Multiple sequence alignment - TraesCS1A01G170000

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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 TraesCS1A01G170000 chr1A 100.000 3882 0 0 1 3882 303730971 303727090 0.000000e+00 7169
1 TraesCS1A01G170000 chr1D 94.608 2207 88 17 1457 3655 239558335 239556152 0.000000e+00 3387
2 TraesCS1A01G170000 chr1D 94.841 1260 44 13 201 1459 239559610 239558371 0.000000e+00 1947
3 TraesCS1A01G170000 chr1D 91.286 241 10 6 3652 3882 239556130 239555891 6.260000e-83 318
4 TraesCS1A01G170000 chr1B 93.641 1950 83 21 1459 3379 334547873 334549810 0.000000e+00 2876
5 TraesCS1A01G170000 chr1B 94.132 1244 50 11 218 1459 334546613 334547835 0.000000e+00 1871


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 TraesCS1A01G170000 chr1A 303727090 303730971 3881 True 7169.0 7169 100.000000 1 3882 1 chr1A.!!$R1 3881
1 TraesCS1A01G170000 chr1D 239555891 239559610 3719 True 1884.0 3387 93.578333 201 3882 3 chr1D.!!$R1 3681
2 TraesCS1A01G170000 chr1B 334546613 334549810 3197 False 2373.5 2876 93.886500 218 3379 2 chr1B.!!$F1 3161

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
42 43 0.108804 ATCAGATTCGTCCACGCGTT 60.109 50.0 10.22 0.00 39.60 4.84 F
492 493 0.179081 GAAGGCCGGTTAGATTCGCT 60.179 55.0 1.90 0.00 0.00 4.93 F
585 586 0.322456 TGGAATCAAGCCCAGTTCGG 60.322 55.0 0.00 0.00 0.00 4.30 F
641 642 0.528684 ACTAAATCAGAGCCGCGAGC 60.529 55.0 8.23 9.98 44.25 5.03 F
642 643 1.218230 CTAAATCAGAGCCGCGAGCC 61.218 60.0 8.23 3.87 45.47 4.70 F
2617 2681 0.322187 TGGAGGACGAGACGATGACA 60.322 55.0 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1707 0.179032 TCGCCACGCATATCCCAATT 60.179 50.000 0.00 0.0 0.00 2.32 R
1663 1713 1.136611 GTTCGAATCGCCACGCATATC 60.137 52.381 0.00 0.0 0.00 1.63 R
2545 2609 3.329542 GAGCCCGGTCTTGATGGCA 62.330 63.158 0.00 0.0 46.45 4.92 R
2617 2681 2.661718 GAGGAAGAGAGGGAGAACGAT 58.338 52.381 0.00 0.0 0.00 3.73 R
2788 2852 1.241990 CCTCGTCGAGAACCCACAGA 61.242 60.000 23.74 0.0 0.00 3.41 R
3453 3532 0.037303 AACATGCCACTCCTGTCCTG 59.963 55.000 0.00 0.0 0.00 3.86 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 3.499918 ACTCTGTGCATACTTGACAAAGC 59.500 43.478 0.00 0.00 36.84 3.51
23 24 3.475575 TCTGTGCATACTTGACAAAGCA 58.524 40.909 0.00 0.00 36.84 3.91
24 25 4.074259 TCTGTGCATACTTGACAAAGCAT 58.926 39.130 0.00 0.00 36.84 3.79
25 26 4.154737 TCTGTGCATACTTGACAAAGCATC 59.845 41.667 0.00 3.88 36.84 3.91
26 27 3.819902 TGTGCATACTTGACAAAGCATCA 59.180 39.130 0.00 5.68 36.84 3.07
27 28 4.083164 TGTGCATACTTGACAAAGCATCAG 60.083 41.667 0.00 0.00 36.84 2.90
28 29 4.154737 GTGCATACTTGACAAAGCATCAGA 59.845 41.667 0.00 0.00 36.84 3.27
29 30 4.945543 TGCATACTTGACAAAGCATCAGAT 59.054 37.500 0.00 0.00 36.84 2.90
30 31 5.416639 TGCATACTTGACAAAGCATCAGATT 59.583 36.000 0.00 0.00 36.84 2.40
31 32 5.970023 GCATACTTGACAAAGCATCAGATTC 59.030 40.000 0.00 0.00 36.84 2.52
32 33 4.675190 ACTTGACAAAGCATCAGATTCG 57.325 40.909 0.00 0.00 36.84 3.34
33 34 4.067896 ACTTGACAAAGCATCAGATTCGT 58.932 39.130 0.00 0.00 36.84 3.85
34 35 4.153117 ACTTGACAAAGCATCAGATTCGTC 59.847 41.667 0.00 0.00 36.84 4.20
35 36 3.002791 TGACAAAGCATCAGATTCGTCC 58.997 45.455 0.00 0.00 0.00 4.79
36 37 3.002791 GACAAAGCATCAGATTCGTCCA 58.997 45.455 0.00 0.00 0.00 4.02
37 38 2.744202 ACAAAGCATCAGATTCGTCCAC 59.256 45.455 0.00 0.00 0.00 4.02
