Multiple sequence alignment - TraesCS3B01G172100

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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 TraesCS3B01G172100 chr3B 100.000 4373 0 0 1 4373 173008734 173004362 0.000000e+00 8076.0
1 TraesCS3B01G172100 chr3B 94.928 2563 123 2 840 3402 172170449 172173004 0.000000e+00 4006.0
2 TraesCS3B01G172100 chr3B 94.853 2545 125 1 858 3402 172052107 172054645 0.000000e+00 3969.0
3 TraesCS3B01G172100 chr3B 92.577 2546 170 9 858 3402 146982498 146979971 0.000000e+00 3637.0
4 TraesCS3B01G172100 chr3B 79.420 345 29 19 4039 4373 172055525 172055837 5.730000e-49 206.0
5 TraesCS3B01G172100 chr3B 78.841 345 31 19 4039 4373 172173884 172174196 1.240000e-45 195.0
6 TraesCS3B01G172100 chr3B 86.264 182 16 4 3799 3972 172055351 172055531 5.770000e-44 189.0
7 TraesCS3B01G172100 chr3B 86.264 182 16 4 3799 3972 172173710 172173890 5.770000e-44 189.0
8 TraesCS3B01G172100 chr3B 100.000 28 0 0 69 96 565436513 565436540 8.000000e-03 52.8
9 TraesCS3B01G172100 chr3B 100.000 28 0 0 69 96 565573900 565573927 8.000000e-03 52.8
10 TraesCS3B01G172100 chr3D 95.771 3571 125 12 111 3672 121342763 121339210 0.000000e+00 5734.0
11 TraesCS3B01G172100 chr3D 91.411 2608 200 16 858 3457 121268860 121266269 0.000000e+00 3554.0
12 TraesCS3B01G172100 chr3D 97.920 577 12 0 3797 4373 121339188 121338612 0.000000e+00 1000.0
13 TraesCS3B01G172100 chr3A 91.902 3606 232 29 125 3698 127859700 127856123 0.000000e+00 4987.0
14 TraesCS3B01G172100 chr3A 82.857 595 49 22 3799 4373 127856105 127855544 6.580000e-133 484.0
15 TraesCS3B01G172100 chr3A 84.052 232 23 7 3483 3705 735448351 735448577 1.230000e-50 211.0
16 TraesCS3B01G172100 chr3A 83.621 232 24 7 3483 3705 735483146 735482920 5.730000e-49 206.0
17 TraesCS3B01G172100 chr1D 91.380 3608 230 30 116 3705 465903906 465900362 0.000000e+00 4865.0
18 TraesCS3B01G172100 chr1D 92.834 2484 165 5 934 3414 341029935 341027462 0.000000e+00 3589.0
19 TraesCS3B01G172100 chr1D 90.576 573 27 5 3802 4373 465900349 465899803 0.000000e+00 734.0
20 TraesCS3B01G172100 chr1D 78.750 320 37 16 3389 3705 341027305 341027014 7.470000e-43 185.0
21 TraesCS3B01G172100 chr1D 74.619 197 39 11 3844 4031 386368566 386368760 4.690000e-10 76.8
22 TraesCS3B01G172100 chr1B 90.768 3607 234 38 116 3705 642702225 642698701 0.000000e+00 4724.0
23 TraesCS3B01G172100 chr1B 88.908 577 28 7 3802 4373 642698687 642698142 0.000000e+00 678.0
24 TraesCS3B01G172100 chr4B 95.789 95 2 2 3706 3800 103890061 103889969 7.570000e-33 152.0
25 TraesCS3B01G172100 chr2B 91.892 111 6 3 3690 3800 774106667 774106560 7.570000e-33 152.0
26 TraesCS3B01G172100 chr2B 83.761 117 14 5 3713 3826 558937396 558937282 5.980000e-19 106.0
27 TraesCS3B01G172100 chrUn 95.699 93 3 1 3712 3804 132121145 132121236 9.800000e-32 148.0
28 TraesCS3B01G172100 chr7D 96.629 89 2 1 3712 3800 25410805 25410718 3.520000e-31 147.0
29 TraesCS3B01G172100 chr7D 92.308 104 5 3 3700 3803 514348288 514348188 1.270000e-30 145.0
30 TraesCS3B01G172100 chr5B 93.878 98 4 2 3713 3810 644607967 644608062 3.520000e-31 147.0
31 TraesCS3B01G172100 chr5B 77.564 156 28 7 3849 3999 63613504 63613657 2.170000e-13 87.9
32 TraesCS3B01G172100 chr6A 92.233 103 6 2 3711 3813 182320744 182320844 1.270000e-30 145.0
33 TraesCS3B01G172100 chr4A 90.566 106 8 2 3696 3800 735738971 735739075 5.900000e-29 139.0
34 TraesCS3B01G172100 chr6B 89.908 109 8 3 3711 3819 288999275 288999170 2.120000e-28 137.0
