Multiple sequence alignment - TraesCS7D01G243700

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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 TraesCS7D01G243700 chr7D 100.000 2801 0 0 1 2801 210126295 210123495 0.000000e+00 5173.0
1 TraesCS7D01G243700 chr7D 89.922 129 13 0 4 132 236956293 236956421 1.730000e-37 167.0
2 TraesCS7D01G243700 chr7D 85.965 114 13 3 82 193 377325366 377325254 4.900000e-23 119.0
3 TraesCS7D01G243700 chr7B 88.850 2009 113 40 180 2147 191138167 191140105 0.000000e+00 2366.0
4 TraesCS7D01G243700 chr7B 92.718 412 18 5 2134 2545 191140122 191140521 4.020000e-163 584.0
5 TraesCS7D01G243700 chr7B 89.222 167 8 4 2640 2801 191140775 191140936 1.700000e-47 200.0
6 TraesCS7D01G243700 chr7A 90.252 1785 93 37 1045 2801 222785790 222784059 0.000000e+00 2257.0
7 TraesCS7D01G243700 chr7A 86.545 602 29 13 397 974 222786664 222786091 1.430000e-172 616.0
8 TraesCS7D01G243700 chr5D 79.317 527 76 25 1098 1618 374661844 374662343 3.460000e-89 339.0
9 TraesCS7D01G243700 chr5B 77.820 523 80 25 1099 1618 447402739 447403228 9.810000e-75 291.0
10 TraesCS7D01G243700 chr6D 86.096 187 24 2 1 185 451627407 451627593 1.700000e-47 200.0
11 TraesCS7D01G243700 chr6D 80.400 250 45 3 4 249 420632715 420632466 1.320000e-43 187.0
12 TraesCS7D01G243700 chr5A 82.051 234 35 5 1 230 693304510 693304740 2.850000e-45 193.0
13 TraesCS7D01G243700 chr5A 84.058 138 16 3 1099 1236 476402840 476402971 8.140000e-26 128.0
14 TraesCS7D01G243700 chr2D 77.215 316 62 9 1 310 478807903 478808214 2.870000e-40 176.0
15 TraesCS7D01G243700 chr2D 89.922 129 13 0 4 132 347335567 347335439 1.730000e-37 167.0
16 TraesCS7D01G243700 chr3A 78.346 254 41 9 58 306 728939227 728939471 4.830000e-33 152.0
17 TraesCS7D01G243700 chr4A 81.053 190 34 2 4 193 9619654 9619841 1.740000e-32 150.0
18 TraesCS7D01G243700 chr3B 75.984 254 46 9 62 310 806048624 806048867 1.760000e-22 117.0
19 TraesCS7D01G243700 chr4B 93.333 45 3 0 141 185 371874572 371874616 1.800000e-07 67.6


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 TraesCS7D01G243700 chr7D 210123495 210126295 2800 True 5173.0 5173 100.000000 1 2801 1 chr7D.!!$R1 2800
1 TraesCS7D01G243700 chr7B 191138167 191140936 2769 False 1050.0 2366 90.263333 180 2801 3 chr7B.!!$F1 2621
2 TraesCS7D01G243700 chr7A 222784059 222786664 2605 True 1436.5 2257 88.398500 397 2801 2 chr7A.!!$R1 2404

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
380 393 0.107703 TGGTCGATGTTGGAGATGCC 60.108 55.0 0.00 0.0 37.10 4.40 F
381 394 0.179000 GGTCGATGTTGGAGATGCCT 59.821 55.0 0.00 0.0 37.63 4.75 F
964 1009 0.321653 TTTCCTCAAAGCCTCGAGCC 60.322 55.0 6.99 0.0 45.47 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1947 0.605319 TTGCTTCAGATTTCGCCGGT 60.605 50.000 1.9 0.0 0.0 5.28 R
1749 2052 1.103398 CCCATCGCCATCTTTCACCC 61.103 60.000 0.0 0.0 0.0 4.61 R
1841 2148 1.149711 CCATCCTCCTCATCTCCTCCT 59.850 57.143 0.0 0.0 0.0 3.69 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
18 19 3.248043 TCATTTGAACGGGGAGCAG 57.752 52.632 0.00 0.00 0.00 4.24
19 20 0.400213 TCATTTGAACGGGGAGCAGT 59.600 50.000 0.00 0.00 0.00 4.40
20 21 0.804989 CATTTGAACGGGGAGCAGTC 59.195 55.000 0.00 0.00 0.00 3.51
21 22 0.322546 ATTTGAACGGGGAGCAGTCC 60.323 55.000 0.00 0.00 43.05 3.85
33 34 3.636231 CAGTCCCCTGCACCGGAA 61.636 66.667 9.46 0.00 0.00 4.30
