Multiple sequence alignment - TraesCS6D01G373000

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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 TraesCS6D01G373000 chr6D 100.000 3430 0 0 2473 5902 458027686 458024257 0.000000e+00 6335.0
1 TraesCS6D01G373000 chr6D 100.000 1982 0 0 1 1982 458030158 458028177 0.000000e+00 3661.0
2 TraesCS6D01G373000 chr6D 88.521 2474 249 24 2564 5012 457697730 457695267 0.000000e+00 2963.0
3 TraesCS6D01G373000 chr6D 91.626 2066 171 1 2869 4932 458057306 458055241 0.000000e+00 2856.0
4 TraesCS6D01G373000 chr6D 87.582 2295 273 11 2505 4794 458018317 458016030 0.000000e+00 2649.0
5 TraesCS6D01G373000 chr6D 88.195 1618 175 10 2772 4387 458049529 458047926 0.000000e+00 1916.0
6 TraesCS6D01G373000 chr6D 87.993 1216 108 20 794 1982 458060701 458059497 0.000000e+00 1402.0
7 TraesCS6D01G373000 chr6D 88.333 960 100 10 1031 1982 457700116 457699161 0.000000e+00 1142.0
8 TraesCS6D01G373000 chr6D 84.339 1028 130 17 963 1982 458019631 458018627 0.000000e+00 977.0
9 TraesCS6D01G373000 chr6D 86.939 758 86 9 1023 1771 458050280 458049527 0.000000e+00 839.0
10 TraesCS6D01G373000 chr6D 88.793 348 25 6 419 764 458061273 458060938 1.180000e-111 414.0
11 TraesCS6D01G373000 chr6D 89.418 189 18 2 5207 5393 458054800 458054612 2.750000e-58 237.0
12 TraesCS6D01G373000 chr6D 83.396 265 16 5 1 252 457693191 457692942 2.770000e-53 220.0
13 TraesCS6D01G373000 chr6D 93.243 74 4 1 180 252 458062170 458062097 2.250000e-19 108.0
14 TraesCS6D01G373000 chr6D 88.525 61 6 1 814 874 458050546 458050487 8.200000e-09 73.1
15 TraesCS6D01G373000 chr6B 88.926 2691 242 30 2733 5380 696343044 696340367 0.000000e+00 3267.0
16 TraesCS6D01G373000 chr6B 86.247 2683 270 55 2505 5154 696177667 696175051 0.000000e+00 2819.0
17 TraesCS6D01G373000 chr6B 85.720 2626 314 42 2505 5088 696250119 696247513 0.000000e+00 2715.0
18 TraesCS6D01G373000 chr6B 86.980 2358 291 13 2505 4856 696151378 696149031 0.000000e+00 2639.0
19 TraesCS6D01G373000 chr6B 85.098 2342 297 36 2515 4844 696357708 696355407 0.000000e+00 2344.0
20 TraesCS6D01G373000 chr6B 88.999 809 89 0 1174 1982 696251224 696250416 0.000000e+00 1002.0
21 TraesCS6D01G373000 chr6B 86.433 914 115 8 1072 1982 696152606 696151699 0.000000e+00 992.0
22 TraesCS6D01G373000 chr6B 88.395 810 93 1 1174 1982 696345274 696344465 0.000000e+00 974.0
23 TraesCS6D01G373000 chr6B 88.005 817 95 2 1166 1982 696179066 696178253 0.000000e+00 963.0
24 TraesCS6D01G373000 chr6B 84.318 880 112 16 1114 1982 696358855 696357991 0.000000e+00 837.0
25 TraesCS6D01G373000 chr6B 83.422 561 60 19 5365 5902 696340342 696339792 1.910000e-134 490.0
26 TraesCS6D01G373000 chr6B 85.000 360 19 7 359 715 696244632 696244305 3.410000e-87 333.0
27 TraesCS6D01G373000 chr6B 84.911 338 25 11 611 936 696251773 696251450 9.540000e-83 318.0
28 TraesCS6D01G373000 chr6B 90.769 195 15 1 5711 5902 696171790 696171596 2.110000e-64 257.0
29 TraesCS6D01G373000 chr6B 90.256 195 16 1 5711 5902 696174533 696174339 9.820000e-63 252.0
30 TraesCS6D01G373000 chr6B 90.206 194 16 2 373 564 696347502 696347310 3.530000e-62 250.0
31 TraesCS6D01G373000 chr6B 86.325 234 20 6 30 252 696194162 696193930 1.640000e-60 244.0
32 TraesCS6D01G373000 chr6B 85.375 253 15 9 1 232 696351821 696351570 5.910000e-60 243.0
33 TraesCS6D01G373000 chr6B 86.449 214 20 5 5350 5554 696172098 696171885 5.950000e-55 226.0
34 TraesCS6D01G373000 chr6B 86.449 214 20 5 5350 5554 696174841 696174628 5.950000e-55 226.0