35 TraesCS3B01G172100 chr1A 88.235 85 10 0 3621 3705 440711898 440711814 7.740000e-18 102.0
36 TraesCS3B01G172100 chr5D 75.393 191 41 6 3849 4034 87848261 87848072 2.170000e-13 87.9


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 TraesCS3B01G172100 chr3B 173004362 173008734 4372 True 8076.000000 8076 100.000000 1 4373 1 chr3B.!!$R2 4372
1 TraesCS3B01G172100 chr3B 146979971 146982498 2527 True 3637.000000 3637 92.577000 858 3402 1 chr3B.!!$R1 2544
2 TraesCS3B01G172100 chr3B 172170449 172174196 3747 False 1463.333333 4006 86.677667 840 4373 3 chr3B.!!$F4 3533
3 TraesCS3B01G172100 chr3B 172052107 172055837 3730 False 1454.666667 3969 86.845667 858 4373 3 chr3B.!!$F3 3515
4 TraesCS3B01G172100 chr3D 121266269 121268860 2591 True 3554.000000 3554 91.411000 858 3457 1 chr3D.!!$R1 2599
5 TraesCS3B01G172100 chr3D 121338612 121342763 4151 True 3367.000000 5734 96.845500 111 4373 2 chr3D.!!$R2 4262
6 TraesCS3B01G172100 chr3A 127855544 127859700 4156 True 2735.500000 4987 87.379500 125 4373 2 chr3A.!!$R2 4248
7 TraesCS3B01G172100 chr1D 465899803 465903906 4103 True 2799.500000 4865 90.978000 116 4373 2 chr1D.!!$R2 4257
8 TraesCS3B01G172100 chr1D 341027014 341029935 2921 True 1887.000000 3589 85.792000 934 3705 2 chr1D.!!$R1 2771
9 TraesCS3B01G172100 chr1B 642698142 642702225 4083 True 2701.000000 4724 89.838000 116 4373 2 chr1B.!!$R1 4257

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
669 677 0.324275 GACAGCAGTCTCCTCCTCCT 60.324 60.0 1.35 0.0 41.64 3.69 F
1005 1031 0.107945 GAGAGTTGAAGGCGATGGCT 60.108 55.0 0.00 0.0 41.24 4.75 F
2478 2504 0.323629 AGCACCCGGAGAAATTCGAA 59.676 50.0 0.73 0.0 0.00 3.71 F
2832 2858 0.529337 CTGTCTTCATCATCGGCGCT 60.529 55.0 7.64 0.0 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 2561 1.318576 CCTTCGCCAACAAGGTCTTT 58.681 50.000 0.00 0.0 40.61 2.52 R
2810 2836 1.469767 CGCCGATGATGAAGACAGTCA 60.470 52.381 2.66 0.0 0.00 3.41 R
3334 3369 0.179054 TCATCCTCATCAGCAGCAGC 60.179 55.000 0.00 0.0 42.56 5.25 R
3844 4316 0.416231 TAACTAGACACCCCCAGGCT 59.584 55.000 0.00 0.0 36.11 4.58 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
36 37 8.851960 TCTAAATACGATGTATCAAGTCACAC 57.148 34.615 0.00 0.00 0.00 3.82
37 38 8.683615 TCTAAATACGATGTATCAAGTCACACT 58.316 33.333 0.00 0.00 0.00 3.55
38 39 9.302345 CTAAATACGATGTATCAAGTCACACTT 57.698 33.333 0.00 0.00 39.39 3.16
39 40 8.547967 AAATACGATGTATCAAGTCACACTTT 57.452 30.769 0.00 0.00 36.03 2.66
40 41 9.647797 AAATACGATGTATCAAGTCACACTTTA 57.352 29.630 0.00 0.00 36.03 1.85
41 42 8.858003 ATACGATGTATCAAGTCACACTTTAG 57.142 34.615 0.00 0.00 36.03 1.85
42 43 5.577164 ACGATGTATCAAGTCACACTTTAGC 59.423 40.000 0.00 0.00 36.03 3.09
43 44 5.576774 CGATGTATCAAGTCACACTTTAGCA 59.423 40.000 0.00 0.00 36.03 3.49
44 45 6.256539 CGATGTATCAAGTCACACTTTAGCAT 59.743 38.462 0.00 0.00 36.03 3.79
45 46 7.201556 CGATGTATCAAGTCACACTTTAGCATT 60.202 37.037 0.00 0.00 36.03 3.56
46 47 9.098355 GATGTATCAAGTCACACTTTAGCATTA 57.902 33.333 0.00 0.00 36.03 1.90
47 48 8.479313 TGTATCAAGTCACACTTTAGCATTAG 57.521 34.615 0.00 0.00 36.03 1.73
48 49 8.311109 TGTATCAAGTCACACTTTAGCATTAGA 58.689 33.333 0.00 0.00 36.03 2.10
49 50 9.319143 GTATCAAGTCACACTTTAGCATTAGAT 57.681 33.333 0.00 0.00 36.03 1.98
51 52 8.703604 TCAAGTCACACTTTAGCATTAGATAC 57.296 34.615 0.00 0.00 36.03 2.24
52 53 8.311109 TCAAGTCACACTTTAGCATTAGATACA 58.689 33.333 0.00 0.00 36.03 2.29
53 54 9.102757 CAAGTCACACTTTAGCATTAGATACAT 57.897 33.333 0.00 0.00 36.03 2.29