34 35 2.852075 AGTCCCCTGCACCGGAAA 60.852 61.111 9.46 0.00 0.00 3.13
35 36 2.359975 GTCCCCTGCACCGGAAAG 60.360 66.667 9.46 1.56 0.00 2.62
36 37 4.344865 TCCCCTGCACCGGAAAGC 62.345 66.667 9.46 10.17 0.00 3.51
56 57 4.838486 CGCGACCGGTGCTCTCTC 62.838 72.222 14.63 0.00 0.00 3.20
57 58 4.838486 GCGACCGGTGCTCTCTCG 62.838 72.222 14.63 8.84 0.00 4.04
59 60 4.500116 GACCGGTGCTCTCTCGGC 62.500 72.222 14.63 0.00 46.87 5.54
61 62 4.504916 CCGGTGCTCTCTCGGCTG 62.505 72.222 0.00 0.00 37.25 4.85
62 63 4.504916 CGGTGCTCTCTCGGCTGG 62.505 72.222 0.00 0.00 0.00 4.85
63 64 4.828925 GGTGCTCTCTCGGCTGGC 62.829 72.222 0.00 0.00 0.00 4.85
87 88 3.114616 CTTCACTGTCGGCGCCAG 61.115 66.667 28.98 17.22 36.01 4.85
88 89 3.865929 CTTCACTGTCGGCGCCAGT 62.866 63.158 28.98 18.81 43.76 4.00
91 92 4.363990 ACTGTCGGCGCCAGTGAG 62.364 66.667 23.73 17.90 41.47 3.51
92 93 4.056125 CTGTCGGCGCCAGTGAGA 62.056 66.667 28.98 12.55 0.00 3.27
93 94 3.573772 CTGTCGGCGCCAGTGAGAA 62.574 63.158 28.98 6.13 0.00 2.87
94 95 2.811317 GTCGGCGCCAGTGAGAAG 60.811 66.667 28.98 7.38 0.00 2.85
95 96 3.303135 TCGGCGCCAGTGAGAAGT 61.303 61.111 28.98 0.00 0.00 3.01
96 97 2.811317 CGGCGCCAGTGAGAAGTC 60.811 66.667 28.98 0.00 0.00 3.01
97 98 2.811317 GGCGCCAGTGAGAAGTCG 60.811 66.667 24.80 0.00 0.00 4.18
98 99 3.482783 GCGCCAGTGAGAAGTCGC 61.483 66.667 0.00 0.00 35.82 5.19
99 100 3.175240 CGCCAGTGAGAAGTCGCG 61.175 66.667 0.00 0.00 38.32 5.87
100 101 2.049063 GCCAGTGAGAAGTCGCGT 60.049 61.111 5.77 0.00 38.32 6.01
101 102 2.089349 GCCAGTGAGAAGTCGCGTC 61.089 63.158 5.77 0.00 38.32 5.19
102 103 1.581954 CCAGTGAGAAGTCGCGTCT 59.418 57.895 5.77 1.88 38.32 4.18
103 104 0.730834 CCAGTGAGAAGTCGCGTCTG 60.731 60.000 6.64 4.01 38.32 3.51
104 105 1.081108 AGTGAGAAGTCGCGTCTGC 60.081 57.895 6.64 4.67 38.32 4.26
105 106 1.081108 GTGAGAAGTCGCGTCTGCT 60.081 57.895 14.00 14.00 39.65 4.24
106 107 1.068287 GTGAGAAGTCGCGTCTGCTC 61.068 60.000 28.04 28.04 39.79 4.26
107 108 1.237954 TGAGAAGTCGCGTCTGCTCT 61.238 55.000 32.10 20.96 39.99 4.09
108 109 0.796491 GAGAAGTCGCGTCTGCTCTG 60.796 60.000 27.65 0.00 37.20 3.35
109 110 1.803519 GAAGTCGCGTCTGCTCTGG 60.804 63.158 6.64 0.00 39.65 3.86
110 111 3.923563 AAGTCGCGTCTGCTCTGGC 62.924 63.158 6.64 0.00 39.65 4.85
120 121 4.802051 GCTCTGGCCGGGCATGAA 62.802 66.667 32.84 18.48 0.00 2.57
121 122 2.194056 CTCTGGCCGGGCATGAAT 59.806 61.111 32.84 0.00 0.00 2.57
122 123 2.124193 TCTGGCCGGGCATGAATG 60.124 61.111 32.84 19.47 0.00 2.67
123 124 2.440796 CTGGCCGGGCATGAATGT 60.441 61.111 32.84 0.00 0.00 2.71
124 125 2.755064 TGGCCGGGCATGAATGTG 60.755 61.111 29.27 0.00 0.00 3.21
125 126 3.530260 GGCCGGGCATGAATGTGG 61.530 66.667 25.33 0.00 0.00 4.17
126 127 4.211502 GCCGGGCATGAATGTGGC 62.212 66.667 15.62 0.00 43.34 5.01
127 128 2.755064 CCGGGCATGAATGTGGCA 60.755 61.111 0.00 0.00 45.63 4.92
128 129 2.491152 CGGGCATGAATGTGGCAC 59.509 61.111 11.55 11.55 45.63 5.01
129 130 2.048023 CGGGCATGAATGTGGCACT 61.048 57.895 19.83 0.00 45.63 4.40
130 131 1.514087 GGGCATGAATGTGGCACTG 59.486 57.895 19.83 9.30 45.63 3.66
131 132 0.966875 GGGCATGAATGTGGCACTGA 60.967 55.000 19.83 0.00 45.63 3.41
132 133 1.108776 GGCATGAATGTGGCACTGAT 58.891 50.000 19.83 1.41 43.52 2.90
133 134 1.202371 GGCATGAATGTGGCACTGATG 60.202 52.381 19.83 14.87 43.52 3.07
170 171 2.172659 GTTTCGGACGGAAAGCGC 59.827 61.111 0.00 0.00 44.95 5.92
171 172 3.408020 TTTCGGACGGAAAGCGCG 61.408 61.111 0.00 0.00 39.67 6.86
