGCAAGCAAGAAGA 59.337 50.000 0.00 0.0 45.62 2.87 R
4679 7674 0.456221 CAGCGTCTAACCGACTGGAT 59.544 55.000 0.00 0.0 40.59 3.41 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 7.677892 AGTTTACAGAGGGAGTAAGTTTTAGG 58.322 38.462 0.00 0.00 33.44 2.69
26 27 6.616237 TTACAGAGGGAGTAAGTTTTAGGG 57.384 41.667 0.00 0.00 0.00 3.53
27 28 3.844804 ACAGAGGGAGTAAGTTTTAGGGG 59.155 47.826 0.00 0.00 0.00 4.79
28 29 4.101856 CAGAGGGAGTAAGTTTTAGGGGA 58.898 47.826 0.00 0.00 0.00 4.81
29 30 4.534897 CAGAGGGAGTAAGTTTTAGGGGAA 59.465 45.833 0.00 0.00 0.00 3.97
30 31 4.783763 AGAGGGAGTAAGTTTTAGGGGAAG 59.216 45.833 0.00 0.00 0.00 3.46
31 32 3.850774 AGGGAGTAAGTTTTAGGGGAAGG 59.149 47.826 0.00 0.00 0.00 3.46
32 33 3.053842 GGGAGTAAGTTTTAGGGGAAGGG 60.054 52.174 0.00 0.00 0.00 3.95
33 34 3.590630 GGAGTAAGTTTTAGGGGAAGGGT 59.409 47.826 0.00 0.00 0.00 4.34
34 35 4.043812 GGAGTAAGTTTTAGGGGAAGGGTT 59.956 45.833 0.00 0.00 0.00 4.11
35 36 5.458654 GGAGTAAGTTTTAGGGGAAGGGTTT 60.459 44.000 0.00 0.00 0.00 3.27
36 37 6.034442 AGTAAGTTTTAGGGGAAGGGTTTT 57.966 37.500 0.00 0.00 0.00 2.43
37 38 6.446451 AGTAAGTTTTAGGGGAAGGGTTTTT 58.554 36.000 0.00 0.00 0.00 1.94
38 39 5.623956 AAGTTTTAGGGGAAGGGTTTTTG 57.376 39.130 0.00 0.00 0.00 2.44
39 40 3.389983 AGTTTTAGGGGAAGGGTTTTTGC 59.610 43.478 0.00 0.00 0.00 3.68
40 41 3.338110 TTTAGGGGAAGGGTTTTTGCT 57.662 42.857 0.00 0.00 0.00 3.91
41 42 3.338110 TTAGGGGAAGGGTTTTTGCTT 57.662 42.857 0.00 0.00 0.00 3.91
42 43 2.190398 AGGGGAAGGGTTTTTGCTTT 57.810 45.000 0.00 0.00 0.00 3.51
43 44 2.487775 AGGGGAAGGGTTTTTGCTTTT 58.512 42.857 0.00 0.00 0.00 2.27
44 45 2.172505 AGGGGAAGGGTTTTTGCTTTTG 59.827 45.455 0.00 0.00 0.00 2.44
45 46 2.092646 GGGGAAGGGTTTTTGCTTTTGT 60.093 45.455 0.00 0.00 0.00 2.83
46 47 2.942376 GGGAAGGGTTTTTGCTTTTGTG 59.058 45.455 0.00 0.00 0.00 3.33
47 48 3.605634 GGAAGGGTTTTTGCTTTTGTGT 58.394 40.909 0.00 0.00 0.00 3.72
48 49 3.373748 GGAAGGGTTTTTGCTTTTGTGTG 59.626 43.478 0.00 0.00 0.00 3.82
49 50 3.694043 AGGGTTTTTGCTTTTGTGTGT 57.306 38.095 0.00 0.00 0.00 3.72
50 51 3.333804 AGGGTTTTTGCTTTTGTGTGTG 58.666 40.909 0.00 0.00 0.00 3.82
51 52 3.070748 GGGTTTTTGCTTTTGTGTGTGT 58.929 40.909 0.00 0.00 0.00 3.72
52 53 3.120373 GGGTTTTTGCTTTTGTGTGTGTG 60.120 43.478 0.00 0.00 0.00 3.82
53 54 3.496507 GGTTTTTGCTTTTGTGTGTGTGT 59.503 39.130 0.00 0.00 0.00 3.72