54 55 8.879342 AGTCACACTTTAGCATTAGATACATC 57.121 34.615 0.00 0.00 0.00 3.06
55 56 7.928706 AGTCACACTTTAGCATTAGATACATCC 59.071 37.037 0.00 0.00 0.00 3.51
56 57 7.710907 GTCACACTTTAGCATTAGATACATCCA 59.289 37.037 0.00 0.00 0.00 3.41
57 58 8.432013 TCACACTTTAGCATTAGATACATCCAT 58.568 33.333 0.00 0.00 0.00 3.41
58 59 9.710900 CACACTTTAGCATTAGATACATCCATA 57.289 33.333 0.00 0.00 0.00 2.74
66 67 8.462811 AGCATTAGATACATCCATAACTAGACG 58.537 37.037 0.00 0.00 0.00 4.18
67 68 8.459635 GCATTAGATACATCCATAACTAGACGA 58.540 37.037 0.00 0.00 0.00 4.20
71 72 8.871629 AGATACATCCATAACTAGACGAATCT 57.128 34.615 0.00 0.00 39.15 2.40
72 73 9.961264 AGATACATCCATAACTAGACGAATCTA 57.039 33.333 0.00 0.00 36.29 1.98
75 76 8.693120 ACATCCATAACTAGACGAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
76 77 8.569641 ACATCCATAACTAGACGAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
77 78 8.568794 CATCCATAACTAGACGAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
78 79 8.515695 TCCATAACTAGACGAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
79 80 8.622157 TCCATAACTAGACGAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
80 81 8.622157 CCATAACTAGACGAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
84 85 9.930693 AACTAGACGAATCTAAGACAAGAATTT 57.069 29.630 0.00 0.00 36.98 1.82
85 86 9.575783 ACTAGACGAATCTAAGACAAGAATTTC 57.424 33.333 0.00 0.00 36.98 2.17
86 87 7.513190 AGACGAATCTAAGACAAGAATTTCG 57.487 36.000 7.64 7.64 40.92 3.46
87 88 7.313646 AGACGAATCTAAGACAAGAATTTCGA 58.686 34.615 13.50 0.00 39.00 3.71
88 89 7.486551 AGACGAATCTAAGACAAGAATTTCGAG 59.513 37.037 13.50 0.00 39.00 4.04
89 90 7.313646 ACGAATCTAAGACAAGAATTTCGAGA 58.686 34.615 13.50 0.00 39.00 4.04
90 91 7.273815 ACGAATCTAAGACAAGAATTTCGAGAC 59.726 37.037 13.50 0.00 39.00 3.36
91 92 7.512272 CGAATCTAAGACAAGAATTTCGAGACG 60.512 40.741 4.43 0.00 39.00 4.18
92 93 5.399858 TCTAAGACAAGAATTTCGAGACGG 58.600 41.667 0.00 0.00 0.00 4.79
93 94 3.936372 AGACAAGAATTTCGAGACGGA 57.064 42.857 0.00 0.00 0.00 4.69
94 95 3.839293 AGACAAGAATTTCGAGACGGAG 58.161 45.455 0.00 0.00 0.00 4.63
95 96 2.924290 GACAAGAATTTCGAGACGGAGG 59.076 50.000 0.00 0.00 0.00 4.30
96 97 2.271800 CAAGAATTTCGAGACGGAGGG 58.728 52.381 0.00 0.00 0.00 4.30
97 98 1.848652 AGAATTTCGAGACGGAGGGA 58.151 50.000 0.00 0.00 0.00 4.20
98 99 1.751924 AGAATTTCGAGACGGAGGGAG 59.248 52.381 0.00 0.00 0.00 4.30
99 100 1.477295 GAATTTCGAGACGGAGGGAGT 59.523 52.381 0.00 0.00 0.00 3.85
100 101 2.431954 ATTTCGAGACGGAGGGAGTA 57.568 50.000 0.00 0.00 0.00 2.59
101 102 2.205022 TTTCGAGACGGAGGGAGTAA 57.795 50.000 0.00 0.00 0.00 2.24
102 103 2.431954 TTCGAGACGGAGGGAGTAAT 57.568 50.000 0.00 0.00 0.00 1.89
103 104 3.565764 TTCGAGACGGAGGGAGTAATA 57.434 47.619 0.00 0.00 0.00 0.98
104 105 2.843701 TCGAGACGGAGGGAGTAATAC 58.156 52.381 0.00 0.00 0.00 1.89
105 106 2.437281 TCGAGACGGAGGGAGTAATACT 59.563 50.000 0.00 0.00 0.00 2.12
106 107 2.807392 CGAGACGGAGGGAGTAATACTC 59.193 54.545 11.79 11.79 44.32 2.59
107 108 3.743584 CGAGACGGAGGGAGTAATACTCA 60.744 52.174 20.57 0.00 46.79 3.41
108 109 4.205587 GAGACGGAGGGAGTAATACTCAA 58.794 47.826 20.57 0.00 46.79 3.02
109 110 3.952967 AGACGGAGGGAGTAATACTCAAC 59.047 47.826 20.57 13.06 46.79 3.18
110 111 2.686915 ACGGAGGGAGTAATACTCAACG 59.313 50.000 20.57 18.57 46.79 4.10
111 112 2.034305 CGGAGGGAGTAATACTCAACGG 59.966 54.545 20.57 11.51 46.79 4.44
112 113 2.223994 GGAGGGAGTAATACTCAACGGC 60.224 54.545 20.57 10.66 46.79 5.68