192 193 1.471829 GGGCAAGGGAGGGTGTTTTG 61.472 60.000 0.00 0.00 0.00 2.44
194 195 0.673985 GCAAGGGAGGGTGTTTTGTC 59.326 55.000 0.00 0.00 0.00 3.18
198 199 1.149854 GGAGGGTGTTTTGTCGGGT 59.850 57.895 0.00 0.00 0.00 5.28
201 202 0.179029 AGGGTGTTTTGTCGGGTCAG 60.179 55.000 0.00 0.00 0.00 3.51
214 215 4.057428 GTCAGGGCGCTCAGACGT 62.057 66.667 17.51 0.00 34.88 4.34
226 227 1.966451 CAGACGTGGGTTTGGGAGC 60.966 63.158 0.00 0.00 0.00 4.70
227 228 3.047877 GACGTGGGTTTGGGAGCG 61.048 66.667 0.00 0.00 0.00 5.03
230 231 2.751688 GTGGGTTTGGGAGCGGTA 59.248 61.111 0.00 0.00 0.00 4.02
262 265 1.522569 AGCCCACACGCTTATCTCC 59.477 57.895 0.00 0.00 34.73 3.71
264 267 1.227263 CCCACACGCTTATCTCCGG 60.227 63.158 0.00 0.00 0.00 5.14
268 271 2.223971 CCACACGCTTATCTCCGGTTAT 60.224 50.000 0.00 0.00 0.00 1.89
272 275 1.616865 CGCTTATCTCCGGTTATGGGA 59.383 52.381 0.00 0.00 0.00 4.37
283 286 4.080975 TCCGGTTATGGGAGAAAATACGTT 60.081 41.667 0.00 0.00 0.00 3.99
288 291 2.963432 TGGGAGAAAATACGTTCGGAC 58.037 47.619 0.00 0.00 32.50 4.79
289 292 2.564062 TGGGAGAAAATACGTTCGGACT 59.436 45.455 0.00 0.00 32.50 3.85
290 293 2.928116 GGGAGAAAATACGTTCGGACTG 59.072 50.000 0.00 0.00 32.50 3.51
291 294 3.582780 GGAGAAAATACGTTCGGACTGT 58.417 45.455 0.00 0.00 32.50 3.55
296 299 1.992170 ATACGTTCGGACTGTTCAGC 58.008 50.000 0.00 0.00 0.00 4.26
306 309 1.067212 GACTGTTCAGCGGACCGATAT 59.933 52.381 20.50 0.00 0.00 1.63
316 319 4.488790 ACCGATATAGGTCCGCGT 57.511 55.556 4.92 0.00 41.46 6.01
319 322 1.007336 CCGATATAGGTCCGCGTTGC 61.007 60.000 4.92 0.00 0.00 4.17
329 332 1.209898 CCGCGTTGCATGACACAAT 59.790 52.632 4.92 0.00 0.00 2.71
331 334 1.529622 CCGCGTTGCATGACACAATAG 60.530 52.381 4.92 0.00 0.00 1.73
332 335 1.538276 GCGTTGCATGACACAATAGC 58.462 50.000 0.00 0.00 0.00 2.97
335 338 2.674852 CGTTGCATGACACAATAGCTCT 59.325 45.455 0.00 0.00 0.00 4.09
344 357 2.563179 ACACAATAGCTCTGTCCGAACT 59.437 45.455 0.00 0.00 0.00 3.01
361 374 3.181524 CGAACTTATGCGGACGTTTTGAT 60.182 43.478 0.00 0.00 0.00 2.57
367 380 1.286354 GCGGACGTTTTGATGGTCGA 61.286 55.000 0.00 0.00 0.00 4.20
368 381 1.355971 CGGACGTTTTGATGGTCGAT 58.644 50.000 0.00 0.00 0.00 3.59
373 386 2.225491 ACGTTTTGATGGTCGATGTTGG 59.775 45.455 0.00 0.00 0.00 3.77
380 393 0.107703 TGGTCGATGTTGGAGATGCC 60.108 55.000 0.00 0.00 37.10 4.40
381 394 0.179000 GGTCGATGTTGGAGATGCCT 59.821 55.000 0.00 0.00 37.63 4.75
382 395 1.407437 GGTCGATGTTGGAGATGCCTT 60.407 52.381 0.00 0.00 37.63 4.35
403 416 6.205464 GCCTTAAGCATAGCATACAAAGATCA 59.795 38.462 0.00 0.00 42.97 2.92
411 424 9.472361 GCATAGCATACAAAGATCAATGAAAAT 57.528 29.630 4.93 0.00 0.00 1.82
442 455 3.498774 AGGACACAACAAAGATGAGCT 57.501 42.857 0.00 0.00 0.00 4.09
449 462 1.446907 ACAAAGATGAGCTTCGCCTG 58.553 50.000 0.00 0.00 35.24 4.85
456 469 3.003173 AGCTTCGCCTGGTAGCCA 61.003 61.111 12.01 0.00 35.53 4.75
529 542 1.207329 AGATGAGTCCACCCGCTAAAC 59.793 52.381 0.00 0.00 0.00 2.01
573 586 3.119096 GAACGCGCACTCCCCTTC 61.119 66.667 5.73 0.00 0.00 3.46
574 587 4.699522 AACGCGCACTCCCCTTCC 62.700 66.667 5.73 0.00 0.00 3.46
651 674 5.656420 TCCCTCCTAAGAAAGAAAGAGACT 58.344 41.667 0.00 0.00 0.00 3.24
652 675 6.085416 TCCCTCCTAAGAAAGAAAGAGACTT 58.915 40.000 0.00 0.00 0.00 3.01
656 679 6.085416 TCCTAAGAAAGAAAGAGACTTCCCT 58.915 40.000 0.00 0.00 0.00 4.20
657 680 6.211785 TCCTAAGAAAGAAAGAGACTTCCCTC 59.788 42.308 0.00 0.00 0.00 4.30
