Multiple sequence alignment - TraesCS1B01G216200

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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 TraesCS1B01G216200 chr1B 100.000 2366 0 0 1 2366 392108001 392105636 0.000000e+00 4370.0
1 TraesCS1B01G216200 chr1B 89.429 946 74 9 1444 2366 555644887 555645829 0.000000e+00 1170.0
2 TraesCS1B01G216200 chr1B 91.250 240 8 2 1154 1392 545798357 545798130 4.910000e-82 315.0
3 TraesCS1B01G216200 chr1B 92.929 99 6 1 979 1077 545798699 545798602 2.450000e-30 143.0
4 TraesCS1B01G216200 chr1B 96.000 50 2 0 1074 1123 545798405 545798356 5.420000e-12 82.4
5 TraesCS1B01G216200 chr4B 91.507 942 59 5 1443 2365 146682526 146681587 0.000000e+00 1277.0
6 TraesCS1B01G216200 chr4B 98.582 141 2 0 1007 1147 619580072 619580212 1.400000e-62 250.0
7 TraesCS1B01G216200 chr4B 95.620 137 6 0 1218 1354 619581850 619581986 1.100000e-53 220.0
8 TraesCS1B01G216200 chr1D 90.609 969 48 14 1 963 290799801 290798870 0.000000e+00 1245.0
9 TraesCS1B01G216200 chr1D 88.448 554 45 6 1832 2366 51551887 51551334 0.000000e+00 651.0
10 TraesCS1B01G216200 chr4D 90.522 939 68 9 1446 2366 351701100 351702035 0.000000e+00 1221.0
11 TraesCS1B01G216200 chr4D 88.024 167 8 4 1225 1391 130542851 130542697 1.120000e-43 187.0
12 TraesCS1B01G216200 chr6D 90.658 942 48 15 1443 2365 9475759 9476679 0.000000e+00 1216.0
13 TraesCS1B01G216200 chr6D 98.058 103 2 0 979 1081 6004247 6004145 1.870000e-41 180.0
14 TraesCS1B01G216200 chr6D 95.652 92 4 0 1205 1296 6004130 6004039 5.270000e-32 148.0
15 TraesCS1B01G216200 chr3D 90.295 948 51 14 1446 2366 407213789 407214722 0.000000e+00 1203.0
16 TraesCS1B01G216200 chr3B 89.894 940 72 5 1446 2366 385393501 385394436 0.000000e+00 1188.0
17 TraesCS1B01G216200 chr7B 89.765 938 72 5 1448 2366 72518422 72517490 0.000000e+00 1179.0
18 TraesCS1B01G216200 chr7B 89.955 667 43 7 1469 2114 150844060 150844723 0.000000e+00 839.0
19 TraesCS1B01G216200 chr2D 90.794 869 57 8 1519 2366 89920706 89921572 0.000000e+00 1140.0
20 TraesCS1B01G216200 chr2A 88.229 943 87 5 1446 2366 592369818 592368878 0.000000e+00 1105.0
21 TraesCS1B01G216200 chr1A 93.713 684 30 4 1 684 363048613 363047943 0.000000e+00 1013.0
22 TraesCS1B01G216200 chr1A 96.330 218 8 0 984 1201 500984738 500984521 2.240000e-95 359.0
23 TraesCS1B01G216200 chr1A 97.525 202 5 0 1193 1394 500984503 500984302 1.740000e-91 346.0
24 TraesCS1B01G216200 chr1A 84.643 280 16 11 721 974 363047946 363047668 1.090000e-63 254.0
25 TraesCS1B01G216200 chr4A 87.963 648 56 7 1738 2366 196018365 196019009 0.000000e+00 745.0
26 TraesCS1B01G216200 chr7A 88.264 605 48 10 1780 2365 716412667 716412067 0.000000e+00 702.0
27 TraesCS1B01G216200 chr2B 91.981 424 29 3 1446 1867 23112261 23112681 7.280000e-165 590.0
28 TraesCS1B01G216200 chrUn 85.629 167 12 4 1225 1391 53482928 53483082 5.230000e-37 165.0


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 TraesCS1B01G216200 chr1B 392105636 392108001 2365 True 4370.0 4370 100.000 1 2366 1 chr1B.!!$R1 2365
1 TraesCS1B01G216200 chr1B 555644887 555645829 942 False 1170.0 1170 89.429 1444 2366 1 chr1B.!!$F1 922
2 TraesCS1B01G216200 chr4B 146681587 146682526 939 True 1277.0 1277 91.507 1443 2365 1 chr4B.!!$R1 922
3 TraesCS1B01G216200 chr4B 619580072 619581986 1914 False 235.0 250 97.101 1007 1354 2 chr4B.!!$F1 347
4 TraesCS1B01G216200 chr1D 290798870 290799801 931 True 1245.0 1245 90.609 1 963 1 chr1D.!!$R2 962
