Multiple sequence alignment - TraesCS6D01G357900

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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 TraesCS6D01G357900 chr6D 100.000 3476 0 0 1 3476 451154571 451158046 0.000000e+00 6420.0
1 TraesCS6D01G357900 chr6D 97.872 47 1 0 362 408 451154878 451154924 8.000000e-12 82.4
2 TraesCS6D01G357900 chr6D 97.872 47 1 0 308 354 451154932 451154978 8.000000e-12 82.4
3 TraesCS6D01G357900 chr6D 86.538 52 7 0 4 55 7866769 7866820 1.350000e-04 58.4
4 TraesCS6D01G357900 chr6A 93.648 2881 102 17 646 3476 596888717 596891566 0.000000e+00 4231.0
5 TraesCS6D01G357900 chr6A 89.030 474 35 7 179 637 596888203 596888674 3.890000e-159 571.0
6 TraesCS6D01G357900 chr6A 98.387 62 1 0 3 64 596888144 596888205 3.670000e-20 110.0
7 TraesCS6D01G357900 chr6A 95.082 61 3 0 303 363 596888391 596888451 2.860000e-16 97.1
8 TraesCS6D01G357900 chr6B 91.888 3082 143 20 469 3476 685303484 685306532 0.000000e+00 4207.0
9 TraesCS6D01G357900 chr6B 81.081 222 23 8 435 637 643163790 643164011 3.590000e-35 159.0
10 TraesCS6D01G357900 chr3D 85.366 205 26 3 435 637 411810190 411810392 3.520000e-50 209.0
11 TraesCS6D01G357900 chr7B 84.729 203 31 0 435 637 673685058 673685260 1.640000e-48 204.0
12 TraesCS6D01G357900 chr7B 93.130 131 6 3 60 189 300087018 300086890 4.580000e-44 189.0
13 TraesCS6D01G357900 chr7B 83.251 203 34 0 435 637 75423995 75423793 1.650000e-43 187.0
14 TraesCS6D01G357900 chr7D 96.667 120 4 0 62 181 253793467 253793586 2.120000e-47 200.0
15 TraesCS6D01G357900 chr7D 95.041 121 6 0 61 181 610248284 610248164 1.270000e-44 191.0
16 TraesCS6D01G357900 chr7D 90.741 54 5 0 11 64 636776750 636776697 4.810000e-09 73.1
17 TraesCS6D01G357900 chr7D 88.679 53 4 2 4 55 519274254 519274203 2.900000e-06 63.9
18 TraesCS6D01G357900 chr7D 100.000 29 0 0 335 363 204685706 204685678 2.000000e-03 54.7
19 TraesCS6D01G357900 chr7A 94.355 124 7 0 64 187 14888140 14888017 1.270000e-44 191.0
20 TraesCS6D01G357900 chr7A 88.889 54 6 0 11 64 729391846 729391899 2.240000e-07 67.6
21 TraesCS6D01G357900 chr1B 95.041 121 6 0 61 181 28559824 28559704 1.270000e-44 191.0
22 TraesCS6D01G357900 chr1B 94.355 124 6 1 59 181 389309879 389309756 4.580000e-44 189.0
23 TraesCS6D01G357900 chr1B 89.216 102 11 0 536 637 486395720 486395619 1.010000e-25 128.0
24 TraesCS6D01G357900 chr1B 91.489 47 4 0 265 311 500986661 500986615 8.050000e-07 65.8
25 TraesCS6D01G357900 chr5B 94.309 123 7 0 61 183 493651425 493651547 4.580000e-44 189.0
26 TraesCS6D01G357900 chr5B 77.333 225 27 12 435 637 488849524 488849302 1.020000e-20 111.0
27 TraesCS6D01G357900 chr5A 94.355 124 5 2 59 181 443739110 443738988 4.580000e-44 189.0
28 TraesCS6D01G357900 chr5A 91.803 61 5 0 4 64 85258887 85258947 6.180000e-13 86.1
29 TraesCS6D01G357900 chr4B 94.309 123 6 1 59 181 311014134 311014013 1.650000e-43 187.0
30 TraesCS6D01G357900 chr4A 90.244 123 12 0 515 637 144607969 144608091 9.980000e-36 161.0
31 TraesCS6D01G357900 chr2D 91.453 117 10 0 521 637 42724360 42724244 9.980000e-36 161.0
32 TraesCS6D01G357900 chr2D 86.207 58 7 1 4 61 558242676 558242732 1.040000e-05 62.1
33 TraesCS6D01G357900 chr1A 90.598 117 11 0 521 637 215803600 215803484 4.650000e-34 156.0
34 TraesCS6D01G357900 chr1A 90.598 117 10 1 521 637 361518024 361517909 1.670000e-33 154.0
35 TraesCS6D01G357900 chr1A 78.049 205 33 6 441 635 182206540 182206338 6.090000e-23 119.0