658 681 4.901197 AGAAAGAAAGAGACTTCCCTCC 57.099 45.455 0.00 0.00 33.76 4.30
660 683 1.959710 AGAAAGAGACTTCCCTCCCC 58.040 55.000 0.00 0.00 33.76 4.81
950 995 2.286121 TCCTCCGCCCCATTTCCT 60.286 61.111 0.00 0.00 0.00 3.36
956 1001 1.512694 CGCCCCATTTCCTCAAAGC 59.487 57.895 0.00 0.00 0.00 3.51
957 1002 1.900351 GCCCCATTTCCTCAAAGCC 59.100 57.895 0.00 0.00 0.00 4.35
958 1003 0.615827 GCCCCATTTCCTCAAAGCCT 60.616 55.000 0.00 0.00 0.00 4.58
959 1004 1.478631 CCCCATTTCCTCAAAGCCTC 58.521 55.000 0.00 0.00 0.00 4.70
960 1005 1.098050 CCCATTTCCTCAAAGCCTCG 58.902 55.000 0.00 0.00 0.00 4.63
961 1006 1.340017 CCCATTTCCTCAAAGCCTCGA 60.340 52.381 0.00 0.00 0.00 4.04
962 1007 2.012673 CCATTTCCTCAAAGCCTCGAG 58.987 52.381 5.13 5.13 0.00 4.04
963 1008 1.399791 CATTTCCTCAAAGCCTCGAGC 59.600 52.381 6.99 2.54 44.25 5.03
964 1009 0.321653 TTTCCTCAAAGCCTCGAGCC 60.322 55.000 6.99 0.00 45.47 4.70
965 1010 2.507110 TTCCTCAAAGCCTCGAGCCG 62.507 60.000 6.99 0.00 45.47 5.52
966 1011 3.191539 CTCAAAGCCTCGAGCCGC 61.192 66.667 6.99 6.20 45.47 6.53
987 1032 2.124860 TCGACTCGCTCGATCCCA 60.125 61.111 1.35 0.00 46.75 4.37
993 1038 1.872197 CTCGCTCGATCCCATCTCCC 61.872 65.000 0.00 0.00 0.00 4.30
996 1041 1.905843 CTCGATCCCATCTCCCGCT 60.906 63.158 0.00 0.00 0.00 5.52
1002 1047 4.899239 CCATCTCCCGCTCACGCC 62.899 72.222 0.00 0.00 38.22 5.68
1078 1366 1.551452 GCGGGATCATCTAGCTACCT 58.449 55.000 0.00 0.00 0.00 3.08
1080 1368 2.300437 GCGGGATCATCTAGCTACCTTT 59.700 50.000 0.00 0.00 0.00 3.11
1319 1619 1.816863 TTCCCGCTCTTCGACAAGCT 61.817 55.000 14.39 0.00 41.67 3.74
1618 1918 1.993370 CCAAGATCGTTCGGTTCTGAC 59.007 52.381 0.00 0.00 0.00 3.51
1624 1924 1.134759 TCGTTCGGTTCTGACCAACAA 60.135 47.619 0.00 0.00 46.91 2.83
1634 1934 1.092921 TGACCAACAAGACACCACGC 61.093 55.000 0.00 0.00 0.00 5.34
1635 1935 2.101209 GACCAACAAGACACCACGCG 62.101 60.000 3.53 3.53 0.00 6.01
1636 1936 2.052237 CAACAAGACACCACGCGC 60.052 61.111 5.73 0.00 0.00 6.86
1637 1937 3.636043 AACAAGACACCACGCGCG 61.636 61.111 30.96 30.96 0.00 6.86
1666 1966 0.605319 ACCGGCGAAATCTGAAGCAA 60.605 50.000 9.30 0.00 0.00 3.91
1667 1967 0.521291 CCGGCGAAATCTGAAGCAAA 59.479 50.000 9.30 0.00 0.00 3.68
1669 1969 2.606795 CCGGCGAAATCTGAAGCAAAAA 60.607 45.455 9.30 0.00 0.00 1.94
1681 1983 5.046663 TCTGAAGCAAAAACCCACTCTTTTT 60.047 36.000 0.00 0.00 32.23 1.94
1815 2122 5.547341 CGATGATAACGTTGTTGTTGTAGG 58.453 41.667 11.99 0.00 33.32 3.18
1816 2123 4.735662 TGATAACGTTGTTGTTGTAGGC 57.264 40.909 11.99 0.00 33.32 3.93
1817 2124 4.382291 TGATAACGTTGTTGTTGTAGGCT 58.618 39.130 11.99 0.00 33.32 4.58
1818 2125 4.817464 TGATAACGTTGTTGTTGTAGGCTT 59.183 37.500 11.99 0.00 33.32 4.35
1819 2126 3.414549 AACGTTGTTGTTGTAGGCTTG 57.585 42.857 0.00 0.00 0.00 4.01
1820 2127 2.361789 ACGTTGTTGTTGTAGGCTTGT 58.638 42.857 0.00 0.00 0.00 3.16
1821 2128 3.533547 ACGTTGTTGTTGTAGGCTTGTA 58.466 40.909 0.00 0.00 0.00 2.41
1822 2129 3.558418 ACGTTGTTGTTGTAGGCTTGTAG 59.442 43.478 0.00 0.00 0.00 2.74
1834 2141 1.599518 CTTGTAGCGGTGGTTGGCA 60.600 57.895 0.00 0.00 0.00 4.92
1840 2147 2.669569 CGGTGGTTGGCAGTGGAG 60.670 66.667 0.00 0.00 0.00 3.86
1841 2148 2.836154 GGTGGTTGGCAGTGGAGA 59.164 61.111 0.00 0.00 0.00 3.71
1842 2149 1.302832 GGTGGTTGGCAGTGGAGAG 60.303 63.158 0.00 0.00 0.00 3.20
1982 2304 5.592054 GCTTTAGCTGTCAACCTTTTTCTT 58.408 37.500 0.00 0.00 38.21 2.52