54 55 4.453339 GTTTTTGCTTTTGTGTGTGTGTG 58.547 39.130 0.00 0.00 0.00 3.82
55 56 2.360553 TTGCTTTTGTGTGTGTGTGG 57.639 45.000 0.00 0.00 0.00 4.17
56 57 0.529833 TGCTTTTGTGTGTGTGTGGG 59.470 50.000 0.00 0.00 0.00 4.61
57 58 0.814457 GCTTTTGTGTGTGTGTGGGA 59.186 50.000 0.00 0.00 0.00 4.37
58 59 1.408702 GCTTTTGTGTGTGTGTGGGAT 59.591 47.619 0.00 0.00 0.00 3.85
59 60 2.543653 GCTTTTGTGTGTGTGTGGGATC 60.544 50.000 0.00 0.00 0.00 3.36
60 61 2.426842 TTTGTGTGTGTGTGGGATCA 57.573 45.000 0.00 0.00 0.00 2.92
61 62 1.674359 TTGTGTGTGTGTGGGATCAC 58.326 50.000 0.00 0.00 43.87 3.06
62 63 0.179032 TGTGTGTGTGTGGGATCACC 60.179 55.000 0.00 0.00 42.98 4.02
71 72 3.955145 TGGGATCACCATGTGACAC 57.045 52.632 0.00 0.00 46.80 3.67
72 73 1.063183 TGGGATCACCATGTGACACA 58.937 50.000 11.41 11.41 46.80 3.72
73 74 1.271325 TGGGATCACCATGTGACACAC 60.271 52.381 11.22 1.42 46.80 3.82
74 75 1.453155 GGATCACCATGTGACACACC 58.547 55.000 11.22 1.67 45.65 4.16
75 76 1.003580 GGATCACCATGTGACACACCT 59.996 52.381 11.22 0.00 45.65 4.00
76 77 2.236146 GGATCACCATGTGACACACCTA 59.764 50.000 11.22 0.00 45.65 3.08
77 78 3.525537 GATCACCATGTGACACACCTAG 58.474 50.000 11.22 2.54 45.65 3.02
78 79 2.325484 TCACCATGTGACACACCTAGT 58.675 47.619 11.22 3.19 37.67 2.57
79 80 3.502356 TCACCATGTGACACACCTAGTA 58.498 45.455 11.22 0.00 37.67 1.82
80 81 3.898741 TCACCATGTGACACACCTAGTAA 59.101 43.478 11.22 0.00 37.67 2.24
81 82 4.021456 TCACCATGTGACACACCTAGTAAG 60.021 45.833 11.22 0.00 37.67 2.34
82 83 3.262420 CCATGTGACACACCTAGTAAGC 58.738 50.000 11.22 0.00 32.73 3.09
83 84 3.306710 CCATGTGACACACCTAGTAAGCA 60.307 47.826 11.22 0.00 32.73 3.91
84 85 4.314961 CATGTGACACACCTAGTAAGCAA 58.685 43.478 11.22 0.00 32.73 3.91
85 86 4.617253 TGTGACACACCTAGTAAGCAAT 57.383 40.909 3.56 0.00 32.73 3.56
86 87 4.566004 TGTGACACACCTAGTAAGCAATC 58.434 43.478 3.56 0.00 32.73 2.67
87 88 3.933332 GTGACACACCTAGTAAGCAATCC 59.067 47.826 0.00 0.00 0.00 3.01
88 89 3.580895 TGACACACCTAGTAAGCAATCCA 59.419 43.478 0.00 0.00 0.00 3.41
89 90 4.041075 TGACACACCTAGTAAGCAATCCAA 59.959 41.667 0.00 0.00 0.00 3.53
90 91 4.980573 ACACACCTAGTAAGCAATCCAAA 58.019 39.130 0.00 0.00 0.00 3.28
91 92 4.760204 ACACACCTAGTAAGCAATCCAAAC 59.240 41.667 0.00 0.00 0.00 2.93
92 93 5.003804 CACACCTAGTAAGCAATCCAAACT 58.996 41.667 0.00 0.00 0.00 2.66
