Multiple sequence alignment - TraesCS2D01G218700

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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 TraesCS2D01G218700 chr2D 100.000 4124 0 0 1 4124 182576914 182572791 0.000000e+00 7616.0
1 TraesCS2D01G218700 chr2D 91.101 2742 184 34 524 3218 156706960 156709688 0.000000e+00 3657.0
2 TraesCS2D01G218700 chr2D 93.118 2136 147 0 1010 3145 156592469 156594604 0.000000e+00 3131.0
3 TraesCS2D01G218700 chr2D 87.482 687 54 13 3365 4050 156710547 156711202 0.000000e+00 763.0
4 TraesCS2D01G218700 chr2A 96.340 3634 94 18 454 4050 197566754 197563123 0.000000e+00 5938.0
5 TraesCS2D01G218700 chr2A 95.328 2333 107 2 1719 4050 197336140 197333809 0.000000e+00 3703.0
6 TraesCS2D01G218700 chr2A 90.760 2619 197 24 634 3218 166627709 166630316 0.000000e+00 3454.0
7 TraesCS2D01G218700 chr2A 88.210 687 58 9 3365 4050 166631166 166631830 0.000000e+00 798.0
8 TraesCS2D01G218700 chr2A 91.117 349 25 6 106 451 197567207 197566862 6.240000e-128 468.0
9 TraesCS2D01G218700 chr2A 83.851 322 32 10 3720 4039 447944655 447944352 5.220000e-74 289.0
10 TraesCS2D01G218700 chr2A 91.503 153 8 1 454 606 197345545 197345398 5.400000e-49 206.0
11 TraesCS2D01G218700 chr2A 89.764 127 12 1 95 221 197346864 197346739 1.190000e-35 161.0
12 TraesCS2D01G218700 chr2A 90.526 95 9 0 467 561 197575755 197575661 4.330000e-25 126.0
13 TraesCS2D01G218700 chr2B 91.260 2643 177 30 605 3218 214312540 214315157 0.000000e+00 3552.0
14 TraesCS2D01G218700 chr2B 90.442 2647 201 25 528 3145 214280666 214283289 0.000000e+00 3439.0
15 TraesCS2D01G218700 chr2B 87.936 688 52 9 3365 4050 214315993 214316651 0.000000e+00 782.0
16 TraesCS2D01G218700 chr2B 85.586 111 12 3 369 475 214280554 214280664 3.370000e-21 113.0
17 TraesCS2D01G218700 chr2B 91.463 82 6 1 523 603 214312421 214312502 1.210000e-20 111.0
18 TraesCS2D01G218700 chr1B 90.062 2576 208 31 615 3169 148416664 148414116 0.000000e+00 3295.0
19 TraesCS2D01G218700 chr1D 89.778 2573 212 30 626 3169 93105547 93102997 0.000000e+00 3247.0
20 TraesCS2D01G218700 chr1A 81.979 283 24 16 626 890 90163845 90163572 8.980000e-52 215.0
21 TraesCS2D01G218700 chr1A 81.651 109 18 2 36 143 565321889 565321782 5.680000e-14 89.8


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 TraesCS2D01G218700 chr2D 182572791 182576914 4123 True 7616.000000 7616 100.000000 1 4124 1 chr2D.!!$R1 4123
1 TraesCS2D01G218700 chr2D 156592469 156594604 2135 False 3131.000000 3131 93.118000 1010 3145 1 chr2D.!!$F1 2135
2 TraesCS2D01G218700 chr2D 156706960 156711202 4242 False 2210.000000 3657 89.291500 524 4050 2 chr2D.!!$F2 3526
3 TraesCS2D01G218700 chr2A 197333809 197336140 2331 True 3703.000000 3703 95.328000 1719 4050 1 chr2A.!!$R1 2331
4 TraesCS2D01G218700 chr2A 197563123 197567207 4084 True 3203.000000 5938 93.728500 106 4050 2 chr2A.!!$R5 3944
5 TraesCS2D01G218700 chr2A 166627709 166631830 4121 False 2126.000000 3454 89.485000 634 4050 2 chr2A.!!$F1 3416
6 TraesCS2D01G218700 chr2B 214280554 214283289 2735 False 1776.000000 3439 88.014000 369 3145 2 chr2B.!!$F1 2776
7 TraesCS2D01G218700 chr2B 214312421 214316651 4230 False 1481.666667 3552 90.219667 523 4050 3 chr2B.!!$F2 3527
8 TraesCS2D01G218700 chr1B 148414116 148416664 2548 True 3295.000000 3295 90.062000 615 3169 1 chr1B.!!$R1 2554
9 TraesCS2D01G218700 chr1D 93102997 93105547 2550 True 3247.000000 3247 89.778000 626 3169 1 chr1D.!!$R1 2543

