Multiple sequence alignment - TraesCS3A01G260700

Loading Multiple Alignment...

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 TraesCS3A01G260700 chr3A 100.000 4331 0 0 1 4331 483485340 483481010 0.000000e+00 7998.0
1 TraesCS3A01G260700 chr3A 97.802 182 2 2 1 181 458239728 458239548 3.250000e-81 313.0
2 TraesCS3A01G260700 chr3D 95.707 4076 109 20 297 4331 363125554 363121504 0.000000e+00 6497.0
3 TraesCS3A01G260700 chr3D 97.283 184 5 0 1 184 522836624 522836807 3.250000e-81 313.0
4 TraesCS3A01G260700 chr3D 97.692 130 3 0 172 301 363128133 363128004 1.570000e-54 224.0
5 TraesCS3A01G260700 chr3D 81.690 213 32 6 3715 3921 17393514 17393303 2.070000e-38 171.0
6 TraesCS3A01G260700 chr3D 98.214 56 1 0 177 232 363128162 363128107 9.910000e-17 99.0
7 TraesCS3A01G260700 chr3D 87.692 65 8 0 3922 3986 528794930 528794994 4.640000e-10 76.8
8 TraesCS3A01G260700 chr3D 88.710 62 7 0 3925 3986 609002179 609002118 4.640000e-10 76.8
9 TraesCS3A01G260700 chr3B 93.374 2777 99 39 682 3405 472913559 472910815 0.000000e+00 4030.0
10 TraesCS3A01G260700 chr3B 97.283 184 4 1 1 184 543911357 543911539 1.170000e-80 311.0
11 TraesCS3A01G260700 chr3B 88.710 62 7 0 3925 3986 525648259 525648198 4.640000e-10 76.8
12 TraesCS3A01G260700 chr4A 85.753 372 33 9 1408 1760 502902592 502902222 4.090000e-100 375.0
13 TraesCS3A01G260700 chr4A 98.324 179 3 0 1 179 132095170 132094992 9.040000e-82 315.0
14 TraesCS3A01G260700 chr7B 95.833 192 7 1 1 192 498151419 498151229 4.210000e-80 309.0
15 TraesCS3A01G260700 chr7B 81.690 213 31 6 3715 3921 725639930 725640140 2.070000e-38 171.0
16 TraesCS3A01G260700 chr7B 81.517 211 31 6 3717 3921 725604337 725604545 2.680000e-37 167.0
17 TraesCS3A01G260700 chr2D 96.277 188 5 2 1 187 485035966 485035780 1.510000e-79 307.0
18 TraesCS3A01G260700 chr2D 77.211 294 41 19 3931 4206 628261291 628261006 9.700000e-32 148.0
19 TraesCS3A01G260700 chr2D 90.323 62 5 1 3933 3993 126974268 126974329 3.590000e-11 80.5
20 TraesCS3A01G260700 chr2D 88.710 62 7 0 3925 3986 532049048 532048987 4.640000e-10 76.8
21 TraesCS3A01G260700 chr5D 95.789 190 5 3 1 189 292204364 292204177 1.960000e-78 303.0
22 TraesCS3A01G260700 chr4B 95.361 194 4 4 1 194 539482241 539482053 1.960000e-78 303.0
23 TraesCS3A01G260700 chr1B 95.361 194 4 5 1 192 159267574 159267384 1.960000e-78 303.0
24 TraesCS3A01G260700 chr7D 81.106 217 35 4 3711 3923 75012884 75012670 7.450000e-38 169.0
25 TraesCS3A01G260700 chrUn 81.517 211 31 6 3717 3921 332190770 332190562 2.680000e-37 167.0
26 TraesCS3A01G260700 chr2B 80.660 212 36 3 3715 3921 106777577 106777788 4.480000e-35 159.0
27 TraesCS3A01G260700 chr7A 80.569 211 36 3 3715 3921 692612123 692611914 1.610000e-34 158.0
28 TraesCS3A01G260700 chr7A 79.812 213 36 5 3715 3921 333639433 333639222 9.700000e-32 148.0
29 TraesCS3A01G260700 chr4D 88.710 62 7 0 3925 3986 381886477 381886416 4.640000e-10 76.8
30 TraesCS3A01G260700 chr1D 88.710 62 7 0 3925 3986 487311158 487311219 4.640000e-10 76.8
31 TraesCS3A01G260700 chr6B 96.875 32 1 0 3350 3381 212194611 212194580 2.000000e-03 54.7


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 TraesCS3A01G260700 chr3A 483481010 483485340 4330 True 7998.000000 7998 100.000000 1 4331 1 chr3A.!!$R2 4330
1 TraesCS3A01G260700 chr3D 363121504 363128162 6658 True 2273.333333 6497 97.204333 172 4331 3 chr3D.!!$R3 4159
2 TraesCS3A01G260700 chr3B 472910815 472913559 2744 True 4030.000000 4030 93.374000 682 3405 1 chr3B.!!$R1 2723