5 TraesCS1B01G216200 chr1D 51551334 51551887 553 True 651.0 651 88.448 1832 2366 1 chr1D.!!$R1 534
6 TraesCS1B01G216200 chr4D 351701100 351702035 935 False 1221.0 1221 90.522 1446 2366 1 chr4D.!!$F1 920
7 TraesCS1B01G216200 chr6D 9475759 9476679 920 False 1216.0 1216 90.658 1443 2365 1 chr6D.!!$F1 922
8 TraesCS1B01G216200 chr3D 407213789 407214722 933 False 1203.0 1203 90.295 1446 2366 1 chr3D.!!$F1 920
9 TraesCS1B01G216200 chr3B 385393501 385394436 935 False 1188.0 1188 89.894 1446 2366 1 chr3B.!!$F1 920
10 TraesCS1B01G216200 chr7B 72517490 72518422 932 True 1179.0 1179 89.765 1448 2366 1 chr7B.!!$R1 918
11 TraesCS1B01G216200 chr7B 150844060 150844723 663 False 839.0 839 89.955 1469 2114 1 chr7B.!!$F1 645
12 TraesCS1B01G216200 chr2D 89920706 89921572 866 False 1140.0 1140 90.794 1519 2366 1 chr2D.!!$F1 847
13 TraesCS1B01G216200 chr2A 592368878 592369818 940 True 1105.0 1105 88.229 1446 2366 1 chr2A.!!$R1 920
14 TraesCS1B01G216200 chr1A 363047668 363048613 945 True 633.5 1013 89.178 1 974 2 chr1A.!!$R1 973
15 TraesCS1B01G216200 chr4A 196018365 196019009 644 False 745.0 745 87.963 1738 2366 1 chr4A.!!$F1 628
16 TraesCS1B01G216200 chr7A 716412067 716412667 600 True 702.0 702 88.264 1780 2365 1 chr7A.!!$R1 585

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
880 900 1.209127 CCGTGATGTTTCGCCCAAC 59.791 57.895 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 3600 0.179081 GGTTATGGTCTCCCGCTCAC 60.179 60.0 0.0 0.0 0.0 3.51 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
23 24 2.159653 GCTCGCCAATGTTCAGTAACTG 60.160 50.000 0.00 0.00 36.51 3.16
35 36 5.105106 TGTTCAGTAACTGTCCAACTTCAGA 60.105 40.000 0.00 0.00 36.51 3.27
43 44 7.540474 AACTGTCCAACTTCAGATTCTACTA 57.460 36.000 0.00 0.00 35.84 1.82
48 49 7.015292 TGTCCAACTTCAGATTCTACTAACACT 59.985 37.037 0.00 0.00 0.00 3.55
49 50 7.873505 GTCCAACTTCAGATTCTACTAACACTT 59.126 37.037 0.00 0.00 0.00 3.16
50 51 7.872993 TCCAACTTCAGATTCTACTAACACTTG 59.127 37.037 0.00 0.00 0.00 3.16
51 52 7.360438 CCAACTTCAGATTCTACTAACACTTGC 60.360 40.741 0.00 0.00 0.00 4.01
52 53 6.998802 ACTTCAGATTCTACTAACACTTGCT 58.001 36.000 0.00 0.00 0.00 3.91
53 54 7.445945 ACTTCAGATTCTACTAACACTTGCTT 58.554 34.615 0.00 0.00 0.00 3.91
54 55 8.585881 ACTTCAGATTCTACTAACACTTGCTTA 58.414 33.333 0.00 0.00 0.00 3.09
55 56 8.988064 TTCAGATTCTACTAACACTTGCTTAG 57.012 34.615 0.00 0.00 0.00 2.18
93 94 4.096732 ACTGTGAAAGCAATTTATCCGC 57.903 40.909 0.00 0.00 0.00 5.54
99 100 6.090628 TGTGAAAGCAATTTATCCGCAAATTC 59.909 34.615 0.00 0.00 36.26 2.17
102 103 4.601019 AGCAATTTATCCGCAAATTCGAG 58.399 39.130 0.00 0.00 36.26 4.04
110 111 2.028839 TCCGCAAATTCGAGGACTAACA 60.029 45.455 0.00 0.00 28.90 2.41
117 118 5.941555 AATTCGAGGACTAACAGAGGAAT 57.058 39.130 0.00 0.00 0.00 3.01
118 119 4.720649 TTCGAGGACTAACAGAGGAATG 57.279 45.455 0.00 0.00 0.00 2.67
119 120 3.698289 TCGAGGACTAACAGAGGAATGT 58.302 45.455 0.00 0.00 33.96 2.71
120 121 4.851843 TCGAGGACTAACAGAGGAATGTA 58.148 43.478 0.00 0.00 31.70 2.29
121 122 5.258841 TCGAGGACTAACAGAGGAATGTAA 58.741 41.667 0.00 0.00 31.70 2.41
122 123 5.892119 TCGAGGACTAACAGAGGAATGTAAT 59.108 40.000 0.00 0.00 31.70 1.89
123 124 5.980116 CGAGGACTAACAGAGGAATGTAATG 59.020 44.000 0.00 0.00 31.70 1.90
124 125 6.240549 AGGACTAACAGAGGAATGTAATGG 57.759 41.667 0.00 0.00 31.70 3.16
130 131 5.964958 ACAGAGGAATGTAATGGTTGTTG 57.035 39.130 0.00 0.00 0.00 3.33
154 155 4.937196 TCCAGATGGGATCTTCGATGAAGA 60.937 45.833 11.30 11.30 42.54 2.87
