Multiple sequence alignment - TraesCS7A01G435800

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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 TraesCS7A01G435800 chr7A 100.000 4380 0 0 1 4380 629779772 629775393 0.000000e+00 8089
1 TraesCS7A01G435800 chr7A 94.019 1371 58 13 2384 3745 308454822 308456177 0.000000e+00 2056
2 TraesCS7A01G435800 chr7A 94.485 272 15 0 3745 4016 53858443 53858714 1.880000e-113 420
3 TraesCS7A01G435800 chr7A 93.548 279 17 1 3741 4018 26451663 26451941 8.760000e-112 414
4 TraesCS7A01G435800 chr1B 94.046 1730 84 13 2026 3741 538916897 538918621 0.000000e+00 2606
5 TraesCS7A01G435800 chr1B 93.920 1727 87 16 2026 3741 117569101 117570820 0.000000e+00 2591
6 TraesCS7A01G435800 chr1B 94.162 1336 62 14 2384 3706 192690476 192689144 0.000000e+00 2021
7 TraesCS7A01G435800 chr1B 96.016 728 28 1 1180 1906 538916175 538916902 0.000000e+00 1182
8 TraesCS7A01G435800 chr1B 95.192 728 34 1 1180 1906 117568379 117569106 0.000000e+00 1149
9 TraesCS7A01G435800 chr1B 90.463 367 30 3 4015 4380 192689123 192688761 3.060000e-131 479
10 TraesCS7A01G435800 chr1B 94.161 137 7 1 1901 2037 623731983 623732118 1.600000e-49 207
11 TraesCS7A01G435800 chr6B 92.758 1726 91 14 2027 3741 207721506 207719804 0.000000e+00 2464
12 TraesCS7A01G435800 chr6B 94.315 1372 66 10 2384 3745 393761050 393762419 0.000000e+00 2091
13 TraesCS7A01G435800 chr6B 94.301 1123 62 2 1 1123 328339267 328340387 0.000000e+00 1718
14 TraesCS7A01G435800 chr6B 92.992 528 37 0 596 1123 207735864 207735337 0.000000e+00 771
15 TraesCS7A01G435800 chr6B 90.110 364 35 1 4015 4377 393762416 393762779 5.130000e-129 472
16 TraesCS7A01G435800 chr6B 95.420 131 6 0 1900 2030 29755089 29755219 4.440000e-50 209
17 TraesCS7A01G435800 chr6D 95.664 1453 50 12 2028 3474 16118921 16120366 0.000000e+00 2322
18 TraesCS7A01G435800 chr6D 96.631 1128 30 4 1 1123 16117077 16118201 0.000000e+00 1866
19 TraesCS7A01G435800 chr6D 97.111 727 21 0 1180 1906 16118198 16118924 0.000000e+00 1227
20 TraesCS7A01G435800 chr6D 94.766 363 19 0 4015 4377 16120534 16120896 2.290000e-157 566
21 TraesCS7A01G435800 chr6D 93.502 277 16 2 3745 4019 470979360 470979084 1.130000e-110 411
22 TraesCS7A01G435800 chr6D 93.220 177 9 2 3572 3745 16120361 16120537 1.560000e-64 257
23 TraesCS7A01G435800 chr6D 94.286 140 7 1 1899 2038 160470643 160470781 3.430000e-51 213
24 TraesCS7A01G435800 chr3D 94.829 1373 56 13 2384 3745 256145692 256144324 0.000000e+00 2128
25 TraesCS7A01G435800 chr3D 90.463 367 27 5 4015 4380 256144327 256143968 1.100000e-130 477
26 TraesCS7A01G435800 chr3D 78.179 692 90 37 958 1614 503995039 503994374 6.870000e-103 385
27 TraesCS7A01G435800 chr3D 93.056 144 8 2 1887 2030 283321265 283321124 4.440000e-50 209
28 TraesCS7A01G435800 chr2B 94.469 1374 61 11 2384 3745 220361240 220362610 0.000000e+00 2102
29 TraesCS7A01G435800 chr2B 91.314 472 30 5 3285 3745 421412783 421412312 6.180000e-178 634
30 TraesCS7A01G435800 chr2B 90.437 366 33 2 4015 4380 421412315 421411952 8.520000e-132 481
31 TraesCS7A01G435800 chr4B 94.096 1372 64 12 2384 3745 414453262 414451898 0.000000e+00 2069
32 TraesCS7A01G435800 chr4B 94.924 1123 43 2 1 1123 149035759 149034651 0.000000e+00 1746
33 TraesCS7A01G435800 chr4B 94.835 1123 44 2 1 1123 148999535 148998427 0.000000e+00 1740
34 TraesCS7A01G435800 chr4B 94.797 788 34 5 337 1123 421859151 421858370 0.000000e+00 1221
35 TraesCS7A01G435800 chr4B 95.646 735 22 4 1180 1906 421858373 421857641 0.000000e+00 1171
36 TraesCS7A01G435800 chr4B 95.186 727 35 0 1180 1906 148998430 148997704 0.000000e+00 1149
