Multiple sequence alignment - TraesCS1D01G162500

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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 TraesCS1D01G162500 chr1D 100.000 4752 0 0 2254 7005 232345512 232350263 0.000000e+00 8776.0
1 TraesCS1D01G162500 chr1D 100.000 1831 0 0 1 1831 232343259 232345089 0.000000e+00 3382.0
2 TraesCS1D01G162500 chr1D 76.773 564 95 30 4224 4767 131148250 131148797 4.140000e-72 283.0
3 TraesCS1D01G162500 chr1B 96.031 4434 126 19 2254 6655 367438293 367442708 0.000000e+00 7167.0
4 TraesCS1D01G162500 chr1B 93.785 901 32 6 922 1799 367437036 367437935 0.000000e+00 1332.0
5 TraesCS1D01G162500 chr1B 75.000 756 123 49 4052 4767 206033480 206034209 8.890000e-74 289.0
6 TraesCS1D01G162500 chr1B 86.747 166 12 3 6657 6813 367442995 367443159 7.220000e-40 176.0
7 TraesCS1D01G162500 chr1B 93.750 64 4 0 6835 6898 367443160 367443223 5.780000e-16 97.1
8 TraesCS1D01G162500 chr1A 98.287 1635 23 3 3193 4826 315837532 315835902 0.000000e+00 2859.0
9 TraesCS1D01G162500 chr1A 96.158 1718 38 7 4827 6516 315835791 315834074 0.000000e+00 2782.0
10 TraesCS1D01G162500 chr1A 97.635 888 20 1 2254 3141 315838414 315837528 0.000000e+00 1522.0
11 TraesCS1D01G162500 chr1A 93.892 835 27 7 886 1703 315839528 315838701 0.000000e+00 1238.0
12 TraesCS1D01G162500 chr1A 93.983 349 17 2 6657 7005 315833994 315833650 6.220000e-145 525.0
13 TraesCS1D01G162500 chr1A 75.166 753 125 48 4052 4767 157831444 157830717 1.480000e-76 298.0
14 TraesCS1D01G162500 chr1A 96.269 134 4 1 1698 1831 315838603 315838471 1.180000e-52 219.0
15 TraesCS1D01G162500 chr1A 97.619 84 2 0 6572 6655 315834131 315834048 2.040000e-30 145.0
16 TraesCS1D01G162500 chr3D 93.712 827 42 3 1 817 349697284 349696458 0.000000e+00 1230.0
17 TraesCS1D01G162500 chr3D 93.924 790 47 1 1 789 162890882 162891671 0.000000e+00 1192.0
18 TraesCS1D01G162500 chr6D 93.237 828 46 3 1 818 60436340 60435513 0.000000e+00 1210.0
19 TraesCS1D01G162500 chr6D 93.932 791 44 4 1 789 394010963 394011751 0.000000e+00 1192.0
20 TraesCS1D01G162500 chr4D 93.245 829 45 4 1 819 173662948 173663775 0.000000e+00 1210.0
21 TraesCS1D01G162500 chr5D 93.116 828 47 3 1 818 334910765 334911592 0.000000e+00 1205.0
22 TraesCS1D01G162500 chr5D 93.116 828 46 4 1 818 212019574 212018748 0.000000e+00 1203.0
23 TraesCS1D01G162500 chr7D 94.177 790 45 1 1 789 407661214 407660425 0.000000e+00 1203.0
24 TraesCS1D01G162500 chr7D 93.924 790 46 2 1 789 541266347 541267135 0.000000e+00 1192.0


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 TraesCS1D01G162500 chr1D 232343259 232350263 7004 False 6079.000000 8776 100.000000 1 7005 2 chr1D.!!$F2 7004
1 TraesCS1D01G162500 chr1D 131148250 131148797 547 False 283.000000 283 76.773000 4224 4767 1 chr1D.!!$F1 543