545 552 5.011738 ACCGTGATAGTTTCTCCTTTCAGAA 59.988 40.000 0.00 0.00 0.00 3.02
580 587 4.711399 TCAGAATGCGATGGAGAAATGAT 58.289 39.130 0.00 0.00 34.76 2.45
653 660 6.552725 TGTGTTAGATTAGAGGATGAGCAGAT 59.447 38.462 0.00 0.00 0.00 2.90
705 712 7.558137 GTGCATGTTTTCATTGTTTTGACTAG 58.442 34.615 0.00 0.00 38.64 2.57
758 765 2.297880 TGAGAAGTCACGGGAATTTCGA 59.702 45.455 0.21 0.00 30.26 3.71
803 810 1.621107 TTCCACGTCGCGAATAGAAC 58.379 50.000 12.06 0.00 0.00 3.01
856 876 7.445402 CCTAAGGTTAATGATGAATAGTGGTGG 59.555 40.741 0.00 0.00 0.00 4.61
880 900 1.209127 CCGTGATGTTTCGCCCAAC 59.791 57.895 0.00 0.00 0.00 3.77
911 943 2.715046 ACGTGTTCATGCTGAATCCAT 58.285 42.857 0.00 0.00 38.79 3.41
912 944 3.084039 ACGTGTTCATGCTGAATCCATT 58.916 40.909 0.00 0.00 38.79 3.16
963 995 5.128008 ACTTGCCTAGTGTTAGAGAATCTCC 59.872 44.000 6.65 0.00 39.72 3.71
964 996 7.259543 ACTTGCCTAGTGTTAGAGAATCTCCA 61.260 42.308 6.65 0.00 39.72 3.86
965 997 8.674198 ACTTGCCTAGTGTTAGAGAATCTCCAA 61.674 40.741 6.65 0.00 39.72 3.53
974 1006 3.272574 GAGAATCTCCAACATCTGCCA 57.727 47.619 0.00 0.00 0.00 4.92
975 1007 3.614092 GAGAATCTCCAACATCTGCCAA 58.386 45.455 0.00 0.00 0.00 4.52
976 1008 4.012374 GAGAATCTCCAACATCTGCCAAA 58.988 43.478 0.00 0.00 0.00 3.28
977 1009 4.410099 AGAATCTCCAACATCTGCCAAAA 58.590 39.130 0.00 0.00 0.00 2.44
978 1010 4.219288 AGAATCTCCAACATCTGCCAAAAC 59.781 41.667 0.00 0.00 0.00 2.43
979 1011 2.942804 TCTCCAACATCTGCCAAAACA 58.057 42.857 0.00 0.00 0.00 2.83
980 1012 3.499338 TCTCCAACATCTGCCAAAACAT 58.501 40.909 0.00 0.00 0.00 2.71
981 1013 3.896888 TCTCCAACATCTGCCAAAACATT 59.103 39.130 0.00 0.00 0.00 2.71
982 1014 4.022068 TCTCCAACATCTGCCAAAACATTC 60.022 41.667 0.00 0.00 0.00 2.67
983 1015 3.640498 TCCAACATCTGCCAAAACATTCA 59.360 39.130 0.00 0.00 0.00 2.57
984 1016 3.991773 CCAACATCTGCCAAAACATTCAG 59.008 43.478 0.00 0.00 0.00 3.02
985 1017 3.947910 ACATCTGCCAAAACATTCAGG 57.052 42.857 0.00 0.00 0.00 3.86
990 1022 2.818130 GCCAAAACATTCAGGCTGAA 57.182 45.000 30.29 30.29 43.70 3.02
991 1023 2.680577 GCCAAAACATTCAGGCTGAAG 58.319 47.619 31.17 24.26 40.05 3.02
992 1024 2.680577 CCAAAACATTCAGGCTGAAGC 58.319 47.619 31.17 0.00 40.05 3.86
993 1025 2.036217 CCAAAACATTCAGGCTGAAGCA 59.964 45.455 31.17 12.75 40.05 3.91
994 1026 3.306502 CCAAAACATTCAGGCTGAAGCAT 60.307 43.478 31.17 18.02 40.05 3.79
995 1027 4.312443 CAAAACATTCAGGCTGAAGCATT 58.688 39.130 31.17 22.03 40.05 3.56
1022 1054 0.822164 ATGCTTGCTTCCCAGATTGC 59.178 50.000 0.00 0.00 0.00 3.56
1077 1109 0.578683 CAGACTATGCGACATTGGCG 59.421 55.000 7.76 7.76 0.00 5.69
1147 1179 0.457443 CAGACCTCAGCTCGCACATA 59.543 55.000 0.00 0.00 0.00 2.29
1148 1180 1.068281 CAGACCTCAGCTCGCACATAT 59.932 52.381 0.00 0.00 0.00 1.78
1149 1181 1.759445 AGACCTCAGCTCGCACATATT 59.241 47.619 0.00 0.00 0.00 1.28
1150 1182 2.959030 AGACCTCAGCTCGCACATATTA 59.041 45.455 0.00 0.00 0.00 0.98
1151 1183 3.384789 AGACCTCAGCTCGCACATATTAA 59.615 43.478 0.00 0.00 0.00 1.40
1152 1184 4.119862 GACCTCAGCTCGCACATATTAAA 58.880 43.478 0.00 0.00 0.00 1.52
1153 1185 4.122776 ACCTCAGCTCGCACATATTAAAG 58.877 43.478 0.00 0.00 0.00 1.85
1154 1186 3.496130 CCTCAGCTCGCACATATTAAAGG 59.504 47.826 0.00 0.00 0.00 3.11
1155 1187 4.122776 CTCAGCTCGCACATATTAAAGGT 58.877 43.478 0.00 0.00 0.00 3.50
1156 1188 4.513442 TCAGCTCGCACATATTAAAGGTT 58.487 39.130 0.00 0.00 0.00 3.50
1157 1189 4.570772 TCAGCTCGCACATATTAAAGGTTC 59.429 41.667 0.00 0.00 0.00 3.62