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
112 113 0.041238 ATCTTCCCGTGAGTCCCTGA 59.959 55.000 0.00 0.0 0.0 3.86 F
115 116 0.041238 TTCCCGTGAGTCCCTGATCT 59.959 55.000 0.00 0.0 0.0 2.75 F
116 117 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.0 0.0 2.40 F
117 118 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.0 0.0 3.02 F
1094 3566 0.829990 CCCTCTCTCCTTTGCCTCTC 59.170 60.000 0.00 0.0 0.0 3.20 F
1352 3824 2.476185 CCGAAATTCATGGACGACTTGC 60.476 50.000 0.00 0.0 0.0 4.01 F
2566 5060 2.279120 GAGCGGATCAGGCAGTCG 60.279 66.667 10.19 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 3944 0.439985 CGTTCAGCTTGTCCATGTCG 59.560 55.000 0.00 0.0 0.00 4.35 R
1492 3977 1.437986 GGCTCGCTCGTTATCCACT 59.562 57.895 0.00 0.0 0.00 4.00 R
1630 4115 1.450312 CTCCTCGGCGCCATTCTTT 60.450 57.895 28.98 0.0 0.00 2.52 R
1711 4205 2.932234 CGCGGACTTCACCTCCAGT 61.932 63.158 0.00 0.0 0.00 4.00 R
2566 5060 2.270527 GCCTCCAGCTCCTTCACC 59.729 66.667 0.00 0.0 38.99 4.02 R
3191 5691 1.805134 GCACGCACTCTGCTCTCTC 60.805 63.158 0.00 0.0 42.25 3.20 R
3467 5974 0.389296 CGGGAGTGCACATACACGAA 60.389 55.000 21.04 0.0 45.45 3.85 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 3.775661 TGATCGAGCACTTGTATTCGA 57.224 42.857 0.00 9.86 44.88 3.71
23 24 3.695816 TGATCGAGCACTTGTATTCGAG 58.304 45.455 0.00 0.00 44.14 4.04
24 25 1.909376 TCGAGCACTTGTATTCGAGC 58.091 50.000 5.19 0.00 37.18 5.03
26 27 1.291132 GAGCACTTGTATTCGAGCCC 58.709 55.000 0.00 0.00 0.00 5.19
27 28 0.905357 AGCACTTGTATTCGAGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
28 29 1.279271 AGCACTTGTATTCGAGCCCTT 59.721 47.619 0.00 0.00 0.00 3.95
29 30 1.398390 GCACTTGTATTCGAGCCCTTG 59.602 52.381 0.00 0.00 0.00 3.61
30 31 2.935238 GCACTTGTATTCGAGCCCTTGA 60.935 50.000 0.00 0.00 0.00 3.02
31 32 2.932614 CACTTGTATTCGAGCCCTTGAG 59.067 50.000 0.00 0.00 0.00 3.02
49 50 4.764143 GCCCCTGGCTTGTATTGT 57.236 55.556 0.00 0.00 46.69 2.71
50 51 2.192605 GCCCCTGGCTTGTATTGTG 58.807 57.895 0.00 0.00 46.69 3.33
51 52 0.323360 GCCCCTGGCTTGTATTGTGA 60.323 55.000 0.00 0.00 46.69 3.58
52 53 1.686115 GCCCCTGGCTTGTATTGTGAT 60.686 52.381 0.00 0.00 46.69 3.06
53 54 2.026641 CCCCTGGCTTGTATTGTGATG 58.973 52.381 0.00 0.00 0.00 3.07
54 55 1.406539 CCCTGGCTTGTATTGTGATGC 59.593 52.381 0.00 0.00 0.00 3.91
55 56 2.372264 CCTGGCTTGTATTGTGATGCT 58.628 47.619 0.00 0.00 0.00 3.79
56 57 2.756760 CCTGGCTTGTATTGTGATGCTT 59.243 45.455 0.00 0.00 0.00 3.91
57 58 3.428452 CCTGGCTTGTATTGTGATGCTTG 60.428 47.826 0.00 0.00 0.00 4.01
58 59 3.156293 TGGCTTGTATTGTGATGCTTGT 58.844 40.909 0.00 0.00 0.00 3.16
59 60 4.331108 TGGCTTGTATTGTGATGCTTGTA 58.669 39.130 0.00 0.00 0.00 2.41
60 61 4.949238 TGGCTTGTATTGTGATGCTTGTAT 59.051 37.500 0.00 0.00 0.00 2.29
61 62 5.163632 TGGCTTGTATTGTGATGCTTGTATG 60.164 40.000 0.00 0.00 0.00 2.39
62 63 5.066375 GGCTTGTATTGTGATGCTTGTATGA 59.934 40.000 0.00 0.00 0.00 2.15
63 64 5.967674 GCTTGTATTGTGATGCTTGTATGAC 59.032 40.000 0.00 0.00 0.00 3.06
64 65 6.183360 GCTTGTATTGTGATGCTTGTATGACT 60.183 38.462 0.00 0.00 0.00 3.41
65 66 7.627088 GCTTGTATTGTGATGCTTGTATGACTT 60.627 37.037 0.00 0.00 0.00 3.01
66 67 8.785329 TTGTATTGTGATGCTTGTATGACTTA 57.215 30.769 0.00 0.00 0.00 2.24
67 68 8.962884 TGTATTGTGATGCTTGTATGACTTAT 57.037 30.769 0.00 0.00 0.00 1.73
68 69 9.394767 TGTATTGTGATGCTTGTATGACTTATT 57.605 29.630 0.00 0.00 0.00 1.40
73 74 9.394767 TGTGATGCTTGTATGACTTATTTATGT 57.605 29.630 0.00 0.00 0.00 2.29
96 97 8.902540 TGTTTTAGAGTTGTGTTGTGATATCT 57.097 30.769 3.98 0.00 0.00 1.98