2 TraesCS1D01G162500 chr1B 367437036 367443223 6187 False 2193.025000 7167 92.578250 922 6898 4 chr1B.!!$F2 5976
3 TraesCS1D01G162500 chr1B 206033480 206034209 729 False 289.000000 289 75.000000 4052 4767 1 chr1B.!!$F1 715
4 TraesCS1D01G162500 chr1A 315833650 315839528 5878 True 1327.142857 2859 96.263286 886 7005 7 chr1A.!!$R2 6119
5 TraesCS1D01G162500 chr1A 157830717 157831444 727 True 298.000000 298 75.166000 4052 4767 1 chr1A.!!$R1 715
6 TraesCS1D01G162500 chr3D 349696458 349697284 826 True 1230.000000 1230 93.712000 1 817 1 chr3D.!!$R1 816
7 TraesCS1D01G162500 chr3D 162890882 162891671 789 False 1192.000000 1192 93.924000 1 789 1 chr3D.!!$F1 788
8 TraesCS1D01G162500 chr6D 60435513 60436340 827 True 1210.000000 1210 93.237000 1 818 1 chr6D.!!$R1 817
9 TraesCS1D01G162500 chr6D 394010963 394011751 788 False 1192.000000 1192 93.932000 1 789 1 chr6D.!!$F1 788
10 TraesCS1D01G162500 chr4D 173662948 173663775 827 False 1210.000000 1210 93.245000 1 819 1 chr4D.!!$F1 818
11 TraesCS1D01G162500 chr5D 334910765 334911592 827 False 1205.000000 1205 93.116000 1 818 1 chr5D.!!$F1 817
12 TraesCS1D01G162500 chr5D 212018748 212019574 826 True 1203.000000 1203 93.116000 1 818 1 chr5D.!!$R1 817
13 TraesCS1D01G162500 chr7D 407660425 407661214 789 True 1203.000000 1203 94.177000 1 789 1 chr7D.!!$R1 788
14 TraesCS1D01G162500 chr7D 541266347 541267135 788 False 1192.000000 1192 93.924000 1 789 1 chr7D.!!$F1 788

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
828 840 0.176680 AGATAGCAGCAACCGACAGG 59.823 55.000 0.0 0.0 45.13 4.00 F
884 896 0.322008 GTCAGGGTTGGGAGCAGAAG 60.322 60.000 0.0 0.0 0.00 2.85 F
1675 1712 0.700564 AGGCATGGACATTCTGTGGT 59.299 50.000 0.0 0.0 0.00 4.16 F
3093 3238 2.687935 TCTTGTTGCTTCCACCAAGTTC 59.312 45.455 0.0 0.0 40.93 3.01 F
4116 4263 1.101049 CAACGGTGAGGGCAACTTGT 61.101 55.000 0.0 0.0 0.00 3.16 F
5007 5289 3.774734 GGGGGCTTTAGGGTATTATTGG 58.225 50.000 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 2793 0.538516 TGGGGTCATTTTGTGGGTCG 60.539 55.000 0.00 0.0 0.00 4.79 R
2992 3135 3.817647 GCTATATAAGGCAGCAAAGCAGT 59.182 43.478 0.00 0.0 35.35 4.40 R
3183 3329 1.279271 AGAACACATGCTGTACTCCCC 59.721 52.381 0.00 0.0 30.51 4.81 R
5096 5380 0.820871 GCTCTTCTGATCTGGGTCGT 59.179 55.000 0.00 0.0 0.00 4.34 R
5270 5562 0.042448 GCGAGCGTTCACGAGTTTTT 60.042 50.000 2.87 0.0 43.02 1.94 R
6514 6932 0.178961 AAAGGCTTGACCAGTTCCCC 60.179 55.000 0.00 0.0 43.14 4.81 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
26 27 7.519328 GCATGATTTGACATTTTTGCAAGTCTT 60.519 33.333 15.17 3.60 31.87 3.01
74 75 6.202570 GCCTACTAGATTGATCTTTCTTGCAG 59.797 42.308 0.00 3.02 38.32 4.41
91 92 1.276421 GCAGTGGGAGAAGTGCTTAGA 59.724 52.381 0.00 0.00 42.21 2.10
