Multiple sequence alignment - TraesCS1A01G398900

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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 TraesCS1A01G398900 chr1A 100.000 3147 0 0 420 3566 563764519 563767665 0.000000e+00 5812.0
1 TraesCS1A01G398900 chr1A 87.620 1559 160 17 1201 2746 563690125 563691663 0.000000e+00 1779.0
2 TraesCS1A01G398900 chr1A 79.958 1442 241 40 1333 2746 563774100 563775521 0.000000e+00 1018.0
3 TraesCS1A01G398900 chr1A 76.621 663 89 43 507 1128 563686213 563686850 4.470000e-79 305.0
4 TraesCS1A01G398900 chr1A 100.000 124 0 0 1 124 563764100 563764223 2.770000e-56 230.0
5 TraesCS1A01G398900 chr1B 92.864 3111 157 32 421 3487 652484995 652488084 0.000000e+00 4455.0
6 TraesCS1A01G398900 chr1B 86.485 1428 171 11 1201 2616 652463151 652464568 0.000000e+00 1548.0
7 TraesCS1A01G398900 chr1B 83.333 1428 194 22 1342 2746 652459742 652461148 0.000000e+00 1279.0
8 TraesCS1A01G398900 chr1B 81.208 1341 217 29 1391 2708 652564682 652566010 0.000000e+00 1048.0
9 TraesCS1A01G398900 chr1B 77.982 654 90 29 505 1128 652459244 652459873 9.410000e-96 361.0
10 TraesCS1A01G398900 chr1D 94.242 2883 115 26 420 3263 470123223 470126093 0.000000e+00 4357.0
11 TraesCS1A01G398900 chr1D 89.754 1464 128 13 1287 2746 470081023 470082468 0.000000e+00 1853.0
12 TraesCS1A01G398900 chr1D 83.356 1460 199 26 1310 2746 470077534 470078972 0.000000e+00 1310.0
13 TraesCS1A01G398900 chr1D 79.264 815 143 19 1891 2690 470191311 470192114 2.420000e-151 545.0
14 TraesCS1A01G398900 chr1D 95.548 292 7 4 3280 3566 470126214 470126504 2.510000e-126 462.0
15 TraesCS1A01G398900 chr1D 87.330 221 21 6 3000 3216 470082628 470082845 2.750000e-61 246.0
16 TraesCS1A01G398900 chr4A 100.000 33 0 0 710 742 722381029 722380997 1.070000e-05 62.1


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 TraesCS1A01G398900 chr1A 563764100 563767665 3565 False 3021.000000 5812 100.000000 1 3566 2 chr1A.!!$F3 3565
1 TraesCS1A01G398900 chr1A 563686213 563691663 5450 False 1042.000000 1779 82.120500 507 2746 2 chr1A.!!$F2 2239
2 TraesCS1A01G398900 chr1A 563774100 563775521 1421 False 1018.000000 1018 79.958000 1333 2746 1 chr1A.!!$F1 1413
3 TraesCS1A01G398900 chr1B 652484995 652488084 3089 False 4455.000000 4455 92.864000 421 3487 1 chr1B.!!$F1 3066
4 TraesCS1A01G398900 chr1B 652459244 652464568 5324 False 1062.666667 1548 82.600000 505 2746 3 chr1B.!!$F3 2241
5 TraesCS1A01G398900 chr1B 652564682 652566010 1328 False 1048.000000 1048 81.208000 1391 2708 1 chr1B.!!$F2 1317
6 TraesCS1A01G398900 chr1D 470123223 470126504 3281 False 2409.500000 4357 94.895000 420 3566 2 chr1D.!!$F3 3146
7 TraesCS1A01G398900 chr1D 470077534 470082845 5311 False 1136.333333 1853 86.813333 1287 3216 3 chr1D.!!$F2 1929
8 TraesCS1A01G398900 chr1D 470191311 470192114 803 False 545.000000 545 79.264000 1891 2690 1 chr1D.!!$F1 799

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
97 98 0.107993 CATCGATGCATCCCCGCTAT 60.108 55.000 20.87 2.8 0.00 2.97 F
1158 1218 0.035056 GAGGTAATGCTGTGGCCTGT 60.035 55.000 3.32 0.0 37.74 4.00 F
1361 4784 0.106335 ATGATGGCGGCAGAGAAGAG 59.894 55.000 19.29 0.0 0.00 2.85 F
2212 5641 1.303317 GTGTGCCGGGTTCCTGAAT 60.303 57.895 2.18 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1301 0.109597 CACAACAGCATTTCCCTCGC 60.110 55.000 0.00 0.0 0.0 5.03 R
2212 5641 0.253044 GCTTCACCATACAGCCCAGA 59.747 55.000 0.00 0.0 0.0 3.86 R
2284 5716 1.758906 TCGACACACTGACCCACCA 60.759 57.895 0.00 0.0 0.0 4.17 R
