Multiple sequence alignment - TraesCS7A01G119700

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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 TraesCS7A01G119700 chr7A 100.000 2411 0 0 1 2411 77149103 77151513 0.000000e+00 4453.0
1 TraesCS7A01G119700 chr7D 89.266 1593 132 29 1 1577 73118123 73116554 0.000000e+00 1958.0
2 TraesCS7A01G119700 chr7D 91.267 813 55 10 989 1789 72128484 72129292 0.000000e+00 1094.0
3 TraesCS7A01G119700 chr7D 90.960 708 50 10 999 1697 71864511 71863809 0.000000e+00 941.0
4 TraesCS7A01G119700 chr7D 92.201 577 37 5 996 1567 71812574 71813147 0.000000e+00 809.0
5 TraesCS7A01G119700 chrUn 90.890 933 66 7 975 1889 82605087 82604156 0.000000e+00 1234.0
6 TraesCS7A01G119700 chrUn 91.358 810 54 10 998 1795 273470864 273470059 0.000000e+00 1094.0
7 TraesCS7A01G119700 chrUn 88.128 935 75 16 975 1889 84317817 84316899 0.000000e+00 1079.0
8 TraesCS7A01G119700 chrUn 91.503 612 40 5 975 1576 82565919 82566528 0.000000e+00 832.0
9 TraesCS7A01G119700 chrUn 91.478 575 42 4 997 1567 84331102 84330531 0.000000e+00 784.0
10 TraesCS7A01G119700 chr7B 89.171 905 74 13 997 1881 14866447 14865547 0.000000e+00 1107.0
11 TraesCS7A01G119700 chr7B 90.926 540 38 8 975 1509 14788524 14787991 0.000000e+00 715.0
12 TraesCS7A01G119700 chr7B 82.134 403 39 16 1893 2283 14981222 14981603 5.000000e-82 315.0
13 TraesCS7A01G119700 chr7B 82.031 128 10 6 2292 2411 14981643 14981765 1.970000e-16 97.1
14 TraesCS7A01G119700 chr3B 73.226 310 63 16 31 325 815284282 815284586 7.100000e-16 95.3
15 TraesCS7A01G119700 chr3D 78.899 109 14 4 334 440 308983351 308983250 5.560000e-07 65.8


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 TraesCS7A01G119700 chr7A 77149103 77151513 2410 False 4453.00 4453 100.0000 1 2411 1 chr7A.!!$F1 2410
1 TraesCS7A01G119700 chr7D 73116554 73118123 1569 True 1958.00 1958 89.2660 1 1577 1 chr7D.!!$R2 1576
2 TraesCS7A01G119700 chr7D 72128484 72129292 808 False 1094.00 1094 91.2670 989 1789 1 chr7D.!!$F2 800
3 TraesCS7A01G119700 chr7D 71863809 71864511 702 True 941.00 941 90.9600 999 1697 1 chr7D.!!$R1 698
4 TraesCS7A01G119700 chr7D 71812574 71813147 573 False 809.00 809 92.2010 996 1567 1 chr7D.!!$F1 571
5 TraesCS7A01G119700 chrUn 82604156 82605087 931 True 1234.00 1234 90.8900 975 1889 1 chrUn.!!$R1 914
6 TraesCS7A01G119700 chrUn 273470059 273470864 805 True 1094.00 1094 91.3580 998 1795 1 chrUn.!!$R4 797
7 TraesCS7A01G119700 chrUn 84316899 84317817 918 True 1079.00 1079 88.1280 975 1889 1 chrUn.!!$R2 914
8 TraesCS7A01G119700 chrUn 82565919 82566528 609 False 832.00 832 91.5030 975 1576 1 chrUn.!!$F1 601
9 TraesCS7A01G119700 chrUn 84330531 84331102 571 True 784.00 784 91.4780 997 1567 1 chrUn.!!$R3 570
10 TraesCS7A01G119700 chr7B 14865547 14866447 900 True 1107.00 1107 89.1710 997 1881 1 chr7B.!!$R2 884
11 TraesCS7A01G119700 chr7B 14787991 14788524 533 True 715.00 715 90.9260 975 1509 1 chr7B.!!$R1 534
12 TraesCS7A01G119700 chr7B 14981222 14981765 543 False 206.05 315 82.0825 1893 2411 2 chr7B.!!$F1 518

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
480 484 0.038166 TGAGGTGCCCAAATGAGTCC 59.962 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1774 0.234625 GAATCACGCAGCGACAAACA 59.765 50.0 24.65 0.0 0.0 2.83 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
60 61 2.050895 CTACGCGCCGGATGAGAG 60.051 66.667 5.05 0.00 0.00 3.20
75 76 2.124695 GAGGGGCCCGACAACATC 60.125 66.667 18.95 2.98 0.00 3.06