1983 2305 5.687730 GCTTTAGCTGTCAACCTTTTTCTTC 59.312 40.000 0.00 0.00 38.21 2.87
1984 2306 5.767816 TTAGCTGTCAACCTTTTTCTTCC 57.232 39.130 0.00 0.00 0.00 3.46
1985 2307 3.903467 AGCTGTCAACCTTTTTCTTCCT 58.097 40.909 0.00 0.00 0.00 3.36
1986 2308 4.281657 AGCTGTCAACCTTTTTCTTCCTT 58.718 39.130 0.00 0.00 0.00 3.36
1987 2309 4.339530 AGCTGTCAACCTTTTTCTTCCTTC 59.660 41.667 0.00 0.00 0.00 3.46
1988 2310 4.339530 GCTGTCAACCTTTTTCTTCCTTCT 59.660 41.667 0.00 0.00 0.00 2.85
1989 2311 5.163509 GCTGTCAACCTTTTTCTTCCTTCTT 60.164 40.000 0.00 0.00 0.00 2.52
2067 2392 2.091102 GATCGGTTCGGCGGGGAATA 62.091 60.000 7.21 0.00 0.00 1.75
2070 2395 0.816421 CGGTTCGGCGGGGAATAATT 60.816 55.000 7.21 0.00 0.00 1.40
2071 2396 1.540797 CGGTTCGGCGGGGAATAATTA 60.541 52.381 7.21 0.00 0.00 1.40
2072 2397 2.786777 GGTTCGGCGGGGAATAATTAT 58.213 47.619 7.21 0.00 0.00 1.28
2130 2485 5.565259 CGTACAAAATCATGTCTGTTTGAGC 59.435 40.000 15.15 9.04 35.44 4.26
2151 2506 2.008752 AAATTTGCAAGGCGTATGGC 57.991 45.000 0.00 0.00 42.51 4.40
2177 2532 1.604755 CGACATGTTTCGGTTGGGAAA 59.395 47.619 0.00 0.00 35.26 3.13
2182 2537 1.241165 GTTTCGGTTGGGAAATCGGT 58.759 50.000 0.00 0.00 38.12 4.69
2185 2540 0.604243 TCGGTTGGGAAATCGGTGTG 60.604 55.000 0.00 0.00 0.00 3.82
2251 2606 1.296715 GCCACGAAGGATGGACAGT 59.703 57.895 2.86 0.00 39.87 3.55
2302 2657 5.186992 TGATCAGAATTCGGAAGTAACAGGA 59.813 40.000 12.38 0.00 0.00 3.86
2303 2658 4.817517 TCAGAATTCGGAAGTAACAGGAC 58.182 43.478 5.77 0.00 0.00 3.85
2359 2714 1.228063 GCCAGCGACATCCATCCAT 60.228 57.895 0.00 0.00 0.00 3.41
2360 2715 1.233285 GCCAGCGACATCCATCCATC 61.233 60.000 0.00 0.00 0.00 3.51
2361 2716 0.604780 CCAGCGACATCCATCCATCC 60.605 60.000 0.00 0.00 0.00 3.51
2362 2717 0.107268 CAGCGACATCCATCCATCCA 59.893 55.000 0.00 0.00 0.00 3.41
2377 2736 4.742201 CCACCGGGTCACAGCTCG 62.742 72.222 6.32 0.00 0.00 5.03
2402 2761 2.184322 GCAGAAGATCCGTCGGCA 59.816 61.111 6.34 0.00 36.38 5.69
2551 2918 5.963092 TCCATCTCATCTCATCTCCTAGTT 58.037 41.667 0.00 0.00 0.00 2.24
2558 2925 5.538053 TCATCTCATCTCCTAGTTGATCCAC 59.462 44.000 0.00 0.00 0.00 4.02
2730 3268 4.891727 GATGGCGACGGCGATGGT 62.892 66.667 18.90 0.00 37.76 3.55
2762 3300 4.871513 TCTCGGATGAATGAAATACTCCG 58.128 43.478 2.51 2.51 45.27 4.63
2769 3307 5.614324 TGAATGAAATACTCCGATGGACT 57.386 39.130 0.00 0.00 0.00 3.85
2773 3311 5.011090 TGAAATACTCCGATGGACTCAAG 57.989 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.400213 ACTGCTCCCCGTTCAAATGA 59.600 50.000 0.00 0.00 0.00 2.57
1 2 0.804989 GACTGCTCCCCGTTCAAATG 59.195 55.000 0.00 0.00 0.00 2.32
2 3 0.322546 GGACTGCTCCCCGTTCAAAT 60.323 55.000 0.00 0.00 0.00 2.32
3 4 1.072505 GGACTGCTCCCCGTTCAAA 59.927 57.895 0.00 0.00 0.00 2.69
4 5 2.747686 GGACTGCTCCCCGTTCAA 59.252 61.111 0.00 0.00 0.00 2.69
17 18 2.852075 TTTCCGGTGCAGGGGACT 60.852 61.111 0.00 0.00 46.44 3.85
18 19 2.359975 CTTTCCGGTGCAGGGGAC 60.360 66.667 0.00 0.00 30.46 4.46
19 20 4.344865 GCTTTCCGGTGCAGGGGA 62.345 66.667 0.00 1.53 0.00 4.81
39 40 4.838486 GAGAGAGCACCGGTCGCG 62.838 72.222 18.95 0.00 35.22 5.87
40 41 4.838486 CGAGAGAGCACCGGTCGC 62.838 72.222 17.87 17.87 35.00 5.19
41 42 4.180946 CCGAGAGAGCACCGGTCG 62.181 72.222 2.59 2.74 38.55 4.79
42 43 4.500116 GCCGAGAGAGCACCGGTC 62.500 72.222 2.59 0.00 44.63 4.79
44 45 4.504916 CAGCCGAGAGAGCACCGG 62.505 72.222 0.00 0.00 45.51 5.28
45 46 4.504916 CCAGCCGAGAGAGCACCG 62.505 72.222 0.00 0.00 0.00 4.94
