Multiple sequence alignment - TraesCS5B01G143200

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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 TraesCS5B01G143200 chr5B 100.000 2867 0 0 1 2867 270439133 270436267 0.000000e+00 5295.0
1 TraesCS5B01G143200 chr5B 96.552 145 3 2 1 145 279099231 279099089 3.690000e-59 239.0
2 TraesCS5B01G143200 chr5B 94.702 151 7 1 1 151 394658172 394658321 1.720000e-57 233.0
3 TraesCS5B01G143200 chr5D 93.758 2403 105 19 138 2528 234145032 234147401 0.000000e+00 3565.0
4 TraesCS5B01G143200 chr5D 93.410 349 20 3 2519 2867 234149159 234149504 5.480000e-142 514.0
5 TraesCS5B01G143200 chr5D 96.528 144 5 0 1 144 502184454 502184311 3.690000e-59 239.0
6 TraesCS5B01G143200 chr5A 93.997 2249 100 16 319 2549 320214245 320212014 0.000000e+00 3373.0
7 TraesCS5B01G143200 chr5A 91.575 273 12 5 2535 2806 320211998 320211736 1.620000e-97 366.0
8 TraesCS5B01G143200 chr5A 88.710 186 8 6 141 320 320214582 320214404 6.220000e-52 215.0
9 TraesCS5B01G143200 chr5A 100.000 44 0 0 2824 2867 320211736 320211693 6.580000e-12 82.4
10 TraesCS5B01G143200 chr7B 85.185 702 70 15 796 1465 531654984 531655683 0.000000e+00 689.0
11 TraesCS5B01G143200 chr7B 83.447 731 94 18 1508 2226 531655917 531656632 0.000000e+00 654.0
12 TraesCS5B01G143200 chr7B 86.620 142 18 1 414 554 531654002 531654143 3.820000e-34 156.0
13 TraesCS5B01G143200 chr7B 85.156 128 11 3 322 445 531650594 531650717 1.080000e-24 124.0
14 TraesCS5B01G143200 chr7D 84.922 703 71 15 796 1465 502873649 502874349 0.000000e+00 678.0
15 TraesCS5B01G143200 chr7D 83.058 726 98 17 1517 2227 502874618 502875333 1.120000e-178 636.0
16 TraesCS5B01G143200 chr7D 87.413 143 13 4 414 554 502872661 502872800 2.960000e-35 159.0
17 TraesCS5B01G143200 chr7A 84.893 609 65 13 889 1475 570113205 570113808 8.850000e-165 590.0
18 TraesCS5B01G143200 chr7A 83.333 516 64 13 1508 2019 570114178 570114675 9.360000e-125 457.0
19 TraesCS5B01G143200 chr7A 96.528 144 5 0 1 144 254417769 254417626 3.690000e-59 239.0
20 TraesCS5B01G143200 chr7A 85.207 169 15 5 322 485 570111919 570112082 6.350000e-37 165.0
21 TraesCS5B01G143200 chr7A 88.333 120 13 1 436 554 570112188 570112307 2.980000e-30 143.0
22 TraesCS5B01G143200 chr7A 90.000 80 4 4 1146 1223 686135841 686135764 1.820000e-17 100.0
23 TraesCS5B01G143200 chr4B 90.909 187 16 1 2238 2423 183525209 183525023 1.710000e-62 250.0
24 TraesCS5B01G143200 chr6B 91.209 182 15 1 2238 2418 650790922 650791103 2.210000e-61 246.0
25 TraesCS5B01G143200 chr6B 94.702 151 7 1 1 150 450644657 450644807 1.720000e-57 233.0
26 TraesCS5B01G143200 chr6B 87.129 202 25 1 2223 2423 454030316 454030517 7.990000e-56 228.0
27 TraesCS5B01G143200 chr2A 97.857 140 3 0 1 140 360744454 360744315 2.850000e-60 243.0
28 TraesCS5B01G143200 chr2D 90.270 185 17 1 2240 2423 548608925 548608741 1.030000e-59 241.0
29 TraesCS5B01G143200 chr3B 87.864 206 21 2 2222 2423 556288468 556288673 3.690000e-59 239.0
30 TraesCS5B01G143200 chr3D 85.000 240 24 7 2222 2452 426050063 426049827 1.720000e-57 233.0
31 TraesCS5B01G143200 chr2B 87.685 203 21 4 2223 2423 493711579 493711779 1.720000e-57 233.0
32 TraesCS5B01G143200 chr3A 94.667 150 6 2 4 152 718945627 718945479 6.180000e-57 231.0
33 TraesCS5B01G143200 chr3A 90.000 80 4 4 1146 1223 647369246 647369323 1.820000e-17 100.0
34 TraesCS5B01G143200 chr3A 90.000 80 4 4 1146 1223 662877612 662877535 1.820000e-17 100.0
35 TraesCS5B01G143200 chr4A 92.500 160 9 3 1 160 314685473 314685629 2.870000e-55 226.0