3317 6937 2.050442 CCCAGCAAACGCGGAAAC 60.050 61.111 12.47 0.0 0.0 2.78 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
24 25 7.873719 TGGGTCGACATCATTTTATTATTGT 57.126 32.000 18.91 0.00 0.00 2.71
25 26 8.287439 TGGGTCGACATCATTTTATTATTGTT 57.713 30.769 18.91 0.00 0.00 2.83
26 27 8.744652 TGGGTCGACATCATTTTATTATTGTTT 58.255 29.630 18.91 0.00 0.00 2.83
27 28 9.233232 GGGTCGACATCATTTTATTATTGTTTC 57.767 33.333 18.91 0.00 0.00 2.78
67 68 9.586435 AAAGACTTAATTTTATAAGGCACATGC 57.414 29.630 3.02 0.00 42.36 4.06
68 69 8.525290 AGACTTAATTTTATAAGGCACATGCT 57.475 30.769 3.48 0.00 42.36 3.79
69 70 8.408601 AGACTTAATTTTATAAGGCACATGCTG 58.591 33.333 3.48 0.00 42.36 4.41
70 71 8.292444 ACTTAATTTTATAAGGCACATGCTGA 57.708 30.769 3.48 0.00 41.70 4.26
71 72 8.190784 ACTTAATTTTATAAGGCACATGCTGAC 58.809 33.333 3.48 0.00 41.70 3.51
72 73 6.780457 AATTTTATAAGGCACATGCTGACT 57.220 33.333 3.48 0.00 41.78 3.41
73 74 7.880160 AATTTTATAAGGCACATGCTGACTA 57.120 32.000 3.48 0.00 37.17 2.59
74 75 7.880160 ATTTTATAAGGCACATGCTGACTAA 57.120 32.000 3.48 0.00 37.17 2.24
75 76 7.695480 TTTTATAAGGCACATGCTGACTAAA 57.305 32.000 3.48 1.97 37.17 1.85
76 77 7.880160 TTTATAAGGCACATGCTGACTAAAT 57.120 32.000 3.48 4.80 37.17 1.40
77 78 8.972458 TTTATAAGGCACATGCTGACTAAATA 57.028 30.769 3.48 4.05 37.17 1.40
78 79 6.867662 ATAAGGCACATGCTGACTAAATAC 57.132 37.500 3.48 0.00 37.17 1.89
79 80 4.220693 AGGCACATGCTGACTAAATACA 57.779 40.909 3.48 0.00 35.89 2.29
80 81 4.785301 AGGCACATGCTGACTAAATACAT 58.215 39.130 3.48 0.00 35.89 2.29
81 82 4.818546 AGGCACATGCTGACTAAATACATC 59.181 41.667 3.48 0.00 35.89 3.06
82 83 4.319046 GGCACATGCTGACTAAATACATCG 60.319 45.833 3.48 0.00 41.70 3.84
83 84 4.507756 GCACATGCTGACTAAATACATCGA 59.492 41.667 0.00 0.00 38.21 3.59
84 85 5.178252 GCACATGCTGACTAAATACATCGAT 59.822 40.000 0.00 0.00 38.21 3.59
85 86 6.587651 CACATGCTGACTAAATACATCGATG 58.412 40.000 23.68 23.68 0.00 3.84
86 87 5.178252 ACATGCTGACTAAATACATCGATGC 59.822 40.000 25.11 7.14 0.00 3.91
87 88 4.692228 TGCTGACTAAATACATCGATGCA 58.308 39.130 25.11 13.56 0.00 3.96
88 89 5.299949 TGCTGACTAAATACATCGATGCAT 58.700 37.500 25.11 15.45 0.00 3.96
89 90 5.406477 TGCTGACTAAATACATCGATGCATC 59.594 40.000 25.11 17.10 0.00 3.91
90 91 5.163913 GCTGACTAAATACATCGATGCATCC 60.164 44.000 25.11 7.19 0.00 3.51
91 92 5.237815 TGACTAAATACATCGATGCATCCC 58.762 41.667 25.11 7.78 0.00 3.85
92 93 4.579869 ACTAAATACATCGATGCATCCCC 58.420 43.478 25.11 0.00 0.00 4.81
93 94 2.099141 AATACATCGATGCATCCCCG 57.901 50.000 25.11 10.45 0.00 5.73
94 95 0.391661 ATACATCGATGCATCCCCGC 60.392 55.000 25.11 0.00 0.00 6.13
95 96 1.471829 TACATCGATGCATCCCCGCT 61.472 55.000 25.11 5.00 0.00 5.52
96 97 1.293179 CATCGATGCATCCCCGCTA 59.707 57.895 20.87 0.49 0.00 4.26
97 98 0.107993 CATCGATGCATCCCCGCTAT 60.108 55.000 20.87 2.80 0.00 2.97
98 99 1.136891 CATCGATGCATCCCCGCTATA 59.863 52.381 20.87 0.00 0.00 1.31
99 100 1.262417 TCGATGCATCCCCGCTATAA 58.738 50.000 20.87 0.00 0.00 0.98
100 101 1.831106 TCGATGCATCCCCGCTATAAT 59.169 47.619 20.87 0.00 0.00 1.28
101 102 3.028130 TCGATGCATCCCCGCTATAATA 58.972 45.455 20.87 0.00 0.00 0.98
102 103 3.449377 TCGATGCATCCCCGCTATAATAA 59.551 43.478 20.87 0.00 0.00 1.40
103 104 4.081365 TCGATGCATCCCCGCTATAATAAA 60.081 41.667 20.87 0.00 0.00 1.40
104 105 4.634004 CGATGCATCCCCGCTATAATAAAA 59.366 41.667 20.87 0.00 0.00 1.52
105 106 5.220662 CGATGCATCCCCGCTATAATAAAAG 60.221 44.000 20.87 0.00 0.00 2.27
106 107 4.980573 TGCATCCCCGCTATAATAAAAGT 58.019 39.130 0.00 0.00 0.00 2.66
