Multiple sequence alignment - TraesCS3A01G116500

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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 TraesCS3A01G116500 chr3A 100.000 3501 0 0 1 3501 85269669 85273169 0.000000e+00 6466
1 TraesCS3A01G116500 chr3A 93.008 2274 78 25 922 3134 85371391 85373644 0.000000e+00 3243
2 TraesCS3A01G116500 chr3A 92.850 1007 69 3 859 1865 85464148 85465151 0.000000e+00 1458
3 TraesCS3A01G116500 chr3A 92.552 1007 72 2 859 1865 85533411 85534414 0.000000e+00 1441
4 TraesCS3A01G116500 chr3A 90.752 984 62 10 883 1841 84649165 84650144 0.000000e+00 1286
5 TraesCS3A01G116500 chr3A 86.598 970 48 27 2387 3296 85544390 85545337 0.000000e+00 996
6 TraesCS3A01G116500 chr3A 86.462 975 45 31 2387 3296 85475520 85476472 0.000000e+00 989
7 TraesCS3A01G116500 chr3A 94.080 625 35 1 131 755 159742824 159743446 0.000000e+00 948
8 TraesCS3A01G116500 chr3A 91.039 558 44 3 1858 2412 84650233 84650787 0.000000e+00 749
9 TraesCS3A01G116500 chr3A 93.443 427 28 0 1860 2286 85475095 85475521 4.930000e-178 634
10 TraesCS3A01G116500 chr3A 91.803 427 35 0 1860 2286 85543965 85544391 2.330000e-166 595
11 TraesCS3A01G116500 chr3A 94.569 313 11 4 3192 3501 85387864 85388173 2.440000e-131 479
12 TraesCS3A01G116500 chr3A 86.230 305 21 12 2401 2697 84650814 84651105 9.440000e-81 311
13 TraesCS3A01G116500 chr3A 92.920 113 5 2 2848 2960 84651308 84651417 1.010000e-35 161
14 TraesCS3A01G116500 chr3A 82.812 128 16 5 760 883 84648974 84649099 3.690000e-20 110
15 TraesCS3A01G116500 chr3D 90.033 1535 81 21 2028 3501 72649817 72651340 0.000000e+00 1921
16 TraesCS3A01G116500 chr3D 96.203 1106 36 3 754 1854 72648559 72649663 0.000000e+00 1805
17 TraesCS3A01G116500 chr3D 90.131 993 63 14 883 1841 72251871 72252862 0.000000e+00 1258
18 TraesCS3A01G116500 chr3D 90.018 561 44 5 1858 2412 72252951 72253505 0.000000e+00 715
19 TraesCS3A01G116500 chr3D 87.213 305 18 13 2401 2697 72253532 72253823 9.370000e-86 327
20 TraesCS3A01G116500 chr3D 96.639 119 4 0 1858 1976 72649701 72649819 7.670000e-47 198
21 TraesCS3A01G116500 chr3D 92.920 113 5 2 2848 2960 72254031 72254140 1.010000e-35 161
22 TraesCS3A01G116500 chr3D 83.333 126 18 3 760 883 72251681 72251805 2.860000e-21 113
23 TraesCS3A01G116500 chr3B 88.118 1456 85 22 1834 3224 118252135 118253567 0.000000e+00 1650
24 TraesCS3A01G116500 chr3B 89.920 1002 58 13 883 1841 118136481 118137482 0.000000e+00 1251
25 TraesCS3A01G116500 chr3B 96.006 626 21 4 883 1505 118251165 118251789 0.000000e+00 1014
26 TraesCS3A01G116500 chr3B 90.018 561 47 3 1858 2412 118137571 118138128 0.000000e+00 717
27 TraesCS3A01G116500 chr3B 97.583 331 7 1 1524 1854 118251778 118252107 1.820000e-157 566
28 TraesCS3A01G116500 chr3B 90.508 295 23 4 3209 3501 118253589 118253880 5.480000e-103 385
29 TraesCS3A01G116500 chr3B 86.306 314 23 10 2401 2697 118138155 118138465 1.210000e-84 324
30 TraesCS3A01G116500 chr2A 96.160 625 23 1 131 755 65684952 65684329 0.000000e+00 1020
31 TraesCS3A01G116500 chr2A 95.447 615 28 0 131 745 164996833 164997447 0.000000e+00 981
32 TraesCS3A01G116500 chr6A 96.006 626 25 0 131 756 21077351 21076726 0.000000e+00 1018
