Multiple sequence alignment - TraesCS1A01G415600

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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 TraesCS1A01G415600 chr1A 100.000 4272 0 0 1 4272 574394922 574399193 0.000000e+00 7890.0
1 TraesCS1A01G415600 chr1A 85.764 288 41 0 3116 3403 574479974 574480261 5.370000e-79 305.0
2 TraesCS1A01G415600 chr1A 100.000 30 0 0 503 532 20031567 20031596 5.970000e-04 56.5
3 TraesCS1A01G415600 chr1A 100.000 29 0 0 503 531 38730041 38730069 2.000000e-03 54.7
4 TraesCS1A01G415600 chr1D 92.398 1276 54 21 122 1379 478183678 478184928 0.000000e+00 1779.0
5 TraesCS1A01G415600 chr1D 94.924 926 46 1 2472 3397 478184925 478185849 0.000000e+00 1448.0
6 TraesCS1A01G415600 chr1D 91.416 932 78 1 2472 3403 478252097 478253026 0.000000e+00 1277.0
7 TraesCS1A01G415600 chr1D 92.054 881 41 10 3421 4272 478185845 478186725 0.000000e+00 1212.0
8 TraesCS1A01G415600 chr1D 92.586 607 40 2 773 1379 478251499 478252100 0.000000e+00 867.0
9 TraesCS1A01G415600 chr1D 93.750 128 7 1 3 129 478182740 478182867 1.570000e-44 191.0
10 TraesCS1A01G415600 chr1D 90.598 117 9 1 525 639 478235312 478235428 2.060000e-33 154.0
11 TraesCS1A01G415600 chr1D 94.937 79 4 0 393 471 478235234 478235312 1.610000e-24 124.0
12 TraesCS1A01G415600 chr1D 92.857 70 4 1 637 706 478249277 478249345 2.720000e-17 100.0
13 TraesCS1A01G415600 chr1D 97.222 36 1 0 463 498 104527489 104527524 1.280000e-05 62.1
14 TraesCS1A01G415600 chr2A 95.968 496 16 4 1983 2477 448540299 448539807 0.000000e+00 802.0
15 TraesCS1A01G415600 chr2A 90.047 633 25 8 1379 1976 448541340 448540711 0.000000e+00 785.0
16 TraesCS1A01G415600 chr2A 85.586 111 10 6 1379 1486 779691421 779691528 1.260000e-20 111.0
17 TraesCS1A01G415600 chr2A 100.000 29 0 0 504 532 522506888 522506860 2.000000e-03 54.7
18 TraesCS1A01G415600 chr2A 100.000 29 0 0 503 531 670700572 670700544 2.000000e-03 54.7
19 TraesCS1A01G415600 chr3A 93.135 539 23 6 1381 1906 676883347 676883884 0.000000e+00 778.0
20 TraesCS1A01G415600 chr3A 94.614 427 21 2 2049 2473 676884327 676884753 0.000000e+00 660.0
21 TraesCS1A01G415600 chr3A 82.323 198 9 2 1845 2020 476309500 476309307 9.570000e-32 148.0
22 TraesCS1A01G415600 chr1B 86.620 568 74 2 2743 3309 665439274 665439840 1.010000e-175 627.0
23 TraesCS1A01G415600 chr1B 100.000 29 0 0 470 498 174643732 174643760 2.000000e-03 54.7
24 TraesCS1A01G415600 chr4A 84.815 270 32 9 2205 2470 614420546 614420810 3.280000e-66 263.0
25 TraesCS1A01G415600 chr4A 79.851 268 44 9 2206 2468 646267489 646267751 2.030000e-43 187.0
26 TraesCS1A01G415600 chr4A 100.000 29 0 0 503 531 683428767 683428739 2.000000e-03 54.7
27 TraesCS1A01G415600 chr4A 100.000 28 0 0 470 497 511021887 511021860 8.000000e-03 52.8
28 TraesCS1A01G415600 chr4A 100.000 28 0 0 470 497 559897515 559897488 8.000000e-03 52.8
29 TraesCS1A01G415600 chr6B 80.475 379 31 21 1382 1720 712335721 712336096 2.550000e-62 250.0
30 TraesCS1A01G415600 chr3B 79.949 389 34 21 1372 1720 20463418 20463802 3.300000e-61 246.0
31 TraesCS1A01G415600 chr2D 84.170 259 36 5 2213 2470 303607783 303608037 3.300000e-61 246.0