97 98 9.337396 TGTTTTAGAGTTGTGTTGTGATATCTT 57.663 29.630 3.98 0.00 0.00 2.40
98 99 9.813080 GTTTTAGAGTTGTGTTGTGATATCTTC 57.187 33.333 3.98 0.00 0.00 2.87
99 100 8.547967 TTTAGAGTTGTGTTGTGATATCTTCC 57.452 34.615 3.98 0.00 0.00 3.46
100 101 5.491982 AGAGTTGTGTTGTGATATCTTCCC 58.508 41.667 3.98 0.00 0.00 3.97
101 102 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
102 103 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
103 104 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
104 105 3.259625 TGTGTTGTGATATCTTCCCGTGA 59.740 43.478 3.98 0.00 0.00 4.35
105 106 3.865745 GTGTTGTGATATCTTCCCGTGAG 59.134 47.826 3.98 0.00 0.00 3.51
106 107 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
107 108 4.113354 GTTGTGATATCTTCCCGTGAGTC 58.887 47.826 3.98 0.00 0.00 3.36
108 109 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
109 110 2.036089 GTGATATCTTCCCGTGAGTCCC 59.964 54.545 3.98 0.00 0.00 4.46
110 111 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
111 112 1.776662 TATCTTCCCGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
112 113 0.041238 ATCTTCCCGTGAGTCCCTGA 59.959 55.000 0.00 0.00 0.00 3.86
113 114 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
114 115 0.461961 CTTCCCGTGAGTCCCTGATC 59.538 60.000 0.00 0.00 0.00 2.92
115 116 0.041238 TTCCCGTGAGTCCCTGATCT 59.959 55.000 0.00 0.00 0.00 2.75
116 117 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.00 0.00 2.40
117 118 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
118 119 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
119 120 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
120 121 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
121 122 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
122 123 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
123 124 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
124 125 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
125 126 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
126 127 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
127 128 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
128 129 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
129 130 3.428999 CCCTGATCTTGATCGTACACGTT 60.429 47.826 1.19 0.00 40.80 3.99
130 131 4.174009 CCTGATCTTGATCGTACACGTTT 58.826 43.478 1.19 0.00 40.80 3.60
131 132 4.031765 CCTGATCTTGATCGTACACGTTTG 59.968 45.833 1.19 0.00 40.80 2.93
132 133 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
133 134 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
145 146 2.525750 CGTTTGCGTGCATGATTAGT 57.474 45.000 10.93 0.00 0.00 2.24
146 147 2.168384 CGTTTGCGTGCATGATTAGTG 58.832 47.619 10.93 0.00 0.00 2.74
147 148 2.412716 CGTTTGCGTGCATGATTAGTGT 60.413 45.455 10.93 0.00 0.00 3.55
148 149 3.181525 CGTTTGCGTGCATGATTAGTGTA 60.182 43.478 10.93 0.00 0.00 2.90
149 150 4.088648 GTTTGCGTGCATGATTAGTGTAC 58.911 43.478 10.93 0.00 0.00 2.90
155 156 5.966636 GTGCATGATTAGTGTACGATTGA 57.033 39.130 0.00 0.00 0.00 2.57
156 157 6.344572 GTGCATGATTAGTGTACGATTGAA 57.655 37.500 0.00 0.00 0.00 2.69
157 158 6.948353 GTGCATGATTAGTGTACGATTGAAT 58.052 36.000 0.00 0.00 0.00 2.57
158 159 7.065894 GTGCATGATTAGTGTACGATTGAATC 58.934 38.462 0.00 0.00 0.00 2.52
167 168 3.732470 GATTGAATCGGGGGCGTC 58.268 61.111 0.00 0.00 0.00 5.19
168 169 1.153249 GATTGAATCGGGGGCGTCA 60.153 57.895 0.00 0.00 0.00 4.35
169 170 1.436983 GATTGAATCGGGGGCGTCAC 61.437 60.000 0.00 0.00 0.00 3.67
170 171 2.191786 ATTGAATCGGGGGCGTCACA 62.192 55.000 0.00 0.00 0.00 3.58
