Multiple sequence alignment - TraesCS1B01G011700

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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 TraesCS1B01G011700 chr1B 100.000 3083 0 0 1 3083 5688693 5685611 0.000000e+00 5694.0
1 TraesCS1B01G011700 chr1B 93.489 2488 132 16 600 3083 5521158 5518697 0.000000e+00 3670.0
2 TraesCS1B01G011700 chr1B 95.599 1136 44 1 1286 2421 5584955 5583826 0.000000e+00 1816.0
3 TraesCS1B01G011700 chr1B 85.164 1247 124 30 656 1900 22185385 22186572 0.000000e+00 1221.0
4 TraesCS1B01G011700 chr1B 92.202 731 47 7 592 1321 5585887 5585166 0.000000e+00 1026.0
5 TraesCS1B01G011700 chr1B 84.789 710 78 19 1202 1899 6437343 6436652 0.000000e+00 686.0
6 TraesCS1B01G011700 chr1B 82.386 528 51 25 2 515 5521659 5521160 3.680000e-114 422.0
7 TraesCS1B01G011700 chr1B 86.207 174 21 2 2911 3083 5581282 5581111 5.250000e-43 185.0
8 TraesCS1B01G011700 chr1D 93.994 2148 107 13 275 2421 98631 100757 0.000000e+00 3232.0
9 TraesCS1B01G011700 chr1D 91.331 1142 77 11 1288 2421 84815 85942 0.000000e+00 1541.0
10 TraesCS1B01G011700 chr1D 85.942 1252 129 32 656 1899 7156968 7155756 0.000000e+00 1293.0
11 TraesCS1B01G011700 chr1D 84.425 1252 161 22 656 1896 4341407 4342635 0.000000e+00 1201.0
12 TraesCS1B01G011700 chr1D 85.875 977 120 12 345 1319 5356113 5357073 0.000000e+00 1024.0
13 TraesCS1B01G011700 chr1D 85.016 961 121 16 401 1349 84072 85021 0.000000e+00 955.0
14 TraesCS1B01G011700 chr1D 86.456 539 65 5 1883 2415 5357469 5358005 4.430000e-163 584.0
15 TraesCS1B01G011700 chr1D 85.660 523 62 6 1895 2412 5139994 5140508 3.500000e-149 538.0
16 TraesCS1B01G011700 chr1D 84.000 575 66 16 1326 1900 3710391 3709843 2.110000e-146 529.0
17 TraesCS1B01G011700 chr1D 87.531 401 43 6 343 742 7157371 7156977 1.010000e-124 457.0
18 TraesCS1B01G011700 chr1D 87.282 401 44 6 343 742 4341004 4341398 4.690000e-123 451.0
19 TraesCS1B01G011700 chr1D 84.153 366 23 17 1 360 98346 98682 3.840000e-84 322.0
20 TraesCS1B01G011700 chr1D 92.105 190 11 4 3 191 83701 83887 6.560000e-67 265.0
21 TraesCS1B01G011700 chr1D 97.059 136 3 1 36 171 5137681 5137815 8.600000e-56 228.0
22 TraesCS1B01G011700 chr1D 81.618 136 18 6 65 193 102203 102338 4.200000e-19 106.0
23 TraesCS1B01G011700 chr1D 100.000 28 0 0 1 28 5137662 5137689 6.000000e-03 52.8
24 TraesCS1B01G011700 chr1A 89.451 948 85 3 1489 2421 4096336 4095389 0.000000e+00 1182.0
25 TraesCS1B01G011700 chr1A 85.890 1141 105 28 1321 2421 4203001 4201877 0.000000e+00 1164.0
26 TraesCS1B01G011700 chr1A 87.841 880 85 11 345 1211 6516769 6517639 0.000000e+00 1013.0
27 TraesCS1B01G011700 chr1A 90.199 755 63 8 318 1062 4204280 4203527 0.000000e+00 974.0
28 TraesCS1B01G011700 chr1A 88.300 812 82 9 407 1211 6561199 6562004 0.000000e+00 961.0
29 TraesCS1B01G011700 chr1A 89.171 748 75 3 318 1062 4097508 4096764 0.000000e+00 928.0
30 TraesCS1B01G011700 chr1A 86.679 533 69 2 1883 2415 6518137 6518667 9.520000e-165 590.0
31 TraesCS1B01G011700 chr1A 89.286 168 13 5 67 233 4097745 4097582 4.030000e-49 206.0
32 TraesCS1B01G011700 chr1A 94.231 52 3 0 345 396 6561060 6561111 2.550000e-11 80.5
33 TraesCS1B01G011700 chr7D 95.588 476 19 2 2436 2910 5846127 5845653 0.000000e+00 761.0
34 TraesCS1B01G011700 chr7D 94.759 477 24 1 2436 2911 133271122 133270646 0.000000e+00 741.0