36 TraesCS6D01G357900 chr5D 79.018 224 24 10 435 637 15226218 15225997 7.830000e-27 132.0
37 TraesCS6D01G357900 chr5D 95.082 61 3 0 4 64 91556545 91556605 2.860000e-16 97.1
38 TraesCS6D01G357900 chr5D 97.297 37 1 0 265 301 460085817 460085853 2.900000e-06 63.9
39 TraesCS6D01G357900 chr4D 90.000 60 6 0 5 64 87957768 87957827 1.030000e-10 78.7


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 TraesCS6D01G357900 chr6D 451154571 451158046 3475 False 2194.933333 6420 98.581333 1 3476 3 chr6D.!!$F2 3475
1 TraesCS6D01G357900 chr6A 596888144 596891566 3422 False 1252.275000 4231 94.036750 3 3476 4 chr6A.!!$F1 3473
2 TraesCS6D01G357900 chr6B 685303484 685306532 3048 False 4207.000000 4207 91.888000 469 3476 1 chr6B.!!$F2 3007

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
167 168 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.0 0.0 0.0 41.36 5.14 F
587 603 0.108662 CTTCGGGCTTGATTTTGGGC 60.109 55.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2126 1.006102 GTCGTAGCTGTGCACCAGT 60.006 57.895 15.69 0.32 43.55 4.00 R
2577 2659 1.449601 GGGTTGATGGCACGTCGAT 60.450 57.895 0.00 0.00 0.00 3.59 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
44 45 3.585990 CGAATGACATGGCGGGCC 61.586 66.667 1.86 1.86 0.00 5.80
61 62 1.307647 CCAGGGCTGGGCTTAACAT 59.692 57.895 0.00 0.00 46.81 2.71
62 63 0.550914 CCAGGGCTGGGCTTAACATA 59.449 55.000 0.00 0.00 46.81 2.29
63 64 1.145738 CCAGGGCTGGGCTTAACATAT 59.854 52.381 0.00 0.00 46.81 1.78
64 65 2.375174 CCAGGGCTGGGCTTAACATATA 59.625 50.000 0.00 0.00 46.81 0.86
65 66 3.412386 CAGGGCTGGGCTTAACATATAC 58.588 50.000 0.00 0.00 0.00 1.47
66 67 3.073062 CAGGGCTGGGCTTAACATATACT 59.927 47.826 0.00 0.00 0.00 2.12
67 68 3.722101 AGGGCTGGGCTTAACATATACTT 59.278 43.478 0.00 0.00 0.00 2.24
68 69 4.072839 GGGCTGGGCTTAACATATACTTC 58.927 47.826 0.00 0.00 0.00 3.01
69 70 4.072839 GGCTGGGCTTAACATATACTTCC 58.927 47.826 0.00 0.00 0.00 3.46
70 71 4.202472 GGCTGGGCTTAACATATACTTCCT 60.202 45.833 0.00 0.00 0.00 3.36
71 72 4.998033 GCTGGGCTTAACATATACTTCCTC 59.002 45.833 0.00 0.00 0.00 3.71
72 73 5.552178 CTGGGCTTAACATATACTTCCTCC 58.448 45.833 0.00 0.00 0.00 4.30
73 74 4.039973 TGGGCTTAACATATACTTCCTCCG 59.960 45.833 0.00 0.00 0.00 4.63
74 75 4.040095 GGGCTTAACATATACTTCCTCCGT 59.960 45.833 0.00 0.00 0.00 4.69
75 76 5.228665 GGCTTAACATATACTTCCTCCGTC 58.771 45.833 0.00 0.00 0.00 4.79
76 77 5.228665 GCTTAACATATACTTCCTCCGTCC 58.771 45.833 0.00 0.00 0.00 4.79
77 78 5.443185 TTAACATATACTTCCTCCGTCCG 57.557 43.478 0.00 0.00 0.00 4.79
78 79 3.219176 ACATATACTTCCTCCGTCCGA 57.781 47.619 0.00 0.00 0.00 4.55
79 80 3.559069 ACATATACTTCCTCCGTCCGAA 58.441 45.455 0.00 0.00 0.00 4.30
80 81 3.956199 ACATATACTTCCTCCGTCCGAAA 59.044 43.478 0.00 0.00 0.00 3.46
81 82 4.403432 ACATATACTTCCTCCGTCCGAAAA 59.597 41.667 0.00 0.00 0.00 2.29
82 83 5.070047 ACATATACTTCCTCCGTCCGAAAAT 59.930 40.000 0.00 0.00 0.00 1.82
83 84 6.266103 ACATATACTTCCTCCGTCCGAAAATA 59.734 38.462 0.00 0.00 0.00 1.40
84 85 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
85 86 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
86 87 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
87 88 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
88 89 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
89 90 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
90 91 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