35 TraesCS6D01G373000 chr6B 90.123 162 12 3 3 161 696145715 696145555 2.160000e-49 207.0
36 TraesCS6D01G373000 chr6B 82.000 250 18 12 554 802 696345691 696345468 2.810000e-43 187.0
37 TraesCS6D01G373000 chr6B 80.142 141 13 11 126 252 696361890 696361751 2.270000e-14 91.6
38 TraesCS6D01G373000 chr6A 86.624 2669 286 36 2505 5132 604609792 604607154 0.000000e+00 2885.0
39 TraesCS6D01G373000 chr6A 88.519 810 91 2 1174 1982 604610885 604610077 0.000000e+00 979.0
40 TraesCS6D01G373000 chr6A 85.650 885 85 22 4794 5646 604838724 604837850 0.000000e+00 893.0
41 TraesCS6D01G373000 chr6A 92.125 546 22 5 359 903 604618661 604618136 0.000000e+00 750.0
42 TraesCS6D01G373000 chr6A 86.651 427 48 3 4424 4850 604852337 604851920 1.160000e-126 464.0
43 TraesCS6D01G373000 chr6A 86.093 302 16 8 1 293 604619579 604619295 9.610000e-78 302.0
44 TraesCS6D01G373000 chr6A 92.262 168 8 2 1013 1176 604618090 604617924 3.560000e-57 233.0


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 TraesCS6D01G373000 chr6D 458024257 458030158 5901 True 4998.000000 6335 100.000000 1 5902 2 chr6D.!!$R3 5901
1 TraesCS6D01G373000 chr6D 458016030 458019631 3601 True 1813.000000 2649 85.960500 963 4794 2 chr6D.!!$R2 3831
2 TraesCS6D01G373000 chr6D 457692942 457700116 7174 True 1441.666667 2963 86.750000 1 5012 3 chr6D.!!$R1 5011
3 TraesCS6D01G373000 chr6D 458054612 458062170 7558 True 1003.400000 2856 90.214600 180 5393 5 chr6D.!!$R5 5213
4 TraesCS6D01G373000 chr6D 458047926 458050546 2620 True 942.700000 1916 87.886333 814 4387 3 chr6D.!!$R4 3573
5 TraesCS6D01G373000 chr6B 696145555 696152606 7051 True 1279.333333 2639 87.845333 3 4856 3 chr6B.!!$R2 4853
6 TraesCS6D01G373000 chr6B 696244305 696251773 7468 True 1092.000000 2715 86.157500 359 5088 4 chr6B.!!$R4 4729
7 TraesCS6D01G373000 chr6B 696339792 696347502 7710 True 1033.600000 3267 86.589800 373 5902 5 chr6B.!!$R5 5529
8 TraesCS6D01G373000 chr6B 696351570 696361890 10320 True 878.900000 2344 83.733250 1 4844 4 chr6B.!!$R6 4843
9 TraesCS6D01G373000 chr6B 696171596 696179066 7470 True 790.500000 2819 88.029167 1166 5902 6 chr6B.!!$R3 4736
10 TraesCS6D01G373000 chr6A 604607154 604610885 3731 True 1932.000000 2885 87.571500 1174 5132 2 chr6A.!!$R3 3958
11 TraesCS6D01G373000 chr6A 604837850 604838724 874 True 893.000000 893 85.650000 4794 5646 1 chr6A.!!$R1 852
12 TraesCS6D01G373000 chr6A 604617924 604619579 1655 True 428.333333 750 90.160000 1 1176 3 chr6A.!!$R4 1175

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
293 308 0.100682 GAGCTCGACGCCTTGACATA 59.899 55.0 0.00 0.0 40.39 2.29 F
957 5335 0.661552 CTCCATATGCTGCACTGCAC 59.338 55.0 3.57 0.0 46.33 4.57 F
1821 6395 0.834687 TTGCAAGGGAGGTCTACCGT 60.835 55.0 0.00 0.0 39.08 4.83 F
2628 8415 0.240678 TAAGCAAAGCACACATGGCG 59.759 50.0 0.00 0.0 36.08 5.69 F
3908 11014 0.824109 TGTCGAAGCTACCATCAGGG 59.176 55.0 0.00 0.0 44.81 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 6377 0.040058 TACGGTAGACCTCCCTTGCA 59.960 55.000 0.0 0.0 0.00 4.08 R
2618 8405 1.085893 TGCTTATGTCGCCATGTGTG 58.914 50.000 0.0 0.0 32.29 3.82 R
3617 10723 1.203052 CCATCACGCTTTGCCAAATCT 59.797 47.619 0.0 0.0 0.00 2.40 R
4469 11578 1.823041 GGCAGGCATCTCTCCAAGC 60.823 63.158 0.0 0.0 0.00 4.01 R
5066 12371 0.034756 AGCACACCATCACGCACTTA 59.965 50.000 0.0 0.0 0.00 2.24 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
35 36 6.973843 TCAGGAAGCATTGTATTATTGATGC 58.026 36.000 0.00 0.00 43.88 3.91
56 57 5.122519 TGCTTACACTGAGTGAATCACAAA 58.877 37.500 20.97 2.06 36.74 2.83