33 TraesCS3A01G116500 chr4A 95.847 626 26 0 130 755 622279635 622280260 0.000000e+00 1013
34 TraesCS3A01G116500 chr4A 95.360 625 27 2 131 755 595871204 595870582 0.000000e+00 992
35 TraesCS3A01G116500 chr4A 94.737 627 33 0 129 755 118627465 118626839 0.000000e+00 976
36 TraesCS3A01G116500 chr6B 93.185 631 42 1 128 757 664720873 664720243 0.000000e+00 926
37 TraesCS3A01G116500 chrUn 93.280 625 42 0 131 755 277522821 277522197 0.000000e+00 922


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 TraesCS3A01G116500 chr3A 85269669 85273169 3500 False 6466.00 6466 100.000000 1 3501 1 chr3A.!!$F1 3500
1 TraesCS3A01G116500 chr3A 85371391 85373644 2253 False 3243.00 3243 93.008000 922 3134 1 chr3A.!!$F2 2212
2 TraesCS3A01G116500 chr3A 85464148 85465151 1003 False 1458.00 1458 92.850000 859 1865 1 chr3A.!!$F4 1006
3 TraesCS3A01G116500 chr3A 85533411 85534414 1003 False 1441.00 1441 92.552000 859 1865 1 chr3A.!!$F5 1006
4 TraesCS3A01G116500 chr3A 159742824 159743446 622 False 948.00 948 94.080000 131 755 1 chr3A.!!$F6 624
5 TraesCS3A01G116500 chr3A 85475095 85476472 1377 False 811.50 989 89.952500 1860 3296 2 chr3A.!!$F8 1436
6 TraesCS3A01G116500 chr3A 85543965 85545337 1372 False 795.50 996 89.200500 1860 3296 2 chr3A.!!$F9 1436
7 TraesCS3A01G116500 chr3A 84648974 84651417 2443 False 523.40 1286 88.750600 760 2960 5 chr3A.!!$F7 2200
8 TraesCS3A01G116500 chr3D 72648559 72651340 2781 False 1308.00 1921 94.291667 754 3501 3 chr3D.!!$F2 2747
9 TraesCS3A01G116500 chr3D 72251681 72254140 2459 False 514.80 1258 88.723000 760 2960 5 chr3D.!!$F1 2200
10 TraesCS3A01G116500 chr3B 118251165 118253880 2715 False 903.75 1650 93.053750 883 3501 4 chr3B.!!$F2 2618
11 TraesCS3A01G116500 chr3B 118136481 118138465 1984 False 764.00 1251 88.748000 883 2697 3 chr3B.!!$F1 1814
12 TraesCS3A01G116500 chr2A 65684329 65684952 623 True 1020.00 1020 96.160000 131 755 1 chr2A.!!$R1 624
13 TraesCS3A01G116500 chr2A 164996833 164997447 614 False 981.00 981 95.447000 131 745 1 chr2A.!!$F1 614
14 TraesCS3A01G116500 chr6A 21076726 21077351 625 True 1018.00 1018 96.006000 131 756 1 chr6A.!!$R1 625
15 TraesCS3A01G116500 chr4A 622279635 622280260 625 False 1013.00 1013 95.847000 130 755 1 chr4A.!!$F1 625
16 TraesCS3A01G116500 chr4A 595870582 595871204 622 True 992.00 992 95.360000 131 755 1 chr4A.!!$R2 624
17 TraesCS3A01G116500 chr4A 118626839 118627465 626 True 976.00 976 94.737000 129 755 1 chr4A.!!$R1 626
18 TraesCS3A01G116500 chr6B 664720243 664720873 630 True 926.00 926 93.185000 128 757 1 chr6B.!!$R1 629
19 TraesCS3A01G116500 chrUn 277522197 277522821 624 True 922.00 922 93.280000 131 755 1 chrUn.!!$R1 624

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
88 89 0.103937 CTGGATTCTCCCTCTCGTGC 59.896 60.0 0.0 0.00 35.03 5.34 F
109 110 0.240945 CCAGGCGAAATGTGTGTTCC 59.759 55.0 0.0 0.00 0.00 3.62 F
110 111 0.950836 CAGGCGAAATGTGTGTTCCA 59.049 50.0 0.0 0.00 0.00 3.53 F
111 112 0.951558 AGGCGAAATGTGTGTTCCAC 59.048 50.0 0.0 0.00 44.78 4.02 F
2276 2616 0.533032 GGAGTTAGCGCTGGAGAAGT 59.467 55.0 22.9 9.17 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1772 0.178941 ACACGGACCTCCACTTACCT 60.179 55.000 0.00 0.0 35.14 3.08 R
1933 2258 1.423056 GTCCAGGTCGTAGTCGTCG 59.577 63.158 0.00 0.0 38.33 5.12 R