37 TraesCS7A01G435800 chr4B 95.186 727 34 1 1180 1906 149034654 149033929 0.000000e+00 1147
38 TraesCS7A01G435800 chr4B 96.961 362 10 1 1 361 421859686 421859325 1.350000e-169 606
39 TraesCS7A01G435800 chr4B 90.634 363 33 1 4015 4376 414451901 414451539 8.520000e-132 481
40 TraesCS7A01G435800 chr4B 90.323 372 25 4 4015 4380 149029565 149029199 1.100000e-130 477
41 TraesCS7A01G435800 chr4B 92.440 291 20 2 3739 4028 656890781 656890492 8.760000e-112 414
42 TraesCS7A01G435800 chrUn 95.557 1193 45 8 2026 3215 286671174 286672361 0.000000e+00 1903
43 TraesCS7A01G435800 chrUn 95.557 1193 45 8 2026 3215 286676041 286674854 0.000000e+00 1903
44 TraesCS7A01G435800 chrUn 95.557 1193 45 8 2026 3215 335064662 335063475 0.000000e+00 1903
45 TraesCS7A01G435800 chrUn 94.505 728 39 1 1180 1906 286670452 286671179 0.000000e+00 1122
46 TraesCS7A01G435800 chrUn 93.561 528 33 1 596 1123 286669929 286670455 0.000000e+00 785
47 TraesCS7A01G435800 chrUn 93.561 528 33 1 596 1123 286677286 286676760 0.000000e+00 785
48 TraesCS7A01G435800 chrUn 93.561 528 33 1 596 1123 316389957 316390483 0.000000e+00 785
49 TraesCS7A01G435800 chr3A 96.260 1123 40 1 1 1123 296899509 296900629 0.000000e+00 1840
50 TraesCS7A01G435800 chr3A 94.661 768 38 2 2026 2793 296901347 296902111 0.000000e+00 1188
51 TraesCS7A01G435800 chr3A 95.742 728 29 2 1180 1906 296900626 296901352 0.000000e+00 1171
52 TraesCS7A01G435800 chr3A 79.274 661 87 31 987 1619 642210266 642209628 2.440000e-112 416
53 TraesCS7A01G435800 chr3A 96.183 131 5 0 1901 2031 580812813 580812683 9.540000e-52 215
54 TraesCS7A01G435800 chr1A 96.171 1123 39 4 1 1122 176409734 176410853 0.000000e+00 1832
55 TraesCS7A01G435800 chr1A 95.052 768 35 2 2026 2793 176411573 176412337 0.000000e+00 1205
56 TraesCS7A01G435800 chr1A 96.429 728 25 1 1180 1906 176410851 176411578 0.000000e+00 1199
57 TraesCS7A01G435800 chr1A 96.183 131 5 0 1901 2031 516009599 516009729 9.540000e-52 215
58 TraesCS7A01G435800 chr3B 95.676 902 34 4 1 901 286888027 286887130 0.000000e+00 1445
59 TraesCS7A01G435800 chr3B 93.284 670 35 6 3085 3745 277659002 277659670 0.000000e+00 979
60 TraesCS7A01G435800 chr3B 91.257 366 27 4 4015 4377 277659667 277660030 1.090000e-135 494
61 TraesCS7A01G435800 chr3B 84.709 412 43 9 1044 1454 378722989 378722597 1.140000e-105 394
62 TraesCS7A01G435800 chr7B 87.407 810 82 10 193 987 141075808 141075004 0.000000e+00 913
63 TraesCS7A01G435800 chr7B 84.709 412 43 9 1044 1454 141075002 141074610 1.140000e-105 394
64 TraesCS7A01G435800 chr5D 91.008 367 28 5 4016 4380 249150259 249149896 1.420000e-134 490
65 TraesCS7A01G435800 chr5D 86.726 226 13 6 373 582 65039254 65039030 7.320000e-58 235
66 TraesCS7A01G435800 chr5D 80.128 312 23 12 274 546 65007385 65007696 3.460000e-46 196
67 TraesCS7A01G435800 chr5A 94.604 278 14 1 3740 4016 392030987 392031264 3.130000e-116 429
68 TraesCS7A01G435800 chr5A 94.604 278 14 1 3740 4016 392032979 392033256 3.130000e-116 429
69 TraesCS7A01G435800 chr5A 93.214 280 18 1 3743 4021 509105065 509104786 1.130000e-110 411
70 TraesCS7A01G435800 chr5A 91.892 148 9 3 1886 2032 243810126 243809981 2.070000e-48 204
71 TraesCS7A01G435800 chr2A 93.380 287 17 2 3742 4026 763863540 763863254 1.460000e-114 424
72 TraesCS7A01G435800 chr4A 93.929 280 16 1 3741 4019 683792551 683792272 5.240000e-114 422
73 TraesCS7A01G435800 chr7D 93.706 143 7 2 1891 2032 598598607 598598466 3.430000e-51 213
74 TraesCS7A01G435800 chr2D 91.892 148 9 3 1900 2046 326403641 326403496 2.070000e-48 204