91 92 2.228582 TCCGTCCGAAAATACTTGTCGA 59.771 45.455 1.13 0.00 36.92 4.20
92 93 2.988493 CCGTCCGAAAATACTTGTCGAA 59.012 45.455 1.13 0.00 36.92 3.71
93 94 3.060363 CCGTCCGAAAATACTTGTCGAAG 59.940 47.826 1.13 0.00 36.92 3.79
94 95 3.916172 CGTCCGAAAATACTTGTCGAAGA 59.084 43.478 1.13 0.00 36.92 2.87
95 96 4.383649 CGTCCGAAAATACTTGTCGAAGAA 59.616 41.667 1.13 0.00 39.69 2.52
96 97 5.107760 CGTCCGAAAATACTTGTCGAAGAAA 60.108 40.000 1.13 0.00 39.69 2.52
97 98 6.400727 CGTCCGAAAATACTTGTCGAAGAAAT 60.401 38.462 1.13 0.00 39.69 2.17
98 99 6.736853 GTCCGAAAATACTTGTCGAAGAAATG 59.263 38.462 1.13 0.00 39.69 2.32
99 100 5.508224 CCGAAAATACTTGTCGAAGAAATGC 59.492 40.000 1.13 0.00 39.69 3.56
100 101 6.077197 CGAAAATACTTGTCGAAGAAATGCA 58.923 36.000 0.00 0.00 39.69 3.96
101 102 6.742718 CGAAAATACTTGTCGAAGAAATGCAT 59.257 34.615 0.00 0.00 39.69 3.96
102 103 7.902917 CGAAAATACTTGTCGAAGAAATGCATA 59.097 33.333 0.00 0.00 39.69 3.14
103 104 9.554724 GAAAATACTTGTCGAAGAAATGCATAA 57.445 29.630 0.00 0.00 39.69 1.90
104 105 9.906660 AAAATACTTGTCGAAGAAATGCATAAA 57.093 25.926 0.00 0.00 39.69 1.40
105 106 9.906660 AAATACTTGTCGAAGAAATGCATAAAA 57.093 25.926 0.00 0.00 39.69 1.52
106 107 9.906660 AATACTTGTCGAAGAAATGCATAAAAA 57.093 25.926 0.00 0.00 39.69 1.94
108 109 8.231304 ACTTGTCGAAGAAATGCATAAAAATG 57.769 30.769 0.00 0.00 39.69 2.32
109 110 8.081633 ACTTGTCGAAGAAATGCATAAAAATGA 58.918 29.630 0.00 0.00 39.69 2.57
110 111 8.809159 TTGTCGAAGAAATGCATAAAAATGAA 57.191 26.923 0.00 0.00 39.69 2.57
111 112 8.984891 TGTCGAAGAAATGCATAAAAATGAAT 57.015 26.923 0.00 0.00 39.69 2.57
112 113 8.862074 TGTCGAAGAAATGCATAAAAATGAATG 58.138 29.630 0.00 0.00 39.69 2.67
113 114 8.863049 GTCGAAGAAATGCATAAAAATGAATGT 58.137 29.630 0.00 0.00 39.69 2.71
150 151 9.781425 AGAATACATCTAGATACATCCATTCCT 57.219 33.333 4.54 0.00 36.32 3.36
152 153 6.865834 ACATCTAGATACATCCATTCCTCC 57.134 41.667 4.54 0.00 0.00 4.30
153 154 5.420421 ACATCTAGATACATCCATTCCTCCG 59.580 44.000 4.54 0.00 0.00 4.63
154 155 5.256806 TCTAGATACATCCATTCCTCCGA 57.743 43.478 0.00 0.00 0.00 4.55
155 156 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
156 157 2.558795 AGATACATCCATTCCTCCGACG 59.441 50.000 0.00 0.00 0.00 5.12
157 158 2.061509 TACATCCATTCCTCCGACGA 57.938 50.000 0.00 0.00 0.00 4.20
158 159 0.747255 ACATCCATTCCTCCGACGAG 59.253 55.000 0.00 0.00 35.72 4.18
159 160 0.747255 CATCCATTCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
160 161 1.954382 CATCCATTCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
161 162 2.359981 TCCATTCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
162 163 2.662866 TCCATTCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
163 164 3.028850 TCCATTCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
164 165 3.067742 TCCATTCCTCCGACGAGTATTTC 59.932 47.826 0.00 0.00 33.93 2.17
165 166 3.381949 CATTCCTCCGACGAGTATTTCC 58.618 50.000 0.00 0.00 33.93 3.13
166 167 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
167 168 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
168 169 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
169 170 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
170 171 0.452987 CCGACGAGTATTTCCGGACA 59.547 55.000 1.83 0.00 42.49 4.02
171 172 1.135315 CCGACGAGTATTTCCGGACAA 60.135 52.381 1.83 2.11 42.49 3.18
172 173 2.598589 CGACGAGTATTTCCGGACAAA 58.401 47.619 1.83 0.00 0.00 2.83