35 TraesCS1B01G011700 chr6D 95.378 476 21 1 2436 2910 82870413 82870888 0.000000e+00 756.0
36 TraesCS1B01G011700 chr6B 95.188 478 22 1 2436 2912 469217309 469216832 0.000000e+00 754.0
37 TraesCS1B01G011700 chr3B 95.541 471 20 1 2436 2905 244767169 244767639 0.000000e+00 752.0
38 TraesCS1B01G011700 chr3B 95.158 475 22 1 2436 2910 244747437 244747910 0.000000e+00 749.0
39 TraesCS1B01G011700 chr4D 95.168 476 22 1 2436 2910 433886363 433885888 0.000000e+00 750.0
40 TraesCS1B01G011700 chr2D 94.947 475 23 1 2437 2910 27733548 27733074 0.000000e+00 743.0


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 TraesCS1B01G011700 chr1B 5685611 5688693 3082 True 5694.000000 5694 100.000000 1 3083 1 chr1B.!!$R1 3082
1 TraesCS1B01G011700 chr1B 5518697 5521659 2962 True 2046.000000 3670 87.937500 2 3083 2 chr1B.!!$R3 3081
2 TraesCS1B01G011700 chr1B 22185385 22186572 1187 False 1221.000000 1221 85.164000 656 1900 1 chr1B.!!$F1 1244
3 TraesCS1B01G011700 chr1B 5581111 5585887 4776 True 1009.000000 1816 91.336000 592 3083 3 chr1B.!!$R4 2491
4 TraesCS1B01G011700 chr1B 6436652 6437343 691 True 686.000000 686 84.789000 1202 1899 1 chr1B.!!$R2 697
5 TraesCS1B01G011700 chr1D 98346 102338 3992 False 1220.000000 3232 86.588333 1 2421 3 chr1D.!!$F2 2420
6 TraesCS1B01G011700 chr1D 83701 85942 2241 False 920.333333 1541 89.484000 3 2421 3 chr1D.!!$F1 2418
7 TraesCS1B01G011700 chr1D 7155756 7157371 1615 True 875.000000 1293 86.736500 343 1899 2 chr1D.!!$R2 1556
8 TraesCS1B01G011700 chr1D 4341004 4342635 1631 False 826.000000 1201 85.853500 343 1896 2 chr1D.!!$F3 1553
9 TraesCS1B01G011700 chr1D 5356113 5358005 1892 False 804.000000 1024 86.165500 345 2415 2 chr1D.!!$F5 2070
10 TraesCS1B01G011700 chr1D 3709843 3710391 548 True 529.000000 529 84.000000 1326 1900 1 chr1D.!!$R1 574
11 TraesCS1B01G011700 chr1D 5137662 5140508 2846 False 272.933333 538 94.239667 1 2412 3 chr1D.!!$F4 2411
12 TraesCS1B01G011700 chr1A 4201877 4204280 2403 True 1069.000000 1164 88.044500 318 2421 2 chr1A.!!$R2 2103
13 TraesCS1B01G011700 chr1A 6516769 6518667 1898 False 801.500000 1013 87.260000 345 2415 2 chr1A.!!$F1 2070
14 TraesCS1B01G011700 chr1A 4095389 4097745 2356 True 772.000000 1182 89.302667 67 2421 3 chr1A.!!$R1 2354
15 TraesCS1B01G011700 chr1A 6561060 6562004 944 False 520.750000 961 91.265500 345 1211 2 chr1A.!!$F2 866

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
187 191 0.460311 CGTTGGGCCTAATCTCTCGT 59.540 55.0 4.25 0.0 0.00 4.18 F
914 1735 0.853530 AAGAAAAGAGGTGGTGCCCT 59.146 50.0 0.00 0.0 38.26 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 2102 0.104671 ATGGTGGTTGTTGTTGCTGC 59.895 50.0 0.0 0.0 0.00 5.25 R
2702 6529 0.467106 TAAAGTGCAGCAAGGTGGCA 60.467 50.0 0.0 0.0 35.83 4.92 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
101 103 2.360475 GAGTGTGGGCTGGGCTTC 60.360 66.667 0.00 0.00 0.00 3.86
161 165 0.476338 TGGTGCCCTAACACACACAT 59.524 50.000 0.00 0.00 42.55 3.21
187 191 0.460311 CGTTGGGCCTAATCTCTCGT 59.540 55.000 4.25 0.00 0.00 4.18
191 225 1.120530 GGGCCTAATCTCTCGTTCCA 58.879 55.000 0.84 0.00 0.00 3.53
227 290 3.513909 TCCAGCCCCATCTATCATTTG 57.486 47.619 0.00 0.00 0.00 2.32
302 414 6.550938 ACATAGATGGAACTGATTGTCTCA 57.449 37.500 0.00 0.00 0.00 3.27
428 1132 6.671614 TGTAAGCAATTACCATCCTTTACG 57.328 37.500 0.00 0.00 0.00 3.18