38 39 1.645034 AAGCATCAGATTCGTCCACG 58.355 50.000 0.00 0.00 41.45 4.94
39 40 0.807667 AGCATCAGATTCGTCCACGC 60.808 55.000 0.00 0.00 39.60 5.34
40 41 1.920051 CATCAGATTCGTCCACGCG 59.080 57.895 3.53 3.53 39.60 6.01
41 42 0.802222 CATCAGATTCGTCCACGCGT 60.802 55.000 5.58 5.58 39.60 6.01
42 43 0.108804 ATCAGATTCGTCCACGCGTT 60.109 50.000 10.22 0.00 39.60 4.84
43 44 1.006825 TCAGATTCGTCCACGCGTTG 61.007 55.000 10.22 6.47 39.60 4.10
44 45 1.006571 AGATTCGTCCACGCGTTGT 60.007 52.632 10.22 0.00 39.60 3.32
56 57 2.726633 ACGCGTTGTGAATTGAAAAGG 58.273 42.857 5.58 0.00 0.00 3.11
57 58 1.451651 CGCGTTGTGAATTGAAAAGGC 59.548 47.619 0.00 2.78 0.00 4.35
58 59 1.451651 GCGTTGTGAATTGAAAAGGCG 59.548 47.619 0.00 0.00 0.00 5.52
59 60 2.856720 GCGTTGTGAATTGAAAAGGCGA 60.857 45.455 0.00 0.00 0.00 5.54
60 61 3.367607 CGTTGTGAATTGAAAAGGCGAA 58.632 40.909 0.00 0.00 0.00 4.70
61 62 3.794028 CGTTGTGAATTGAAAAGGCGAAA 59.206 39.130 0.00 0.00 0.00 3.46
62 63 4.444056 CGTTGTGAATTGAAAAGGCGAAAT 59.556 37.500 0.00 0.00 0.00 2.17
63 64 5.610124 CGTTGTGAATTGAAAAGGCGAAATG 60.610 40.000 0.00 0.00 0.00 2.32
64 65 3.740321 TGTGAATTGAAAAGGCGAAATGC 59.260 39.130 0.00 0.00 45.38 3.56
74 75 4.763593 CGAAATGCCGCAACGAAT 57.236 50.000 0.00 0.00 0.00 3.34
75 76 3.887777 CGAAATGCCGCAACGAATA 57.112 47.368 0.00 0.00 0.00 1.75
76 77 1.730176 CGAAATGCCGCAACGAATAG 58.270 50.000 0.00 0.00 0.00 1.73
77 78 1.062002 CGAAATGCCGCAACGAATAGT 59.938 47.619 0.00 0.00 0.00 2.12
78 79 2.283086 CGAAATGCCGCAACGAATAGTA 59.717 45.455 0.00 0.00 0.00 1.82
79 80 3.059868 CGAAATGCCGCAACGAATAGTAT 60.060 43.478 0.00 0.00 0.00 2.12
80 81 4.149221 CGAAATGCCGCAACGAATAGTATA 59.851 41.667 0.00 0.00 0.00 1.47
81 82 4.985044 AATGCCGCAACGAATAGTATAC 57.015 40.909 0.00 0.00 0.00 1.47
82 83 3.439895 TGCCGCAACGAATAGTATACA 57.560 42.857 5.50 0.00 0.00 2.29
83 84 3.783191 TGCCGCAACGAATAGTATACAA 58.217 40.909 5.50 0.00 0.00 2.41
84 85 4.182339 TGCCGCAACGAATAGTATACAAA 58.818 39.130 5.50 0.00 0.00 2.83
85 86 4.630505 TGCCGCAACGAATAGTATACAAAA 59.369 37.500 5.50 0.00 0.00 2.44
86 87 4.959757 GCCGCAACGAATAGTATACAAAAC 59.040 41.667 5.50 0.00 0.00 2.43
87 88 5.220529 GCCGCAACGAATAGTATACAAAACT 60.221 40.000 5.50 0.00 0.00 2.66
88 89 6.408428 CCGCAACGAATAGTATACAAAACTC 58.592 40.000 5.50 0.00 0.00 3.01
89 90 6.035220 CCGCAACGAATAGTATACAAAACTCA 59.965 38.462 5.50 0.00 0.00 3.41
90 91 7.412129 CCGCAACGAATAGTATACAAAACTCAA 60.412 37.037 5.50 0.00 0.00 3.02
91 92 8.114290 CGCAACGAATAGTATACAAAACTCAAT 58.886 33.333 5.50 0.00 0.00 2.57
92 93 9.210426 GCAACGAATAGTATACAAAACTCAATG 57.790 33.333 5.50 0.00 0.00 2.82
106 107 9.008965 ACAAAACTCAATGTTGTATGTATAGCA 57.991 29.630 0.00 0.00 39.13 3.49
109 110 7.969536 ACTCAATGTTGTATGTATAGCATCC 57.030 36.000 0.00 0.00 38.94 3.51
110 111 6.936900 ACTCAATGTTGTATGTATAGCATCCC 59.063 38.462 0.00 0.00 38.94 3.85
111 112 7.078249 TCAATGTTGTATGTATAGCATCCCT 57.922 36.000 0.00 0.00 38.94 4.20
112 113 7.517320 TCAATGTTGTATGTATAGCATCCCTT 58.483 34.615 0.00 0.00 38.94 3.95
113 114 7.661437 TCAATGTTGTATGTATAGCATCCCTTC 59.339 37.037 0.00 0.00 38.94 3.46
114 115 5.538118 TGTTGTATGTATAGCATCCCTTCG 58.462 41.667 0.00 0.00 38.94 3.79
115 116 5.069914 TGTTGTATGTATAGCATCCCTTCGT 59.930 40.000 0.00 0.00 38.94 3.85
116 117 5.801531 TGTATGTATAGCATCCCTTCGTT 57.198 39.130 0.00 0.00 38.94 3.85