1158 1190 3.877508 AGCTCGCACATATTAAAGGTTCC 59.122 43.478 0.00 0.00 0.00 3.62
1159 1191 3.625764 GCTCGCACATATTAAAGGTTCCA 59.374 43.478 0.00 0.00 0.00 3.53
1160 1192 4.495844 GCTCGCACATATTAAAGGTTCCAC 60.496 45.833 0.00 0.00 0.00 4.02
1161 1193 3.619483 TCGCACATATTAAAGGTTCCACG 59.381 43.478 0.00 0.00 0.00 4.94
1162 1194 3.242608 CGCACATATTAAAGGTTCCACGG 60.243 47.826 0.00 0.00 0.00 4.94
1163 1195 3.488553 GCACATATTAAAGGTTCCACGGC 60.489 47.826 0.00 0.00 0.00 5.68
1164 1196 2.940410 ACATATTAAAGGTTCCACGGCG 59.060 45.455 4.80 4.80 0.00 6.46
1165 1197 2.766345 TATTAAAGGTTCCACGGCGT 57.234 45.000 6.77 6.77 0.00 5.68
1166 1198 1.900245 ATTAAAGGTTCCACGGCGTT 58.100 45.000 11.19 0.00 0.00 4.84
1167 1199 1.677942 TTAAAGGTTCCACGGCGTTT 58.322 45.000 11.19 2.40 0.00 3.60
1168 1200 0.945813 TAAAGGTTCCACGGCGTTTG 59.054 50.000 11.19 4.61 0.00 2.93
1169 1201 0.748729 AAAGGTTCCACGGCGTTTGA 60.749 50.000 11.19 7.47 0.00 2.69
1170 1202 0.536460 AAGGTTCCACGGCGTTTGAT 60.536 50.000 11.19 0.00 0.00 2.57
1171 1203 0.322322 AGGTTCCACGGCGTTTGATA 59.678 50.000 11.19 0.00 0.00 2.15
1172 1204 1.065709 AGGTTCCACGGCGTTTGATAT 60.066 47.619 11.19 0.00 0.00 1.63
1173 1205 1.329599 GGTTCCACGGCGTTTGATATC 59.670 52.381 11.19 0.00 0.00 1.63
1174 1206 2.004017 GTTCCACGGCGTTTGATATCA 58.996 47.619 11.19 0.00 0.00 2.15
1175 1207 1.647346 TCCACGGCGTTTGATATCAC 58.353 50.000 11.19 0.00 0.00 3.06
1176 1208 1.066787 TCCACGGCGTTTGATATCACA 60.067 47.619 11.19 0.00 0.00 3.58
1177 1209 1.735018 CCACGGCGTTTGATATCACAA 59.265 47.619 11.19 0.79 0.00 3.33
1178 1210 2.223021 CCACGGCGTTTGATATCACAAG 60.223 50.000 11.19 2.45 0.00 3.16
1179 1211 2.006888 ACGGCGTTTGATATCACAAGG 58.993 47.619 6.77 9.71 0.00 3.61
1180 1212 1.330521 CGGCGTTTGATATCACAAGGG 59.669 52.381 4.48 0.88 0.00 3.95
1181 1213 2.365582 GGCGTTTGATATCACAAGGGT 58.634 47.619 4.48 0.00 0.00 4.34
1182 1214 2.354821 GGCGTTTGATATCACAAGGGTC 59.645 50.000 4.48 0.00 0.00 4.46
1183 1215 3.270877 GCGTTTGATATCACAAGGGTCT 58.729 45.455 4.48 0.00 0.00 3.85
1184 1216 4.439057 GCGTTTGATATCACAAGGGTCTA 58.561 43.478 4.48 0.00 0.00 2.59
1185 1217 4.270325 GCGTTTGATATCACAAGGGTCTAC 59.730 45.833 4.48 0.00 0.00 2.59
1186 1218 4.809426 CGTTTGATATCACAAGGGTCTACC 59.191 45.833 4.48 0.00 40.67 3.18
1187 1219 5.625886 CGTTTGATATCACAAGGGTCTACCA 60.626 44.000 4.48 0.00 43.89 3.25
1188 1220 5.353394 TTGATATCACAAGGGTCTACCAC 57.647 43.478 4.48 0.00 43.89 4.16
1189 1221 4.358214 TGATATCACAAGGGTCTACCACA 58.642 43.478 0.00 0.00 43.89 4.17
1190 1222 4.968719 TGATATCACAAGGGTCTACCACAT 59.031 41.667 0.00 0.00 43.89 3.21
1191 1223 5.428457 TGATATCACAAGGGTCTACCACATT 59.572 40.000 0.00 0.00 43.89 2.71
1192 1224 6.613679 TGATATCACAAGGGTCTACCACATTA 59.386 38.462 0.00 0.00 43.89 1.90
1193 1225 5.772393 ATCACAAGGGTCTACCACATTAA 57.228 39.130 0.81 0.00 43.89 1.40
1194 1226 4.901868 TCACAAGGGTCTACCACATTAAC 58.098 43.478 0.81 0.00 43.89 2.01
1195 1227 4.348461 TCACAAGGGTCTACCACATTAACA 59.652 41.667 0.81 0.00 43.89 2.41
1262 2905 9.219603 TCTCAAAATTCAGAATACACCTTACAG 57.780 33.333 0.00 0.00 0.00 2.74
1279 2922 3.618690 ACAGGTTCAGATGCTTAGGAC 57.381 47.619 0.00 0.00 0.00 3.85
1291 2934 4.142609 TGCTTAGGACTAGGCAATGAAG 57.857 45.455 12.90 0.00 43.67 3.02
1304 2947 0.822164 AATGAAGCCTGCCTCAATGC 59.178 50.000 0.00 0.00 0.00 3.56
1354 2997 7.094420 TGCTTAACTGCACAATTGTACATGTAT 60.094 33.333 11.53 1.50 38.12 2.29
1355 2998 7.218773 GCTTAACTGCACAATTGTACATGTATG 59.781 37.037 11.53 5.76 0.00 2.39
