Multiple sequence alignment - TraesCS6D01G395200

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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 TraesCS6D01G395200 chr6D 100.000 5397 0 0 1 5397 467997574 467992178 0.000000e+00 9930.0
1 TraesCS6D01G395200 chr6D 86.473 1035 126 12 977 2002 468657737 468656708 0.000000e+00 1123.0
2 TraesCS6D01G395200 chr6D 78.006 1555 272 43 2714 4238 468089451 468087937 0.000000e+00 913.0
3 TraesCS6D01G395200 chr6D 80.976 205 32 4 5191 5395 468654007 468653810 7.240000e-34 156.0
4 TraesCS6D01G395200 chrUn 95.897 3071 98 13 2346 5397 79514404 79511343 0.000000e+00 4948.0
5 TraesCS6D01G395200 chrUn 96.254 2776 76 11 2321 5079 79551524 79548760 0.000000e+00 4525.0
6 TraesCS6D01G395200 chrUn 97.367 1671 30 3 634 2294 79516195 79514529 0.000000e+00 2830.0
7 TraesCS6D01G395200 chrUn 97.239 1666 32 3 634 2289 79553593 79551932 0.000000e+00 2809.0
8 TraesCS6D01G395200 chrUn 97.910 1340 23 2 634 1972 270623800 270625135 0.000000e+00 2314.0
9 TraesCS6D01G395200 chrUn 91.163 1539 112 10 3656 5188 79710139 79711659 0.000000e+00 2067.0
10 TraesCS6D01G395200 chrUn 91.163 1539 112 10 3656 5188 297258400 297256880 0.000000e+00 2067.0
11 TraesCS6D01G395200 chrUn 92.792 874 49 9 2784 3649 461243088 461242221 0.000000e+00 1253.0
12 TraesCS6D01G395200 chrUn 85.951 1025 133 10 976 1993 79688895 79689915 0.000000e+00 1085.0
13 TraesCS6D01G395200 chrUn 84.541 925 130 7 1065 1980 79468549 79467629 0.000000e+00 904.0
14 TraesCS6D01G395200 chrUn 80.274 1095 178 21 2949 4028 322139425 322140496 0.000000e+00 791.0
15 TraesCS6D01G395200 chrUn 90.698 516 45 2 992 1504 298375455 298374940 0.000000e+00 684.0
16 TraesCS6D01G395200 chrUn 91.064 470 38 1 1517 1986 79776837 79776372 2.740000e-177 632.0
17 TraesCS6D01G395200 chrUn 94.587 351 14 5 5051 5397 79548763 79548414 6.150000e-149 538.0
18 TraesCS6D01G395200 chrUn 85.139 323 34 7 205 524 79516699 79516388 8.720000e-83 318.0
19 TraesCS6D01G395200 chrUn 85.139 323 34 7 205 524 79554097 79553786 8.720000e-83 318.0
20 TraesCS6D01G395200 chrUn 85.139 323 34 7 205 524 270623296 270623607 8.720000e-83 318.0
21 TraesCS6D01G395200 chrUn 91.150 226 5 2 5172 5397 79712160 79712370 5.290000e-75 292.0
22 TraesCS6D01G395200 chrUn 91.480 223 4 2 5175 5397 297256376 297256169 5.290000e-75 292.0
23 TraesCS6D01G395200 chrUn 95.152 165 8 0 5233 5397 477240458 477240294 1.490000e-65 261.0
24 TraesCS6D01G395200 chrUn 81.860 215 19 3 2342 2536 79776276 79776062 4.330000e-36 163.0
25 TraesCS6D01G395200 chrUn 84.564 149 18 3 992 1135 79566222 79566370 5.630000e-30 143.0
26 TraesCS6D01G395200 chrUn 94.737 57 2 1 4446 4502 79710993 79711048 2.680000e-13 87.9
27 TraesCS6D01G395200 chrUn 94.737 57 2 1 4446 4502 297257546 297257491 2.680000e-13 87.9
28 TraesCS6D01G395200 chr6B 96.759 2561 46 9 2308 4845 714122332 714119786 0.000000e+00 4235.0
29 TraesCS6D01G395200 chr6B 96.318 2444 83 4 2955 5397 714308139 714305702 0.000000e+00 4008.0
30 TraesCS6D01G395200 chr6B 95.579 1674 45 7 634 2297 714124033 714122379 0.000000e+00 2654.0
31 TraesCS6D01G395200 chr6B 97.910 1340 23 2 634 1972 714274883 714273548 0.000000e+00 2314.0
32 TraesCS6D01G395200 chr6B 93.369 558 32 2 4840 5397 714095250 714094698 0.000000e+00 821.0
33 TraesCS6D01G395200 chr6B 77.092 1458 287 35 2987 4411 714265159 714263716 0.000000e+00 798.0
34 TraesCS6D01G395200 chr6B 81.414 877 138 18 1329 2196 714271296 714270436 0.000000e+00 693.0
35 TraesCS6D01G395200 chr6B 75.714 1470 302 41 2995 4426 714190715 714189263 0.000000e+00 686.0