117 118 5.779922 TGTATGTATAGCATCCCTTCGTTC 58.220 41.667 0.00 0.00 38.94 3.95
118 119 3.746045 TGTATAGCATCCCTTCGTTCC 57.254 47.619 0.00 0.00 0.00 3.62
119 120 3.035363 TGTATAGCATCCCTTCGTTCCA 58.965 45.455 0.00 0.00 0.00 3.53
120 121 3.452990 TGTATAGCATCCCTTCGTTCCAA 59.547 43.478 0.00 0.00 0.00 3.53
121 122 3.644966 ATAGCATCCCTTCGTTCCAAA 57.355 42.857 0.00 0.00 0.00 3.28
122 123 2.286365 AGCATCCCTTCGTTCCAAAA 57.714 45.000 0.00 0.00 0.00 2.44
123 124 2.807676 AGCATCCCTTCGTTCCAAAAT 58.192 42.857 0.00 0.00 0.00 1.82
124 125 3.165071 AGCATCCCTTCGTTCCAAAATT 58.835 40.909 0.00 0.00 0.00 1.82
125 126 3.578282 AGCATCCCTTCGTTCCAAAATTT 59.422 39.130 0.00 0.00 0.00 1.82
126 127 4.040339 AGCATCCCTTCGTTCCAAAATTTT 59.960 37.500 0.00 0.00 0.00 1.82
127 128 4.388773 GCATCCCTTCGTTCCAAAATTTTC 59.611 41.667 0.00 0.00 0.00 2.29
128 129 5.537188 CATCCCTTCGTTCCAAAATTTTCA 58.463 37.500 0.00 0.00 0.00 2.69
129 130 5.799827 TCCCTTCGTTCCAAAATTTTCAT 57.200 34.783 0.00 0.00 0.00 2.57
130 131 6.168270 TCCCTTCGTTCCAAAATTTTCATT 57.832 33.333 0.00 0.00 0.00 2.57
131 132 6.587273 TCCCTTCGTTCCAAAATTTTCATTT 58.413 32.000 0.00 0.00 33.72 2.32
132 133 6.704050 TCCCTTCGTTCCAAAATTTTCATTTC 59.296 34.615 0.00 0.00 30.80 2.17
133 134 6.481644 CCCTTCGTTCCAAAATTTTCATTTCA 59.518 34.615 0.00 0.00 30.80 2.69
134 135 7.307337 CCCTTCGTTCCAAAATTTTCATTTCAG 60.307 37.037 0.00 0.00 30.80 3.02
135 136 7.437862 CCTTCGTTCCAAAATTTTCATTTCAGA 59.562 33.333 0.00 0.00 30.80 3.27
136 137 8.885494 TTCGTTCCAAAATTTTCATTTCAGAT 57.115 26.923 0.00 0.00 30.80 2.90
137 138 8.885494 TCGTTCCAAAATTTTCATTTCAGATT 57.115 26.923 0.00 0.00 30.80 2.40
138 139 9.323985 TCGTTCCAAAATTTTCATTTCAGATTT 57.676 25.926 0.00 0.00 30.80 2.17
139 140 9.372541 CGTTCCAAAATTTTCATTTCAGATTTG 57.627 29.630 0.00 0.00 30.80 2.32
178 179 9.982651 TCTAAGATAAGAATTTTATGACGGAGG 57.017 33.333 0.00 0.00 0.00 4.30
179 180 9.765795 CTAAGATAAGAATTTTATGACGGAGGT 57.234 33.333 0.00 0.00 0.00 3.85
195 196 9.883142 ATGACGGAGGTAATAGTATACTACTAC 57.117 37.037 18.87 18.87 43.46 2.73
196 197 8.314751 TGACGGAGGTAATAGTATACTACTACC 58.685 40.741 30.48 30.48 46.30 3.18
264 265 6.406177 GGACCACATACGGACTAAAATGAGTA 60.406 42.308 0.00 0.00 0.00 2.59
336 337 9.793259 AGTGAAGACATCTTAAAAATAGGAACA 57.207 29.630 0.00 0.00 36.11 3.18
374 375 3.982058 CCGTATTGTTTAGAGGAGATCGC 59.018 47.826 0.00 0.00 0.00 4.58
469 470 6.112734 TCTTGAACTTGTGCTCTTTTGACTA 58.887 36.000 0.00 0.00 0.00 2.59
477 478 4.249661 GTGCTCTTTTGACTAGGAGAAGG 58.750 47.826 0.00 0.00 0.00 3.46
482 483 0.252103 TTGACTAGGAGAAGGCCGGT 60.252 55.000 1.90 0.00 0.00 5.28
492 493 0.179081 GAAGGCCGGTTAGATTCGCT 60.179 55.000 1.90 0.00 0.00 4.93
553 554 3.677527 GCAAGATGCACCACTGCT 58.322 55.556 0.00 0.00 44.26 4.24
584 585 1.089920 CTGGAATCAAGCCCAGTTCG 58.910 55.000 0.00 0.00 43.71 3.95
585 586 0.322456 TGGAATCAAGCCCAGTTCGG 60.322 55.000 0.00 0.00 0.00 4.30
593 594 4.821589 CCCAGTTCGGCTCGGCTC 62.822 72.222 0.00 0.00 0.00 4.70
637 638 3.124560 GGTTCTACTAAATCAGAGCCGC 58.875 50.000 0.00 0.00 33.28 6.53
639 640 2.294979 TCTACTAAATCAGAGCCGCGA 58.705 47.619 8.23 0.00 0.00 5.87
640 641 2.290916 TCTACTAAATCAGAGCCGCGAG 59.709 50.000 8.23 0.00 0.00 5.03
641 642 0.528684 ACTAAATCAGAGCCGCGAGC 60.529 55.000 8.23 9.98 44.25 5.03
642 643 1.218230 CTAAATCAGAGCCGCGAGCC 61.218 60.000 8.23 3.87 45.47 4.70