113 114 2.429610 GAGGGAGTAATACTCAACGGCA 59.570 50.000 20.57 0.00 46.79 5.69
114 115 2.835764 AGGGAGTAATACTCAACGGCAA 59.164 45.455 20.57 0.00 46.79 4.52
118 119 4.270325 GGAGTAATACTCAACGGCAATGTC 59.730 45.833 20.57 0.00 46.79 3.06
143 144 6.808008 AGAAGAATTGAAACATGTCGATGT 57.192 33.333 0.00 0.00 45.24 3.06
151 152 0.374758 ACATGTCGATGTCGCAATGC 59.625 50.000 13.45 0.00 38.53 3.56
172 176 2.477825 CAAGCTGGACGAATCGATCAT 58.522 47.619 10.55 0.00 0.00 2.45
178 182 2.687935 TGGACGAATCGATCATGTCTGA 59.312 45.455 10.55 7.96 35.41 3.27
186 190 2.101415 TCGATCATGTCTGACACCCATC 59.899 50.000 13.50 12.74 33.22 3.51
267 274 2.179517 CTCCTTCTCGCGCGTCTT 59.820 61.111 30.98 0.00 0.00 3.01
626 634 4.057428 GACTGAGCGGCTCCGTGT 62.057 66.667 28.02 21.73 42.09 4.49
646 654 3.440415 TCCGTCTCGCATCGCACT 61.440 61.111 0.00 0.00 0.00 4.40
665 673 1.133407 CTAACGACAGCAGTCTCCTCC 59.867 57.143 7.71 0.00 42.73 4.30
666 674 0.540830 AACGACAGCAGTCTCCTCCT 60.541 55.000 7.71 0.00 42.73 3.69
667 675 0.963355 ACGACAGCAGTCTCCTCCTC 60.963 60.000 7.71 0.00 42.73 3.71
668 676 1.662438 CGACAGCAGTCTCCTCCTCC 61.662 65.000 7.71 0.00 42.73 4.30
669 677 0.324275 GACAGCAGTCTCCTCCTCCT 60.324 60.000 1.35 0.00 41.64 3.69
670 678 0.324275 ACAGCAGTCTCCTCCTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
711 719 3.566261 CGCAGCCAGGTACAACTG 58.434 61.111 0.00 0.00 38.21 3.16
756 764 1.883084 CCGATCGTGCCAAGGTAGC 60.883 63.158 15.09 0.00 0.00 3.58
778 786 5.053811 GCAGGAAGATAGTAGGAAAAGAGC 58.946 45.833 0.00 0.00 0.00 4.09
1005 1031 0.107945 GAGAGTTGAAGGCGATGGCT 60.108 55.000 0.00 0.00 41.24 4.75
1009 1035 0.744414 GTTGAAGGCGATGGCTAGCA 60.744 55.000 18.24 2.97 37.50 3.49
1114 1140 1.372087 GGCCACAATGGAGAAGCTCG 61.372 60.000 0.00 0.00 40.96 5.03
1156 1182 2.518112 TGCTCAAGGGCAAACGCA 60.518 55.556 0.00 0.00 39.43 5.24
1926 1952 1.179814 AGAAGACTCACGGCGAGGTT 61.180 55.000 16.62 0.00 46.98 3.50
2355 2381 4.947147 GGCACCAACCCGTCTGCA 62.947 66.667 0.00 0.00 0.00 4.41
2478 2504 0.323629 AGCACCCGGAGAAATTCGAA 59.676 50.000 0.73 0.00 0.00 3.71
2832 2858 0.529337 CTGTCTTCATCATCGGCGCT 60.529 55.000 7.64 0.00 0.00 5.92
3197 3232 2.805546 GATGAGGTACGCGAGGCA 59.194 61.111 15.93 3.52 0.00 4.75
3363 3398 4.501229 GCTGATGAGGATGAAGACGATCTT 60.501 45.833 0.00 0.00 39.87 2.40
3394 3429 7.390718 AGTGATCCAGTAACCATTGTTAGAAAC 59.609 37.037 0.00 0.00 37.62 2.78
3559 4015 8.968242 TCGTGAATTAGAATCTCATTATTGTCG 58.032 33.333 0.00 0.00 0.00 4.35
3719 4191 9.982651 TGATATGCTTGATTTACTTAGTACTCC 57.017 33.333 0.00 0.00 0.00 3.85
3720 4192 9.425577 GATATGCTTGATTTACTTAGTACTCCC 57.574 37.037 0.00 0.00 0.00 4.30
3721 4193 6.869206 TGCTTGATTTACTTAGTACTCCCT 57.131 37.500 0.00 0.00 0.00 4.20
3722 4194 6.875076 TGCTTGATTTACTTAGTACTCCCTC 58.125 40.000 0.00 0.00 0.00 4.30
3723 4195 6.127140 TGCTTGATTTACTTAGTACTCCCTCC 60.127 42.308 0.00 0.00 0.00 4.30
3724 4196 6.461110 TTGATTTACTTAGTACTCCCTCCG 57.539 41.667 0.00 0.00 0.00 4.63
3725 4197 5.513233 TGATTTACTTAGTACTCCCTCCGT 58.487 41.667 0.00 0.00 0.00 4.69
3726 4198 6.662755 TGATTTACTTAGTACTCCCTCCGTA 58.337 40.000 0.00 0.00 0.00 4.02
3727 4199 7.118723 TGATTTACTTAGTACTCCCTCCGTAA 58.881 38.462 0.00 0.00 0.00 3.18
3728 4200 7.615365 TGATTTACTTAGTACTCCCTCCGTAAA 59.385 37.037 0.00 6.28 32.36 2.01
3729 4201 6.759497 TTACTTAGTACTCCCTCCGTAAAC 57.241 41.667 0.00 0.00 0.00 2.01
3730 4202 4.928263 ACTTAGTACTCCCTCCGTAAACT 58.072 43.478 0.00 0.00 0.00 2.66
3731 4203 6.067217 ACTTAGTACTCCCTCCGTAAACTA 57.933 41.667 0.00 0.00 0.00 2.24