36 TraesCS5B01G143200 chr4A 91.463 164 10 4 4 166 393386582 393386422 3.720000e-54 222.0


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 TraesCS5B01G143200 chr5B 270436267 270439133 2866 True 5295.00 5295 100.0000 1 2867 1 chr5B.!!$R1 2866
1 TraesCS5B01G143200 chr5D 234145032 234149504 4472 False 2039.50 3565 93.5840 138 2867 2 chr5D.!!$F1 2729
2 TraesCS5B01G143200 chr5A 320211693 320214582 2889 True 1009.10 3373 93.5705 141 2867 4 chr5A.!!$R1 2726
3 TraesCS5B01G143200 chr7B 531650594 531656632 6038 False 405.75 689 85.1020 322 2226 4 chr7B.!!$F1 1904
4 TraesCS5B01G143200 chr7D 502872661 502875333 2672 False 491.00 678 85.1310 414 2227 3 chr7D.!!$F1 1813
5 TraesCS5B01G143200 chr7A 570111919 570114675 2756 False 338.75 590 85.4415 322 2019 4 chr7A.!!$F1 1697

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
51 52 0.179037 TGCTATCCATGTGCCAGAGC 60.179 55.0 0.0 0.0 40.48 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 6825 1.001487 CTTGCCTGATGAAACAACGCA 60.001 47.619 0.0 0.0 0.0 5.24 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
20 21 2.399580 GAACTAGCTATGGACAGGGGT 58.600 52.381 0.00 0.00 0.00 4.95
21 22 1.794714 ACTAGCTATGGACAGGGGTG 58.205 55.000 0.00 0.00 0.00 4.61
22 23 0.394565 CTAGCTATGGACAGGGGTGC 59.605 60.000 0.00 0.00 35.66 5.01
23 24 1.399744 TAGCTATGGACAGGGGTGCG 61.400 60.000 0.00 0.00 38.35 5.34
24 25 3.031417 GCTATGGACAGGGGTGCGT 62.031 63.158 0.00 0.00 38.35 5.24
25 26 1.153369 CTATGGACAGGGGTGCGTG 60.153 63.158 0.00 0.00 38.35 5.34
26 27 2.593468 CTATGGACAGGGGTGCGTGG 62.593 65.000 0.00 0.00 38.35 4.94
28 29 3.948719 GGACAGGGGTGCGTGGAA 61.949 66.667 0.00 0.00 0.00 3.53
29 30 2.358737 GACAGGGGTGCGTGGAAG 60.359 66.667 0.00 0.00 0.00 3.46
30 31 4.643387 ACAGGGGTGCGTGGAAGC 62.643 66.667 0.00 0.00 37.71 3.86
31 32 4.335647 CAGGGGTGCGTGGAAGCT 62.336 66.667 0.00 0.00 38.13 3.74
32 33 3.570212 AGGGGTGCGTGGAAGCTT 61.570 61.111 0.00 0.00 38.13 3.74
33 34 3.365265 GGGGTGCGTGGAAGCTTG 61.365 66.667 2.10 0.00 38.13 4.01
34 35 4.043200 GGGTGCGTGGAAGCTTGC 62.043 66.667 11.58 11.58 38.13 4.01
35 36 2.980233 GGTGCGTGGAAGCTTGCT 60.980 61.111 19.34 0.00 38.13 3.91
36 37 1.671054 GGTGCGTGGAAGCTTGCTA 60.671 57.895 19.34 2.82 38.13 3.49
37 38 1.026718 GGTGCGTGGAAGCTTGCTAT 61.027 55.000 19.34 0.00 38.13 2.97
38 39 0.375106 GTGCGTGGAAGCTTGCTATC 59.625 55.000 19.34 8.59 38.13 2.08
39 40 0.744414 TGCGTGGAAGCTTGCTATCC 60.744 55.000 19.34 6.99 38.13 2.59
40 41 0.744414 GCGTGGAAGCTTGCTATCCA 60.744 55.000 19.34 9.80 40.84 3.41
41 42 1.959042 CGTGGAAGCTTGCTATCCAT 58.041 50.000 19.34 0.00 44.55 3.41
42 43 1.600957 CGTGGAAGCTTGCTATCCATG 59.399 52.381 19.34 20.51 44.55 3.66
43 44 2.648059 GTGGAAGCTTGCTATCCATGT 58.352 47.619 19.34 0.00 44.55 3.21
44 45 2.357009 GTGGAAGCTTGCTATCCATGTG 59.643 50.000 19.34 0.00 44.55 3.21
45 46 1.336125 GGAAGCTTGCTATCCATGTGC 59.664 52.381 11.19 0.00 33.30 4.57
46 47 1.336125 GAAGCTTGCTATCCATGTGCC 59.664 52.381 2.10 0.00 0.00 5.01
47 48 0.256752 AGCTTGCTATCCATGTGCCA 59.743 50.000 0.00 0.00 0.00 4.92
48 49 0.666913 GCTTGCTATCCATGTGCCAG 59.333 55.000 0.00 0.00 0.00 4.85
49 50 1.748244 GCTTGCTATCCATGTGCCAGA 60.748 52.381 0.00 0.00 0.00 3.86
50 51 2.219458 CTTGCTATCCATGTGCCAGAG 58.781 52.381 0.00 0.00 0.00 3.35
51 52 0.179037 TGCTATCCATGTGCCAGAGC 60.179 55.000 0.00 0.00 40.48 4.09
52 53 0.888285 GCTATCCATGTGCCAGAGCC 60.888 60.000 0.00 0.00 38.69 4.70