32 TraesCS1A01G415600 chr2D 95.349 86 4 0 1633 1718 511438784 511438869 2.070000e-28 137.0
33 TraesCS1A01G415600 chr2D 96.491 57 2 0 1578 1634 511438617 511438673 1.260000e-15 95.3
34 TraesCS1A01G415600 chr2D 100.000 28 0 0 1758 1785 511439029 511439056 8.000000e-03 52.8
35 TraesCS1A01G415600 chr2D 94.286 35 0 2 504 538 628259956 628259924 8.000000e-03 52.8
36 TraesCS1A01G415600 chr4B 91.765 170 9 4 1742 1906 41870786 41870617 9.240000e-57 231.0
37 TraesCS1A01G415600 chr4B 96.970 33 1 0 466 498 368857261 368857293 5.970000e-04 56.5
38 TraesCS1A01G415600 chr3D 82.625 259 44 1 2215 2473 418165458 418165201 1.200000e-55 228.0
39 TraesCS1A01G415600 chr5A 90.000 170 12 4 1742 1906 666723931 666723762 9.300000e-52 215.0
40 TraesCS1A01G415600 chr7B 80.741 270 46 6 2206 2473 664352674 664352939 5.600000e-49 206.0
41 TraesCS1A01G415600 chr7B 79.926 269 49 5 2206 2473 664324734 664324998 4.360000e-45 193.0
42 TraesCS1A01G415600 chr7B 88.158 152 12 6 1381 1529 664323441 664323589 4.390000e-40 176.0
43 TraesCS1A01G415600 chr7B 87.500 152 13 6 1381 1529 664351614 664351762 2.040000e-38 171.0
44 TraesCS1A01G415600 chrUn 88.485 165 18 1 2206 2370 10654960 10655123 9.370000e-47 198.0
45 TraesCS1A01G415600 chrUn 86.087 115 13 3 1379 1490 79260489 79260375 2.090000e-23 121.0
46 TraesCS1A01G415600 chrUn 85.217 115 14 3 1379 1490 79291842 79291728 9.710000e-22 115.0
47 TraesCS1A01G415600 chr2B 97.753 89 2 0 1632 1720 600442487 600442575 2.060000e-33 154.0
48 TraesCS1A01G415600 chr2B 96.491 57 2 0 1578 1634 600442324 600442380 1.260000e-15 95.3
49 TraesCS1A01G415600 chr2B 88.462 52 6 0 3666 3717 88852769 88852718 3.570000e-06 63.9
50 TraesCS1A01G415600 chr2B 96.875 32 0 1 466 497 258065552 258065522 8.000000e-03 52.8
51 TraesCS1A01G415600 chr2B 100.000 28 0 0 1758 1785 600442730 600442757 8.000000e-03 52.8
52 TraesCS1A01G415600 chr5D 85.321 109 14 2 1382 1489 542973784 542973891 1.260000e-20 111.0
53 TraesCS1A01G415600 chr6A 96.970 33 1 0 466 498 59695334 59695366 5.970000e-04 56.5
54 TraesCS1A01G415600 chr6D 96.970 33 0 1 504 535 32920189 32920157 2.000000e-03 54.7
55 TraesCS1A01G415600 chr5B 100.000 29 0 0 503 531 580833498 580833526 2.000000e-03 54.7
56 TraesCS1A01G415600 chr5B 100.000 29 0 0 470 498 610345963 610345991 2.000000e-03 54.7


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 TraesCS1A01G415600 chr1A 574394922 574399193 4271 False 7890.0 7890 100.000000 1 4272 1 chr1A.!!$F3 4271
1 TraesCS1A01G415600 chr1D 478182740 478186725 3985 False 1157.5 1779 93.281500 3 4272 4 chr1D.!!$F2 4269
2 TraesCS1A01G415600 chr1D 478249277 478253026 3749 False 748.0 1277 92.286333 637 3403 3 chr1D.!!$F4 2766
3 TraesCS1A01G415600 chr2A 448539807 448541340 1533 True 793.5 802 93.007500 1379 2477 2 chr2A.!!$R3 1098
4 TraesCS1A01G415600 chr3A 676883347 676884753 1406 False 719.0 778 93.874500 1381 2473 2 chr3A.!!$F1 1092
5 TraesCS1A01G415600 chr1B 665439274 665439840 566 False 627.0 627 86.620000 2743 3309 1 chr1B.!!$F2 566

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
283 1103 0.242825 TACGCAAGAACTCGGGTGAG 59.757 55.0 0.00 0.0 44.84 3.51 F