93 94 6.170506 CACACCTAGTAAGCAATCCAAACTA 58.829 40.000 0.00 0.00 0.00 2.24
94 95 6.823689 CACACCTAGTAAGCAATCCAAACTAT 59.176 38.462 0.00 0.00 0.00 2.12
95 96 7.336931 CACACCTAGTAAGCAATCCAAACTATT 59.663 37.037 0.00 0.00 0.00 1.73
96 97 8.545472 ACACCTAGTAAGCAATCCAAACTATTA 58.455 33.333 0.00 0.00 0.00 0.98
97 98 9.391006 CACCTAGTAAGCAATCCAAACTATTAA 57.609 33.333 0.00 0.00 0.00 1.40
98 99 9.969001 ACCTAGTAAGCAATCCAAACTATTAAA 57.031 29.630 0.00 0.00 0.00 1.52
143 145 0.527565 AAAGGATGTGCGCATGAACC 59.472 50.000 19.33 12.87 35.07 3.62
169 171 3.188895 GTGCAACCTAGCTCTTTTTCG 57.811 47.619 0.00 0.00 34.99 3.46
170 172 2.806244 GTGCAACCTAGCTCTTTTTCGA 59.194 45.455 0.00 0.00 34.99 3.71
236 238 2.665185 ACAAACACGAGGCTCGGC 60.665 61.111 36.81 1.19 45.59 5.54
626 628 6.319715 TCCTCCAAACCTTAATTAGCCTTTT 58.680 36.000 0.00 0.00 0.00 2.27
656 939 0.041576 TTAGTCGCGTCCGATCGATG 60.042 55.000 18.66 9.37 46.38 3.84
870 1162 0.109919 CTTTAAAACCCCGCGCTGTC 60.110 55.000 5.56 0.00 0.00 3.51
900 1192 0.613260 TGCTATCACCAAGCCGTTCT 59.387 50.000 0.00 0.00 39.30 3.01
939 1231 2.124778 GCTTGAGCTCCAGCCTCC 60.125 66.667 25.55 1.79 43.38 4.30
940 1232 2.964310 GCTTGAGCTCCAGCCTCCA 61.964 63.158 25.55 0.00 43.38 3.86
941 1233 1.221293 CTTGAGCTCCAGCCTCCAG 59.779 63.158 12.15 0.00 43.38 3.86
953 1245 0.667453 GCCTCCAGCTACGTACCTAC 59.333 60.000 0.00 0.00 38.99 3.18
959 1251 4.899502 TCCAGCTACGTACCTACCTATAC 58.100 47.826 0.00 0.00 0.00 1.47
960 1252 4.006319 CCAGCTACGTACCTACCTATACC 58.994 52.174 0.00 0.00 0.00 2.73
961 1253 4.006319 CAGCTACGTACCTACCTATACCC 58.994 52.174 0.00 0.00 0.00 3.69
962 1254 3.009584 AGCTACGTACCTACCTATACCCC 59.990 52.174 0.00 0.00 0.00 4.95
963 1255 2.980246 ACGTACCTACCTATACCCCC 57.020 55.000 0.00 0.00 0.00 5.40
964 1256 2.143602 ACGTACCTACCTATACCCCCA 58.856 52.381 0.00 0.00 0.00 4.96
965 1257 2.108952 ACGTACCTACCTATACCCCCAG 59.891 54.545 0.00 0.00 0.00 4.45
966 1258 2.556114 CGTACCTACCTATACCCCCAGG 60.556 59.091 0.00 0.00 37.97 4.45
1397 1689 3.847602 CAGCCTCTCCCGCCTCAG 61.848 72.222 0.00 0.00 0.00 3.35
1587 1879 2.584608 CAGGGCTCGATTCCGGTT 59.415 61.111 0.00 0.00 36.24 4.44
1604 1896 2.856628 TTGAGCTCACGCGTGTCCT 61.857 57.895 35.74 30.23 42.32 3.85
1611 1903 2.022129 CACGCGTGTCCTGAACCTC 61.022 63.158 30.50 0.00 0.00 3.85