1997 2331 3.799753 GCCATTGCTGTCGTCGAT 58.200 55.556 0.00 0.0 33.53 3.59 R
2335 2675 0.249238 GTAGGCACTCGATCTGCAGG 60.249 60.000 15.13 0.0 41.75 4.85 R
3093 3565 1.302993 GGTTTTCGGTGCTGGCCTA 60.303 57.895 3.32 0.0 0.00 3.93 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
22 23 4.153958 TGTTTGTATCGGTGATGTTTGC 57.846 40.909 0.00 0.00 0.00 3.68
23 24 3.818210 TGTTTGTATCGGTGATGTTTGCT 59.182 39.130 0.00 0.00 0.00 3.91
24 25 4.277174 TGTTTGTATCGGTGATGTTTGCTT 59.723 37.500 0.00 0.00 0.00 3.91
25 26 5.219633 GTTTGTATCGGTGATGTTTGCTTT 58.780 37.500 0.00 0.00 0.00 3.51
26 27 4.678509 TGTATCGGTGATGTTTGCTTTC 57.321 40.909 0.00 0.00 0.00 2.62
27 28 4.323417 TGTATCGGTGATGTTTGCTTTCT 58.677 39.130 0.00 0.00 0.00 2.52
28 29 5.483811 TGTATCGGTGATGTTTGCTTTCTA 58.516 37.500 0.00 0.00 0.00 2.10
29 30 5.935206 TGTATCGGTGATGTTTGCTTTCTAA 59.065 36.000 0.00 0.00 0.00 2.10
30 31 6.597672 TGTATCGGTGATGTTTGCTTTCTAAT 59.402 34.615 0.00 0.00 0.00 1.73
31 32 7.766738 TGTATCGGTGATGTTTGCTTTCTAATA 59.233 33.333 0.00 0.00 0.00 0.98
32 33 6.417191 TCGGTGATGTTTGCTTTCTAATAC 57.583 37.500 0.00 0.00 0.00 1.89
33 34 5.935206 TCGGTGATGTTTGCTTTCTAATACA 59.065 36.000 0.00 0.00 0.00 2.29
34 35 6.428465 TCGGTGATGTTTGCTTTCTAATACAA 59.572 34.615 0.00 0.00 0.00 2.41
35 36 7.041030 TCGGTGATGTTTGCTTTCTAATACAAA 60.041 33.333 0.00 0.00 0.00 2.83
36 37 7.593273 CGGTGATGTTTGCTTTCTAATACAAAA 59.407 33.333 0.00 0.00 34.10 2.44
37 38 9.255304 GGTGATGTTTGCTTTCTAATACAAAAA 57.745 29.630 0.00 0.00 34.10 1.94
39 40 9.474920 TGATGTTTGCTTTCTAATACAAAAAGG 57.525 29.630 0.00 0.00 34.10 3.11
40 41 8.831715 ATGTTTGCTTTCTAATACAAAAAGGG 57.168 30.769 0.00 0.00 34.10 3.95
41 42 7.213678 TGTTTGCTTTCTAATACAAAAAGGGG 58.786 34.615 0.00 0.00 34.10 4.79
42 43 5.993748 TGCTTTCTAATACAAAAAGGGGG 57.006 39.130 0.00 0.00 32.01 5.40
43 44 5.646215 TGCTTTCTAATACAAAAAGGGGGA 58.354 37.500 0.00 0.00 32.01 4.81
44 45 6.078664 TGCTTTCTAATACAAAAAGGGGGAA 58.921 36.000 0.00 0.00 32.01 3.97
45 46 6.555360 TGCTTTCTAATACAAAAAGGGGGAAA 59.445 34.615 0.00 0.00 32.01 3.13
46 47 6.872020 GCTTTCTAATACAAAAAGGGGGAAAC 59.128 38.462 0.00 0.00 32.01 2.78
47 48 8.007390 GCTTTCTAATACAAAAAGGGGGAAACC 61.007 40.741 0.00 0.00 38.87 3.27
62 63 3.617284 GGAAACCCTATTTCGTCATGGT 58.383 45.455 0.00 0.00 0.00 3.55
63 64 4.773013 GGAAACCCTATTTCGTCATGGTA 58.227 43.478 0.00 0.00 0.00 3.25
64 65 5.187687 GGAAACCCTATTTCGTCATGGTAA 58.812 41.667 0.00 0.00 0.00 2.85
65 66 5.065602 GGAAACCCTATTTCGTCATGGTAAC 59.934 44.000 0.00 0.00 0.00 2.50
81 82 4.302559 GGTAACAAACTGGATTCTCCCT 57.697 45.455 0.00 0.00 35.03 4.20
82 83 4.262617 GGTAACAAACTGGATTCTCCCTC 58.737 47.826 0.00 0.00 35.03 4.30
83 84 4.019231 GGTAACAAACTGGATTCTCCCTCT 60.019 45.833 0.00 0.00 35.03 3.69
84 85 3.990959 ACAAACTGGATTCTCCCTCTC 57.009 47.619 0.00 0.00 35.03 3.20
85 86 2.234908 ACAAACTGGATTCTCCCTCTCG 59.765 50.000 0.00 0.00 35.03 4.04
86 87 2.234908 CAAACTGGATTCTCCCTCTCGT 59.765 50.000 0.00 0.00 35.03 4.18
87 88 1.479709 ACTGGATTCTCCCTCTCGTG 58.520 55.000 0.00 0.00 35.03 4.35
88 89 0.103937 CTGGATTCTCCCTCTCGTGC 59.896 60.000 0.00 0.00 35.03 5.34
89 90 0.324738 TGGATTCTCCCTCTCGTGCT 60.325 55.000 0.00 0.00 35.03 4.40