1356 2999 4.985413 ACTGCACAATTGTACATGTATGC 58.015 39.130 11.53 16.42 0.00 3.14
1357 3000 4.701651 ACTGCACAATTGTACATGTATGCT 59.298 37.500 21.31 5.88 0.00 3.79
1358 3001 4.984205 TGCACAATTGTACATGTATGCTG 58.016 39.130 21.31 13.74 0.00 4.41
1359 3002 4.458642 TGCACAATTGTACATGTATGCTGT 59.541 37.500 21.31 14.23 0.00 4.40
1360 3003 5.048154 TGCACAATTGTACATGTATGCTGTT 60.048 36.000 21.31 7.09 0.00 3.16
1361 3004 6.150140 TGCACAATTGTACATGTATGCTGTTA 59.850 34.615 21.31 5.04 0.00 2.41
1362 3005 6.468956 GCACAATTGTACATGTATGCTGTTAC 59.531 38.462 11.53 2.58 0.00 2.50
1363 3006 7.626240 GCACAATTGTACATGTATGCTGTTACT 60.626 37.037 11.53 0.00 0.00 2.24
1364 3007 8.878769 CACAATTGTACATGTATGCTGTTACTA 58.121 33.333 11.53 0.00 0.00 1.82
1365 3008 9.443323 ACAATTGTACATGTATGCTGTTACTAA 57.557 29.630 9.97 0.00 0.00 2.24
1400 3043 9.468532 AATTTCTCTGTTAAAAAGAACATCTGC 57.531 29.630 0.00 0.00 38.60 4.26
1401 3044 6.560253 TCTCTGTTAAAAAGAACATCTGCC 57.440 37.500 0.00 0.00 38.60 4.85
1402 3045 6.061441 TCTCTGTTAAAAAGAACATCTGCCA 58.939 36.000 0.00 0.00 38.60 4.92
1403 3046 6.545666 TCTCTGTTAAAAAGAACATCTGCCAA 59.454 34.615 0.00 0.00 38.60 4.52
1404 3047 7.068103 TCTCTGTTAAAAAGAACATCTGCCAAA 59.932 33.333 0.00 0.00 38.60 3.28
1405 3048 7.551585 TCTGTTAAAAAGAACATCTGCCAAAA 58.448 30.769 0.00 0.00 38.60 2.44
1406 3049 8.037758 TCTGTTAAAAAGAACATCTGCCAAAAA 58.962 29.630 0.00 0.00 38.60 1.94
1429 3072 6.964807 AAAAACTTCCCGTAAAGTGGTATT 57.035 33.333 0.94 0.00 39.40 1.89
1431 3074 7.439157 AAAACTTCCCGTAAAGTGGTATTAC 57.561 36.000 0.94 0.00 39.40 1.89
1440 3083 3.832615 AAGTGGTATTACGGGATGACC 57.167 47.619 0.00 0.00 0.00 4.02
1512 3159 9.381038 AGGGTACATGGCTATATATATTGGTAG 57.619 37.037 0.00 0.00 0.00 3.18
1878 3539 1.807142 GGTGCAGTTCTAAGAGCAACC 59.193 52.381 0.00 0.00 38.71 3.77
1914 3589 0.452184 ATCAGCGACAGTGGTACTCG 59.548 55.000 0.00 0.00 0.00 4.18
1925 3600 2.202756 GTACTCGGCTTCAGCGGG 60.203 66.667 6.53 0.00 43.26 6.13
1977 3654 6.514947 TGAGGACCAAGAAATCAAATTGTTG 58.485 36.000 0.00 0.00 34.37 3.33
1981 3658 3.432933 CCAAGAAATCAAATTGTTGCCCG 59.567 43.478 0.00 0.00 33.53 6.13
2084 3769 6.157645 AGGAGTGGACTTATTGATGTGAAGAT 59.842 38.462 0.00 0.00 0.00 2.40
2242 3927 4.080687 GGAGAGCCTCGGTTATACTACAT 58.919 47.826 0.00 0.00 0.00 2.29
2247 3932 6.720288 AGAGCCTCGGTTATACTACATTACAT 59.280 38.462 0.00 0.00 0.00 2.29
2269 3954 2.766828 AGTAGGATCCTGGAAAGGTTCG 59.233 50.000 25.28 0.00 0.00 3.95
2302 3987 7.839837 GCGAATAGTTTGAAACTAGTATCAACG 59.160 37.037 20.82 17.46 46.32 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.379750 AGTGTTAGTAGAATCTGAAGTTGGAC 58.620 38.462 0.00 0.00 0.00 4.02
43 44 7.801716 TGATCAAAGTAACTAAGCAAGTGTT 57.198 32.000 0.00 0.00 38.88 3.32
48 49 9.066892 AGTTTGATGATCAAAGTAACTAAGCAA 57.933 29.630 22.85 0.00 45.83 3.91
49 50 8.506437 CAGTTTGATGATCAAAGTAACTAAGCA 58.494 33.333 23.45 0.00 45.35 3.91
50 51 8.507249 ACAGTTTGATGATCAAAGTAACTAAGC 58.493 33.333 23.45 8.98 45.35 3.09
51 52 9.817365 CACAGTTTGATGATCAAAGTAACTAAG 57.183 33.333 23.45 14.55 45.35 2.18
52 53 9.554395 TCACAGTTTGATGATCAAAGTAACTAA 57.446 29.630 23.45 8.83 45.35 2.24
53 54 9.554395 TTCACAGTTTGATGATCAAAGTAACTA 57.446 29.630 23.45 10.23 45.35 2.24
54 55 8.450578 TTCACAGTTTGATGATCAAAGTAACT 57.549 30.769 23.45 14.33 45.35 2.24
55 56 9.173939 CTTTCACAGTTTGATGATCAAAGTAAC 57.826 33.333 23.45 12.49 45.35 2.50
62 63 5.771153 TTGCTTTCACAGTTTGATGATCA 57.229 34.783 0.00 0.00 32.84 2.92