36 TraesCS6D01G395200 chr6B 87.719 342 31 6 634 974 714126556 714126225 6.560000e-104 388.0
37 TraesCS6D01G395200 chr6B 88.125 320 25 8 205 524 714127055 714126749 8.540000e-98 368.0
38 TraesCS6D01G395200 chr6B 85.139 323 34 7 205 524 714275387 714275076 8.720000e-83 318.0
39 TraesCS6D01G395200 chr6B 84.127 252 29 8 272 523 714128246 714128006 3.250000e-57 233.0
40 TraesCS6D01G395200 chr6B 86.555 119 12 2 1 116 714124624 714124507 1.580000e-25 128.0
41 TraesCS6D01G395200 chr6B 79.679 187 26 6 5214 5395 714262924 714262745 2.040000e-24 124.0
42 TraesCS6D01G395200 chr6B 91.525 59 2 2 29 84 714127279 714127221 1.610000e-10 78.7
43 TraesCS6D01G395200 chr6A 87.320 347 31 7 634 974 614110838 614110499 8.480000e-103 385.0
44 TraesCS6D01G395200 chr6A 85.625 320 33 6 205 524 614111337 614111031 1.870000e-84 324.0
45 TraesCS6D01G395200 chr6A 80.620 387 41 18 243 629 614113789 614113437 8.910000e-68 268.0
46 TraesCS6D01G395200 chr5D 78.351 291 42 15 5052 5330 87806064 87806345 9.300000e-38 169.0
47 TraesCS6D01G395200 chr7B 94.737 38 2 0 106 143 234647863 234647826 5.840000e-05 60.2
48 TraesCS6D01G395200 chr7B 92.683 41 3 0 103 143 479258229 479258269 5.840000e-05 60.2
49 TraesCS6D01G395200 chr3B 92.683 41 3 0 103 143 785669621 785669661 5.840000e-05 60.2
50 TraesCS6D01G395200 chr2B 92.683 41 3 0 103 143 197584656 197584696 5.840000e-05 60.2
51 TraesCS6D01G395200 chr1A 94.737 38 2 0 106 143 51821280 51821243 5.840000e-05 60.2
52 TraesCS6D01G395200 chr1A 94.737 38 2 0 106 143 115526789 115526752 5.840000e-05 60.2


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 TraesCS6D01G395200 chr6D 467992178 467997574 5396 True 9930.000000 9930 100.000000 1 5397 1 chr6D.!!$R1 5396
1 TraesCS6D01G395200 chr6D 468087937 468089451 1514 True 913.000000 913 78.006000 2714 4238 1 chr6D.!!$R2 1524
2 TraesCS6D01G395200 chr6D 468653810 468657737 3927 True 639.500000 1123 83.724500 977 5395 2 chr6D.!!$R3 4418
3 TraesCS6D01G395200 chrUn 79511343 79516699 5356 True 2698.666667 4948 92.801000 205 5397 3 chrUn.!!$R5 5192
4 TraesCS6D01G395200 chrUn 79548414 79554097 5683 True 2047.500000 4525 93.304750 205 5397 4 chrUn.!!$R6 5192
5 TraesCS6D01G395200 chrUn 270623296 270625135 1839 False 1316.000000 2314 91.524500 205 1972 2 chrUn.!!$F5 1767
6 TraesCS6D01G395200 chrUn 461242221 461243088 867 True 1253.000000 1253 92.792000 2784 3649 1 chrUn.!!$R3 865
7 TraesCS6D01G395200 chrUn 79688895 79689915 1020 False 1085.000000 1085 85.951000 976 1993 1 chrUn.!!$F2 1017
8 TraesCS6D01G395200 chrUn 79467629 79468549 920 True 904.000000 904 84.541000 1065 1980 1 chrUn.!!$R1 915
9 TraesCS6D01G395200 chrUn 79710139 79712370 2231 False 815.633333 2067 92.350000 3656 5397 3 chrUn.!!$F4 1741
10 TraesCS6D01G395200 chrUn 297256169 297258400 2231 True 815.633333 2067 92.460000 3656 5397 3 chrUn.!!$R8 1741
11 TraesCS6D01G395200 chrUn 322139425 322140496 1071 False 791.000000 791 80.274000 2949 4028 1 chrUn.!!$F3 1079
12 TraesCS6D01G395200 chrUn 298374940 298375455 515 True 684.000000 684 90.698000 992 1504 1 chrUn.!!$R2 512
13 TraesCS6D01G395200 chrUn 79776062 79776837 775 True 397.500000 632 86.462000 1517 2536 2 chrUn.!!$R7 1019
14 TraesCS6D01G395200 chr6B 714305702 714308139 2437 True 4008.000000 4008 96.318000 2955 5397 1 chr6B.!!$R3 2442
15 TraesCS6D01G395200 chr6B 714119786 714128246 8460 True 1154.957143 4235 90.055571 1 4845 7 chr6B.!!$R4 4844
16 TraesCS6D01G395200 chr6B 714270436 714275387 4951 True 1108.333333 2314 88.154333 205 2196 3 chr6B.!!$R6 1991
17 TraesCS6D01G395200 chr6B 714094698 714095250 552 True 821.000000 821 93.369000 4840 5397 1 chr6B.!!$R1 557