171 172 2.046700 GAATCGGGGGCGTCACAA 60.047 61.111 0.00 0.00 0.00 3.33
172 173 1.451387 GAATCGGGGGCGTCACAAT 60.451 57.895 0.00 0.00 0.00 2.71
173 174 1.436983 GAATCGGGGGCGTCACAATC 61.437 60.000 0.00 0.00 0.00 2.67
174 175 2.191786 AATCGGGGGCGTCACAATCA 62.192 55.000 0.00 0.00 0.00 2.57
175 176 1.983119 ATCGGGGGCGTCACAATCAT 61.983 55.000 0.00 0.00 0.00 2.45
274 275 2.119009 GCCCAAGGCTTGAATAGGC 58.881 57.895 28.18 25.41 46.69 3.93
306 2761 2.504175 AGGATTTTGGGCTAAGCGTCTA 59.496 45.455 0.00 0.00 0.00 2.59
460 2917 3.178046 TGTGTGGGAATAAGACCTAGCA 58.822 45.455 0.00 0.00 0.00 3.49
485 2942 3.224007 ATTTTCACCCTGGCGGCCT 62.224 57.895 21.46 0.00 33.26 5.19
497 2954 1.515954 GCGGCCTGTCTTAGTGCTA 59.484 57.895 0.00 0.00 0.00 3.49
510 2967 5.517054 GTCTTAGTGCTAGTGTTGTAGATGC 59.483 44.000 0.00 0.00 0.00 3.91
670 3127 4.389374 AGAAAAGAAGAAGCCGAATGACA 58.611 39.130 0.00 0.00 0.00 3.58
798 3270 3.119884 CGAGCCACTTGCAATTTATGTGA 60.120 43.478 15.22 0.00 44.83 3.58
808 3280 3.684305 GCAATTTATGTGACCAAAAGGCC 59.316 43.478 0.00 0.00 0.00 5.19
814 3286 3.431725 GACCAAAAGGCCTCGCGG 61.432 66.667 5.23 9.47 0.00 6.46
824 3296 1.823899 GCCTCGCGGAAAATCCCAT 60.824 57.895 6.13 0.00 31.13 4.00
852 3324 1.573108 TACTCCAAAGCCCCAGAGAG 58.427 55.000 0.00 0.00 0.00 3.20
978 3450 1.706305 ACAGGGTGGATAAAACGGGAA 59.294 47.619 0.00 0.00 0.00 3.97
987 3459 0.948678 TAAAACGGGAACAGCTGTGC 59.051 50.000 22.49 19.82 0.00 4.57
1058 3530 2.032808 GCTGAAACACTTGTCCTCGTTC 60.033 50.000 0.00 0.00 0.00 3.95
1094 3566 0.829990 CCCTCTCTCCTTTGCCTCTC 59.170 60.000 0.00 0.00 0.00 3.20
1142 3614 2.807045 GGTCTGCGTCGCTGTGAG 60.807 66.667 19.50 7.38 0.00 3.51
1352 3824 2.476185 CCGAAATTCATGGACGACTTGC 60.476 50.000 0.00 0.00 0.00 4.01
1391 3876 8.762426 GTTTCTTGGAGTACTGTTTAACTGTAG 58.238 37.037 13.69 4.96 34.03 2.74
1444 3929 4.694509 CAGAACCTGTCCTCTGAAATGAAG 59.305 45.833 0.00 0.00 41.38 3.02
2133 4627 2.821991 ACCACGAGACAGAAGAAAGG 57.178 50.000 0.00 0.00 0.00 3.11
2515 5009 4.457496 TGCGTGCTAGCAGAGGCC 62.457 66.667 20.03 4.77 42.92 5.19
2566 5060 2.279120 GAGCGGATCAGGCAGTCG 60.279 66.667 10.19 0.00 0.00 4.18
3295 5802 4.736473 TGATCCCCGTTCTATATGTCTCA 58.264 43.478 0.00 0.00 0.00 3.27
3418 5925 7.069085 GGTCTACCAAGTATAGGTGTTGTCATA 59.931 40.741 0.00 0.00 40.26 2.15
3437 5944 6.420903 TGTCATATATAGTCTGCGTGAAAAGC 59.579 38.462 0.00 0.00 43.47 3.51
3467 5974 6.936900 ACTTTATCTGTTTCATGCACTAGTGT 59.063 34.615 23.44 2.22 0.00 3.55
3484 5991 1.459592 GTGTTCGTGTATGTGCACTCC 59.540 52.381 19.41 6.22 37.24 3.85
3782 6313 7.574607 ACCTTGATCGGGTTTATAGAGAAAAT 58.425 34.615 4.58 0.00 32.46 1.82
3837 6368 8.093307 ACATATGAGGCTACAACTTATGATGAG 58.907 37.037 10.38 0.00 0.00 2.90
3889 6420 8.690884 TGTCAATATTTTTCTCCACAAACTTGA 58.309 29.630 0.00 0.00 0.00 3.02
3895 6426 8.652810 ATTTTTCTCCACAAACTTGATCAAAG 57.347 30.769 9.88 6.49 42.07 2.77
3911 6442 8.696410 TTGATCAAAGTTTGTAAGTTTTGACC 57.304 30.769 15.08 0.00 31.88 4.02
3912 6443 8.062065 TGATCAAAGTTTGTAAGTTTTGACCT 57.938 30.769 15.08 0.00 31.88 3.85
3980 6511 8.755696 TCATTCCATTAAATGAAAGAAAACCG 57.244 30.769 0.00 0.00 41.47 4.44
4063 6594 5.809001 TGAGGCATCAACTAACTTCTCATT 58.191 37.500 0.00 0.00 30.61 2.57
4078 6609 4.581309 TCTCATTTGCAAAGAGAGGGAT 57.419 40.909 29.27 7.90 33.75 3.85
4079 6610 4.267536 TCTCATTTGCAAAGAGAGGGATG 58.732 43.478 29.27 17.27 33.75 3.51
4101 6632 2.580815 GCAAGGGCCCTGCAATTC 59.419 61.111 29.50 7.27 0.00 2.17
4130 6661 4.664150 AAAAACGAGAAAAAGCATCCCA 57.336 36.364 0.00 0.00 0.00 4.37