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
392 395 0.028242 CAGAGCTCCGCTACAGTACG 59.972 60.0 10.93 0.00 39.88 3.67 F
502 614 0.320374 CTGGAACACTAACGGGAGCA 59.680 55.0 0.00 0.00 0.00 4.26 F
965 1198 0.465287 TCTCTCACACAACTGCTGCA 59.535 50.0 0.88 0.88 0.00 4.41 F
1389 1625 0.899720 TCATCCGGTTCCTTAACGCT 59.100 50.0 0.00 0.00 36.39 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1566 0.105658 CCCTCCTTGGTCCTCCGATA 60.106 60.000 0.00 0.0 36.30 2.92 R
1677 1913 2.099756 GCCCGCAATCTTAAATGCTTCT 59.900 45.455 6.14 0.0 40.39 2.85 R
2694 2930 1.623081 CGTCCGCGTATGCAAACACT 61.623 55.000 4.92 0.0 42.97 3.55 R
3262 3576 2.819608 GTGCCCTTTTGCTTACATCAGA 59.180 45.455 0.00 0.0 0.00 3.27 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 2.078849 TATGGTATGCATCCGCTTCG 57.921 50.000 0.19 0.00 39.64 3.79
23 24 0.106708 ATGGTATGCATCCGCTTCGT 59.893 50.000 0.19 0.00 39.64 3.85
24 25 0.747852 TGGTATGCATCCGCTTCGTA 59.252 50.000 0.19 0.00 39.64 3.43
25 26 1.137513 GGTATGCATCCGCTTCGTAC 58.862 55.000 0.19 0.00 39.64 3.67
26 27 1.537348 GGTATGCATCCGCTTCGTACA 60.537 52.381 0.19 0.00 39.64 2.90
27 28 2.404215 GTATGCATCCGCTTCGTACAT 58.596 47.619 0.19 0.00 39.64 2.29
28 29 1.220529 ATGCATCCGCTTCGTACATG 58.779 50.000 0.00 0.00 39.64 3.21
29 30 0.809636 TGCATCCGCTTCGTACATGG 60.810 55.000 0.00 0.00 39.64 3.66
30 31 0.529773 GCATCCGCTTCGTACATGGA 60.530 55.000 0.00 0.00 34.30 3.41
31 32 1.209128 CATCCGCTTCGTACATGGAC 58.791 55.000 0.00 0.00 0.00 4.02
32 33 1.112113 ATCCGCTTCGTACATGGACT 58.888 50.000 6.49 0.00 0.00 3.85
33 34 1.753930 TCCGCTTCGTACATGGACTA 58.246 50.000 6.49 0.00 0.00 2.59
34 35 1.402968 TCCGCTTCGTACATGGACTAC 59.597 52.381 6.49 0.00 0.00 2.73
35 36 1.463805 CGCTTCGTACATGGACTACG 58.536 55.000 6.49 7.24 38.67 3.51
36 37 1.197910 GCTTCGTACATGGACTACGC 58.802 55.000 6.49 0.32 37.49 4.42
37 38 1.202268 GCTTCGTACATGGACTACGCT 60.202 52.381 6.49 0.00 37.49 5.07
38 39 2.032550 GCTTCGTACATGGACTACGCTA 59.967 50.000 6.49 0.00 37.49 4.26
39 40 3.615614 CTTCGTACATGGACTACGCTAC 58.384 50.000 6.49 0.00 37.49 3.58
40 41 2.631267 TCGTACATGGACTACGCTACA 58.369 47.619 6.49 0.00 37.49 2.74
41 42 3.208594 TCGTACATGGACTACGCTACAT 58.791 45.455 6.49 0.00 37.49 2.29
42 43 3.249320 TCGTACATGGACTACGCTACATC 59.751 47.826 6.49 0.00 37.49 3.06
43 44 2.776312 ACATGGACTACGCTACATCG 57.224 50.000 0.00 0.00 0.00 3.84
44 45 2.294979 ACATGGACTACGCTACATCGA 58.705 47.619 0.00 0.00 0.00 3.59
45 46 2.686405 ACATGGACTACGCTACATCGAA 59.314 45.455 0.00 0.00 0.00 3.71
46 47 2.838386 TGGACTACGCTACATCGAAC 57.162 50.000 0.00 0.00 0.00 3.95
47 48 2.086094 TGGACTACGCTACATCGAACA 58.914 47.619 0.00 0.00 0.00 3.18
48 49 2.159476 TGGACTACGCTACATCGAACAC 60.159 50.000 0.00 0.00 0.00 3.32
49 50 2.159476 GGACTACGCTACATCGAACACA 60.159 50.000 0.00 0.00 0.00 3.72
50 51 3.099362 GACTACGCTACATCGAACACAG 58.901 50.000 0.00 0.00 0.00 3.66
51 52 2.486982 ACTACGCTACATCGAACACAGT 59.513 45.455 0.00 0.00 0.00 3.55
52 53 3.686241 ACTACGCTACATCGAACACAGTA 59.314 43.478 0.00 0.00 0.00 2.74
53 54 2.860062 ACGCTACATCGAACACAGTAC 58.140 47.619 0.00 0.00 0.00 2.73
54 55 2.182825 CGCTACATCGAACACAGTACC 58.817 52.381 0.00 0.00 0.00 3.34
55 56 2.414957 CGCTACATCGAACACAGTACCA 60.415 50.000 0.00 0.00 0.00 3.25
56 57 3.581755 GCTACATCGAACACAGTACCAA 58.418 45.455 0.00 0.00 0.00 3.67
57 58 3.367025 GCTACATCGAACACAGTACCAAC 59.633 47.826 0.00 0.00 0.00 3.77