3732 4204 6.485171 ACTTAGTACTCCCTCCGTAAACTAA 58.515 40.000 0.00 0.00 0.00 2.24
3733 4205 7.122048 ACTTAGTACTCCCTCCGTAAACTAAT 58.878 38.462 0.00 0.00 0.00 1.73
3734 4206 8.275040 ACTTAGTACTCCCTCCGTAAACTAATA 58.725 37.037 0.00 0.00 0.00 0.98
3735 4207 9.294614 CTTAGTACTCCCTCCGTAAACTAATAT 57.705 37.037 0.00 0.00 0.00 1.28
3738 4210 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
3739 4211 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3740 4212 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3741 4213 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3742 4214 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3743 4215 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3744 4216 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3745 4217 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3746 4218 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3747 4219 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3748 4220 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3762 4234 8.680039 AGAGCGTTTAGATCACTACTTATAGT 57.320 34.615 0.00 0.00 42.74 2.12
3763 4235 9.775854 AGAGCGTTTAGATCACTACTTATAGTA 57.224 33.333 0.00 0.00 39.80 1.82
3795 4267 8.617290 ATGCTTTTATATTAGTTTACGGAGGG 57.383 34.615 0.00 0.00 0.00 4.30
3796 4268 7.794041 TGCTTTTATATTAGTTTACGGAGGGA 58.206 34.615 0.00 0.00 0.00 4.20
3797 4269 7.929785 TGCTTTTATATTAGTTTACGGAGGGAG 59.070 37.037 0.00 0.00 0.00 4.30
3810 4282 4.805744 ACGGAGGGAGTAATTGAGTAGAT 58.194 43.478 0.00 0.00 0.00 1.98
3844 4316 4.583489 ACAGACGAGTCAAGGAAAAGAGTA 59.417 41.667 5.99 0.00 0.00 2.59
4077 4559 3.259625 GCCCTTGCAAAAACCTATTACCA 59.740 43.478 0.00 0.00 37.47 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.464714 GTGTGACTTGATACATCGTATTTAGAT 57.535 33.333 0.00 0.00 0.00 1.98
11 12 8.683615 AGTGTGACTTGATACATCGTATTTAGA 58.316 33.333 0.00 0.00 0.00 2.10
12 13 8.858003 AGTGTGACTTGATACATCGTATTTAG 57.142 34.615 0.00 0.00 0.00 1.85
13 14 9.647797 AAAGTGTGACTTGATACATCGTATTTA 57.352 29.630 0.00 0.00 38.66 1.40
14 15 8.547967 AAAGTGTGACTTGATACATCGTATTT 57.452 30.769 0.00 0.00 38.66 1.40
15 16 9.302345 CTAAAGTGTGACTTGATACATCGTATT 57.698 33.333 0.00 0.00 38.66 1.89
16 17 7.435488 GCTAAAGTGTGACTTGATACATCGTAT 59.565 37.037 0.00 0.00 38.66 3.06
17 18 6.750501 GCTAAAGTGTGACTTGATACATCGTA 59.249 38.462 0.00 0.00 38.66 3.43
18 19 5.577164 GCTAAAGTGTGACTTGATACATCGT 59.423 40.000 0.00 0.00 38.66 3.73
19 20 5.576774 TGCTAAAGTGTGACTTGATACATCG 59.423 40.000 0.00 0.00 38.66 3.84
20 21 6.968131 TGCTAAAGTGTGACTTGATACATC 57.032 37.500 0.00 0.00 38.66 3.06
21 22 7.928307 AATGCTAAAGTGTGACTTGATACAT 57.072 32.000 0.00 0.00 38.66 2.29
22 23 8.311109 TCTAATGCTAAAGTGTGACTTGATACA 58.689 33.333 0.00 0.00 38.66 2.29
23 24 8.703604 TCTAATGCTAAAGTGTGACTTGATAC 57.296 34.615 0.00 0.00 38.66 2.24
25 26 9.319143 GTATCTAATGCTAAAGTGTGACTTGAT 57.681 33.333 0.00 0.00 38.66 2.57
26 27 8.311109 TGTATCTAATGCTAAAGTGTGACTTGA 58.689 33.333 0.00 0.00 38.66 3.02
27 28 8.479313 TGTATCTAATGCTAAAGTGTGACTTG 57.521 34.615 0.00 0.00 38.66 3.16
28 29 9.319143 GATGTATCTAATGCTAAAGTGTGACTT 57.681 33.333 0.00 0.00 40.80 3.01
29 30 7.928706 GGATGTATCTAATGCTAAAGTGTGACT 59.071 37.037 0.00 0.00 0.00 3.41
30 31 7.710907 TGGATGTATCTAATGCTAAAGTGTGAC 59.289 37.037 0.00 0.00 0.00 3.67
31 32 7.791029 TGGATGTATCTAATGCTAAAGTGTGA 58.209 34.615 0.00 0.00 0.00 3.58
32 33 8.613060 ATGGATGTATCTAATGCTAAAGTGTG 57.387 34.615 0.00 0.00 0.00 3.82