363 1183 0.611062 TGGGAGTACGCACTACTGCT 60.611 55.0 0.00 0.0 42.20 4.24 F
1240 4181 0.458025 CCTCGGCTTCTACGTCAACC 60.458 60.0 0.00 0.0 0.00 3.77 F
2479 5875 0.179936 CTGGAGATGCCCTCAAGTCC 59.820 60.0 5.71 0.0 43.76 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 4160 1.134560 GTTGACGTAGAAGCCGAGGAT 59.865 52.381 0.0 0.0 0.00 3.24 R
1374 4315 1.153005 GGCTGGAGATGCCTTGAGG 60.153 63.158 0.0 0.0 46.38 3.86 R
2978 6374 0.038618 TCACCGTTGTCGTCCATCTG 60.039 55.000 0.0 0.0 35.01 2.90 R
3903 7326 0.452184 GGCAGTCGAAGAGATGTCGA 59.548 55.000 0.0 0.0 44.82 4.20 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
108 110 6.474819 TTTTCGCATTCTAAGATTTCGTCA 57.525 33.333 0.00 0.00 0.00 4.35
120 122 5.948992 AGATTTCGTCAAAAGAAAGGGAG 57.051 39.130 0.00 0.00 40.39 4.30
226 1046 1.206132 ACTCATACGGGACAATTCGCA 59.794 47.619 0.00 0.00 34.29 5.10
227 1047 1.593006 CTCATACGGGACAATTCGCAC 59.407 52.381 0.00 0.00 34.29 5.34
228 1048 1.066787 TCATACGGGACAATTCGCACA 60.067 47.619 0.00 0.00 34.29 4.57
238 1058 1.205655 CAATTCGCACAGAGGAGGAGA 59.794 52.381 0.00 0.00 0.00 3.71
273 1093 1.872237 GCCGCCAGATATACGCAAGAA 60.872 52.381 0.00 0.00 43.62 2.52
274 1094 1.792949 CCGCCAGATATACGCAAGAAC 59.207 52.381 0.00 0.00 43.62 3.01
275 1095 2.545952 CCGCCAGATATACGCAAGAACT 60.546 50.000 0.00 0.00 43.62 3.01
276 1096 2.726760 CGCCAGATATACGCAAGAACTC 59.273 50.000 0.00 0.00 43.62 3.01
279 1099 3.309388 CAGATATACGCAAGAACTCGGG 58.691 50.000 0.00 0.00 43.62 5.14
280 1100 2.957006 AGATATACGCAAGAACTCGGGT 59.043 45.455 0.00 0.00 43.62 5.28
281 1101 2.572191 TATACGCAAGAACTCGGGTG 57.428 50.000 0.00 0.00 43.62 4.61
282 1102 0.892755 ATACGCAAGAACTCGGGTGA 59.107 50.000 0.00 0.00 43.62 4.02
283 1103 0.242825 TACGCAAGAACTCGGGTGAG 59.757 55.000 0.00 0.00 44.84 3.51
284 1104 1.738099 CGCAAGAACTCGGGTGAGG 60.738 63.158 0.00 0.00 43.89 3.86
285 1105 2.154798 CGCAAGAACTCGGGTGAGGA 62.155 60.000 0.00 0.00 43.89 3.71
319 1139 3.701040 CCCTCCACAAATTTCGATCCAAT 59.299 43.478 0.00 0.00 0.00 3.16
353 1173 1.429463 GCTCAGTTTGTGGGAGTACG 58.571 55.000 0.00 0.00 0.00 3.67
354 1174 1.429463 CTCAGTTTGTGGGAGTACGC 58.571 55.000 0.00 0.00 0.00 4.42
363 1183 0.611062 TGGGAGTACGCACTACTGCT 60.611 55.000 0.00 0.00 42.20 4.24
407 1227 0.676782 ACGGTAATGGTGCTGGCTTC 60.677 55.000 0.00 0.00 0.00 3.86
410 1230 1.077787 TAATGGTGCTGGCTTCCGG 60.078 57.895 0.00 0.00 0.00 5.14
448 1268 6.089249 ACTCTGAATTTTTGGACAATCACC 57.911 37.500 0.00 0.00 0.00 4.02
460 1280 1.202927 ACAATCACCACAACCTCCTGG 60.203 52.381 0.00 0.00 39.83 4.45
481 1301 1.677052 CTGCTAAGTACTCCCTCCGTC 59.323 57.143 0.00 0.00 0.00 4.79
498 1318 4.008330 TCCGTCTCGAAATAAGTGTCTCT 58.992 43.478 0.00 0.00 0.00 3.10
499 1319 4.094590 TCCGTCTCGAAATAAGTGTCTCTC 59.905 45.833 0.00 0.00 0.00 3.20
500 1320 4.095185 CCGTCTCGAAATAAGTGTCTCTCT 59.905 45.833 0.00 0.00 0.00 3.10
544 1380 4.926238 GGGAGTATATGCGTGAATCTTGAG 59.074 45.833 0.00 0.00 0.00 3.02
576 1412 2.354103 CCTGCCGACTGAAATGAGAAGA 60.354 50.000 0.00 0.00 0.00 2.87
577 1413 2.928757 CTGCCGACTGAAATGAGAAGAG 59.071 50.000 0.00 0.00 0.00 2.85