58 59 3.462483 ACATCGAACACAGTACCAACA 57.538 42.857 0.00 0.00 0.00 3.33
59 60 3.390135 ACATCGAACACAGTACCAACAG 58.610 45.455 0.00 0.00 0.00 3.16
60 61 3.181469 ACATCGAACACAGTACCAACAGT 60.181 43.478 0.00 0.00 0.00 3.55
61 62 3.530265 TCGAACACAGTACCAACAGTT 57.470 42.857 0.00 0.00 0.00 3.16
62 63 3.191669 TCGAACACAGTACCAACAGTTG 58.808 45.455 6.28 6.28 0.00 3.16
63 64 2.933906 CGAACACAGTACCAACAGTTGT 59.066 45.455 12.42 3.45 0.00 3.32
64 65 3.372822 CGAACACAGTACCAACAGTTGTT 59.627 43.478 12.42 0.00 39.12 2.83
65 66 4.493545 CGAACACAGTACCAACAGTTGTTC 60.494 45.833 12.42 6.49 35.83 3.18
66 67 3.945346 ACACAGTACCAACAGTTGTTCA 58.055 40.909 12.42 0.00 35.83 3.18
67 68 4.328536 ACACAGTACCAACAGTTGTTCAA 58.671 39.130 12.42 0.00 35.83 2.69
68 69 4.394920 ACACAGTACCAACAGTTGTTCAAG 59.605 41.667 12.42 0.00 35.83 3.02
69 70 4.634004 CACAGTACCAACAGTTGTTCAAGA 59.366 41.667 12.42 0.00 35.83 3.02
70 71 5.296780 CACAGTACCAACAGTTGTTCAAGAT 59.703 40.000 12.42 0.00 35.83 2.40
71 72 5.296780 ACAGTACCAACAGTTGTTCAAGATG 59.703 40.000 12.42 4.50 35.83 2.90
72 73 5.527214 CAGTACCAACAGTTGTTCAAGATGA 59.473 40.000 12.42 0.00 35.83 2.92
73 74 6.205464 CAGTACCAACAGTTGTTCAAGATGAT 59.795 38.462 12.42 0.00 35.83 2.45
74 75 5.443185 ACCAACAGTTGTTCAAGATGATG 57.557 39.130 12.42 0.00 35.83 3.07
75 76 4.232221 CCAACAGTTGTTCAAGATGATGC 58.768 43.478 12.42 0.00 35.83 3.91
76 77 3.818961 ACAGTTGTTCAAGATGATGCG 57.181 42.857 5.18 0.00 0.00 4.73
77 78 3.141398 ACAGTTGTTCAAGATGATGCGT 58.859 40.909 5.18 0.00 0.00 5.24
78 79 4.314961 ACAGTTGTTCAAGATGATGCGTA 58.685 39.130 5.18 0.00 0.00 4.42
79 80 4.937620 ACAGTTGTTCAAGATGATGCGTAT 59.062 37.500 0.00 0.00 0.00 3.06
80 81 6.106003 ACAGTTGTTCAAGATGATGCGTATA 58.894 36.000 0.00 0.00 0.00 1.47
81 82 6.036083 ACAGTTGTTCAAGATGATGCGTATAC 59.964 38.462 0.00 0.00 0.00 1.47
82 83 6.035975 CAGTTGTTCAAGATGATGCGTATACA 59.964 38.462 3.32 0.00 0.00 2.29
83 84 6.593770 AGTTGTTCAAGATGATGCGTATACAA 59.406 34.615 3.32 0.00 0.00 2.41
84 85 6.976636 TGTTCAAGATGATGCGTATACAAA 57.023 33.333 3.32 0.00 0.00 2.83
85 86 7.552458 TGTTCAAGATGATGCGTATACAAAT 57.448 32.000 3.32 0.00 0.00 2.32
86 87 7.408910 TGTTCAAGATGATGCGTATACAAATG 58.591 34.615 3.32 0.00 0.00 2.32
87 88 6.544038 TCAAGATGATGCGTATACAAATGG 57.456 37.500 3.32 0.00 0.00 3.16
88 89 6.287525 TCAAGATGATGCGTATACAAATGGA 58.712 36.000 3.32 0.00 0.00 3.41
89 90 6.424812 TCAAGATGATGCGTATACAAATGGAG 59.575 38.462 3.32 0.00 0.00 3.86
90 91 4.692625 AGATGATGCGTATACAAATGGAGC 59.307 41.667 3.32 0.00 0.00 4.70
91 92 2.799978 TGATGCGTATACAAATGGAGCG 59.200 45.455 3.32 0.00 0.00 5.03
92 93 1.577468 TGCGTATACAAATGGAGCGG 58.423 50.000 3.32 0.00 0.00 5.52
93 94 0.865769 GCGTATACAAATGGAGCGGG 59.134 55.000 3.32 0.00 0.00 6.13
94 95 1.808891 GCGTATACAAATGGAGCGGGT 60.809 52.381 3.32 0.00 0.00 5.28
95 96 1.864711 CGTATACAAATGGAGCGGGTG 59.135 52.381 3.32 0.00 0.00 4.61
96 97 2.218603 GTATACAAATGGAGCGGGTGG 58.781 52.381 0.00 0.00 0.00 4.61
97 98 0.751643 ATACAAATGGAGCGGGTGGC 60.752 55.000 0.00 0.00 44.05 5.01
98 99 2.830186 TACAAATGGAGCGGGTGGCC 62.830 60.000 0.00 0.00 45.17 5.36
99 100 3.978193 AAATGGAGCGGGTGGCCA 61.978 61.111 0.00 0.00 45.17 5.36
100 101 3.944250 AAATGGAGCGGGTGGCCAG 62.944 63.158 5.11 0.00 45.17 4.85
104 105 4.154347 GAGCGGGTGGCCAGAGAG 62.154 72.222 5.11 0.00 45.17 3.20
113 114 0.696501 TGGCCAGAGAGGGTTTTACC 59.303 55.000 0.00 0.00 38.09 2.85