40 41 8.462811 CGTCTAGTTATGGATGTATCTAATGCT 58.537 37.037 0.00 0.00 0.00 3.79
41 42 8.459635 TCGTCTAGTTATGGATGTATCTAATGC 58.540 37.037 0.00 0.00 0.00 3.56
45 46 9.961264 AGATTCGTCTAGTTATGGATGTATCTA 57.039 33.333 0.00 0.00 37.89 1.98
46 47 8.871629 AGATTCGTCTAGTTATGGATGTATCT 57.128 34.615 0.00 0.00 36.14 1.98
49 50 9.788889 TCTTAGATTCGTCTAGTTATGGATGTA 57.211 33.333 0.00 0.00 0.00 2.29
50 51 8.569641 GTCTTAGATTCGTCTAGTTATGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
51 52 8.568794 TGTCTTAGATTCGTCTAGTTATGGATG 58.431 37.037 0.00 0.00 0.00 3.51
52 53 8.693120 TGTCTTAGATTCGTCTAGTTATGGAT 57.307 34.615 0.00 0.00 0.00 3.41
53 54 8.515695 TTGTCTTAGATTCGTCTAGTTATGGA 57.484 34.615 0.00 0.00 0.00 3.41
54 55 8.622157 TCTTGTCTTAGATTCGTCTAGTTATGG 58.378 37.037 0.00 0.00 0.00 2.74
58 59 9.930693 AAATTCTTGTCTTAGATTCGTCTAGTT 57.069 29.630 0.00 0.00 0.00 2.24
59 60 9.575783 GAAATTCTTGTCTTAGATTCGTCTAGT 57.424 33.333 0.00 0.00 0.00 2.57
60 61 8.738554 CGAAATTCTTGTCTTAGATTCGTCTAG 58.261 37.037 4.38 0.00 34.42 2.43
61 62 8.456471 TCGAAATTCTTGTCTTAGATTCGTCTA 58.544 33.333 10.33 0.00 37.65 2.59
62 63 7.313646 TCGAAATTCTTGTCTTAGATTCGTCT 58.686 34.615 10.33 0.00 37.65 4.18
63 64 7.485277 TCTCGAAATTCTTGTCTTAGATTCGTC 59.515 37.037 10.33 0.00 37.65 4.20
64 65 7.273815 GTCTCGAAATTCTTGTCTTAGATTCGT 59.726 37.037 10.33 0.00 37.65 3.85
65 66 7.512272 CGTCTCGAAATTCTTGTCTTAGATTCG 60.512 40.741 5.78 5.78 37.71 3.34
66 67 7.253817 CCGTCTCGAAATTCTTGTCTTAGATTC 60.254 40.741 0.00 0.00 0.00 2.52
67 68 6.531948 CCGTCTCGAAATTCTTGTCTTAGATT 59.468 38.462 0.00 0.00 0.00 2.40
68 69 6.037098 CCGTCTCGAAATTCTTGTCTTAGAT 58.963 40.000 0.00 0.00 0.00 1.98
69 70 5.182570 TCCGTCTCGAAATTCTTGTCTTAGA 59.817 40.000 0.00 0.00 0.00 2.10
70 71 5.399858 TCCGTCTCGAAATTCTTGTCTTAG 58.600 41.667 0.00 0.00 0.00 2.18
71 72 5.381174 TCCGTCTCGAAATTCTTGTCTTA 57.619 39.130 0.00 0.00 0.00 2.10
72 73 4.238514 CTCCGTCTCGAAATTCTTGTCTT 58.761 43.478 0.00 0.00 0.00 3.01
73 74 3.367498 CCTCCGTCTCGAAATTCTTGTCT 60.367 47.826 0.00 0.00 0.00 3.41
74 75 2.924290 CCTCCGTCTCGAAATTCTTGTC 59.076 50.000 0.00 0.00 0.00 3.18
75 76 2.353803 CCCTCCGTCTCGAAATTCTTGT 60.354 50.000 0.00 0.00 0.00 3.16
76 77 2.094182 TCCCTCCGTCTCGAAATTCTTG 60.094 50.000 0.00 0.00 0.00 3.02
77 78 2.166664 CTCCCTCCGTCTCGAAATTCTT 59.833 50.000 0.00 0.00 0.00 2.52
78 79 1.751924 CTCCCTCCGTCTCGAAATTCT 59.248 52.381 0.00 0.00 0.00 2.40
79 80 1.477295 ACTCCCTCCGTCTCGAAATTC 59.523 52.381 0.00 0.00 0.00 2.17
80 81 1.558233 ACTCCCTCCGTCTCGAAATT 58.442 50.000 0.00 0.00 0.00 1.82
81 82 2.431954 TACTCCCTCCGTCTCGAAAT 57.568 50.000 0.00 0.00 0.00 2.17
82 83 2.205022 TTACTCCCTCCGTCTCGAAA 57.795 50.000 0.00 0.00 0.00 3.46
83 84 2.431954 ATTACTCCCTCCGTCTCGAA 57.568 50.000 0.00 0.00 0.00 3.71
84 85 2.437281 AGTATTACTCCCTCCGTCTCGA 59.563 50.000 0.00 0.00 0.00 4.04
85 86 2.807392 GAGTATTACTCCCTCCGTCTCG 59.193 54.545 12.06 0.00 39.28 4.04
86 87 3.818180 TGAGTATTACTCCCTCCGTCTC 58.182 50.000 18.81 0.00 44.44 3.36
87 88 3.947612 TGAGTATTACTCCCTCCGTCT 57.052 47.619 18.81 0.00 44.44 4.18
88 89 3.243002 CGTTGAGTATTACTCCCTCCGTC 60.243 52.174 18.81 3.74 44.44 4.79
89 90 2.686915 CGTTGAGTATTACTCCCTCCGT 59.313 50.000 18.81 0.00 44.44 4.69
90 91 2.034305 CCGTTGAGTATTACTCCCTCCG 59.966 54.545 18.81 14.55 44.44 4.63
91 92 2.223994 GCCGTTGAGTATTACTCCCTCC 60.224 54.545 18.81 5.55 44.44 4.30
92 93 2.429610 TGCCGTTGAGTATTACTCCCTC 59.570 50.000 18.81 9.60 44.44 4.30
93 94 2.463752 TGCCGTTGAGTATTACTCCCT 58.536 47.619 18.81 0.00 44.44 4.20