464 1170 5.354767 TCAATGAGTCATGTCATGCTCTAC 58.645 41.667 24.82 13.44 37.24 2.59
473 1179 1.114627 TCATGCTCTACAGGCGTCAT 58.885 50.000 0.00 0.00 0.00 3.06
547 1262 2.685897 CGAGTCTAGAAGAACCCTCCAG 59.314 54.545 0.00 0.00 0.00 3.86
643 1361 4.261994 GCCTTTCTTGTTTATGGCTGACAA 60.262 41.667 0.00 0.00 37.58 3.18
685 1403 6.636705 ACTCGGTTGCAAAAGTGATACTATA 58.363 36.000 0.00 0.00 0.00 1.31
729 1447 7.665559 TGTAAAGTGAATAAGGCAAGTCATCTT 59.334 33.333 0.00 0.00 0.00 2.40
736 1454 6.690194 ATAAGGCAAGTCATCTTTAGCAAG 57.310 37.500 0.00 0.00 0.00 4.01
838 1651 2.767505 AGCTAGTGCAACCTAACACAC 58.232 47.619 0.00 0.00 42.74 3.82
843 1656 4.351874 AGTGCAACCTAACACACTGTAT 57.648 40.909 0.00 0.00 41.63 2.29
914 1735 0.853530 AAGAAAAGAGGTGGTGCCCT 59.146 50.000 0.00 0.00 38.26 5.19
955 1776 8.623903 GGCATGAAGTATAAAGATCATCACAAA 58.376 33.333 0.00 0.00 30.39 2.83
973 1794 4.033129 CACAAACACAAGCATCAAAACCAG 59.967 41.667 0.00 0.00 0.00 4.00
975 1796 2.665165 ACACAAGCATCAAAACCAGGA 58.335 42.857 0.00 0.00 0.00 3.86
1145 1966 3.569250 AACATTATCGCACCAACAACC 57.431 42.857 0.00 0.00 0.00 3.77
1155 1976 0.899019 ACCAACAACCACAACAACCC 59.101 50.000 0.00 0.00 0.00 4.11
1156 1977 0.898320 CCAACAACCACAACAACCCA 59.102 50.000 0.00 0.00 0.00 4.51
1157 1978 1.484240 CCAACAACCACAACAACCCAT 59.516 47.619 0.00 0.00 0.00 4.00
1158 1979 2.482839 CCAACAACCACAACAACCCATC 60.483 50.000 0.00 0.00 0.00 3.51
1159 1980 1.408969 ACAACCACAACAACCCATCC 58.591 50.000 0.00 0.00 0.00 3.51
1160 1981 1.342474 ACAACCACAACAACCCATCCA 60.342 47.619 0.00 0.00 0.00 3.41
1161 1982 1.759445 CAACCACAACAACCCATCCAA 59.241 47.619 0.00 0.00 0.00 3.53
1162 1983 1.408969 ACCACAACAACCCATCCAAC 58.591 50.000 0.00 0.00 0.00 3.77
1163 1984 1.342474 ACCACAACAACCCATCCAACA 60.342 47.619 0.00 0.00 0.00 3.33
1164 1985 1.759445 CCACAACAACCCATCCAACAA 59.241 47.619 0.00 0.00 0.00 2.83
1165 1986 2.482839 CCACAACAACCCATCCAACAAC 60.483 50.000 0.00 0.00 0.00 3.32
1166 1987 2.167281 CACAACAACCCATCCAACAACA 59.833 45.455 0.00 0.00 0.00 3.33
1167 1988 2.834549 ACAACAACCCATCCAACAACAA 59.165 40.909 0.00 0.00 0.00 2.83
1168 1989 3.194062 CAACAACCCATCCAACAACAAC 58.806 45.455 0.00 0.00 0.00 3.32
1169 1990 1.760029 ACAACCCATCCAACAACAACC 59.240 47.619 0.00 0.00 0.00 3.77
1170 1991 1.759445 CAACCCATCCAACAACAACCA 59.241 47.619 0.00 0.00 0.00 3.67
1171 1992 1.408969 ACCCATCCAACAACAACCAC 58.591 50.000 0.00 0.00 0.00 4.16
1172 1993 1.342474 ACCCATCCAACAACAACCACA 60.342 47.619 0.00 0.00 0.00 4.17
1173 1994 1.759445 CCCATCCAACAACAACCACAA 59.241 47.619 0.00 0.00 0.00 3.33
1174 1995 2.482839 CCCATCCAACAACAACCACAAC 60.483 50.000 0.00 0.00 0.00 3.32
1175 1996 2.167281 CCATCCAACAACAACCACAACA 59.833 45.455 0.00 0.00 0.00 3.33
1176 1997 3.368843 CCATCCAACAACAACCACAACAA 60.369 43.478 0.00 0.00 0.00 2.83
1177 1998 4.440880 CATCCAACAACAACCACAACAAT 58.559 39.130 0.00 0.00 0.00 2.71
1178 1999 4.543590 TCCAACAACAACCACAACAATT 57.456 36.364 0.00 0.00 0.00 2.32
1179 2000 4.899502 TCCAACAACAACCACAACAATTT 58.100 34.783 0.00 0.00 0.00 1.82
1180 2001 4.932200 TCCAACAACAACCACAACAATTTC 59.068 37.500 0.00 0.00 0.00 2.17
1181 2002 4.094146 CCAACAACAACCACAACAATTTCC 59.906 41.667 0.00 0.00 0.00 3.13
1182 2003 4.543590 ACAACAACCACAACAATTTCCA 57.456 36.364 0.00 0.00 0.00 3.53
1183 2004 4.249661 ACAACAACCACAACAATTTCCAC 58.750 39.130 0.00 0.00 0.00 4.02