643 644 2.954020 TAAATCAGAGCCGCGAGCCG 62.954 60.000 8.23 1.27 45.47 5.52
646 647 4.880537 CAGAGCCGCGAGCCGATT 62.881 66.667 8.23 0.00 45.47 3.34
647 648 4.880537 AGAGCCGCGAGCCGATTG 62.881 66.667 8.23 0.00 45.47 2.67
774 775 2.360767 CCGACCCCACCCGTCATAA 61.361 63.158 0.00 0.00 0.00 1.90
948 950 3.313012 GAAAAATTTCCCCTTCCCACG 57.687 47.619 0.00 0.00 0.00 4.94
1359 1361 4.351054 CCTCTTGTTGGCCCCGCT 62.351 66.667 0.00 0.00 0.00 5.52
1453 1455 4.935702 TGTTCAAGATTGGAGTTTTGCTG 58.064 39.130 0.00 0.00 0.00 4.41
1577 1627 6.011981 TGTTCCTCTCCCCATTGTAGTAAAAT 60.012 38.462 0.00 0.00 0.00 1.82
1581 1631 8.616598 TCCTCTCCCCATTGTAGTAAAATAAAA 58.383 33.333 0.00 0.00 0.00 1.52
1582 1632 9.250246 CCTCTCCCCATTGTAGTAAAATAAAAA 57.750 33.333 0.00 0.00 0.00 1.94
1657 1707 1.406887 GCGTGGAGAATTTGGCCTAGA 60.407 52.381 3.32 0.00 0.00 2.43
1663 1713 3.638627 GGAGAATTTGGCCTAGAATTGGG 59.361 47.826 3.32 0.00 0.00 4.12
1712 1765 8.301002 GTGGCTAGTAGTATCTGATAAAGAAGG 58.699 40.741 0.00 0.00 38.79 3.46
1899 1960 4.269844 GGTTCAGAAATTGCGCTTTTTGAA 59.730 37.500 18.26 18.26 37.07 2.69
2001 2062 3.751175 TGTTTTTGGCGTTAGATCTGAGG 59.249 43.478 5.18 3.93 0.00 3.86
2011 2072 6.238239 GGCGTTAGATCTGAGGAATTTTTCTC 60.238 42.308 11.04 0.00 0.00 2.87
2020 2081 3.084786 AGGAATTTTTCTCGCCCTCTTG 58.915 45.455 0.00 0.00 0.00 3.02
2173 2237 3.958860 AAGAAGCAGCTGGGCGGT 61.959 61.111 17.12 0.00 39.27 5.68
2287 2351 2.756283 CGCTCCGTCTCCTCCCTT 60.756 66.667 0.00 0.00 0.00 3.95
2617 2681 0.322187 TGGAGGACGAGACGATGACA 60.322 55.000 0.00 0.00 0.00 3.58
2812 2876 0.752376 GGGTTCTCGACGAGGAGGAT 60.752 60.000 23.92 0.00 34.74 3.24
2851 2915 1.512522 CGTCACGTTCGCCGACATA 60.513 57.895 13.05 0.00 40.70 2.29
2893 2957 1.227205 GCAGTGAGGCGGAGATGAG 60.227 63.158 0.00 0.00 0.00 2.90
2951 3015 0.813821 GGAGAGGATTTGCTGTTGGC 59.186 55.000 0.00 0.00 42.22 4.52
3043 3108 4.035091 TGTTCTTTGTTGAGACATGTTCCG 59.965 41.667 0.00 0.00 35.29 4.30
3066 3133 6.291585 CCGAGTTTGCTGTGTTATTTTTGTTC 60.292 38.462 0.00 0.00 0.00 3.18
3083 3150 1.812571 GTTCGCTTGGTGGTGATGAAT 59.187 47.619 0.00 0.00 0.00 2.57
3104 3171 6.432162 TGAATCTGAAGACTTGCTTATGCTTT 59.568 34.615 0.00 0.00 36.83 3.51
3172 3247 4.155462 TGTTTCTAAGCTGACGACGTAGAT 59.845 41.667 0.00 0.00 0.00 1.98
3174 3249 5.401033 TTCTAAGCTGACGACGTAGATAC 57.599 43.478 0.00 0.00 0.00 2.24
3180 3255 2.130395 TGACGACGTAGATACTAGCCG 58.870 52.381 0.00 0.00 0.00 5.52
3204 3282 7.118390 CCGTCCATTTTTATTGGTGCATTTTTA 59.882 33.333 0.00 0.00 35.64 1.52
3218 3296 7.768120 TGGTGCATTTTTAGTTTTGTGAGATTT 59.232 29.630 0.00 0.00 0.00 2.17
3239 3317 9.965824 AGATTTTACATAGGAAAACAAACAGTG 57.034 29.630 0.00 0.00 0.00 3.66
3300 3378 3.871594 CCGATAAACTGAACATCTGGACC 59.128 47.826 0.00 0.00 0.00 4.46
3328 3406 6.551385 CACTGGAGTGGCATCTATTTATTC 57.449 41.667 0.00 0.00 42.10 1.75
3411 3490 0.744874 GATGCCGTGACCTACAGCTA 59.255 55.000 0.00 0.00 0.00 3.32
3445 3524 1.554160 AGCCTCAGAGATGGAAGTGTG 59.446 52.381 0.00 0.00 0.00 3.82
3453 3532 5.538053 TCAGAGATGGAAGTGTGGATAGATC 59.462 44.000 0.00 0.00 0.00 2.75
3557 3636 0.242017 GTCTCATTGTGCTTGTGGCC 59.758 55.000 0.00 0.00 40.92 5.36
3569 3648 2.354259 CTTGTGGCCACTGAATCTCTC 58.646 52.381 34.75 6.57 0.00 3.20
3643 3722 2.552743 CTGTCGGATAACTCTGGCGATA 59.447 50.000 0.00 0.00 34.96 2.92
3647 3726 3.050619 CGGATAACTCTGGCGATAACAC 58.949 50.000 0.00 0.00 0.00 3.32