53 54 0.471191 CTATCCATGTGCCAGAGCCA 59.529 55.000 0.00 0.00 38.69 4.75
54 55 1.073444 CTATCCATGTGCCAGAGCCAT 59.927 52.381 0.00 0.00 38.69 4.40
55 56 0.467474 ATCCATGTGCCAGAGCCATG 60.467 55.000 8.59 8.59 42.54 3.66
56 57 1.077285 CCATGTGCCAGAGCCATGA 60.077 57.895 14.22 0.00 44.14 3.07
57 58 1.381928 CCATGTGCCAGAGCCATGAC 61.382 60.000 14.22 0.00 44.14 3.06
58 59 0.393944 CATGTGCCAGAGCCATGACT 60.394 55.000 0.00 0.00 44.14 3.41
59 60 0.330604 ATGTGCCAGAGCCATGACTT 59.669 50.000 0.00 0.00 38.69 3.01
60 61 0.607217 TGTGCCAGAGCCATGACTTG 60.607 55.000 0.00 0.00 38.69 3.16
68 69 3.786101 CCATGACTTGGTCGCGAG 58.214 61.111 10.24 0.00 40.99 5.03
69 70 1.215382 CCATGACTTGGTCGCGAGA 59.785 57.895 10.24 0.00 40.99 4.04
70 71 0.179100 CCATGACTTGGTCGCGAGAT 60.179 55.000 10.24 0.00 45.19 2.75
71 72 1.203928 CATGACTTGGTCGCGAGATC 58.796 55.000 10.24 2.63 45.19 2.75
72 73 1.107114 ATGACTTGGTCGCGAGATCT 58.893 50.000 10.24 0.00 43.23 2.75
73 74 0.888619 TGACTTGGTCGCGAGATCTT 59.111 50.000 10.24 0.00 43.23 2.40
74 75 2.089201 TGACTTGGTCGCGAGATCTTA 58.911 47.619 10.24 0.00 43.23 2.10
75 76 2.688446 TGACTTGGTCGCGAGATCTTAT 59.312 45.455 10.24 0.00 43.23 1.73
76 77 3.046390 GACTTGGTCGCGAGATCTTATG 58.954 50.000 10.24 0.00 43.23 1.90
77 78 2.223829 ACTTGGTCGCGAGATCTTATGG 60.224 50.000 10.24 0.00 43.23 2.74
78 79 0.673985 TGGTCGCGAGATCTTATGGG 59.326 55.000 10.24 0.00 43.23 4.00
79 80 0.674534 GGTCGCGAGATCTTATGGGT 59.325 55.000 10.24 0.00 45.19 4.51
80 81 1.068741 GGTCGCGAGATCTTATGGGTT 59.931 52.381 10.24 0.00 45.19 4.11
81 82 2.483188 GGTCGCGAGATCTTATGGGTTT 60.483 50.000 10.24 0.00 45.19 3.27
82 83 2.795470 GTCGCGAGATCTTATGGGTTTC 59.205 50.000 10.24 0.00 45.19 2.78
83 84 2.429250 TCGCGAGATCTTATGGGTTTCA 59.571 45.455 3.71 0.00 33.31 2.69
84 85 2.540101 CGCGAGATCTTATGGGTTTCAC 59.460 50.000 0.00 0.00 0.00 3.18
85 86 2.872858 GCGAGATCTTATGGGTTTCACC 59.127 50.000 0.00 0.00 37.60 4.02
86 87 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
87 88 4.372656 CGAGATCTTATGGGTTTCACCTC 58.627 47.826 0.00 0.00 38.64 3.85
88 89 4.100189 CGAGATCTTATGGGTTTCACCTCT 59.900 45.833 0.00 0.00 38.64 3.69
89 90 5.302059 CGAGATCTTATGGGTTTCACCTCTA 59.698 44.000 0.00 0.00 38.64 2.43
90 91 6.515862 CGAGATCTTATGGGTTTCACCTCTAG 60.516 46.154 0.00 0.00 38.64 2.43
91 92 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
92 93 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
93 94 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
94 95 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
95 96 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
96 97 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
97 98 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
98 99 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
99 100 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
100 101 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
101 102 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
102 103 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
103 104 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
104 105 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
105 106 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
106 107 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
107 108 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
108 109 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
119 120 4.385358 CAACTTGTTTGGCACTAAAGGT 57.615 40.909 0.00 0.00 0.00 3.50