127 129 2.534903 GCCCCGAAGCGTTATCTGC 61.535 63.158 0.00 0.00 0.00 4.26
136 138 1.141881 CGTTATCTGCTGTCGCCCT 59.858 57.895 0.00 0.00 34.43 5.19
144 146 1.300542 GCTGTCGCCCTGATCTAGC 60.301 63.158 0.00 0.00 0.00 3.42
187 190 0.615331 AGAGCGACCACATCCATGTT 59.385 50.000 0.00 0.00 39.39 2.71
196 199 4.012374 ACCACATCCATGTTGAAGTCATC 58.988 43.478 0.00 0.00 39.39 2.92
197 200 4.011698 CCACATCCATGTTGAAGTCATCA 58.988 43.478 0.00 0.00 39.39 3.07
204 207 4.392754 CCATGTTGAAGTCATCATTGTCGA 59.607 41.667 2.73 0.00 38.03 4.20
209 212 4.641396 TGAAGTCATCATTGTCGAAACCT 58.359 39.130 0.00 0.00 31.50 3.50
212 215 3.997021 AGTCATCATTGTCGAAACCTGTC 59.003 43.478 0.00 0.00 0.00 3.51
220 223 1.597854 CGAAACCTGTCCTGCTGCA 60.598 57.895 0.88 0.88 0.00 4.41
224 227 1.699054 AACCTGTCCTGCTGCAGTCA 61.699 55.000 26.41 21.92 0.00 3.41
225 228 1.071987 CCTGTCCTGCTGCAGTCAA 59.928 57.895 26.41 10.31 0.00 3.18
248 251 5.614324 ACGACATAGATCAGATTGGGAAA 57.386 39.130 0.00 0.00 0.00 3.13
258 261 3.010584 TCAGATTGGGAAAGAAGAAGGGG 59.989 47.826 0.00 0.00 0.00 4.79
260 263 0.251165 TTGGGAAAGAAGAAGGGGCG 60.251 55.000 0.00 0.00 0.00 6.13
265 268 1.210722 GAAAGAAGAAGGGGCGGAGAT 59.789 52.381 0.00 0.00 0.00 2.75
267 270 2.176247 AGAAGAAGGGGCGGAGATAA 57.824 50.000 0.00 0.00 0.00 1.75
277 280 0.603975 GCGGAGATAATGGAGTGGCC 60.604 60.000 0.00 0.00 37.10 5.36
283 286 0.475906 ATAATGGAGTGGCCTGGAGC 59.524 55.000 3.32 0.00 42.60 4.70
294 297 2.716017 CCTGGAGCGGTCTGAGGTC 61.716 68.421 15.18 0.00 35.57 3.85
305 309 3.487711 CGGTCTGAGGTCTAGTTTCATCG 60.488 52.174 0.00 0.00 0.00 3.84
307 311 3.024547 TCTGAGGTCTAGTTTCATCGGG 58.975 50.000 0.00 0.00 0.00 5.14
317 321 4.519906 AGTTTCATCGGGTTGGGATATT 57.480 40.909 0.00 0.00 0.00 1.28
328 332 2.758423 GTTGGGATATTTGTGGGGTCAC 59.242 50.000 0.00 0.00 43.87 3.67
414 418 4.142271 CGCCTCATATCCTTCCTACATCTC 60.142 50.000 0.00 0.00 0.00 2.75
420 424 1.063942 TCCTTCCTACATCTCGGCTGA 60.064 52.381 0.00 0.00 0.00 4.26
423 427 3.388308 CTTCCTACATCTCGGCTGAATG 58.612 50.000 13.09 13.09 0.00 2.67
432 436 1.002134 CGGCTGAATGTGAGGGGTT 60.002 57.895 0.00 0.00 0.00 4.11
433 437 1.026718 CGGCTGAATGTGAGGGGTTC 61.027 60.000 0.00 0.00 0.00 3.62
436 440 0.324943 CTGAATGTGAGGGGTTCGGT 59.675 55.000 0.00 0.00 0.00 4.69
472 476 2.203422 CCGGTTTGAGGTGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
480 484 0.038166 TGAGGTGCCCAAATGAGTCC 59.962 55.000 0.00 0.00 0.00 3.85
485 489 3.161866 GGTGCCCAAATGAGTCCTTTTA 58.838 45.455 0.00 0.00 0.00 1.52
500 504 4.331992 GTCCTTTTATTCTTACCGGTCAGC 59.668 45.833 12.40 0.00 0.00 4.26
544 550 1.223487 GATTTGGGGCGCCTGACTA 59.777 57.895 28.56 11.26 0.00 2.59
569 575 5.794894 AGAAGCTTTTACATTCTCTTCCGA 58.205 37.500 0.00 0.00 32.62 4.55
577 583 3.265791 ACATTCTCTTCCGAGTCAATGC 58.734 45.455 0.00 0.00 36.04 3.56
583 589 3.589988 TCTTCCGAGTCAATGCTCTTTC 58.410 45.455 0.00 0.00 33.55 2.62
593 599 3.758554 TCAATGCTCTTTCTTTGCTACCC 59.241 43.478 0.00 0.00 0.00 3.69
594 600 3.728385 ATGCTCTTTCTTTGCTACCCT 57.272 42.857 0.00 0.00 0.00 4.34
596 602 2.371841 TGCTCTTTCTTTGCTACCCTCA 59.628 45.455 0.00 0.00 0.00 3.86
597 603 3.181445 TGCTCTTTCTTTGCTACCCTCAA 60.181 43.478 0.00 0.00 0.00 3.02
638 647 2.676342 GCTGAATTCCGGTGAAATACGT 59.324 45.455 0.00 0.00 33.32 3.57
650 660 6.018588 CCGGTGAAATACGTATCAGCAAATTA 60.019 38.462 21.69 0.00 42.62 1.40
662 672 4.286910 TCAGCAAATTAAAACGAGCACAC 58.713 39.130 0.00 0.00 0.00 3.82
678 688 5.791974 CGAGCACACATTAGAAATTGTTCTG 59.208 40.000 0.00 0.00 44.12 3.02