3673 3777 0.398318 AGGGCAAGTGTTCCTCTGAC 59.602 55.000 0.00 0.00 0.00 3.51
3758 3862 4.688021 AGAAACTGAGGAGATAACATCGC 58.312 43.478 0.00 0.00 0.00 4.58
3767 3871 2.226912 GAGATAACATCGCGGCTCTACT 59.773 50.000 6.13 0.00 0.00 2.57
3791 3903 0.109342 CCCAGTGCTTCACCTGTTCT 59.891 55.000 0.00 0.00 34.49 3.01
3796 3908 3.249559 CAGTGCTTCACCTGTTCTTTCTC 59.750 47.826 0.00 0.00 34.49 2.87
3799 3911 5.012561 AGTGCTTCACCTGTTCTTTCTCTAT 59.987 40.000 0.00 0.00 34.49 1.98
3804 3916 7.387948 GCTTCACCTGTTCTTTCTCTATTGTAA 59.612 37.037 0.00 0.00 0.00 2.41
3832 3946 2.834638 AAGGATTTGGCCTGCACTAT 57.165 45.000 3.32 0.00 38.58 2.12
3869 3983 0.033208 TAGAATTGCAGGCTTGGGGG 60.033 55.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.499918 GCTTTGTCAAGTATGCACAGAGT 59.500 43.478 0.00 0.00 31.86 3.24
1 2 3.499537 TGCTTTGTCAAGTATGCACAGAG 59.500 43.478 0.00 0.00 31.86 3.35
2 3 3.475575 TGCTTTGTCAAGTATGCACAGA 58.524 40.909 0.00 0.00 31.86 3.41
3 4 3.902261 TGCTTTGTCAAGTATGCACAG 57.098 42.857 0.00 0.00 31.86 3.66
4 5 3.819902 TGATGCTTTGTCAAGTATGCACA 59.180 39.130 0.00 0.00 35.62 4.57
5 6 4.154737 TCTGATGCTTTGTCAAGTATGCAC 59.845 41.667 0.00 0.00 35.62 4.57
6 7 4.325972 TCTGATGCTTTGTCAAGTATGCA 58.674 39.130 0.00 0.00 35.62 3.96
7 8 4.952262 TCTGATGCTTTGTCAAGTATGC 57.048 40.909 0.00 0.00 35.62 3.14
8 9 6.183360 ACGAATCTGATGCTTTGTCAAGTATG 60.183 38.462 0.00 0.00 35.62 2.39
9 10 5.877012 ACGAATCTGATGCTTTGTCAAGTAT 59.123 36.000 0.00 0.00 37.99 2.12
10 11 5.237815 ACGAATCTGATGCTTTGTCAAGTA 58.762 37.500 0.00 0.00 31.86 2.24
11 12 4.067896 ACGAATCTGATGCTTTGTCAAGT 58.932 39.130 0.00 0.00 31.86 3.16
12 13 4.436584 GGACGAATCTGATGCTTTGTCAAG 60.437 45.833 10.48 0.00 37.46 3.02
13 14 3.436704 GGACGAATCTGATGCTTTGTCAA 59.563 43.478 10.48 0.00 37.46 3.18
14 15 3.002791 GGACGAATCTGATGCTTTGTCA 58.997 45.455 10.48 0.00 37.46 3.58
15 16 3.002791 TGGACGAATCTGATGCTTTGTC 58.997 45.455 0.00 0.00 35.77 3.18
16 17 2.744202 GTGGACGAATCTGATGCTTTGT 59.256 45.455 0.00 0.00 0.00 2.83
17 18 2.222886 CGTGGACGAATCTGATGCTTTG 60.223 50.000 0.00 0.00 43.02 2.77
18 19 2.002586 CGTGGACGAATCTGATGCTTT 58.997 47.619 0.00 0.00 43.02 3.51
19 20 1.645034 CGTGGACGAATCTGATGCTT 58.355 50.000 0.00 0.00 43.02 3.91
20 21 0.807667 GCGTGGACGAATCTGATGCT 60.808 55.000 2.73 0.00 43.02 3.79
21 22 1.638467 GCGTGGACGAATCTGATGC 59.362 57.895 2.73 0.00 43.02 3.91
22 23 0.802222 ACGCGTGGACGAATCTGATG 60.802 55.000 12.93 0.00 43.02 3.07
23 24 0.108804 AACGCGTGGACGAATCTGAT 60.109 50.000 14.98 0.00 43.02 2.90
24 25 1.006825 CAACGCGTGGACGAATCTGA 61.007 55.000 14.98 0.00 43.02 3.27
25 26 1.282248 ACAACGCGTGGACGAATCTG 61.282 55.000 23.00 10.61 43.02 2.90
26 27 1.006571 ACAACGCGTGGACGAATCT 60.007 52.632 23.00 0.00 43.02 2.40
27 28 1.129809 CACAACGCGTGGACGAATC 59.870 57.895 23.00 0.00 42.34 2.52
28 29 0.876777 TTCACAACGCGTGGACGAAT 60.877 50.000 23.00 0.00 46.36 3.34
29 30 0.876777 ATTCACAACGCGTGGACGAA 60.877 50.000 23.00 21.21 46.36 3.85
30 31 0.876777 AATTCACAACGCGTGGACGA 60.877 50.000 23.00 13.49 46.36 4.20
31 32 0.721155 CAATTCACAACGCGTGGACG 60.721 55.000 23.00 11.13 46.36 4.79
32 33 0.584396 TCAATTCACAACGCGTGGAC 59.416 50.000 23.00 0.00 46.36 4.02
33 34 1.300481 TTCAATTCACAACGCGTGGA 58.700 45.000 23.00 12.66 46.36 4.02
34 35 2.112475 TTTCAATTCACAACGCGTGG 57.888 45.000 14.98 14.06 46.36 4.94