63 64 4.694509 ACTGAGTGAATCACAAAGAGATGC 59.305 41.667 16.38 0.00 36.74 3.91
65 66 4.694037 TGAGTGAATCACAAAGAGATGCAG 59.306 41.667 16.38 0.00 36.74 4.41
79 80 4.430423 GCAGCTGCACGTACACGC 62.430 66.667 33.36 1.04 44.43 5.34
80 81 3.777925 CAGCTGCACGTACACGCC 61.778 66.667 0.00 0.00 44.43 5.68
81 82 3.991051 AGCTGCACGTACACGCCT 61.991 61.111 1.02 0.00 44.43 5.52
82 83 2.126228 GCTGCACGTACACGCCTA 60.126 61.111 0.85 0.00 44.43 3.93
83 84 2.442188 GCTGCACGTACACGCCTAC 61.442 63.158 0.85 0.00 44.43 3.18
84 85 1.804326 CTGCACGTACACGCCTACC 60.804 63.158 0.85 0.00 44.43 3.18
85 86 2.259204 GCACGTACACGCCTACCA 59.741 61.111 0.85 0.00 44.43 3.25
86 87 1.804326 GCACGTACACGCCTACCAG 60.804 63.158 0.85 0.00 44.43 4.00
87 88 1.878070 CACGTACACGCCTACCAGA 59.122 57.895 0.85 0.00 44.43 3.86
88 89 0.454600 CACGTACACGCCTACCAGAT 59.545 55.000 0.85 0.00 44.43 2.90
89 90 0.454600 ACGTACACGCCTACCAGATG 59.545 55.000 0.85 0.00 44.43 2.90
90 91 0.870307 CGTACACGCCTACCAGATGC 60.870 60.000 0.00 0.00 0.00 3.91
99 100 2.666596 CTACCAGATGCCGCCTTCCC 62.667 65.000 0.00 0.00 0.00 3.97
101 102 2.203126 CAGATGCCGCCTTCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
124 125 1.880027 GCCTTGAACCATCAGACGTTT 59.120 47.619 0.00 0.00 36.78 3.60
131 132 1.308069 CCATCAGACGTTTGCCCTGG 61.308 60.000 0.23 4.72 0.00 4.45
221 236 1.838073 CGGCCCCAAGTTCAGGTACT 61.838 60.000 0.00 0.00 43.88 2.73
269 284 1.001378 GCAGTTTGGGTTGTGCTACTG 60.001 52.381 0.00 0.00 36.85 2.74
293 308 0.100682 GAGCTCGACGCCTTGACATA 59.899 55.000 0.00 0.00 40.39 2.29
294 309 0.747255 AGCTCGACGCCTTGACATAT 59.253 50.000 3.66 0.00 40.39 1.78
295 310 0.855349 GCTCGACGCCTTGACATATG 59.145 55.000 0.00 0.00 0.00 1.78
300 315 2.288457 CGACGCCTTGACATATGGATCT 60.288 50.000 7.80 0.00 0.00 2.75
304 319 2.225019 GCCTTGACATATGGATCTTGCG 59.775 50.000 7.80 0.00 0.00 4.85
306 321 4.129380 CCTTGACATATGGATCTTGCGAA 58.871 43.478 7.80 0.00 0.00 4.70
307 322 4.024556 CCTTGACATATGGATCTTGCGAAC 60.025 45.833 7.80 0.00 0.00 3.95
308 323 3.466836 TGACATATGGATCTTGCGAACC 58.533 45.455 7.80 0.00 33.00 3.62
309 324 3.134623 TGACATATGGATCTTGCGAACCT 59.865 43.478 7.80 0.00 33.52 3.50
310 325 4.130118 GACATATGGATCTTGCGAACCTT 58.870 43.478 7.80 0.00 33.52 3.50
311 326 3.879295 ACATATGGATCTTGCGAACCTTG 59.121 43.478 7.80 0.00 33.52 3.61
312 327 1.098050 ATGGATCTTGCGAACCTTGC 58.902 50.000 0.00 0.00 33.52 4.01
313 328 1.298157 TGGATCTTGCGAACCTTGCG 61.298 55.000 0.00 0.00 33.52 4.85
314 329 1.019278 GGATCTTGCGAACCTTGCGA 61.019 55.000 0.00 0.00 34.24 5.10
315 330 0.796312 GATCTTGCGAACCTTGCGAA 59.204 50.000 0.00 0.00 34.24 4.70
316 331 0.798776 ATCTTGCGAACCTTGCGAAG 59.201 50.000 0.00 0.00 34.24 3.79
334 1177 8.481974 TTGCGAAGTATAAAAGTATAAGTGCA 57.518 30.769 0.00 0.00 0.00 4.57
335 1178 8.657074 TGCGAAGTATAAAAGTATAAGTGCAT 57.343 30.769 0.00 0.00 0.00 3.96
354 1216 0.875728 TAAATGCACCGTGGGTTTCG 59.124 50.000 0.00 0.00 31.02 3.46
357 1780 1.234615 ATGCACCGTGGGTTTCGAAG 61.235 55.000 0.00 0.00 31.02 3.79
375 1798 2.861147 AGGCACAGTAAGGAAGGAAC 57.139 50.000 0.00 0.00 0.00 3.62
432 2816 8.191446 TGCATGACTCACTTAACTAATAGAGAC 58.809 37.037 0.00 0.00 0.00 3.36
437 2821 9.944663 GACTCACTTAACTAATAGAGACATGAG 57.055 37.037 0.00 4.52 35.82 2.90
474 2860 8.202745 ACAAGTAAAAGAATATGCTGCTAGTC 57.797 34.615 0.00 0.15 0.00 2.59
829 5056 8.229253 ACATATACCTTTGAGATGTACGTACA 57.771 34.615 29.15 29.15 40.98 2.90
833 5060 6.579666 ACCTTTGAGATGTACGTACACTTA 57.420 37.500 29.54 20.41 39.30 2.24