90 91 0.387565 GGATTCTCCCTCTCGTGCTC 59.612 60.000 0.00 0.00 0.00 4.26
91 92 0.387565 GATTCTCCCTCTCGTGCTCC 59.612 60.000 0.00 0.00 0.00 4.70
92 93 0.324738 ATTCTCCCTCTCGTGCTCCA 60.325 55.000 0.00 0.00 0.00 3.86
93 94 0.967887 TTCTCCCTCTCGTGCTCCAG 60.968 60.000 0.00 0.00 0.00 3.86
94 95 2.363018 TCCCTCTCGTGCTCCAGG 60.363 66.667 0.00 0.00 0.00 4.45
95 96 4.154347 CCCTCTCGTGCTCCAGGC 62.154 72.222 0.00 0.00 42.22 4.85
96 97 4.504916 CCTCTCGTGCTCCAGGCG 62.505 72.222 0.00 0.00 45.43 5.52
97 98 3.443925 CTCTCGTGCTCCAGGCGA 61.444 66.667 0.00 0.00 45.43 5.54
98 99 2.989253 TCTCGTGCTCCAGGCGAA 60.989 61.111 0.00 0.00 45.43 4.70
99 100 2.048222 CTCGTGCTCCAGGCGAAA 60.048 61.111 0.00 0.00 45.43 3.46
100 101 1.448540 CTCGTGCTCCAGGCGAAAT 60.449 57.895 0.00 0.00 45.43 2.17
101 102 1.699656 CTCGTGCTCCAGGCGAAATG 61.700 60.000 0.00 0.00 45.43 2.32
102 103 2.034879 CGTGCTCCAGGCGAAATGT 61.035 57.895 0.00 0.00 45.43 2.71
103 104 1.503542 GTGCTCCAGGCGAAATGTG 59.496 57.895 0.00 0.00 45.43 3.21
104 105 1.073025 TGCTCCAGGCGAAATGTGT 59.927 52.632 0.00 0.00 45.43 3.72
105 106 1.236616 TGCTCCAGGCGAAATGTGTG 61.237 55.000 0.00 0.00 45.43 3.82
106 107 1.237285 GCTCCAGGCGAAATGTGTGT 61.237 55.000 0.00 0.00 0.00 3.72
107 108 1.238439 CTCCAGGCGAAATGTGTGTT 58.762 50.000 0.00 0.00 0.00 3.32
108 109 1.197721 CTCCAGGCGAAATGTGTGTTC 59.802 52.381 0.00 0.00 0.00 3.18
109 110 0.240945 CCAGGCGAAATGTGTGTTCC 59.759 55.000 0.00 0.00 0.00 3.62
110 111 0.950836 CAGGCGAAATGTGTGTTCCA 59.049 50.000 0.00 0.00 0.00 3.53
111 112 0.951558 AGGCGAAATGTGTGTTCCAC 59.048 50.000 0.00 0.00 44.78 4.02
118 119 2.939022 GTGTGTTCCACAGCGAGC 59.061 61.111 0.00 0.00 45.43 5.03
119 120 2.280797 TGTGTTCCACAGCGAGCC 60.281 61.111 0.00 0.00 39.62 4.70
120 121 3.414700 GTGTTCCACAGCGAGCCG 61.415 66.667 0.00 0.00 34.08 5.52
121 122 3.611674 TGTTCCACAGCGAGCCGA 61.612 61.111 0.00 0.00 0.00 5.54
122 123 2.811317 GTTCCACAGCGAGCCGAG 60.811 66.667 0.00 0.00 0.00 4.63
123 124 4.069232 TTCCACAGCGAGCCGAGG 62.069 66.667 0.00 0.00 0.00 4.63
125 126 4.504916 CCACAGCGAGCCGAGGAG 62.505 72.222 0.00 0.00 0.00 3.69
199 200 4.122143 ACCGAACCGAACCGATTTTATA 57.878 40.909 0.00 0.00 0.00 0.98
480 481 5.970317 TCAACAGATGAATCAATGCAAGT 57.030 34.783 0.00 0.00 34.30 3.16
590 591 7.492669 TCATTTTCAAATTTGCGTTAGGTTTGA 59.507 29.630 13.54 4.32 37.11 2.69
653 654 6.096141 TGGTATATACTGAAACCGAACCGTAA 59.904 38.462 12.54 0.00 34.60 3.18
658 659 9.768662 ATATACTGAAACCGAACCGTAATTTAT 57.231 29.630 0.00 0.00 0.00 1.40
749 751 1.194997 CCGAATAAACCGAACGCACAA 59.805 47.619 0.00 0.00 0.00 3.33
840 844 3.368571 GCACAGAAGCAGCCACCC 61.369 66.667 0.00 0.00 0.00 4.61
1180 1340 4.308458 CTCCACCACGCCAACGGA 62.308 66.667 0.00 0.00 46.04 4.69
1933 2258 1.567357 AAGAGGCTGAAGAGGAGGAC 58.433 55.000 0.00 0.00 0.00 3.85
2276 2616 0.533032 GGAGTTAGCGCTGGAGAAGT 59.467 55.000 22.90 9.17 0.00 3.01
2353 2693 2.021068 GCCTGCAGATCGAGTGCCTA 62.021 60.000 17.39 2.13 40.43 3.93
2647 3037 7.485970 CGATTCGTTGTAATCAGCAGTAGCG 62.486 48.000 0.00 0.00 36.60 4.26
2697 3092 5.771666 TGCCTTGAATTGAGAAGTTTCAGAT 59.228 36.000 0.00 0.00 31.54 2.90
2698 3093 6.942005 TGCCTTGAATTGAGAAGTTTCAGATA 59.058 34.615 0.00 0.00 31.54 1.98