94 95 2.973694 TGCCGTTGAGTATTACTCCC 57.026 50.000 18.81 9.98 44.44 4.30
95 96 4.189231 ACATTGCCGTTGAGTATTACTCC 58.811 43.478 18.81 5.86 44.44 3.85
96 97 4.868171 TGACATTGCCGTTGAGTATTACTC 59.132 41.667 15.57 15.57 45.26 2.59
97 98 4.827692 TGACATTGCCGTTGAGTATTACT 58.172 39.130 0.00 0.00 0.00 2.24
98 99 5.350365 TCTTGACATTGCCGTTGAGTATTAC 59.650 40.000 0.00 0.00 0.00 1.89
99 100 5.483811 TCTTGACATTGCCGTTGAGTATTA 58.516 37.500 0.00 0.00 0.00 0.98
100 101 4.323417 TCTTGACATTGCCGTTGAGTATT 58.677 39.130 0.00 0.00 0.00 1.89
101 102 3.937814 TCTTGACATTGCCGTTGAGTAT 58.062 40.909 0.00 0.00 0.00 2.12
102 103 3.394674 TCTTGACATTGCCGTTGAGTA 57.605 42.857 0.00 0.00 0.00 2.59
103 104 2.254546 TCTTGACATTGCCGTTGAGT 57.745 45.000 0.00 0.00 0.00 3.41
104 105 2.807967 TCTTCTTGACATTGCCGTTGAG 59.192 45.455 0.00 0.00 0.00 3.02
105 106 2.844946 TCTTCTTGACATTGCCGTTGA 58.155 42.857 0.00 0.00 0.00 3.18
106 107 3.624326 TTCTTCTTGACATTGCCGTTG 57.376 42.857 0.00 0.00 0.00 4.10
107 108 4.278170 TCAATTCTTCTTGACATTGCCGTT 59.722 37.500 0.00 0.00 30.34 4.44
108 109 3.820467 TCAATTCTTCTTGACATTGCCGT 59.180 39.130 0.00 0.00 30.34 5.68
109 110 4.424061 TCAATTCTTCTTGACATTGCCG 57.576 40.909 0.00 0.00 30.34 5.69
110 111 5.984926 TGTTTCAATTCTTCTTGACATTGCC 59.015 36.000 0.00 0.00 34.96 4.52
111 112 7.170320 ACATGTTTCAATTCTTCTTGACATTGC 59.830 33.333 0.00 0.00 34.96 3.56
112 113 8.583810 ACATGTTTCAATTCTTCTTGACATTG 57.416 30.769 0.00 0.00 34.96 2.82
113 114 7.592533 CGACATGTTTCAATTCTTCTTGACATT 59.407 33.333 0.00 0.00 34.96 2.71
114 115 7.041167 TCGACATGTTTCAATTCTTCTTGACAT 60.041 33.333 0.00 0.00 34.96 3.06
118 119 7.080099 ACATCGACATGTTTCAATTCTTCTTG 58.920 34.615 0.00 0.00 40.66 3.02
143 144 2.033911 TCCAGCTTGGCATTGCGA 59.966 55.556 1.91 0.00 37.47 5.10
151 152 1.212616 GATCGATTCGTCCAGCTTGG 58.787 55.000 5.89 0.00 39.43 3.61
172 176 1.591703 GAGCGATGGGTGTCAGACA 59.408 57.895 0.00 0.00 0.00 3.41
178 182 2.261671 GTGACGAGCGATGGGTGT 59.738 61.111 0.00 0.00 0.00 4.16
186 190 0.926174 GAGATGCTACGTGACGAGCG 60.926 60.000 13.70 0.00 41.83 5.03
380 388 1.517832 CGGAAGTGCGGGAGAAGAT 59.482 57.895 0.00 0.00 0.00 2.40
463 471 2.036098 CTGATGCACCAGGCCCAA 59.964 61.111 0.00 0.00 43.89 4.12
626 634 2.506217 GCGATGCGAGACGGACAA 60.506 61.111 0.00 0.00 0.00 3.18
646 654 1.174783 GGAGGAGACTGCTGTCGTTA 58.825 55.000 16.87 0.00 46.74 3.18
711 719 1.000618 AGAACCCTTCGAACTCGGAAC 59.999 52.381 3.58 0.71 40.29 3.62
756 764 6.478512 AGCTCTTTTCCTACTATCTTCCTG 57.521 41.667 0.00 0.00 0.00 3.86
778 786 0.307146 GTGCCGTACTAGGACGCTAG 59.693 60.000 22.52 9.87 41.56 3.42
1114 1140 0.250901 ATGTCGCCCTGGAATATGGC 60.251 55.000 0.00 0.00 41.85 4.40
1156 1182 2.591715 GCAGACCGTGTTGTGGCT 60.592 61.111 0.00 0.00 0.00 4.75
1435 1461 4.862092 CTCGACGCTCCGCATGCT 62.862 66.667 17.13 0.00 0.00 3.79
1682 1708 2.210711 CCGTAGAGGAGGATGCCCC 61.211 68.421 0.00 0.00 45.00 5.80
1926 1952 2.775856 GGAGACGATGCGCCTCTCA 61.776 63.158 17.92 0.00 36.64 3.27
2355 2381 2.156917 TCGACAATGGTCTCACGTAGT 58.843 47.619 0.00 0.00 41.94 2.73
2535 2561 1.318576 CCTTCGCCAACAAGGTCTTT 58.681 50.000 0.00 0.00 40.61 2.52
2810 2836 1.469767 CGCCGATGATGAAGACAGTCA 60.470 52.381 2.66 0.00 0.00 3.41
2832 2858 4.348461 TCAATTATGTCCGGCCTATTGGTA 59.652 41.667 0.00 0.00 35.27 3.25
3197 3232 2.202716 CAGCATCGCTCACGCTCT 60.203 61.111 0.00 0.00 36.40 4.09
3334 3369 0.179054 TCATCCTCATCAGCAGCAGC 60.179 55.000 0.00 0.00 42.56 5.25