36 37 2.726633 CCTTTTCAATTCACAACGCGT 58.273 42.857 5.58 5.58 0.00 6.01
37 38 1.451651 GCCTTTTCAATTCACAACGCG 59.548 47.619 3.53 3.53 0.00 6.01
38 39 1.451651 CGCCTTTTCAATTCACAACGC 59.548 47.619 0.00 0.00 0.00 4.84
39 40 2.993545 TCGCCTTTTCAATTCACAACG 58.006 42.857 0.00 0.00 0.00 4.10
40 41 5.669122 CATTTCGCCTTTTCAATTCACAAC 58.331 37.500 0.00 0.00 0.00 3.32
41 42 4.210955 GCATTTCGCCTTTTCAATTCACAA 59.789 37.500 0.00 0.00 32.94 3.33
42 43 3.740321 GCATTTCGCCTTTTCAATTCACA 59.260 39.130 0.00 0.00 32.94 3.58
43 44 4.312097 GCATTTCGCCTTTTCAATTCAC 57.688 40.909 0.00 0.00 32.94 3.18
57 58 1.062002 ACTATTCGTTGCGGCATTTCG 59.938 47.619 2.28 9.76 0.00 3.46
58 59 2.825086 ACTATTCGTTGCGGCATTTC 57.175 45.000 2.28 0.00 0.00 2.17
59 60 4.812091 TGTATACTATTCGTTGCGGCATTT 59.188 37.500 2.28 0.00 0.00 2.32
60 61 4.373527 TGTATACTATTCGTTGCGGCATT 58.626 39.130 2.28 0.00 0.00 3.56
61 62 3.985008 TGTATACTATTCGTTGCGGCAT 58.015 40.909 2.28 0.00 0.00 4.40
62 63 3.439895 TGTATACTATTCGTTGCGGCA 57.560 42.857 0.00 0.00 0.00 5.69
63 64 4.782252 TTTGTATACTATTCGTTGCGGC 57.218 40.909 4.17 0.00 0.00 6.53
64 65 6.035220 TGAGTTTTGTATACTATTCGTTGCGG 59.965 38.462 4.17 0.00 0.00 5.69
65 66 6.985013 TGAGTTTTGTATACTATTCGTTGCG 58.015 36.000 4.17 0.00 0.00 4.85
66 67 9.210426 CATTGAGTTTTGTATACTATTCGTTGC 57.790 33.333 4.17 0.00 0.00 4.17
80 81 9.008965 TGCTATACATACAACATTGAGTTTTGT 57.991 29.630 0.00 0.00 38.74 2.83
83 84 8.840321 GGATGCTATACATACAACATTGAGTTT 58.160 33.333 0.00 0.00 39.69 2.66
84 85 7.445402 GGGATGCTATACATACAACATTGAGTT 59.555 37.037 0.00 0.00 42.01 3.01
85 86 6.936900 GGGATGCTATACATACAACATTGAGT 59.063 38.462 0.00 0.00 42.01 3.41
86 87 7.164122 AGGGATGCTATACATACAACATTGAG 58.836 38.462 0.00 0.00 42.01 3.02
87 88 7.078249 AGGGATGCTATACATACAACATTGA 57.922 36.000 0.00 0.00 42.01 2.57
88 89 7.360353 CGAAGGGATGCTATACATACAACATTG 60.360 40.741 0.00 0.00 42.01 2.82
89 90 6.650807 CGAAGGGATGCTATACATACAACATT 59.349 38.462 0.00 0.00 42.01 2.71
90 91 6.166279 CGAAGGGATGCTATACATACAACAT 58.834 40.000 0.00 0.00 42.01 2.71
91 92 5.069914 ACGAAGGGATGCTATACATACAACA 59.930 40.000 0.00 0.00 42.01 3.33
92 93 5.539048 ACGAAGGGATGCTATACATACAAC 58.461 41.667 0.00 0.00 42.01 3.32
93 94 5.801531 ACGAAGGGATGCTATACATACAA 57.198 39.130 0.00 0.00 42.01 2.41
94 95 5.279306 GGAACGAAGGGATGCTATACATACA 60.279 44.000 0.00 0.00 42.01 2.29
95 96 5.169295 GGAACGAAGGGATGCTATACATAC 58.831 45.833 0.00 0.00 39.84 2.39
96 97 4.836175 TGGAACGAAGGGATGCTATACATA 59.164 41.667 0.00 0.00 39.84 2.29
97 98 3.646162 TGGAACGAAGGGATGCTATACAT 59.354 43.478 0.00 0.00 43.54 2.29
98 99 3.035363 TGGAACGAAGGGATGCTATACA 58.965 45.455 0.00 0.00 0.00 2.29
99 100 3.746045 TGGAACGAAGGGATGCTATAC 57.254 47.619 0.00 0.00 0.00 1.47
100 101 4.764050 TTTGGAACGAAGGGATGCTATA 57.236 40.909 0.00 0.00 0.00 1.31
101 102 3.644966 TTTGGAACGAAGGGATGCTAT 57.355 42.857 0.00 0.00 0.00 2.97
102 103 3.426787 TTTTGGAACGAAGGGATGCTA 57.573 42.857 0.00 0.00 0.00 3.49
103 104 2.286365 TTTTGGAACGAAGGGATGCT 57.714 45.000 0.00 0.00 0.00 3.79
104 105 3.592898 AATTTTGGAACGAAGGGATGC 57.407 42.857 0.00 0.00 0.00 3.91
105 106 5.537188 TGAAAATTTTGGAACGAAGGGATG 58.463 37.500 8.47 0.00 0.00 3.51
106 107 5.799827 TGAAAATTTTGGAACGAAGGGAT 57.200 34.783 8.47 0.00 0.00 3.85
107 108 5.799827 ATGAAAATTTTGGAACGAAGGGA 57.200 34.783 8.47 0.00 0.00 4.20