1989 2281 2.881352 CCGTTCTTCGCCTCGCTC 60.881 66.667 0.00 0.00 38.35 5.03
1992 2284 2.126463 TTCTTCGCCTCGCTCACG 60.126 61.111 0.00 0.00 42.01 4.35
2244 2536 4.828925 GAGCGGCTGCACCTCTCC 62.829 72.222 21.93 0.00 43.43 3.71
2417 2709 4.148825 GCGAGGCGTGATCCCAGT 62.149 66.667 0.00 0.00 0.00 4.00
2568 2860 3.771160 ACGATTCCGCCGGAGCTT 61.771 61.111 5.05 0.00 39.95 3.74
3666 3961 0.179004 TCACCGGATTGTTGCAAGGT 60.179 50.000 9.46 0.00 0.00 3.50
3695 3990 2.544267 GCTACATCGCACCAGGTAAATC 59.456 50.000 0.00 0.00 0.00 2.17
3727 4039 9.107177 TCAAATTAACAGAAACAAATGCATGTT 57.893 25.926 0.00 0.00 45.12 2.71
3764 4085 2.927429 TCAACATTTTCATGGCGTTCG 58.073 42.857 0.00 0.00 34.27 3.95
3765 4086 2.550180 TCAACATTTTCATGGCGTTCGA 59.450 40.909 0.00 0.00 34.27 3.71
3766 4087 3.190327 TCAACATTTTCATGGCGTTCGAT 59.810 39.130 0.00 0.00 34.27 3.59
3767 4088 3.405170 ACATTTTCATGGCGTTCGATC 57.595 42.857 0.00 0.00 34.27 3.69
3807 4128 0.822944 GAGTACGGACTAGGAGGCCC 60.823 65.000 0.00 0.00 41.74 5.80
4138 4465 2.029964 GACCTCGCCAAACACGGA 59.970 61.111 0.00 0.00 0.00 4.69
4208 4535 4.747543 CGGACTCGTCGTTCTGAG 57.252 61.111 0.00 0.00 38.21 3.35
4289 4852 2.987149 AGCTAGTTTGAACACGTCATCG 59.013 45.455 0.00 0.00 43.34 3.84
4290 4853 2.472397 GCTAGTTTGAACACGTCATCGC 60.472 50.000 0.00 0.00 41.18 4.58
4421 7409 1.539388 TCCAATGCACCGACACATTTC 59.461 47.619 0.00 0.00 34.32 2.17
4440 7428 4.340019 TCCACGCGCGTCCGTTTA 62.340 61.111 35.61 11.87 39.83 2.01
4441 7429 3.183323 CCACGCGCGTCCGTTTAT 61.183 61.111 35.61 5.82 39.83 1.40
4474 7462 0.519961 GAAACAACGGCCTAATGCGT 59.480 50.000 0.00 0.00 42.61 5.24
4491 7479 2.890961 TTGTCGCAAACGGACGCA 60.891 55.556 0.00 0.00 40.63 5.24
4631 7620 1.459539 CGCTATTCTCCCCTCCCCA 60.460 63.158 0.00 0.00 0.00 4.96
4643 7633 1.811266 CTCCCCATTCACAGACGCG 60.811 63.158 3.53 3.53 0.00 6.01
4882 7930 0.181114 ACTTTGACAGGTCTGCTGCA 59.819 50.000 0.88 0.88 0.00 4.41
4930 7982 4.329545 GCCGGCTTCTCCACCACA 62.330 66.667 22.15 0.00 34.01 4.17
5097 8167 1.336980 GGTTTAGGGGATCGATCTCGC 60.337 57.143 23.96 20.17 39.60 5.03
5108 8179 1.365633 GATCTCGCGCCATTCTCCT 59.634 57.895 0.00 0.00 0.00 3.69
5160 8235 1.602416 GCCTACTCTTCGCCGATTACC 60.602 57.143 0.00 0.00 0.00 2.85
5178 8253 4.308458 TTCGGTGCACGTCCCCAG 62.308 66.667 11.45 0.00 44.69 4.45