635 1473 2.430694 TCATGTTCTCCATACAGGTCGG 59.569 50.000 0.00 0.00 39.02 4.79
669 1507 2.159296 TCGTAGTCATGATTCACGTGGG 60.159 50.000 17.00 0.00 36.29 4.61
870 3811 2.927477 GGCTTTTGGGCTTTATTTACGC 59.073 45.455 0.00 0.00 37.53 4.42
957 3898 3.317150 CAAGTACAAGATCACGAGTGCA 58.683 45.455 0.00 0.00 0.00 4.57
966 3907 3.071206 ACGAGTGCATCCTCCGCT 61.071 61.111 0.00 0.00 0.00 5.52
975 3916 1.992277 ATCCTCCGCTGCCAGACTT 60.992 57.895 0.00 0.00 0.00 3.01
1011 3952 1.831286 CCGCGGTATGGACCTACCT 60.831 63.158 19.50 0.00 44.46 3.08
1051 3992 4.214327 GAAGGAGAGGCGGCGAGG 62.214 72.222 12.98 0.00 0.00 4.63
1131 4072 1.448013 CTTCCCGGCTTTCCTCGTC 60.448 63.158 0.00 0.00 0.00 4.20
1134 4075 2.584608 CCGGCTTTCCTCGTCCAT 59.415 61.111 0.00 0.00 0.00 3.41
1143 4084 3.536917 CTCGTCCATGCCGCCCTA 61.537 66.667 0.00 0.00 0.00 3.53
1240 4181 0.458025 CCTCGGCTTCTACGTCAACC 60.458 60.000 0.00 0.00 0.00 3.77
1258 4199 4.254709 ACTGCTCCACCTTGCGCA 62.255 61.111 5.66 5.66 0.00 6.09
1266 4207 3.276846 ACCTTGCGCACGGTGTTC 61.277 61.111 34.86 2.62 31.12 3.18
1812 4777 4.704103 AGGCACGCTCCTCCTCCA 62.704 66.667 0.00 0.00 0.00 3.86
1813 4778 3.474570 GGCACGCTCCTCCTCCAT 61.475 66.667 0.00 0.00 0.00 3.41
2228 5623 3.491598 AAAGAGCACGTGGGTGGGG 62.492 63.158 18.88 0.00 44.54 4.96
2254 5649 4.382685 CGGGAGAAAAAGTATACAGAGCCA 60.383 45.833 5.50 0.00 0.00 4.75
2392 5787 1.626825 CGAAAAGTAGGGTCTTGGGGA 59.373 52.381 0.00 0.00 0.00 4.81
2473 5869 3.162505 CTCGGCTGGAGATGCCCTC 62.163 68.421 0.00 0.00 46.23 4.30
2475 5871 3.001514 GGCTGGAGATGCCCTCAA 58.998 61.111 5.71 0.00 44.32 3.02
2476 5872 1.153005 GGCTGGAGATGCCCTCAAG 60.153 63.158 3.83 3.83 44.32 3.02
2477 5873 1.606531 GCTGGAGATGCCCTCAAGT 59.393 57.895 8.78 0.00 43.56 3.16
2478 5874 0.463474 GCTGGAGATGCCCTCAAGTC 60.463 60.000 8.78 0.23 43.56 3.01
2479 5875 0.179936 CTGGAGATGCCCTCAAGTCC 59.820 60.000 5.71 0.00 43.76 3.85
2480 5876 1.274703 TGGAGATGCCCTCAAGTCCC 61.275 60.000 5.71 0.00 43.76 4.46
2481 5877 1.144936 GAGATGCCCTCAAGTCCCG 59.855 63.158 0.00 0.00 41.58 5.14
2482 5878 2.190578 GATGCCCTCAAGTCCCGG 59.809 66.667 0.00 0.00 0.00 5.73
2483 5879 4.115199 ATGCCCTCAAGTCCCGGC 62.115 66.667 0.00 0.00 41.99 6.13
2488 5884 1.000896 CCTCAAGTCCCGGCCATTT 60.001 57.895 2.24 0.00 0.00 2.32
2585 5981 5.505780 AGCTATTACACATTGGCAGGTTAA 58.494 37.500 0.00 0.00 0.00 2.01
2636 6032 8.092687 GTCTCTACTTGTTATTTAGGGACAACA 58.907 37.037 3.48 0.00 41.30 3.33
2643 6039 1.868469 TTTAGGGACAACAACGACGG 58.132 50.000 0.00 0.00 0.00 4.79
2645 6041 1.746322 TAGGGACAACAACGACGGCA 61.746 55.000 0.00 0.00 0.00 5.69
2650 6046 1.796459 GACAACAACGACGGCATAGTT 59.204 47.619 0.00 0.00 0.00 2.24
2674 6070 4.056125 TCTGTGCGTCTCAGCGGG 62.056 66.667 4.67 0.00 40.67 6.13
2731 6127 2.440980 GCCTGGGGTGAAGCCATC 60.441 66.667 0.27 0.00 39.65 3.51
2764 6160 2.019984 GAGCTCCCTGTGCCATTAAAG 58.980 52.381 0.87 0.00 0.00 1.85
2776 6172 2.908626 GCCATTAAAGTTTGTTCGCTCG 59.091 45.455 0.00 0.00 0.00 5.03
2853 6249 2.393764 GTTGGATTTTGTTGCTCCACG 58.606 47.619 0.00 0.00 38.75 4.94
2856 6252 1.880027 GGATTTTGTTGCTCCACGTCT 59.120 47.619 0.00 0.00 0.00 4.18
2859 6255 1.493772 TTTGTTGCTCCACGTCTACG 58.506 50.000 0.04 0.04 46.33 3.51