173 174 2.597305 CGACGAGTATTTCCGGACAAAG 59.403 50.000 1.83 0.00 0.00 2.77
174 175 2.928116 GACGAGTATTTCCGGACAAAGG 59.072 50.000 1.83 0.00 0.00 3.11
175 176 2.277084 CGAGTATTTCCGGACAAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
176 177 2.093869 CGAGTATTTCCGGACAAAGGGA 60.094 50.000 1.83 0.00 0.00 4.20
177 178 3.532542 GAGTATTTCCGGACAAAGGGAG 58.467 50.000 1.83 0.00 33.01 4.30
257 270 2.024941 CCTGAATTCTAGGCCCAAAGGT 60.025 50.000 7.05 0.00 34.57 3.50
307 320 1.303806 TTTTTAGGCCCGACCCTGC 60.304 57.895 0.00 0.00 40.58 4.85
323 336 2.203209 GCCCGAGTTATGGCCTGG 60.203 66.667 3.32 0.00 41.97 4.45
341 354 3.181472 CCTGGTATACCCGTGACTAAACC 60.181 52.174 19.42 0.00 35.15 3.27
354 367 0.322997 CTAAACCCGGGCATGGACAA 60.323 55.000 24.08 0.00 0.00 3.18
360 373 2.750237 GGGCATGGACAACCCGAC 60.750 66.667 0.00 0.00 37.93 4.79
389 402 0.399376 TGGCCTGGTATACCCGTGAT 60.399 55.000 19.42 0.00 35.15 3.06
462 475 1.000938 GGCTCAGGACTTGTTTTGCAG 60.001 52.381 0.00 0.00 0.00 4.41
465 478 1.035139 CAGGACTTGTTTTGCAGCCT 58.965 50.000 0.00 0.00 0.00 4.58
506 519 2.871633 GCTCAGGCTTCTCTATTTCTGC 59.128 50.000 0.00 0.00 35.22 4.26
512 525 5.356190 CAGGCTTCTCTATTTCTGCATTTCA 59.644 40.000 0.00 0.00 0.00 2.69
519 532 5.255687 TCTATTTCTGCATTTCAAGCTGGA 58.744 37.500 0.00 0.00 0.00 3.86
530 543 1.447643 AAGCTGGACTTGCACGTCT 59.552 52.632 21.17 0.30 37.17 4.18
587 603 0.108662 CTTCGGGCTTGATTTTGGGC 60.109 55.000 0.00 0.00 0.00 5.36
608 624 0.600057 GGGCTCAGGCTTGAAAACAG 59.400 55.000 0.00 0.00 38.73 3.16
618 634 6.772716 TCAGGCTTGAAAACAGAGAGTATTTT 59.227 34.615 0.00 0.00 0.00 1.82
654 704 0.856641 TCTCGAGAAAACGTTTGCCG 59.143 50.000 15.46 17.27 44.03 5.69
871 921 1.938329 GCTCGGCTTACGCTACGTC 60.938 63.158 0.00 0.00 43.86 4.34
903 953 1.886542 GAGTTCCCAATGACCAACACC 59.113 52.381 0.00 0.00 0.00 4.16
922 972 2.735237 CCCCTACGCTTCGATCCC 59.265 66.667 0.00 0.00 0.00 3.85
1736 1804 2.317609 CCGAGGTGTTCAACTGCGG 61.318 63.158 11.76 11.76 38.44 5.69
1737 1805 2.317609 CGAGGTGTTCAACTGCGGG 61.318 63.158 0.00 0.00 0.00 6.13
1800 1868 2.511600 CCGCCCAACCAGATCGTC 60.512 66.667 0.00 0.00 0.00 4.20
2058 2126 0.251386 AGAGCTTCAGGACGGTCTCA 60.251 55.000 8.23 0.00 33.04 3.27
2268 2336 5.873164 AGTCCGTCTGTATCATGGTTTTTAC 59.127 40.000 0.00 0.00 0.00 2.01
2269 2337 5.064325 GTCCGTCTGTATCATGGTTTTTACC 59.936 44.000 0.00 0.00 0.00 2.85
2300 2373 0.662619 TGCTACTTGTGCTGTTGTGC 59.337 50.000 0.00 0.00 0.00 4.57
2359 2434 8.543774 GTGGAGTGGACAATGGAGAATATATAT 58.456 37.037 0.00 0.00 0.00 0.86
2383 2459 8.736097 ATACATGGAGTGATACTTTATACCCA 57.264 34.615 0.00 0.00 0.00 4.51
2384 2460 7.446106 ACATGGAGTGATACTTTATACCCAA 57.554 36.000 0.00 0.00 0.00 4.12
2385 2461 7.867921 ACATGGAGTGATACTTTATACCCAAA 58.132 34.615 0.00 0.00 0.00 3.28
2386 2462 8.502738 ACATGGAGTGATACTTTATACCCAAAT 58.497 33.333 0.00 0.00 0.00 2.32
2387 2463 8.786898 CATGGAGTGATACTTTATACCCAAATG 58.213 37.037 0.00 0.00 0.00 2.32
2388 2464 7.867921 TGGAGTGATACTTTATACCCAAATGT 58.132 34.615 0.00 0.00 0.00 2.71
2389 2465 8.333235 TGGAGTGATACTTTATACCCAAATGTT 58.667 33.333 0.00 0.00 0.00 2.71
2390 2466 9.841295 GGAGTGATACTTTATACCCAAATGTTA 57.159 33.333 0.00 0.00 0.00 2.41
2404 2480 8.257602 ACCCAAATGTTAAAATGTTTCCTACT 57.742 30.769 0.00 0.00 0.00 2.57
2405 2481 8.710239 ACCCAAATGTTAAAATGTTTCCTACTT 58.290 29.630 0.00 0.00 0.00 2.24
2445 2521 0.039256 GCAAGGAAACGCAAGCATCA 60.039 50.000 0.00 0.00 45.62 3.07