4132 6663 3.643159 AACGAGAAAAAGCATCCCAAC 57.357 42.857 0.00 0.00 0.00 3.77
4133 6664 2.582052 ACGAGAAAAAGCATCCCAACA 58.418 42.857 0.00 0.00 0.00 3.33
4134 6665 2.554032 ACGAGAAAAAGCATCCCAACAG 59.446 45.455 0.00 0.00 0.00 3.16
4135 6666 2.669391 CGAGAAAAAGCATCCCAACAGC 60.669 50.000 0.00 0.00 0.00 4.40
4137 6668 1.620323 GAAAAAGCATCCCAACAGCCT 59.380 47.619 0.00 0.00 0.00 4.58
4138 6669 0.971386 AAAAGCATCCCAACAGCCTG 59.029 50.000 0.00 0.00 0.00 4.85
4139 6670 0.178953 AAAGCATCCCAACAGCCTGT 60.179 50.000 0.00 0.00 0.00 4.00
4140 6671 0.610232 AAGCATCCCAACAGCCTGTC 60.610 55.000 0.00 0.00 0.00 3.51
4141 6672 2.048603 GCATCCCAACAGCCTGTCC 61.049 63.158 0.00 0.00 0.00 4.02
4142 6673 1.379044 CATCCCAACAGCCTGTCCC 60.379 63.158 0.00 0.00 0.00 4.46
4143 6674 2.971598 ATCCCAACAGCCTGTCCCG 61.972 63.158 0.00 0.00 0.00 5.14
4144 6675 4.722700 CCCAACAGCCTGTCCCGG 62.723 72.222 0.00 0.00 0.00 5.73
4152 6683 2.511600 CCTGTCCCGGCTAAAGCG 60.512 66.667 0.00 0.00 43.26 4.68
4236 6767 3.999663 CCAGCCTCTACTCTTGTTGAAAG 59.000 47.826 0.00 0.00 0.00 2.62
4245 6776 5.424121 ACTCTTGTTGAAAGAACCATTCG 57.576 39.130 0.00 0.00 34.02 3.34
4262 6793 0.613260 TCGCCACCTCAATTAGCAGT 59.387 50.000 0.00 0.00 0.00 4.40
4289 6820 0.873054 CCTCCTGCATGATCGATTGC 59.127 55.000 13.93 13.93 39.33 3.56
4303 6834 5.360999 TGATCGATTGCTTTCCTCTTCTCTA 59.639 40.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.432885 TCGAATACAAGTGCTCGATCATA 57.567 39.130 0.00 0.00 35.52 2.15
1 2 4.294232 CTCGAATACAAGTGCTCGATCAT 58.706 43.478 8.31 0.00 39.39 2.45
3 4 2.469516 GCTCGAATACAAGTGCTCGATC 59.530 50.000 8.31 2.80 39.39 3.69
4 5 2.464865 GCTCGAATACAAGTGCTCGAT 58.535 47.619 8.31 0.00 39.39 3.59
5 6 1.469251 GGCTCGAATACAAGTGCTCGA 60.469 52.381 7.80 7.80 37.95 4.04
7 8 1.134670 AGGGCTCGAATACAAGTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
9 10 1.398390 CAAGGGCTCGAATACAAGTGC 59.602 52.381 0.00 0.00 0.00 4.40
11 12 2.093447 CCTCAAGGGCTCGAATACAAGT 60.093 50.000 0.00 0.00 0.00 3.16
12 13 2.555199 CCTCAAGGGCTCGAATACAAG 58.445 52.381 0.00 0.00 0.00 3.16
13 14 2.691409 CCTCAAGGGCTCGAATACAA 57.309 50.000 0.00 0.00 0.00 2.41
33 34 2.026641 CATCACAATACAAGCCAGGGG 58.973 52.381 0.00 0.00 0.00 4.79
34 35 1.406539 GCATCACAATACAAGCCAGGG 59.593 52.381 0.00 0.00 0.00 4.45
35 36 2.372264 AGCATCACAATACAAGCCAGG 58.628 47.619 0.00 0.00 0.00 4.45
36 37 3.192001 ACAAGCATCACAATACAAGCCAG 59.808 43.478 0.00 0.00 0.00 4.85
37 38 3.156293 ACAAGCATCACAATACAAGCCA 58.844 40.909 0.00 0.00 0.00 4.75
38 39 3.855689 ACAAGCATCACAATACAAGCC 57.144 42.857 0.00 0.00 0.00 4.35
39 40 5.967674 GTCATACAAGCATCACAATACAAGC 59.032 40.000 0.00 0.00 0.00 4.01
40 41 7.312657 AGTCATACAAGCATCACAATACAAG 57.687 36.000 0.00 0.00 0.00 3.16
41 42 7.686438 AAGTCATACAAGCATCACAATACAA 57.314 32.000 0.00 0.00 0.00 2.41
42 43 8.962884 ATAAGTCATACAAGCATCACAATACA 57.037 30.769 0.00 0.00 0.00 2.29
47 48 9.394767 ACATAAATAAGTCATACAAGCATCACA 57.605 29.630 0.00 0.00 0.00 3.58
70 71 9.507329 AGATATCACAACACAACTCTAAAACAT 57.493 29.630 5.32 0.00 0.00 2.71
71 72 8.902540 AGATATCACAACACAACTCTAAAACA 57.097 30.769 5.32 0.00 0.00 2.83
72 73 9.813080 GAAGATATCACAACACAACTCTAAAAC 57.187 33.333 5.32 0.00 0.00 2.43
73 74 8.999431 GGAAGATATCACAACACAACTCTAAAA 58.001 33.333 5.32 0.00 0.00 1.52
74 75 7.606456 GGGAAGATATCACAACACAACTCTAAA 59.394 37.037 5.32 0.00 0.00 1.85
75 76 7.103641 GGGAAGATATCACAACACAACTCTAA 58.896 38.462 5.32 0.00 0.00 2.10
76 77 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