104 105 5.649782 AGTGCTTAGATTTGGGTTCAATG 57.350 39.130 0.00 0.00 32.28 2.82
245 246 4.994907 TCTTGCCTAATGCGTTACTCTA 57.005 40.909 0.00 0.00 45.60 2.43
252 253 6.921857 TGCCTAATGCGTTACTCTATTCTTAC 59.078 38.462 0.00 0.00 45.60 2.34
279 280 7.060383 ACTTAATACTCTAGATGCATGCTGT 57.940 36.000 20.33 7.62 0.00 4.40
294 295 2.983402 GCTGTATAGCGGTCGATGTA 57.017 50.000 0.00 0.00 40.67 2.29
475 476 5.363005 GGAGAAGCCACTAGTGAAACCTATA 59.637 44.000 24.68 0.00 34.65 1.31
527 528 9.995003 TTAGTTTATCATCAACTTGCCAATTTT 57.005 25.926 0.00 0.00 35.95 1.82
677 679 1.335496 GCGTTGGTTGCAAGGTTCTTA 59.665 47.619 0.00 0.00 0.00 2.10
709 711 2.026641 AGGTACTAGGCGATTTGCGTA 58.973 47.619 0.00 0.00 41.35 4.42
775 778 8.215736 AGGGAAATACTTACACTACTTTGTTGT 58.784 33.333 0.00 0.00 0.00 3.32
811 823 2.472695 AACCAACGCATGCTAAGAGA 57.527 45.000 17.13 0.00 0.00 3.10
824 836 3.717400 CTAAGAGATAGCAGCAACCGA 57.283 47.619 0.00 0.00 0.00 4.69
825 837 2.301577 AAGAGATAGCAGCAACCGAC 57.698 50.000 0.00 0.00 0.00 4.79
826 838 1.186200 AGAGATAGCAGCAACCGACA 58.814 50.000 0.00 0.00 0.00 4.35
827 839 1.135915 AGAGATAGCAGCAACCGACAG 59.864 52.381 0.00 0.00 0.00 3.51
828 840 0.176680 AGATAGCAGCAACCGACAGG 59.823 55.000 0.00 0.00 45.13 4.00
829 841 0.811616 GATAGCAGCAACCGACAGGG 60.812 60.000 0.00 0.00 43.47 4.45
840 852 4.373771 GACAGGGTTTGGTCGTCC 57.626 61.111 0.00 0.00 0.00 4.79
841 853 1.666872 GACAGGGTTTGGTCGTCCG 60.667 63.158 0.00 0.00 36.30 4.79
842 854 3.047877 CAGGGTTTGGTCGTCCGC 61.048 66.667 0.00 0.00 36.30 5.54
843 855 4.324991 AGGGTTTGGTCGTCCGCC 62.325 66.667 0.00 0.00 36.30 6.13
861 873 4.314440 GCACGAGTGTGGGCTCCA 62.314 66.667 5.07 0.00 46.51 3.86
870 882 2.930019 TGGGCTCCACAGGTCAGG 60.930 66.667 0.00 0.00 0.00 3.86
871 883 3.721706 GGGCTCCACAGGTCAGGG 61.722 72.222 0.00 0.00 0.00 4.45
872 884 2.930562 GGCTCCACAGGTCAGGGT 60.931 66.667 0.00 0.00 0.00 4.34
873 885 2.529744 GGCTCCACAGGTCAGGGTT 61.530 63.158 0.00 0.00 0.00 4.11
874 886 1.302832 GCTCCACAGGTCAGGGTTG 60.303 63.158 0.00 0.00 0.00 3.77
875 887 1.376466 CTCCACAGGTCAGGGTTGG 59.624 63.158 0.00 0.00 0.00 3.77
876 888 2.129555 CTCCACAGGTCAGGGTTGGG 62.130 65.000 0.00 0.00 0.00 4.12
877 889 2.153401 CCACAGGTCAGGGTTGGGA 61.153 63.158 0.00 0.00 0.00 4.37
878 890 1.376466 CACAGGTCAGGGTTGGGAG 59.624 63.158 0.00 0.00 0.00 4.30
879 891 2.352805 CAGGTCAGGGTTGGGAGC 59.647 66.667 0.00 0.00 0.00 4.70
880 892 2.121963 AGGTCAGGGTTGGGAGCA 60.122 61.111 0.00 0.00 34.11 4.26
881 893 2.227036 AGGTCAGGGTTGGGAGCAG 61.227 63.158 0.00 0.00 34.11 4.24
882 894 2.224159 GGTCAGGGTTGGGAGCAGA 61.224 63.158 0.00 0.00 0.00 4.26
883 895 1.761174 GTCAGGGTTGGGAGCAGAA 59.239 57.895 0.00 0.00 0.00 3.02
884 896 0.322008 GTCAGGGTTGGGAGCAGAAG 60.322 60.000 0.00 0.00 0.00 2.85