5187 8262 1.609794 ACGTCCCCAGTCCTCTTCC 60.610 63.158 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.256583 CCCTAAAACTTACTCCCTCTGTAAACT 60.257 40.741 0.00 0.00 30.72 2.66
1 2 6.877855 CCCTAAAACTTACTCCCTCTGTAAAC 59.122 42.308 0.00 0.00 30.72 2.01
2 3 6.013119 CCCCTAAAACTTACTCCCTCTGTAAA 60.013 42.308 0.00 0.00 30.72 2.01
3 4 5.486419 CCCCTAAAACTTACTCCCTCTGTAA 59.514 44.000 0.00 0.00 0.00 2.41
4 5 5.028131 CCCCTAAAACTTACTCCCTCTGTA 58.972 45.833 0.00 0.00 0.00 2.74
5 6 3.844804 CCCCTAAAACTTACTCCCTCTGT 59.155 47.826 0.00 0.00 0.00 3.41
6 7 4.101856 TCCCCTAAAACTTACTCCCTCTG 58.898 47.826 0.00 0.00 0.00 3.35
7 8 4.431158 TCCCCTAAAACTTACTCCCTCT 57.569 45.455 0.00 0.00 0.00 3.69
8 9 4.080469 CCTTCCCCTAAAACTTACTCCCTC 60.080 50.000 0.00 0.00 0.00 4.30
9 10 3.850774 CCTTCCCCTAAAACTTACTCCCT 59.149 47.826 0.00 0.00 0.00 4.20
10 11 3.053842 CCCTTCCCCTAAAACTTACTCCC 60.054 52.174 0.00 0.00 0.00 4.30
11 12 3.590630 ACCCTTCCCCTAAAACTTACTCC 59.409 47.826 0.00 0.00 0.00 3.85
12 13 4.923516 ACCCTTCCCCTAAAACTTACTC 57.076 45.455 0.00 0.00 0.00 2.59
13 14 5.674799 AAACCCTTCCCCTAAAACTTACT 57.325 39.130 0.00 0.00 0.00 2.24
14 15 6.518493 CAAAAACCCTTCCCCTAAAACTTAC 58.482 40.000 0.00 0.00 0.00 2.34
15 16 5.070714 GCAAAAACCCTTCCCCTAAAACTTA 59.929 40.000 0.00 0.00 0.00 2.24
16 17 4.141574 GCAAAAACCCTTCCCCTAAAACTT 60.142 41.667 0.00 0.00 0.00 2.66
17 18 3.389983 GCAAAAACCCTTCCCCTAAAACT 59.610 43.478 0.00 0.00 0.00 2.66
18 19 3.389983 AGCAAAAACCCTTCCCCTAAAAC 59.610 43.478 0.00 0.00 0.00 2.43
19 20 3.659841 AGCAAAAACCCTTCCCCTAAAA 58.340 40.909 0.00 0.00 0.00 1.52
20 21 3.338110 AGCAAAAACCCTTCCCCTAAA 57.662 42.857 0.00 0.00 0.00 1.85
21 22 3.338110 AAGCAAAAACCCTTCCCCTAA 57.662 42.857 0.00 0.00 0.00 2.69
22 23 3.338110 AAAGCAAAAACCCTTCCCCTA 57.662 42.857 0.00 0.00 0.00 3.53
23 24 2.172505 CAAAAGCAAAAACCCTTCCCCT 59.827 45.455 0.00 0.00 0.00 4.79
24 25 2.092646 ACAAAAGCAAAAACCCTTCCCC 60.093 45.455 0.00 0.00 0.00 4.81
25 26 2.942376 CACAAAAGCAAAAACCCTTCCC 59.058 45.455 0.00 0.00 0.00 3.97
26 27 3.373748 CACACAAAAGCAAAAACCCTTCC 59.626 43.478 0.00 0.00 0.00 3.46
27 28 4.000325 ACACACAAAAGCAAAAACCCTTC 59.000 39.130 0.00 0.00 0.00 3.46
28 29 3.750652 CACACACAAAAGCAAAAACCCTT 59.249 39.130 0.00 0.00 0.00 3.95
29 30 3.244387 ACACACACAAAAGCAAAAACCCT 60.244 39.130 0.00 0.00 0.00 4.34