127 128 3.570550 GGTTTTACCCAACATGTGTAGCA 59.429 43.478 0.00 0.00 30.04 3.49
147 148 4.024893 AGCAACATAATCTACGAATTGCCG 60.025 41.667 0.00 0.00 41.41 5.69
220 221 6.030228 GGTTATGCAAAGCTGAGTATTGTTC 58.970 40.000 0.00 0.00 0.00 3.18
222 223 2.095768 TGCAAAGCTGAGTATTGTTCGC 60.096 45.455 0.00 0.00 0.00 4.70
227 229 4.410492 AGCTGAGTATTGTTCGCTTTTG 57.590 40.909 0.00 0.00 0.00 2.44
241 243 3.316588 TCGCTTTTGTGTTTTGGCTATGA 59.683 39.130 0.00 0.00 0.00 2.15
248 250 5.606348 TGTGTTTTGGCTATGAAAAACCT 57.394 34.783 8.15 0.00 42.80 3.50
254 256 5.860941 TTGGCTATGAAAAACCTGTTTGA 57.139 34.783 0.00 0.00 32.36 2.69
270 272 9.665719 AACCTGTTTGATGTTTTATTTTGAGTT 57.334 25.926 0.00 0.00 0.00 3.01
335 338 1.523758 AATCTCCCGTGTGAACTTGC 58.476 50.000 0.00 0.00 0.00 4.01
339 342 2.604174 CCCGTGTGAACTTGCCGTC 61.604 63.158 0.00 0.00 0.00 4.79
363 366 3.896888 TCAAGTCATGGTCAAAAAGCCAT 59.103 39.130 0.00 0.00 45.55 4.40
370 373 2.295909 TGGTCAAAAAGCCATGCTGTAC 59.704 45.455 0.00 0.00 39.62 2.90
392 395 0.028242 CAGAGCTCCGCTACAGTACG 59.972 60.000 10.93 0.00 39.88 3.67
425 432 1.239347 GCAAAGAACCAGTCTCACCC 58.761 55.000 0.00 0.00 34.56 4.61
495 607 7.964604 ATCTAAAACTGACTGGAACACTAAC 57.035 36.000 0.00 0.00 0.00 2.34
502 614 0.320374 CTGGAACACTAACGGGAGCA 59.680 55.000 0.00 0.00 0.00 4.26
507 619 1.267121 ACACTAACGGGAGCACATCT 58.733 50.000 0.00 0.00 0.00 2.90
706 876 3.434179 AGGCCACCAACCCAACCA 61.434 61.111 5.01 0.00 0.00 3.67
766 961 1.678970 GTCCACACCAATCCCCAGC 60.679 63.158 0.00 0.00 0.00 4.85
805 1000 5.172934 CGTGCAGTCCACTACCTATTTAAA 58.827 41.667 0.00 0.00 42.42 1.52
809 1004 6.157994 TGCAGTCCACTACCTATTTAAATCCT 59.842 38.462 3.39 0.00 0.00 3.24
819 1015 5.976870 ACCTATTTAAATCCTTCCCTCTCCA 59.023 40.000 3.39 0.00 0.00 3.86
826 1022 1.081174 TCCTTCCCTCTCCACCATTCT 59.919 52.381 0.00 0.00 0.00 2.40
828 1024 1.488393 CTTCCCTCTCCACCATTCTCC 59.512 57.143 0.00 0.00 0.00 3.71
850 1049 0.539051 CAAGAAGAGCATCCCGACCT 59.461 55.000 0.00 0.00 33.66 3.85
952 1183 2.290008 ACAGTCGAGCTCTTCTCTCTCA 60.290 50.000 12.85 0.00 39.70 3.27
963 1196 2.808523 TCTCTCTCACACAACTGCTG 57.191 50.000 0.00 0.00 0.00 4.41
965 1198 0.465287 TCTCTCACACAACTGCTGCA 59.535 50.000 0.88 0.88 0.00 4.41
967 1200 1.263484 CTCTCACACAACTGCTGCAAG 59.737 52.381 3.02 0.51 0.00 4.01
1266 1502 2.125753 GAGAGCAGCGACTGGGTG 60.126 66.667 8.57 0.00 46.88 4.61
1389 1625 0.899720 TCATCCGGTTCCTTAACGCT 59.100 50.000 0.00 0.00 36.39 5.07
1677 1913 1.872197 GCACCAAGGTTAATGCCGCA 61.872 55.000 0.00 0.00 31.71 5.69
1737 1973 1.531602 GCTGCAACCCAAGGAAGGT 60.532 57.895 0.00 0.00 40.14 3.50
1938 2174 3.517140 GCCGCGGCAATCATGGAA 61.517 61.111 43.55 0.00 41.49 3.53
2139 2375 1.531149 GACAACCCACTCATTGACGTG 59.469 52.381 0.00 8.44 0.00 4.49
2298 2534 2.028561 ACAATGGTTTGCCCTCCAAT 57.971 45.000 0.00 0.00 37.27 3.16
2508 2744 2.280971 CGACATTCTGAAGCTCATGTCG 59.719 50.000 21.56 21.56 44.99 4.35
2577 2813 3.196469 TCGAGGAGAATGTCAAGAATGCT 59.804 43.478 0.00 0.00 0.00 3.79
2848 3084 0.677731 TGCCAAATTCGAGCAGGAGG 60.678 55.000 0.00 0.00 31.65 4.30
3196 3435 9.722056 GCACCACAATTTCTAAAGTGATAATAG 57.278 33.333 9.62 0.00 37.42 1.73
3257 3571 1.434622 CGCCATGCAGCAACTAGAGG 61.435 60.000 0.00 0.00 0.00 3.69
3286 3600 2.880963 TGTAAGCAAAAGGGCACAAC 57.119 45.000 0.00 0.00 35.83 3.32
3342 3656 4.705507 TGTCGAAAGAAGCCAGTCTACTAT 59.294 41.667 0.00 0.00 45.01 2.12
3755 4747 7.032580 CGGAATTGCAGAAAACCAAACATATA 58.967 34.615 0.00 0.00 0.00 0.86