93 94 5.073311 TCCTCTGTTAGTCCTCGAATTTG 57.927 43.478 0.00 0.00 0.00 2.32
99 100 5.578005 TTACATTCCTCTGTTAGTCCTCG 57.422 43.478 0.00 0.00 0.00 4.63
102 103 5.990668 ACCATTACATTCCTCTGTTAGTCC 58.009 41.667 0.00 0.00 0.00 3.85
110 111 5.010282 GGACAACAACCATTACATTCCTCT 58.990 41.667 0.00 0.00 0.00 3.69
117 118 4.078537 CCATCTGGACAACAACCATTACA 58.921 43.478 0.00 0.00 36.79 2.41
118 119 3.443681 CCCATCTGGACAACAACCATTAC 59.556 47.826 0.00 0.00 36.79 1.89
119 120 3.332187 TCCCATCTGGACAACAACCATTA 59.668 43.478 0.00 0.00 38.61 1.90
120 121 2.109834 TCCCATCTGGACAACAACCATT 59.890 45.455 0.00 0.00 38.61 3.16
121 122 1.710244 TCCCATCTGGACAACAACCAT 59.290 47.619 0.00 0.00 38.61 3.55
122 123 1.144691 TCCCATCTGGACAACAACCA 58.855 50.000 0.00 0.00 38.61 3.67
130 131 4.798924 CTTCATCGAAGATCCCATCTGGAC 60.799 50.000 0.00 0.00 45.12 4.02
154 155 0.888619 TGCTCGTCGAAGATGGTTCT 59.111 50.000 0.35 0.00 45.05 3.01
342 343 4.636435 CGGTGGAGGTGCCGGTTT 62.636 66.667 1.90 0.00 43.85 3.27
580 587 2.259204 CGACCTACGCCCGTTTGA 59.741 61.111 0.00 0.00 34.51 2.69
647 654 2.418910 CCCACCTCGACGATCTGCT 61.419 63.158 0.00 0.00 0.00 4.24
653 660 2.753043 GCCTACCCACCTCGACGA 60.753 66.667 0.00 0.00 0.00 4.20
758 765 4.741928 ACTGTTTCCCCTAAAACTCCAT 57.258 40.909 1.73 0.00 39.39 3.41
803 810 0.457166 CATCACGCAATGCACAAGGG 60.457 55.000 5.91 0.00 0.00 3.95
849 869 3.941188 CACGGCACTCCCACCACT 61.941 66.667 0.00 0.00 0.00 4.00
856 876 1.787847 CGAAACATCACGGCACTCC 59.212 57.895 0.00 0.00 0.00 3.85
880 900 0.462937 TGAACACGTTGTGAGGGTGG 60.463 55.000 3.61 0.00 36.96 4.61
911 943 2.342279 CGGCAACAGACGGAGGAA 59.658 61.111 0.00 0.00 0.00 3.36
963 995 3.991773 CCTGAATGTTTTGGCAGATGTTG 59.008 43.478 0.00 0.00 0.00 3.33
964 996 3.555586 GCCTGAATGTTTTGGCAGATGTT 60.556 43.478 0.00 0.00 44.34 2.71
965 997 2.028748 GCCTGAATGTTTTGGCAGATGT 60.029 45.455 0.00 0.00 44.34 3.06
966 998 2.613691 GCCTGAATGTTTTGGCAGATG 58.386 47.619 0.00 0.00 44.34 2.90
971 1003 2.680577 CTTCAGCCTGAATGTTTTGGC 58.319 47.619 7.75 0.00 45.21 4.52
972 1004 2.036217 TGCTTCAGCCTGAATGTTTTGG 59.964 45.455 7.75 0.00 41.18 3.28
973 1005 3.374220 TGCTTCAGCCTGAATGTTTTG 57.626 42.857 7.75 0.00 41.18 2.44
974 1006 4.039488 TGAATGCTTCAGCCTGAATGTTTT 59.961 37.500 7.75 0.14 41.18 2.43
975 1007 3.575256 TGAATGCTTCAGCCTGAATGTTT 59.425 39.130 7.75 1.90 41.18 2.83
976 1008 3.159472 TGAATGCTTCAGCCTGAATGTT 58.841 40.909 7.75 3.44 41.18 2.71
977 1009 2.799017 TGAATGCTTCAGCCTGAATGT 58.201 42.857 7.75 0.00 41.18 2.71
987 1019 2.863401 GCATCATGCTGAATGCTTCA 57.137 45.000 1.02 0.00 40.96 3.02
998 1030 0.102481 CTGGGAAGCAAGCATCATGC 59.898 55.000 0.00 0.00 45.46 4.06
999 1031 1.758936 TCTGGGAAGCAAGCATCATG 58.241 50.000 0.00 0.00 0.00 3.07
1000 1032 2.693591 CAATCTGGGAAGCAAGCATCAT 59.306 45.455 0.00 0.00 0.00 2.45
1001 1033 2.097036 CAATCTGGGAAGCAAGCATCA 58.903 47.619 0.00 0.00 0.00 3.07
1002 1034 1.202382 GCAATCTGGGAAGCAAGCATC 60.202 52.381 0.00 0.00 0.00 3.91
1003 1035 0.822164 GCAATCTGGGAAGCAAGCAT 59.178 50.000 0.00 0.00 0.00 3.79
1004 1036 0.251474 AGCAATCTGGGAAGCAAGCA 60.251 50.000 0.00 0.00 0.00 3.91
1005 1037 0.455005 GAGCAATCTGGGAAGCAAGC 59.545 55.000 0.00 0.00 0.00 4.01
1022 1054 5.220624 GCATGTTGAAGATTGAGTAGCTGAG 60.221 44.000 0.00 0.00 0.00 3.35
1077 1109 3.991121 GGTCTTGAGAAACTACAGCTGAC 59.009 47.826 23.35 2.48 0.00 3.51
1147 1179 1.900245 AACGCCGTGGAACCTTTAAT 58.100 45.000 0.00 0.00 0.00 1.40
1148 1180 1.334243 CAAACGCCGTGGAACCTTTAA 59.666 47.619 0.00 0.00 0.00 1.52