1258 1295 4.631377 CCGAGATTTGATTCTGTGTTGCTA 59.369 41.667 0.00 0.00 0.00 3.49
1261 1298 6.904011 CGAGATTTGATTCTGTGTTGCTATTC 59.096 38.462 0.00 0.00 0.00 1.75
1406 1443 3.003689 GGTAATTCCCATCGTGCATCTTG 59.996 47.826 0.00 0.00 0.00 3.02
1591 1628 4.301027 CCCGAGTATGCTCCGCCC 62.301 72.222 5.13 0.00 38.49 6.13
1629 1666 4.747583 ACTAGGGTATGTTTTTGGCCTTT 58.252 39.130 3.32 0.00 0.00 3.11
1644 1681 1.740043 GCCTTTGTTGCTGCAGTTTGT 60.740 47.619 16.64 0.00 0.00 2.83
1675 1712 0.700564 AGGCATGGACATTCTGTGGT 59.299 50.000 0.00 0.00 0.00 4.16
1738 1878 7.164230 AGATATAGTACCTCTTATGTGCAGC 57.836 40.000 0.00 0.00 0.00 5.25
1802 1942 6.127897 TGTGCTCATGATCATATAGTACCTCG 60.128 42.308 23.65 6.16 0.00 4.63
2509 2649 9.706529 AAATAGGCTGAAAAGAAGGATAGAATT 57.293 29.630 0.00 0.00 0.00 2.17
2749 2892 9.713684 TTTACCCCATCATTCAGATTTTCTTAT 57.286 29.630 0.00 0.00 33.72 1.73
2992 3135 2.969262 GTGGGTGAAATCTGGGGAAAAA 59.031 45.455 0.00 0.00 0.00 1.94
2993 3136 2.969262 TGGGTGAAATCTGGGGAAAAAC 59.031 45.455 0.00 0.00 0.00 2.43
3093 3238 2.687935 TCTTGTTGCTTCCACCAAGTTC 59.312 45.455 0.00 0.00 40.93 3.01
3174 3320 8.126700 GCTGTTAGTTAGCTTTGTTCTGTTTAA 58.873 33.333 0.00 0.00 38.14 1.52
3238 3384 6.702716 TCCAAAGAACGTTGAAAACCTATT 57.297 33.333 5.00 0.00 46.28 1.73
3615 3762 8.267620 TGATGCTCGATTTCTTGAGAAAAATA 57.732 30.769 9.96 0.00 45.81 1.40
3868 4015 9.070149 GTGAGTAGTATTTGTAGTTACTTTCCG 57.930 37.037 0.00 0.00 31.37 4.30
4036 4183 6.101150 ACCCTGCACTATTATCACCTTGATTA 59.899 38.462 0.00 0.00 38.26 1.75
4116 4263 1.101049 CAACGGTGAGGGCAACTTGT 61.101 55.000 0.00 0.00 0.00 3.16
4524 4694 4.389077 CACTCGGGACATGAAAAGTAAGTC 59.611 45.833 0.00 0.00 0.00 3.01
4555 4725 5.769662 TCATTCAAACTCAATGTAGGCTTGT 59.230 36.000 0.00 0.00 33.61 3.16
4916 5198 7.476540 TGTTGATATATCAGGGTATAACGCT 57.523 36.000 14.86 0.00 42.51 5.07
4929 5211 5.467399 GGGTATAACGCTGTATTAACATGCA 59.533 40.000 0.00 0.00 34.37 3.96
5007 5289 3.774734 GGGGGCTTTAGGGTATTATTGG 58.225 50.000 0.00 0.00 0.00 3.16
5013 5297 5.889289 GGCTTTAGGGTATTATTGGTGTTGA 59.111 40.000 0.00 0.00 0.00 3.18
5023 5307 5.866335 TTATTGGTGTTGACCGTATGTTC 57.134 39.130 0.00 0.00 46.62 3.18
5087 5371 5.046014 ACCACTTATCAGAGAGCAACAGAAT 60.046 40.000 0.00 0.00 0.00 2.40
5270 5562 1.135489 CGGGAAAGAGATCGTGACGAA 60.135 52.381 13.14 0.00 39.99 3.85
5525 5817 1.927174 GATTACGAGCGTGCAAGTCAT 59.073 47.619 5.69 0.00 0.00 3.06
5615 5907 3.072944 GGAGAGTGATGCTGATTATGGC 58.927 50.000 0.00 0.00 0.00 4.40
5887 6179 3.316868 GCTGTGGTAAGGCTTTGTTAACA 59.683 43.478 4.45 3.59 0.00 2.41
5944 6236 3.058846 GGTTCTCTCGCCTTTTTCTTGTC 60.059 47.826 0.00 0.00 0.00 3.18
5974 6266 7.611855 ACTTCCAGTCTTATCCCACTTATTTTG 59.388 37.037 0.00 0.00 0.00 2.44
5975 6267 7.027874 TCCAGTCTTATCCCACTTATTTTGT 57.972 36.000 0.00 0.00 0.00 2.83