108 109 6.481644 TGAAATGAAAATTTTGGAACGAAGGG 59.518 34.615 8.47 0.00 0.00 3.95
109 110 7.437862 TCTGAAATGAAAATTTTGGAACGAAGG 59.562 33.333 8.47 0.00 0.00 3.46
110 111 8.351495 TCTGAAATGAAAATTTTGGAACGAAG 57.649 30.769 8.47 0.00 0.00 3.79
111 112 8.885494 ATCTGAAATGAAAATTTTGGAACGAA 57.115 26.923 8.47 0.00 0.00 3.85
112 113 8.885494 AATCTGAAATGAAAATTTTGGAACGA 57.115 26.923 8.47 0.00 0.00 3.85
113 114 9.372541 CAAATCTGAAATGAAAATTTTGGAACG 57.627 29.630 8.47 0.00 0.00 3.95
152 153 9.982651 CCTCCGTCATAAAATTCTTATCTTAGA 57.017 33.333 0.00 0.00 0.00 2.10
153 154 9.765795 ACCTCCGTCATAAAATTCTTATCTTAG 57.234 33.333 0.00 0.00 0.00 2.18
225 226 7.935210 CCGTATGTGGTCCCTACTAAAATATTT 59.065 37.037 0.00 0.00 0.00 1.40
235 236 1.772836 AGTCCGTATGTGGTCCCTAC 58.227 55.000 0.00 0.00 0.00 3.18
238 239 3.615224 TTTTAGTCCGTATGTGGTCCC 57.385 47.619 0.00 0.00 0.00 4.46
243 244 8.246908 TGTTTACTCATTTTAGTCCGTATGTG 57.753 34.615 0.00 0.00 0.00 3.21
264 265 4.634443 AGACGTGTTTTAGAGTGCTTGTTT 59.366 37.500 0.00 0.00 0.00 2.83
336 337 9.948964 AAACAATACGGTATTTAGTACTTTCCT 57.051 29.630 10.59 0.00 33.64 3.36
374 375 8.138074 TCTTTGGTTCAGATTCGATCTACATAG 58.862 37.037 0.00 0.00 37.58 2.23
469 470 1.763545 GAATCTAACCGGCCTTCTCCT 59.236 52.381 0.00 0.00 0.00 3.69
477 478 2.534903 GCCAGCGAATCTAACCGGC 61.535 63.158 0.00 0.00 0.00 6.13
482 483 0.387929 CCCGTAGCCAGCGAATCTAA 59.612 55.000 0.00 0.00 0.00 2.10
553 554 5.061853 GCTTGATTCCAGAAGATATGCAGA 58.938 41.667 0.00 0.00 0.00 4.26
590 591 3.491652 GTTTGAGCCGAGCCGAGC 61.492 66.667 0.00 0.00 0.00 5.03
591 592 1.807573 GAGTTTGAGCCGAGCCGAG 60.808 63.158 0.00 0.00 0.00 4.63
592 593 2.094757 TTGAGTTTGAGCCGAGCCGA 62.095 55.000 0.00 0.00 0.00 5.54
593 594 1.630244 CTTGAGTTTGAGCCGAGCCG 61.630 60.000 0.00 0.00 0.00 5.52
594 595 1.916697 GCTTGAGTTTGAGCCGAGCC 61.917 60.000 0.00 0.00 32.55 4.70
637 638 0.861837 GCTGTATTCCAATCGGCTCG 59.138 55.000 0.00 0.00 0.00 5.03
639 640 1.486310 TGAGCTGTATTCCAATCGGCT 59.514 47.619 0.00 0.00 44.93 5.52
640 641 1.953559 TGAGCTGTATTCCAATCGGC 58.046 50.000 0.00 0.00 0.00 5.54
641 642 3.070018 GGATGAGCTGTATTCCAATCGG 58.930 50.000 0.00 0.00 0.00 4.18
642 643 3.496130 GTGGATGAGCTGTATTCCAATCG 59.504 47.826 0.00 0.00 39.84 3.34
643 644 4.274459 GTGTGGATGAGCTGTATTCCAATC 59.726 45.833 0.00 0.00 39.84 2.67
644 645 4.202441 GTGTGGATGAGCTGTATTCCAAT 58.798 43.478 0.00 0.00 39.84 3.16
645 646 3.609853 GTGTGGATGAGCTGTATTCCAA 58.390 45.455 0.00 0.00 39.84 3.53
646 647 2.092968 GGTGTGGATGAGCTGTATTCCA 60.093 50.000 0.00 0.00 35.93 3.53
647 648 2.092968 TGGTGTGGATGAGCTGTATTCC 60.093 50.000 0.00 0.00 0.00 3.01
1358 1360 6.019801 CGGAATCACAGTAAATTAACCGAGAG 60.020 42.308 0.00 0.00 39.11 3.20
1359 1361 5.808540 CGGAATCACAGTAAATTAACCGAGA 59.191 40.000 0.00 0.00 39.11 4.04
1417 1419 2.966309 GAACAGGCGTCCGCAAAGG 61.966 63.158 14.19 2.16 44.11 3.11
1453 1455 8.553459 TCAATTAGATCTTGACTTGAACCTTC 57.447 34.615 0.00 0.00 0.00 3.46
1540 1583 3.326006 GGAGAGGAACATGGCATATCTCA 59.674 47.826 18.91 0.00 34.71 3.27
1581 1631 3.020984 TGTTCCTCCTGAAACGCTTTTT 58.979 40.909 0.00 0.00 33.94 1.94
1582 1632 2.650322 TGTTCCTCCTGAAACGCTTTT 58.350 42.857 0.00 0.00 33.94 2.27
1583 1633 2.341846 TGTTCCTCCTGAAACGCTTT 57.658 45.000 0.00 0.00 33.94 3.51
1584 1634 2.568623 ATGTTCCTCCTGAAACGCTT 57.431 45.000 0.00 0.00 33.94 4.68