1184 2005 4.248859 CAACAACCACAACAATTTCCACA 58.751 39.130 0.00 0.00 0.00 4.17
1185 2006 4.543590 ACAACCACAACAATTTCCACAA 57.456 36.364 0.00 0.00 0.00 3.33
1186 2007 4.249661 ACAACCACAACAATTTCCACAAC 58.750 39.130 0.00 0.00 0.00 3.32
1187 2008 4.248859 CAACCACAACAATTTCCACAACA 58.751 39.130 0.00 0.00 0.00 3.33
1188 2009 4.122143 ACCACAACAATTTCCACAACAG 57.878 40.909 0.00 0.00 0.00 3.16
1189 2010 2.865551 CCACAACAATTTCCACAACAGC 59.134 45.455 0.00 0.00 0.00 4.40
1190 2011 3.519579 CACAACAATTTCCACAACAGCA 58.480 40.909 0.00 0.00 0.00 4.41
1191 2012 3.931468 CACAACAATTTCCACAACAGCAA 59.069 39.130 0.00 0.00 0.00 3.91
1192 2013 3.932089 ACAACAATTTCCACAACAGCAAC 59.068 39.130 0.00 0.00 0.00 4.17
1193 2014 3.177997 ACAATTTCCACAACAGCAACC 57.822 42.857 0.00 0.00 0.00 3.77
1194 2015 2.499289 ACAATTTCCACAACAGCAACCA 59.501 40.909 0.00 0.00 0.00 3.67
1195 2016 3.134442 ACAATTTCCACAACAGCAACCAT 59.866 39.130 0.00 0.00 0.00 3.55
1196 2017 2.886862 TTTCCACAACAGCAACCATG 57.113 45.000 0.00 0.00 0.00 3.66
1197 2018 1.774110 TTCCACAACAGCAACCATGT 58.226 45.000 0.00 0.00 0.00 3.21
1198 2019 1.774110 TCCACAACAGCAACCATGTT 58.226 45.000 0.00 0.00 41.47 2.71
1199 2020 1.680735 TCCACAACAGCAACCATGTTC 59.319 47.619 0.00 0.00 38.80 3.18
1200 2021 1.408340 CCACAACAGCAACCATGTTCA 59.592 47.619 0.00 0.00 38.80 3.18
1214 2035 4.240888 CCATGTTCACAACAACAACAACA 58.759 39.130 0.00 0.00 45.86 3.33
1215 2036 4.687948 CCATGTTCACAACAACAACAACAA 59.312 37.500 0.00 0.00 45.86 2.83
1216 2037 5.389307 CCATGTTCACAACAACAACAACAAC 60.389 40.000 0.00 0.00 45.86 3.32
1217 2038 4.682787 TGTTCACAACAACAACAACAACA 58.317 34.783 0.00 0.00 38.72 3.33
1218 2039 5.109210 TGTTCACAACAACAACAACAACAA 58.891 33.333 0.00 0.00 38.72 2.83
1229 2050 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1235 2056 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1237 2058 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1238 2059 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1240 2061 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1241 2062 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1242 2063 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1245 2066 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1248 2069 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1262 2083 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1263 2084 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1264 2085 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1265 2086 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1266 2087 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1274 2095 4.271291 ACAACAACAACAACAACAACAACC 59.729 37.500 0.00 0.00 0.00 3.77
1276 2097 4.636249 ACAACAACAACAACAACAACCAT 58.364 34.783 0.00 0.00 0.00 3.55
1277 2098 5.059833 ACAACAACAACAACAACAACCATT 58.940 33.333 0.00 0.00 0.00 3.16
1279 2100 6.876257 ACAACAACAACAACAACAACCATTAT 59.124 30.769 0.00 0.00 0.00 1.28
1280 2101 7.064016 ACAACAACAACAACAACAACCATTATC 59.936 33.333 0.00 0.00 0.00 1.75
1281 2102 5.746245 ACAACAACAACAACAACCATTATCG 59.254 36.000 0.00 0.00 0.00 2.92
1283 2104 4.202060 ACAACAACAACAACCATTATCGCA 60.202 37.500 0.00 0.00 0.00 5.10
1284 2105 4.159377 ACAACAACAACCATTATCGCAG 57.841 40.909 0.00 0.00 0.00 5.18
1285 2106 2.916716 CAACAACAACCATTATCGCAGC 59.083 45.455 0.00 0.00 0.00 5.25