701 711 2.833913 CCTGGCCCACTCACCAAGT 61.834 63.158 0.00 0.00 39.44 3.16
782 792 1.700042 ATCCCTCCCTGATCCAACGC 61.700 60.000 0.00 0.00 0.00 4.84
789 799 2.933287 TGATCCAACGCCCCACCT 60.933 61.111 0.00 0.00 0.00 4.00
834 844 2.813179 CGCGAAGATCCGGCCAAAG 61.813 63.158 0.00 0.00 0.00 2.77
866 876 1.432270 GGCTCGAAATTCTCAGGCCG 61.432 60.000 0.00 0.00 33.51 6.13
888 898 1.620259 GCCATCCTCCAAATCCCCA 59.380 57.895 0.00 0.00 0.00 4.96
889 899 0.756815 GCCATCCTCCAAATCCCCAC 60.757 60.000 0.00 0.00 0.00 4.61
901 911 2.084121 ATCCCCACCCCCTTCTTAAA 57.916 50.000 0.00 0.00 0.00 1.52
932 942 0.912487 TCCGGCTAATCCCCACAACT 60.912 55.000 0.00 0.00 0.00 3.16
935 945 1.743772 CGGCTAATCCCCACAACTCAG 60.744 57.143 0.00 0.00 0.00 3.35
936 946 1.559682 GGCTAATCCCCACAACTCAGA 59.440 52.381 0.00 0.00 0.00 3.27
937 947 2.173569 GGCTAATCCCCACAACTCAGAT 59.826 50.000 0.00 0.00 0.00 2.90
964 974 0.744771 GCACCCGATCTCCCAAGAAC 60.745 60.000 0.00 0.00 34.49 3.01
968 978 1.676014 CCCGATCTCCCAAGAACACAC 60.676 57.143 0.00 0.00 34.49 3.82
979 989 0.469917 AGAACACACCACCACCAGAG 59.530 55.000 0.00 0.00 0.00 3.35
1209 1219 2.930562 AAGCTCCCCTTCCAGCGT 60.931 61.111 0.00 0.00 40.84 5.07
1272 1282 2.752238 CAGTCCTCCGCCGTCTCT 60.752 66.667 0.00 0.00 0.00 3.10
1436 1452 1.449601 CTGGTCGCCGGTAATGCTT 60.450 57.895 1.90 0.00 0.00 3.91
1453 1473 1.127582 GCTTGCTAGCTGTTCTTGTCG 59.872 52.381 17.23 0.00 44.27 4.35
1462 1482 2.868044 GCTGTTCTTGTCGTGTGATCCT 60.868 50.000 0.00 0.00 0.00 3.24
1471 1499 1.568612 CGTGTGATCCTGGTGTGTGC 61.569 60.000 0.00 0.00 0.00 4.57
1495 1531 1.003866 GTGCTTCTGTTTGTCGGTGTC 60.004 52.381 0.00 0.00 0.00 3.67
1509 1545 2.685897 TCGGTGTCGATATGATGTGTCA 59.314 45.455 0.00 0.00 40.88 3.58
1532 1569 3.903714 TCTGGTCCTATGTATGGTGATGG 59.096 47.826 0.00 0.00 0.00 3.51
1592 1636 9.327529 GATCTGATGCTCGAATGAATTTAATTC 57.672 33.333 10.47 10.47 39.70 2.17
1637 1681 1.333308 TGCAATGGTGTTCTTGTCACG 59.667 47.619 0.00 0.00 36.76 4.35
1654 1702 1.018910 ACGTGTACCAAGTTGTTGCC 58.981 50.000 1.45 0.00 31.64 4.52
1829 1886 4.141711 TGTGATTCTGAACTATGGTAGGGC 60.142 45.833 0.00 0.00 0.00 5.19
1877 1947 4.574421 ACGACATGTGTTGTGATTCTGAAA 59.426 37.500 1.15 0.00 40.93 2.69
1883 1953 8.239314 ACATGTGTTGTGATTCTGAAATATGTC 58.761 33.333 0.00 0.00 37.11 3.06
1889 1959 6.042777 TGTGATTCTGAAATATGTCTCGTCC 58.957 40.000 0.00 0.00 0.00 4.79
1890 1960 5.174035 GTGATTCTGAAATATGTCTCGTCCG 59.826 44.000 0.00 0.00 0.00 4.79
1891 1961 3.710326 TCTGAAATATGTCTCGTCCGG 57.290 47.619 0.00 0.00 0.00 5.14
1965 2036 1.592400 TAGTCCACCCGTGCTTCGAG 61.592 60.000 3.69 0.00 42.86 4.04
1974 2045 1.455786 CCGTGCTTCGAGTTGTTACTG 59.544 52.381 3.69 0.00 42.86 2.74
1988 2059 6.456501 AGTTGTTACTGCTAGGTTCTAGTTG 58.543 40.000 4.20 1.02 31.99 3.16
1990 2061 6.852420 TGTTACTGCTAGGTTCTAGTTGAT 57.148 37.500 4.20 0.00 0.00 2.57
1995 2066 7.425224 ACTGCTAGGTTCTAGTTGATGTAAT 57.575 36.000 4.20 0.00 0.00 1.89
2027 2098 5.304101 TGCTGTTGATTACCAGTTGGAAAAT 59.696 36.000 4.92 4.41 38.94 1.82
2029 2100 6.146021 GCTGTTGATTACCAGTTGGAAAATTG 59.854 38.462 4.92 0.00 38.94 2.32
2030 2101 5.988561 TGTTGATTACCAGTTGGAAAATTGC 59.011 36.000 4.92 1.21 38.94 3.56
2031 2102 5.798125 TGATTACCAGTTGGAAAATTGCA 57.202 34.783 4.92 0.00 38.94 4.08
2033 2104 6.767456 TGATTACCAGTTGGAAAATTGCAAT 58.233 32.000 5.99 5.99 40.59 3.56
2034 2105 6.649973 TGATTACCAGTTGGAAAATTGCAATG 59.350 34.615 13.82 0.00 40.59 2.82
2036 2107 3.390639 ACCAGTTGGAAAATTGCAATGGA 59.609 39.130 22.61 0.00 40.59 3.41