120 121 4.754322 CAACTTGTTTGGCACTAAAGGTT 58.246 39.130 0.00 0.00 0.00 3.50
121 122 5.175127 CAACTTGTTTGGCACTAAAGGTTT 58.825 37.500 0.00 0.00 0.00 3.27
122 123 5.414789 ACTTGTTTGGCACTAAAGGTTTT 57.585 34.783 0.00 0.00 0.00 2.43
123 124 5.175127 ACTTGTTTGGCACTAAAGGTTTTG 58.825 37.500 0.00 0.00 0.00 2.44
124 125 4.810191 TGTTTGGCACTAAAGGTTTTGT 57.190 36.364 0.00 0.00 0.00 2.83
125 126 5.153950 TGTTTGGCACTAAAGGTTTTGTT 57.846 34.783 0.00 0.00 0.00 2.83
126 127 4.932200 TGTTTGGCACTAAAGGTTTTGTTG 59.068 37.500 0.00 0.00 0.00 3.33
127 128 4.810191 TTGGCACTAAAGGTTTTGTTGT 57.190 36.364 0.00 0.00 0.00 3.32
128 129 4.810191 TGGCACTAAAGGTTTTGTTGTT 57.190 36.364 0.00 0.00 0.00 2.83
129 130 4.499183 TGGCACTAAAGGTTTTGTTGTTG 58.501 39.130 0.00 0.00 0.00 3.33
130 131 4.021016 TGGCACTAAAGGTTTTGTTGTTGT 60.021 37.500 0.00 0.00 0.00 3.32
131 132 4.932799 GGCACTAAAGGTTTTGTTGTTGTT 59.067 37.500 0.00 0.00 0.00 2.83
132 133 5.163903 GGCACTAAAGGTTTTGTTGTTGTTG 60.164 40.000 0.00 0.00 0.00 3.33
133 134 5.670094 GCACTAAAGGTTTTGTTGTTGTTGC 60.670 40.000 0.00 0.00 0.00 4.17
134 135 5.637387 CACTAAAGGTTTTGTTGTTGTTGCT 59.363 36.000 0.00 0.00 0.00 3.91
135 136 5.637387 ACTAAAGGTTTTGTTGTTGTTGCTG 59.363 36.000 0.00 0.00 0.00 4.41
136 137 3.676291 AGGTTTTGTTGTTGTTGCTGT 57.324 38.095 0.00 0.00 0.00 4.40
137 138 4.001618 AGGTTTTGTTGTTGTTGCTGTT 57.998 36.364 0.00 0.00 0.00 3.16
138 139 3.745458 AGGTTTTGTTGTTGTTGCTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
139 140 3.496507 GGTTTTGTTGTTGTTGCTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
143 144 3.722147 TGTTGTTGTTGCTGTTGTTTGT 58.278 36.364 0.00 0.00 0.00 2.83
211 212 7.154435 TCTATTCTCTACAGGTTGTGTACAC 57.846 40.000 19.36 19.36 40.94 2.90
212 213 5.801531 ATTCTCTACAGGTTGTGTACACA 57.198 39.130 24.62 24.62 40.94 3.72
213 214 4.848562 TCTCTACAGGTTGTGTACACAG 57.151 45.455 26.52 18.10 42.94 3.66
214 215 4.212716 TCTCTACAGGTTGTGTACACAGT 58.787 43.478 26.52 22.30 42.94 3.55
215 216 5.379187 TCTCTACAGGTTGTGTACACAGTA 58.621 41.667 26.52 22.23 42.94 2.74
216 217 5.240183 TCTCTACAGGTTGTGTACACAGTAC 59.760 44.000 26.52 22.21 42.94 2.73
217 218 4.888823 TCTACAGGTTGTGTACACAGTACA 59.111 41.667 26.52 11.20 42.94 2.90
293 300 6.089249 AGTTGTTGTGAGAATCCCAAATTC 57.911 37.500 0.00 0.00 0.00 2.17
424 3911 6.250344 TGAGCTTCACTGAAAATCTTGATG 57.750 37.500 0.00 0.00 0.00 3.07
545 4149 8.321353 TGAAATGTCTAATGTCCACTATCAAGT 58.679 33.333 0.00 0.00 35.91 3.16
685 4289 3.354948 TGACCACAGCTTGCTAATGAT 57.645 42.857 7.39 0.00 0.00 2.45
686 4290 3.689347 TGACCACAGCTTGCTAATGATT 58.311 40.909 7.39 0.00 0.00 2.57
698 4302 7.941238 AGCTTGCTAATGATTCCACAGTATTAT 59.059 33.333 0.00 0.00 0.00 1.28
706 4310 7.616528 TGATTCCACAGTATTATCATCCTGA 57.383 36.000 0.00 0.00 0.00 3.86
735 4339 5.674569 GCCGCTGATTACCATAGCATATTTG 60.675 44.000 0.00 0.00 37.29 2.32
763 4367 5.410602 AGCCTCCTATCTGGATAACTTCAT 58.589 41.667 0.00 0.00 45.16 2.57
934 5343 6.857956 TCTCAACTCTTCTGTCTTGTATAGC 58.142 40.000 0.00 0.00 0.00 2.97
950 5359 5.294356 TGTATAGCTGTATTACTTTGGCCG 58.706 41.667 0.00 0.00 0.00 6.13
1006 5416 1.269778 GCTGATACTGCAGTATGGCGA 60.270 52.381 37.57 19.77 40.99 5.54
1126 5536 1.079127 CCGTGGAAGTCGATTGCCT 60.079 57.895 6.49 0.00 0.00 4.75
1311 5728 7.017645 CCGTATTAAGATTGATATGCAACTGC 58.982 38.462 0.00 0.00 39.78 4.40
1562 6354 2.288666 GAGACAAGGTGCACTGTTGAA 58.711 47.619 28.18 0.00 0.00 2.69
1629 6422 3.317603 CCCGTTTTGGCATCTCAATTT 57.682 42.857 0.00 0.00 35.87 1.82