1286 2107 2.158559 ACAACAACCATTATCGCAGCA 58.841 42.857 0.00 0.00 0.00 4.41
1287 2108 2.556189 ACAACAACCATTATCGCAGCAA 59.444 40.909 0.00 0.00 0.00 3.91
1289 2110 2.158559 ACAACCATTATCGCAGCAACA 58.841 42.857 0.00 0.00 0.00 3.33
1295 2116 2.697431 TTATCGCAGCAACAACAACC 57.303 45.000 0.00 0.00 0.00 3.77
1300 2121 0.104671 GCAGCAACAACAACCACCAT 59.895 50.000 0.00 0.00 0.00 3.55
1302 2123 2.903798 CAGCAACAACAACCACCATTT 58.096 42.857 0.00 0.00 0.00 2.32
1305 2126 3.055530 AGCAACAACAACCACCATTTTCA 60.056 39.130 0.00 0.00 0.00 2.69
1306 2127 3.063316 GCAACAACAACCACCATTTTCAC 59.937 43.478 0.00 0.00 0.00 3.18
1307 2128 4.248859 CAACAACAACCACCATTTTCACA 58.751 39.130 0.00 0.00 0.00 3.58
1308 2129 4.122143 ACAACAACCACCATTTTCACAG 57.878 40.909 0.00 0.00 0.00 3.66
1319 2140 3.309410 CCATTTTCACAGCAACAACAACC 59.691 43.478 0.00 0.00 0.00 3.77
1327 2148 3.269178 CAGCAACAACAACCACCATTTT 58.731 40.909 0.00 0.00 0.00 1.82
1380 3330 1.531149 CAACCAGTTCTACCGCAACAG 59.469 52.381 0.00 0.00 0.00 3.16
1493 3512 3.369147 CCATTTTCGCAACAACAACAACA 59.631 39.130 0.00 0.00 0.00 3.33
1494 3513 4.143030 CCATTTTCGCAACAACAACAACAA 60.143 37.500 0.00 0.00 0.00 2.83
1495 3514 4.376450 TTTTCGCAACAACAACAACAAC 57.624 36.364 0.00 0.00 0.00 3.32
1496 3515 2.706555 TCGCAACAACAACAACAACA 57.293 40.000 0.00 0.00 0.00 3.33
1519 3559 4.479158 ACCAATTCTACCACAACAACCAT 58.521 39.130 0.00 0.00 0.00 3.55
1544 3584 2.999507 TCGCAACAACAACAACAACT 57.000 40.000 0.00 0.00 0.00 3.16
1599 3642 1.874231 CCATCTATCTTGCAGCAGCTG 59.126 52.381 18.93 18.93 42.74 4.24
1808 3878 2.159448 TGCAAGAACAACAACAGGTTCG 60.159 45.455 0.00 0.00 46.09 3.95
2000 4130 2.590092 GCTCCGTACCCTGCCAAT 59.410 61.111 0.00 0.00 0.00 3.16
2031 4161 3.063452 GTGTCAATGTGCCGTTGTATAGG 59.937 47.826 6.92 0.00 32.76 2.57
2052 4182 1.144913 ACCACCACTAGTGTGCCATTT 59.855 47.619 21.18 0.00 45.74 2.32
2285 4419 3.055891 TGTGTGGATGTCGATCTGATTGT 60.056 43.478 4.85 0.00 0.00 2.71
2450 5167 4.094739 CCGTGTCAATGTTTCATGCTATGA 59.905 41.667 0.00 0.00 37.55 2.15
2514 5231 6.068010 TGCAATAGGGGTTAATCATAAGTGG 58.932 40.000 0.00 0.00 0.00 4.00
2522 5239 6.303839 GGGTTAATCATAAGTGGGATGCTTA 58.696 40.000 0.00 0.00 33.59 3.09
2536 5253 4.202441 GGATGCTTATCCAAGAAAGAGCA 58.798 43.478 1.55 0.00 43.35 4.26
2540 5257 5.994250 TGCTTATCCAAGAAAGAGCAGTAT 58.006 37.500 0.00 0.00 35.43 2.12
2542 5259 5.468409 GCTTATCCAAGAAAGAGCAGTATCC 59.532 44.000 0.00 0.00 33.20 2.59
2565 5409 1.476833 GCACCGGTCCATCCACATATT 60.477 52.381 2.59 0.00 35.57 1.28
2702 6529 5.163602 TGTCGTTTGCTACAAAAAGGATTGT 60.164 36.000 0.00 0.00 45.14 2.71
2728 6555 5.156355 CACCTTGCTGCACTTTATTTACTG 58.844 41.667 0.00 0.00 0.00 2.74
2838 7186 3.695830 ACCGCTTGTCATTTCCTTCTA 57.304 42.857 0.00 0.00 0.00 2.10
2848 7196 5.103687 GTCATTTCCTTCTACTCCTCGTTC 58.896 45.833 0.00 0.00 0.00 3.95
2880 7228 7.760437 ACACTCTTACTTATCGAAAGGACTAC 58.240 38.462 10.65 0.00 0.00 2.73
2938 7421 2.268920 CAGGCGGTGGCTACATGT 59.731 61.111 2.69 2.69 36.44 3.21
3046 7530 4.823442 TCTTGTTGAAGACACATGCAGATT 59.177 37.500 0.00 0.00 38.18 2.40
3050 7534 3.273434 TGAAGACACATGCAGATTAGCC 58.727 45.455 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 4.760047 CGGAGGCCCCAACGTCAG 62.760 72.222 0.00 0.00 34.14 3.51
161 165 0.538118 ATTAGGCCCAACGTAAGCGA 59.462 50.000 0.00 0.00 45.62 4.93