2884 6280 0.682852 TTGTCGTCAAAGTCCCGGAT 59.317 50.000 0.73 0.00 0.00 4.18
2946 6342 2.490903 CTGGGCTTTTTCTCATCCACAG 59.509 50.000 0.00 0.00 0.00 3.66
2951 6347 4.067896 GCTTTTTCTCATCCACAGAGACA 58.932 43.478 0.00 0.00 41.53 3.41
2952 6348 4.153835 GCTTTTTCTCATCCACAGAGACAG 59.846 45.833 0.00 0.00 41.53 3.51
2965 6361 1.830477 AGAGACAGGTTCCATCTCAGC 59.170 52.381 18.65 0.00 41.18 4.26
2978 6374 1.374758 CTCAGCGTCTGGAACCACC 60.375 63.158 6.95 0.00 39.54 4.61
3033 6429 1.203523 GGTTGACAGGTTTGTTGTGCA 59.796 47.619 0.00 0.00 37.76 4.57
3072 6468 1.079503 GAGAGATTTCGGGTGTGTGC 58.920 55.000 0.00 0.00 0.00 4.57
3122 6518 7.771361 TGTTCTTATGTTTGTGGACAAGTAGAA 59.229 33.333 0.00 0.00 37.15 2.10
3161 6557 1.178276 GAGAAGCAGGAAGGAGACGA 58.822 55.000 0.00 0.00 0.00 4.20
3387 6783 0.396139 AAGCCGATGGGAATGCATGT 60.396 50.000 0.00 0.00 34.06 3.21
3399 6795 9.199982 GATGGGAATGCATGTGAAATATTAAAG 57.800 33.333 0.00 0.00 0.00 1.85
3403 6799 9.101655 GGAATGCATGTGAAATATTAAAGCTTT 57.898 29.630 17.30 17.30 0.00 3.51
3419 6815 9.628500 ATTAAAGCTTTTATCGGATTAGAACCT 57.372 29.630 18.47 0.00 0.00 3.50
3454 6850 4.160252 TGCAAAAGAAAAAGGTTCTCTGCT 59.840 37.500 17.21 0.00 0.00 4.24
3537 6933 3.440173 CCATGTTCGTGCCAAATAAGACT 59.560 43.478 0.00 0.00 0.00 3.24
3582 6978 9.153721 TCAAAATTGATTCAAGCAAATATGGAC 57.846 29.630 5.21 0.00 31.01 4.02
3597 6994 2.847959 TGGACGCATTATGCACAATG 57.152 45.000 17.75 13.44 45.36 2.82
3612 7009 7.643569 ATGCACAATGTAGAATTCATACCAA 57.356 32.000 8.44 0.00 0.00 3.67
3615 7012 8.363390 TGCACAATGTAGAATTCATACCAAAAA 58.637 29.630 8.44 0.00 0.00 1.94
3616 7013 8.863049 GCACAATGTAGAATTCATACCAAAAAG 58.137 33.333 8.44 0.00 0.00 2.27
3617 7014 8.863049 CACAATGTAGAATTCATACCAAAAAGC 58.137 33.333 8.44 0.00 0.00 3.51
3618 7015 8.806146 ACAATGTAGAATTCATACCAAAAAGCT 58.194 29.630 8.44 0.00 0.00 3.74
3630 7040 0.261696 AAAAAGCTGGGTCACCTGGT 59.738 50.000 0.00 0.00 46.68 4.00
3705 7115 3.262420 AGATACTAAAGCGTGCAACCTG 58.738 45.455 0.00 0.00 0.00 4.00
3714 7124 1.001378 GCGTGCAACCTGAATGAAACT 60.001 47.619 0.00 0.00 0.00 2.66
3719 7129 3.253188 TGCAACCTGAATGAAACTACAGC 59.747 43.478 0.00 0.00 0.00 4.40
3768 7178 4.148825 CTCCGACCCTGCCTTCCG 62.149 72.222 0.00 0.00 0.00 4.30
3802 7224 2.264794 CGGCACCTCGGCTACTTT 59.735 61.111 0.00 0.00 38.27 2.66
3807 7229 0.320374 CACCTCGGCTACTTTGTGGA 59.680 55.000 0.00 0.00 0.00 4.02
3858 7281 1.079127 CGTGTCCATCCCAGGTGAC 60.079 63.158 0.00 0.00 0.00 3.67
3903 7326 2.648454 GTCAAAATTGCCGGCCGT 59.352 55.556 26.77 9.84 0.00 5.68
3916 7339 1.586564 GGCCGTCGACATCTCTTCG 60.587 63.158 17.16 0.00 37.85 3.79
3940 7363 1.078214 CGAAATGGCTGCCTCCTCA 60.078 57.895 21.03 0.00 0.00 3.86
3941 7364 1.372087 CGAAATGGCTGCCTCCTCAC 61.372 60.000 21.03 5.76 0.00 3.51
3945 7368 2.045536 GGCTGCCTCCTCACCAAG 60.046 66.667 12.43 0.00 0.00 3.61
3958 7381 6.931840 CCTCCTCACCAAGTATTTAGATAAGC 59.068 42.308 0.00 0.00 0.00 3.09
4000 7423 1.300620 TGCCCGACACGAAGAGTTG 60.301 57.895 0.00 0.00 32.15 3.16
4008 7431 1.978580 ACACGAAGAGTTGATCCCCTT 59.021 47.619 0.00 0.00 0.00 3.95
4147 7572 2.196295 CGACACGGAAGATCTTCTCC 57.804 55.000 29.64 17.58 39.45 3.71