46 47 4.828925 GCCAGCCGAGAGAGCACC 62.829 72.222 0.00 0.00 0.00 5.01
70 71 3.114616 CTGGCGCCGACAGTGAAG 61.115 66.667 23.90 6.88 33.29 3.02
75 76 3.573772 TTCTCACTGGCGCCGACAG 62.574 63.158 20.42 20.42 45.62 3.51
76 77 3.573772 CTTCTCACTGGCGCCGACA 62.574 63.158 23.90 2.68 0.00 4.35
77 78 2.811317 CTTCTCACTGGCGCCGAC 60.811 66.667 23.90 0.00 0.00 4.79
78 79 3.282745 GACTTCTCACTGGCGCCGA 62.283 63.158 23.90 12.42 0.00 5.54
79 80 2.811317 GACTTCTCACTGGCGCCG 60.811 66.667 23.90 18.98 0.00 6.46
80 81 2.811317 CGACTTCTCACTGGCGCC 60.811 66.667 22.73 22.73 0.00 6.53
81 82 3.482783 GCGACTTCTCACTGGCGC 61.483 66.667 0.00 0.00 37.60 6.53
82 83 3.175240 CGCGACTTCTCACTGGCG 61.175 66.667 0.00 0.00 37.56 5.69
83 84 2.049063 ACGCGACTTCTCACTGGC 60.049 61.111 15.93 0.00 0.00 4.85
84 85 0.730834 CAGACGCGACTTCTCACTGG 60.731 60.000 15.93 0.00 0.00 4.00
85 86 1.340657 GCAGACGCGACTTCTCACTG 61.341 60.000 15.93 9.59 0.00 3.66
86 87 1.081108 GCAGACGCGACTTCTCACT 60.081 57.895 15.93 0.00 0.00 3.41
87 88 1.068287 GAGCAGACGCGACTTCTCAC 61.068 60.000 26.49 7.17 45.49 3.51
88 89 1.210413 GAGCAGACGCGACTTCTCA 59.790 57.895 26.49 0.00 45.49 3.27
89 90 0.796491 CAGAGCAGACGCGACTTCTC 60.796 60.000 24.83 24.83 45.49 2.87
90 91 1.211449 CAGAGCAGACGCGACTTCT 59.789 57.895 15.93 12.82 45.49 2.85
91 92 1.803519 CCAGAGCAGACGCGACTTC 60.804 63.158 15.93 6.62 45.49 3.01
92 93 2.259818 CCAGAGCAGACGCGACTT 59.740 61.111 15.93 0.00 45.49 3.01
93 94 4.427661 GCCAGAGCAGACGCGACT 62.428 66.667 15.93 10.02 45.49 4.18
103 104 4.802051 TTCATGCCCGGCCAGAGC 62.802 66.667 7.03 1.95 38.76 4.09
104 105 2.191513 CATTCATGCCCGGCCAGAG 61.192 63.158 7.03 0.00 0.00 3.35
105 106 2.124193 CATTCATGCCCGGCCAGA 60.124 61.111 7.03 1.44 0.00 3.86
106 107 2.440796 ACATTCATGCCCGGCCAG 60.441 61.111 7.03 0.00 0.00 4.85
107 108 2.755064 CACATTCATGCCCGGCCA 60.755 61.111 7.03 0.00 0.00 5.36
108 109 3.530260 CCACATTCATGCCCGGCC 61.530 66.667 7.03 0.00 0.00 6.13
109 110 4.211502 GCCACATTCATGCCCGGC 62.212 66.667 1.04 1.04 34.96 6.13
110 111 2.755064 TGCCACATTCATGCCCGG 60.755 61.111 0.00 0.00 0.00 5.73
111 112 2.048023 AGTGCCACATTCATGCCCG 61.048 57.895 0.00 0.00 0.00 6.13
112 113 0.966875 TCAGTGCCACATTCATGCCC 60.967 55.000 0.00 0.00 0.00 5.36
113 114 1.108776 ATCAGTGCCACATTCATGCC 58.891 50.000 0.00 0.00 0.00 4.40
114 115 1.801395 GCATCAGTGCCACATTCATGC 60.801 52.381 0.00 1.23 45.76 4.06
115 116 2.203800 GCATCAGTGCCACATTCATG 57.796 50.000 0.00 0.00 45.76 3.07
153 154 2.172659 GCGCTTTCCGTCCGAAAC 59.827 61.111 0.00 0.00 35.49 2.78
154 155 3.408020 CGCGCTTTCCGTCCGAAA 61.408 61.111 5.56 0.00 38.16 3.46
172 173 2.994643 AAAACACCCTCCCTTGCCCG 62.995 60.000 0.00 0.00 0.00 6.13
173 174 1.152333 AAAACACCCTCCCTTGCCC 60.152 57.895 0.00 0.00 0.00 5.36
174 175 0.759060 ACAAAACACCCTCCCTTGCC 60.759 55.000 0.00 0.00 0.00 4.52
175 176 0.673985 GACAAAACACCCTCCCTTGC 59.326 55.000 0.00 0.00 0.00 4.01
176 177 0.951558 CGACAAAACACCCTCCCTTG 59.048 55.000 0.00 0.00 0.00 3.61
177 178 0.179001 CCGACAAAACACCCTCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
178 179 1.454539 CCGACAAAACACCCTCCCT 59.545 57.895 0.00 0.00 0.00 4.20
182 183 0.179029 CTGACCCGACAAAACACCCT 60.179 55.000 0.00 0.00 0.00 4.34
198 199 4.056125 CACGTCTGAGCGCCCTGA 62.056 66.667 2.29 0.00 34.88 3.86
206 207 0.320771 CTCCCAAACCCACGTCTGAG 60.321 60.000 0.00 0.00 0.00 3.35
209 210 2.430367 GCTCCCAAACCCACGTCT 59.570 61.111 0.00 0.00 0.00 4.18