355 590 4.634883 TCCTAACTCTAGACACGTCATCAC 59.365 45.833 0.00 0.00 0.00 3.06
428 1132 6.817765 TGACTCATTGAATTCCCTTTACAC 57.182 37.500 2.27 0.00 0.00 2.90
443 1149 5.349061 TGTAGAGCATGACATGACTCATT 57.651 39.130 27.07 17.17 36.53 2.57
464 1170 5.699915 AGATGATAAGATGAAATGACGCCTG 59.300 40.000 0.00 0.00 0.00 4.85
547 1262 2.158841 TCGATTGTTAAAGCCTTGCGTC 59.841 45.455 0.00 0.00 0.00 5.19
562 1277 4.153117 GGGCTGTTAAGATATGCTCGATTG 59.847 45.833 0.00 0.00 0.00 2.67
685 1403 7.171508 CACTTTACATGTCACACACTTATCTGT 59.828 37.037 0.00 0.00 0.00 3.41
729 1447 7.739825 AGTATAGAAATCCTGATGCTTGCTAA 58.260 34.615 0.00 0.00 0.00 3.09
736 1454 7.559590 ACACAAAGTATAGAAATCCTGATGC 57.440 36.000 0.00 0.00 0.00 3.91
811 1621 0.669318 GGTTGCACTAGCTACACGCA 60.669 55.000 3.45 3.45 46.27 5.24
843 1656 9.722184 TTTGGATGCATCTAAAATGATTTTTGA 57.278 25.926 29.38 15.04 38.40 2.69
914 1735 7.316393 ACTTCATGCCTATTTATAGTAGCCA 57.684 36.000 0.00 0.00 0.00 4.75
955 1776 2.665165 TCCTGGTTTTGATGCTTGTGT 58.335 42.857 0.00 0.00 0.00 3.72
993 1814 1.630878 AGGAAGGTCTTCATGGTGGAC 59.369 52.381 12.13 0.00 41.20 4.02
1145 1966 2.167281 TGTTGTTGGATGGGTTGTTGTG 59.833 45.455 0.00 0.00 0.00 3.33
1155 1976 3.516981 TGTTGTGGTTGTTGTTGGATG 57.483 42.857 0.00 0.00 0.00 3.51
1156 1977 4.751767 ATTGTTGTGGTTGTTGTTGGAT 57.248 36.364 0.00 0.00 0.00 3.41
1157 1978 4.543590 AATTGTTGTGGTTGTTGTTGGA 57.456 36.364 0.00 0.00 0.00 3.53
1158 1979 4.094146 GGAAATTGTTGTGGTTGTTGTTGG 59.906 41.667 0.00 0.00 0.00 3.77
1159 1980 4.692625 TGGAAATTGTTGTGGTTGTTGTTG 59.307 37.500 0.00 0.00 0.00 3.33
1160 1981 4.693095 GTGGAAATTGTTGTGGTTGTTGTT 59.307 37.500 0.00 0.00 0.00 2.83
1161 1982 4.249661 GTGGAAATTGTTGTGGTTGTTGT 58.750 39.130 0.00 0.00 0.00 3.32
1162 1983 4.248859 TGTGGAAATTGTTGTGGTTGTTG 58.751 39.130 0.00 0.00 0.00 3.33
1163 1984 4.543590 TGTGGAAATTGTTGTGGTTGTT 57.456 36.364 0.00 0.00 0.00 2.83
1164 1985 4.249661 GTTGTGGAAATTGTTGTGGTTGT 58.750 39.130 0.00 0.00 0.00 3.32
1165 1986 4.248859 TGTTGTGGAAATTGTTGTGGTTG 58.751 39.130 0.00 0.00 0.00 3.77
1166 1987 4.502962 CTGTTGTGGAAATTGTTGTGGTT 58.497 39.130 0.00 0.00 0.00 3.67
1167 1988 3.678529 GCTGTTGTGGAAATTGTTGTGGT 60.679 43.478 0.00 0.00 0.00 4.16
1168 1989 2.865551 GCTGTTGTGGAAATTGTTGTGG 59.134 45.455 0.00 0.00 0.00 4.17
1169 1990 3.519579 TGCTGTTGTGGAAATTGTTGTG 58.480 40.909 0.00 0.00 0.00 3.33
1170 1991 3.883830 TGCTGTTGTGGAAATTGTTGT 57.116 38.095 0.00 0.00 0.00 3.32
1171 1992 3.309410 GGTTGCTGTTGTGGAAATTGTTG 59.691 43.478 0.00 0.00 0.00 3.33
1172 1993 3.055530 TGGTTGCTGTTGTGGAAATTGTT 60.056 39.130 0.00 0.00 0.00 2.83
1173 1994 2.499289 TGGTTGCTGTTGTGGAAATTGT 59.501 40.909 0.00 0.00 0.00 2.71
1174 1995 3.176552 TGGTTGCTGTTGTGGAAATTG 57.823 42.857 0.00 0.00 0.00 2.32
1175 1996 3.134442 ACATGGTTGCTGTTGTGGAAATT 59.866 39.130 0.00 0.00 0.00 1.82
1176 1997 2.699846 ACATGGTTGCTGTTGTGGAAAT 59.300 40.909 0.00 0.00 0.00 2.17
1177 1998 2.106566 ACATGGTTGCTGTTGTGGAAA 58.893 42.857 0.00 0.00 0.00 3.13
1178 1999 1.774110 ACATGGTTGCTGTTGTGGAA 58.226 45.000 0.00 0.00 0.00 3.53
1179 2000 1.680735 GAACATGGTTGCTGTTGTGGA 59.319 47.619 0.00 0.00 36.98 4.02
1180 2001 1.408340 TGAACATGGTTGCTGTTGTGG 59.592 47.619 0.00 0.00 36.98 4.17
1181 2002 2.159268 TGTGAACATGGTTGCTGTTGTG 60.159 45.455 0.00 0.00 36.98 3.33