107 108 6.116711 TGCATCCCCGCTATAATAAAAGTA 57.883 37.500 0.00 0.00 0.00 2.24
108 109 6.535540 TGCATCCCCGCTATAATAAAAGTAA 58.464 36.000 0.00 0.00 0.00 2.24
109 110 6.999272 TGCATCCCCGCTATAATAAAAGTAAA 59.001 34.615 0.00 0.00 0.00 2.01
110 111 7.502895 TGCATCCCCGCTATAATAAAAGTAAAA 59.497 33.333 0.00 0.00 0.00 1.52
111 112 8.520351 GCATCCCCGCTATAATAAAAGTAAAAT 58.480 33.333 0.00 0.00 0.00 1.82
464 465 1.192146 TGTAGGACGCCAGCTCCTTT 61.192 55.000 13.49 0.00 39.09 3.11
467 468 0.912486 AGGACGCCAGCTCCTTTAAT 59.088 50.000 5.21 0.00 34.11 1.40
813 843 2.876368 CTTGCTAGCCCGGGTTCTGG 62.876 65.000 24.63 14.77 0.00 3.86
913 962 0.961019 ATGTTGCTGTGCCGTGATTT 59.039 45.000 0.00 0.00 0.00 2.17
927 976 4.553156 GCCGTGATTTTTCTCGTTGTGTTA 60.553 41.667 0.00 0.00 0.00 2.41
939 993 3.749088 TCGTTGTGTTATGTTGGATGGTC 59.251 43.478 0.00 0.00 0.00 4.02
1023 1077 1.649664 CGGCAGAGGAGAAATCACAG 58.350 55.000 0.00 0.00 0.00 3.66
1095 1155 3.111939 CTCCGCCTACTCCACTCG 58.888 66.667 0.00 0.00 0.00 4.18
1096 1156 1.749638 CTCCGCCTACTCCACTCGT 60.750 63.158 0.00 0.00 0.00 4.18
1097 1157 0.463295 CTCCGCCTACTCCACTCGTA 60.463 60.000 0.00 0.00 0.00 3.43
1099 1159 1.351012 CGCCTACTCCACTCGTACG 59.649 63.158 9.53 9.53 0.00 3.67
1100 1160 1.063811 GCCTACTCCACTCGTACGC 59.936 63.158 11.24 0.00 0.00 4.42
1102 1162 1.028330 CCTACTCCACTCGTACGCCA 61.028 60.000 11.24 0.00 0.00 5.69
1103 1163 0.377554 CTACTCCACTCGTACGCCAG 59.622 60.000 11.24 6.40 0.00 4.85
1104 1164 1.651240 TACTCCACTCGTACGCCAGC 61.651 60.000 11.24 0.00 0.00 4.85
1130 1190 2.972505 CTTCGCCGCAGTGTGGTT 60.973 61.111 23.38 0.00 35.34 3.67
1131 1191 2.954753 CTTCGCCGCAGTGTGGTTC 61.955 63.158 23.38 7.39 35.34 3.62
1144 1204 3.384532 GGTTCGCACGGGGAGGTA 61.385 66.667 0.00 0.00 0.00 3.08
1145 1205 2.658422 GTTCGCACGGGGAGGTAA 59.342 61.111 0.00 0.00 0.00 2.85
1146 1206 1.219935 GTTCGCACGGGGAGGTAAT 59.780 57.895 0.00 0.00 0.00 1.89
1147 1207 1.087771 GTTCGCACGGGGAGGTAATG 61.088 60.000 0.00 0.00 0.00 1.90
1148 1208 2.862674 TTCGCACGGGGAGGTAATGC 62.863 60.000 0.00 0.00 0.00 3.56
1149 1209 2.590092 GCACGGGGAGGTAATGCT 59.410 61.111 0.00 0.00 33.44 3.79
1150 1210 1.819632 GCACGGGGAGGTAATGCTG 60.820 63.158 0.00 0.00 33.44 4.41
1151 1211 1.602237 CACGGGGAGGTAATGCTGT 59.398 57.895 0.00 0.00 0.00 4.40
1152 1212 0.744414 CACGGGGAGGTAATGCTGTG 60.744 60.000 0.00 0.00 0.00 3.66
1153 1213 1.153168 CGGGGAGGTAATGCTGTGG 60.153 63.158 0.00 0.00 0.00 4.17
1154 1214 1.453928 GGGGAGGTAATGCTGTGGC 60.454 63.158 0.00 0.00 39.26 5.01
1156 1216 1.609783 GGAGGTAATGCTGTGGCCT 59.390 57.895 3.32 0.00 37.74 5.19
1157 1217 0.749454 GGAGGTAATGCTGTGGCCTG 60.749 60.000 3.32 0.00 37.74 4.85
1158 1218 0.035056 GAGGTAATGCTGTGGCCTGT 60.035 55.000 3.32 0.00 37.74 4.00
1160 1220 1.315257 GGTAATGCTGTGGCCTGTGG 61.315 60.000 3.32 0.00 37.74 4.17
1164 1224 4.603535 GCTGTGGCCTGTGGGGTT 62.604 66.667 3.32 0.00 37.43 4.11
1165 1225 2.198426 CTGTGGCCTGTGGGGTTT 59.802 61.111 3.32 0.00 37.43 3.27
1166 1226 2.123511 TGTGGCCTGTGGGGTTTG 60.124 61.111 3.32 0.00 37.43 2.93
1167 1227 2.917227 GTGGCCTGTGGGGTTTGG 60.917 66.667 3.32 0.00 37.43 3.28
1168 1228 4.932105 TGGCCTGTGGGGTTTGGC 62.932 66.667 3.32 0.00 44.22 4.52
1171 1231 4.596585 CCTGTGGGGTTTGGCCGT 62.597 66.667 0.00 0.00 38.44 5.68
1172 1232 2.520741 CTGTGGGGTTTGGCCGTT 60.521 61.111 0.00 0.00 38.44 4.44
1175 1235 2.840102 TGGGGTTTGGCCGTTTGG 60.840 61.111 0.00 0.00 38.44 3.28
1176 1236 3.621805 GGGGTTTGGCCGTTTGGG 61.622 66.667 0.00 0.00 38.44 4.12