4172 7597 0.471617 AGCTTGTGTCCTGCAGAAGT 59.528 50.000 17.39 0.00 46.54 3.01
4176 7601 0.394192 TGTGTCCTGCAGAAGTCTGG 59.606 55.000 17.39 0.00 43.94 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.140286 CATAGGACTACAATATAATGTTGACCG 57.860 37.037 14.39 2.44 42.23 4.79
66 68 4.946784 AAAGCTGCAAAATAGAGTACCG 57.053 40.909 1.02 0.00 0.00 4.02
67 69 5.324697 CGAAAAGCTGCAAAATAGAGTACC 58.675 41.667 1.02 0.00 0.00 3.34
196 1016 7.502120 TTGTCCCGTATGAGTAGTAGATTAC 57.498 40.000 0.00 0.00 0.00 1.89
211 1031 0.604073 TCTGTGCGAATTGTCCCGTA 59.396 50.000 0.00 0.00 0.00 4.02
226 1046 2.041686 GCGTCGTCTCCTCCTCTGT 61.042 63.158 0.00 0.00 0.00 3.41
227 1047 2.766400 GGCGTCGTCTCCTCCTCTG 61.766 68.421 0.00 0.00 0.00 3.35
228 1048 2.438795 GGCGTCGTCTCCTCCTCT 60.439 66.667 0.00 0.00 0.00 3.69
271 1091 0.528470 CTCAGTCCTCACCCGAGTTC 59.472 60.000 0.00 0.00 37.59 3.01
273 1093 1.304547 CCTCAGTCCTCACCCGAGT 60.305 63.158 0.00 0.00 37.59 4.18
274 1094 1.000771 TCCTCAGTCCTCACCCGAG 60.001 63.158 0.00 0.00 39.16 4.63
275 1095 1.000771 CTCCTCAGTCCTCACCCGA 60.001 63.158 0.00 0.00 0.00 5.14
276 1096 0.034380 TACTCCTCAGTCCTCACCCG 60.034 60.000 0.00 0.00 33.62 5.28
279 1099 1.476477 GGGTACTCCTCAGTCCTCAC 58.524 60.000 0.00 0.00 33.62 3.51
280 1100 0.335361 GGGGTACTCCTCAGTCCTCA 59.665 60.000 3.84 0.00 33.58 3.86
281 1101 0.632294 AGGGGTACTCCTCAGTCCTC 59.368 60.000 9.09 0.00 36.47 3.71
282 1102 2.822118 AGGGGTACTCCTCAGTCCT 58.178 57.895 9.09 0.00 36.47 3.85
327 1147 0.100325 CCACAAACTGAGCGCAACAA 59.900 50.000 11.47 0.00 0.00 2.83
328 1148 1.723608 CCCACAAACTGAGCGCAACA 61.724 55.000 11.47 8.79 0.00 3.33
354 1174 4.820897 TCAGTAAATCACCAGCAGTAGTG 58.179 43.478 0.00 0.00 35.24 2.74
363 1183 5.559770 TCTGCTGAAATCAGTAAATCACCA 58.440 37.500 11.77 0.00 45.45 4.17
389 1209 1.376609 GGAAGCCAGCACCATTACCG 61.377 60.000 0.00 0.00 0.00 4.02
390 1210 1.376609 CGGAAGCCAGCACCATTACC 61.377 60.000 6.67 0.00 0.00 2.85
407 1227 2.498941 TAGAGGAAGATGCGGCCGG 61.499 63.158 29.38 8.95 0.00 6.13
410 1230 1.036707 AGAGTAGAGGAAGATGCGGC 58.963 55.000 0.00 0.00 0.00 6.53
418 1238 6.837312 TGTCCAAAAATTCAGAGTAGAGGAA 58.163 36.000 0.00 0.00 0.00 3.36
448 1268 0.036732 TTAGCAGCCAGGAGGTTGTG 59.963 55.000 0.00 0.00 46.80 3.33
460 1280 0.386113 CGGAGGGAGTACTTAGCAGC 59.614 60.000 0.00 0.00 0.00 5.25
481 1301 7.728580 GTGTAAGAGAGACACTTATTTCGAG 57.271 40.000 0.00 0.00 43.19 4.04
498 1318 3.763360 TCCGTCCCGAAATAAGTGTAAGA 59.237 43.478 0.00 0.00 0.00 2.10
499 1319 4.110482 CTCCGTCCCGAAATAAGTGTAAG 58.890 47.826 0.00 0.00 0.00 2.34
500 1320 3.119029 CCTCCGTCCCGAAATAAGTGTAA 60.119 47.826 0.00 0.00 0.00 2.41
544 1380 4.347453 CGGCAGGGCACACAAAGC 62.347 66.667 0.00 0.00 0.00 3.51
587 1423 4.022589 CCTGATGGCATTATTGTGTCCATC 60.023 45.833 0.00 11.46 44.28 3.51
635 1473 2.232399 GACTACGATCCCTCCTCCTTC 58.768 57.143 0.00 0.00 0.00 3.46
775 3716 3.018423 TCCGTGGAGATCATGAAGAGA 57.982 47.619 0.00 0.00 34.35 3.10
776 3717 3.651206 CATCCGTGGAGATCATGAAGAG 58.349 50.000 0.00 0.00 34.35 2.85
870 3811 1.424403 TCTGTTCCGTTGCATGTACG 58.576 50.000 13.39 13.39 38.67 3.67