18 TraesCS6D01G395200 chr6B 714189263 714190715 1452 True 686.000000 686 75.714000 2995 4426 1 chr6B.!!$R2 1431
19 TraesCS6D01G395200 chr6B 714262745 714265159 2414 True 461.000000 798 78.385500 2987 5395 2 chr6B.!!$R5 2408
20 TraesCS6D01G395200 chr6A 614110499 614113789 3290 True 325.666667 385 84.521667 205 974 3 chr6A.!!$R1 769

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
202 1145 0.107654 AGCCTCCTGATGTTTACGGC 60.108 55.0 0.00 0.0 36.36 5.68 F
340 2589 0.107703 CAGGAAGCTAATGCCGACCA 60.108 55.0 0.00 0.0 40.80 4.02 F
359 2608 1.014352 ATTGGCGCGGTGAGAAATAC 58.986 50.0 8.83 0.0 0.00 1.89 F
2268 7287 1.149964 GAAGGCGGAATAACGTCGGG 61.150 60.0 0.00 0.0 44.42 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 6116 0.394352 GGAATCCATGACCGGCAAGT 60.394 55.000 0.00 0.0 0.00 3.16 R
2268 7287 1.421410 CGAATGTGTCGCCTACCTGC 61.421 60.000 0.00 0.0 44.14 4.85 R
2347 7742 0.868602 GCGCAGGCGAATCGTAGTAA 60.869 55.000 18.96 0.0 42.83 2.24 R
4440 9963 3.264450 AGATCCGAAACCTCCAATTGTCT 59.736 43.478 4.43 0.0 0.00 3.41 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
45 985 7.238710 ACCACTCACCCTTAATTACAAGATTT 58.761 34.615 0.00 0.00 0.00 2.17
85 1028 8.927675 TTAATAACATAAACACCACTGGAACT 57.072 30.769 0.71 0.00 0.00 3.01
87 1030 8.561738 AATAACATAAACACCACTGGAACTAG 57.438 34.615 0.71 0.00 0.00 2.57
89 1032 6.675413 ACATAAACACCACTGGAACTAGTA 57.325 37.500 0.71 0.00 0.00 1.82
90 1033 7.069877 ACATAAACACCACTGGAACTAGTAA 57.930 36.000 0.71 0.00 0.00 2.24
91 1034 7.159372 ACATAAACACCACTGGAACTAGTAAG 58.841 38.462 0.71 0.00 0.00 2.34
92 1035 5.881923 AAACACCACTGGAACTAGTAAGA 57.118 39.130 0.71 0.00 0.00 2.10
93 1036 5.881923 AACACCACTGGAACTAGTAAGAA 57.118 39.130 0.71 0.00 0.00 2.52
94 1037 5.211174 ACACCACTGGAACTAGTAAGAAC 57.789 43.478 0.71 0.00 0.00 3.01
95 1038 4.652421 ACACCACTGGAACTAGTAAGAACA 59.348 41.667 0.71 0.00 0.00 3.18
96 1039 5.221461 ACACCACTGGAACTAGTAAGAACAG 60.221 44.000 0.71 3.43 0.00 3.16
97 1040 5.010719 CACCACTGGAACTAGTAAGAACAGA 59.989 44.000 0.71 0.00 0.00 3.41
98 1041 5.010820 ACCACTGGAACTAGTAAGAACAGAC 59.989 44.000 0.71 0.00 0.00 3.51
99 1042 5.010719 CCACTGGAACTAGTAAGAACAGACA 59.989 44.000 14.92 0.00 0.00 3.41
100 1043 5.921408 CACTGGAACTAGTAAGAACAGACAC 59.079 44.000 14.92 0.00 0.00 3.67
103 1046 6.309357 TGGAACTAGTAAGAACAGACACCTA 58.691 40.000 0.00 0.00 0.00 3.08
105 1048 6.208204 GGAACTAGTAAGAACAGACACCTACA 59.792 42.308 0.00 0.00 0.00 2.74
107 1050 6.979465 ACTAGTAAGAACAGACACCTACAAC 58.021 40.000 0.00 0.00 0.00 3.32
108 1051 5.864418 AGTAAGAACAGACACCTACAACA 57.136 39.130 0.00 0.00 0.00 3.33
109 1052 6.229936 AGTAAGAACAGACACCTACAACAA 57.770 37.500 0.00 0.00 0.00 2.83
110 1053 6.646267 AGTAAGAACAGACACCTACAACAAA 58.354 36.000 0.00 0.00 0.00 2.83
114 1057 4.481368 ACAGACACCTACAACAAACTCA 57.519 40.909 0.00 0.00 0.00 3.41
115 1058 4.189231 ACAGACACCTACAACAAACTCAC 58.811 43.478 0.00 0.00 0.00 3.51
116 1059 4.188462 CAGACACCTACAACAAACTCACA 58.812 43.478 0.00 0.00 0.00 3.58
121 1064 5.475564 ACACCTACAACAAACTCACAAAAGT 59.524 36.000 0.00 0.00 0.00 2.66
122 1065 5.799936 CACCTACAACAAACTCACAAAAGTG 59.200 40.000 0.00 0.00 0.00 3.16
123 1066 5.708230 ACCTACAACAAACTCACAAAAGTGA 59.292 36.000 0.00 0.00 0.00 3.41
124 1067 6.027749 CCTACAACAAACTCACAAAAGTGAC 58.972 40.000 0.00 0.00 0.00 3.67
125 1068 5.446143 ACAACAAACTCACAAAAGTGACA 57.554 34.783 0.00 0.00 0.00 3.58
126 1069 5.460646 ACAACAAACTCACAAAAGTGACAG 58.539 37.500 0.00 0.00 0.00 3.51
127 1070 4.701956 ACAAACTCACAAAAGTGACAGG 57.298 40.909 0.00 0.00 0.00 4.00