1672 6465 5.946942 TTCCTACTCTTCTGCATCTCAAT 57.053 39.130 0.00 0.00 0.00 2.57
1781 6576 6.358118 ACGTGTACATATTTACATGGCTTG 57.642 37.500 20.19 0.00 41.49 4.01
1899 6694 4.744795 AACTCATCTACTGGGCAGTAAG 57.255 45.455 0.00 0.00 42.72 2.34
2029 6825 6.466812 TGTGTTGATTCTATGTCACATGACT 58.533 36.000 12.98 2.16 44.99 3.41
2031 6827 5.352293 TGTTGATTCTATGTCACATGACTGC 59.648 40.000 12.98 0.00 44.99 4.40
2091 6905 1.861971 AAGCTGCTCTTTTGCTTTGC 58.138 45.000 1.00 0.00 43.47 3.68
2092 6906 1.038280 AGCTGCTCTTTTGCTTTGCT 58.962 45.000 0.00 0.00 32.61 3.91
2093 6907 1.411612 AGCTGCTCTTTTGCTTTGCTT 59.588 42.857 0.00 0.00 33.76 3.91
2094 6908 1.525619 GCTGCTCTTTTGCTTTGCTTG 59.474 47.619 0.00 0.00 0.00 4.01
2095 6909 2.800629 GCTGCTCTTTTGCTTTGCTTGA 60.801 45.455 0.00 0.00 0.00 3.02
2096 6910 3.650139 CTGCTCTTTTGCTTTGCTTGAT 58.350 40.909 0.00 0.00 0.00 2.57
2097 6911 4.056050 CTGCTCTTTTGCTTTGCTTGATT 58.944 39.130 0.00 0.00 0.00 2.57
2227 7047 9.678260 AAGATACTACATATTACCCCGTACTAG 57.322 37.037 0.00 0.00 0.00 2.57
2230 7050 6.310149 ACTACATATTACCCCGTACTAGCTT 58.690 40.000 0.00 0.00 0.00 3.74
2233 7053 0.826062 TTACCCCGTACTAGCTTGGC 59.174 55.000 0.00 0.00 0.00 4.52
2243 7063 1.923148 ACTAGCTTGGCCCTGGTTTAT 59.077 47.619 0.00 0.00 0.00 1.40
2438 7259 8.657387 TTGACCCAAATGGACTAATAAATCAA 57.343 30.769 0.00 0.00 37.39 2.57
2440 7261 7.893302 TGACCCAAATGGACTAATAAATCAAGT 59.107 33.333 0.00 0.00 37.39 3.16
2520 7343 3.273434 TGGATGCTGATACTTGAACTGC 58.727 45.455 0.00 0.00 0.00 4.40
2573 9192 6.686630 TGTTATGCGATCTTTGGTTTCAAAT 58.313 32.000 0.00 0.00 41.45 2.32
2577 9196 4.278170 TGCGATCTTTGGTTTCAAATGACT 59.722 37.500 0.00 0.00 41.45 3.41
2688 9307 7.065803 TCCAGTTTGTTTGTTTGTTTGTTTTCA 59.934 29.630 0.00 0.00 0.00 2.69
2773 9392 4.214119 TCCTAAATGCAAGAGCGATTATGC 59.786 41.667 4.87 4.87 46.23 3.14
2775 9394 0.870393 ATGCAAGAGCGATTATGCCG 59.130 50.000 8.79 0.00 46.23 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.103263 CACCCCTGTCCATAGCTAGTTC 59.897 54.545 0.00 0.00 0.00 3.01
1 2 2.119495 CACCCCTGTCCATAGCTAGTT 58.881 52.381 0.00 0.00 0.00 2.24
3 4 0.394565 GCACCCCTGTCCATAGCTAG 59.605 60.000 0.00 0.00 0.00 3.42
5 6 2.735772 CGCACCCCTGTCCATAGCT 61.736 63.158 0.00 0.00 0.00 3.32
6 7 2.203070 CGCACCCCTGTCCATAGC 60.203 66.667 0.00 0.00 0.00 2.97
7 8 1.153369 CACGCACCCCTGTCCATAG 60.153 63.158 0.00 0.00 0.00 2.23
8 9 2.665089 CCACGCACCCCTGTCCATA 61.665 63.158 0.00 0.00 0.00 2.74
9 10 4.033776 CCACGCACCCCTGTCCAT 62.034 66.667 0.00 0.00 0.00 3.41
11 12 3.901797 CTTCCACGCACCCCTGTCC 62.902 68.421 0.00 0.00 0.00 4.02
12 13 2.358737 CTTCCACGCACCCCTGTC 60.359 66.667 0.00 0.00 0.00 3.51
13 14 4.643387 GCTTCCACGCACCCCTGT 62.643 66.667 0.00 0.00 0.00 4.00
14 15 3.850098 AAGCTTCCACGCACCCCTG 62.850 63.158 0.00 0.00 0.00 4.45
15 16 3.570212 AAGCTTCCACGCACCCCT 61.570 61.111 0.00 0.00 0.00 4.79
16 17 3.365265 CAAGCTTCCACGCACCCC 61.365 66.667 0.00 0.00 0.00 4.95
17 18 4.043200 GCAAGCTTCCACGCACCC 62.043 66.667 0.00 0.00 0.00 4.61
18 19 1.026718 ATAGCAAGCTTCCACGCACC 61.027 55.000 8.96 0.00 0.00 5.01
19 20 0.375106 GATAGCAAGCTTCCACGCAC 59.625 55.000 8.96 0.00 0.00 5.34
20 21 0.744414 GGATAGCAAGCTTCCACGCA 60.744 55.000 8.96 0.00 0.00 5.24
21 22 0.744414 TGGATAGCAAGCTTCCACGC 60.744 55.000 16.61 0.00 34.65 5.34
22 23 1.600957 CATGGATAGCAAGCTTCCACG 59.399 52.381 20.41 13.24 42.09 4.94
23 24 2.357009 CACATGGATAGCAAGCTTCCAC 59.643 50.000 20.41 0.00 42.09 4.02
24 25 2.646930 CACATGGATAGCAAGCTTCCA 58.353 47.619 20.33 20.33 43.37 3.53