30 31 3.070748 ACACACACAAAAGCAAAAACCC 58.929 40.909 0.00 0.00 0.00 4.11
31 32 3.496507 ACACACACACAAAAGCAAAAACC 59.503 39.130 0.00 0.00 0.00 3.27
32 33 4.453339 CACACACACACAAAAGCAAAAAC 58.547 39.130 0.00 0.00 0.00 2.43
33 34 3.496130 CCACACACACACAAAAGCAAAAA 59.504 39.130 0.00 0.00 0.00 1.94
34 35 3.062763 CCACACACACACAAAAGCAAAA 58.937 40.909 0.00 0.00 0.00 2.44
35 36 2.611473 CCCACACACACACAAAAGCAAA 60.611 45.455 0.00 0.00 0.00 3.68
36 37 1.067283 CCCACACACACACAAAAGCAA 60.067 47.619 0.00 0.00 0.00 3.91
37 38 0.529833 CCCACACACACACAAAAGCA 59.470 50.000 0.00 0.00 0.00 3.91
38 39 0.814457 TCCCACACACACACAAAAGC 59.186 50.000 0.00 0.00 0.00 3.51
39 40 2.687425 TGATCCCACACACACACAAAAG 59.313 45.455 0.00 0.00 0.00 2.27
40 41 2.425312 GTGATCCCACACACACACAAAA 59.575 45.455 0.00 0.00 42.72 2.44
41 42 2.020720 GTGATCCCACACACACACAAA 58.979 47.619 0.00 0.00 42.72 2.83
42 43 1.674359 GTGATCCCACACACACACAA 58.326 50.000 0.00 0.00 42.72 3.33
43 44 0.179032 GGTGATCCCACACACACACA 60.179 55.000 0.00 0.00 44.93 3.72
44 45 0.179032 TGGTGATCCCACACACACAC 60.179 55.000 0.00 0.00 44.93 3.82
45 46 2.225792 TGGTGATCCCACACACACA 58.774 52.632 0.00 0.00 44.93 3.72
54 55 1.453155 GTGTGTCACATGGTGATCCC 58.547 55.000 9.31 0.00 44.63 3.85
55 56 1.003580 AGGTGTGTCACATGGTGATCC 59.996 52.381 9.31 3.70 44.63 3.36
56 57 2.479566 AGGTGTGTCACATGGTGATC 57.520 50.000 9.31 0.00 44.63 2.92
57 58 2.906389 ACTAGGTGTGTCACATGGTGAT 59.094 45.455 9.31 0.00 44.63 3.06
58 59 2.325484 ACTAGGTGTGTCACATGGTGA 58.675 47.619 9.31 0.00 38.32 4.02
59 60 2.839486 ACTAGGTGTGTCACATGGTG 57.161 50.000 9.31 3.52 38.32 4.17
60 61 3.306780 GCTTACTAGGTGTGTCACATGGT 60.307 47.826 9.31 4.94 41.98 3.55
61 62 3.262420 GCTTACTAGGTGTGTCACATGG 58.738 50.000 9.31 0.00 35.86 3.66
62 63 3.925379 TGCTTACTAGGTGTGTCACATG 58.075 45.455 9.31 3.18 35.86 3.21
63 64 4.617253 TTGCTTACTAGGTGTGTCACAT 57.383 40.909 9.31 0.00 35.86 3.21
64 65 4.562757 GGATTGCTTACTAGGTGTGTCACA 60.563 45.833 0.18 0.18 35.86 3.58
65 66 3.933332 GGATTGCTTACTAGGTGTGTCAC 59.067 47.826 0.00 0.00 0.00 3.67
66 67 3.580895 TGGATTGCTTACTAGGTGTGTCA 59.419 43.478 0.00 0.00 0.00 3.58
67 68 4.202245 TGGATTGCTTACTAGGTGTGTC 57.798 45.455 0.00 0.00 0.00 3.67
68 69 4.634012 TTGGATTGCTTACTAGGTGTGT 57.366 40.909 0.00 0.00 0.00 3.72