128 1071 4.331968 ACAAACTCACAAAAGTGACAGGA 58.668 39.130 0.00 0.00 0.00 3.86
129 1072 4.396166 ACAAACTCACAAAAGTGACAGGAG 59.604 41.667 0.00 0.00 0.00 3.69
130 1073 3.199880 ACTCACAAAAGTGACAGGAGG 57.800 47.619 0.00 0.00 0.00 4.30
132 1075 2.104792 CTCACAAAAGTGACAGGAGGGA 59.895 50.000 0.00 0.00 0.00 4.20
133 1076 2.104792 TCACAAAAGTGACAGGAGGGAG 59.895 50.000 0.00 0.00 0.00 4.30
135 1078 2.104963 ACAAAAGTGACAGGAGGGAGAC 59.895 50.000 0.00 0.00 0.00 3.36
149 1092 2.195741 GGAGACCCAAAACCTACCAC 57.804 55.000 0.00 0.00 0.00 4.16
150 1093 1.422402 GGAGACCCAAAACCTACCACA 59.578 52.381 0.00 0.00 0.00 4.17
151 1094 2.501261 GAGACCCAAAACCTACCACAC 58.499 52.381 0.00 0.00 0.00 3.82
156 1099 2.101750 CCCAAAACCTACCACACAAACC 59.898 50.000 0.00 0.00 0.00 3.27
159 1102 2.651382 AACCTACCACACAAACCTCC 57.349 50.000 0.00 0.00 0.00 4.30
163 1106 3.914435 ACCTACCACACAAACCTCCTATT 59.086 43.478 0.00 0.00 0.00 1.73
165 1108 3.434940 ACCACACAAACCTCCTATTCC 57.565 47.619 0.00 0.00 0.00 3.01
166 1109 2.041216 ACCACACAAACCTCCTATTCCC 59.959 50.000 0.00 0.00 0.00 3.97
167 1110 2.620627 CCACACAAACCTCCTATTCCCC 60.621 54.545 0.00 0.00 0.00 4.81
170 1113 2.311841 CACAAACCTCCTATTCCCCCTT 59.688 50.000 0.00 0.00 0.00 3.95
171 1114 2.581246 ACAAACCTCCTATTCCCCCTTC 59.419 50.000 0.00 0.00 0.00 3.46
172 1115 2.853077 CAAACCTCCTATTCCCCCTTCT 59.147 50.000 0.00 0.00 0.00 2.85
175 1118 4.379263 ACCTCCTATTCCCCCTTCTTAA 57.621 45.455 0.00 0.00 0.00 1.85
176 1119 4.921661 ACCTCCTATTCCCCCTTCTTAAT 58.078 43.478 0.00 0.00 0.00 1.40
177 1120 5.306182 ACCTCCTATTCCCCCTTCTTAATT 58.694 41.667 0.00 0.00 0.00 1.40
178 1121 5.134509 ACCTCCTATTCCCCCTTCTTAATTG 59.865 44.000 0.00 0.00 0.00 2.32
181 1124 7.291991 TCCTATTCCCCCTTCTTAATTGAAA 57.708 36.000 0.00 0.00 0.00 2.69
182 1125 7.714500 TCCTATTCCCCCTTCTTAATTGAAAA 58.286 34.615 0.00 0.00 0.00 2.29
183 1126 8.180844 TCCTATTCCCCCTTCTTAATTGAAAAA 58.819 33.333 0.00 0.00 0.00 1.94
185 1128 5.738619 TCCCCCTTCTTAATTGAAAAAGC 57.261 39.130 0.00 0.00 0.00 3.51
188 1131 5.337571 CCCCCTTCTTAATTGAAAAAGCCTC 60.338 44.000 0.00 0.00 0.00 4.70
189 1132 5.337571 CCCCTTCTTAATTGAAAAAGCCTCC 60.338 44.000 0.00 0.00 0.00 4.30
190 1133 5.481824 CCCTTCTTAATTGAAAAAGCCTCCT 59.518 40.000 0.00 0.00 0.00 3.69
195 1138 6.721208 TCTTAATTGAAAAAGCCTCCTGATGT 59.279 34.615 0.00 0.00 0.00 3.06
196 1139 5.813513 AATTGAAAAAGCCTCCTGATGTT 57.186 34.783 0.00 0.00 0.00 2.71
197 1140 5.813513 ATTGAAAAAGCCTCCTGATGTTT 57.186 34.783 0.00 0.00 0.00 2.83
198 1141 6.916360 ATTGAAAAAGCCTCCTGATGTTTA 57.084 33.333 0.00 0.00 0.00 2.01
200 1143 4.215399 TGAAAAAGCCTCCTGATGTTTACG 59.785 41.667 0.00 0.00 0.00 3.18
201 1144 2.403252 AAGCCTCCTGATGTTTACGG 57.597 50.000 0.00 0.00 0.00 4.02
202 1145 0.107654 AGCCTCCTGATGTTTACGGC 60.108 55.000 0.00 0.00 36.36 5.68
203 1146 1.095807 GCCTCCTGATGTTTACGGCC 61.096 60.000 0.00 0.00 0.00 6.13
224 2473 1.525077 GAACAGCCACCGACCACAA 60.525 57.895 0.00 0.00 0.00 3.33
230 2479 2.539338 CCACCGACCACAAACCACG 61.539 63.158 0.00 0.00 0.00 4.94
231 2480 1.816259 CACCGACCACAAACCACGT 60.816 57.895 0.00 0.00 0.00 4.49
232 2481 1.078285 ACCGACCACAAACCACGTT 60.078 52.632 0.00 0.00 0.00 3.99
233 2482 0.177604 ACCGACCACAAACCACGTTA 59.822 50.000 0.00 0.00 0.00 3.18
272 2521 5.799213 AGCATGATTATGTTAGTCTAGCCC 58.201 41.667 0.00 0.00 36.65 5.19
279 2528 6.956202 TTATGTTAGTCTAGCCCTAGTGTC 57.044 41.667 2.53 0.00 34.84 3.67
298 2547 9.651718 CTAGTGTCAATTTCAACAGTTTTCTAC 57.348 33.333 0.00 0.00 31.68 2.59
301 2550 6.094325 TGTCAATTTCAACAGTTTTCTACCGT 59.906 34.615 0.00 0.00 0.00 4.83
318 2567 0.108851 CGTTTTGTATTGGCTGGCCC 60.109 55.000 9.28 0.00 34.56 5.80