942 5320 2.046023 CAGTCAATGCGGGCTCCA 60.046 61.111 0.00 0.00 0.00 3.86
943 5321 1.452651 CAGTCAATGCGGGCTCCAT 60.453 57.895 0.00 0.00 0.00 3.41
957 5335 0.661552 CTCCATATGCTGCACTGCAC 59.338 55.000 3.57 0.00 46.33 4.57
958 5336 1.091197 TCCATATGCTGCACTGCACG 61.091 55.000 3.57 0.00 46.33 5.34
961 5339 3.898167 TATGCTGCACTGCACGCCA 62.898 57.895 3.57 8.97 46.33 5.69
979 5357 1.238439 CATGTTTGTCCGACAAGGCT 58.762 50.000 13.51 0.75 39.53 4.58
1108 5596 3.108376 ACCCCATTAGTCAGTCCTCTTC 58.892 50.000 0.00 0.00 0.00 2.87
1122 5610 2.187100 CCTCTTCCCTGCTCTTCTCTT 58.813 52.381 0.00 0.00 0.00 2.85
1225 5790 2.983592 GCGTGTTGGGTCCCTTGG 60.984 66.667 10.00 0.00 0.00 3.61
1252 5817 1.737355 GCTCACTGGTTTGCTTGCCA 61.737 55.000 0.00 0.00 0.00 4.92
1338 5903 2.745884 CATGGCGCGGTCCAGAAA 60.746 61.111 8.83 0.00 39.89 2.52
1377 5942 1.296392 CGATGTCCAGGTGAAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
1590 6155 5.771666 TCGTCTCAAGGAGGTAAAAGAGTTA 59.228 40.000 0.00 0.00 0.00 2.24
1623 6188 7.775561 AGTTACAAGTTGGATGATATTCCCTTC 59.224 37.037 7.96 0.00 34.67 3.46
1672 6246 4.704540 TGTCTGCTCTTTTTGTTGAGGAAA 59.295 37.500 0.00 0.00 30.64 3.13
1745 6319 5.652014 TGTTGGAAGATAAAAATGGCTCGAT 59.348 36.000 0.00 0.00 0.00 3.59
1803 6377 4.383661 GGTGGATTGGGAAAAACAACACTT 60.384 41.667 0.00 0.00 30.25 3.16
1821 6395 0.834687 TTGCAAGGGAGGTCTACCGT 60.835 55.000 0.00 0.00 39.08 4.83
1929 6504 2.079158 CAGATGCCTTGCGAGAAAGAA 58.921 47.619 1.22 0.00 0.00 2.52
2521 7822 9.655769 GTAGCAAATAAATGATGTGTGTATGAG 57.344 33.333 0.00 0.00 0.00 2.90
2603 8390 6.598064 TGTTACATCTATGTCTGAAGTCTCGA 59.402 38.462 0.00 0.00 41.97 4.04
2618 8405 6.090898 TGAAGTCTCGATTAAGTAAGCAAAGC 59.909 38.462 0.00 0.00 0.00 3.51
2628 8415 0.240678 TAAGCAAAGCACACATGGCG 59.759 50.000 0.00 0.00 36.08 5.69
2658 8470 5.824624 AGCAATAATCACATGGTAGACCTTG 59.175 40.000 11.91 11.91 44.21 3.61
2667 8483 8.877864 TCACATGGTAGACCTTGAATAATTTT 57.122 30.769 18.63 0.00 42.04 1.82
2760 8591 2.564062 CCCCTTGGAGTTCGTAGTGTTA 59.436 50.000 0.00 0.00 0.00 2.41
2800 8632 6.772233 TGGTTGGATTCCTTATACATGACATG 59.228 38.462 14.02 14.02 0.00 3.21
2802 8634 5.316167 TGGATTCCTTATACATGACATGGC 58.684 41.667 19.39 0.00 33.60 4.40
2811 8643 8.774586 CCTTATACATGACATGGCTAACTTTAC 58.225 37.037 19.39 0.00 33.60 2.01
2924 10029 3.552132 TCAGCATGGGACGCTATTAAA 57.448 42.857 0.00 0.00 37.72 1.52
3119 10225 3.004106 GCTGCCCTGATATGCTAAAACAG 59.996 47.826 0.00 0.00 0.00 3.16
3237 10343 1.190643 GGAGAGGGTCAGAAGGTCTG 58.809 60.000 0.00 0.00 45.59 3.51
3378 10484 6.612863 TCCTGAGGATTATGTGATTGAGAGAA 59.387 38.462 0.00 0.00 0.00 2.87
3381 10487 8.672823 TGAGGATTATGTGATTGAGAGAAATG 57.327 34.615 0.00 0.00 0.00 2.32
3467 10573 2.067013 GTTGCCGAGAACCACTTCTAC 58.933 52.381 0.00 0.00 36.82 2.59
3617 10723 1.907807 GGCAGGCCATGGTCAAACA 60.908 57.895 20.74 0.00 35.81 2.83
3689 10795 1.404391 GACCAAGAGCTTGCATCCATG 59.596 52.381 4.72 0.00 39.16 3.66
3692 10798 2.159282 CCAAGAGCTTGCATCCATGTTC 60.159 50.000 4.72 0.00 39.16 3.18
3693 10799 2.490509 CAAGAGCTTGCATCCATGTTCA 59.509 45.455 0.00 0.00 33.45 3.18
3694 10800 2.366533 AGAGCTTGCATCCATGTTCAG 58.633 47.619 0.00 0.00 31.57 3.02
3768 10874 3.780804 TCAAACACTTGCCTAGGCTTA 57.219 42.857 33.07 20.14 42.51 3.09
3772 10878 5.538433 TCAAACACTTGCCTAGGCTTATTTT 59.462 36.000 33.07 21.15 42.51 1.82
3794 10900 3.127895 TGTTTGAAGCTTTGCGTGTACTT 59.872 39.130 0.00 0.00 0.00 2.24
3804 10910 5.402270 GCTTTGCGTGTACTTGAATTTCAAT 59.598 36.000 12.04 5.96 35.59 2.57