3847 4839 6.012745 ACTCCTTAAATGCCTGAAACAATCT 58.987 36.000 0.00 0.00 0.00 2.40
4053 5046 9.886132 AGTTAAACAGTATGAATACTTAGGGTG 57.114 33.333 0.07 0.00 41.44 4.61
4054 5047 8.610035 GTTAAACAGTATGAATACTTAGGGTGC 58.390 37.037 0.07 0.00 41.44 5.01
4055 5048 5.950544 ACAGTATGAATACTTAGGGTGCA 57.049 39.130 0.07 0.00 41.44 4.57
4056 5049 6.500589 ACAGTATGAATACTTAGGGTGCAT 57.499 37.500 0.07 0.00 41.44 3.96
4057 5050 6.900194 ACAGTATGAATACTTAGGGTGCATT 58.100 36.000 0.07 0.00 41.44 3.56
4058 5051 7.346471 ACAGTATGAATACTTAGGGTGCATTT 58.654 34.615 0.07 0.00 41.44 2.32
4059 5052 7.834181 ACAGTATGAATACTTAGGGTGCATTTT 59.166 33.333 0.07 0.00 41.44 1.82
4060 5053 8.686334 CAGTATGAATACTTAGGGTGCATTTTT 58.314 33.333 0.07 0.00 41.44 1.94
4061 5054 8.686334 AGTATGAATACTTAGGGTGCATTTTTG 58.314 33.333 0.00 0.00 40.54 2.44
4062 5055 6.909550 TGAATACTTAGGGTGCATTTTTGT 57.090 33.333 0.00 0.00 0.00 2.83
4063 5056 7.296628 TGAATACTTAGGGTGCATTTTTGTT 57.703 32.000 0.00 0.00 0.00 2.83
4064 5057 8.410673 TGAATACTTAGGGTGCATTTTTGTTA 57.589 30.769 0.00 0.00 0.00 2.41
4065 5058 8.861086 TGAATACTTAGGGTGCATTTTTGTTAA 58.139 29.630 0.00 0.00 0.00 2.01
4066 5059 9.353999 GAATACTTAGGGTGCATTTTTGTTAAG 57.646 33.333 0.00 0.00 0.00 1.85
4067 5060 6.724893 ACTTAGGGTGCATTTTTGTTAAGT 57.275 33.333 0.00 0.00 0.00 2.24
4068 5061 7.826918 ACTTAGGGTGCATTTTTGTTAAGTA 57.173 32.000 0.00 0.00 30.71 2.24
4069 5062 8.417273 ACTTAGGGTGCATTTTTGTTAAGTAT 57.583 30.769 0.00 0.00 30.71 2.12
4070 5063 8.866093 ACTTAGGGTGCATTTTTGTTAAGTATT 58.134 29.630 0.00 0.00 30.71 1.89
4108 5101 8.816640 AGATTTTTGGATAAACATTGTCACAC 57.183 30.769 0.00 0.00 0.00 3.82
4109 5102 8.641541 AGATTTTTGGATAAACATTGTCACACT 58.358 29.630 0.00 0.00 0.00 3.55
4110 5103 9.906660 GATTTTTGGATAAACATTGTCACACTA 57.093 29.630 0.00 0.00 0.00 2.74
4116 5109 9.337396 TGGATAAACATTGTCACACTAATATCC 57.663 33.333 8.11 8.11 0.00 2.59
4117 5110 8.784043 GGATAAACATTGTCACACTAATATCCC 58.216 37.037 0.00 0.00 0.00 3.85
4118 5111 9.561069 GATAAACATTGTCACACTAATATCCCT 57.439 33.333 0.00 0.00 0.00 4.20
4119 5112 9.920946 ATAAACATTGTCACACTAATATCCCTT 57.079 29.630 0.00 0.00 0.00 3.95
4121 5114 8.732746 AACATTGTCACACTAATATCCCTTAC 57.267 34.615 0.00 0.00 0.00 2.34
4122 5115 7.857456 ACATTGTCACACTAATATCCCTTACA 58.143 34.615 0.00 0.00 0.00 2.41
4123 5116 8.325787 ACATTGTCACACTAATATCCCTTACAA 58.674 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.180817 CGAAGCGGATGCATACCATATAA 58.819 43.478 2.50 0.00 46.23 0.98
1 2 3.194755 ACGAAGCGGATGCATACCATATA 59.805 43.478 2.50 0.00 46.23 0.86
3 4 1.343142 ACGAAGCGGATGCATACCATA 59.657 47.619 2.50 0.00 46.23 2.74
5 6 0.747852 TACGAAGCGGATGCATACCA 59.252 50.000 2.50 0.00 46.23 3.25
6 7 1.137513 GTACGAAGCGGATGCATACC 58.862 55.000 2.50 4.26 46.23 2.73
7 8 1.847818 TGTACGAAGCGGATGCATAC 58.152 50.000 0.00 0.00 46.23 2.39
8 9 2.403259 CATGTACGAAGCGGATGCATA 58.597 47.619 0.00 0.00 46.23 3.14
9 10 1.220529 CATGTACGAAGCGGATGCAT 58.779 50.000 0.00 0.00 46.23 3.96
10 11 0.809636 CCATGTACGAAGCGGATGCA 60.810 55.000 0.00 0.00 46.23 3.96
11 12 0.529773 TCCATGTACGAAGCGGATGC 60.530 55.000 0.00 0.00 43.24 3.91
12 13 1.202417 AGTCCATGTACGAAGCGGATG 60.202 52.381 0.00 0.00 0.00 3.51
13 14 1.112113 AGTCCATGTACGAAGCGGAT 58.888 50.000 0.00 0.00 0.00 4.18
14 15 1.402968 GTAGTCCATGTACGAAGCGGA 59.597 52.381 0.00 0.00 0.00 5.54
15 16 1.836383 GTAGTCCATGTACGAAGCGG 58.164 55.000 0.00 0.00 0.00 5.52