340 2589 0.107703 CAGGAAGCTAATGCCGACCA 60.108 55.000 0.00 0.00 40.80 4.02
359 2608 1.014352 ATTGGCGCGGTGAGAAATAC 58.986 50.000 8.83 0.00 0.00 1.89
378 2631 8.215050 AGAAATACCAAATGGATCGTATTACCA 58.785 33.333 6.42 0.00 38.94 3.25
379 2632 8.934023 AAATACCAAATGGATCGTATTACCAT 57.066 30.769 6.42 0.00 44.87 3.55
430 2683 7.802738 TCTTACAATCATAAACAACTTGGACG 58.197 34.615 0.00 0.00 0.00 4.79
471 2724 4.839668 GGGCACCGCATATTAATTAACA 57.160 40.909 0.00 0.00 40.86 2.41
512 2765 7.595502 GTGATCTAGTATTGATAGTGAAACGGG 59.404 40.741 0.00 0.00 45.86 5.28
517 2770 3.791953 TTGATAGTGAAACGGGGGAAA 57.208 42.857 0.00 0.00 45.86 3.13
518 2771 4.310022 TTGATAGTGAAACGGGGGAAAT 57.690 40.909 0.00 0.00 45.86 2.17
519 2772 5.438698 TTGATAGTGAAACGGGGGAAATA 57.561 39.130 0.00 0.00 45.86 1.40
520 2773 4.773013 TGATAGTGAAACGGGGGAAATAC 58.227 43.478 0.00 0.00 45.86 1.89
521 2774 2.502142 AGTGAAACGGGGGAAATACC 57.498 50.000 0.00 0.00 45.86 2.73
522 2775 1.706305 AGTGAAACGGGGGAAATACCA 59.294 47.619 0.00 0.00 45.86 3.25
523 2776 2.108601 AGTGAAACGGGGGAAATACCAA 59.891 45.455 0.00 0.00 45.86 3.67
524 2777 2.892215 GTGAAACGGGGGAAATACCAAA 59.108 45.455 0.00 0.00 41.20 3.28
525 2778 3.321396 GTGAAACGGGGGAAATACCAAAA 59.679 43.478 0.00 0.00 41.20 2.44
526 2779 3.965347 TGAAACGGGGGAAATACCAAAAA 59.035 39.130 0.00 0.00 41.20 1.94
603 2856 5.356190 TCAGATCATTGCTTGGAAATGAGAC 59.644 40.000 6.99 4.43 44.81 3.36
629 2882 1.953686 TGTTCAAGGGCTAACAACTGC 59.046 47.619 0.00 0.00 32.86 4.40
882 5777 3.243367 TGTGCACAAGTTTGATACAAGGC 60.243 43.478 19.28 0.00 0.00 4.35
897 5792 2.359975 GGCCGTCTTGGTTCCTGG 60.360 66.667 0.00 0.00 41.21 4.45
911 5806 4.342951 TGGTTCCTGGTATATACGAGTTGG 59.657 45.833 19.73 9.04 31.13 3.77
912 5807 4.304939 GTTCCTGGTATATACGAGTTGGC 58.695 47.826 19.73 7.03 31.13 4.52
913 5808 3.840991 TCCTGGTATATACGAGTTGGCT 58.159 45.455 19.73 0.00 31.13 4.75
914 5809 4.989277 TCCTGGTATATACGAGTTGGCTA 58.011 43.478 19.73 0.71 31.13 3.93
947 5855 4.450080 CCAGCACTCGTACGACTATATACA 59.550 45.833 15.28 0.00 0.00 2.29
951 5859 6.426025 AGCACTCGTACGACTATATACATTCA 59.574 38.462 15.28 0.00 0.00 2.57
952 5860 6.737301 GCACTCGTACGACTATATACATTCAG 59.263 42.308 15.28 1.74 0.00 3.02
953 5861 7.359849 GCACTCGTACGACTATATACATTCAGA 60.360 40.741 15.28 0.00 0.00 3.27
954 5862 8.493547 CACTCGTACGACTATATACATTCAGAA 58.506 37.037 15.28 0.00 0.00 3.02
955 5863 9.217278 ACTCGTACGACTATATACATTCAGAAT 57.783 33.333 15.28 0.00 0.00 2.40
956 5864 9.691795 CTCGTACGACTATATACATTCAGAATC 57.308 37.037 15.28 0.00 0.00 2.52
957 5865 9.211485 TCGTACGACTATATACATTCAGAATCA 57.789 33.333 15.28 0.00 0.00 2.57
958 5866 9.821662 CGTACGACTATATACATTCAGAATCAA 57.178 33.333 10.44 0.00 0.00 2.57
961 5869 8.861086 ACGACTATATACATTCAGAATCAACCT 58.139 33.333 0.00 0.00 0.00 3.50
962 5870 9.698309 CGACTATATACATTCAGAATCAACCTT 57.302 33.333 0.00 0.00 0.00 3.50
1042 5950 2.750350 CTCCTGCCTCACCCGTTT 59.250 61.111 0.00 0.00 0.00 3.60
1060 5968 2.833943 GTTTTGGGAAATGCTCCTCCAT 59.166 45.455 1.77 0.00 44.68 3.41
1792 6711 1.737236 TGGAAAACAGAATCATCGCCG 59.263 47.619 0.00 0.00 0.00 6.46
2268 7287 1.149964 GAAGGCGGAATAACGTCGGG 61.150 60.000 0.00 0.00 44.42 5.14
2365 7760 1.552226 TTTACTACGATTCGCCTGCG 58.448 50.000 5.86 4.92 41.35 5.18
2455 7869 4.171005 CGGAGCTCACGAGTTAATTGTAA 58.829 43.478 17.19 0.00 0.00 2.41
2597 8012 7.962964 TTGTTATCATAGGCAAGTACATAGC 57.037 36.000 0.00 0.00 0.00 2.97
2601 8016 5.614324 TCATAGGCAAGTACATAGCACTT 57.386 39.130 0.00 0.00 36.68 3.16
2920 8341 0.819582 CAAAACTGGGCAGGCATAGG 59.180 55.000 0.00 0.00 0.00 2.57
2941 8362 3.181482 GGGTTTAGAGGCGGTACTCTTAC 60.181 52.174 9.11 8.19 45.21 2.34