2038 2109 4.453136 CCAGTTGGAAAATTGCAATGGAAG 59.547 41.667 13.82 0.00 40.59 3.46
2039 2110 4.067192 AGTTGGAAAATTGCAATGGAAGC 58.933 39.130 13.82 1.32 40.59 3.86
2073 2145 8.510358 TTATCCCCATTTCTGAGATCTTATGA 57.490 34.615 0.00 0.00 0.00 2.15
2076 2148 7.819500 TCCCCATTTCTGAGATCTTATGAATT 58.180 34.615 0.00 0.00 0.00 2.17
2079 2151 9.128404 CCCATTTCTGAGATCTTATGAATTGAA 57.872 33.333 18.75 5.62 0.00 2.69
2087 2159 7.986889 TGAGATCTTATGAATTGAATTCCGTGA 59.013 33.333 14.73 8.45 38.50 4.35
2099 2171 4.142403 TGAATTCCGTGATTGGATGCTTTC 60.142 41.667 2.27 0.00 38.00 2.62
2101 2173 3.071874 TCCGTGATTGGATGCTTTCTT 57.928 42.857 0.00 0.00 31.53 2.52
2102 2174 3.009723 TCCGTGATTGGATGCTTTCTTC 58.990 45.455 0.00 0.00 31.53 2.87
2113 2185 5.163353 TGGATGCTTTCTTCGGTGTATGATA 60.163 40.000 0.00 0.00 0.00 2.15
2114 2186 5.177696 GGATGCTTTCTTCGGTGTATGATAC 59.822 44.000 0.00 0.00 0.00 2.24
2115 2187 4.439057 TGCTTTCTTCGGTGTATGATACC 58.561 43.478 0.00 0.00 34.81 2.73
2116 2188 4.081365 TGCTTTCTTCGGTGTATGATACCA 60.081 41.667 0.00 0.00 38.11 3.25
2117 2189 4.873827 GCTTTCTTCGGTGTATGATACCAA 59.126 41.667 0.00 0.00 38.11 3.67
2119 2191 4.036567 TCTTCGGTGTATGATACCAACG 57.963 45.455 0.00 3.50 38.11 4.10
2120 2192 3.695556 TCTTCGGTGTATGATACCAACGA 59.304 43.478 9.83 9.83 38.11 3.85
2121 2193 4.340097 TCTTCGGTGTATGATACCAACGAT 59.660 41.667 13.13 0.00 38.11 3.73
2122 2194 4.659111 TCGGTGTATGATACCAACGATT 57.341 40.909 9.83 0.00 38.11 3.34
2145 2226 6.554334 TTTCTCGTACTGAATTTTTCTGGG 57.446 37.500 0.00 0.00 33.45 4.45
2146 2227 5.223449 TCTCGTACTGAATTTTTCTGGGT 57.777 39.130 0.00 0.00 33.45 4.51
2149 2230 4.023536 TCGTACTGAATTTTTCTGGGTTGC 60.024 41.667 0.00 0.00 33.45 4.17
2150 2231 3.369546 ACTGAATTTTTCTGGGTTGCG 57.630 42.857 0.00 0.00 33.45 4.85
2154 2235 2.368655 ATTTTTCTGGGTTGCGCATC 57.631 45.000 12.75 11.18 0.00 3.91
2164 2245 2.682856 GGGTTGCGCATCAGAAATTCTA 59.317 45.455 12.75 0.00 0.00 2.10
2170 2251 4.142425 TGCGCATCAGAAATTCTATTGCAA 60.142 37.500 21.35 0.00 34.88 4.08
2171 2252 4.205792 GCGCATCAGAAATTCTATTGCAAC 59.794 41.667 21.35 13.09 34.88 4.17
2172 2253 5.575957 CGCATCAGAAATTCTATTGCAACT 58.424 37.500 21.35 0.00 34.88 3.16
2173 2254 5.454554 CGCATCAGAAATTCTATTGCAACTG 59.545 40.000 21.35 1.83 34.88 3.16
2174 2255 6.558009 GCATCAGAAATTCTATTGCAACTGA 58.442 36.000 18.54 12.70 35.13 3.41
2175 2256 6.471519 GCATCAGAAATTCTATTGCAACTGAC 59.528 38.462 18.54 0.99 35.13 3.51
2176 2257 7.532571 CATCAGAAATTCTATTGCAACTGACA 58.467 34.615 12.61 2.55 36.29 3.58
2177 2258 7.509141 TCAGAAATTCTATTGCAACTGACAA 57.491 32.000 0.00 0.00 0.00 3.18
2178 2259 8.114331 TCAGAAATTCTATTGCAACTGACAAT 57.886 30.769 0.00 0.00 40.68 2.71
2179 2260 8.579006 TCAGAAATTCTATTGCAACTGACAATT 58.421 29.630 0.00 0.00 38.62 2.32
2180 2261 9.844790 CAGAAATTCTATTGCAACTGACAATTA 57.155 29.630 0.00 0.00 38.62 1.40
2181 2262 9.846248 AGAAATTCTATTGCAACTGACAATTAC 57.154 29.630 0.00 0.00 38.62 1.89
2182 2263 8.986477 AAATTCTATTGCAACTGACAATTACC 57.014 30.769 0.00 0.00 38.62 2.85
2183 2264 5.794687 TCTATTGCAACTGACAATTACCG 57.205 39.130 0.00 0.00 38.62 4.02
2184 2265 5.242434 TCTATTGCAACTGACAATTACCGT 58.758 37.500 0.00 0.00 38.62 4.83
2185 2266 6.399743 TCTATTGCAACTGACAATTACCGTA 58.600 36.000 0.00 0.00 38.62 4.02
2186 2267 5.545658 ATTGCAACTGACAATTACCGTAG 57.454 39.130 0.00 0.00 34.05 3.51
2187 2268 4.394920 ATTGCAACTGACAATTACCGTAGG 59.605 41.667 0.00 0.00 44.62 3.18
2188 2269 6.603014 ATTGCAACTGACAATTACCGTAGGG 61.603 44.000 0.00 0.00 43.75 3.53