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 TraesCS7A01G435800 chr7A 629775393 629779772 4379 True 8089.000000 8089 100.000000 1 4380 1 chr7A.!!$R1 4379
1 TraesCS7A01G435800 chr7A 308454822 308456177 1355 False 2056.000000 2056 94.019000 2384 3745 1 chr7A.!!$F3 1361
2 TraesCS7A01G435800 chr1B 538916175 538918621 2446 False 1894.000000 2606 95.031000 1180 3741 2 chr1B.!!$F3 2561
3 TraesCS7A01G435800 chr1B 117568379 117570820 2441 False 1870.000000 2591 94.556000 1180 3741 2 chr1B.!!$F2 2561
4 TraesCS7A01G435800 chr1B 192688761 192690476 1715 True 1250.000000 2021 92.312500 2384 4380 2 chr1B.!!$R1 1996
5 TraesCS7A01G435800 chr6B 207719804 207721506 1702 True 2464.000000 2464 92.758000 2027 3741 1 chr6B.!!$R1 1714
6 TraesCS7A01G435800 chr6B 328339267 328340387 1120 False 1718.000000 1718 94.301000 1 1123 1 chr6B.!!$F2 1122
7 TraesCS7A01G435800 chr6B 393761050 393762779 1729 False 1281.500000 2091 92.212500 2384 4377 2 chr6B.!!$F3 1993
8 TraesCS7A01G435800 chr6B 207735337 207735864 527 True 771.000000 771 92.992000 596 1123 1 chr6B.!!$R2 527
9 TraesCS7A01G435800 chr6D 16117077 16120896 3819 False 1247.600000 2322 95.478400 1 4377 5 chr6D.!!$F2 4376
10 TraesCS7A01G435800 chr3D 256143968 256145692 1724 True 1302.500000 2128 92.646000 2384 4380 2 chr3D.!!$R3 1996
11 TraesCS7A01G435800 chr3D 503994374 503995039 665 True 385.000000 385 78.179000 958 1614 1 chr3D.!!$R2 656
12 TraesCS7A01G435800 chr2B 220361240 220362610 1370 False 2102.000000 2102 94.469000 2384 3745 1 chr2B.!!$F1 1361
13 TraesCS7A01G435800 chr2B 421411952 421412783 831 True 557.500000 634 90.875500 3285 4380 2 chr2B.!!$R1 1095
14 TraesCS7A01G435800 chr4B 149033929 149035759 1830 True 1446.500000 1746 95.055000 1 1906 2 chr4B.!!$R4 1905
15 TraesCS7A01G435800 chr4B 148997704 148999535 1831 True 1444.500000 1740 95.010500 1 1906 2 chr4B.!!$R3 1905
16 TraesCS7A01G435800 chr4B 414451539 414453262 1723 True 1275.000000 2069 92.365000 2384 4376 2 chr4B.!!$R5 1992
17 TraesCS7A01G435800 chr4B 421857641 421859686 2045 True 999.333333 1221 95.801333 1 1906 3 chr4B.!!$R6 1905
18 TraesCS7A01G435800 chrUn 335063475 335064662 1187 True 1903.000000 1903 95.557000 2026 3215 1 chrUn.!!$R1 1189
19 TraesCS7A01G435800 chrUn 286674854 286677286 2432 True 1344.000000 1903 94.559000 596 3215 2 chrUn.!!$R2 2619
20 TraesCS7A01G435800 chrUn 286669929 286672361 2432 False 1270.000000 1903 94.541000 596 3215 3 chrUn.!!$F2 2619
21 TraesCS7A01G435800 chrUn 316389957 316390483 526 False 785.000000 785 93.561000 596 1123 1 chrUn.!!$F1 527
22 TraesCS7A01G435800 chr3A 296899509 296902111 2602 False 1399.666667 1840 95.554333 1 2793 3 chr3A.!!$F1 2792
23 TraesCS7A01G435800 chr3A 642209628 642210266 638 True 416.000000 416 79.274000 987 1619 1 chr3A.!!$R2 632
24 TraesCS7A01G435800 chr1A 176409734 176412337 2603 False 1412.000000 1832 95.884000 1 2793 3 chr1A.!!$F2 2792
25 TraesCS7A01G435800 chr3B 286887130 286888027 897 True 1445.000000 1445 95.676000 1 901 1 chr3B.!!$R1 900
26 TraesCS7A01G435800 chr3B 277659002 277660030 1028 False 736.500000 979 92.270500 3085 4377 2 chr3B.!!$F1 1292
27 TraesCS7A01G435800 chr7B 141074610 141075808 1198 True 653.500000 913 86.058000 193 1454 2 chr7B.!!$R1 1261
28 TraesCS7A01G435800 chr5A 392030987 392033256 2269 False 429.000000 429 94.604000 3740 4016 2 chr5A.!!$F1 276

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
699 908 1.859427 AACTGCAGAGCAACATGGCG 61.859 55.0 23.35 0.0 38.41 5.69 F
1917 2182 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.0 0.00 0.0 0.00 4.37 F