210 211 3.047877 CGCTCCCAAACCCACGTC 61.048 66.667 0.00 0.00 0.00 4.34
214 215 2.751688 GTACCGCTCCCAAACCCA 59.248 61.111 0.00 0.00 0.00 4.51
245 246 1.883084 CGGAGATAAGCGTGTGGGC 60.883 63.158 0.00 0.00 0.00 5.36
249 250 2.223971 CCATAACCGGAGATAAGCGTGT 60.224 50.000 9.46 0.00 0.00 4.49
250 251 2.404215 CCATAACCGGAGATAAGCGTG 58.596 52.381 9.46 0.00 0.00 5.34
251 252 1.343465 CCCATAACCGGAGATAAGCGT 59.657 52.381 9.46 0.00 0.00 5.07
252 253 1.616865 TCCCATAACCGGAGATAAGCG 59.383 52.381 9.46 0.00 0.00 4.68
260 261 3.451902 ACGTATTTTCTCCCATAACCGGA 59.548 43.478 9.46 0.00 0.00 5.14
262 265 4.026310 CGAACGTATTTTCTCCCATAACCG 60.026 45.833 0.00 0.00 0.00 4.44
264 267 5.006068 GTCCGAACGTATTTTCTCCCATAAC 59.994 44.000 0.00 0.00 0.00 1.89
268 271 2.564062 AGTCCGAACGTATTTTCTCCCA 59.436 45.455 0.00 0.00 0.00 4.37
272 275 4.624015 TGAACAGTCCGAACGTATTTTCT 58.376 39.130 0.00 0.00 0.00 2.52
278 281 0.386352 CGCTGAACAGTCCGAACGTA 60.386 55.000 3.77 0.00 0.00 3.57
280 283 2.372690 CCGCTGAACAGTCCGAACG 61.373 63.158 3.77 0.00 0.00 3.95
283 286 2.649034 GTCCGCTGAACAGTCCGA 59.351 61.111 3.77 0.00 0.00 4.55
288 291 2.351835 CCTATATCGGTCCGCTGAACAG 60.352 54.545 6.34 0.00 33.10 3.16
289 292 1.611977 CCTATATCGGTCCGCTGAACA 59.388 52.381 6.34 0.00 33.10 3.18
290 293 1.612463 ACCTATATCGGTCCGCTGAAC 59.388 52.381 6.34 0.00 33.10 3.18
291 294 1.884579 GACCTATATCGGTCCGCTGAA 59.115 52.381 14.19 0.00 46.19 3.02
306 309 1.447140 GTCATGCAACGCGGACCTA 60.447 57.895 12.47 0.00 32.12 3.08
310 313 1.233950 ATTGTGTCATGCAACGCGGA 61.234 50.000 12.47 0.00 32.25 5.54
315 318 3.438087 ACAGAGCTATTGTGTCATGCAAC 59.562 43.478 2.73 0.00 0.00 4.17
316 319 3.678289 ACAGAGCTATTGTGTCATGCAA 58.322 40.909 2.73 0.00 0.00 4.08
329 332 2.223502 CGCATAAGTTCGGACAGAGCTA 60.224 50.000 0.00 0.00 39.62 3.32
331 334 0.924090 CGCATAAGTTCGGACAGAGC 59.076 55.000 0.00 0.00 0.00 4.09
344 357 2.417239 GACCATCAAAACGTCCGCATAA 59.583 45.455 0.00 0.00 0.00 1.90
352 365 2.225491 CCAACATCGACCATCAAAACGT 59.775 45.455 0.00 0.00 0.00 3.99
361 374 0.107703 GGCATCTCCAACATCGACCA 60.108 55.000 0.00 0.00 34.01 4.02
380 393 9.608617 CATTGATCTTTGTATGCTATGCTTAAG 57.391 33.333 0.00 0.00 0.00 1.85
381 394 9.341078 TCATTGATCTTTGTATGCTATGCTTAA 57.659 29.630 0.00 0.00 0.00 1.85
382 395 8.907222 TCATTGATCTTTGTATGCTATGCTTA 57.093 30.769 0.00 0.00 0.00 3.09
414 427 8.287439 TCATCTTTGTTGTGTCCTTTTCTTTA 57.713 30.769 0.00 0.00 0.00 1.85
419 432 4.646492 AGCTCATCTTTGTTGTGTCCTTTT 59.354 37.500 0.00 0.00 0.00 2.27
456 469 1.272313 TGGGTACTCTGCTTCGTAGGT 60.272 52.381 0.00 0.00 0.00 3.08
570 583 0.332632 TGATGCAAGGGGAAGGGAAG 59.667 55.000 0.00 0.00 0.00 3.46
571 584 1.009997 ATGATGCAAGGGGAAGGGAA 58.990 50.000 0.00 0.00 0.00 3.97
572 585 1.009997 AATGATGCAAGGGGAAGGGA 58.990 50.000 0.00 0.00 0.00 4.20
573 586 1.342275 TGAATGATGCAAGGGGAAGGG 60.342 52.381 0.00 0.00 0.00 3.95
574 587 1.753073 GTGAATGATGCAAGGGGAAGG 59.247 52.381 0.00 0.00 0.00 3.46
684 707 6.624204 CGTTGGTTAAACAAGTGGAGTTTTCT 60.624 38.462 6.08 0.00 39.65 2.52
928 973 2.840203 AAATGGGGCGGAGGAGGAGA 62.840 60.000 0.00 0.00 0.00 3.71
1067 1355 3.301274 AGCCGAGAAAAGGTAGCTAGAT 58.699 45.455 0.00 0.00 0.00 1.98
1078 1366 1.153901 CGCCTACGAGCCGAGAAAA 60.154 57.895 1.50 0.00 43.93 2.29
1080 1368 2.749044 ACGCCTACGAGCCGAGAA 60.749 61.111 1.50 0.00 43.93 2.87