2446 2522 1.602668 GCAAGGAAACGCAAGCATCAA 60.603 47.619 0.00 0.00 45.62 2.57
2449 2525 1.537202 AGGAAACGCAAGCATCAAGAC 59.463 47.619 0.00 0.00 45.62 3.01
2520 2602 8.856103 ACAATGCATCATGAGATCATTTTATCA 58.144 29.630 0.00 0.00 33.59 2.15
2577 2659 7.532571 CAAACTGCTCATGACTGATGATTTAA 58.467 34.615 0.00 0.00 40.46 1.52
2612 2694 1.066143 ACCCAAGGAGCGTATGAGTTG 60.066 52.381 0.00 0.00 0.00 3.16
2614 2696 2.167693 CCCAAGGAGCGTATGAGTTGTA 59.832 50.000 0.00 0.00 0.00 2.41
2628 2710 3.072211 GAGTTGTACCCGAGGGAAAAAG 58.928 50.000 16.26 0.00 38.96 2.27
2630 2712 1.732117 TGTACCCGAGGGAAAAAGGA 58.268 50.000 16.26 0.00 38.96 3.36
2655 2737 2.507339 ACAAACCATCAAAACAGCCG 57.493 45.000 0.00 0.00 0.00 5.52
2656 2738 2.028130 ACAAACCATCAAAACAGCCGA 58.972 42.857 0.00 0.00 0.00 5.54
2712 2794 0.453950 CGGTGTTCGTCGATCTCGTT 60.454 55.000 0.00 0.00 40.80 3.85
2847 2955 3.367395 GGCAGGCCAATTTTAGTTCAGAC 60.367 47.826 5.01 0.00 35.81 3.51
2902 3010 3.197333 ACTCACTCTTGCATGCTATGACT 59.803 43.478 20.33 0.00 0.00 3.41
2978 3086 2.743664 TGATGAGTTCCAACTTGCATCG 59.256 45.455 12.83 0.00 40.43 3.84
2986 3094 1.135859 CCAACTTGCATCGACAGCTTC 60.136 52.381 12.28 0.00 0.00 3.86
3011 3119 1.019278 TTCTCCGATGAAGCAACGCC 61.019 55.000 0.00 0.00 0.00 5.68
3014 3122 2.745884 CGATGAAGCAACGCCCCA 60.746 61.111 0.00 0.00 0.00 4.96
3095 3203 2.345760 GCAACCCCCAGCATCTGTG 61.346 63.158 0.00 0.00 0.00 3.66
3131 3239 1.065491 TCTTGAATGATGACCACCCCG 60.065 52.381 0.00 0.00 0.00 5.73
3251 3359 2.031163 ACACGCAGAGGCTGGTTC 59.969 61.111 0.00 0.00 38.10 3.62
3259 3367 0.402121 AGAGGCTGGTTCCTGGAAAC 59.598 55.000 17.63 17.63 36.38 2.78
3266 3374 1.408969 GGTTCCTGGAAACCAAGCAA 58.591 50.000 13.66 0.00 46.62 3.91
3269 3377 3.181455 GGTTCCTGGAAACCAAGCAAAAT 60.181 43.478 13.66 0.00 46.62 1.82
3273 3381 6.432403 TCCTGGAAACCAAGCAAAATAAAT 57.568 33.333 0.00 0.00 30.80 1.40
3274 3382 6.463360 TCCTGGAAACCAAGCAAAATAAATC 58.537 36.000 0.00 0.00 30.80 2.17
3311 3419 3.619419 ACCAAAAGCCAAAACTTGCAAT 58.381 36.364 0.00 0.00 0.00 3.56
3355 3463 5.070001 ACAAGAGTAAAATGCTAGCACCAA 58.930 37.500 22.07 2.93 0.00 3.67
3368 3476 5.218139 GCTAGCACCAATTCATTCTAATGC 58.782 41.667 10.63 0.00 36.36 3.56
3379 3487 6.463995 TTCATTCTAATGCCCATGTAAACC 57.536 37.500 0.00 0.00 36.36 3.27
3380 3488 5.514169 TCATTCTAATGCCCATGTAAACCA 58.486 37.500 0.00 0.00 36.36 3.67
3429 3544 6.127925 TGCCAACTAGCACAAGAAAATCTATG 60.128 38.462 0.00 0.00 38.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.664402 ATATGTTAAGCCCAGCCCTG 57.336 50.000 0.00 0.00 0.00 4.45
61 62 5.829924 AGTATTTTCGGACGGAGGAAGTATA 59.170 40.000 0.00 0.00 0.00 1.47
62 63 4.648307 AGTATTTTCGGACGGAGGAAGTAT 59.352 41.667 0.00 0.00 0.00 2.12
63 64 4.019174 AGTATTTTCGGACGGAGGAAGTA 58.981 43.478 0.00 0.00 0.00 2.24
64 65 2.830321 AGTATTTTCGGACGGAGGAAGT 59.170 45.455 0.00 0.00 0.00 3.01
65 66 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
66 67 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
67 68 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
68 69 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
69 70 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
70 71 2.228582 TCGACAAGTATTTTCGGACGGA 59.771 45.455 0.00 0.00 33.50 4.69
71 72 2.598589 TCGACAAGTATTTTCGGACGG 58.401 47.619 0.00 0.00 33.50 4.79
72 73 3.916172 TCTTCGACAAGTATTTTCGGACG 59.084 43.478 0.00 0.00 33.50 4.79
73 74 5.834239 TTCTTCGACAAGTATTTTCGGAC 57.166 39.130 0.00 0.00 33.50 4.79