3335 3370 2.158943 TCTTCATCCTCATCAGCAGCAG 60.159 50.000 0.00 0.00 0.00 4.24
3336 3371 1.835531 TCTTCATCCTCATCAGCAGCA 59.164 47.619 0.00 0.00 0.00 4.41
3337 3372 2.211806 GTCTTCATCCTCATCAGCAGC 58.788 52.381 0.00 0.00 0.00 5.25
3338 3373 2.100418 TCGTCTTCATCCTCATCAGCAG 59.900 50.000 0.00 0.00 0.00 4.24
3339 3374 2.102578 TCGTCTTCATCCTCATCAGCA 58.897 47.619 0.00 0.00 0.00 4.41
3363 3398 6.539173 ACAATGGTTACTGGATCACTTGTAA 58.461 36.000 0.00 0.00 0.00 2.41
3559 4015 0.591236 TCACGCACGCTTTCTTTTGC 60.591 50.000 0.00 0.00 0.00 3.68
3680 4149 6.175471 TCAAGCATATCAGTGTCTGACAAAT 58.825 36.000 12.81 9.09 43.63 2.32
3698 4170 6.127140 GGAGGGAGTACTAAGTAAATCAAGCA 60.127 42.308 0.00 0.00 0.00 3.91
3715 4187 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3716 4188 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3717 4189 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3718 4190 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3719 4191 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3720 4192 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3721 4193 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3722 4194 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3736 4208 9.122779 ACTATAAGTAGTGATCTAAACGCTCTT 57.877 33.333 0.00 0.00 39.66 2.85
3737 4209 8.680039 ACTATAAGTAGTGATCTAAACGCTCT 57.320 34.615 0.00 0.00 39.66 4.09
3769 4241 9.063615 CCCTCCGTAAACTAATATAAAAGCATT 57.936 33.333 0.00 0.00 0.00 3.56
3770 4242 8.434392 TCCCTCCGTAAACTAATATAAAAGCAT 58.566 33.333 0.00 0.00 0.00 3.79
3771 4243 7.794041 TCCCTCCGTAAACTAATATAAAAGCA 58.206 34.615 0.00 0.00 0.00 3.91
3772 4244 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
3778 4250 9.151177 TCAATTACTCCCTCCGTAAACTAATAT 57.849 33.333 0.00 0.00 31.36 1.28
3779 4251 8.537728 TCAATTACTCCCTCCGTAAACTAATA 57.462 34.615 0.00 0.00 31.36 0.98
3780 4252 7.125356 ACTCAATTACTCCCTCCGTAAACTAAT 59.875 37.037 0.00 0.00 31.36 1.73
3781 4253 6.438425 ACTCAATTACTCCCTCCGTAAACTAA 59.562 38.462 0.00 0.00 31.36 2.24
3782 4254 5.954150 ACTCAATTACTCCCTCCGTAAACTA 59.046 40.000 0.00 0.00 31.36 2.24
3783 4255 4.776308 ACTCAATTACTCCCTCCGTAAACT 59.224 41.667 0.00 0.00 31.36 2.66
3784 4256 5.082251 ACTCAATTACTCCCTCCGTAAAC 57.918 43.478 0.00 0.00 31.36 2.01
3785 4257 6.189859 TCTACTCAATTACTCCCTCCGTAAA 58.810 40.000 0.00 0.00 31.36 2.01
3786 4258 5.759059 TCTACTCAATTACTCCCTCCGTAA 58.241 41.667 0.00 0.00 0.00 3.18
3787 4259 5.378230 TCTACTCAATTACTCCCTCCGTA 57.622 43.478 0.00 0.00 0.00 4.02
3788 4260 4.246712 TCTACTCAATTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
3789 4261 4.559704 GCATCTACTCAATTACTCCCTCCG 60.560 50.000 0.00 0.00 0.00 4.63
3790 4262 4.345257 TGCATCTACTCAATTACTCCCTCC 59.655 45.833 0.00 0.00 0.00 4.30
3791 4263 5.069781 ACTGCATCTACTCAATTACTCCCTC 59.930 44.000 0.00 0.00 0.00 4.30
3792 4264 4.965532 ACTGCATCTACTCAATTACTCCCT 59.034 41.667 0.00 0.00 0.00 4.20
3793 4265 5.069781 AGACTGCATCTACTCAATTACTCCC 59.930 44.000 0.00 0.00 35.15 4.30
3794 4266 6.155475 AGACTGCATCTACTCAATTACTCC 57.845 41.667 0.00 0.00 35.15 3.85
3795 4267 8.160521 TCTAGACTGCATCTACTCAATTACTC 57.839 38.462 0.00 0.00 39.04 2.59
3796 4268 8.410141 GTTCTAGACTGCATCTACTCAATTACT 58.590 37.037 0.00 0.00 39.04 2.24
3797 4269 8.191446 TGTTCTAGACTGCATCTACTCAATTAC 58.809 37.037 0.00 0.00 39.04 1.89
3844 4316 0.416231 TAACTAGACACCCCCAGGCT 59.584 55.000 0.00 0.00 36.11 4.58
4077 4559 2.727123 TGTTGTTGTCTGTGTGGGAT 57.273 45.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.