16 17 1.463805 CGTAGTCCATGTACGAAGCG 58.536 55.000 8.28 0.00 44.90 4.68
17 18 1.197910 GCGTAGTCCATGTACGAAGC 58.802 55.000 16.04 6.18 44.90 3.86
18 19 2.846039 AGCGTAGTCCATGTACGAAG 57.154 50.000 16.04 0.00 44.90 3.79
19 20 3.009026 TGTAGCGTAGTCCATGTACGAA 58.991 45.455 16.04 3.14 44.90 3.85
20 21 2.631267 TGTAGCGTAGTCCATGTACGA 58.369 47.619 16.04 0.00 44.90 3.43
21 22 3.552541 GATGTAGCGTAGTCCATGTACG 58.447 50.000 9.36 9.36 44.90 3.67
22 23 3.249320 TCGATGTAGCGTAGTCCATGTAC 59.751 47.826 0.00 0.00 0.00 2.90
23 24 3.469739 TCGATGTAGCGTAGTCCATGTA 58.530 45.455 0.00 0.00 0.00 2.29
24 25 2.294979 TCGATGTAGCGTAGTCCATGT 58.705 47.619 0.00 0.00 0.00 3.21
25 26 3.043586 GTTCGATGTAGCGTAGTCCATG 58.956 50.000 0.00 0.00 0.00 3.66
26 27 2.686405 TGTTCGATGTAGCGTAGTCCAT 59.314 45.455 0.00 0.00 0.00 3.41
27 28 2.086094 TGTTCGATGTAGCGTAGTCCA 58.914 47.619 0.00 0.00 0.00 4.02
28 29 2.159476 TGTGTTCGATGTAGCGTAGTCC 60.159 50.000 0.00 0.00 0.00 3.85
29 30 3.099362 CTGTGTTCGATGTAGCGTAGTC 58.901 50.000 0.00 0.00 0.00 2.59
30 31 2.486982 ACTGTGTTCGATGTAGCGTAGT 59.513 45.455 0.00 0.00 0.00 2.73
31 32 3.132629 ACTGTGTTCGATGTAGCGTAG 57.867 47.619 0.00 0.00 0.00 3.51
32 33 3.181507 GGTACTGTGTTCGATGTAGCGTA 60.182 47.826 0.00 0.00 0.00 4.42
33 34 2.415090 GGTACTGTGTTCGATGTAGCGT 60.415 50.000 0.00 0.00 0.00 5.07
34 35 2.182825 GGTACTGTGTTCGATGTAGCG 58.817 52.381 0.00 0.00 0.00 4.26
35 36 3.226346 TGGTACTGTGTTCGATGTAGC 57.774 47.619 0.00 0.00 34.98 3.58
36 37 4.552355 TGTTGGTACTGTGTTCGATGTAG 58.448 43.478 0.00 0.00 0.00 2.74
37 38 4.038282 ACTGTTGGTACTGTGTTCGATGTA 59.962 41.667 0.00 0.00 35.42 2.29
38 39 3.181469 ACTGTTGGTACTGTGTTCGATGT 60.181 43.478 0.00 0.00 35.42 3.06
39 40 3.390135 ACTGTTGGTACTGTGTTCGATG 58.610 45.455 0.00 0.00 35.42 3.84
40 41 3.746045 ACTGTTGGTACTGTGTTCGAT 57.254 42.857 0.00 0.00 35.42 3.59
41 42 3.191669 CAACTGTTGGTACTGTGTTCGA 58.808 45.455 12.66 0.00 36.67 3.71
42 43 2.933906 ACAACTGTTGGTACTGTGTTCG 59.066 45.455 23.15 0.00 36.67 3.95
43 44 4.393680 TGAACAACTGTTGGTACTGTGTTC 59.606 41.667 23.15 15.67 40.09 3.18
44 45 4.328536 TGAACAACTGTTGGTACTGTGTT 58.671 39.130 23.15 7.62 38.56 3.32
45 46 3.945346 TGAACAACTGTTGGTACTGTGT 58.055 40.909 23.15 0.00 38.56 3.72
46 47 4.634004 TCTTGAACAACTGTTGGTACTGTG 59.366 41.667 23.15 7.60 38.56 3.66
47 48 4.839121 TCTTGAACAACTGTTGGTACTGT 58.161 39.130 23.15 0.01 38.56 3.55
48 49 5.527214 TCATCTTGAACAACTGTTGGTACTG 59.473 40.000 23.15 10.75 38.56 2.74
49 50 5.680619 TCATCTTGAACAACTGTTGGTACT 58.319 37.500 23.15 6.02 38.56 2.73
50 51 6.373779 CATCATCTTGAACAACTGTTGGTAC 58.626 40.000 23.15 14.08 38.56 3.34
51 52 5.048782 GCATCATCTTGAACAACTGTTGGTA 60.049 40.000 23.15 3.39 38.56 3.25
52 53 4.261741 GCATCATCTTGAACAACTGTTGGT 60.262 41.667 23.15 18.16 38.56 3.67
53 54 4.232221 GCATCATCTTGAACAACTGTTGG 58.768 43.478 23.15 6.46 38.56 3.77
54 55 3.910170 CGCATCATCTTGAACAACTGTTG 59.090 43.478 18.44 18.44 38.56 3.33
55 56 3.565482 ACGCATCATCTTGAACAACTGTT 59.435 39.130 0.00 0.00 41.64 3.16
56 57 3.141398 ACGCATCATCTTGAACAACTGT 58.859 40.909 0.00 0.00 0.00 3.55
57 58 3.818961 ACGCATCATCTTGAACAACTG 57.181 42.857 0.00 0.00 0.00 3.16
58 59 6.106003 TGTATACGCATCATCTTGAACAACT 58.894 36.000 0.00 0.00 0.00 3.16
59 60 6.344572 TGTATACGCATCATCTTGAACAAC 57.655 37.500 0.00 0.00 0.00 3.32
60 61 6.976636 TTGTATACGCATCATCTTGAACAA 57.023 33.333 0.00 0.00 0.00 2.83