1618 1918 2.631428 CGCGTGGTGTCTTGTTGG 59.369 61.111 0.00 0.00 0.00 3.77
1645 1945 1.706287 GCTTCAGATTTCGCCGGTCC 61.706 60.000 1.90 0.00 0.00 4.46
1646 1946 1.019278 TGCTTCAGATTTCGCCGGTC 61.019 55.000 1.90 0.00 0.00 4.79
1647 1947 0.605319 TTGCTTCAGATTTCGCCGGT 60.605 50.000 1.90 0.00 0.00 5.28
1666 1966 7.038302 AGGAAAGAAAGAAAAAGAGTGGGTTTT 60.038 33.333 0.00 0.00 0.00 2.43
1667 1967 6.440647 AGGAAAGAAAGAAAAAGAGTGGGTTT 59.559 34.615 0.00 0.00 0.00 3.27
1669 1969 5.519808 AGGAAAGAAAGAAAAAGAGTGGGT 58.480 37.500 0.00 0.00 0.00 4.51
1749 2052 1.103398 CCCATCGCCATCTTTCACCC 61.103 60.000 0.00 0.00 0.00 4.61
1815 2122 2.978018 GCCAACCACCGCTACAAGC 61.978 63.158 0.00 0.00 38.02 4.01
1816 2123 1.577328 CTGCCAACCACCGCTACAAG 61.577 60.000 0.00 0.00 0.00 3.16
1817 2124 1.599518 CTGCCAACCACCGCTACAA 60.600 57.895 0.00 0.00 0.00 2.41
1818 2125 2.031919 CTGCCAACCACCGCTACA 59.968 61.111 0.00 0.00 0.00 2.74
1819 2126 2.032071 ACTGCCAACCACCGCTAC 59.968 61.111 0.00 0.00 0.00 3.58
1820 2127 2.031919 CACTGCCAACCACCGCTA 59.968 61.111 0.00 0.00 0.00 4.26
1821 2128 4.954970 CCACTGCCAACCACCGCT 62.955 66.667 0.00 0.00 0.00 5.52
1822 2129 4.947147 TCCACTGCCAACCACCGC 62.947 66.667 0.00 0.00 0.00 5.68
1834 2141 1.217689 CCTCATCTCCTCCTCTCCACT 59.782 57.143 0.00 0.00 0.00 4.00
1840 2147 2.528564 CATCCTCCTCATCTCCTCCTC 58.471 57.143 0.00 0.00 0.00 3.71
1841 2148 1.149711 CCATCCTCCTCATCTCCTCCT 59.850 57.143 0.00 0.00 0.00 3.69
1842 2149 1.643310 CCATCCTCCTCATCTCCTCC 58.357 60.000 0.00 0.00 0.00 4.30
1934 2252 9.140286 GCTAACGAATACTGCATCATAGAAATA 57.860 33.333 0.00 0.00 0.00 1.40
1982 2304 3.068881 CGGCCAGTGGAAGAAGGA 58.931 61.111 15.20 0.00 0.00 3.36
1983 2305 2.747855 GCGGCCAGTGGAAGAAGG 60.748 66.667 15.20 0.00 0.00 3.46
1984 2306 3.121030 CGCGGCCAGTGGAAGAAG 61.121 66.667 15.20 0.00 0.00 2.85
1985 2307 2.463589 ATTCGCGGCCAGTGGAAGAA 62.464 55.000 15.20 11.95 0.00 2.52
1986 2308 2.463589 AATTCGCGGCCAGTGGAAGA 62.464 55.000 15.20 2.62 0.00 2.87
1987 2309 2.040544 AATTCGCGGCCAGTGGAAG 61.041 57.895 15.20 6.65 0.00 3.46
1988 2310 2.033448 AATTCGCGGCCAGTGGAA 59.967 55.556 15.20 0.00 0.00 3.53
1989 2311 2.745884 CAATTCGCGGCCAGTGGA 60.746 61.111 15.20 0.00 0.00 4.02
2114 2442 7.416154 CAAATTTTGCTCAAACAGACATGAT 57.584 32.000 0.00 0.00 0.00 2.45
2130 2485 2.094099 GCCATACGCCTTGCAAATTTTG 59.906 45.455 0.00 4.72 0.00 2.44
2151 2506 1.909376 ACCGAAACATGTCGATCTCG 58.091 50.000 8.40 7.63 43.86 4.04
2154 2509 1.396996 CCCAACCGAAACATGTCGATC 59.603 52.381 8.40 2.84 43.86 3.69
2182 2537 2.904866 GACGCCTTTGGTGCCACA 60.905 61.111 0.00 0.00 36.54 4.17
2185 2540 2.676471 ATGGACGCCTTTGGTGCC 60.676 61.111 0.00 1.17 36.54 5.01
2251 2606 2.975799 GCAGAAAACGGGGCGTCA 60.976 61.111 0.00 0.00 39.99 4.35
2302 2657 4.996434 GCAGCTGGCTGGACGTGT 62.996 66.667 21.76 0.00 43.77 4.49
2359 2714 3.311110 GAGCTGTGACCCGGTGGA 61.311 66.667 0.00 0.00 34.81 4.02
2360 2715 4.742201 CGAGCTGTGACCCGGTGG 62.742 72.222 0.00 0.00 37.80 4.61
2361 2716 4.742201 CCGAGCTGTGACCCGGTG 62.742 72.222 0.00 0.00 37.40 4.94
2402 2761 2.093447 CCACCGCTCTGAATTTCTACCT 60.093 50.000 0.00 0.00 0.00 3.08
2762 3300 8.512956 CATCCATCATTATTTCTTGAGTCCATC 58.487 37.037 0.00 0.00 0.00 3.51
2769 3307 8.644216 CCCAATTCATCCATCATTATTTCTTGA 58.356 33.333 0.00 0.00 0.00 3.02
2773 3311 8.413309 TCTCCCAATTCATCCATCATTATTTC 57.587 34.615 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.