3873 10979 3.402628 TTCAACTGAAGTACCTGAGCC 57.597 47.619 0.00 0.00 0.00 4.70
3908 11014 0.824109 TGTCGAAGCTACCATCAGGG 59.176 55.000 0.00 0.00 44.81 4.45
3955 11061 3.743911 ACGCTAGATCTCAGAGATACACG 59.256 47.826 13.26 15.59 34.53 4.49
3973 11079 2.940410 CACGTATAAAGGAATTGCCCGT 59.060 45.455 0.00 0.00 37.37 5.28
3981 11087 1.550072 AGGAATTGCCCGTTGGAATTG 59.450 47.619 6.43 0.00 37.37 2.32
3991 11097 1.798223 CGTTGGAATTGTTCAGCTCGA 59.202 47.619 0.00 0.00 0.00 4.04
4020 11126 5.300969 GCAACATCTACTCATTGCAAGAA 57.699 39.130 4.94 0.00 45.38 2.52
4041 11150 7.592885 AGAAATCCATATTCCAATGTTCCTG 57.407 36.000 0.00 0.00 0.00 3.86
4152 11261 1.279271 CAGTCGAGGAACTGGGGAATT 59.721 52.381 0.00 0.00 41.55 2.17
4166 11275 5.221702 ACTGGGGAATTTGACCAATTTGAAG 60.222 40.000 0.00 0.00 35.02 3.02
4354 11463 5.954752 TGCCATATAACCTCCAAATGTTTCA 59.045 36.000 0.00 0.00 0.00 2.69
4365 11474 3.828451 CCAAATGTTTCAGATGTCCACCT 59.172 43.478 0.00 0.00 0.00 4.00
4366 11475 4.082571 CCAAATGTTTCAGATGTCCACCTC 60.083 45.833 0.00 0.00 0.00 3.85
4469 11578 0.249784 CACAGGAGGATCTGCGGATG 60.250 60.000 14.17 0.78 38.26 3.51
4638 11747 1.613437 CGTTTGAAGAAGGGGCAATGT 59.387 47.619 0.00 0.00 0.00 2.71
4844 11953 1.005215 CCCAATCATCCCAGGCTATCC 59.995 57.143 0.00 0.00 0.00 2.59
4851 11960 1.843376 CCCAGGCTATCCATCCGGT 60.843 63.158 0.00 0.00 33.74 5.28
4866 12002 1.003118 TCCGGTGTGAAATGGAAGAGG 59.997 52.381 0.00 0.00 0.00 3.69
4875 12017 1.589414 AATGGAAGAGGGCTACAGCT 58.411 50.000 0.54 0.00 41.70 4.24
4963 12228 5.147330 TCAGTACCAACACAAGAGGTATG 57.853 43.478 0.00 0.00 39.83 2.39
4976 12242 9.857656 ACACAAGAGGTATGAATCATAATCAAT 57.142 29.630 4.30 0.00 0.00 2.57
5017 12315 3.403968 TGTACGCAACCTTTCTTATGCA 58.596 40.909 0.00 0.00 38.69 3.96
5019 12317 3.492421 ACGCAACCTTTCTTATGCATG 57.508 42.857 10.16 0.00 38.69 4.06
5055 12359 6.430962 TCTTTCATCTATTCAGGGGATCTG 57.569 41.667 0.00 0.00 44.68 2.90
5066 12371 1.628846 AGGGGATCTGCTGTTAAACGT 59.371 47.619 0.00 0.00 0.00 3.99
5091 12396 0.884259 CGTGATGGTGTGCTGTTGGA 60.884 55.000 0.00 0.00 0.00 3.53
5190 12663 8.511604 TTCAGGGAATCTTGTATCAGAATTTC 57.488 34.615 0.00 0.00 0.00 2.17
5202 12675 7.022979 TGTATCAGAATTTCTTGCGTTGATTG 58.977 34.615 0.00 0.00 0.00 2.67
5276 13386 6.422701 TGCATGTACTTGTGTGTAACTTAGTC 59.577 38.462 10.17 0.00 38.04 2.59
5292 13402 6.763715 ACTTAGTCTAATGGGCCATTCATA 57.236 37.500 33.85 16.88 35.54 2.15
5371 15617 4.174411 TGTTCTGTCACTCCAATACTCG 57.826 45.455 0.00 0.00 0.00 4.18
5399 15686 5.655488 TCTTCTATGTAGCTTGAACTGCTC 58.345 41.667 0.00 0.00 41.46 4.26
5404 15691 4.179926 TGTAGCTTGAACTGCTCTACTG 57.820 45.455 0.00 0.00 41.46 2.74
5463 16077 0.395724 GGGGCGTGAGATTTGGGATT 60.396 55.000 0.00 0.00 0.00 3.01
5490 16306 6.126652 ACAGTAGGGTAATGATTCAGCAGAAT 60.127 38.462 3.70 3.70 46.85 2.40
5528 16349 1.228644 TGGCCAGCTGCATCAACTT 60.229 52.632 8.66 0.00 43.89 2.66
5603 16476 2.818714 CTTCCTCTGCTGCCTGCG 60.819 66.667 0.00 0.00 46.63 5.18
5638 16650 4.039245 TGGAATCAATCGAGTACCTCCATC 59.961 45.833 5.23 0.00 0.00 3.51
5651 16690 1.455773 TCCATCGATCGAGTGGGCT 60.456 57.895 29.71 12.23 33.78 5.19
5653 16692 1.735973 CATCGATCGAGTGGGCTGA 59.264 57.895 23.84 0.00 0.00 4.26
5695 16734 2.731217 GCAAGGTGTGACACAATCAAC 58.269 47.619 18.40 0.00 39.72 3.18
5704 16743 3.960002 GTGACACAATCAACGAGAAAACG 59.040 43.478 0.00 0.00 39.72 3.60
5779 16827 3.612517 TGCACAGGTAGCACAAGAG 57.387 52.632 0.00 0.00 37.02 2.85
5801 16852 0.842030 AGATGCAGGGTGTTGAGGGA 60.842 55.000 0.00 0.00 0.00 4.20