930 3871 2.271800 GTGATCTTGTACTTGGAGCCG 58.728 52.381 0.00 0.00 0.00 5.52
931 3872 2.094182 TCGTGATCTTGTACTTGGAGCC 60.094 50.000 0.00 0.00 0.00 4.70
932 3873 3.182967 CTCGTGATCTTGTACTTGGAGC 58.817 50.000 0.00 0.00 0.00 4.70
933 3874 4.169508 CACTCGTGATCTTGTACTTGGAG 58.830 47.826 0.00 0.00 0.00 3.86
957 3898 0.687757 TAAGTCTGGCAGCGGAGGAT 60.688 55.000 10.34 0.00 0.00 3.24
966 3907 2.404566 TTTGGGCGCTAAGTCTGGCA 62.405 55.000 7.64 0.00 0.00 4.92
975 3916 2.202824 CGGACGATTTGGGCGCTA 60.203 61.111 7.64 0.00 0.00 4.26
1011 3952 2.159819 GAAGGTGGAGCAGCTCGTCA 62.160 60.000 16.47 6.80 41.59 4.35
1131 4072 2.423446 GAGACTAGGGCGGCATGG 59.577 66.667 12.47 8.76 0.00 3.66
1134 4075 2.284331 TTGGAGACTAGGGCGGCA 60.284 61.111 12.47 0.00 0.00 5.69
1171 4112 2.273912 GGAGGAAGACGGTGTCGGT 61.274 63.158 0.00 0.00 41.39 4.69
1219 4160 1.134560 GTTGACGTAGAAGCCGAGGAT 59.865 52.381 0.00 0.00 0.00 3.24
1240 4181 3.730761 GCGCAAGGTGGAGCAGTG 61.731 66.667 0.30 0.00 33.48 3.66
1321 4262 4.696877 TCTTACAGATTGATTGCAGTGGTG 59.303 41.667 0.00 0.00 0.00 4.17
1374 4315 1.153005 GGCTGGAGATGCCTTGAGG 60.153 63.158 0.00 0.00 46.38 3.86
1452 4393 3.230134 TGGAACAAATCTCACCCCAAAG 58.770 45.455 0.00 0.00 31.92 2.77
1455 4396 1.780309 ACTGGAACAAATCTCACCCCA 59.220 47.619 0.00 0.00 38.70 4.96
1796 4761 3.453070 GATGGAGGAGGAGCGTGCC 62.453 68.421 0.00 0.00 0.00 5.01
2083 5475 2.277072 CTCTCTCCCTCCCTCGCA 59.723 66.667 0.00 0.00 0.00 5.10
2155 5549 1.925972 GCCCCAACCTCTCTCCCTT 60.926 63.158 0.00 0.00 0.00 3.95
2211 5605 3.953775 CCCCACCCACGTGCTCTT 61.954 66.667 10.91 0.00 38.79 2.85
2228 5623 3.118519 TCTGTATACTTTTTCTCCCGGGC 60.119 47.826 18.49 0.00 0.00 6.13
2231 5626 4.120589 GGCTCTGTATACTTTTTCTCCCG 58.879 47.826 4.17 0.00 0.00 5.14
2254 5649 2.526873 ACCGTCAGCCTCCCACTT 60.527 61.111 0.00 0.00 0.00 3.16
2370 5765 2.224695 CCCCAAGACCCTACTTTTCGTT 60.225 50.000 0.00 0.00 0.00 3.85
2371 5766 1.350019 CCCCAAGACCCTACTTTTCGT 59.650 52.381 0.00 0.00 0.00 3.85
2392 5787 1.923356 AAAAATCATCCCAGCCACGT 58.077 45.000 0.00 0.00 0.00 4.49
2404 5799 1.198178 GACACCGGCGCTTAAAAATCA 59.802 47.619 7.64 0.00 0.00 2.57
2473 5869 2.350458 CCCAAATGGCCGGGACTTG 61.350 63.158 7.67 0.00 46.34 3.16
2475 5871 3.264845 ACCCAAATGGCCGGGACT 61.265 61.111 19.45 0.00 46.34 3.85
2476 5872 3.068064 CACCCAAATGGCCGGGAC 61.068 66.667 19.45 0.00 46.34 4.46
2488 5884 4.460683 GTGTATCCGCCGCACCCA 62.461 66.667 0.00 0.00 0.00 4.51
2537 5933 0.960286 GGTAGTCGGATAGGGAGCAC 59.040 60.000 0.00 0.00 0.00 4.40
2636 6032 3.656559 ACACTAAAACTATGCCGTCGTT 58.343 40.909 0.00 0.00 0.00 3.85
2643 6039 3.432252 ACGCACAGACACTAAAACTATGC 59.568 43.478 0.00 0.00 31.84 3.14
2645 6041 5.135508 AGACGCACAGACACTAAAACTAT 57.864 39.130 0.00 0.00 0.00 2.12
2650 6046 2.862530 GCTGAGACGCACAGACACTAAA 60.863 50.000 8.00 0.00 37.54 1.85
2674 6070 1.488261 CTCGGGCCGATAACTTTCGC 61.488 60.000 31.23 0.00 37.80 4.70
2731 6127 0.107752 GGAGCTCTCCTTCAGCCAAG 60.108 60.000 14.64 0.00 46.16 3.61
2764 6160 3.933155 ATCATCATCGAGCGAACAAAC 57.067 42.857 0.00 0.00 0.00 2.93
2946 6342 1.470632 CGCTGAGATGGAACCTGTCTC 60.471 57.143 14.87 14.87 39.02 3.36