2221 2302 2.150390 TGTTCATGTTGGTGTGATCCG 58.850 47.619 0.00 0.00 0.00 4.18
2227 2308 3.478857 TGTTGGTGTGATCCGTTTACT 57.521 42.857 0.00 0.00 0.00 2.24
2228 2309 3.135225 TGTTGGTGTGATCCGTTTACTG 58.865 45.455 0.00 0.00 0.00 2.74
2235 2316 1.557371 TGATCCGTTTACTGCCATCCA 59.443 47.619 0.00 0.00 0.00 3.41
2244 2325 6.430451 CGTTTACTGCCATCCATTTAATCTC 58.570 40.000 0.00 0.00 0.00 2.75
2246 2327 6.942532 TTACTGCCATCCATTTAATCTCAC 57.057 37.500 0.00 0.00 0.00 3.51
2252 2333 6.127647 TGCCATCCATTTAATCTCACAAGTTC 60.128 38.462 0.00 0.00 0.00 3.01
2258 2339 7.284261 TCCATTTAATCTCACAAGTTCACAACA 59.716 33.333 0.00 0.00 0.00 3.33
2283 2364 4.076394 TGGTACATAGGCAAACAAGTTCC 58.924 43.478 0.00 0.00 0.00 3.62
2284 2365 3.442625 GGTACATAGGCAAACAAGTTCCC 59.557 47.826 0.00 0.00 0.00 3.97
2286 2367 4.650972 ACATAGGCAAACAAGTTCCCTA 57.349 40.909 12.03 12.03 33.75 3.53
2287 2368 4.332828 ACATAGGCAAACAAGTTCCCTAC 58.667 43.478 11.93 0.00 32.77 3.18
2288 2369 2.287977 AGGCAAACAAGTTCCCTACC 57.712 50.000 4.02 0.00 0.00 3.18
2289 2370 1.497286 AGGCAAACAAGTTCCCTACCA 59.503 47.619 4.02 0.00 0.00 3.25
2290 2371 2.110011 AGGCAAACAAGTTCCCTACCAT 59.890 45.455 4.02 0.00 0.00 3.55
2296 2408 6.389906 CAAACAAGTTCCCTACCATTCATTC 58.610 40.000 0.00 0.00 0.00 2.67
2299 2411 6.314917 ACAAGTTCCCTACCATTCATTCTTT 58.685 36.000 0.00 0.00 0.00 2.52
2302 2414 6.552008 AGTTCCCTACCATTCATTCTTTTCA 58.448 36.000 0.00 0.00 0.00 2.69
2306 2418 5.163581 CCCTACCATTCATTCTTTTCAGCTG 60.164 44.000 7.63 7.63 0.00 4.24
2326 2438 7.171508 TCAGCTGTTAACTGAAAGATTGTGTAG 59.828 37.037 14.67 0.00 41.10 2.74
2331 2443 8.402472 TGTTAACTGAAAGATTGTGTAGTTTGG 58.598 33.333 7.22 0.00 37.43 3.28
2332 2444 8.403236 GTTAACTGAAAGATTGTGTAGTTTGGT 58.597 33.333 0.00 0.00 37.43 3.67
2333 2445 6.377327 ACTGAAAGATTGTGTAGTTTGGTG 57.623 37.500 0.00 0.00 37.43 4.17
2334 2446 5.299279 ACTGAAAGATTGTGTAGTTTGGTGG 59.701 40.000 0.00 0.00 37.43 4.61
2375 2487 6.671190 TCTGAATAAACTTGTTGTGATGCTG 58.329 36.000 0.00 0.00 0.00 4.41
2377 2489 5.301551 TGAATAAACTTGTTGTGATGCTGGT 59.698 36.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.203209 CCAGATAGGTTGCCCCGC 60.203 66.667 0.00 0.00 38.74 6.13
55 56 3.319198 GTTGTCGGGCCCCTCTCA 61.319 66.667 18.66 7.51 0.00 3.27
115 117 2.373938 GCGACAGCAGATAACGCTT 58.626 52.632 0.00 0.00 44.67 4.68
127 129 1.365633 GGCTAGATCAGGGCGACAG 59.634 63.158 0.00 0.00 0.00 3.51
169 172 0.729116 CAACATGGATGTGGTCGCTC 59.271 55.000 0.00 0.00 41.61 5.03
173 176 3.411446 TGACTTCAACATGGATGTGGTC 58.589 45.455 0.00 9.08 41.61 4.02
187 190 4.452114 CAGGTTTCGACAATGATGACTTCA 59.548 41.667 0.00 0.00 39.12 3.02
196 199 1.197721 GCAGGACAGGTTTCGACAATG 59.802 52.381 0.00 0.00 0.00 2.82
197 200 1.072331 AGCAGGACAGGTTTCGACAAT 59.928 47.619 0.00 0.00 0.00 2.71
204 207 0.536006 GACTGCAGCAGGACAGGTTT 60.536 55.000 26.38 2.19 38.25 3.27
209 212 1.159713 CGTTTGACTGCAGCAGGACA 61.160 55.000 26.38 21.10 35.51 4.02
212 215 1.159713 TGTCGTTTGACTGCAGCAGG 61.160 55.000 26.38 7.53 45.70 4.85
220 223 6.045318 CCAATCTGATCTATGTCGTTTGACT 58.955 40.000 0.00 0.00 45.70 3.41
224 227 5.614324 TCCCAATCTGATCTATGTCGTTT 57.386 39.130 0.00 0.00 0.00 3.60
225 228 5.614324 TTCCCAATCTGATCTATGTCGTT 57.386 39.130 0.00 0.00 0.00 3.85
248 251 2.176247 TTATCTCCGCCCCTTCTTCT 57.824 50.000 0.00 0.00 0.00 2.85
258 261 0.603975 GGCCACTCCATTATCTCCGC 60.604 60.000 0.00 0.00 34.01 5.54
260 263 1.072965 CCAGGCCACTCCATTATCTCC 59.927 57.143 5.01 0.00 37.29 3.71
265 268 1.915228 GCTCCAGGCCACTCCATTA 59.085 57.895 5.01 0.00 37.29 1.90