1177 1237 2.840572 GGGTTTGGCCGTTTGGGT 60.841 61.111 0.00 0.00 38.44 4.51
1178 1238 2.436544 GGGTTTGGCCGTTTGGGTT 61.437 57.895 0.00 0.00 38.44 4.11
1179 1239 1.523046 GGTTTGGCCGTTTGGGTTT 59.477 52.632 0.00 0.00 38.44 3.27
1181 1241 0.462375 GTTTGGCCGTTTGGGTTTCT 59.538 50.000 0.00 0.00 38.44 2.52
1182 1242 0.461961 TTTGGCCGTTTGGGTTTCTG 59.538 50.000 0.00 0.00 38.44 3.02
1183 1243 0.684805 TTGGCCGTTTGGGTTTCTGT 60.685 50.000 0.00 0.00 38.44 3.41
1186 1246 1.802337 GCCGTTTGGGTTTCTGTCCC 61.802 60.000 0.00 0.00 44.81 4.46
1210 1270 4.170062 CTGCGTTCGCTGGCCATG 62.170 66.667 5.51 1.37 0.00 3.66
1223 1283 2.360350 CCATGAGCGCCAGGTGTT 60.360 61.111 2.29 0.00 0.00 3.32
1234 1294 1.081242 CAGGTGTTGGACGCATTGC 60.081 57.895 0.00 0.00 0.00 3.56
1235 1295 2.258286 GGTGTTGGACGCATTGCC 59.742 61.111 2.41 0.00 0.00 4.52
1236 1296 2.268076 GGTGTTGGACGCATTGCCT 61.268 57.895 2.41 0.00 0.00 4.75
1238 1298 1.073025 TGTTGGACGCATTGCCTCT 59.927 52.632 2.41 0.00 0.00 3.69
1239 1299 1.236616 TGTTGGACGCATTGCCTCTG 61.237 55.000 2.41 0.00 0.00 3.35
1240 1300 2.334946 TTGGACGCATTGCCTCTGC 61.335 57.895 2.41 0.00 36.26 4.26
1245 1305 4.233635 GCATTGCCTCTGCGCGAG 62.234 66.667 12.10 18.33 41.78 5.03
1252 1312 3.403277 CTCTGCGCGAGGGAAATG 58.597 61.111 12.10 0.00 36.06 2.32
1254 1314 2.821366 CTGCGCGAGGGAAATGCT 60.821 61.111 12.10 0.00 0.00 3.79
1255 1315 3.104602 CTGCGCGAGGGAAATGCTG 62.105 63.158 12.10 0.00 0.00 4.41
1256 1316 3.127533 GCGCGAGGGAAATGCTGT 61.128 61.111 12.10 0.00 0.00 4.40
1257 1317 2.690778 GCGCGAGGGAAATGCTGTT 61.691 57.895 12.10 0.00 0.00 3.16
1258 1318 1.135315 CGCGAGGGAAATGCTGTTG 59.865 57.895 0.00 0.00 0.00 3.33
1262 1322 0.244721 GAGGGAAATGCTGTTGTGCC 59.755 55.000 0.00 0.00 0.00 5.01
1264 1324 1.659794 GGAAATGCTGTTGTGCCGT 59.340 52.632 0.00 0.00 0.00 5.68
1265 1325 0.664166 GGAAATGCTGTTGTGCCGTG 60.664 55.000 0.00 0.00 0.00 4.94
1266 1326 0.310543 GAAATGCTGTTGTGCCGTGA 59.689 50.000 0.00 0.00 0.00 4.35
1268 1328 0.961019 AATGCTGTTGTGCCGTGATT 59.039 45.000 0.00 0.00 0.00 2.57
1271 1331 0.593128 GCTGTTGTGCCGTGATTCTT 59.407 50.000 0.00 0.00 0.00 2.52
1272 1332 1.400242 GCTGTTGTGCCGTGATTCTTC 60.400 52.381 0.00 0.00 0.00 2.87
1273 1333 2.146342 CTGTTGTGCCGTGATTCTTCT 58.854 47.619 0.00 0.00 0.00 2.85
1275 1335 2.290367 TGTTGTGCCGTGATTCTTCTTG 59.710 45.455 0.00 0.00 0.00 3.02
1276 1336 1.522668 TGTGCCGTGATTCTTCTTGG 58.477 50.000 0.00 0.00 0.00 3.61
1277 1337 1.202758 TGTGCCGTGATTCTTCTTGGT 60.203 47.619 0.00 0.00 0.00 3.67
1278 1338 1.197721 GTGCCGTGATTCTTCTTGGTG 59.802 52.381 0.00 0.00 0.00 4.17
1279 1339 1.202758 TGCCGTGATTCTTCTTGGTGT 60.203 47.619 0.00 0.00 0.00 4.16
1280 1340 1.197721 GCCGTGATTCTTCTTGGTGTG 59.802 52.381 0.00 0.00 0.00 3.82
1281 1341 2.494059 CCGTGATTCTTCTTGGTGTGT 58.506 47.619 0.00 0.00 0.00 3.72
1282 1342 2.480419 CCGTGATTCTTCTTGGTGTGTC 59.520 50.000 0.00 0.00 0.00 3.67
1283 1343 3.393800 CGTGATTCTTCTTGGTGTGTCT 58.606 45.455 0.00 0.00 0.00 3.41
1284 1344 3.809832 CGTGATTCTTCTTGGTGTGTCTT 59.190 43.478 0.00 0.00 0.00 3.01
1286 1346 4.816385 GTGATTCTTCTTGGTGTGTCTTCA 59.184 41.667 0.00 0.00 0.00 3.02
1287 1347 5.296780 GTGATTCTTCTTGGTGTGTCTTCAA 59.703 40.000 0.00 0.00 0.00 2.69
1290 1350 4.780815 TCTTCTTGGTGTGTCTTCAATGT 58.219 39.130 0.00 0.00 0.00 2.71
1361 4784 0.106335 ATGATGGCGGCAGAGAAGAG 59.894 55.000 19.29 0.00 0.00 2.85
1624 5050 3.393360 GGTACCAGAGTGCCTGCT 58.607 61.111 7.15 0.00 44.81 4.24
1987 5416 2.265367 TGTCATTCTACCAGGGCAAGA 58.735 47.619 0.00 0.00 0.00 3.02