1919 2184 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2276 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 R
2756 3022 0.034380 AGTCCTAGTAGCACGCTCCA 60.034 55.0 0.0 0.0 0.0 3.86 R
3905 4196 2.233676 GGGACTTAAAGTGGGCATTTGG 59.766 50.0 0.0 0.0 0.0 3.28 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
131 132 2.170260 AAACGAATGTGCAGGCGACG 62.170 55.000 0.00 0.00 0.00 5.12
642 851 5.278604 GTTGTCACCATTAGGACACAAAAC 58.721 41.667 0.00 0.00 43.22 2.43
699 908 1.859427 AACTGCAGAGCAACATGGCG 61.859 55.000 23.35 0.00 38.41 5.69
845 1056 9.831737 CTGCTGCATTTGTTTTATATATCCTAC 57.168 33.333 1.31 0.00 0.00 3.18
881 1092 6.692849 TCCTATATGCTGTCATGATCCTTT 57.307 37.500 0.00 0.00 34.22 3.11
882 1093 7.083062 TCCTATATGCTGTCATGATCCTTTT 57.917 36.000 0.00 0.00 34.22 2.27
906 1117 7.528996 TTTCAGTGATCATGTTGATTTTCCT 57.471 32.000 0.00 0.00 37.20 3.36
1077 1310 1.805539 CGTCGACGTGATGGCACAT 60.806 57.895 29.08 0.00 45.41 3.21
1338 1597 1.153568 CGATGTCGGCATGGTCACT 60.154 57.895 7.54 0.00 35.07 3.41
1696 1959 7.745620 TTAGGAAAGAAGAACAAGGATCAAC 57.254 36.000 0.00 0.00 0.00 3.18
1697 1960 5.073428 AGGAAAGAAGAACAAGGATCAACC 58.927 41.667 0.00 0.00 39.35 3.77
1794 2058 5.621197 TGCACACTGTCAATTATGTTACC 57.379 39.130 0.00 0.00 0.00 2.85
1862 2127 8.132362 ACTCGCTAAAGTACTAAATCTGATGAG 58.868 37.037 0.00 0.00 0.00 2.90
1911 2176 7.421087 AACTGAATACTAAAGTACTCCCTCC 57.579 40.000 0.00 0.00 32.72 4.30
1912 2177 5.593502 ACTGAATACTAAAGTACTCCCTCCG 59.406 44.000 0.00 0.00 32.72 4.63
1913 2178 5.513233 TGAATACTAAAGTACTCCCTCCGT 58.487 41.667 0.00 0.00 32.72 4.69
1914 2179 5.591877 TGAATACTAAAGTACTCCCTCCGTC 59.408 44.000 0.00 0.00 32.72 4.79
1915 2180 2.732763 ACTAAAGTACTCCCTCCGTCC 58.267 52.381 0.00 0.00 0.00 4.79
1916 2181 2.030371 CTAAAGTACTCCCTCCGTCCC 58.970 57.143 0.00 0.00 0.00 4.46
1917 2182 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
1918 2183 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1919 2184 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1920 2185 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1921 2186 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1922 2187 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1923 2188 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1924 2189 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1925 2190 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1926 2191 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1927 2192 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1928 2193 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1929 2194 2.147958 TCCGTCCCAAAATTCTTGTCG 58.852 47.619 0.00 0.00 0.00 4.35
1930 2195 1.877443 CCGTCCCAAAATTCTTGTCGT 59.123 47.619 0.00 0.00 0.00 4.34
1931 2196 3.068560 CCGTCCCAAAATTCTTGTCGTA 58.931 45.455 0.00 0.00 0.00 3.43
1932 2197 3.124636 CCGTCCCAAAATTCTTGTCGTAG 59.875 47.826 0.00 0.00 0.00 3.51
1933 2198 3.991773 CGTCCCAAAATTCTTGTCGTAGA 59.008 43.478 0.00 0.00 0.00 2.59
1934 2199 4.630069 CGTCCCAAAATTCTTGTCGTAGAT 59.370 41.667 0.00 0.00 40.67 1.98
1935 2200 5.121768 CGTCCCAAAATTCTTGTCGTAGATT 59.878 40.000 0.00 0.00 40.67 2.40
1936 2201 6.348213 CGTCCCAAAATTCTTGTCGTAGATTT 60.348 38.462 0.00 0.00 40.67 2.17
1937 2202 6.801862 GTCCCAAAATTCTTGTCGTAGATTTG 59.198 38.462 0.00 0.00 40.67 2.32
1938 2203 6.488683 TCCCAAAATTCTTGTCGTAGATTTGT 59.511 34.615 0.00 0.00 40.67 2.83
1939 2204 6.801862 CCCAAAATTCTTGTCGTAGATTTGTC 59.198 38.462 0.00 0.00 40.67 3.18
1940 2205 7.308589 CCCAAAATTCTTGTCGTAGATTTGTCT 60.309 37.037 0.00 0.00 40.67 3.41
1941 2206 8.717821 CCAAAATTCTTGTCGTAGATTTGTCTA 58.282 33.333 0.00 0.00 40.67 2.59