1182 2003 2.098614 TGTGAACATGGTTGCTGTTGT 58.901 42.857 0.00 0.00 36.98 3.32
1183 2004 2.859538 GTTGTGAACATGGTTGCTGTTG 59.140 45.455 0.00 0.00 36.98 3.33
1184 2005 2.495270 TGTTGTGAACATGGTTGCTGTT 59.505 40.909 0.00 0.00 39.46 3.16
1185 2006 2.098614 TGTTGTGAACATGGTTGCTGT 58.901 42.857 0.00 0.00 36.25 4.40
1186 2007 2.859538 GTTGTTGTGAACATGGTTGCTG 59.140 45.455 0.00 0.00 41.79 4.41
1187 2008 2.495270 TGTTGTTGTGAACATGGTTGCT 59.505 40.909 0.00 0.00 41.79 3.91
1188 2009 2.886081 TGTTGTTGTGAACATGGTTGC 58.114 42.857 0.00 0.00 41.79 4.17
1189 2010 4.240888 TGTTGTTGTTGTGAACATGGTTG 58.759 39.130 0.00 0.00 41.79 3.77
1190 2011 4.527509 TGTTGTTGTTGTGAACATGGTT 57.472 36.364 0.00 0.00 41.79 3.67
1191 2012 4.241681 GTTGTTGTTGTTGTGAACATGGT 58.758 39.130 0.00 0.00 41.79 3.55
1192 2013 4.240888 TGTTGTTGTTGTTGTGAACATGG 58.759 39.130 0.00 0.00 41.79 3.66
1193 2014 5.176406 TGTTGTTGTTGTTGTTGTGAACATG 59.824 36.000 0.00 0.00 41.79 3.21
1194 2015 5.292765 TGTTGTTGTTGTTGTTGTGAACAT 58.707 33.333 0.00 0.00 41.79 2.71
1195 2016 4.682787 TGTTGTTGTTGTTGTTGTGAACA 58.317 34.783 0.00 0.00 40.21 3.18
1196 2017 5.005779 TGTTGTTGTTGTTGTTGTTGTGAAC 59.994 36.000 0.00 0.00 0.00 3.18
1197 2018 5.109210 TGTTGTTGTTGTTGTTGTTGTGAA 58.891 33.333 0.00 0.00 0.00 3.18
1198 2019 4.682787 TGTTGTTGTTGTTGTTGTTGTGA 58.317 34.783 0.00 0.00 0.00 3.58
1199 2020 5.193936 GTTGTTGTTGTTGTTGTTGTTGTG 58.806 37.500 0.00 0.00 0.00 3.33
1200 2021 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1214 2035 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1215 2036 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1216 2037 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1217 2038 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1218 2039 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1229 2050 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1235 2056 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1237 2058 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1238 2059 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1240 2061 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1241 2062 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
1242 2063 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1245 2066 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1248 2069 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
1262 2083 4.545610 CTGCGATAATGGTTGTTGTTGTT 58.454 39.130 0.00 0.00 0.00 2.83
1263 2084 3.611530 GCTGCGATAATGGTTGTTGTTGT 60.612 43.478 0.00 0.00 0.00 3.32
1264 2085 2.916716 GCTGCGATAATGGTTGTTGTTG 59.083 45.455 0.00 0.00 0.00 3.33
1265 2086 2.556189 TGCTGCGATAATGGTTGTTGTT 59.444 40.909 0.00 0.00 0.00 2.83
1266 2087 2.158559 TGCTGCGATAATGGTTGTTGT 58.841 42.857 0.00 0.00 0.00 3.32
1274 2095 2.916716 GGTTGTTGTTGCTGCGATAATG 59.083 45.455 2.26 0.00 0.00 1.90
1276 2097 1.950216 TGGTTGTTGTTGCTGCGATAA 59.050 42.857 0.00 0.00 0.00 1.75
1277 2098 1.265635 GTGGTTGTTGTTGCTGCGATA 59.734 47.619 0.00 0.00 0.00 2.92
1279 2100 1.431440 GTGGTTGTTGTTGCTGCGA 59.569 52.632 0.00 0.00 0.00 5.10
1280 2101 1.588667 GGTGGTTGTTGTTGCTGCG 60.589 57.895 0.00 0.00 0.00 5.18
1281 2102 0.104671 ATGGTGGTTGTTGTTGCTGC 59.895 50.000 0.00 0.00 0.00 5.25
1283 2104 3.055530 TGAAAATGGTGGTTGTTGTTGCT 60.056 39.130 0.00 0.00 0.00 3.91
1284 2105 3.063316 GTGAAAATGGTGGTTGTTGTTGC 59.937 43.478 0.00 0.00 0.00 4.17