2212 5641 1.303317 GTGTGCCGGGTTCCTGAAT 60.303 57.895 2.18 0.00 0.00 2.57
2284 5716 3.083122 AGGCTGACTTTGAGCATTCAT 57.917 42.857 0.00 0.00 38.27 2.57
2814 6318 5.702865 ACTATGCAAGTTGTTAACTGCATG 58.297 37.500 29.23 23.07 46.11 4.06
2821 6325 5.351948 AGTTGTTAACTGCATGGGTTTTT 57.648 34.783 7.22 0.00 41.01 1.94
2822 6326 5.115480 AGTTGTTAACTGCATGGGTTTTTG 58.885 37.500 7.22 0.00 41.01 2.44
2851 6355 1.066002 CTGTGGTTGTTTCTGTGCCTG 59.934 52.381 0.00 0.00 0.00 4.85
2931 6435 9.886132 AGTAATCGTCTGAAGTAATTATGGTTT 57.114 29.630 0.00 0.00 0.00 3.27
2976 6483 0.948678 TTTTCAACTAGTGCCGTGGC 59.051 50.000 3.30 3.30 42.35 5.01
3012 6519 3.665745 AGATTTGCGATGTTTTTGGCT 57.334 38.095 0.00 0.00 0.00 4.75
3270 6785 5.901336 GCGTGAGGTTTGCTTTTAATTTTTG 59.099 36.000 0.00 0.00 0.00 2.44
3317 6937 0.106519 AAAATCATCTGCCCCCTCCG 60.107 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.233232 GAAACAATAATAAAATGATGTCGACCC 57.767 33.333 14.12 5.58 0.00 4.46
41 42 9.586435 GCATGTGCCTTATAAAATTAAGTCTTT 57.414 29.630 0.00 0.00 34.31 2.52
42 43 8.971073 AGCATGTGCCTTATAAAATTAAGTCTT 58.029 29.630 0.57 0.00 43.38 3.01
43 44 8.408601 CAGCATGTGCCTTATAAAATTAAGTCT 58.591 33.333 0.57 0.00 43.38 3.24
44 45 8.405531 TCAGCATGTGCCTTATAAAATTAAGTC 58.594 33.333 0.57 0.00 43.38 3.01
45 46 8.190784 GTCAGCATGTGCCTTATAAAATTAAGT 58.809 33.333 0.57 0.00 43.38 2.24
46 47 8.408601 AGTCAGCATGTGCCTTATAAAATTAAG 58.591 33.333 0.57 0.00 43.38 1.85
47 48 8.292444 AGTCAGCATGTGCCTTATAAAATTAA 57.708 30.769 0.57 0.00 43.38 1.40
48 49 7.880160 AGTCAGCATGTGCCTTATAAAATTA 57.120 32.000 0.57 0.00 43.38 1.40
49 50 6.780457 AGTCAGCATGTGCCTTATAAAATT 57.220 33.333 0.57 0.00 43.38 1.82
50 51 7.880160 TTAGTCAGCATGTGCCTTATAAAAT 57.120 32.000 0.57 0.00 43.38 1.82
51 52 7.695480 TTTAGTCAGCATGTGCCTTATAAAA 57.305 32.000 0.57 0.00 43.38 1.52
52 53 7.880160 ATTTAGTCAGCATGTGCCTTATAAA 57.120 32.000 0.57 3.98 43.38 1.40
53 54 7.990314 TGTATTTAGTCAGCATGTGCCTTATAA 59.010 33.333 0.57 0.00 43.38 0.98
54 55 7.505258 TGTATTTAGTCAGCATGTGCCTTATA 58.495 34.615 0.57 0.00 43.38 0.98
55 56 6.356556 TGTATTTAGTCAGCATGTGCCTTAT 58.643 36.000 0.57 0.00 43.38 1.73
56 57 5.739959 TGTATTTAGTCAGCATGTGCCTTA 58.260 37.500 0.57 0.00 43.38 2.69
57 58 4.588899 TGTATTTAGTCAGCATGTGCCTT 58.411 39.130 0.57 0.00 43.38 4.35
58 59 4.220693 TGTATTTAGTCAGCATGTGCCT 57.779 40.909 0.57 0.00 43.38 4.75
59 60 4.319046 CGATGTATTTAGTCAGCATGTGCC 60.319 45.833 0.57 0.00 43.38 5.01
60 61 4.507756 TCGATGTATTTAGTCAGCATGTGC 59.492 41.667 0.00 0.00 42.49 4.57
61 62 6.587651 CATCGATGTATTTAGTCAGCATGTG 58.412 40.000 17.50 0.00 37.40 3.21
62 63 5.178252 GCATCGATGTATTTAGTCAGCATGT 59.822 40.000 25.47 0.00 37.40 3.21
63 64 5.178067 TGCATCGATGTATTTAGTCAGCATG 59.822 40.000 25.47 0.00 37.54 4.06
64 65 5.299949 TGCATCGATGTATTTAGTCAGCAT 58.700 37.500 25.47 0.00 0.00 3.79
65 66 4.692228 TGCATCGATGTATTTAGTCAGCA 58.308 39.130 25.47 10.54 0.00 4.41
66 67 5.163913 GGATGCATCGATGTATTTAGTCAGC 60.164 44.000 26.58 15.55 33.17 4.26
67 68 5.349817 GGGATGCATCGATGTATTTAGTCAG 59.650 44.000 26.58 0.00 33.17 3.51
68 69 5.237815 GGGATGCATCGATGTATTTAGTCA 58.762 41.667 26.58 14.09 33.17 3.41
69 70 4.631813 GGGGATGCATCGATGTATTTAGTC 59.368 45.833 26.58 15.89 33.17 2.59
70 71 4.579869 GGGGATGCATCGATGTATTTAGT 58.420 43.478 26.58 8.25 33.17 2.24
71 72 3.618594 CGGGGATGCATCGATGTATTTAG 59.381 47.826 26.58 15.82 33.17 1.85
72 73 3.595173 CGGGGATGCATCGATGTATTTA 58.405 45.455 26.58 9.93 33.17 1.40