61 62 6.976636 TTTGTATACGCATCATCTTGAACA 57.023 33.333 0.00 0.00 0.00 3.18
62 63 6.852853 CCATTTGTATACGCATCATCTTGAAC 59.147 38.462 0.00 0.00 0.00 3.18
63 64 6.765512 TCCATTTGTATACGCATCATCTTGAA 59.234 34.615 0.00 0.00 0.00 2.69
64 65 6.287525 TCCATTTGTATACGCATCATCTTGA 58.712 36.000 0.00 0.00 0.00 3.02
65 66 6.544038 TCCATTTGTATACGCATCATCTTG 57.456 37.500 0.00 0.00 0.00 3.02
66 67 5.180117 GCTCCATTTGTATACGCATCATCTT 59.820 40.000 0.00 0.00 0.00 2.40
67 68 4.692625 GCTCCATTTGTATACGCATCATCT 59.307 41.667 0.00 0.00 0.00 2.90
68 69 4.434725 CGCTCCATTTGTATACGCATCATC 60.435 45.833 0.00 0.00 0.00 2.92
69 70 3.433274 CGCTCCATTTGTATACGCATCAT 59.567 43.478 0.00 0.00 0.00 2.45
70 71 2.799978 CGCTCCATTTGTATACGCATCA 59.200 45.455 0.00 0.00 0.00 3.07
71 72 2.157668 CCGCTCCATTTGTATACGCATC 59.842 50.000 0.00 0.00 0.00 3.91
72 73 2.143122 CCGCTCCATTTGTATACGCAT 58.857 47.619 0.00 0.00 0.00 4.73
73 74 1.577468 CCGCTCCATTTGTATACGCA 58.423 50.000 0.00 0.00 0.00 5.24
74 75 0.865769 CCCGCTCCATTTGTATACGC 59.134 55.000 0.00 0.00 0.00 4.42
75 76 1.864711 CACCCGCTCCATTTGTATACG 59.135 52.381 0.00 0.00 0.00 3.06
76 77 2.218603 CCACCCGCTCCATTTGTATAC 58.781 52.381 0.00 0.00 0.00 1.47
77 78 1.476110 GCCACCCGCTCCATTTGTATA 60.476 52.381 0.00 0.00 0.00 1.47
78 79 0.751643 GCCACCCGCTCCATTTGTAT 60.752 55.000 0.00 0.00 0.00 2.29
79 80 1.377987 GCCACCCGCTCCATTTGTA 60.378 57.895 0.00 0.00 0.00 2.41
80 81 2.676471 GCCACCCGCTCCATTTGT 60.676 61.111 0.00 0.00 0.00 2.83
81 82 3.451894 GGCCACCCGCTCCATTTG 61.452 66.667 0.00 0.00 37.74 2.32
82 83 3.944250 CTGGCCACCCGCTCCATTT 62.944 63.158 0.00 0.00 37.74 2.32
83 84 4.431131 CTGGCCACCCGCTCCATT 62.431 66.667 0.00 0.00 37.74 3.16
87 88 4.154347 CTCTCTGGCCACCCGCTC 62.154 72.222 0.00 0.00 37.74 5.03
91 92 2.081585 AAAACCCTCTCTGGCCACCC 62.082 60.000 0.00 0.00 0.00 4.61
92 93 0.696501 TAAAACCCTCTCTGGCCACC 59.303 55.000 0.00 0.00 0.00 4.61
93 94 1.613520 GGTAAAACCCTCTCTGGCCAC 60.614 57.143 0.00 0.00 30.04 5.01
94 95 0.696501 GGTAAAACCCTCTCTGGCCA 59.303 55.000 4.71 4.71 30.04 5.36
95 96 3.571748 GGTAAAACCCTCTCTGGCC 57.428 57.895 0.00 0.00 30.04 5.36
113 114 6.441093 AGATTATGTTGCTACACATGTTGG 57.559 37.500 2.28 0.00 37.93 3.77
121 122 6.018262 GGCAATTCGTAGATTATGTTGCTACA 60.018 38.462 2.82 2.82 40.06 2.74
127 128 7.602644 ACATATCGGCAATTCGTAGATTATGTT 59.397 33.333 0.00 0.00 35.04 2.71
181 182 4.327357 TGCATAACCAAAACACAAAACACG 59.673 37.500 0.00 0.00 0.00 4.49
185 186 5.645497 AGCTTTGCATAACCAAAACACAAAA 59.355 32.000 0.00 0.00 34.59 2.44
220 221 3.637432 TCATAGCCAAAACACAAAAGCG 58.363 40.909 0.00 0.00 0.00 4.68
222 223 7.065683 AGGTTTTTCATAGCCAAAACACAAAAG 59.934 33.333 9.15 0.00 42.35 2.27
227 229 5.356426 ACAGGTTTTTCATAGCCAAAACAC 58.644 37.500 9.15 0.85 42.35 3.32
303 306 2.084546 GGGAGATTTGGACGAGTTTGG 58.915 52.381 0.00 0.00 0.00 3.28
315 318 1.880027 GCAAGTTCACACGGGAGATTT 59.120 47.619 0.00 0.00 0.00 2.17
319 322 2.317609 CGGCAAGTTCACACGGGAG 61.318 63.158 0.00 0.00 0.00 4.30
335 338 2.455674 TGACCATGACTTGAAGACGG 57.544 50.000 0.00 0.00 0.00 4.79
339 342 4.202141 TGGCTTTTTGACCATGACTTGAAG 60.202 41.667 0.00 0.00 0.00 3.02
363 366 1.883732 GGAGCTCTGACGTACAGCA 59.116 57.895 14.64 0.00 45.38 4.41
425 432 8.200120 TGTCCTAGTCTGATTCTTGTATGATTG 58.800 37.037 0.00 0.00 0.00 2.67
480 592 1.616865 CTCCCGTTAGTGTTCCAGTCA 59.383 52.381 0.00 0.00 0.00 3.41
502 614 4.042062 TGATCAAGTCTGGTTTGGAGATGT 59.958 41.667 0.00 0.00 0.00 3.06