2741 3172 3.014604 ACTACTTGTCAGCGTTGAGTC 57.985 47.619 0.73 0.00 32.98 3.36
2742 3173 2.623889 ACTACTTGTCAGCGTTGAGTCT 59.376 45.455 0.73 0.00 32.98 3.24
2743 3174 2.604046 ACTTGTCAGCGTTGAGTCTT 57.396 45.000 0.73 0.00 32.98 3.01
2744 3175 2.205074 ACTTGTCAGCGTTGAGTCTTG 58.795 47.619 0.73 0.00 32.98 3.02
2745 3176 2.159099 ACTTGTCAGCGTTGAGTCTTGA 60.159 45.455 0.73 0.00 32.98 3.02
2746 3177 2.140065 TGTCAGCGTTGAGTCTTGAG 57.860 50.000 0.73 0.00 32.98 3.02
2747 3178 1.409064 TGTCAGCGTTGAGTCTTGAGT 59.591 47.619 0.73 0.00 32.98 3.41
2796 3228 1.383109 TCCATGGGCATCTCCGAGT 60.383 57.895 13.02 0.00 34.94 4.18
2800 3232 1.630126 ATGGGCATCTCCGAGTTGCT 61.630 55.000 24.11 8.18 40.01 3.91
2857 3317 2.631012 GATCCCCATGGTCCACTGCC 62.631 65.000 11.73 0.00 0.00 4.85
2908 3368 2.223845 GCTCTACCTAGGAATCGTCGAC 59.776 54.545 17.98 5.18 0.00 4.20
2937 3397 2.442262 ACCTTTCTCCTCCCCTTTCT 57.558 50.000 0.00 0.00 0.00 2.52
2938 3398 2.719676 ACCTTTCTCCTCCCCTTTCTT 58.280 47.619 0.00 0.00 0.00 2.52
2939 3399 2.645297 ACCTTTCTCCTCCCCTTTCTTC 59.355 50.000 0.00 0.00 0.00 2.87
2941 3401 2.320681 TTCTCCTCCCCTTTCTTCGA 57.679 50.000 0.00 0.00 0.00 3.71
2943 3403 2.111384 TCTCCTCCCCTTTCTTCGATG 58.889 52.381 0.00 0.00 0.00 3.84
2944 3404 1.139853 CTCCTCCCCTTTCTTCGATGG 59.860 57.143 0.00 0.00 0.00 3.51
2945 3405 0.912486 CCTCCCCTTTCTTCGATGGT 59.088 55.000 0.00 0.00 0.00 3.55
2952 3424 2.160417 CCTTTCTTCGATGGTCAACTGC 59.840 50.000 0.00 0.00 0.00 4.40
2960 3432 2.034179 CGATGGTCAACTGCGTATCCTA 59.966 50.000 0.00 0.00 0.00 2.94
2961 3433 3.490249 CGATGGTCAACTGCGTATCCTAA 60.490 47.826 0.00 0.00 0.00 2.69
2979 3451 4.773674 TCCTAAACTGTGATCGGGTCTTTA 59.226 41.667 0.00 0.00 0.00 1.85
2980 3452 5.424252 TCCTAAACTGTGATCGGGTCTTTAT 59.576 40.000 0.00 0.00 0.00 1.40
2990 3462 8.644216 TGTGATCGGGTCTTTATAATTAGCTAA 58.356 33.333 8.99 8.99 0.00 3.09
3063 3535 1.618837 TGGGTTCCTCTCTCGAAGTTG 59.381 52.381 0.00 0.00 0.00 3.16
3064 3536 1.893801 GGGTTCCTCTCTCGAAGTTGA 59.106 52.381 0.00 0.00 0.00 3.18
3093 3565 6.245408 TCTGCTGTTTAAATGTCCAGGTATT 58.755 36.000 5.89 0.00 0.00 1.89
3142 3614 1.509463 GTCGGATCCTACGCACACA 59.491 57.895 10.75 0.00 0.00 3.72
3165 3637 0.040058 ATTGTCATGCCCTCTTGCCA 59.960 50.000 0.00 0.00 0.00 4.92
3181 3658 2.492418 CCACGCCTGGCAATTACAT 58.508 52.632 20.29 0.00 0.00 2.29
3182 3659 0.101040 CCACGCCTGGCAATTACATG 59.899 55.000 20.29 1.70 0.00 3.21
3219 3696 2.535012 TACGCTCCAACACATCACAA 57.465 45.000 0.00 0.00 0.00 3.33
3320 3837 1.141858 CCCAACCTTATGAGAGAGCCC 59.858 57.143 0.00 0.00 0.00 5.19
3344 3861 5.601662 TCTCAAGAACAATGTCTCTTTCGT 58.398 37.500 7.67 0.00 29.29 3.85
3382 3899 5.107375 GCATGTTTAGCAACACAGAAAATGG 60.107 40.000 0.00 0.00 45.88 3.16
3391 3909 4.345859 ACACAGAAAATGGTCTTCCGTA 57.654 40.909 0.00 0.00 36.30 4.02
3399 3917 4.939509 AATGGTCTTCCGTAATTGAACG 57.060 40.909 0.00 0.00 42.49 3.95
3423 3941 6.008696 TCCTCTTTTGGACAGAAGGTTTAA 57.991 37.500 3.20 0.00 0.00 1.52
3443 3961 7.148820 GGTTTAAATGGTCGAACAAACATGATG 60.149 37.037 7.51 0.09 0.00 3.07
3455 3973 7.060979 CGAACAAACATGATGAACCAACAATAG 59.939 37.037 0.00 0.00 0.00 1.73
3465 3983 7.337689 TGATGAACCAACAATAGAGAGAATTGG 59.662 37.037 0.00 0.00 41.92 3.16