1942 2207 9.746711 CAAAATTCTTGTCGTAGATTTGTCTAG 57.253 33.333 0.00 0.00 40.67 2.43
1943 2208 9.706691 AAAATTCTTGTCGTAGATTTGTCTAGA 57.293 29.630 0.00 0.00 40.67 2.43
1944 2209 9.877178 AAATTCTTGTCGTAGATTTGTCTAGAT 57.123 29.630 0.00 0.00 40.67 1.98
1947 2212 9.952188 TTCTTGTCGTAGATTTGTCTAGATATG 57.048 33.333 0.00 0.00 40.67 1.78
1948 2213 8.568794 TCTTGTCGTAGATTTGTCTAGATATGG 58.431 37.037 0.00 0.00 40.67 2.74
1949 2214 8.459911 TTGTCGTAGATTTGTCTAGATATGGA 57.540 34.615 0.00 0.00 40.67 3.41
1950 2215 8.637196 TGTCGTAGATTTGTCTAGATATGGAT 57.363 34.615 0.00 0.00 40.67 3.41
1951 2216 8.515414 TGTCGTAGATTTGTCTAGATATGGATG 58.485 37.037 0.00 0.00 40.67 3.51
1952 2217 8.516234 GTCGTAGATTTGTCTAGATATGGATGT 58.484 37.037 0.00 0.00 40.67 3.06
1953 2218 9.734984 TCGTAGATTTGTCTAGATATGGATGTA 57.265 33.333 0.00 0.00 0.00 2.29
1985 2250 8.547967 ACTAAAATGTGACTTGATACATTCGT 57.452 30.769 0.00 0.00 44.32 3.85
1986 2251 9.647797 ACTAAAATGTGACTTGATACATTCGTA 57.352 29.630 0.00 0.00 44.32 3.43
1993 2258 9.297586 TGTGACTTGATACATTCGTATTTAGAC 57.702 33.333 0.00 0.00 38.48 2.59
1994 2259 9.297586 GTGACTTGATACATTCGTATTTAGACA 57.702 33.333 0.00 0.00 38.48 3.41
1995 2260 9.863845 TGACTTGATACATTCGTATTTAGACAA 57.136 29.630 0.00 0.00 38.48 3.18
2008 2273 9.917129 TCGTATTTAGACAAATGTAAGACAAGA 57.083 29.630 0.00 0.00 35.88 3.02
2016 2281 8.143835 AGACAAATGTAAGACAAGAATTTTGGG 58.856 33.333 7.26 0.00 31.16 4.12
2017 2282 8.017418 ACAAATGTAAGACAAGAATTTTGGGA 57.983 30.769 7.26 0.00 31.16 4.37
2018 2283 7.926018 ACAAATGTAAGACAAGAATTTTGGGAC 59.074 33.333 7.26 0.00 31.16 4.46
2019 2284 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
2020 2285 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
2021 2286 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2022 2287 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2023 2288 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2024 2289 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2048 2313 7.832685 GGGAGTACTAAATTTGGTGTTCCTAAT 59.167 37.037 24.83 6.08 39.95 1.73
2257 2523 7.758076 GGTTATGGTAGTAATTTGGACAAAAGC 59.242 37.037 1.17 0.00 33.56 3.51
2303 2569 7.062957 CAGTTTATTCTACCATGGATTCCCTT 58.937 38.462 21.47 0.00 0.00 3.95
2448 2714 7.233348 ACATTCAGGAAATATGTGACCAACTTT 59.767 33.333 0.00 0.00 31.66 2.66
2458 2724 1.850345 TGACCAACTTTCCCAAGGTCT 59.150 47.619 10.79 0.00 46.81 3.85
2465 2731 0.690192 TTTCCCAAGGTCTCGCATCA 59.310 50.000 0.00 0.00 0.00 3.07
2504 2770 2.701951 TCGGTCTACAACCTCCAAAACT 59.298 45.455 0.00 0.00 46.87 2.66
2639 2905 9.474920 TTTTTAAGTTTTCATGCTGATTACTGG 57.525 29.630 0.00 0.00 0.00 4.00
2756 3022 8.576442 CATGTAGGTTTTTGTAAGAATCCTGTT 58.424 33.333 0.00 0.00 0.00 3.16
2762 3028 2.972625 TGTAAGAATCCTGTTGGAGCG 58.027 47.619 0.00 0.00 46.91 5.03
2806 3074 7.683578 AGATTGGCTATTCTAGACATTGCATA 58.316 34.615 16.49 2.95 44.79 3.14
2881 3150 7.012799 TGTGTTAAATAACTGTCAGCACAATGA 59.987 33.333 0.00 0.00 37.12 2.57
3021 3296 8.324191 TCAGATATGTAAAATCCAGGACTCTT 57.676 34.615 0.00 0.00 0.00 2.85
3033 3308 3.804325 CCAGGACTCTTATGTAATGTGCG 59.196 47.826 0.00 0.00 0.00 5.34
3044 3319 8.764287 TCTTATGTAATGTGCGTTCAATATCTG 58.236 33.333 0.00 0.00 0.00 2.90
3119 3394 7.663081 TCATGCTCTCTAACTTCTTGACATTTT 59.337 33.333 0.00 0.00 0.00 1.82
3251 3526 7.750229 ATACTGATGTTTGTCTTGTGATTGT 57.250 32.000 0.00 0.00 0.00 2.71
3271 3546 3.266772 TGTTTCAGGATATTCTGTGCCCT 59.733 43.478 10.92 0.00 36.25 5.19
3363 3645 1.410882 AGAAGCGGCTTACTCAGATCC 59.589 52.381 16.38 0.00 0.00 3.36
3426 3708 9.622637 AGATATTCCTAGAGTAAATAAAGGGCT 57.377 33.333 0.00 0.00 0.00 5.19