77 78 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
78 79 4.330074 CGGGAAGATATCACAACACAACTC 59.670 45.833 5.32 0.00 0.00 3.01
79 80 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
80 81 4.000988 ACGGGAAGATATCACAACACAAC 58.999 43.478 5.32 0.00 0.00 3.32
81 82 4.000325 CACGGGAAGATATCACAACACAA 59.000 43.478 5.32 0.00 0.00 3.33
82 83 3.259625 TCACGGGAAGATATCACAACACA 59.740 43.478 5.32 0.00 0.00 3.72
83 84 3.857052 TCACGGGAAGATATCACAACAC 58.143 45.455 5.32 0.00 0.00 3.32
84 85 3.513912 ACTCACGGGAAGATATCACAACA 59.486 43.478 5.32 0.00 0.00 3.33
85 86 4.113354 GACTCACGGGAAGATATCACAAC 58.887 47.826 5.32 0.00 0.00 3.32
86 87 3.132289 GGACTCACGGGAAGATATCACAA 59.868 47.826 5.32 0.00 0.00 3.33
87 88 2.693591 GGACTCACGGGAAGATATCACA 59.306 50.000 5.32 0.00 0.00 3.58
88 89 2.036089 GGGACTCACGGGAAGATATCAC 59.964 54.545 5.32 0.00 0.00 3.06
89 90 2.091278 AGGGACTCACGGGAAGATATCA 60.091 50.000 5.32 0.00 0.00 2.15
90 91 2.297597 CAGGGACTCACGGGAAGATATC 59.702 54.545 0.00 0.00 34.60 1.63
91 92 2.091278 TCAGGGACTCACGGGAAGATAT 60.091 50.000 0.00 0.00 34.60 1.63
92 93 1.286849 TCAGGGACTCACGGGAAGATA 59.713 52.381 0.00 0.00 34.60 1.98
93 94 0.041238 TCAGGGACTCACGGGAAGAT 59.959 55.000 0.00 0.00 34.60 2.40
94 95 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
95 96 0.461961 GATCAGGGACTCACGGGAAG 59.538 60.000 0.00 0.00 34.60 3.46
96 97 0.041238 AGATCAGGGACTCACGGGAA 59.959 55.000 0.00 0.00 34.60 3.97
97 98 0.041238 AAGATCAGGGACTCACGGGA 59.959 55.000 0.00 0.00 34.60 5.14
98 99 0.176680 CAAGATCAGGGACTCACGGG 59.823 60.000 0.00 0.00 34.60 5.28
99 100 1.186200 TCAAGATCAGGGACTCACGG 58.814 55.000 0.00 0.00 34.60 4.94
100 101 2.542618 CGATCAAGATCAGGGACTCACG 60.543 54.545 10.39 0.00 34.60 4.35
101 102 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
102 103 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
103 104 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
104 105 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
105 106 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
106 107 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
107 108 2.099263 ACGTGTACGATCAAGATCAGGG 59.901 50.000 11.79 0.00 43.02 4.45
108 109 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
109 110 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
110 111 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
111 112 3.539592 CGCAAACGTGTACGATCAAGATC 60.540 47.826 11.79 0.00 43.02 2.75
112 113 2.344441 CGCAAACGTGTACGATCAAGAT 59.656 45.455 11.79 0.00 43.02 2.40
113 114 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
114 115 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
127 128 3.201726 ACACTAATCATGCACGCAAAC 57.798 42.857 0.00 0.00 0.00 2.93
128 129 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
129 130 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
130 131 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
131 132 2.190161 TCGTACACTAATCATGCACGC 58.810 47.619 0.00 0.00 36.88 5.34
132 133 4.502645 TCAATCGTACACTAATCATGCACG 59.497 41.667 0.00 0.00 38.02 5.34
133 134 5.966636 TCAATCGTACACTAATCATGCAC 57.033 39.130 0.00 0.00 0.00 4.57
134 135 7.177498 GATTCAATCGTACACTAATCATGCA 57.823 36.000 0.00 0.00 0.00 3.96
150 151 1.153249 TGACGCCCCCGATTCAATC 60.153 57.895 0.00 0.00 38.29 2.67
151 152 1.451387 GTGACGCCCCCGATTCAAT 60.451 57.895 0.00 0.00 38.29 2.57
152 153 2.046700 GTGACGCCCCCGATTCAA 60.047 61.111 0.00 0.00 38.29 2.69
153 154 2.191786 ATTGTGACGCCCCCGATTCA 62.192 55.000 0.00 0.00 38.29 2.57