5834 20270 6.323739 GCTATTATTTGGTTTTCAGGGGATCA 59.676 38.462 0.00 0.00 0.00 2.92
5837 20273 1.851304 TGGTTTTCAGGGGATCATGC 58.149 50.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.925718 TCTCTTTGTGATTCACTCAGTGTAAG 59.074 38.462 17.26 9.20 35.11 2.34
41 42 4.694037 TGCATCTCTTTGTGATTCACTCAG 59.306 41.667 17.26 12.46 35.11 3.35
63 64 2.812542 TAGGCGTGTACGTGCAGCTG 62.813 60.000 20.54 10.11 42.22 4.24
65 66 2.126228 TAGGCGTGTACGTGCAGC 60.126 61.111 6.58 12.52 42.22 5.25
78 79 3.406595 AAGGCGGCATCTGGTAGGC 62.407 63.158 13.08 0.00 0.00 3.93
79 80 1.227674 GAAGGCGGCATCTGGTAGG 60.228 63.158 13.08 0.00 0.00 3.18
80 81 1.227674 GGAAGGCGGCATCTGGTAG 60.228 63.158 13.08 0.00 0.00 3.18
81 82 2.742116 GGGAAGGCGGCATCTGGTA 61.742 63.158 13.08 0.00 0.00 3.25
82 83 4.115199 GGGAAGGCGGCATCTGGT 62.115 66.667 13.08 0.00 0.00 4.00
83 84 3.764160 GAGGGAAGGCGGCATCTGG 62.764 68.421 13.08 0.00 0.00 3.86
84 85 2.203126 GAGGGAAGGCGGCATCTG 60.203 66.667 13.08 0.00 0.00 2.90
85 86 2.074948 ATGAGGGAAGGCGGCATCT 61.075 57.895 13.08 2.13 0.00 2.90
86 87 1.895707 CATGAGGGAAGGCGGCATC 60.896 63.158 13.08 9.11 0.00 3.91
87 88 2.194056 CATGAGGGAAGGCGGCAT 59.806 61.111 13.08 0.00 0.00 4.40
88 89 4.802051 GCATGAGGGAAGGCGGCA 62.802 66.667 13.08 0.00 0.00 5.69
90 91 3.350031 AAGGCATGAGGGAAGGCGG 62.350 63.158 0.00 0.00 0.00 6.13
99 100 2.681848 GTCTGATGGTTCAAGGCATGAG 59.318 50.000 0.00 0.00 39.77 2.90
101 102 1.399440 CGTCTGATGGTTCAAGGCATG 59.601 52.381 0.00 0.00 0.00 4.06
124 125 2.527624 AGCAGACTGTCCAGGGCA 60.528 61.111 3.76 0.00 0.00 5.36
131 132 2.505118 GTCGGCGAGCAGACTGTC 60.505 66.667 11.20 0.00 37.97 3.51
211 226 2.550208 CCTGGTGGACAAGTACCTGAAC 60.550 54.545 0.00 0.00 37.92 3.18
221 236 2.203337 GCTGTGCCTGGTGGACAA 60.203 61.111 0.00 0.00 34.57 3.18
300 315 1.803334 ATACTTCGCAAGGTTCGCAA 58.197 45.000 1.84 0.00 38.47 4.85
306 321 9.095065 CACTTATACTTTTATACTTCGCAAGGT 57.905 33.333 1.84 0.00 38.47 3.50
307 322 8.062448 GCACTTATACTTTTATACTTCGCAAGG 58.938 37.037 1.84 0.00 38.47 3.61
308 323 8.600625 TGCACTTATACTTTTATACTTCGCAAG 58.399 33.333 0.00 0.00 0.00 4.01
309 324 8.481974 TGCACTTATACTTTTATACTTCGCAA 57.518 30.769 0.00 0.00 0.00 4.85
310 325 8.657074 ATGCACTTATACTTTTATACTTCGCA 57.343 30.769 0.00 0.00 0.00 5.10
334 1177 1.470890 CGAAACCCACGGTGCATTTAT 59.529 47.619 1.68 0.00 35.34 1.40
335 1178 0.875728 CGAAACCCACGGTGCATTTA 59.124 50.000 1.68 0.00 35.34 1.40
337 1180 0.820074 TTCGAAACCCACGGTGCATT 60.820 50.000 1.68 0.00 35.34 3.56
341 1203 2.613506 GCCTTCGAAACCCACGGTG 61.614 63.158 0.00 0.00 35.34 4.94
354 1216 3.075148 GTTCCTTCCTTACTGTGCCTTC 58.925 50.000 0.00 0.00 0.00 3.46
357 1780 2.561478 TGTTCCTTCCTTACTGTGCC 57.439 50.000 0.00 0.00 0.00 5.01
375 1798 5.336744 TCCGTTTTTCTTACTGCAAACTTG 58.663 37.500 0.00 0.00 0.00 3.16
459 2845 5.009410 AGCCAATTTGACTAGCAGCATATTC 59.991 40.000 0.00 0.00 0.00 1.75
463 2849 2.731572 AGCCAATTTGACTAGCAGCAT 58.268 42.857 0.00 0.00 0.00 3.79
474 2860 5.484173 TCGTGCTTAATCTAGCCAATTTG 57.516 39.130 0.00 0.00 40.49 2.32
547 2935 5.249420 TGCACATAACCAAGTGTTAGCATA 58.751 37.500 0.00 0.00 42.50 3.14
957 5335 0.110238 CTTGTCGGACAAACATGGCG 60.110 55.000 22.60 7.24 37.69 5.69
958 5336 0.240945 CCTTGTCGGACAAACATGGC 59.759 55.000 22.60 0.00 37.69 4.40
961 5339 1.981256 AAGCCTTGTCGGACAAACAT 58.019 45.000 22.60 9.63 37.69 2.71
979 5357 0.966179 TCTGCTTCACGGCTCTGTAA 59.034 50.000 0.00 0.00 0.00 2.41
1048 5428 6.450545 AGATTCCTTGAGTTTTTGCTTTAGC 58.549 36.000 0.00 0.00 42.50 3.09