2951 6347 0.534412 CAGACGCTGAGATGGAACCT 59.466 55.000 1.18 0.00 32.44 3.50
2952 6348 0.460987 CCAGACGCTGAGATGGAACC 60.461 60.000 8.20 0.00 33.90 3.62
2978 6374 0.038618 TCACCGTTGTCGTCCATCTG 60.039 55.000 0.00 0.00 35.01 2.90
3072 6468 1.186200 TCCACCATCTTCCGAGACTG 58.814 55.000 0.00 0.00 33.99 3.51
3122 6518 6.611613 TCTCAGGTCAACAGAAATGATAGT 57.388 37.500 0.00 0.00 0.00 2.12
3161 6557 3.181447 CCCTGCACCTTGATCTCATATGT 60.181 47.826 1.90 0.00 0.00 2.29
3329 6725 5.187186 AGAGGGCGAATACAAAAGTCTTAGA 59.813 40.000 0.00 0.00 0.00 2.10
3403 6799 9.485206 GCAACTAATAAGGTTCTAATCCGATAA 57.515 33.333 0.00 0.00 0.00 1.75
3404 6800 8.092687 GGCAACTAATAAGGTTCTAATCCGATA 58.907 37.037 0.00 0.00 0.00 2.92
3405 6801 6.935208 GGCAACTAATAAGGTTCTAATCCGAT 59.065 38.462 0.00 0.00 0.00 4.18
3406 6802 6.285990 GGCAACTAATAAGGTTCTAATCCGA 58.714 40.000 0.00 0.00 0.00 4.55
3407 6803 6.541111 GGCAACTAATAAGGTTCTAATCCG 57.459 41.667 0.00 0.00 0.00 4.18
3454 6850 6.667414 AGTAACCCAATTATGATTTTGCTGGA 59.333 34.615 0.00 0.00 0.00 3.86
3464 6860 7.925483 GCAAATGCATAAGTAACCCAATTATGA 59.075 33.333 0.00 0.00 38.57 2.15
3537 6933 3.217626 TGATGCACCACAACACATGTTA 58.782 40.909 0.00 0.00 41.46 2.41
3597 6994 6.152831 ACCCAGCTTTTTGGTATGAATTCTAC 59.847 38.462 7.05 6.74 36.45 2.59
3612 7009 0.468029 CACCAGGTGACCCAGCTTTT 60.468 55.000 15.35 0.00 40.40 2.27
3615 7012 3.958860 GCACCAGGTGACCCAGCT 61.959 66.667 24.96 0.00 43.33 4.24
3617 7014 2.833913 AAGGCACCAGGTGACCCAG 61.834 63.158 23.18 0.00 43.69 4.45
3618 7015 2.776526 AAGGCACCAGGTGACCCA 60.777 61.111 23.18 0.00 43.69 4.51
3630 7040 3.626930 ACTTTGTAAGTTCACCAAGGCA 58.373 40.909 0.00 0.00 39.04 4.75
3705 7115 6.238320 GGATGATGTGAGCTGTAGTTTCATTC 60.238 42.308 0.00 0.00 0.00 2.67
3714 7124 4.256110 CAACTTGGATGATGTGAGCTGTA 58.744 43.478 0.00 0.00 0.00 2.74
3807 7229 4.680537 ACAGGGCGTCGGAGTCCT 62.681 66.667 7.77 0.00 0.00 3.85
3837 7260 0.673644 CACCTGGGATGGACACGAAC 60.674 60.000 0.00 0.00 0.00 3.95
3838 7261 0.834261 TCACCTGGGATGGACACGAA 60.834 55.000 0.00 0.00 0.00 3.85
3847 7270 1.217057 AGCATTGGGTCACCTGGGAT 61.217 55.000 0.00 0.00 37.76 3.85
3882 7305 2.647875 CCGGCAATTTTGACCGCA 59.352 55.556 15.87 0.00 42.42 5.69
3884 7307 2.126110 GGCCGGCAATTTTGACCG 60.126 61.111 30.85 14.91 42.96 4.79
3903 7326 0.452184 GGCAGTCGAAGAGATGTCGA 59.548 55.000 0.00 0.00 44.82 4.20
3927 7350 2.853542 TTGGTGAGGAGGCAGCCA 60.854 61.111 15.80 0.00 35.50 4.75
3940 7363 5.291905 AGCCGCTTATCTAAATACTTGGT 57.708 39.130 0.00 0.00 0.00 3.67
3941 7364 4.386049 CGAGCCGCTTATCTAAATACTTGG 59.614 45.833 0.00 0.00 0.00 3.61
3997 7420 2.513897 CGGCGGAAGGGGATCAAC 60.514 66.667 0.00 0.00 0.00 3.18
4023 7446 1.305381 AAGACTGGGTAGCGGCTCT 60.305 57.895 5.39 0.00 0.00 4.09
4028 7451 2.494918 CCCGAAGACTGGGTAGCG 59.505 66.667 0.00 0.00 42.07 4.26
4111 7534 3.585990 GGCGCCATCGGGAACATG 61.586 66.667 24.80 0.00 35.59 3.21
4147 7572 1.280746 CAGGACACAAGCTTGCACG 59.719 57.895 26.27 16.76 0.00 5.34
4213 7638 2.012673 GTGATTCTGGACCATGCAGTC 58.987 52.381 0.00 0.00 37.12 3.51


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

AutoCloner maintained by Alex Coulton.