267 270 3.790437 CGCTCCAGGCCACTCCAT 61.790 66.667 5.01 0.00 37.74 3.41
277 280 0.394488 TAGACCTCAGACCGCTCCAG 60.394 60.000 0.00 0.00 0.00 3.86
283 286 3.487711 CGATGAAACTAGACCTCAGACCG 60.488 52.174 0.00 0.00 0.00 4.79
294 297 3.560636 ATCCCAACCCGATGAAACTAG 57.439 47.619 0.00 0.00 0.00 2.57
305 309 1.007842 ACCCCACAAATATCCCAACCC 59.992 52.381 0.00 0.00 0.00 4.11
307 311 2.758423 GTGACCCCACAAATATCCCAAC 59.242 50.000 0.00 0.00 42.72 3.77
317 321 1.074775 GCCATCAGTGACCCCACAA 59.925 57.895 0.00 0.00 45.54 3.33
383 387 3.909086 GATATGAGGCGGCCTGGGC 62.909 68.421 29.31 13.10 41.06 5.36
384 388 2.348998 GATATGAGGCGGCCTGGG 59.651 66.667 29.31 0.00 31.76 4.45
385 389 1.772819 AAGGATATGAGGCGGCCTGG 61.773 60.000 29.31 0.00 31.76 4.45
386 390 0.321122 GAAGGATATGAGGCGGCCTG 60.321 60.000 29.31 0.00 31.76 4.85
387 391 1.484444 GGAAGGATATGAGGCGGCCT 61.484 60.000 24.13 24.13 36.03 5.19
388 392 1.003233 GGAAGGATATGAGGCGGCC 60.003 63.158 12.11 12.11 0.00 6.13
389 393 1.066787 GTAGGAAGGATATGAGGCGGC 60.067 57.143 0.00 0.00 0.00 6.53
414 418 1.002134 AACCCCTCACATTCAGCCG 60.002 57.895 0.00 0.00 0.00 5.52
420 424 0.324943 CTGACCGAACCCCTCACATT 59.675 55.000 0.00 0.00 0.00 2.71
423 427 2.047179 GCTGACCGAACCCCTCAC 60.047 66.667 0.00 0.00 0.00 3.51
432 436 1.122632 TAAACACCTGGGCTGACCGA 61.123 55.000 0.00 0.00 44.64 4.69
433 437 0.673644 CTAAACACCTGGGCTGACCG 60.674 60.000 0.00 0.00 44.64 4.79
436 440 2.074967 CCCTAAACACCTGGGCTGA 58.925 57.895 0.00 0.00 33.88 4.26
472 476 6.718294 ACCGGTAAGAATAAAAGGACTCATT 58.282 36.000 4.49 0.00 0.00 2.57
480 484 4.032558 GTCGCTGACCGGTAAGAATAAAAG 59.967 45.833 24.25 4.26 37.59 2.27
485 489 0.175073 GGTCGCTGACCGGTAAGAAT 59.825 55.000 24.25 0.00 43.14 2.40
506 510 0.034896 GGTCTCAAAAGTCCGAGCCA 59.965 55.000 0.00 0.00 0.00 4.75
507 511 2.842320 GGTCTCAAAAGTCCGAGCC 58.158 57.895 0.00 0.00 0.00 4.70
544 550 7.556844 TCGGAAGAGAATGTAAAAGCTTCTAT 58.443 34.615 0.00 0.00 33.95 1.98
569 575 4.457257 GGTAGCAAAGAAAGAGCATTGACT 59.543 41.667 0.00 0.00 0.00 3.41
577 583 6.391227 TTTTTGAGGGTAGCAAAGAAAGAG 57.609 37.500 0.00 0.00 36.68 2.85
629 638 9.268255 CGTTTTAATTTGCTGATACGTATTTCA 57.732 29.630 9.92 4.07 0.00 2.69
638 647 6.083630 GTGTGCTCGTTTTAATTTGCTGATA 58.916 36.000 0.00 0.00 0.00 2.15
650 660 6.503524 ACAATTTCTAATGTGTGCTCGTTTT 58.496 32.000 0.00 0.00 0.00 2.43
662 672 5.865552 CAGGTTGCCAGAACAATTTCTAATG 59.134 40.000 0.00 0.00 40.34 1.90
701 711 0.035152 ATCCGTGGCAGCATTTCTCA 60.035 50.000 0.00 0.00 0.00 3.27
847 857 1.432270 CGGCCTGAGAATTTCGAGCC 61.432 60.000 0.00 10.25 41.09 4.70
848 858 2.009888 CGGCCTGAGAATTTCGAGC 58.990 57.895 0.00 0.00 0.00 5.03
866 876 3.186390 GATTTGGAGGATGGCGCGC 62.186 63.158 25.94 25.94 0.00 6.86
876 886 1.518431 AAGGGGGTGGGGATTTGGAG 61.518 60.000 0.00 0.00 0.00 3.86
888 898 0.781920 GGGTGGTTTAAGAAGGGGGT 59.218 55.000 0.00 0.00 0.00 4.95
889 899 0.781278 TGGGTGGTTTAAGAAGGGGG 59.219 55.000 0.00 0.00 0.00 5.40
919 929 2.158957 GCGATCTGAGTTGTGGGGATTA 60.159 50.000 0.00 0.00 0.00 1.75
958 968 1.024271 CTGGTGGTGGTGTGTTCTTG 58.976 55.000 0.00 0.00 0.00 3.02
964 974 2.281761 GGCTCTGGTGGTGGTGTG 60.282 66.667 0.00 0.00 0.00 3.82
984 994 3.168528 ATCGGGGATTGGGGGTCG 61.169 66.667 0.00 0.00 0.00 4.79
986 996 3.103213 CCATCGGGGATTGGGGGT 61.103 66.667 0.00 0.00 40.01 4.95
1418 1431 1.449601 AAGCATTACCGGCGACCAG 60.450 57.895 9.30 0.00 36.08 4.00
1436 1452 1.068588 ACACGACAAGAACAGCTAGCA 59.931 47.619 18.83 0.00 0.00 3.49