73 74 2.426522 CGGGGATGCATCGATGTATTT 58.573 47.619 26.58 9.71 33.17 1.40
74 75 1.945819 GCGGGGATGCATCGATGTATT 60.946 52.381 26.58 12.94 33.17 1.89
75 76 0.391661 GCGGGGATGCATCGATGTAT 60.392 55.000 26.26 26.26 35.78 2.29
76 77 1.005037 GCGGGGATGCATCGATGTA 60.005 57.895 25.47 22.25 34.15 2.29
77 78 1.471829 TAGCGGGGATGCATCGATGT 61.472 55.000 25.47 7.78 37.31 3.06
78 79 0.107993 ATAGCGGGGATGCATCGATG 60.108 55.000 21.27 21.27 37.31 3.84
79 80 1.485124 TATAGCGGGGATGCATCGAT 58.515 50.000 20.15 11.19 37.31 3.59
80 81 1.262417 TTATAGCGGGGATGCATCGA 58.738 50.000 20.15 1.99 37.31 3.59
81 82 2.315925 ATTATAGCGGGGATGCATCG 57.684 50.000 20.15 11.08 37.31 3.84
82 83 5.648092 ACTTTTATTATAGCGGGGATGCATC 59.352 40.000 18.81 18.81 37.31 3.91
83 84 5.570320 ACTTTTATTATAGCGGGGATGCAT 58.430 37.500 0.00 0.00 37.31 3.96
84 85 4.980573 ACTTTTATTATAGCGGGGATGCA 58.019 39.130 0.00 0.00 37.31 3.96
85 86 7.443259 TTTACTTTTATTATAGCGGGGATGC 57.557 36.000 0.00 0.00 0.00 3.91
431 432 4.377897 CGTCCTACAGAAAGACCAGTTTT 58.622 43.478 0.00 0.00 0.00 2.43
433 434 2.288886 GCGTCCTACAGAAAGACCAGTT 60.289 50.000 0.00 0.00 0.00 3.16
464 465 1.134699 CACGCAGGCAAGAGGAGATTA 60.135 52.381 0.00 0.00 0.00 1.75
467 468 1.758440 AACACGCAGGCAAGAGGAGA 61.758 55.000 0.00 0.00 0.00 3.71
499 506 2.757868 CAGTGGAGTAGAGTGGAAGAGG 59.242 54.545 0.00 0.00 0.00 3.69
501 508 3.422796 GTCAGTGGAGTAGAGTGGAAGA 58.577 50.000 0.00 0.00 0.00 2.87
502 509 2.162608 CGTCAGTGGAGTAGAGTGGAAG 59.837 54.545 0.00 0.00 0.00 3.46
552 581 3.917760 CCGGAGCTGGGGTCGATC 61.918 72.222 0.00 0.00 0.00 3.69
813 843 1.232621 CGAGACGGAAACCCAAACCC 61.233 60.000 0.00 0.00 0.00 4.11
897 946 1.680735 AGAAAAATCACGGCACAGCAA 59.319 42.857 0.00 0.00 0.00 3.91
913 962 5.049060 CCATCCAACATAACACAACGAGAAA 60.049 40.000 0.00 0.00 0.00 2.52
927 976 2.093711 TCGAACATCGACCATCCAACAT 60.094 45.455 0.00 0.00 44.82 2.71
939 993 1.328680 CTGCCCTTTCATCGAACATCG 59.671 52.381 0.00 0.00 42.10 3.84
962 1016 5.346822 GCAAAGAAACAAAATCATCAGCGAT 59.653 36.000 0.00 0.00 0.00 4.58
1086 1146 2.991076 GCTGGCGTACGAGTGGAGT 61.991 63.158 21.65 0.00 0.00 3.85
1113 1173 2.954753 GAACCACACTGCGGCGAAG 61.955 63.158 14.72 14.72 0.00 3.79
1114 1174 2.970324 GAACCACACTGCGGCGAA 60.970 61.111 12.98 0.00 0.00 4.70
1119 1179 4.354212 CGTGCGAACCACACTGCG 62.354 66.667 0.00 0.00 44.91 5.18
1120 1180 4.012895 CCGTGCGAACCACACTGC 62.013 66.667 0.00 0.00 44.91 4.40
1121 1181 3.345808 CCCGTGCGAACCACACTG 61.346 66.667 0.00 0.00 44.91 3.66
1122 1182 4.619227 CCCCGTGCGAACCACACT 62.619 66.667 0.00 0.00 44.91 3.55
1123 1183 4.612412 TCCCCGTGCGAACCACAC 62.612 66.667 0.00 0.00 44.91 3.82
1124 1184 4.308458 CTCCCCGTGCGAACCACA 62.308 66.667 0.00 0.00 44.91 4.17
1128 1188 1.087771 CATTACCTCCCCGTGCGAAC 61.088 60.000 0.00 0.00 0.00 3.95
1129 1189 1.219664 CATTACCTCCCCGTGCGAA 59.780 57.895 0.00 0.00 0.00 4.70
1130 1190 2.897207 CATTACCTCCCCGTGCGA 59.103 61.111 0.00 0.00 0.00 5.10
1131 1191 2.895372 GCATTACCTCCCCGTGCG 60.895 66.667 0.00 0.00 0.00 5.34
1133 1193 0.744414 CACAGCATTACCTCCCCGTG 60.744 60.000 0.00 0.00 0.00 4.94
1134 1194 1.602237 CACAGCATTACCTCCCCGT 59.398 57.895 0.00 0.00 0.00 5.28
1136 1196 1.453928 GCCACAGCATTACCTCCCC 60.454 63.158 0.00 0.00 39.53 4.81
1137 1197 1.453928 GGCCACAGCATTACCTCCC 60.454 63.158 0.00 0.00 42.56 4.30
1138 1198 0.749454 CAGGCCACAGCATTACCTCC 60.749 60.000 5.01 0.00 42.56 4.30
1142 1202 1.315257 CCCACAGGCCACAGCATTAC 61.315 60.000 5.01 0.00 42.56 1.89
1143 1203 1.001020 CCCACAGGCCACAGCATTA 60.001 57.895 5.01 0.00 42.56 1.90