3468 3986 4.018050 ACCAACAATAGAGAGAATTGGCCT 60.018 41.667 3.32 0.00 40.23 5.19
3475 3993 1.747924 GAGAGAATTGGCCTTGGCTTC 59.252 52.381 11.71 7.68 0.00 3.86
3479 3997 3.701040 GAGAATTGGCCTTGGCTTCATAA 59.299 43.478 11.71 0.92 0.00 1.90
3491 4009 2.576615 GCTTCATAAACCTAGCCTGGG 58.423 52.381 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.083324 AGCAAACATCACCGATACAAACAG 60.083 41.667 0.00 0.00 0.00 3.16
1 2 3.818210 AGCAAACATCACCGATACAAACA 59.182 39.130 0.00 0.00 0.00 2.83
5 6 4.323417 AGAAAGCAAACATCACCGATACA 58.677 39.130 0.00 0.00 0.00 2.29
6 7 4.946784 AGAAAGCAAACATCACCGATAC 57.053 40.909 0.00 0.00 0.00 2.24
7 8 7.766738 TGTATTAGAAAGCAAACATCACCGATA 59.233 33.333 0.00 0.00 0.00 2.92
8 9 6.597672 TGTATTAGAAAGCAAACATCACCGAT 59.402 34.615 0.00 0.00 0.00 4.18
9 10 5.935206 TGTATTAGAAAGCAAACATCACCGA 59.065 36.000 0.00 0.00 0.00 4.69
10 11 6.176975 TGTATTAGAAAGCAAACATCACCG 57.823 37.500 0.00 0.00 0.00 4.94
11 12 8.810652 TTTTGTATTAGAAAGCAAACATCACC 57.189 30.769 0.00 0.00 31.62 4.02
13 14 9.474920 CCTTTTTGTATTAGAAAGCAAACATCA 57.525 29.630 0.00 0.00 31.62 3.07
14 15 8.925700 CCCTTTTTGTATTAGAAAGCAAACATC 58.074 33.333 0.00 0.00 31.62 3.06
15 16 7.877612 CCCCTTTTTGTATTAGAAAGCAAACAT 59.122 33.333 0.00 0.00 31.62 2.71
16 17 7.213678 CCCCTTTTTGTATTAGAAAGCAAACA 58.786 34.615 0.00 0.00 31.62 2.83
17 18 6.649141 CCCCCTTTTTGTATTAGAAAGCAAAC 59.351 38.462 0.00 0.00 31.62 2.93
18 19 6.555360 TCCCCCTTTTTGTATTAGAAAGCAAA 59.445 34.615 0.00 0.00 0.00 3.68
19 20 6.078664 TCCCCCTTTTTGTATTAGAAAGCAA 58.921 36.000 0.00 0.00 0.00 3.91
20 21 5.646215 TCCCCCTTTTTGTATTAGAAAGCA 58.354 37.500 0.00 0.00 0.00 3.91
21 22 6.599356 TTCCCCCTTTTTGTATTAGAAAGC 57.401 37.500 0.00 0.00 0.00 3.51
22 23 7.383687 GGTTTCCCCCTTTTTGTATTAGAAAG 58.616 38.462 0.00 0.00 0.00 2.62
23 24 7.305813 GGTTTCCCCCTTTTTGTATTAGAAA 57.694 36.000 0.00 0.00 0.00 2.52
24 25 6.921486 GGTTTCCCCCTTTTTGTATTAGAA 57.079 37.500 0.00 0.00 0.00 2.10
40 41 2.949644 CCATGACGAAATAGGGTTTCCC 59.050 50.000 0.00 0.00 45.90 3.97
41 42 3.617284 ACCATGACGAAATAGGGTTTCC 58.383 45.455 0.00 0.00 0.00 3.13
42 43 5.644636 TGTTACCATGACGAAATAGGGTTTC 59.355 40.000 0.00 0.00 0.00 2.78
43 44 5.562635 TGTTACCATGACGAAATAGGGTTT 58.437 37.500 0.00 0.00 0.00 3.27
44 45 5.168647 TGTTACCATGACGAAATAGGGTT 57.831 39.130 0.00 0.00 0.00 4.11
45 46 4.829872 TGTTACCATGACGAAATAGGGT 57.170 40.909 0.00 0.00 0.00 4.34
46 47 5.646360 AGTTTGTTACCATGACGAAATAGGG 59.354 40.000 0.00 0.00 0.00 3.53
47 48 6.403200 CCAGTTTGTTACCATGACGAAATAGG 60.403 42.308 0.00 0.00 0.00 2.57
48 49 6.370442 TCCAGTTTGTTACCATGACGAAATAG 59.630 38.462 0.00 0.00 0.00 1.73
49 50 6.231951 TCCAGTTTGTTACCATGACGAAATA 58.768 36.000 0.00 0.00 0.00 1.40
50 51 5.067273 TCCAGTTTGTTACCATGACGAAAT 58.933 37.500 0.00 0.00 0.00 2.17
51 52 4.452825 TCCAGTTTGTTACCATGACGAAA 58.547 39.130 0.00 0.00 0.00 3.46
52 53 4.074627 TCCAGTTTGTTACCATGACGAA 57.925 40.909 0.00 0.00 0.00 3.85
53 54 3.755112 TCCAGTTTGTTACCATGACGA 57.245 42.857 0.00 0.00 0.00 4.20
54 55 4.695455 AGAATCCAGTTTGTTACCATGACG 59.305 41.667 0.00 0.00 0.00 4.35
55 56 6.183309 GAGAATCCAGTTTGTTACCATGAC 57.817 41.667 0.00 0.00 0.00 3.06
72 73 0.387565 GGAGCACGAGAGGGAGAATC 59.612 60.000 0.00 0.00 35.60 2.52