25 26 1.336125 GCACATGGATAGCAAGCTTCC 59.664 52.381 0.00 7.95 0.00 3.46
26 27 1.336125 GGCACATGGATAGCAAGCTTC 59.664 52.381 0.00 0.00 0.00 3.86
27 28 1.341285 TGGCACATGGATAGCAAGCTT 60.341 47.619 0.00 0.00 0.00 3.74
28 29 0.256752 TGGCACATGGATAGCAAGCT 59.743 50.000 0.00 0.00 0.00 3.74
29 30 0.666913 CTGGCACATGGATAGCAAGC 59.333 55.000 0.00 0.00 38.20 4.01
30 31 2.219458 CTCTGGCACATGGATAGCAAG 58.781 52.381 0.00 0.00 38.20 4.01
31 32 1.748244 GCTCTGGCACATGGATAGCAA 60.748 52.381 0.00 0.00 38.20 3.91
32 33 0.179037 GCTCTGGCACATGGATAGCA 60.179 55.000 0.00 0.00 38.20 3.49
33 34 0.888285 GGCTCTGGCACATGGATAGC 60.888 60.000 0.00 0.00 38.20 2.97
34 35 0.471191 TGGCTCTGGCACATGGATAG 59.529 55.000 0.00 0.00 38.20 2.08
35 36 1.142936 ATGGCTCTGGCACATGGATA 58.857 50.000 0.00 0.00 41.84 2.59
36 37 0.467474 CATGGCTCTGGCACATGGAT 60.467 55.000 7.68 0.00 41.84 3.41
37 38 1.077285 CATGGCTCTGGCACATGGA 60.077 57.895 7.68 0.00 41.84 3.41
38 39 1.077285 TCATGGCTCTGGCACATGG 60.077 57.895 13.76 0.00 41.84 3.66
39 40 0.393944 AGTCATGGCTCTGGCACATG 60.394 55.000 8.97 8.97 41.84 3.21
40 41 0.330604 AAGTCATGGCTCTGGCACAT 59.669 50.000 0.00 0.00 41.84 3.21
41 42 0.607217 CAAGTCATGGCTCTGGCACA 60.607 55.000 0.00 0.00 41.84 4.57
42 43 1.310933 CCAAGTCATGGCTCTGGCAC 61.311 60.000 13.29 0.00 43.80 5.01
43 44 1.001764 CCAAGTCATGGCTCTGGCA 60.002 57.895 13.29 0.00 43.80 4.92
44 45 3.915575 CCAAGTCATGGCTCTGGC 58.084 61.111 13.29 0.00 43.80 4.85
52 53 1.202348 AGATCTCGCGACCAAGTCATG 60.202 52.381 3.71 0.00 32.09 3.07
53 54 1.107114 AGATCTCGCGACCAAGTCAT 58.893 50.000 3.71 0.00 32.09 3.06
54 55 0.888619 AAGATCTCGCGACCAAGTCA 59.111 50.000 3.71 0.00 32.09 3.41
55 56 2.846039 TAAGATCTCGCGACCAAGTC 57.154 50.000 3.71 0.00 0.00 3.01
56 57 2.223829 CCATAAGATCTCGCGACCAAGT 60.224 50.000 3.71 0.00 0.00 3.16
57 58 2.398498 CCATAAGATCTCGCGACCAAG 58.602 52.381 3.71 0.00 0.00 3.61
58 59 1.068588 CCCATAAGATCTCGCGACCAA 59.931 52.381 3.71 0.00 0.00 3.67
59 60 0.673985 CCCATAAGATCTCGCGACCA 59.326 55.000 3.71 0.00 0.00 4.02
60 61 0.674534 ACCCATAAGATCTCGCGACC 59.325 55.000 3.71 0.00 0.00 4.79
61 62 2.510768 AACCCATAAGATCTCGCGAC 57.489 50.000 3.71 0.00 0.00 5.19
62 63 2.429250 TGAAACCCATAAGATCTCGCGA 59.571 45.455 9.26 9.26 0.00 5.87
63 64 2.540101 GTGAAACCCATAAGATCTCGCG 59.460 50.000 0.00 0.00 0.00 5.87
78 79 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
79 80 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
80 81 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
81 82 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
82 83 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
83 84 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
84 85 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
85 86 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
86 87 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
87 88 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
88 89 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
89 90 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
98 99 4.385358 ACCTTTAGTGCCAAACAAGTTG 57.615 40.909 0.00 0.00 36.94 3.16
99 100 5.414789 AAACCTTTAGTGCCAAACAAGTT 57.585 34.783 0.00 0.00 0.00 2.66
100 101 5.175127 CAAAACCTTTAGTGCCAAACAAGT 58.825 37.500 0.00 0.00 0.00 3.16
101 102 5.175127 ACAAAACCTTTAGTGCCAAACAAG 58.825 37.500 0.00 0.00 0.00 3.16
102 103 5.153950 ACAAAACCTTTAGTGCCAAACAA 57.846 34.783 0.00 0.00 0.00 2.83
103 104 4.810191 ACAAAACCTTTAGTGCCAAACA 57.190 36.364 0.00 0.00 0.00 2.83