74 75 6.619874 GCATTTCTTCGACAAGTATTTTCGGA 60.620 38.462 0.00 0.00 33.50 4.55
75 76 5.508224 GCATTTCTTCGACAAGTATTTTCGG 59.492 40.000 0.00 0.00 33.50 4.30
76 77 6.077197 TGCATTTCTTCGACAAGTATTTTCG 58.923 36.000 0.00 0.00 0.00 3.46
77 78 9.554724 TTATGCATTTCTTCGACAAGTATTTTC 57.445 29.630 3.54 0.00 0.00 2.29
78 79 9.906660 TTTATGCATTTCTTCGACAAGTATTTT 57.093 25.926 3.54 0.00 0.00 1.82
79 80 9.906660 TTTTATGCATTTCTTCGACAAGTATTT 57.093 25.926 3.54 0.00 0.00 1.40
80 81 9.906660 TTTTTATGCATTTCTTCGACAAGTATT 57.093 25.926 3.54 0.00 0.00 1.89
82 83 9.340695 CATTTTTATGCATTTCTTCGACAAGTA 57.659 29.630 3.54 0.00 0.00 2.24
83 84 8.081633 TCATTTTTATGCATTTCTTCGACAAGT 58.918 29.630 3.54 0.00 0.00 3.16
84 85 8.451687 TCATTTTTATGCATTTCTTCGACAAG 57.548 30.769 3.54 0.00 0.00 3.16
85 86 8.809159 TTCATTTTTATGCATTTCTTCGACAA 57.191 26.923 3.54 0.00 0.00 3.18
86 87 8.862074 CATTCATTTTTATGCATTTCTTCGACA 58.138 29.630 3.54 0.00 0.00 4.35
87 88 8.863049 ACATTCATTTTTATGCATTTCTTCGAC 58.137 29.630 3.54 0.00 0.00 4.20
88 89 8.984891 ACATTCATTTTTATGCATTTCTTCGA 57.015 26.923 3.54 0.00 0.00 3.71
124 125 9.781425 AGGAATGGATGTATCTAGATGTATTCT 57.219 33.333 15.79 0.00 38.57 2.40
126 127 8.986991 GGAGGAATGGATGTATCTAGATGTATT 58.013 37.037 15.79 6.57 0.00 1.89
127 128 7.286546 CGGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
128 129 6.603599 CGGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
129 130 5.420421 CGGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
130 131 5.654209 TCGGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
131 132 5.654650 GTCGGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
132 133 5.010933 GTCGGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
133 134 4.142578 CGTCGGAGGAATGGATGTATCTAG 60.143 50.000 0.00 0.00 0.00 2.43
134 135 3.756963 CGTCGGAGGAATGGATGTATCTA 59.243 47.826 0.00 0.00 0.00 1.98
135 136 2.558795 CGTCGGAGGAATGGATGTATCT 59.441 50.000 0.00 0.00 0.00 1.98
136 137 2.557056 TCGTCGGAGGAATGGATGTATC 59.443 50.000 0.00 0.00 0.00 2.24
137 138 2.558795 CTCGTCGGAGGAATGGATGTAT 59.441 50.000 1.73 0.00 36.61 2.29
138 139 1.954382 CTCGTCGGAGGAATGGATGTA 59.046 52.381 1.73 0.00 36.61 2.29
139 140 0.747255 CTCGTCGGAGGAATGGATGT 59.253 55.000 1.73 0.00 36.61 3.06
140 141 0.747255 ACTCGTCGGAGGAATGGATG 59.253 55.000 1.73 0.00 44.93 3.51
141 142 2.359981 TACTCGTCGGAGGAATGGAT 57.640 50.000 1.73 0.00 44.93 3.41
142 143 2.359981 ATACTCGTCGGAGGAATGGA 57.640 50.000 1.73 0.00 44.93 3.41
143 144 3.381949 GAAATACTCGTCGGAGGAATGG 58.618 50.000 1.73 0.00 44.93 3.16
144 145 3.381949 GGAAATACTCGTCGGAGGAATG 58.618 50.000 1.73 0.00 44.93 2.67
145 146 2.034305 CGGAAATACTCGTCGGAGGAAT 59.966 50.000 1.73 0.00 44.93 3.01
146 147 1.402968 CGGAAATACTCGTCGGAGGAA 59.597 52.381 1.73 0.00 44.93 3.36
147 148 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
148 149 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
149 150 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
150 151 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
151 152 0.452987 TGTCCGGAAATACTCGTCGG 59.547 55.000 5.23 0.00 41.80 4.79
152 153 2.267188 TTGTCCGGAAATACTCGTCG 57.733 50.000 5.23 0.00 0.00 5.12
153 154 2.928116 CCTTTGTCCGGAAATACTCGTC 59.072 50.000 5.23 0.00 0.00 4.20
154 155 2.354403 CCCTTTGTCCGGAAATACTCGT 60.354 50.000 5.23 0.00 0.00 4.18
155 156 2.093869 TCCCTTTGTCCGGAAATACTCG 60.094 50.000 5.23 0.00 0.00 4.18