1108 5596 2.094078 CAGAGTGAAGAGAAGAGCAGGG 60.094 54.545 0.00 0.00 0.00 4.45
1122 5610 0.106708 GCTTGGTGTGGTCAGAGTGA 59.893 55.000 0.00 0.00 0.00 3.41
1222 5787 1.455849 CAGTGAGCTTCCCCACCAA 59.544 57.895 0.00 0.00 34.00 3.67
1225 5790 0.178990 AAACCAGTGAGCTTCCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
1252 5817 2.360350 CAGGCGGGCACACTCATT 60.360 61.111 3.78 0.00 0.00 2.57
1338 5903 1.560923 GATCTTGCAGCGTCGTGTAT 58.439 50.000 0.00 0.00 0.00 2.29
1377 5942 2.301296 CTCCCTCAGCAACGATATCCAT 59.699 50.000 0.00 0.00 0.00 3.41
1623 6188 3.338249 AGGATCCACAGTTGAATGTTCG 58.662 45.455 15.82 0.00 0.00 3.95
1684 6258 2.028420 TCTCTTGGACCATCAATGCG 57.972 50.000 0.00 0.00 0.00 4.73
1745 6319 1.202758 ACAACACCTTGCGATCCTTGA 60.203 47.619 0.00 0.00 0.00 3.02
1803 6377 0.040058 TACGGTAGACCTCCCTTGCA 59.960 55.000 0.00 0.00 0.00 4.08
1821 6395 3.924114 TCAAAATGCCCTCGGATCTTA 57.076 42.857 0.00 0.00 0.00 2.10
1929 6504 5.760253 CCAAGTGTCGATGCCTTCTATAAAT 59.240 40.000 0.00 0.00 0.00 1.40
2495 7073 9.655769 CTCATACACACATCATTTATTTGCTAC 57.344 33.333 0.00 0.00 0.00 3.58
2498 7076 6.974048 TGCTCATACACACATCATTTATTTGC 59.026 34.615 0.00 0.00 0.00 3.68
2502 7080 7.174426 CCTCATGCTCATACACACATCATTTAT 59.826 37.037 0.00 0.00 0.00 1.40
2521 7822 4.990426 ACTTTAACAATGTTTGCCTCATGC 59.010 37.500 3.17 0.00 41.77 4.06
2572 8352 9.507329 ACTTCAGACATAGATGTAACACAAAAT 57.493 29.630 0.00 0.00 41.95 1.82
2603 8390 5.713025 CCATGTGTGCTTTGCTTACTTAAT 58.287 37.500 0.00 0.00 0.00 1.40
2618 8405 1.085893 TGCTTATGTCGCCATGTGTG 58.914 50.000 0.00 0.00 32.29 3.82
2628 8415 8.499162 GTCTACCATGTGATTATTGCTTATGTC 58.501 37.037 0.00 0.00 0.00 3.06
2667 8483 7.254898 GCATCATATAAGCTGCAAGTACTCAAA 60.255 37.037 1.02 0.00 35.30 2.69
2924 10029 4.647564 ATCATTCTCCGGGAAAGCATAT 57.352 40.909 0.00 0.00 37.49 1.78
2982 10087 6.862711 ATGAGAACATGATCTTGCTACATG 57.137 37.500 6.96 0.00 44.42 3.21
3237 10343 5.408299 GGTTTTTATCCAATGCAGAACCAAC 59.592 40.000 0.00 0.00 36.27 3.77
3378 10484 3.950397 TCCATCGCCTCACTAAAACATT 58.050 40.909 0.00 0.00 0.00 2.71
3381 10487 3.495001 GCTATCCATCGCCTCACTAAAAC 59.505 47.826 0.00 0.00 0.00 2.43
3467 10573 7.065324 TGGACCATACTTTTGTTTATTAGCTCG 59.935 37.037 0.00 0.00 0.00 5.03
3617 10723 1.203052 CCATCACGCTTTGCCAAATCT 59.797 47.619 0.00 0.00 0.00 2.40
3689 10795 6.992063 TGGCTTAGATCTTCATTTCTGAAC 57.008 37.500 0.00 0.00 36.46 3.18
3692 10798 6.939132 ACATGGCTTAGATCTTCATTTCTG 57.061 37.500 0.00 0.00 0.00 3.02
3693 10799 6.703607 CGTACATGGCTTAGATCTTCATTTCT 59.296 38.462 0.00 0.00 0.00 2.52
3694 10800 6.701841 TCGTACATGGCTTAGATCTTCATTTC 59.298 38.462 0.00 0.00 0.00 2.17
3768 10874 3.932089 ACACGCAAAGCTTCAAACAAAAT 59.068 34.783 0.00 0.00 0.00 1.82
3772 10878 2.680841 AGTACACGCAAAGCTTCAAACA 59.319 40.909 0.00 0.00 0.00 2.83
3794 10900 7.391275 TGCAGACTCTCACAATATTGAAATTCA 59.609 33.333 22.16 0.00 0.00 2.57
3804 10910 6.322201 TCATACTCATGCAGACTCTCACAATA 59.678 38.462 0.00 0.00 31.73 1.90
3857 10963 3.100671 CCTAAGGCTCAGGTACTTCAGT 58.899 50.000 0.00 0.00 34.60 3.41
3873 10979 2.628178 TCGACATATGAGTGCCCCTAAG 59.372 50.000 10.38 0.00 0.00 2.18
3887 10993 2.628178 CCCTGATGGTAGCTTCGACATA 59.372 50.000 0.00 0.00 0.00 2.29
3908 11014 6.661377 TCTCTAGACCATATAGCCTCACAATC 59.339 42.308 0.00 0.00 0.00 2.67
3944 11050 7.095607 GGCAATTCCTTTATACGTGTATCTCTG 60.096 40.741 0.00 0.00 0.00 3.35
3955 11061 3.949113 TCCAACGGGCAATTCCTTTATAC 59.051 43.478 0.00 0.00 34.39 1.47
3973 11079 5.801350 CTTATCGAGCTGAACAATTCCAA 57.199 39.130 0.00 0.00 0.00 3.53