507 619 5.445069 TCTTTTGATCAAGTCTGGTTTGGA 58.555 37.500 8.41 0.00 0.00 3.53
509 621 6.154445 CCATCTTTTGATCAAGTCTGGTTTG 58.846 40.000 8.41 0.86 36.97 2.93
510 622 5.279156 GCCATCTTTTGATCAAGTCTGGTTT 60.279 40.000 20.37 0.25 36.97 3.27
511 623 4.219288 GCCATCTTTTGATCAAGTCTGGTT 59.781 41.667 20.37 1.46 36.97 3.67
606 755 7.420002 CAGTATAATATGCAGTGCAAATGTGT 58.580 34.615 23.90 6.91 43.62 3.72
805 1000 2.131023 GAATGGTGGAGAGGGAAGGAT 58.869 52.381 0.00 0.00 0.00 3.24
809 1004 1.081174 AGGAGAATGGTGGAGAGGGAA 59.919 52.381 0.00 0.00 0.00 3.97
819 1015 2.238395 GCTCTTCTTGGAGGAGAATGGT 59.762 50.000 10.19 0.00 37.89 3.55
826 1022 1.207791 GGGATGCTCTTCTTGGAGGA 58.792 55.000 0.00 0.00 38.01 3.71
828 1024 0.826715 TCGGGATGCTCTTCTTGGAG 59.173 55.000 0.00 0.00 36.50 3.86
850 1049 0.331954 AGAGCTCGTTGGAGTAGGGA 59.668 55.000 8.37 0.00 42.53 4.20
952 1183 1.779025 CTCGCTTGCAGCAGTTGTGT 61.779 55.000 0.00 0.00 42.58 3.72
963 1196 3.254060 TGTATCTTGAAGTCTCGCTTGC 58.746 45.455 0.00 0.00 37.59 4.01
965 1198 4.021894 ACACTGTATCTTGAAGTCTCGCTT 60.022 41.667 0.00 0.00 40.76 4.68
967 1200 3.839293 ACACTGTATCTTGAAGTCTCGC 58.161 45.455 0.00 0.00 0.00 5.03
1122 1358 2.760385 GGCCTGCGGTACTCCTCT 60.760 66.667 0.00 0.00 0.00 3.69
1266 1502 1.723870 GTTCGCCATGCTGGTCATC 59.276 57.895 4.45 0.00 40.46 2.92
1330 1566 0.105658 CCCTCCTTGGTCCTCCGATA 60.106 60.000 0.00 0.00 36.30 2.92
1677 1913 2.099756 GCCCGCAATCTTAAATGCTTCT 59.900 45.455 6.14 0.00 40.39 2.85
1737 1973 2.942376 CGTGCCATTAACCATAGCAAGA 59.058 45.455 0.00 0.00 35.36 3.02
1938 2174 2.976490 GCTGCCCTCCAGGATGTGT 61.976 63.158 0.00 0.00 42.03 3.72
2139 2375 2.151202 TGAATTGCCTTTCCACGAGAC 58.849 47.619 0.00 0.00 0.00 3.36
2298 2534 2.922503 TTGCGGCCACCTGAGAGA 60.923 61.111 2.24 0.00 0.00 3.10
2508 2744 2.979813 CAGCGCAACCAAAAATGTAGAC 59.020 45.455 11.47 0.00 0.00 2.59
2577 2813 5.065090 CACTCTTGTGACACAATTCTTGACA 59.935 40.000 20.86 0.00 46.55 3.58
2694 2930 1.623081 CGTCCGCGTATGCAAACACT 61.623 55.000 4.92 0.00 42.97 3.55
3257 3571 4.479619 CCTTTTGCTTACATCAGAACAGC 58.520 43.478 0.00 0.00 0.00 4.40
3262 3576 2.819608 GTGCCCTTTTGCTTACATCAGA 59.180 45.455 0.00 0.00 0.00 3.27
3286 3600 8.583810 AGAACATCAACATTTGTCATGAAAAG 57.416 30.769 0.00 0.00 0.00 2.27
3342 3656 5.743026 TTAGTTTCAACGTGCTGATTCAA 57.257 34.783 0.00 0.00 0.00 2.69
3847 4839 5.645929 ACCAAATGCGATATGTTAACTCACA 59.354 36.000 7.22 0.00 0.00 3.58
4034 5027 7.807977 AAATGCACCCTAAGTATTCATACTG 57.192 36.000 0.07 0.00 42.47 2.74
4082 5075 9.260002 GTGTGACAATGTTTATCCAAAAATCTT 57.740 29.630 0.00 0.00 0.00 2.40
4083 5076 8.641541 AGTGTGACAATGTTTATCCAAAAATCT 58.358 29.630 0.00 0.00 0.00 2.40
4084 5077 8.816640 AGTGTGACAATGTTTATCCAAAAATC 57.183 30.769 0.00 0.00 0.00 2.17
4090 5083 9.337396 GGATATTAGTGTGACAATGTTTATCCA 57.663 33.333 17.76 0.00 0.00 3.41
4091 5084 8.784043 GGGATATTAGTGTGACAATGTTTATCC 58.216 37.037 15.88 15.88 0.00 2.59
4092 5085 9.561069 AGGGATATTAGTGTGACAATGTTTATC 57.439 33.333 0.00 0.22 0.00 1.75
4093 5086 9.920946 AAGGGATATTAGTGTGACAATGTTTAT 57.079 29.630 0.00 0.00 0.00 1.40
4095 5088 9.174166 GTAAGGGATATTAGTGTGACAATGTTT 57.826 33.333 0.00 0.00 0.00 2.83
4096 5089 8.325787 TGTAAGGGATATTAGTGTGACAATGTT 58.674 33.333 0.00 0.00 0.00 2.71
4097 5090 7.857456 TGTAAGGGATATTAGTGTGACAATGT 58.143 34.615 0.00 0.00 0.00 2.71
4098 5091 8.731275 TTGTAAGGGATATTAGTGTGACAATG 57.269 34.615 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.