1149 1181 0.945813 CAAACGCCGTGGAACCTTTA 59.054 50.000 0.00 0.00 0.00 1.85
1150 1182 0.748729 TCAAACGCCGTGGAACCTTT 60.749 50.000 0.00 0.00 0.00 3.11
1151 1183 0.536460 ATCAAACGCCGTGGAACCTT 60.536 50.000 0.00 0.00 0.00 3.50
1152 1184 0.322322 TATCAAACGCCGTGGAACCT 59.678 50.000 0.00 0.00 0.00 3.50
1153 1185 1.329599 GATATCAAACGCCGTGGAACC 59.670 52.381 0.00 0.00 0.00 3.62
1154 1186 2.004017 TGATATCAAACGCCGTGGAAC 58.996 47.619 1.98 0.00 0.00 3.62
1155 1187 2.004017 GTGATATCAAACGCCGTGGAA 58.996 47.619 7.07 0.00 0.00 3.53
1156 1188 1.066787 TGTGATATCAAACGCCGTGGA 60.067 47.619 7.07 0.00 0.00 4.02
1157 1189 1.364721 TGTGATATCAAACGCCGTGG 58.635 50.000 7.07 0.00 0.00 4.94
1158 1190 2.223021 CCTTGTGATATCAAACGCCGTG 60.223 50.000 7.07 0.00 0.00 4.94
1159 1191 2.006888 CCTTGTGATATCAAACGCCGT 58.993 47.619 7.07 0.00 0.00 5.68
1160 1192 1.330521 CCCTTGTGATATCAAACGCCG 59.669 52.381 7.07 0.00 0.00 6.46
1161 1193 2.354821 GACCCTTGTGATATCAAACGCC 59.645 50.000 7.07 0.00 0.00 5.68
1162 1194 3.270877 AGACCCTTGTGATATCAAACGC 58.729 45.455 7.07 0.00 0.00 4.84
1163 1195 4.809426 GGTAGACCCTTGTGATATCAAACG 59.191 45.833 7.07 0.00 0.00 3.60
1164 1196 5.585047 GTGGTAGACCCTTGTGATATCAAAC 59.415 44.000 7.07 0.00 34.29 2.93
1165 1197 5.249622 TGTGGTAGACCCTTGTGATATCAAA 59.750 40.000 7.07 0.00 34.29 2.69
1166 1198 4.780554 TGTGGTAGACCCTTGTGATATCAA 59.219 41.667 7.07 0.00 34.29 2.57
1167 1199 4.358214 TGTGGTAGACCCTTGTGATATCA 58.642 43.478 0.00 0.00 34.29 2.15
1168 1200 5.552870 ATGTGGTAGACCCTTGTGATATC 57.447 43.478 0.00 0.00 34.29 1.63
1169 1201 5.975988 AATGTGGTAGACCCTTGTGATAT 57.024 39.130 0.00 0.00 34.29 1.63
1170 1202 6.213802 TGTTAATGTGGTAGACCCTTGTGATA 59.786 38.462 0.00 0.00 34.29 2.15
1171 1203 5.013704 TGTTAATGTGGTAGACCCTTGTGAT 59.986 40.000 0.00 0.00 34.29 3.06
1172 1204 4.348461 TGTTAATGTGGTAGACCCTTGTGA 59.652 41.667 0.00 0.00 34.29 3.58
1173 1205 4.647611 TGTTAATGTGGTAGACCCTTGTG 58.352 43.478 0.00 0.00 34.29 3.33
1174 1206 4.595781 TCTGTTAATGTGGTAGACCCTTGT 59.404 41.667 0.00 0.00 34.29 3.16
1175 1207 5.160607 TCTGTTAATGTGGTAGACCCTTG 57.839 43.478 0.00 0.00 34.29 3.61
1176 1208 4.225267 CCTCTGTTAATGTGGTAGACCCTT 59.775 45.833 0.00 0.00 34.29 3.95
1177 1209 3.775316 CCTCTGTTAATGTGGTAGACCCT 59.225 47.826 0.00 0.00 34.29 4.34
1178 1210 3.681874 GCCTCTGTTAATGTGGTAGACCC 60.682 52.174 0.00 0.00 34.29 4.46
1179 1211 3.197983 AGCCTCTGTTAATGTGGTAGACC 59.802 47.826 0.00 0.00 0.00 3.85
1180 1212 4.473477 AGCCTCTGTTAATGTGGTAGAC 57.527 45.455 0.00 0.00 0.00 2.59
1181 1213 7.907841 TTATAGCCTCTGTTAATGTGGTAGA 57.092 36.000 0.00 0.00 0.00 2.59
1182 1214 9.561069 AAATTATAGCCTCTGTTAATGTGGTAG 57.439 33.333 0.00 0.00 0.00 3.18
1183 1215 9.914834 AAAATTATAGCCTCTGTTAATGTGGTA 57.085 29.630 0.00 0.00 0.00 3.25
1184 1216 8.823220 AAAATTATAGCCTCTGTTAATGTGGT 57.177 30.769 0.00 0.00 0.00 4.16
1185 1217 8.070171 CGAAAATTATAGCCTCTGTTAATGTGG 58.930 37.037 0.00 0.00 0.00 4.17
1186 1218 8.612619 ACGAAAATTATAGCCTCTGTTAATGTG 58.387 33.333 0.00 0.00 0.00 3.21
1187 1219 8.612619 CACGAAAATTATAGCCTCTGTTAATGT 58.387 33.333 0.00 0.00 0.00 2.71
1188 1220 7.587757 GCACGAAAATTATAGCCTCTGTTAATG 59.412 37.037 0.00 0.00 0.00 1.90
1189 1221 7.499232 AGCACGAAAATTATAGCCTCTGTTAAT 59.501 33.333 0.00 0.00 0.00 1.40
1190 1222 6.821665 AGCACGAAAATTATAGCCTCTGTTAA 59.178 34.615 0.00 0.00 0.00 2.01
1191 1223 6.346096 AGCACGAAAATTATAGCCTCTGTTA 58.654 36.000 0.00 0.00 0.00 2.41