156 157 3.055312 ACTCCCTTTGTCCGGAAATACTC 60.055 47.826 5.23 0.00 0.00 2.59
157 158 2.910977 ACTCCCTTTGTCCGGAAATACT 59.089 45.455 5.23 0.00 0.00 2.12
158 159 3.345508 ACTCCCTTTGTCCGGAAATAC 57.654 47.619 5.23 0.00 0.00 1.89
159 160 4.472108 ACATACTCCCTTTGTCCGGAAATA 59.528 41.667 5.23 0.00 0.00 1.40
160 161 3.265995 ACATACTCCCTTTGTCCGGAAAT 59.734 43.478 5.23 0.00 0.00 2.17
161 162 2.640826 ACATACTCCCTTTGTCCGGAAA 59.359 45.455 5.23 0.00 0.00 3.13
162 163 2.027561 CACATACTCCCTTTGTCCGGAA 60.028 50.000 5.23 0.00 0.00 4.30
163 164 1.553248 CACATACTCCCTTTGTCCGGA 59.447 52.381 0.00 0.00 0.00 5.14
164 165 1.278127 ACACATACTCCCTTTGTCCGG 59.722 52.381 0.00 0.00 0.00 5.14
165 166 2.289444 ACACACATACTCCCTTTGTCCG 60.289 50.000 0.00 0.00 0.00 4.79
166 167 3.418684 ACACACATACTCCCTTTGTCC 57.581 47.619 0.00 0.00 0.00 4.02
167 168 5.767816 AAAACACACATACTCCCTTTGTC 57.232 39.130 0.00 0.00 0.00 3.18
168 169 5.768164 CCTAAAACACACATACTCCCTTTGT 59.232 40.000 0.00 0.00 0.00 2.83
169 170 5.183140 CCCTAAAACACACATACTCCCTTTG 59.817 44.000 0.00 0.00 0.00 2.77
170 171 5.073965 TCCCTAAAACACACATACTCCCTTT 59.926 40.000 0.00 0.00 0.00 3.11
171 172 4.600111 TCCCTAAAACACACATACTCCCTT 59.400 41.667 0.00 0.00 0.00 3.95
172 173 4.172807 TCCCTAAAACACACATACTCCCT 58.827 43.478 0.00 0.00 0.00 4.20
173 174 4.563140 TCCCTAAAACACACATACTCCC 57.437 45.455 0.00 0.00 0.00 4.30
174 175 5.801380 TCTTCCCTAAAACACACATACTCC 58.199 41.667 0.00 0.00 0.00 3.85
175 176 5.875359 CCTCTTCCCTAAAACACACATACTC 59.125 44.000 0.00 0.00 0.00 2.59
176 177 5.803470 GCCTCTTCCCTAAAACACACATACT 60.803 44.000 0.00 0.00 0.00 2.12
177 178 4.395231 GCCTCTTCCCTAAAACACACATAC 59.605 45.833 0.00 0.00 0.00 2.39
206 207 1.978617 CCCGCCAGTGGAAAAGCAT 60.979 57.895 15.20 0.00 0.00 3.79
240 253 1.064685 CCGACCTTTGGGCCTAGAATT 60.065 52.381 4.53 0.00 35.63 2.17
264 277 1.886542 CACAACAGAAAACCTAGGCCC 59.113 52.381 9.30 0.00 0.00 5.80
307 320 1.056660 ATACCAGGCCATAACTCGGG 58.943 55.000 5.01 0.00 0.00 5.14
309 322 2.028385 GGGTATACCAGGCCATAACTCG 60.028 54.545 23.33 0.00 39.85 4.18
323 336 3.084070 CGGGTTTAGTCACGGGTATAC 57.916 52.381 0.00 0.00 0.00 1.47
359 372 2.375345 CCAGGCCATAACTCGGGGT 61.375 63.158 5.01 0.00 0.00 4.95
360 373 1.052124 TACCAGGCCATAACTCGGGG 61.052 60.000 5.01 0.00 0.00 5.73
389 402 0.322997 CTGTCCATGCCCGGGTTTAA 60.323 55.000 24.63 6.02 0.00 1.52
438 451 3.553095 AACAAGTCCTGAGCCCGGC 62.553 63.158 0.00 0.00 0.00 6.13
447 460 1.035139 CAGGCTGCAAAACAAGTCCT 58.965 50.000 0.00 0.00 0.00 3.85
462 475 1.134371 AGCCCGAACTATCTTTCAGGC 60.134 52.381 2.43 2.43 45.85 4.85
465 478 1.209504 CCCAGCCCGAACTATCTTTCA 59.790 52.381 0.00 0.00 0.00 2.69
512 525 0.882042 CAGACGTGCAAGTCCAGCTT 60.882 55.000 26.13 7.35 41.83 3.74
519 532 3.720949 TTAGTGTACAGACGTGCAAGT 57.279 42.857 4.50 4.50 39.61 3.16
587 603 1.603455 TTTTCAAGCCTGAGCCCGG 60.603 57.895 0.00 0.00 41.25 5.73
608 624 2.289565 CCCGAAGCCCAAAATACTCTC 58.710 52.381 0.00 0.00 0.00 3.20
631 647 1.194772 CAAACGTTTTCTCGAGAGCCC 59.805 52.381 15.94 6.26 34.70 5.19
637 653 1.500512 CCCGGCAAACGTTTTCTCGA 61.501 55.000 21.31 0.00 42.24 4.04
638 654 1.082366 CCCGGCAAACGTTTTCTCG 60.082 57.895 11.66 14.38 42.24 4.04
640 656 1.038681 AACCCCGGCAAACGTTTTCT 61.039 50.000 11.66 0.00 42.24 2.52
641 657 0.179105 AAACCCCGGCAAACGTTTTC 60.179 50.000 11.66 6.44 42.24 2.29
642 658 1.109609 TAAACCCCGGCAAACGTTTT 58.890 45.000 11.66 0.00 42.24 2.43