73 74 0.324738 TGGAGCACGAGAGGGAGAAT 60.325 55.000 0.00 0.00 35.60 2.40
74 75 0.967887 CTGGAGCACGAGAGGGAGAA 60.968 60.000 0.00 0.00 35.60 2.87
75 76 1.379176 CTGGAGCACGAGAGGGAGA 60.379 63.158 0.00 0.00 35.60 3.71
76 77 2.422231 CCTGGAGCACGAGAGGGAG 61.422 68.421 0.00 0.00 35.60 4.30
77 78 2.363018 CCTGGAGCACGAGAGGGA 60.363 66.667 0.00 0.00 35.60 4.20
78 79 4.154347 GCCTGGAGCACGAGAGGG 62.154 72.222 0.00 0.00 42.97 4.30
79 80 4.504916 CGCCTGGAGCACGAGAGG 62.505 72.222 0.00 0.00 44.04 3.69
80 81 2.492449 TTTCGCCTGGAGCACGAGAG 62.492 60.000 0.00 0.00 44.04 3.20
81 82 1.888436 ATTTCGCCTGGAGCACGAGA 61.888 55.000 0.00 0.00 44.04 4.04
82 83 1.448540 ATTTCGCCTGGAGCACGAG 60.449 57.895 0.00 0.00 44.04 4.18
83 84 1.741401 CATTTCGCCTGGAGCACGA 60.741 57.895 0.00 0.00 44.04 4.35
84 85 2.034879 ACATTTCGCCTGGAGCACG 61.035 57.895 0.00 0.00 44.04 5.34
85 86 1.237285 ACACATTTCGCCTGGAGCAC 61.237 55.000 0.00 0.00 44.04 4.40
86 87 1.073025 ACACATTTCGCCTGGAGCA 59.927 52.632 0.00 0.00 44.04 4.26
87 88 1.237285 ACACACATTTCGCCTGGAGC 61.237 55.000 0.00 0.00 38.52 4.70
88 89 1.197721 GAACACACATTTCGCCTGGAG 59.802 52.381 0.00 0.00 0.00 3.86
89 90 1.234821 GAACACACATTTCGCCTGGA 58.765 50.000 0.00 0.00 0.00 3.86
90 91 0.240945 GGAACACACATTTCGCCTGG 59.759 55.000 0.00 0.00 0.00 4.45
91 92 0.950836 TGGAACACACATTTCGCCTG 59.049 50.000 0.00 0.00 0.00 4.85
92 93 3.412722 TGGAACACACATTTCGCCT 57.587 47.368 0.00 0.00 0.00 5.52
105 106 2.811317 CTCGGCTCGCTGTGGAAC 60.811 66.667 0.00 0.00 37.35 3.62
106 107 4.069232 CCTCGGCTCGCTGTGGAA 62.069 66.667 12.29 0.00 37.99 3.53
108 109 4.504916 CTCCTCGGCTCGCTGTGG 62.505 72.222 11.59 11.59 37.32 4.17
119 120 2.752238 AGAGTGACCCGCTCCTCG 60.752 66.667 4.13 0.00 41.38 4.63
120 121 1.979693 ACAGAGTGACCCGCTCCTC 60.980 63.158 4.13 0.00 41.38 3.71
121 122 2.118513 ACAGAGTGACCCGCTCCT 59.881 61.111 4.13 0.00 41.38 3.69
122 123 2.262915 CACAGAGTGACCCGCTCC 59.737 66.667 4.13 0.00 41.38 4.70
123 124 2.433318 GCACAGAGTGACCCGCTC 60.433 66.667 0.58 0.00 40.84 5.03
124 125 2.116983 AATGCACAGAGTGACCCGCT 62.117 55.000 0.58 0.00 35.23 5.52
125 126 1.237285 AAATGCACAGAGTGACCCGC 61.237 55.000 0.58 0.00 35.23 6.13
126 127 0.518636 CAAATGCACAGAGTGACCCG 59.481 55.000 0.58 0.00 35.23 5.28
127 128 1.896220 TCAAATGCACAGAGTGACCC 58.104 50.000 0.58 0.00 35.23 4.46
199 200 5.361571 ACCGAAACCAGAAACCATAAAAACT 59.638 36.000 0.00 0.00 0.00 2.66
324 325 7.835822 TGTATGGTTGTTTATCCCAAGAAATG 58.164 34.615 0.00 0.00 0.00 2.32
749 751 3.710722 CTGGCCCGCTCCTCACTT 61.711 66.667 0.00 0.00 0.00 3.16
806 809 0.105964 TGCACAGCTTGTAACCGAGT 59.894 50.000 0.00 0.00 0.00 4.18
840 844 0.462047 ACCTAGGATTCTTTGCGCCG 60.462 55.000 17.98 0.00 0.00 6.46
1180 1340 2.530151 TGCTGGACCTGGAAGCCT 60.530 61.111 0.00 0.00 36.05 4.58
1543 1772 0.178941 ACACGGACCTCCACTTACCT 60.179 55.000 0.00 0.00 35.14 3.08
1933 2258 1.423056 GTCCAGGTCGTAGTCGTCG 59.577 63.158 0.00 0.00 38.33 5.12
1997 2331 3.799753 GCCATTGCTGTCGTCGAT 58.200 55.556 0.00 0.00 33.53 3.59
2335 2675 0.249238 GTAGGCACTCGATCTGCAGG 60.249 60.000 15.13 0.00 41.75 4.85
2340 2680 2.049475 GACGCGTAGGCACTCGATCT 62.049 60.000 13.97 0.00 41.75 2.75
2587 2976 1.167851 CATGCTGGCGAAGGAAAAGA 58.832 50.000 0.00 0.00 0.00 2.52