1192 1224 5.186198 AGCACGAAAATTATAGCCTCTGTT 58.814 37.500 0.00 0.00 0.00 3.16
1193 1225 4.770795 AGCACGAAAATTATAGCCTCTGT 58.229 39.130 0.00 0.00 0.00 3.41
1194 1226 4.811024 TGAGCACGAAAATTATAGCCTCTG 59.189 41.667 0.00 0.00 0.00 3.35
1195 1227 5.023533 TGAGCACGAAAATTATAGCCTCT 57.976 39.130 0.00 0.00 0.00 3.69
1262 2905 3.493524 GCCTAGTCCTAAGCATCTGAACC 60.494 52.174 0.00 0.00 0.00 3.62
1264 2907 3.374764 TGCCTAGTCCTAAGCATCTGAA 58.625 45.455 0.00 0.00 28.42 3.02
1304 2947 4.624882 CAGTAGAAAGAGCAGCTACAACTG 59.375 45.833 0.00 0.28 37.54 3.16
1374 3017 9.468532 GCAGATGTTCTTTTTAACAGAGAAATT 57.531 29.630 0.00 0.00 42.33 1.82
1375 3018 8.084684 GGCAGATGTTCTTTTTAACAGAGAAAT 58.915 33.333 0.00 0.00 42.33 2.17
1376 3019 7.068103 TGGCAGATGTTCTTTTTAACAGAGAAA 59.932 33.333 0.00 0.00 42.33 2.52
1377 3020 6.545666 TGGCAGATGTTCTTTTTAACAGAGAA 59.454 34.615 0.00 0.00 42.33 2.87
1378 3021 6.061441 TGGCAGATGTTCTTTTTAACAGAGA 58.939 36.000 0.00 0.00 42.33 3.10
1379 3022 6.317789 TGGCAGATGTTCTTTTTAACAGAG 57.682 37.500 0.00 0.00 42.33 3.35
1380 3023 6.707440 TTGGCAGATGTTCTTTTTAACAGA 57.293 33.333 0.00 0.00 42.33 3.41
1381 3024 7.769272 TTTTGGCAGATGTTCTTTTTAACAG 57.231 32.000 0.00 0.00 42.33 3.16
1406 3049 6.964807 AATACCACTTTACGGGAAGTTTTT 57.035 33.333 3.29 0.00 37.76 1.94
1407 3050 6.147656 CGTAATACCACTTTACGGGAAGTTTT 59.852 38.462 7.82 0.00 44.95 2.43
1408 3051 5.639082 CGTAATACCACTTTACGGGAAGTTT 59.361 40.000 7.82 0.00 44.95 2.66
1409 3052 5.170748 CGTAATACCACTTTACGGGAAGTT 58.829 41.667 7.82 0.00 44.95 2.66
1410 3053 4.747810 CGTAATACCACTTTACGGGAAGT 58.252 43.478 7.82 0.44 44.95 3.01
1417 3060 5.052481 GGTCATCCCGTAATACCACTTTAC 58.948 45.833 0.00 0.00 0.00 2.01
1418 3061 5.280654 GGTCATCCCGTAATACCACTTTA 57.719 43.478 0.00 0.00 0.00 1.85
1419 3062 4.146745 GGTCATCCCGTAATACCACTTT 57.853 45.455 0.00 0.00 0.00 2.66
1420 3063 3.832615 GGTCATCCCGTAATACCACTT 57.167 47.619 0.00 0.00 0.00 3.16
1432 3075 5.661056 TCATCTATCAATACGGTCATCCC 57.339 43.478 0.00 0.00 0.00 3.85
1433 3076 9.653287 TTTATTCATCTATCAATACGGTCATCC 57.347 33.333 0.00 0.00 0.00 3.51
1467 3110 7.883833 TGTACCCTGTGCTAAACATTATACAAA 59.116 33.333 0.00 0.00 38.39 2.83
1474 3117 4.016444 CCATGTACCCTGTGCTAAACATT 58.984 43.478 0.00 0.00 38.39 2.71
1539 3186 1.900486 AGTTTCCTAGTCCAAGTCGGG 59.100 52.381 0.00 0.00 34.36 5.14
1603 3263 1.682684 AACGTCATCGAGCCTCCCT 60.683 57.895 0.00 0.00 40.62 4.20
1845 3506 2.244436 CTGCACCAACCGATTGAGCG 62.244 60.000 0.00 0.00 38.64 5.03
1857 3518 2.494059 GTTGCTCTTAGAACTGCACCA 58.506 47.619 0.00 0.00 35.01 4.17
1878 3539 3.489785 GCTGATACTATTTGGGTTCGTCG 59.510 47.826 0.00 0.00 0.00 5.12
1925 3600 0.179081 GGTTATGGTCTCCCGCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
1949 3624 7.712205 ACAATTTGATTTCTTGGTCCTCAAAAG 59.288 33.333 2.79 5.19 38.77 2.27
1977 3654 0.966179 ATCCTTGTGTTTTTCCGGGC 59.034 50.000 0.00 0.00 0.00 6.13
2084 3769 9.383519 GTATTTGAAAGGTACTCTTGATCATGA 57.616 33.333 10.59 10.59 38.49 3.07
2114 3799 7.696035 GCATTATAATCATGTCAAACGTGTTCA 59.304 33.333 0.00 0.00 36.53 3.18
2242 3927 6.449956 ACCTTTCCAGGATCCTACTATGTAA 58.550 40.000 15.67 1.62 44.19 2.41
2247 3932 3.958798 CGAACCTTTCCAGGATCCTACTA 59.041 47.826 15.67 0.00 44.19 1.82
2257 3942 1.291877 CTGACGGCGAACCTTTCCAG 61.292 60.000 16.62 3.65 0.00 3.86
2269 3954 1.355971 TCAAACTATTCGCTGACGGC 58.644 50.000 0.00 0.00 40.63 5.68
2302 3987 1.566298 ATCAGTCCTCTTGCACCCCC 61.566 60.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.