154 155 1.436983 GATTGTGACGCCCCCGATTC 61.437 60.000 0.00 0.00 38.29 2.52
155 156 1.451387 GATTGTGACGCCCCCGATT 60.451 57.895 0.00 0.00 38.29 3.34
156 157 1.983119 ATGATTGTGACGCCCCCGAT 61.983 55.000 0.00 0.00 38.29 4.18
157 158 2.587322 GATGATTGTGACGCCCCCGA 62.587 60.000 0.00 0.00 38.29 5.14
158 159 2.124736 ATGATTGTGACGCCCCCG 60.125 61.111 0.00 0.00 41.14 5.73
159 160 2.180204 CGATGATTGTGACGCCCCC 61.180 63.158 0.00 0.00 0.00 5.40
160 161 1.429148 GACGATGATTGTGACGCCCC 61.429 60.000 0.00 0.00 0.00 5.80
161 162 0.460284 AGACGATGATTGTGACGCCC 60.460 55.000 0.00 0.00 0.00 6.13
162 163 0.924090 GAGACGATGATTGTGACGCC 59.076 55.000 0.00 0.00 0.00 5.68
163 164 0.924090 GGAGACGATGATTGTGACGC 59.076 55.000 0.00 0.00 0.00 5.19
164 165 2.278026 TGGAGACGATGATTGTGACG 57.722 50.000 0.00 0.00 0.00 4.35
165 166 2.673368 GGTTGGAGACGATGATTGTGAC 59.327 50.000 0.00 0.00 0.00 3.67
166 167 2.673893 CGGTTGGAGACGATGATTGTGA 60.674 50.000 0.00 0.00 0.00 3.58
167 168 1.660607 CGGTTGGAGACGATGATTGTG 59.339 52.381 0.00 0.00 0.00 3.33
168 169 1.275291 ACGGTTGGAGACGATGATTGT 59.725 47.619 0.00 0.00 0.00 2.71
169 170 1.927174 GACGGTTGGAGACGATGATTG 59.073 52.381 0.00 0.00 0.00 2.67
170 171 1.134788 GGACGGTTGGAGACGATGATT 60.135 52.381 0.00 0.00 0.00 2.57
171 172 0.460311 GGACGGTTGGAGACGATGAT 59.540 55.000 0.00 0.00 0.00 2.45
172 173 1.601419 GGGACGGTTGGAGACGATGA 61.601 60.000 0.00 0.00 0.00 2.92
173 174 1.153628 GGGACGGTTGGAGACGATG 60.154 63.158 0.00 0.00 0.00 3.84
174 175 1.189524 TTGGGACGGTTGGAGACGAT 61.190 55.000 0.00 0.00 0.00 3.73
175 176 1.401318 TTTGGGACGGTTGGAGACGA 61.401 55.000 0.00 0.00 0.00 4.20
262 263 1.202651 TCCTAAGCGCCTATTCAAGCC 60.203 52.381 2.29 0.00 0.00 4.35
274 275 3.676049 GCCCAAAATCCTTTTCCTAAGCG 60.676 47.826 0.00 0.00 0.00 4.68
431 2888 1.757682 TATTCCCACACAAATCCCGC 58.242 50.000 0.00 0.00 0.00 6.13
441 2898 3.451178 GTCTGCTAGGTCTTATTCCCACA 59.549 47.826 0.00 0.00 0.00 4.17
460 2917 1.272147 GCCAGGGTGAAAATCCTGTCT 60.272 52.381 4.40 0.00 46.75 3.41
485 2942 6.621613 CATCTACAACACTAGCACTAAGACA 58.378 40.000 0.00 0.00 0.00 3.41
641 3098 6.451064 TCGGCTTCTTCTTTTCTTTCTTTT 57.549 33.333 0.00 0.00 0.00 2.27
644 3101 5.765182 TCATTCGGCTTCTTCTTTTCTTTCT 59.235 36.000 0.00 0.00 0.00 2.52
645 3102 5.853810 GTCATTCGGCTTCTTCTTTTCTTTC 59.146 40.000 0.00 0.00 0.00 2.62
647 3104 4.821805 TGTCATTCGGCTTCTTCTTTTCTT 59.178 37.500 0.00 0.00 0.00 2.52
648 3105 4.389374 TGTCATTCGGCTTCTTCTTTTCT 58.611 39.130 0.00 0.00 0.00 2.52
649 3106 4.452455 TCTGTCATTCGGCTTCTTCTTTTC 59.548 41.667 0.00 0.00 0.00 2.29
650 3107 4.389374 TCTGTCATTCGGCTTCTTCTTTT 58.611 39.130 0.00 0.00 0.00 2.27
651 3108 4.008074 TCTGTCATTCGGCTTCTTCTTT 57.992 40.909 0.00 0.00 0.00 2.52
808 3280 2.017049 AGAAATGGGATTTTCCGCGAG 58.983 47.619 8.23 0.00 37.43 5.03
814 3286 7.666623 TGGAGTAAAACAGAAATGGGATTTTC 58.333 34.615 0.00 0.00 36.13 2.29
824 3296 3.639561 GGGGCTTTGGAGTAAAACAGAAA 59.360 43.478 0.00 0.00 0.00 2.52
852 3324 4.303086 TCGCTTGTAGCACTAGAATACC 57.697 45.455 0.00 0.00 42.58 2.73
987 3459 1.203523 GAGGAGCTCACTACCACACAG 59.796 57.143 17.19 0.00 0.00 3.66
1058 3530 1.098050 GGGGAGTTTATGTGCTGCTG 58.902 55.000 0.00 0.00 0.00 4.41
1094 3566 2.325661 ATTTGGTTGGAAGGGGAAGG 57.674 50.000 0.00 0.00 0.00 3.46
1149 3621 6.085555 TCGTATATCCTCACCAGACAAATC 57.914 41.667 0.00 0.00 0.00 2.17
1281 3753 1.882623 CTTGTCTGCCTTTCTTCCACC 59.117 52.381 0.00 0.00 0.00 4.61
1352 3824 5.116084 TCCAAGAAACAGGGAAGATATGG 57.884 43.478 0.00 0.00 0.00 2.74