1144 1204 2.283388 CCCACAGGCCACAGCATT 60.283 61.111 5.01 0.00 42.56 3.56
1145 1205 4.371417 CCCCACAGGCCACAGCAT 62.371 66.667 5.01 0.00 42.56 3.79
1147 1207 4.603535 AACCCCACAGGCCACAGC 62.604 66.667 5.01 0.00 40.58 4.40
1148 1208 2.198426 AAACCCCACAGGCCACAG 59.802 61.111 5.01 0.00 40.58 3.66
1149 1209 2.123511 CAAACCCCACAGGCCACA 60.124 61.111 5.01 0.00 40.58 4.17
1150 1210 2.917227 CCAAACCCCACAGGCCAC 60.917 66.667 5.01 0.00 40.58 5.01
1151 1211 4.932105 GCCAAACCCCACAGGCCA 62.932 66.667 5.01 0.00 41.25 5.36
1154 1214 4.596585 ACGGCCAAACCCCACAGG 62.597 66.667 2.24 0.00 43.78 4.00
1156 1216 2.042843 AAACGGCCAAACCCCACA 60.043 55.556 2.24 0.00 33.26 4.17
1157 1217 2.419620 CAAACGGCCAAACCCCAC 59.580 61.111 2.24 0.00 33.26 4.61
1158 1218 2.840102 CCAAACGGCCAAACCCCA 60.840 61.111 2.24 0.00 33.26 4.96
1160 1220 1.973816 AAACCCAAACGGCCAAACCC 61.974 55.000 2.24 0.00 33.26 4.11
1163 1223 0.461961 CAGAAACCCAAACGGCCAAA 59.538 50.000 2.24 0.00 33.26 3.28
1164 1224 0.684805 ACAGAAACCCAAACGGCCAA 60.685 50.000 2.24 0.00 33.26 4.52
1165 1225 1.076632 ACAGAAACCCAAACGGCCA 60.077 52.632 2.24 0.00 33.26 5.36
1166 1226 1.658114 GACAGAAACCCAAACGGCC 59.342 57.895 0.00 0.00 33.26 6.13
1167 1227 1.658114 GGACAGAAACCCAAACGGC 59.342 57.895 0.00 0.00 33.26 5.68
1168 1228 2.337361 GGGACAGAAACCCAAACGG 58.663 57.895 0.00 0.00 46.05 4.44
1207 1267 2.693762 CCAACACCTGGCGCTCATG 61.694 63.158 7.64 3.51 38.76 3.07
1208 1268 2.360350 CCAACACCTGGCGCTCAT 60.360 61.111 7.64 0.00 38.76 2.90
1209 1269 3.555324 TCCAACACCTGGCGCTCA 61.555 61.111 7.64 2.39 45.98 4.26
1210 1270 3.050275 GTCCAACACCTGGCGCTC 61.050 66.667 7.64 0.00 45.98 5.03
1214 1274 2.268076 AATGCGTCCAACACCTGGC 61.268 57.895 0.00 0.00 45.98 4.85
1217 1277 2.268076 GGCAATGCGTCCAACACCT 61.268 57.895 0.00 0.00 0.00 4.00
1218 1278 2.200170 GAGGCAATGCGTCCAACACC 62.200 60.000 16.20 0.00 37.46 4.16
1219 1279 1.210155 GAGGCAATGCGTCCAACAC 59.790 57.895 16.20 0.00 37.46 3.32
1221 1281 1.503542 CAGAGGCAATGCGTCCAAC 59.496 57.895 22.23 0.41 43.36 3.77
1222 1282 2.334946 GCAGAGGCAATGCGTCCAA 61.335 57.895 22.23 0.00 43.36 3.53
1223 1283 2.747460 GCAGAGGCAATGCGTCCA 60.747 61.111 22.23 0.00 43.36 4.02
1228 1288 4.233635 CTCGCGCAGAGGCAATGC 62.234 66.667 17.74 0.00 43.20 3.56
1235 1295 2.817423 GCATTTCCCTCGCGCAGAG 61.817 63.158 18.33 18.33 46.44 3.35
1236 1296 2.819595 GCATTTCCCTCGCGCAGA 60.820 61.111 8.75 4.86 0.00 4.26
1238 1298 3.126879 CAGCATTTCCCTCGCGCA 61.127 61.111 8.75 0.00 0.00 6.09
1239 1299 2.690778 AACAGCATTTCCCTCGCGC 61.691 57.895 0.00 0.00 0.00 6.86
1240 1300 1.135315 CAACAGCATTTCCCTCGCG 59.865 57.895 0.00 0.00 0.00 5.87
1241 1301 0.109597 CACAACAGCATTTCCCTCGC 60.110 55.000 0.00 0.00 0.00 5.03
1243 1303 0.244721 GGCACAACAGCATTTCCCTC 59.755 55.000 0.00 0.00 35.83 4.30
1244 1304 1.526575 CGGCACAACAGCATTTCCCT 61.527 55.000 0.00 0.00 35.83 4.20
1245 1305 1.080569 CGGCACAACAGCATTTCCC 60.081 57.895 0.00 0.00 35.83 3.97
1246 1306 0.664166 CACGGCACAACAGCATTTCC 60.664 55.000 0.00 0.00 35.83 3.13
1247 1307 0.310543 TCACGGCACAACAGCATTTC 59.689 50.000 0.00 0.00 35.83 2.17
1248 1308 0.961019 ATCACGGCACAACAGCATTT 59.039 45.000 0.00 0.00 35.83 2.32
1249 1309 0.961019 AATCACGGCACAACAGCATT 59.039 45.000 0.00 0.00 35.83 3.56
1250 1310 0.523072 GAATCACGGCACAACAGCAT 59.477 50.000 0.00 0.00 35.83 3.79
1252 1312 0.593128 AAGAATCACGGCACAACAGC 59.407 50.000 0.00 0.00 0.00 4.40
1254 1314 2.254546 AGAAGAATCACGGCACAACA 57.745 45.000 0.00 0.00 0.00 3.33