1285 2106 4.248859 TGTGAAAATGGTGGTTGTTGTTG 58.751 39.130 0.00 0.00 0.00 3.33
1286 2107 4.502962 CTGTGAAAATGGTGGTTGTTGTT 58.497 39.130 0.00 0.00 0.00 2.83
1287 2108 3.678529 GCTGTGAAAATGGTGGTTGTTGT 60.679 43.478 0.00 0.00 0.00 3.32
1289 2110 2.499289 TGCTGTGAAAATGGTGGTTGTT 59.501 40.909 0.00 0.00 0.00 2.83
1295 2116 3.519579 TGTTGTTGCTGTGAAAATGGTG 58.480 40.909 0.00 0.00 0.00 4.17
1300 2121 3.321497 GTGGTTGTTGTTGCTGTGAAAA 58.679 40.909 0.00 0.00 0.00 2.29
1302 2123 1.203523 GGTGGTTGTTGTTGCTGTGAA 59.796 47.619 0.00 0.00 0.00 3.18
1305 2126 1.484038 ATGGTGGTTGTTGTTGCTGT 58.516 45.000 0.00 0.00 0.00 4.40
1306 2127 2.600470 AATGGTGGTTGTTGTTGCTG 57.400 45.000 0.00 0.00 0.00 4.41
1307 2128 3.055530 TGAAAATGGTGGTTGTTGTTGCT 60.056 39.130 0.00 0.00 0.00 3.91
1308 2129 3.063316 GTGAAAATGGTGGTTGTTGTTGC 59.937 43.478 0.00 0.00 0.00 4.17
1319 2140 2.865551 GGTTGTTGCTGTGAAAATGGTG 59.134 45.455 0.00 0.00 0.00 4.17
1327 2148 1.774110 AATGGTGGTTGTTGCTGTGA 58.226 45.000 0.00 0.00 0.00 3.58
1380 3330 0.994263 GTTGCTGCGAAAATGATGGC 59.006 50.000 0.00 0.00 0.00 4.40
1493 3512 5.394773 GGTTGTTGTGGTAGAATTGGTTGTT 60.395 40.000 0.00 0.00 0.00 2.83
1494 3513 4.098807 GGTTGTTGTGGTAGAATTGGTTGT 59.901 41.667 0.00 0.00 0.00 3.32
1495 3514 4.098654 TGGTTGTTGTGGTAGAATTGGTTG 59.901 41.667 0.00 0.00 0.00 3.77
1496 3515 4.282496 TGGTTGTTGTGGTAGAATTGGTT 58.718 39.130 0.00 0.00 0.00 3.67
1519 3559 4.237724 TGTTGTTGTTGTTGCGAAAATGA 58.762 34.783 0.00 0.00 0.00 2.57
1544 3584 5.409214 GGTATTTGTTGTTGCGGTAGAACTA 59.591 40.000 0.00 0.00 0.00 2.24
1599 3642 3.018423 AGGAATACCTTGCATGGGTTC 57.982 47.619 21.67 21.35 45.36 3.62
1808 3878 1.839424 CTGAGTTTGGATGGAACCCC 58.161 55.000 0.00 0.00 0.00 4.95
2000 4130 0.873721 CACATTGACACGGCACATCA 59.126 50.000 0.00 0.00 0.00 3.07
2052 4182 3.414136 AACTCCAGTGCCAACGCCA 62.414 57.895 0.00 0.00 0.00 5.69
2285 4419 5.710513 AACTTATGAACTTGCAAGCATGA 57.289 34.783 26.27 16.65 0.00 3.07
2468 5185 2.622942 AGCATCCGCAACTCAAAAGAAA 59.377 40.909 0.00 0.00 42.27 2.52
2476 5193 1.580942 TTGCAAGCATCCGCAACTC 59.419 52.632 0.00 0.00 42.93 3.01
2477 5194 3.762293 TTGCAAGCATCCGCAACT 58.238 50.000 0.00 0.00 42.93 3.16
2522 5239 5.435291 CTTGGATACTGCTCTTTCTTGGAT 58.565 41.667 0.00 0.00 37.61 3.41
2536 5253 0.907704 TGGACCGGTGCTTGGATACT 60.908 55.000 27.28 0.00 37.61 2.12
2540 5257 2.668632 GATGGACCGGTGCTTGGA 59.331 61.111 27.28 7.02 0.00 3.53
2542 5259 2.040544 GTGGATGGACCGGTGCTTG 61.041 63.158 27.28 0.00 42.61 4.01
2587 5431 6.539826 AGTTTTCATCACGCTCATATGATTCA 59.460 34.615 5.72 0.00 33.18 2.57
2702 6529 0.467106 TAAAGTGCAGCAAGGTGGCA 60.467 50.000 0.00 0.00 35.83 4.92
2728 6555 4.742659 TCGTAACGGGTAACAAGTAACAAC 59.257 41.667 0.00 0.00 39.74 3.32
2744 6571 8.437742 AGTTTTGTGATAAGGTAATTCGTAACG 58.562 33.333 0.00 0.00 0.00 3.18
2838 7186 1.168407 TGTCGAACCGAACGAGGAGT 61.168 55.000 0.00 0.00 40.37 3.85
2848 7196 4.027065 CGATAAGTAAGAGTGTCGAACCG 58.973 47.826 0.00 0.00 0.00 4.44
2880 7228 3.005897 CCACAAGTGTAGGGGATCTATCG 59.994 52.174 0.00 0.00 0.00 2.92
2938 7421 1.604308 TCGACCACCCTACTTCGCA 60.604 57.895 0.00 0.00 0.00 5.10
3032 7516 1.945387 CGGCTAATCTGCATGTGTCT 58.055 50.000 0.00 0.00 34.04 3.41


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

AutoCloner maintained by Alex Coulton.