1444 3929 1.058903 GTCGGATTTCGCTCGTTGC 59.941 57.895 0.00 0.00 39.05 4.17
1459 3944 0.439985 CGTTCAGCTTGTCCATGTCG 59.560 55.000 0.00 0.00 0.00 4.35
1492 3977 1.437986 GGCTCGCTCGTTATCCACT 59.562 57.895 0.00 0.00 0.00 4.00
1630 4115 1.450312 CTCCTCGGCGCCATTCTTT 60.450 57.895 28.98 0.00 0.00 2.52
1681 4175 4.443266 AGCTCCCTCTTGACGCGC 62.443 66.667 5.73 0.00 0.00 6.86
1711 4205 2.932234 CGCGGACTTCACCTCCAGT 61.932 63.158 0.00 0.00 0.00 4.00
2133 4627 4.154347 CCCTGTCCTGCGCCTCTC 62.154 72.222 4.18 0.00 0.00 3.20
2566 5060 2.270527 GCCTCCAGCTCCTTCACC 59.729 66.667 0.00 0.00 38.99 4.02
3191 5691 1.805134 GCACGCACTCTGCTCTCTC 60.805 63.158 0.00 0.00 42.25 3.20
3192 5692 1.886253 ATGCACGCACTCTGCTCTCT 61.886 55.000 0.00 0.00 42.25 3.10
3295 5802 9.154632 AGACAAACCTAAAATGGGAACTAAAAT 57.845 29.630 0.00 0.00 0.00 1.82
3418 5925 5.874810 TCTTTGCTTTTCACGCAGACTATAT 59.125 36.000 0.00 0.00 38.80 0.86
3422 5929 2.032178 GTCTTTGCTTTTCACGCAGACT 59.968 45.455 0.00 0.00 38.80 3.24
3437 5944 7.365741 AGTGCATGAAACAGATAAAGTCTTTG 58.634 34.615 8.14 0.00 34.00 2.77
3467 5974 0.389296 CGGGAGTGCACATACACGAA 60.389 55.000 21.04 0.00 45.45 3.85
3521 6028 6.507958 TCTCGGATTCAACATTAATTGCAA 57.492 33.333 0.00 0.00 0.00 4.08
3617 6124 5.068067 TCCAATTTGTAGCCATCACATCATG 59.932 40.000 0.00 0.00 0.00 3.07
3646 6153 9.798994 TCAATCATCTATATCGAATGTCTCATG 57.201 33.333 0.00 0.00 0.00 3.07
3738 6269 8.754991 TCAAGGTTTGTAGATTTGACCTTTTA 57.245 30.769 3.49 0.00 45.76 1.52
3759 6290 8.662781 TCATTTTCTCTATAAACCCGATCAAG 57.337 34.615 0.00 0.00 0.00 3.02
3889 6420 9.719355 AAAAGGTCAAAACTTACAAACTTTGAT 57.281 25.926 8.55 0.00 39.32 2.57
4007 6538 1.834822 GCTCCGGCACTAGGATCCT 60.835 63.158 20.48 20.48 37.13 3.24
4041 6572 6.549952 CAAATGAGAAGTTAGTTGATGCCTC 58.450 40.000 0.00 0.00 0.00 4.70
4063 6594 0.405198 TGGCATCCCTCTCTTTGCAA 59.595 50.000 0.00 0.00 36.82 4.08
4114 6645 2.669391 GCTGTTGGGATGCTTTTTCTCG 60.669 50.000 0.00 0.00 0.00 4.04
4115 6646 2.353109 GGCTGTTGGGATGCTTTTTCTC 60.353 50.000 0.00 0.00 0.00 2.87
4123 6654 2.048603 GGACAGGCTGTTGGGATGC 61.049 63.158 22.98 6.65 0.00 3.91
4135 6666 2.511600 CGCTTTAGCCGGGACAGG 60.512 66.667 2.18 0.00 37.91 4.00
4137 6668 2.577059 CTCGCTTTAGCCGGGACA 59.423 61.111 2.18 0.00 37.91 4.02
4138 6669 2.890961 GCTCGCTTTAGCCGGGAC 60.891 66.667 2.18 0.00 36.45 4.46
4139 6670 3.075005 AGCTCGCTTTAGCCGGGA 61.075 61.111 2.18 0.00 43.86 5.14
4140 6671 2.586357 GAGCTCGCTTTAGCCGGG 60.586 66.667 2.18 0.00 43.86 5.73
4141 6672 2.586357 GGAGCTCGCTTTAGCCGG 60.586 66.667 7.83 0.00 43.86 6.13
4142 6673 1.019278 TTTGGAGCTCGCTTTAGCCG 61.019 55.000 7.83 0.00 43.86 5.52
4143 6674 1.383523 ATTTGGAGCTCGCTTTAGCC 58.616 50.000 7.83 0.00 43.86 3.93
4144 6675 4.616181 TTTATTTGGAGCTCGCTTTAGC 57.384 40.909 7.83 0.00 43.11 3.09
4145 6676 4.972440 GCATTTATTTGGAGCTCGCTTTAG 59.028 41.667 7.83 0.00 0.00 1.85
4152 6683 8.532977 TTAGTTTTTGCATTTATTTGGAGCTC 57.467 30.769 4.71 4.71 0.00 4.09
4236 6767 1.463674 ATTGAGGTGGCGAATGGTTC 58.536 50.000 0.00 0.00 0.00 3.62
4245 6776 0.453390 GCACTGCTAATTGAGGTGGC 59.547 55.000 0.00 0.00 0.00 5.01
4275 6806 2.615447 GAGGAAAGCAATCGATCATGCA 59.385 45.455 20.96 0.00 44.95 3.96
4279 6810 4.161189 AGAGAAGAGGAAAGCAATCGATCA 59.839 41.667 0.00 0.00 0.00 2.92
4289 6820 3.257127 CGGGCCTATAGAGAAGAGGAAAG 59.743 52.174 0.84 0.00 31.45 2.62
4303 6834 1.151899 TCCTATTGGGCGGGCCTAT 60.152 57.895 22.12 21.01 36.10 2.57


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

AutoCloner maintained by Alex Coulton.