69 70 5.003804 AGTTTGGATTGCTTACTAGGTGTG 58.996 41.667 0.00 0.00 0.00 3.82
70 71 5.242795 AGTTTGGATTGCTTACTAGGTGT 57.757 39.130 0.00 0.00 0.00 4.16
71 72 7.865706 AATAGTTTGGATTGCTTACTAGGTG 57.134 36.000 0.00 0.00 0.00 4.00
72 73 9.969001 TTTAATAGTTTGGATTGCTTACTAGGT 57.031 29.630 0.00 0.00 0.00 3.08
122 123 2.610232 GGTTCATGCGCACATCCTTTTT 60.610 45.455 14.90 0.00 32.87 1.94
167 169 4.373527 TGGTCTTTTTGTTCTTCGATCGA 58.626 39.130 15.15 15.15 0.00 3.59
168 170 4.725556 TGGTCTTTTTGTTCTTCGATCG 57.274 40.909 9.36 9.36 0.00 3.69
169 171 8.669243 AGAATATGGTCTTTTTGTTCTTCGATC 58.331 33.333 0.00 0.00 0.00 3.69
170 172 8.567285 AGAATATGGTCTTTTTGTTCTTCGAT 57.433 30.769 0.00 0.00 0.00 3.59
595 597 8.799367 GCTAATTAAGGTTTGGAGGAGTAAAAA 58.201 33.333 0.00 0.00 0.00 1.94
596 598 7.395206 GGCTAATTAAGGTTTGGAGGAGTAAAA 59.605 37.037 0.00 0.00 0.00 1.52
597 599 6.888088 GGCTAATTAAGGTTTGGAGGAGTAAA 59.112 38.462 0.00 0.00 0.00 2.01
598 600 6.216868 AGGCTAATTAAGGTTTGGAGGAGTAA 59.783 38.462 0.00 0.00 0.00 2.24
656 939 2.178235 GCCTCGCGGTTTGGATACC 61.178 63.158 6.13 0.00 34.72 2.73
900 1192 2.698274 TCACATCGGAGCTAGGCAAATA 59.302 45.455 0.00 0.00 0.00 1.40
935 1227 1.133853 AGGTAGGTACGTAGCTGGAGG 60.134 57.143 31.93 0.00 35.39 4.30
936 1228 2.345124 AGGTAGGTACGTAGCTGGAG 57.655 55.000 31.93 0.00 35.39 3.86
937 1229 4.263068 GGTATAGGTAGGTACGTAGCTGGA 60.263 50.000 31.93 14.51 35.39 3.86
938 1230 4.006319 GGTATAGGTAGGTACGTAGCTGG 58.994 52.174 31.93 0.00 35.39 4.85
939 1231 4.006319 GGGTATAGGTAGGTACGTAGCTG 58.994 52.174 31.93 0.00 35.39 4.24
940 1232 3.009584 GGGGTATAGGTAGGTACGTAGCT 59.990 52.174 28.36 28.36 37.80 3.32
941 1233 3.348119 GGGGTATAGGTAGGTACGTAGC 58.652 54.545 16.85 16.85 31.13 3.58
953 1245 2.531942 GGGGCCTGGGGGTATAGG 60.532 72.222 0.84 0.00 37.14 2.57
963 1255 3.694058 CTAGCACTGCTGGGGCCTG 62.694 68.421 14.15 0.00 40.10 4.85
964 1256 3.406200 CTAGCACTGCTGGGGCCT 61.406 66.667 14.15 0.00 40.10 5.19
1287 1579 3.766496 GAGCGCGGAAGAGAGCTCC 62.766 68.421 10.93 1.70 43.64 4.70
1604 1896 3.170717 AGGTTGAGGTATTCGAGGTTCA 58.829 45.455 0.00 0.00 0.00 3.18
1611 1903 0.870307 CGCCGAGGTTGAGGTATTCG 60.870 60.000 0.00 0.00 0.00 3.34
1665 1957 1.078143 GGCGGAGAGGTTGCAGAAT 60.078 57.895 0.00 0.00 0.00 2.40
1807 2099 0.093705 GTCGAGTTTGACAGCGATGC 59.906 55.000 0.00 0.00 38.75 3.91