3242 8709 8.690203 TTACCATCAATGTCTTTCTTCAGAAA 57.310 30.769 2.07 2.07 41.29 2.52
3628 9110 8.344098 ACAATTAAGTTGCATGGTTCAAAATTG 58.656 29.630 13.18 13.18 41.69 2.32
3638 9120 9.118300 TGCATGGTTCAAAATTGACTTATTTTT 57.882 25.926 0.00 0.00 35.98 1.94
3683 9165 5.741388 AAAAATACATCTAGCGCTCCAAG 57.259 39.130 16.34 6.18 0.00 3.61
4440 9963 9.754382 GACGTATATTACCATCTTTAAGTGGAA 57.246 33.333 16.42 9.22 38.86 3.53
4618 10151 1.536766 GTGTGCTGCTGTGCTTTGATA 59.463 47.619 0.00 0.00 0.00 2.15
4864 10472 4.490743 GGTCATTTTTATCACCAAACCCG 58.509 43.478 0.00 0.00 0.00 5.28
4888 10496 6.549912 TTGAAGAATCAACAGACATCACTG 57.450 37.500 0.00 0.00 40.59 3.66
4975 10583 2.746277 GCTGAAATCCACGCGGGT 60.746 61.111 12.47 0.00 38.11 5.28
5194 11510 7.112122 AGAAACACCATCAGCACATAATCTTA 58.888 34.615 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.879400 AGTGGTTTAGACTTGTATCCATCTC 58.121 40.000 0.00 0.00 0.00 2.75
2 3 6.440647 TGAGTGGTTTAGACTTGTATCCATCT 59.559 38.462 0.00 0.00 0.00 2.90
80 1023 5.725325 AGGTGTCTGTTCTTACTAGTTCC 57.275 43.478 0.00 0.00 0.00 3.62
84 1027 6.978338 TGTTGTAGGTGTCTGTTCTTACTAG 58.022 40.000 0.00 0.00 0.00 2.57
85 1028 6.964807 TGTTGTAGGTGTCTGTTCTTACTA 57.035 37.500 0.00 0.00 0.00 1.82
87 1030 6.537660 AGTTTGTTGTAGGTGTCTGTTCTTAC 59.462 38.462 0.00 0.00 0.00 2.34
89 1032 5.497474 AGTTTGTTGTAGGTGTCTGTTCTT 58.503 37.500 0.00 0.00 0.00 2.52
90 1033 5.099042 AGTTTGTTGTAGGTGTCTGTTCT 57.901 39.130 0.00 0.00 0.00 3.01
91 1034 4.873827 TGAGTTTGTTGTAGGTGTCTGTTC 59.126 41.667 0.00 0.00 0.00 3.18
92 1035 4.634443 GTGAGTTTGTTGTAGGTGTCTGTT 59.366 41.667 0.00 0.00 0.00 3.16
93 1036 4.189231 GTGAGTTTGTTGTAGGTGTCTGT 58.811 43.478 0.00 0.00 0.00 3.41
94 1037 4.188462 TGTGAGTTTGTTGTAGGTGTCTG 58.812 43.478 0.00 0.00 0.00 3.51
95 1038 4.481368 TGTGAGTTTGTTGTAGGTGTCT 57.519 40.909 0.00 0.00 0.00 3.41
96 1039 5.554822 TTTGTGAGTTTGTTGTAGGTGTC 57.445 39.130 0.00 0.00 0.00 3.67
97 1040 5.475564 ACTTTTGTGAGTTTGTTGTAGGTGT 59.524 36.000 0.00 0.00 0.00 4.16
98 1041 5.949735 ACTTTTGTGAGTTTGTTGTAGGTG 58.050 37.500 0.00 0.00 0.00 4.00
114 1057 2.104963 GTCTCCCTCCTGTCACTTTTGT 59.895 50.000 0.00 0.00 0.00 2.83
115 1058 2.551071 GGTCTCCCTCCTGTCACTTTTG 60.551 54.545 0.00 0.00 0.00 2.44
116 1059 1.700186 GGTCTCCCTCCTGTCACTTTT 59.300 52.381 0.00 0.00 0.00 2.27
121 1064 0.104672 TTTGGGTCTCCCTCCTGTCA 60.105 55.000 6.38 0.00 45.70 3.58
122 1065 1.064825 TTTTGGGTCTCCCTCCTGTC 58.935 55.000 6.38 0.00 45.70 3.51
123 1066 0.771755 GTTTTGGGTCTCCCTCCTGT 59.228 55.000 6.38 0.00 45.70 4.00
124 1067 0.038310 GGTTTTGGGTCTCCCTCCTG 59.962 60.000 6.38 0.00 45.70 3.86
125 1068 0.103876 AGGTTTTGGGTCTCCCTCCT 60.104 55.000 6.38 6.13 45.70 3.69
126 1069 1.281287 GTAGGTTTTGGGTCTCCCTCC 59.719 57.143 6.38 4.20 45.70 4.30
127 1070 1.281287 GGTAGGTTTTGGGTCTCCCTC 59.719 57.143 6.38 0.00 45.70 4.30
128 1071 1.369403 GGTAGGTTTTGGGTCTCCCT 58.631 55.000 6.38 0.00 45.70 4.20
129 1072 1.069775 TGGTAGGTTTTGGGTCTCCC 58.930 55.000 0.00 0.00 45.71 4.30
130 1073 1.422402 TGTGGTAGGTTTTGGGTCTCC 59.578 52.381 0.00 0.00 0.00 3.71
132 1075 1.847737 TGTGTGGTAGGTTTTGGGTCT 59.152 47.619 0.00 0.00 0.00 3.85
133 1076 2.351706 TGTGTGGTAGGTTTTGGGTC 57.648 50.000 0.00 0.00 0.00 4.46
135 1078 2.101750 GGTTTGTGTGGTAGGTTTTGGG 59.898 50.000 0.00 0.00 0.00 4.12
137 1080 3.067601 GGAGGTTTGTGTGGTAGGTTTTG 59.932 47.826 0.00 0.00 0.00 2.44
139 1082 2.512476 AGGAGGTTTGTGTGGTAGGTTT 59.488 45.455 0.00 0.00 0.00 3.27
143 1086 4.514401 GGAATAGGAGGTTTGTGTGGTAG 58.486 47.826 0.00 0.00 0.00 3.18
144 1087 3.264964 GGGAATAGGAGGTTTGTGTGGTA 59.735 47.826 0.00 0.00 0.00 3.25