2647 3037 4.216411 TCTTACAGGTTATTGGTCAGCC 57.784 45.455 0.00 0.00 0.00 4.85
2653 3043 3.316308 GCAGGCATCTTACAGGTTATTGG 59.684 47.826 0.00 0.00 0.00 3.16
2741 3172 6.050432 AGGTAGATACTCGAGTACACTCAAG 58.950 44.000 26.87 3.12 43.00 3.02
2742 3173 5.987098 AGGTAGATACTCGAGTACACTCAA 58.013 41.667 26.87 12.30 43.00 3.02
2743 3174 5.599732 GAGGTAGATACTCGAGTACACTCA 58.400 45.833 26.87 6.68 43.00 3.41
2800 3232 3.663176 GCAGTTGCAGAGCGCCAA 61.663 61.111 2.29 0.00 41.33 4.52
2869 3329 1.301165 CCACTGCAAAAGGCCAAGC 60.301 57.895 5.01 3.31 43.89 4.01
2937 3397 2.536365 GATACGCAGTTGACCATCGAA 58.464 47.619 0.00 0.00 37.78 3.71
2938 3398 1.202371 GGATACGCAGTTGACCATCGA 60.202 52.381 0.00 0.00 37.78 3.59
2939 3399 1.202417 AGGATACGCAGTTGACCATCG 60.202 52.381 0.00 0.00 37.78 3.84
2941 3401 4.081087 AGTTTAGGATACGCAGTTGACCAT 60.081 41.667 0.00 0.00 37.78 3.55
2943 3403 3.617263 CAGTTTAGGATACGCAGTTGACC 59.383 47.826 0.00 0.00 37.78 4.02
2944 3404 4.091509 CACAGTTTAGGATACGCAGTTGAC 59.908 45.833 0.00 0.00 37.78 3.18
2945 3405 4.021807 TCACAGTTTAGGATACGCAGTTGA 60.022 41.667 0.00 0.00 37.78 3.18
2952 3424 3.067742 ACCCGATCACAGTTTAGGATACG 59.932 47.826 0.00 0.00 46.39 3.06
2960 3432 9.326413 CTAATTATAAAGACCCGATCACAGTTT 57.674 33.333 0.00 0.00 0.00 2.66
2961 3433 7.441458 GCTAATTATAAAGACCCGATCACAGTT 59.559 37.037 0.00 0.00 0.00 3.16
2979 3451 7.064253 GGACGCCGTATTGATTTAGCTAATTAT 59.936 37.037 7.08 0.00 0.00 1.28
2980 3452 6.366877 GGACGCCGTATTGATTTAGCTAATTA 59.633 38.462 7.08 0.00 0.00 1.40
3063 3535 6.503524 TGGACATTTAAACAGCAGAAAAGTC 58.496 36.000 0.00 0.00 32.65 3.01
3064 3536 6.461509 CCTGGACATTTAAACAGCAGAAAAGT 60.462 38.462 0.00 0.00 0.00 2.66
3093 3565 1.302993 GGTTTTCGGTGCTGGCCTA 60.303 57.895 3.32 0.00 0.00 3.93
3142 3614 2.028748 GCAAGAGGGCATGACAATTTGT 60.029 45.455 0.00 0.63 0.00 2.83
3165 3637 2.411628 TACATGTAATTGCCAGGCGT 57.588 45.000 7.03 0.00 0.00 5.68
3171 3643 4.334203 TCACGATGGTTACATGTAATTGCC 59.666 41.667 20.72 16.98 37.47 4.52
3178 3655 3.034721 ACGTTCACGATGGTTACATGT 57.965 42.857 6.30 2.69 43.02 3.21
3181 3658 3.424861 CGTAAACGTTCACGATGGTTACA 59.575 43.478 19.19 0.00 43.02 2.41
3182 3659 3.718898 GCGTAAACGTTCACGATGGTTAC 60.719 47.826 27.44 9.27 43.02 2.50
3219 3696 5.605488 TCACCTAGGAAGTTTTACTGAACCT 59.395 40.000 17.98 0.00 33.80 3.50
3320 3837 5.694006 ACGAAAGAGACATTGTTCTTGAGAG 59.306 40.000 12.09 8.37 34.09 3.20
3323 3840 5.356426 TGACGAAAGAGACATTGTTCTTGA 58.644 37.500 12.09 0.00 34.09 3.02
3325 3842 6.316390 AGTTTGACGAAAGAGACATTGTTCTT 59.684 34.615 0.00 7.83 35.25 2.52
3344 3861 4.734398 AAACATGCCAGTTTCAGTTTGA 57.266 36.364 0.00 0.00 37.11 2.69
3382 3899 3.582780 AGGACGTTCAATTACGGAAGAC 58.417 45.455 0.00 0.00 45.44 3.01
3423 3941 5.460646 GTTCATCATGTTTGTTCGACCATT 58.539 37.500 0.00 0.00 0.00 3.16
3443 3961 5.163612 GGCCAATTCTCTCTATTGTTGGTTC 60.164 44.000 0.00 0.00 38.61 3.62
3455 3973 1.747924 GAAGCCAAGGCCAATTCTCTC 59.252 52.381 5.01 0.00 43.17 3.20
3465 3983 2.359214 GCTAGGTTTATGAAGCCAAGGC 59.641 50.000 2.02 2.02 42.33 4.35
3475 3993 4.141390 ACTTGATCCCAGGCTAGGTTTATG 60.141 45.833 0.00 0.00 0.00 1.90
3479 3997 1.972588 ACTTGATCCCAGGCTAGGTT 58.027 50.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.