3506 3789 5.368523 TCCTCGGACATTTTATTCCACCTAT 59.631 40.000 0.00 0.00 0.00 2.57
3535 3820 7.321153 ACCCCAATATCGAATATCTACTTTCG 58.679 38.462 0.00 0.00 44.53 3.46
3542 3827 5.647589 TCGAATATCTACTTTCGCACTGTT 58.352 37.500 0.49 0.00 43.26 3.16
3600 3885 5.767816 TTGTCTTAAGTGGGCTTTCTTTC 57.232 39.130 1.63 0.00 36.22 2.62
3749 4039 1.066929 CATTTGGTGCAACTAAGGCCC 60.067 52.381 2.04 0.00 38.96 5.80
3817 4108 3.074094 GTCCCAAGTCCCTAAAAAGTCCT 59.926 47.826 0.00 0.00 0.00 3.85
3832 4123 7.418337 AAAAAGTCCTTACATGTTTGGTTCT 57.582 32.000 2.30 7.39 0.00 3.01
3838 4129 4.772100 CCTTACATGTTTGGTTCTTGGGAT 59.228 41.667 2.30 0.00 0.00 3.85
3849 4140 9.457436 GTTTGGTTCTTGGGATTTATAAGTCTA 57.543 33.333 7.79 0.00 0.00 2.59
3911 4202 9.401058 AGAGTCTTATTTCATAAGTCCCAAATG 57.599 33.333 3.93 0.00 42.21 2.32
3932 4223 5.782677 TGCCCACTTTAAGTCCCTATAAA 57.217 39.130 0.00 0.00 0.00 1.40
3939 4230 7.225011 CACTTTAAGTCCCTATAAATCCCTCC 58.775 42.308 0.00 0.00 0.00 4.30
4016 4307 5.130477 AGTCTCTGAAAACAAACACCCTCTA 59.870 40.000 0.00 0.00 0.00 2.43
4030 4853 3.434641 CACCCTCTAAATCTATGCATGCG 59.565 47.826 14.09 0.00 0.00 4.73
4038 4863 5.779529 AAATCTATGCATGCGGAGAAATT 57.220 34.783 21.21 16.66 0.00 1.82
4058 5844 5.913946 ATTTGAGGTAATAGGAAGGGAGG 57.086 43.478 0.00 0.00 0.00 4.30
4076 5862 2.996621 GAGGAATCTCACCAGTTTCACG 59.003 50.000 0.00 0.00 39.74 4.35
4108 5938 2.970987 TCACTAGGTAGCATATGGGCA 58.029 47.619 4.56 0.00 35.83 5.36
4134 5964 1.729586 ATACCCGTGCCTCCATATGT 58.270 50.000 1.24 0.00 0.00 2.29
4218 6190 5.369409 AACCCTCCTTAGCAGGTTTATAC 57.631 43.478 0.00 0.00 39.59 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 7.759489 TGGATATAACACTAATCAAATGGCC 57.241 36.000 0.00 0.00 0.00 5.36
282 288 6.145534 GCCGTAGATGAATCGATAATCAAACA 59.854 38.462 18.30 4.64 0.00 2.83
699 908 3.697166 AGGACATGGAACCATTGTAACC 58.303 45.455 3.35 5.27 33.90 2.85
737 948 2.612212 AGATAATACGCCTGCAAAACGG 59.388 45.455 7.48 0.00 0.00 4.44
881 1092 7.868922 CAGGAAAATCAACATGATCACTGAAAA 59.131 33.333 0.00 0.00 35.76 2.29
882 1093 7.231115 TCAGGAAAATCAACATGATCACTGAAA 59.769 33.333 0.00 0.00 35.76 2.69
906 1117 1.313772 CACAACACCCGACCAAATCA 58.686 50.000 0.00 0.00 0.00 2.57
933 1147 1.538047 GATCAAAGAGCACAAGGGCA 58.462 50.000 0.00 0.00 35.83 5.36
944 1158 2.897436 CCAGAGCACATCGATCAAAGA 58.103 47.619 0.00 0.00 0.00 2.52
1077 1310 2.364842 GAGCCCAGCCTCCTCTGA 60.365 66.667 0.00 0.00 36.19 3.27
1338 1597 3.338249 GGAGTCAATGTTGCTGAAGCTA 58.662 45.455 3.61 0.00 42.66 3.32
1568 1830 2.510012 CAAGCGATGCTCTGCGGA 60.510 61.111 0.00 0.00 38.25 5.54
1696 1959 1.828768 CAGCCTCCTTAGCCTCTGG 59.171 63.158 0.00 0.00 0.00 3.86
1697 1960 1.145819 GCAGCCTCCTTAGCCTCTG 59.854 63.158 0.00 0.00 0.00 3.35
1794 2058 7.337689 TCCTGGTGAAATTTTCATCTCTATGTG 59.662 37.037 20.13 4.73 41.40 3.21
1862 2127 4.990543 TCGCTAAATATGCAGCATGTAC 57.009 40.909 18.81 1.71 39.31 2.90
1906 2171 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1907 2172 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1908 2173 2.159627 CGACAAGAATTTTGGGACGGAG 59.840 50.000 0.00 0.00 0.00 4.63
1909 2174 2.147958 CGACAAGAATTTTGGGACGGA 58.852 47.619 0.00 0.00 0.00 4.69
1910 2175 1.877443 ACGACAAGAATTTTGGGACGG 59.123 47.619 0.00 0.00 0.00 4.79
1911 2176 3.991773 TCTACGACAAGAATTTTGGGACG 59.008 43.478 0.00 0.00 0.00 4.79
1912 2177 6.496338 AATCTACGACAAGAATTTTGGGAC 57.504 37.500 0.00 0.00 0.00 4.46
1913 2178 6.488683 ACAAATCTACGACAAGAATTTTGGGA 59.511 34.615 0.00 0.00 33.04 4.37
1914 2179 6.677913 ACAAATCTACGACAAGAATTTTGGG 58.322 36.000 0.00 1.31 33.04 4.12