145 1088 2.041216 GGGAATAGGAGGTTTGTGTGGT 59.959 50.000 0.00 0.00 0.00 4.16
146 1089 2.620627 GGGGAATAGGAGGTTTGTGTGG 60.621 54.545 0.00 0.00 0.00 4.17
147 1090 2.620627 GGGGGAATAGGAGGTTTGTGTG 60.621 54.545 0.00 0.00 0.00 3.82
149 1092 1.923148 AGGGGGAATAGGAGGTTTGTG 59.077 52.381 0.00 0.00 0.00 3.33
150 1093 2.378308 AGGGGGAATAGGAGGTTTGT 57.622 50.000 0.00 0.00 0.00 2.83
151 1094 2.853077 AGAAGGGGGAATAGGAGGTTTG 59.147 50.000 0.00 0.00 0.00 2.93
156 1099 6.515512 TCAATTAAGAAGGGGGAATAGGAG 57.484 41.667 0.00 0.00 0.00 3.69
159 1102 7.981789 GCTTTTTCAATTAAGAAGGGGGAATAG 59.018 37.037 0.00 0.00 31.48 1.73
163 1106 4.530553 GGCTTTTTCAATTAAGAAGGGGGA 59.469 41.667 0.00 0.00 31.48 4.81
165 1108 5.337571 GGAGGCTTTTTCAATTAAGAAGGGG 60.338 44.000 0.00 0.00 31.48 4.79
166 1109 5.481824 AGGAGGCTTTTTCAATTAAGAAGGG 59.518 40.000 0.00 0.00 31.48 3.95
167 1110 6.209391 TCAGGAGGCTTTTTCAATTAAGAAGG 59.791 38.462 0.00 0.00 31.48 3.46
170 1113 6.721208 ACATCAGGAGGCTTTTTCAATTAAGA 59.279 34.615 0.00 0.00 0.00 2.10
171 1114 6.928520 ACATCAGGAGGCTTTTTCAATTAAG 58.071 36.000 0.00 0.00 0.00 1.85
172 1115 6.916360 ACATCAGGAGGCTTTTTCAATTAA 57.084 33.333 0.00 0.00 0.00 1.40
175 1118 5.813513 AAACATCAGGAGGCTTTTTCAAT 57.186 34.783 0.00 0.00 0.00 2.57
176 1119 5.278266 CGTAAACATCAGGAGGCTTTTTCAA 60.278 40.000 0.00 0.00 0.00 2.69
177 1120 4.215399 CGTAAACATCAGGAGGCTTTTTCA 59.785 41.667 0.00 0.00 0.00 2.69
178 1121 4.379499 CCGTAAACATCAGGAGGCTTTTTC 60.379 45.833 0.00 0.00 0.00 2.29
181 1124 2.711542 CCGTAAACATCAGGAGGCTTT 58.288 47.619 0.00 0.00 0.00 3.51
182 1125 1.679032 GCCGTAAACATCAGGAGGCTT 60.679 52.381 0.00 0.00 39.92 4.35
183 1126 0.107654 GCCGTAAACATCAGGAGGCT 60.108 55.000 0.00 0.00 39.92 4.58
185 1128 0.251916 TGGCCGTAAACATCAGGAGG 59.748 55.000 0.00 0.00 0.00 4.30
188 1131 2.107950 TCTTGGCCGTAAACATCAGG 57.892 50.000 0.00 0.00 0.00 3.86
189 1132 2.811431 TGTTCTTGGCCGTAAACATCAG 59.189 45.455 11.36 0.00 0.00 2.90
190 1133 2.811431 CTGTTCTTGGCCGTAAACATCA 59.189 45.455 14.66 0.00 31.73 3.07
195 1138 2.636299 GGCTGTTCTTGGCCGTAAA 58.364 52.632 0.00 0.00 38.91 2.01
196 1139 4.390048 GGCTGTTCTTGGCCGTAA 57.610 55.556 0.00 0.00 38.91 3.18
201 1144 2.281484 TCGGTGGCTGTTCTTGGC 60.281 61.111 0.00 0.00 0.00 4.52
202 1145 1.966451 GGTCGGTGGCTGTTCTTGG 60.966 63.158 0.00 0.00 0.00 3.61
203 1146 1.227823 TGGTCGGTGGCTGTTCTTG 60.228 57.895 0.00 0.00 0.00 3.02
217 2466 3.870419 TGTAACTAACGTGGTTTGTGGTC 59.130 43.478 11.46 0.49 32.59 4.02
224 2473 4.768583 TCAACCTTGTAACTAACGTGGTT 58.231 39.130 11.07 11.07 42.99 3.67
230 2479 6.872020 TCATGCTACTCAACCTTGTAACTAAC 59.128 38.462 0.00 0.00 0.00 2.34
231 2480 6.999950 TCATGCTACTCAACCTTGTAACTAA 58.000 36.000 0.00 0.00 0.00 2.24
232 2481 6.599356 TCATGCTACTCAACCTTGTAACTA 57.401 37.500 0.00 0.00 0.00 2.24
233 2482 5.483685 TCATGCTACTCAACCTTGTAACT 57.516 39.130 0.00 0.00 0.00 2.24
272 2521 9.651718 GTAGAAAACTGTTGAAATTGACACTAG 57.348 33.333 0.00 0.00 0.00 2.57
298 2547 0.108851 GGCCAGCCAATACAAAACGG 60.109 55.000 3.12 0.00 35.81 4.44
301 2550 1.265236 CAGGGCCAGCCAATACAAAA 58.735 50.000 11.50 0.00 37.98 2.44
318 2567 0.462581 TCGGCATTAGCTTCCTGCAG 60.463 55.000 6.78 6.78 45.94 4.41
340 2589 1.014352 GTATTTCTCACCGCGCCAAT 58.986 50.000 0.00 0.00 0.00 3.16
346 2595 3.013921 TCCATTTGGTATTTCTCACCGC 58.986 45.455 0.00 0.00 39.04 5.68
359 2608 9.830975 TCATATATGGTAATACGATCCATTTGG 57.169 33.333 12.78 0.00 41.45 3.28
421 2674 0.745128 TCACAAACGGCGTCCAAGTT 60.745 50.000 15.17 0.00 0.00 2.66
429 2682 3.586039 GTGATCATCACAAACGGCG 57.414 52.632 13.26 4.80 46.22 6.46