1255 1315 2.350772 CCAAGAAGAATCACGGCACAAC 60.351 50.000 0.00 0.00 0.00 3.32
1256 1316 1.879380 CCAAGAAGAATCACGGCACAA 59.121 47.619 0.00 0.00 0.00 3.33
1257 1317 1.202758 ACCAAGAAGAATCACGGCACA 60.203 47.619 0.00 0.00 0.00 4.57
1258 1318 1.197721 CACCAAGAAGAATCACGGCAC 59.802 52.381 0.00 0.00 0.00 5.01
1262 1322 3.393800 AGACACACCAAGAAGAATCACG 58.606 45.455 0.00 0.00 0.00 4.35
1264 1324 5.034852 TGAAGACACACCAAGAAGAATCA 57.965 39.130 0.00 0.00 0.00 2.57
1265 1325 6.016777 ACATTGAAGACACACCAAGAAGAATC 60.017 38.462 0.00 0.00 0.00 2.52
1266 1326 5.829924 ACATTGAAGACACACCAAGAAGAAT 59.170 36.000 0.00 0.00 0.00 2.40
1268 1328 4.780815 ACATTGAAGACACACCAAGAAGA 58.219 39.130 0.00 0.00 0.00 2.87
1271 1331 3.130633 CGACATTGAAGACACACCAAGA 58.869 45.455 0.00 0.00 0.00 3.02
1272 1332 2.224079 CCGACATTGAAGACACACCAAG 59.776 50.000 0.00 0.00 0.00 3.61
1273 1333 2.158885 TCCGACATTGAAGACACACCAA 60.159 45.455 0.00 0.00 0.00 3.67
1275 1335 2.163818 TCCGACATTGAAGACACACC 57.836 50.000 0.00 0.00 0.00 4.16
1276 1336 3.607078 GCTTTCCGACATTGAAGACACAC 60.607 47.826 0.00 0.00 0.00 3.82
1277 1337 2.548057 GCTTTCCGACATTGAAGACACA 59.452 45.455 0.00 0.00 0.00 3.72
1278 1338 2.411547 CGCTTTCCGACATTGAAGACAC 60.412 50.000 0.00 0.00 40.02 3.67
1279 1339 1.798223 CGCTTTCCGACATTGAAGACA 59.202 47.619 0.00 0.00 40.02 3.41
1280 1340 2.066262 TCGCTTTCCGACATTGAAGAC 58.934 47.619 0.00 0.00 41.89 3.01
1281 1341 2.337583 CTCGCTTTCCGACATTGAAGA 58.662 47.619 0.00 0.00 41.89 2.87
1282 1342 1.394917 CCTCGCTTTCCGACATTGAAG 59.605 52.381 0.00 0.00 41.89 3.02
1283 1343 1.438651 CCTCGCTTTCCGACATTGAA 58.561 50.000 0.00 0.00 41.89 2.69
1284 1344 1.019278 GCCTCGCTTTCCGACATTGA 61.019 55.000 0.00 0.00 41.89 2.57
1286 1346 0.605319 TTGCCTCGCTTTCCGACATT 60.605 50.000 0.00 0.00 41.89 2.71
1287 1347 1.003839 TTGCCTCGCTTTCCGACAT 60.004 52.632 0.00 0.00 41.89 3.06
1290 1350 2.736995 CGTTGCCTCGCTTTCCGA 60.737 61.111 0.00 0.00 45.15 4.55
1361 4784 4.043200 GCGGCTGCAAGTTGGGTC 62.043 66.667 14.08 0.00 42.15 4.46
1382 4805 3.465701 TGGACGACCATGACAGCA 58.534 55.556 1.37 0.00 41.77 4.41
1624 5050 1.601759 GGAAGACAAGCCAGCTGCA 60.602 57.895 8.66 0.00 44.83 4.41
1987 5416 0.541863 CCTTTGGTGAGGGCGTAGAT 59.458 55.000 0.00 0.00 32.94 1.98
2212 5641 0.253044 GCTTCACCATACAGCCCAGA 59.747 55.000 0.00 0.00 0.00 3.86
2284 5716 1.758906 TCGACACACTGACCCACCA 60.759 57.895 0.00 0.00 0.00 4.17
2535 5979 2.044252 AAGAGCCATGCAGCCAGG 60.044 61.111 0.00 0.00 0.00 4.45
2814 6318 5.128205 ACCACAGTACTAGTTCAAAAACCC 58.872 41.667 0.00 0.00 35.92 4.11
2821 6325 6.046593 CAGAAACAACCACAGTACTAGTTCA 58.953 40.000 0.00 0.00 0.00 3.18
2822 6326 6.018994 CACAGAAACAACCACAGTACTAGTTC 60.019 42.308 0.00 0.00 0.00 3.01
2891 6395 2.286294 CGATTACTGATGCTCTGCAACC 59.714 50.000 0.00 0.00 43.62 3.77
2931 6435 7.663905 ACCAATGCAATAACTTAGACAGTAACA 59.336 33.333 0.00 0.00 32.94 2.41
2976 6483 4.802039 GCAAATCTTCCATATGCACAACAG 59.198 41.667 0.00 0.00 37.00 3.16
3012 6519 2.224159 GGGAGTCAGAGGCCACCAA 61.224 63.158 5.01 0.00 0.00 3.67
3149 6657 5.989168 TGTTCCACTGTCTAATAACTGTGTG 59.011 40.000 11.42 0.00 43.57 3.82
3304 6923 2.680370 GGAAACGGAGGGGGCAGAT 61.680 63.158 0.00 0.00 0.00 2.90
3317 6937 2.050442 CCCAGCAAACGCGGAAAC 60.050 61.111 12.47 0.00 0.00 2.78
3520 7147 8.230472 ACAAATTATTTTGAAATTGCCCAACA 57.770 26.923 15.19 0.00 44.11 3.33
3521 7148 9.526713 AAACAAATTATTTTGAAATTGCCCAAC 57.473 25.926 15.19 0.00 44.11 3.77


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

AutoCloner maintained by Alex Coulton.