1915 2180 7.584987 AGACAAATCTACGACAAGAATTTTGG 58.415 34.615 0.00 0.00 33.04 3.28
1916 2181 9.746711 CTAGACAAATCTACGACAAGAATTTTG 57.253 33.333 0.00 1.14 36.29 2.44
1917 2182 9.706691 TCTAGACAAATCTACGACAAGAATTTT 57.293 29.630 0.00 0.00 36.29 1.82
1918 2183 9.877178 ATCTAGACAAATCTACGACAAGAATTT 57.123 29.630 0.00 0.00 36.29 1.82
1921 2186 9.952188 CATATCTAGACAAATCTACGACAAGAA 57.048 33.333 0.00 0.00 36.29 2.52
1922 2187 8.568794 CCATATCTAGACAAATCTACGACAAGA 58.431 37.037 0.00 0.00 36.29 3.02
1923 2188 8.568794 TCCATATCTAGACAAATCTACGACAAG 58.431 37.037 0.00 0.00 36.29 3.16
1924 2189 8.459911 TCCATATCTAGACAAATCTACGACAA 57.540 34.615 0.00 0.00 36.29 3.18
1925 2190 8.515414 CATCCATATCTAGACAAATCTACGACA 58.485 37.037 0.00 0.00 36.29 4.35
1926 2191 8.516234 ACATCCATATCTAGACAAATCTACGAC 58.484 37.037 0.00 0.00 36.29 4.34
1927 2192 8.637196 ACATCCATATCTAGACAAATCTACGA 57.363 34.615 0.00 0.00 36.29 3.43
1959 2224 9.647797 ACGAATGTATCAAGTCACATTTTAGTA 57.352 29.630 1.86 0.00 43.58 1.82
1960 2225 8.547967 ACGAATGTATCAAGTCACATTTTAGT 57.452 30.769 1.86 1.50 43.58 2.24
1967 2232 9.297586 GTCTAAATACGAATGTATCAAGTCACA 57.702 33.333 0.00 0.00 40.42 3.58
1968 2233 9.297586 TGTCTAAATACGAATGTATCAAGTCAC 57.702 33.333 0.00 0.00 40.42 3.67
1969 2234 9.863845 TTGTCTAAATACGAATGTATCAAGTCA 57.136 29.630 0.00 0.00 40.42 3.41
1982 2247 9.917129 TCTTGTCTTACATTTGTCTAAATACGA 57.083 29.630 0.00 0.00 34.81 3.43
1990 2255 8.143835 CCCAAAATTCTTGTCTTACATTTGTCT 58.856 33.333 0.00 0.00 27.14 3.41
1991 2256 8.141268 TCCCAAAATTCTTGTCTTACATTTGTC 58.859 33.333 0.00 0.00 27.14 3.18
1992 2257 7.926018 GTCCCAAAATTCTTGTCTTACATTTGT 59.074 33.333 0.00 0.00 27.14 2.83
1993 2258 7.114811 CGTCCCAAAATTCTTGTCTTACATTTG 59.885 37.037 0.00 0.00 0.00 2.32
1994 2259 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
1995 2260 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
1996 2261 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
1997 2262 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
1998 2263 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
1999 2264 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2000 2265 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2001 2266 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2002 2267 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2003 2268 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2004 2269 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2005 2270 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2006 2271 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2007 2272 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2008 2273 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2009 2274 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2010 2275 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2011 2276 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2012 2277 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2013 2278 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2014 2279 2.149973 TTTAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
2015 2280 4.439968 CAAATTTAGTACTCCCTCCGTCC 58.560 47.826 0.00 0.00 0.00 4.79
2016 2281 4.081254 ACCAAATTTAGTACTCCCTCCGTC 60.081 45.833 0.00 0.00 0.00 4.79
2017 2282 3.842436 ACCAAATTTAGTACTCCCTCCGT 59.158 43.478 0.00 0.00 0.00 4.69
2018 2283 4.189231 CACCAAATTTAGTACTCCCTCCG 58.811 47.826 0.00 0.00 0.00 4.63
2019 2284 5.175388 ACACCAAATTTAGTACTCCCTCC 57.825 43.478 0.00 0.00 0.00 4.30
2020 2285 5.646793 GGAACACCAAATTTAGTACTCCCTC 59.353 44.000 0.00 0.00 0.00 4.30