1585 1635 3.914426 ATATGTTCCTCCTGAAACGCT 57.086 42.857 0.00 0.00 33.94 5.07
1586 1636 4.058817 CCTATATGTTCCTCCTGAAACGC 58.941 47.826 0.00 0.00 33.94 4.84
1587 1637 5.050490 CACCTATATGTTCCTCCTGAAACG 58.950 45.833 0.00 0.00 33.94 3.60
1637 1687 1.017387 CTAGGCCAAATTCTCCACGC 58.983 55.000 5.01 0.00 0.00 5.34
1657 1707 0.179032 TCGCCACGCATATCCCAATT 60.179 50.000 0.00 0.00 0.00 2.32
1663 1713 1.136611 GTTCGAATCGCCACGCATATC 60.137 52.381 0.00 0.00 0.00 1.63
1922 1983 9.875691 ATCAAAGATCCTTAATAAAAAGTTGCC 57.124 29.630 0.00 0.00 0.00 4.52
1933 1994 5.126067 CCACGGACATCAAAGATCCTTAAT 58.874 41.667 0.00 0.00 0.00 1.40
1961 2022 9.271828 CCAAAAACAAAAAGGTAAGCATATTCT 57.728 29.630 0.00 0.00 0.00 2.40
2001 2062 5.622770 TTACAAGAGGGCGAGAAAAATTC 57.377 39.130 0.00 0.00 0.00 2.17
2011 2072 6.618287 TTCATGATTTATTACAAGAGGGCG 57.382 37.500 0.00 0.00 0.00 6.13
2545 2609 3.329542 GAGCCCGGTCTTGATGGCA 62.330 63.158 0.00 0.00 46.45 4.92
2617 2681 2.661718 GAGGAAGAGAGGGAGAACGAT 58.338 52.381 0.00 0.00 0.00 3.73
2788 2852 1.241990 CCTCGTCGAGAACCCACAGA 61.242 60.000 23.74 0.00 0.00 3.41
2851 2915 0.106149 GTTCACGGAACACCCTCAGT 59.894 55.000 10.67 0.00 41.62 3.41
2893 2957 3.804325 GCAAAAACTCCAAGCCTTTCTTC 59.196 43.478 0.00 0.00 31.27 2.87
3043 3108 6.627274 CGAACAAAAATAACACAGCAAACTC 58.373 36.000 0.00 0.00 0.00 3.01
3066 3133 1.399440 CAGATTCATCACCACCAAGCG 59.601 52.381 0.00 0.00 0.00 4.68
3083 3150 5.764686 TCAAAAGCATAAGCAAGTCTTCAGA 59.235 36.000 0.00 0.00 45.49 3.27
3104 3171 4.335037 TGCACGATGCTGCTTTATTATCAA 59.665 37.500 0.00 0.00 45.31 2.57
3172 3247 5.587043 CACCAATAAAAATGGACGGCTAGTA 59.413 40.000 0.00 0.00 40.56 1.82
3174 3249 4.733523 GCACCAATAAAAATGGACGGCTAG 60.734 45.833 0.00 0.00 40.56 3.42
3180 3255 8.998377 ACTAAAAATGCACCAATAAAAATGGAC 58.002 29.630 0.00 0.00 40.56 4.02
3218 3296 6.952773 AGCACTGTTTGTTTTCCTATGTAA 57.047 33.333 0.00 0.00 0.00 2.41
3239 3317 6.374565 ACTCATGATTCAGAAAATGCTAGC 57.625 37.500 8.10 8.10 0.00 3.42
3270 3348 7.595502 CAGATGTTCAGTTTATCGGAGTATACC 59.404 40.741 0.00 0.00 0.00 2.73
3300 3378 1.004560 ATGCCACTCCAGTGTGTCG 60.005 57.895 5.99 0.00 44.21 4.35
3328 3406 3.961480 TGTGGGATATTCTAGCATCGG 57.039 47.619 0.00 0.00 0.00 4.18
3445 3524 2.896685 CCACTCCTGTCCTGATCTATCC 59.103 54.545 0.00 0.00 0.00 2.59
3453 3532 0.037303 AACATGCCACTCCTGTCCTG 59.963 55.000 0.00 0.00 0.00 3.86
3513 3592 5.878116 TGCCAGGTTTAACATCTGTACATAC 59.122 40.000 0.00 0.00 0.00 2.39
3557 3636 6.981762 AAGCATAACTTGAGAGATTCAGTG 57.018 37.500 0.00 0.00 37.17 3.66
3569 3648 3.921119 TGGACAGCAAAGCATAACTTG 57.079 42.857 0.00 0.00 39.09 3.16
3643 3722 1.072331 CACTTGCCCTCTACTGGTGTT 59.928 52.381 0.00 0.00 0.00 3.32
3647 3726 1.339151 GGAACACTTGCCCTCTACTGG 60.339 57.143 0.00 0.00 0.00 4.00
3706 3810 5.392811 CGTTTATCTCCTCTCAAGGTTACGT 60.393 44.000 0.00 0.00 43.82 3.57
3708 3812 6.205101 TCGTTTATCTCCTCTCAAGGTTAC 57.795 41.667 0.00 0.00 43.82 2.50
3758 3862 0.681564 ACTGGGACTGAGTAGAGCCG 60.682 60.000 0.00 0.00 0.00 5.52
3767 3871 0.764369 AGGTGAAGCACTGGGACTGA 60.764 55.000 0.00 0.00 34.40 3.41
3791 3903 8.380099 TCCTTTTGGCTACTTACAATAGAGAAA 58.620 33.333 0.00 0.00 40.12 2.52
3837 3951 1.632965 AATTCTAGGTCGGGCCACCC 61.633 60.000 17.97 10.41 41.09 4.61
3849 3963 1.396653 CCCCAAGCCTGCAATTCTAG 58.603 55.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.