3991 11097 5.008415 GCAATGAGTAGATGTTGCAGCTTAT 59.992 40.000 1.17 0.00 44.63 1.73
3998 11104 4.952262 TCTTGCAATGAGTAGATGTTGC 57.048 40.909 0.00 2.25 45.27 4.17
4020 11126 5.532406 CGTCAGGAACATTGGAATATGGATT 59.468 40.000 0.00 0.00 0.00 3.01
4041 11150 3.587797 TGGTATCTTCACTTCACCGTC 57.412 47.619 0.00 0.00 31.64 4.79
4076 11185 5.490139 AGATCGCCTGTAAATTGTTCATG 57.510 39.130 0.00 0.00 0.00 3.07
4082 11191 1.867233 CCCGAGATCGCCTGTAAATTG 59.133 52.381 0.00 0.00 38.18 2.32
4152 11261 4.541705 TGGAGTTCCTTCAAATTGGTCAA 58.458 39.130 0.00 0.00 36.82 3.18
4166 11275 3.676324 CGTCCAACTGTAGATGGAGTTCC 60.676 52.174 10.71 0.04 45.77 3.62
4354 11463 2.757894 ATCGTAGGAGGTGGACATCT 57.242 50.000 0.00 0.00 0.00 2.90
4365 11474 4.080807 TGGCATCTTTGGTAAATCGTAGGA 60.081 41.667 0.00 0.00 0.00 2.94
4366 11475 4.196193 TGGCATCTTTGGTAAATCGTAGG 58.804 43.478 0.00 0.00 0.00 3.18
4469 11578 1.823041 GGCAGGCATCTCTCCAAGC 60.823 63.158 0.00 0.00 0.00 4.01
4694 11803 1.992557 TGGCCAAGACCCAAGTAGAAT 59.007 47.619 0.61 0.00 0.00 2.40
4844 11953 2.679837 CTCTTCCATTTCACACCGGATG 59.320 50.000 9.46 6.25 0.00 3.51
4851 11960 2.642311 TGTAGCCCTCTTCCATTTCACA 59.358 45.455 0.00 0.00 0.00 3.58
4866 12002 2.761208 TCTCTTCCTTGTAGCTGTAGCC 59.239 50.000 0.00 0.00 43.38 3.93
4875 12017 2.753452 CGGTGTAGCTCTCTTCCTTGTA 59.247 50.000 0.00 0.00 0.00 2.41
4944 12202 6.170506 TGATTCATACCTCTTGTGTTGGTAC 58.829 40.000 0.00 0.00 38.89 3.34
4976 12242 7.851963 GCGTACAGAAAGTGTTGTACAAAATTA 59.148 33.333 10.51 0.00 46.22 1.40
5017 12315 6.185511 AGATGAAAGAACATGTCACATCCAT 58.814 36.000 18.08 10.84 35.80 3.41
5019 12317 7.798596 ATAGATGAAAGAACATGTCACATCC 57.201 36.000 18.08 3.49 35.80 3.51
5055 12359 2.219216 TCACGCACTTACGTTTAACAGC 59.781 45.455 0.00 0.00 45.75 4.40
5066 12371 0.034756 AGCACACCATCACGCACTTA 59.965 50.000 0.00 0.00 0.00 2.24
5091 12396 4.220693 TCACCACGAGATTCCAATCAAT 57.779 40.909 2.21 0.00 37.89 2.57
5161 12592 7.020827 TCTGATACAAGATTCCCTGAAAACT 57.979 36.000 0.00 0.00 0.00 2.66
5230 12787 6.013379 TGCACAATAGGGAAAATTCACCTAA 58.987 36.000 11.77 0.00 40.05 2.69
5276 13386 8.237811 ACTTAACTTTATGAATGGCCCATTAG 57.762 34.615 9.43 5.29 33.90 1.73
5292 13402 4.158949 AGCCAACCGTTTCAACTTAACTTT 59.841 37.500 0.00 0.00 0.00 2.66
5371 15617 6.533367 CAGTTCAAGCTACATAGAAGAGTTCC 59.467 42.308 0.00 0.00 0.00 3.62
5399 15686 5.482908 ACCAGATGAAGCAGTTTACAGTAG 58.517 41.667 0.00 0.00 0.00 2.57
5404 15691 5.689383 TGAAACCAGATGAAGCAGTTTAC 57.311 39.130 0.00 0.00 31.14 2.01
5463 16077 4.469586 TGCTGAATCATTACCCTACTGTGA 59.530 41.667 0.00 0.00 0.00 3.58
5549 16422 0.907486 AGCAGCAGAGCACCAGAATA 59.093 50.000 0.00 0.00 36.85 1.75
5603 16476 3.334583 TTGATTCCACTAGGCACTCAC 57.665 47.619 0.00 0.00 41.75 3.51
5638 16650 2.288457 ACATAATCAGCCCACTCGATCG 60.288 50.000 9.36 9.36 0.00 3.69
5651 16690 6.238621 GCGATGGTGGTTATTCAACATAATCA 60.239 38.462 0.00 0.00 44.25 2.57
5653 16692 5.592282 TGCGATGGTGGTTATTCAACATAAT 59.408 36.000 0.00 0.00 44.25 1.28
5695 16734 9.210426 CTTGATTATAAACATTCCGTTTTCTCG 57.790 33.333 0.00 0.00 45.79 4.04
5704 16743 7.753132 TGCAACGAACTTGATTATAAACATTCC 59.247 33.333 0.00 0.00 30.42 3.01
5779 16827 1.457346 CTCAACACCCTGCATCTTCC 58.543 55.000 0.00 0.00 0.00 3.46
5813 20249 5.104982 GCATGATCCCCTGAAAACCAAATAA 60.105 40.000 0.00 0.00 0.00 1.40
5837 20273 8.381387 CACTCGATGCAAGAGATTATGATAATG 58.619 37.037 23.80 8.22 38.97 1.90


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

AutoCloner maintained by Alex Coulton.