1453 1473 1.237285 GGCACACACCAGGATCACAC 61.237 60.000 0.00 0.00 0.00 3.82
1471 1499 0.588252 CGACAAACAGAAGCACCAGG 59.412 55.000 0.00 0.00 0.00 4.45
1495 1531 4.021632 AGGACCAGATGACACATCATATCG 60.022 45.833 13.06 0.00 46.01 2.92
1509 1545 4.533707 CCATCACCATACATAGGACCAGAT 59.466 45.833 0.00 0.00 0.00 2.90
1532 1569 5.634859 ACTTTCCATTGCAATTTCATTCGAC 59.365 36.000 9.83 0.00 0.00 4.20
1592 1636 6.313905 AGAATCACGGAGTAATTTACAAGCAG 59.686 38.462 9.15 2.14 41.61 4.24
1637 1681 1.018910 ACGGCAACAACTTGGTACAC 58.981 50.000 0.00 0.00 39.29 2.90
1654 1702 6.648310 ACAGCATATCTTCTAATTCCATCACG 59.352 38.462 0.00 0.00 0.00 4.35
1724 1774 0.234625 GAATCACGCAGCGACAAACA 59.765 50.000 24.65 0.00 0.00 2.83
1725 1775 0.234625 TGAATCACGCAGCGACAAAC 59.765 50.000 24.65 10.20 0.00 2.93
1728 1778 0.599991 AACTGAATCACGCAGCGACA 60.600 50.000 24.65 7.43 36.86 4.35
1736 1786 4.539870 ACATGCAAAGAAACTGAATCACG 58.460 39.130 0.00 0.00 0.00 4.35
1829 1886 5.971763 ACTTCACCTTCAGCTATCAACTAG 58.028 41.667 0.00 0.00 0.00 2.57
1864 1934 6.535150 GGACGAGACATATTTCAGAATCACAA 59.465 38.462 0.00 0.00 0.00 3.33
1877 1947 3.039988 CGGCCGGACGAGACATAT 58.960 61.111 30.37 0.00 35.47 1.78
1890 1960 3.219198 GATGGAACCATGGCGGCC 61.219 66.667 13.04 13.32 39.03 6.13
1891 1961 3.219198 GGATGGAACCATGGCGGC 61.219 66.667 13.04 0.00 39.03 6.53
1898 1968 2.025981 CAGGATCAACAGGATGGAACCA 60.026 50.000 0.00 0.00 43.62 3.67
1936 2007 3.446161 CACGGGTGGACTAGAATAACAGA 59.554 47.826 0.00 0.00 0.00 3.41
1965 2036 6.453092 TCAACTAGAACCTAGCAGTAACAAC 58.547 40.000 0.00 0.00 0.00 3.32
1974 2045 6.583562 ACCATTACATCAACTAGAACCTAGC 58.416 40.000 0.00 0.00 0.00 3.42
1988 2059 4.083537 TCAACAGCAAACGACCATTACATC 60.084 41.667 0.00 0.00 0.00 3.06
1990 2061 3.206964 TCAACAGCAAACGACCATTACA 58.793 40.909 0.00 0.00 0.00 2.41
1995 2066 2.550606 GGTAATCAACAGCAAACGACCA 59.449 45.455 0.00 0.00 0.00 4.02
2027 2098 5.726980 AAAATAGACAGCTTCCATTGCAA 57.273 34.783 0.00 0.00 0.00 4.08
2029 2100 6.442112 GGATAAAATAGACAGCTTCCATTGC 58.558 40.000 0.00 0.00 0.00 3.56
2030 2101 6.015940 GGGGATAAAATAGACAGCTTCCATTG 60.016 42.308 0.00 0.00 0.00 2.82
2031 2102 6.071320 GGGGATAAAATAGACAGCTTCCATT 58.929 40.000 0.00 0.00 0.00 3.16
2033 2104 4.476846 TGGGGATAAAATAGACAGCTTCCA 59.523 41.667 0.00 0.00 0.00 3.53
2034 2105 5.048846 TGGGGATAAAATAGACAGCTTCC 57.951 43.478 0.00 0.00 0.00 3.46
2036 2107 7.286316 CAGAAATGGGGATAAAATAGACAGCTT 59.714 37.037 0.00 0.00 0.00 3.74
2038 2109 6.772716 TCAGAAATGGGGATAAAATAGACAGC 59.227 38.462 0.00 0.00 0.00 4.40
2039 2110 8.213679 TCTCAGAAATGGGGATAAAATAGACAG 58.786 37.037 0.00 0.00 0.00 3.51
2073 2145 4.403432 AGCATCCAATCACGGAATTCAATT 59.597 37.500 7.93 0.00 38.95 2.32
2076 2148 3.003394 AGCATCCAATCACGGAATTCA 57.997 42.857 7.93 0.00 38.95 2.57
2079 2151 3.624777 AGAAAGCATCCAATCACGGAAT 58.375 40.909 0.00 0.00 38.95 3.01
2082 2154 2.223112 CGAAGAAAGCATCCAATCACGG 60.223 50.000 0.00 0.00 0.00 4.94
2083 2155 2.223112 CCGAAGAAAGCATCCAATCACG 60.223 50.000 0.00 0.00 0.00 4.35
2087 2159 2.795329 ACACCGAAGAAAGCATCCAAT 58.205 42.857 0.00 0.00 0.00 3.16
2099 2171 4.036567 TCGTTGGTATCATACACCGAAG 57.963 45.455 0.00 0.00 39.04 3.79
2101 2173 4.659111 AATCGTTGGTATCATACACCGA 57.341 40.909 0.00 1.51 39.04 4.69
2102 2174 5.522460 AGAAAATCGTTGGTATCATACACCG 59.478 40.000 0.00 0.00 39.04 4.94
2119 2191 7.750903 CCCAGAAAAATTCAGTACGAGAAAATC 59.249 37.037 7.68 5.02 0.00 2.17
2120 2192 7.230712 ACCCAGAAAAATTCAGTACGAGAAAAT 59.769 33.333 7.68 0.00 0.00 1.82