2021 2286 5.312443 AGGAACACCAAATTTAGTACTCCCT 59.688 40.000 0.00 4.12 0.00 4.20
2022 2287 5.567430 AGGAACACCAAATTTAGTACTCCC 58.433 41.667 0.00 2.40 0.00 4.30
2023 2288 8.803397 ATTAGGAACACCAAATTTAGTACTCC 57.197 34.615 0.00 7.71 0.00 3.85
2024 2289 8.890718 GGATTAGGAACACCAAATTTAGTACTC 58.109 37.037 0.00 0.00 0.00 2.59
2048 2313 0.534203 GGCAACACTTCCAACTCGGA 60.534 55.000 0.00 0.00 44.40 4.55
2148 2414 8.447833 CGACAGAAAGTATAGCCAACATTTAAA 58.552 33.333 0.00 0.00 0.00 1.52
2303 2569 4.826733 AGTTCTGAAACATGCACATACCAA 59.173 37.500 0.00 0.00 37.88 3.67
2411 2677 4.853468 TTCCTGAATGTGTATTGGCCTA 57.147 40.909 3.32 0.00 0.00 3.93
2448 2714 0.465705 GATGATGCGAGACCTTGGGA 59.534 55.000 0.00 0.00 0.00 4.37
2458 2724 5.791336 ATTAACCTGAGTAGATGATGCGA 57.209 39.130 0.00 0.00 0.00 5.10
2465 2731 6.130569 AGACCGAGAATTAACCTGAGTAGAT 58.869 40.000 0.00 0.00 0.00 1.98
2520 2786 4.180057 CAATGGGCGCTTAAGCATTTTAA 58.820 39.130 26.29 7.54 42.21 1.52
2571 2837 2.294233 TGTTCAGGAAAGCATGAAGCAC 59.706 45.455 0.00 0.00 44.44 4.40
2639 2905 1.336240 GCACAATTCAGCTCCCACAAC 60.336 52.381 0.00 0.00 0.00 3.32
2756 3022 0.034380 AGTCCTAGTAGCACGCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
2762 3028 7.371936 CCAATCTACATAAGTCCTAGTAGCAC 58.628 42.308 0.00 0.00 35.19 4.40
2806 3074 7.183475 ACCATATATAGGATGCAGACCATTCTT 59.817 37.037 13.88 0.00 36.29 2.52
2907 3176 6.476378 AGACATTGCCTCATATATACCAACC 58.524 40.000 0.00 0.00 0.00 3.77
3021 3296 8.432110 AACAGATATTGAACGCACATTACATA 57.568 30.769 0.00 0.00 0.00 2.29
3209 3484 7.241042 TCAGTATTAAGCAAGGACTACAGTT 57.759 36.000 0.00 0.00 0.00 3.16
3251 3526 5.684704 CTTAGGGCACAGAATATCCTGAAA 58.315 41.667 0.00 0.00 37.59 2.69
3271 3546 3.719479 TGGGCATTATTCTGTAGGGCTTA 59.281 43.478 0.00 0.00 0.00 3.09
3363 3645 3.872511 TTTTCTAAGTGCATGCCCATG 57.127 42.857 16.68 3.93 41.60 3.66
3426 3708 7.492669 GCTTCTGTCTAACTTATGAGCACATAA 59.507 37.037 14.67 14.67 43.80 1.90
3535 3820 4.273480 ACATCAGTTTCTGTACAACAGTGC 59.727 41.667 6.93 0.08 46.03 4.40
3711 4001 5.922544 CCAAATGACAGAGTCCAATTTGAAC 59.077 40.000 17.46 0.00 37.75 3.18
3749 4039 5.875359 GTCCTAGGACTTATGAACCAAACAG 59.125 44.000 31.12 0.00 41.57 3.16
3785 4076 5.437191 AGGGACTTGGGACTTATAAGTTG 57.563 43.478 18.96 9.81 34.84 3.16
3798 4089 5.627135 TGTAAGGACTTTTTAGGGACTTGG 58.373 41.667 0.00 0.00 41.75 3.61
3817 4108 6.739331 AAATCCCAAGAACCAAACATGTAA 57.261 33.333 0.00 0.00 0.00 2.41
3905 4196 2.233676 GGGACTTAAAGTGGGCATTTGG 59.766 50.000 0.00 0.00 0.00 3.28
3911 4202 5.768662 GGATTTATAGGGACTTAAAGTGGGC 59.231 44.000 0.00 0.00 41.75 5.36
3932 4223 4.325344 CCATCTAAACCAAACAGGAGGGAT 60.325 45.833 0.00 0.00 41.22 3.85
3939 4230 7.499232 CCTATAAGTCCCATCTAAACCAAACAG 59.501 40.741 0.00 0.00 0.00 3.16
3996 4287 7.060421 AGATTTAGAGGGTGTTTGTTTTCAGA 58.940 34.615 0.00 0.00 0.00 3.27
4016 4307 5.779529 AATTTCTCCGCATGCATAGATTT 57.220 34.783 19.57 12.33 0.00 2.17
4030 4853 6.773200 CCCTTCCTATTACCTCAAATTTCTCC 59.227 42.308 0.00 0.00 0.00 3.71
4038 4863 4.637288 TCCTCCCTTCCTATTACCTCAA 57.363 45.455 0.00 0.00 0.00 3.02
4058 5844 2.737252 GACCGTGAAACTGGTGAGATTC 59.263 50.000 0.00 0.00 42.25 2.52
4108 5938 2.291282 TGGAGGCACGGGTATTTGAAAT 60.291 45.455 0.00 0.00 0.00 2.17
4134 5964 5.181056 TGCATGAAAAGAATAACTTCTCGCA 59.819 36.000 0.00 0.00 40.93 5.10
4258 6230 2.458592 AATGCGCACGCTAAGAATTC 57.541 45.000 14.90 0.00 42.51 2.17
4318 6314 4.201980 GCCCAAGTTTAAATCATCCCGTAC 60.202 45.833 0.00 0.00 0.00 3.67
4319 6315 3.949113 GCCCAAGTTTAAATCATCCCGTA 59.051 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.