643 659 0.385029 GTAAACCCCGGCAAACGTTT 59.615 50.000 7.96 7.96 42.24 3.60
801 851 2.586357 GGCGGCATCCTTCGAGAC 60.586 66.667 3.07 0.00 0.00 3.36
1965 2033 1.153369 CACGGCCATGGTGAGGTAG 60.153 63.158 14.67 0.00 37.60 3.18
2058 2126 1.006102 GTCGTAGCTGTGCACCAGT 60.006 57.895 15.69 0.32 43.55 4.00
2268 2336 5.107375 GCACAAGTAGCAATTTTTCACATGG 60.107 40.000 0.00 0.00 0.00 3.66
2269 2337 5.693104 AGCACAAGTAGCAATTTTTCACATG 59.307 36.000 0.00 0.00 0.00 3.21
2271 2339 5.042593 CAGCACAAGTAGCAATTTTTCACA 58.957 37.500 0.00 0.00 0.00 3.58
2272 2340 5.043248 ACAGCACAAGTAGCAATTTTTCAC 58.957 37.500 0.00 0.00 0.00 3.18
2273 2341 5.261209 ACAGCACAAGTAGCAATTTTTCA 57.739 34.783 0.00 0.00 0.00 2.69
2274 2342 5.519927 ACAACAGCACAAGTAGCAATTTTTC 59.480 36.000 0.00 0.00 0.00 2.29
2300 2373 8.504005 AGGAAAAATACAGTCACACGAATTTAG 58.496 33.333 0.00 0.00 0.00 1.85
2359 2434 8.555896 TTGGGTATAAAGTATCACTCCATGTA 57.444 34.615 0.00 0.00 0.00 2.29
2445 2521 6.240894 TGCCTTCAGTTATTCTCATTGTCTT 58.759 36.000 0.00 0.00 0.00 3.01
2446 2522 5.809001 TGCCTTCAGTTATTCTCATTGTCT 58.191 37.500 0.00 0.00 0.00 3.41
2520 2602 6.936279 TGATAACTCGAATCTCTGAACCTTT 58.064 36.000 0.00 0.00 0.00 3.11
2577 2659 1.449601 GGGTTGATGGCACGTCGAT 60.450 57.895 0.00 0.00 0.00 3.59
2612 2694 2.865119 TTCCTTTTTCCCTCGGGTAC 57.135 50.000 1.18 0.00 36.47 3.34
2614 2696 1.708551 TCATTCCTTTTTCCCTCGGGT 59.291 47.619 1.18 0.00 36.47 5.28
2628 2710 6.311200 GCTGTTTTGATGGTTTGTATCATTCC 59.689 38.462 0.00 0.00 34.76 3.01
2630 2712 6.165577 GGCTGTTTTGATGGTTTGTATCATT 58.834 36.000 0.00 0.00 34.76 2.57
2712 2794 2.938451 CTGCTCATAAACAATCTGCGGA 59.062 45.455 0.00 0.00 0.00 5.54
2847 2955 7.432252 AGAACTTTTGCTCTGTTTTTATCAACG 59.568 33.333 0.00 0.00 0.00 4.10
2902 3010 3.057245 GTCAGATAGATGGCGTGATGCTA 60.057 47.826 0.00 0.00 45.43 3.49
2910 3018 3.305676 CCCTTACAGTCAGATAGATGGCG 60.306 52.174 0.00 0.00 0.00 5.69
2978 3086 3.074412 TCGGAGAATTTTGGAAGCTGTC 58.926 45.455 0.00 0.00 0.00 3.51
2986 3094 4.168760 GTTGCTTCATCGGAGAATTTTGG 58.831 43.478 0.00 0.00 43.58 3.28
3011 3119 3.817647 GAGGCATAATAGCTTGTTCTGGG 59.182 47.826 0.00 0.00 34.17 4.45
3014 3122 5.363939 GACAGAGGCATAATAGCTTGTTCT 58.636 41.667 0.00 0.00 34.17 3.01
3083 3191 0.392193 GAGTGGTCACAGATGCTGGG 60.392 60.000 3.82 0.00 36.00 4.45
3086 3194 0.322975 GTGGAGTGGTCACAGATGCT 59.677 55.000 3.82 0.00 35.39 3.79
3095 3203 1.484444 AAGAGGCTGGTGGAGTGGTC 61.484 60.000 0.00 0.00 0.00 4.02
3131 3239 0.254178 AGATATGGGATCATGCCGCC 59.746 55.000 0.00 0.00 34.96 6.13
3251 3359 6.229733 TGATTTATTTTGCTTGGTTTCCAGG 58.770 36.000 0.00 0.00 33.81 4.45
3284 3392 5.767269 CAAGTTTTGGCTTTTGGTTGTTTT 58.233 33.333 0.00 0.00 0.00 2.43
3285 3393 4.320861 GCAAGTTTTGGCTTTTGGTTGTTT 60.321 37.500 0.00 0.00 0.00 2.83
3287 3395 2.746904 GCAAGTTTTGGCTTTTGGTTGT 59.253 40.909 0.00 0.00 0.00 3.32
3290 3398 2.777832 TGCAAGTTTTGGCTTTTGGT 57.222 40.000 0.00 0.00 0.00 3.67
3311 3419 1.810853 CGTGTCATCTGCATGCGGA 60.811 57.895 30.50 30.50 35.60 5.54
3355 3463 6.610830 TGGTTTACATGGGCATTAGAATGAAT 59.389 34.615 6.43 0.00 38.70 2.57
3368 3476 7.403312 TGAATAGTGAATTGGTTTACATGGG 57.597 36.000 0.00 0.00 0.00 4.00
3379 3487 9.836076 CATATGGTATTGCTGAATAGTGAATTG 57.164 33.333 0.00 0.00 0.00 2.32
3380 3488 8.517878 GCATATGGTATTGCTGAATAGTGAATT 58.482 33.333 4.56 0.00 35.95 2.17


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

AutoCloner maintained by Alex Coulton.