1989 2281 4.988598 AGGCCGGTGCAGTTCGTG 62.989 66.667 1.90 0.00 40.13 4.35
1992 2284 2.743928 CTCAGGCCGGTGCAGTTC 60.744 66.667 1.90 0.00 40.13 3.01
2028 2320 3.384532 GTGCCGGGGAGGTCGTTA 61.385 66.667 2.18 0.00 43.70 3.18
2244 2536 2.328099 GCCGGAGAGCAGGTTGTTG 61.328 63.158 5.05 0.00 0.00 3.33
2417 2709 2.922503 TCAGCTCCGACAAGCCCA 60.923 61.111 0.00 0.00 43.56 5.36
2653 2945 1.289066 CGTCGAGGACCTGCAAGAA 59.711 57.895 0.00 0.00 34.07 2.52
2710 3002 0.681733 AGCGACGCCATATTCTCCAT 59.318 50.000 17.79 0.00 0.00 3.41
2737 3029 3.671716 AGCCGTTGTAGGAAAAGTTAGG 58.328 45.455 0.00 0.00 0.00 2.69
3666 3961 2.185867 GCGATGTAGCCCACGGAA 59.814 61.111 0.00 0.00 0.00 4.30
3727 4039 0.671796 TGAAGAGAAGAACGTCGGCA 59.328 50.000 0.00 0.00 0.00 5.69
3764 4085 1.160137 ACCACGCAAGCAAGAAGATC 58.840 50.000 0.00 0.00 45.62 2.75
3765 4086 1.267806 CAACCACGCAAGCAAGAAGAT 59.732 47.619 0.00 0.00 45.62 2.40
3766 4087 0.662619 CAACCACGCAAGCAAGAAGA 59.337 50.000 0.00 0.00 45.62 2.87
3767 4088 0.936297 GCAACCACGCAAGCAAGAAG 60.936 55.000 0.00 0.00 45.62 2.85
4208 4535 7.047891 TGAACTATATCTTCCACAACCACATC 58.952 38.462 0.00 0.00 0.00 3.06
4322 4893 7.706179 TGAACTAAAGAAAATGAAAGGCACAAG 59.294 33.333 0.00 0.00 0.00 3.16
4380 7367 4.822350 GGAGTTGCCCTAATTTCTCCATAC 59.178 45.833 0.00 0.00 40.51 2.39
4440 7428 5.120208 CCGTTGTTTCTGTCTGTTTCGATAT 59.880 40.000 0.00 0.00 0.00 1.63
4441 7429 4.446385 CCGTTGTTTCTGTCTGTTTCGATA 59.554 41.667 0.00 0.00 0.00 2.92
4474 7462 2.890961 TGCGTCCGTTTGCGACAA 60.891 55.556 0.00 0.00 41.33 3.18
4570 7558 3.003763 GGGAGGACAAGGGCGAGT 61.004 66.667 0.00 0.00 0.00 4.18
4673 7668 2.431057 GTCTAACCGACTGGATGTGGAT 59.569 50.000 0.00 0.00 39.61 3.41
4679 7674 0.456221 CAGCGTCTAACCGACTGGAT 59.544 55.000 0.00 0.00 40.59 3.41
4811 7813 4.326227 AGGCGAGGGGGTGGTGTA 62.326 66.667 0.00 0.00 0.00 2.90
4882 7930 3.480133 GCGCCCCTCCCTGTACAT 61.480 66.667 0.00 0.00 0.00 2.29
5108 8179 3.812609 TCTCTCTGTTGCAATTTAACGCA 59.187 39.130 0.59 0.00 36.05 5.24
5160 8235 4.308458 TGGGGACGTGCACCGAAG 62.308 66.667 12.15 0.00 46.01 3.79
5180 8255 4.394712 AAGTGGCGCCGGAAGAGG 62.395 66.667 23.90 0.00 0.00 3.69
5187 8262 3.197790 CATCTGGAAGTGGCGCCG 61.198 66.667 23.90 5.27 33.76 6.46


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

AutoCloner maintained by Alex Coulton.