104 105 4.932799 ACAACAAAACCTTTAGTGCCAAAC 59.067 37.500 0.00 0.00 0.00 2.93
105 106 5.153950 ACAACAAAACCTTTAGTGCCAAA 57.846 34.783 0.00 0.00 0.00 3.28
106 107 4.810191 ACAACAAAACCTTTAGTGCCAA 57.190 36.364 0.00 0.00 0.00 4.52
107 108 4.021016 ACAACAACAAAACCTTTAGTGCCA 60.021 37.500 0.00 0.00 0.00 4.92
108 109 4.500127 ACAACAACAAAACCTTTAGTGCC 58.500 39.130 0.00 0.00 0.00 5.01
109 110 5.670094 GCAACAACAACAAAACCTTTAGTGC 60.670 40.000 0.00 0.00 0.00 4.40
110 111 5.637387 AGCAACAACAACAAAACCTTTAGTG 59.363 36.000 0.00 0.00 0.00 2.74
111 112 5.637387 CAGCAACAACAACAAAACCTTTAGT 59.363 36.000 0.00 0.00 0.00 2.24
112 113 5.637387 ACAGCAACAACAACAAAACCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
113 114 5.542779 ACAGCAACAACAACAAAACCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
114 115 4.384940 ACAGCAACAACAACAAAACCTTT 58.615 34.783 0.00 0.00 0.00 3.11
115 116 4.001618 ACAGCAACAACAACAAAACCTT 57.998 36.364 0.00 0.00 0.00 3.50
116 117 3.676291 ACAGCAACAACAACAAAACCT 57.324 38.095 0.00 0.00 0.00 3.50
117 118 3.496507 ACAACAGCAACAACAACAAAACC 59.503 39.130 0.00 0.00 0.00 3.27
118 119 4.723879 ACAACAGCAACAACAACAAAAC 57.276 36.364 0.00 0.00 0.00 2.43
119 120 5.065218 ACAAACAACAGCAACAACAACAAAA 59.935 32.000 0.00 0.00 0.00 2.44
120 121 4.572389 ACAAACAACAGCAACAACAACAAA 59.428 33.333 0.00 0.00 0.00 2.83
121 122 4.122776 ACAAACAACAGCAACAACAACAA 58.877 34.783 0.00 0.00 0.00 2.83
122 123 3.722147 ACAAACAACAGCAACAACAACA 58.278 36.364 0.00 0.00 0.00 3.33
123 124 5.667644 GCTTACAAACAACAGCAACAACAAC 60.668 40.000 0.00 0.00 32.17 3.32
124 125 4.387256 GCTTACAAACAACAGCAACAACAA 59.613 37.500 0.00 0.00 32.17 2.83
125 126 3.923461 GCTTACAAACAACAGCAACAACA 59.077 39.130 0.00 0.00 32.17 3.33
126 127 4.031652 CAGCTTACAAACAACAGCAACAAC 59.968 41.667 0.00 0.00 34.49 3.32
127 128 4.172505 CAGCTTACAAACAACAGCAACAA 58.827 39.130 0.00 0.00 34.49 2.83
128 129 3.192422 ACAGCTTACAAACAACAGCAACA 59.808 39.130 0.00 0.00 34.49 3.33
129 130 3.547468 CACAGCTTACAAACAACAGCAAC 59.453 43.478 0.00 0.00 34.49 4.17
130 131 3.192422 ACACAGCTTACAAACAACAGCAA 59.808 39.130 0.00 0.00 34.49 3.91
131 132 2.752354 ACACAGCTTACAAACAACAGCA 59.248 40.909 0.00 0.00 34.49 4.41
132 133 3.065371 AGACACAGCTTACAAACAACAGC 59.935 43.478 0.00 0.00 0.00 4.40
133 134 4.882671 AGACACAGCTTACAAACAACAG 57.117 40.909 0.00 0.00 0.00 3.16
134 135 4.941263 AGAAGACACAGCTTACAAACAACA 59.059 37.500 0.00 0.00 0.00 3.33
135 136 5.485662 AGAAGACACAGCTTACAAACAAC 57.514 39.130 0.00 0.00 0.00 3.32
136 137 6.479001 GTCTAGAAGACACAGCTTACAAACAA 59.521 38.462 0.00 0.00 44.45 2.83
137 138 5.983720 GTCTAGAAGACACAGCTTACAAACA 59.016 40.000 0.00 0.00 44.45 2.83
138 139 6.455045 GTCTAGAAGACACAGCTTACAAAC 57.545 41.667 0.00 0.00 44.45 2.93
193 194 4.585955 ACTGTGTACACAACCTGTAGAG 57.414 45.455 27.66 15.64 41.33 2.43
211 212 7.591426 GGCTTTACTTCAAAATCACTTGTACTG 59.409 37.037 0.00 0.00 0.00 2.74
212 213 7.284489 TGGCTTTACTTCAAAATCACTTGTACT 59.716 33.333 0.00 0.00 0.00 2.73
213 214 7.422399 TGGCTTTACTTCAAAATCACTTGTAC 58.578 34.615 0.00 0.00 0.00 2.90
214 215 7.575414 TGGCTTTACTTCAAAATCACTTGTA 57.425 32.000 0.00 0.00 0.00 2.41
215 216 6.463995 TGGCTTTACTTCAAAATCACTTGT 57.536 33.333 0.00 0.00 0.00 3.16
216 217 9.132521 CTTATGGCTTTACTTCAAAATCACTTG 57.867 33.333 0.00 0.00 0.00 3.16
217 218 7.814587 GCTTATGGCTTTACTTCAAAATCACTT 59.185 33.333 0.00 0.00 38.06 3.16
277 284 5.065731 CAGCTACAGAATTTGGGATTCTCAC 59.934 44.000 0.00 0.00 36.32 3.51