467 2720 8.862325 AGATCACACATGGTTCTAAATTGTTA 57.138 30.769 0.00 0.00 0.00 2.41
468 2721 7.765695 AGATCACACATGGTTCTAAATTGTT 57.234 32.000 0.00 0.00 0.00 2.83
469 2722 8.103305 ACTAGATCACACATGGTTCTAAATTGT 58.897 33.333 0.00 0.00 0.00 2.71
470 2723 8.498054 ACTAGATCACACATGGTTCTAAATTG 57.502 34.615 0.00 0.00 0.00 2.32
535 2788 9.992910 CATTTTCAATTGATATCAGTTTCTCGA 57.007 29.630 9.40 3.23 0.00 4.04
536 2789 9.992910 TCATTTTCAATTGATATCAGTTTCTCG 57.007 29.630 9.40 1.00 0.00 4.04
579 2832 5.356190 GTCTCATTTCCAAGCAATGATCTGA 59.644 40.000 0.00 0.00 39.40 3.27
603 2856 5.010012 AGTTGTTAGCCCTTGAACAATTCTG 59.990 40.000 3.75 0.00 44.81 3.02
629 2882 4.922719 TGTTAACACTTGGTTTTAAGCGG 58.077 39.130 3.59 0.00 40.96 5.52
882 5777 4.558095 CGTATATACCAGGAACCAAGACGG 60.558 50.000 7.30 0.00 42.50 4.79
897 5792 4.167268 GCAGCTAGCCAACTCGTATATAC 58.833 47.826 12.13 2.53 37.23 1.47
947 5855 6.068010 TGTGGTTACAAGGTTGATTCTGAAT 58.932 36.000 1.81 1.81 32.88 2.57
951 5859 5.221244 GCTTTGTGGTTACAAGGTTGATTCT 60.221 40.000 0.00 0.00 46.63 2.40
952 5860 4.982295 GCTTTGTGGTTACAAGGTTGATTC 59.018 41.667 0.00 0.00 46.63 2.52
953 5861 4.649218 AGCTTTGTGGTTACAAGGTTGATT 59.351 37.500 0.00 0.00 46.63 2.57
954 5862 4.215109 AGCTTTGTGGTTACAAGGTTGAT 58.785 39.130 0.00 0.00 46.63 2.57
955 5863 3.626930 AGCTTTGTGGTTACAAGGTTGA 58.373 40.909 0.00 0.00 46.63 3.18
956 5864 4.819630 TCTAGCTTTGTGGTTACAAGGTTG 59.180 41.667 0.00 0.00 46.63 3.77
957 5865 5.043737 TCTAGCTTTGTGGTTACAAGGTT 57.956 39.130 0.00 0.00 46.63 3.50
958 5866 4.102681 ACTCTAGCTTTGTGGTTACAAGGT 59.897 41.667 0.00 0.00 46.63 3.50
959 5867 4.642429 ACTCTAGCTTTGTGGTTACAAGG 58.358 43.478 0.00 0.00 46.63 3.61
960 5868 6.293462 GGAAACTCTAGCTTTGTGGTTACAAG 60.293 42.308 0.00 0.00 46.63 3.16
961 5869 5.529800 GGAAACTCTAGCTTTGTGGTTACAA 59.470 40.000 0.00 0.00 44.66 2.41
962 5870 5.061179 GGAAACTCTAGCTTTGTGGTTACA 58.939 41.667 0.00 0.00 34.31 2.41
963 5871 5.306394 AGGAAACTCTAGCTTTGTGGTTAC 58.694 41.667 0.00 0.00 32.90 2.50
1060 5968 2.112297 GGCTTCCGTGGTCACCAA 59.888 61.111 0.00 0.00 34.18 3.67
1205 6116 0.394352 GGAATCCATGACCGGCAAGT 60.394 55.000 0.00 0.00 0.00 3.16
1440 6351 2.350522 CCATCTTCCTCCAAGTTGTCG 58.649 52.381 1.45 0.00 31.96 4.35
1792 6711 3.184581 CGGCTCAACTTGTAGAGTGTTTC 59.815 47.826 0.00 0.00 39.00 2.78
2268 7287 1.421410 CGAATGTGTCGCCTACCTGC 61.421 60.000 0.00 0.00 44.14 4.85
2309 7365 7.215789 AGTCATCATCAGTACTTGATTCCATC 58.784 38.462 7.24 0.00 44.14 3.51
2314 7370 9.896645 ATTTGTAGTCATCATCAGTACTTGATT 57.103 29.630 7.24 1.84 44.14 2.57
2347 7742 0.868602 GCGCAGGCGAATCGTAGTAA 60.869 55.000 18.96 0.00 42.83 2.24
2348 7743 1.298863 GCGCAGGCGAATCGTAGTA 60.299 57.895 18.96 0.00 42.83 1.82
2455 7869 5.011125 CCTACGGGAACTGAATCTATCACAT 59.989 44.000 0.00 0.00 38.67 3.21
2737 8152 2.169769 AGCTGGGCATTCCAATTGATTG 59.830 45.455 7.12 2.58 46.51 2.67
2873 8294 1.819288 TGAGTGCTCTGCCTACACTAC 59.181 52.381 0.00 0.00 44.40 2.73
2920 8341 3.698539 AGTAAGAGTACCGCCTCTAAACC 59.301 47.826 0.00 0.00 40.93 3.27
4440 9963 3.264450 AGATCCGAAACCTCCAATTGTCT 59.736 43.478 4.43 0.00 0.00 3.41
4618 10151 8.196771 TGCACATTAACTCTTCAACAAAGAAAT 58.803 29.630 0.00 0.00 43.39 2.17
4886 10494 0.392193 CTGTCTAGGTTGGGCAGCAG 60.392 60.000 0.00 0.00 0.00 4.24
4887 10495 1.679311 CTGTCTAGGTTGGGCAGCA 59.321 57.895 0.00 0.00 0.00 4.41
4888 10496 1.746991 GCTGTCTAGGTTGGGCAGC 60.747 63.158 3.33 3.33 44.24 5.25
5194 11510 2.106566 CAGTGAGCTGATGGACCTACT 58.893 52.381 0.00 0.00 45.28 2.57


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

AutoCloner maintained by Alex Coulton.