2121 2193 6.544564 ACCCAGAAAAATTCAGTACGAGAAAA 59.455 34.615 7.68 0.00 0.00 2.29
2122 2194 6.059484 ACCCAGAAAAATTCAGTACGAGAAA 58.941 36.000 7.68 0.00 0.00 2.52
2130 2211 2.545742 GCGCAACCCAGAAAAATTCAGT 60.546 45.455 0.30 0.00 0.00 3.41
2135 2216 1.617850 TGATGCGCAACCCAGAAAAAT 59.382 42.857 17.11 0.00 0.00 1.82
2141 2222 0.813184 ATTTCTGATGCGCAACCCAG 59.187 50.000 17.11 21.33 0.00 4.45
2145 2226 4.205792 GCAATAGAATTTCTGATGCGCAAC 59.794 41.667 17.11 13.83 32.54 4.17
2146 2227 4.142425 TGCAATAGAATTTCTGATGCGCAA 60.142 37.500 17.11 0.00 40.20 4.85
2149 2230 5.454554 CAGTTGCAATAGAATTTCTGATGCG 59.545 40.000 22.42 11.73 40.20 4.73
2150 2231 6.471519 GTCAGTTGCAATAGAATTTCTGATGC 59.528 38.462 21.77 21.77 38.81 3.91
2154 2235 8.752766 AATTGTCAGTTGCAATAGAATTTCTG 57.247 30.769 0.59 2.55 35.73 3.02
2164 2245 4.394920 CCTACGGTAATTGTCAGTTGCAAT 59.605 41.667 0.59 0.00 38.09 3.56
2170 2251 5.910614 GTAATCCCTACGGTAATTGTCAGT 58.089 41.667 0.00 0.00 0.00 3.41
2183 2264 6.790285 TGAACAAGAAAACGTAATCCCTAC 57.210 37.500 0.00 0.00 0.00 3.18
2184 2265 6.938030 ACATGAACAAGAAAACGTAATCCCTA 59.062 34.615 0.00 0.00 0.00 3.53
2185 2266 5.768164 ACATGAACAAGAAAACGTAATCCCT 59.232 36.000 0.00 0.00 0.00 4.20
2186 2267 6.009115 ACATGAACAAGAAAACGTAATCCC 57.991 37.500 0.00 0.00 0.00 3.85
2187 2268 6.362283 CCAACATGAACAAGAAAACGTAATCC 59.638 38.462 0.00 0.00 0.00 3.01
2188 2269 6.915843 ACCAACATGAACAAGAAAACGTAATC 59.084 34.615 0.00 0.00 0.00 1.75
2194 2275 5.406649 TCACACCAACATGAACAAGAAAAC 58.593 37.500 0.00 0.00 0.00 2.43
2199 2280 3.365264 CGGATCACACCAACATGAACAAG 60.365 47.826 0.00 0.00 0.00 3.16
2221 2302 7.148086 TGTGAGATTAAATGGATGGCAGTAAAC 60.148 37.037 0.00 0.00 0.00 2.01
2227 2308 5.263599 ACTTGTGAGATTAAATGGATGGCA 58.736 37.500 0.00 0.00 0.00 4.92
2228 2309 5.841957 ACTTGTGAGATTAAATGGATGGC 57.158 39.130 0.00 0.00 0.00 4.40
2235 2316 8.686334 ACTTGTTGTGAACTTGTGAGATTAAAT 58.314 29.630 0.00 0.00 0.00 1.40
2252 2333 3.407698 TGCCTATGTACCACTTGTTGTG 58.592 45.455 0.00 0.00 45.80 3.33
2258 2339 4.725490 ACTTGTTTGCCTATGTACCACTT 58.275 39.130 0.00 0.00 0.00 3.16
2271 2352 3.572255 TGAATGGTAGGGAACTTGTTTGC 59.428 43.478 0.00 0.00 43.67 3.68
2272 2353 5.982890 ATGAATGGTAGGGAACTTGTTTG 57.017 39.130 0.00 0.00 43.67 2.93
2283 2364 5.416952 ACAGCTGAAAAGAATGAATGGTAGG 59.583 40.000 23.35 0.00 0.00 3.18
2284 2365 6.506500 ACAGCTGAAAAGAATGAATGGTAG 57.493 37.500 23.35 0.00 0.00 3.18
2286 2367 5.796424 AACAGCTGAAAAGAATGAATGGT 57.204 34.783 23.35 0.00 0.00 3.55
2287 2368 7.327761 CAGTTAACAGCTGAAAAGAATGAATGG 59.672 37.037 23.35 0.00 36.12 3.16
2288 2369 8.077991 TCAGTTAACAGCTGAAAAGAATGAATG 58.922 33.333 23.35 5.19 39.70 2.67
2289 2370 8.169977 TCAGTTAACAGCTGAAAAGAATGAAT 57.830 30.769 23.35 0.00 39.70 2.57
2290 2371 7.566760 TCAGTTAACAGCTGAAAAGAATGAA 57.433 32.000 23.35 0.00 39.70 2.57
2302 2414 6.992715 ACTACACAATCTTTCAGTTAACAGCT 59.007 34.615 8.61 0.00 0.00 4.24
2306 2418 8.403236 ACCAAACTACACAATCTTTCAGTTAAC 58.597 33.333 0.00 0.00 0.00 2.01
2321 2433 1.602377 GCTGACACCACCAAACTACAC 59.398 52.381 0.00 0.00 0.00 2.90
2322 2434 1.210722 TGCTGACACCACCAAACTACA 59.789 47.619 0.00 0.00 0.00 2.74
2326 2438 0.814457 TGTTGCTGACACCACCAAAC 59.186 50.000 0.00 0.00 32.00 2.93
2347 2459 7.520453 GCATCACAACAAGTTTATTCAGAGACA 60.520 37.037 0.00 0.00 0.00 3.41
2348 2460 6.798959 GCATCACAACAAGTTTATTCAGAGAC 59.201 38.462 0.00 0.00 0.00 3.36
2353 2465 5.301551 ACCAGCATCACAACAAGTTTATTCA 59.698 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.