293 300 5.757850 AACAAAAGTTCTTCCAGCTACAG 57.242 39.130 0.00 0.00 0.00 2.74
342 509 8.509690 CAACTGAATGAACATGTAGAAGAACAT 58.490 33.333 0.00 0.00 40.75 2.71
424 3911 9.591404 CTTCATTATATGATCAAGAAAGCGTTC 57.409 33.333 0.00 3.99 39.39 3.95
645 4249 5.703130 GGTCATTAGTCTATGAATCCAAGGC 59.297 44.000 0.00 0.00 36.37 4.35
706 4310 2.591715 GGTAATCAGCGGCGGCAT 60.592 61.111 19.21 0.83 43.41 4.40
763 4367 7.816513 TCAAGACAATGACATGTTTCACAAAAA 59.183 29.630 0.00 0.00 32.57 1.94
934 5343 5.525199 ACAAAAACGGCCAAAGTAATACAG 58.475 37.500 2.24 0.00 0.00 2.74
950 5359 8.823818 ACATACTGTGACTACAAGTACAAAAAC 58.176 33.333 0.00 0.00 36.14 2.43
1126 5536 3.846588 AGGAAGAGGAGGAACAATGCTAA 59.153 43.478 0.00 0.00 0.00 3.09
1188 5598 1.417890 CTATCACCCTCCATGTGACCC 59.582 57.143 0.00 0.00 44.85 4.46
1311 5728 9.775854 AGACAATATTCATACTGGAAGATGAAG 57.224 33.333 3.93 0.00 40.83 3.02
1562 6354 5.542779 GCCTATAGCAGCTACTGTTACATT 58.457 41.667 3.59 0.00 42.97 2.71
1629 6422 7.781056 AGGAAAAGTTCTGTTTTCAGCATAAA 58.219 30.769 10.37 0.00 44.81 1.40
1716 6509 5.357257 TGAAAAGTGGATCGGTTCTATAGC 58.643 41.667 0.00 0.00 0.00 2.97
1781 6576 2.614057 CGGGTCTCATAAAATCCTGCAC 59.386 50.000 0.00 0.00 0.00 4.57
1899 6694 3.282021 TGGCTCTTGCTGTTCAATATCC 58.718 45.455 0.00 0.00 39.59 2.59
1946 6741 9.490663 GTACAAACATAACAATAAGTGCTCATC 57.509 33.333 0.00 0.00 0.00 2.92
2029 6825 1.001487 CTTGCCTGATGAAACAACGCA 60.001 47.619 0.00 0.00 0.00 5.24
2031 6827 1.267806 AGCTTGCCTGATGAAACAACG 59.732 47.619 0.00 0.00 0.00 4.10
2083 6881 4.524316 ACATAGCAATCAAGCAAAGCAA 57.476 36.364 0.00 0.00 36.85 3.91
2089 6903 6.825213 AGTTCAATCTACATAGCAATCAAGCA 59.175 34.615 0.00 0.00 36.85 3.91
2090 6904 7.256756 AGTTCAATCTACATAGCAATCAAGC 57.743 36.000 0.00 0.00 0.00 4.01
2091 6905 9.107177 AGAAGTTCAATCTACATAGCAATCAAG 57.893 33.333 5.50 0.00 0.00 3.02
2092 6906 8.886719 CAGAAGTTCAATCTACATAGCAATCAA 58.113 33.333 5.50 0.00 0.00 2.57
2093 6907 7.496920 CCAGAAGTTCAATCTACATAGCAATCA 59.503 37.037 5.50 0.00 0.00 2.57
2094 6908 7.712639 TCCAGAAGTTCAATCTACATAGCAATC 59.287 37.037 5.50 0.00 0.00 2.67
2095 6909 7.568349 TCCAGAAGTTCAATCTACATAGCAAT 58.432 34.615 5.50 0.00 0.00 3.56
2096 6910 6.946340 TCCAGAAGTTCAATCTACATAGCAA 58.054 36.000 5.50 0.00 0.00 3.91
2097 6911 6.155221 ACTCCAGAAGTTCAATCTACATAGCA 59.845 38.462 5.50 0.00 33.03 3.49
2192 7010 6.749216 AATATGTAGTATCTTCAACACGCG 57.251 37.500 3.53 3.53 0.00 6.01
2227 7047 0.536724 CCAATAAACCAGGGCCAAGC 59.463 55.000 6.18 0.00 0.00 4.01
2230 7050 3.681909 GACCAATAAACCAGGGCCA 57.318 52.632 6.18 0.00 0.00 5.36
2423 7244 5.424252 ACCTCCGACTTGATTTATTAGTCCA 59.576 40.000 0.00 0.00 35.91 4.02
2438 7259 6.251255 AGAGATAAAGTACTACCTCCGACT 57.749 41.667 0.00 0.00 0.00 4.18
2440 7261 7.372260 ACTAGAGATAAAGTACTACCTCCGA 57.628 40.000 0.00 0.00 0.00 4.55
2520 7343 4.999950 GGTGAGGATTGGCATACTTAGATG 59.000 45.833 0.00 0.00 0.00 2.90
2573 9192 3.005050 CGGACAAGTAGTACAACCAGTCA 59.995 47.826 2.52 0.00 0.00 3.41
2577 9196 4.766373 TGTATCGGACAAGTAGTACAACCA 59.234 41.667 2.52 0.00 34.15 3.67
2688 9307 7.255730 GGTGCTTGCATATTTCAGGATAAGAAT 60.256 37.037 0.00 0.00 0.00 2.40
2703 9322 5.588648 GGTTGATAAACTAGGTGCTTGCATA 59.411 40.000 0.00 0.00 0.00 3.14
2710 9329 3.947834 AGCATGGTTGATAAACTAGGTGC 59.052 43.478 0.00 0.00 0.00 5.01
2773 9392 1.308069 CCCCTGAAACTGATGTGCGG 61.308 60.000 0.00 0.00 0.00 5.69
2775 9394 1.620822 AACCCCTGAAACTGATGTGC 58.379 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.