6126 6418 1.755179 ATGCGGCTTGAGTTTATGCT 58.245 45.000 0.00 0.00 0.00 3.79
6364 6658 3.366719 GTCTTTGCAGTTTGCTTCTGTC 58.633 45.455 2.48 0.00 45.31 3.51
6448 6755 6.699575 AACTCCTTTTGAATCGGATATTGG 57.300 37.500 0.00 0.00 0.00 3.16
6489 6907 3.947834 CCCGATTTCTCTATGGTTTTGCT 59.052 43.478 0.00 0.00 0.00 3.91
6490 6908 4.201950 CCCGATTTCTCTATGGTTTTGCTG 60.202 45.833 0.00 0.00 0.00 4.41
6491 6909 4.635765 CCGATTTCTCTATGGTTTTGCTGA 59.364 41.667 0.00 0.00 0.00 4.26
6492 6910 5.123820 CCGATTTCTCTATGGTTTTGCTGAA 59.876 40.000 0.00 0.00 0.00 3.02
6493 6911 6.024049 CGATTTCTCTATGGTTTTGCTGAAC 58.976 40.000 0.00 0.00 0.00 3.18
6494 6912 6.128172 CGATTTCTCTATGGTTTTGCTGAACT 60.128 38.462 3.43 0.00 0.00 3.01
6495 6913 6.959639 TTTCTCTATGGTTTTGCTGAACTT 57.040 33.333 3.43 0.00 0.00 2.66
6496 6914 5.947228 TCTCTATGGTTTTGCTGAACTTG 57.053 39.130 3.43 0.00 0.00 3.16
6497 6915 4.216257 TCTCTATGGTTTTGCTGAACTTGC 59.784 41.667 3.43 0.00 0.00 4.01
6498 6916 2.531522 ATGGTTTTGCTGAACTTGCC 57.468 45.000 3.43 0.00 0.00 4.52
6499 6917 1.484038 TGGTTTTGCTGAACTTGCCT 58.516 45.000 3.43 0.00 0.00 4.75
6500 6918 1.830477 TGGTTTTGCTGAACTTGCCTT 59.170 42.857 3.43 0.00 0.00 4.35
6501 6919 2.235898 TGGTTTTGCTGAACTTGCCTTT 59.764 40.909 3.43 0.00 0.00 3.11
6502 6920 3.270027 GGTTTTGCTGAACTTGCCTTTT 58.730 40.909 3.43 0.00 0.00 2.27
6503 6921 3.063861 GGTTTTGCTGAACTTGCCTTTTG 59.936 43.478 3.43 0.00 0.00 2.44
6504 6922 2.600470 TTGCTGAACTTGCCTTTTGG 57.400 45.000 0.00 0.00 44.18 3.28
6505 6923 0.752054 TGCTGAACTTGCCTTTTGGG 59.248 50.000 0.00 0.00 40.82 4.12
6526 6944 1.368374 CCTTTAGGGGGAACTGGTCA 58.632 55.000 0.00 0.00 0.00 4.02
6527 6945 1.708551 CCTTTAGGGGGAACTGGTCAA 59.291 52.381 0.00 0.00 0.00 3.18
6528 6946 2.290960 CCTTTAGGGGGAACTGGTCAAG 60.291 54.545 0.00 0.00 0.00 3.02
6529 6947 0.696501 TTAGGGGGAACTGGTCAAGC 59.303 55.000 0.00 0.00 0.00 4.01
6530 6948 1.205460 TAGGGGGAACTGGTCAAGCC 61.205 60.000 0.00 0.00 37.90 4.35
6531 6949 2.539081 GGGGGAACTGGTCAAGCCT 61.539 63.158 0.00 0.00 38.35 4.58
6532 6950 1.460699 GGGGAACTGGTCAAGCCTT 59.539 57.895 0.00 0.00 38.35 4.35
6533 6951 0.178961 GGGGAACTGGTCAAGCCTTT 60.179 55.000 0.00 0.00 38.35 3.11
6534 6952 0.961753 GGGAACTGGTCAAGCCTTTG 59.038 55.000 0.00 0.00 38.35 2.77
6535 6953 0.961753 GGAACTGGTCAAGCCTTTGG 59.038 55.000 0.00 0.00 38.35 3.28
6536 6954 0.961753 GAACTGGTCAAGCCTTTGGG 59.038 55.000 0.00 0.00 38.35 4.12
6546 6964 4.293610 CCTTTGGGCCTTTGTGGT 57.706 55.556 4.53 0.00 38.35 4.16
6547 6965 2.526958 CCTTTGGGCCTTTGTGGTT 58.473 52.632 4.53 0.00 38.35 3.67
6548 6966 0.392706 CCTTTGGGCCTTTGTGGTTC 59.607 55.000 4.53 0.00 38.35 3.62
6549 6967 1.413118 CTTTGGGCCTTTGTGGTTCT 58.587 50.000 4.53 0.00 38.35 3.01
6550 6968 1.762370 CTTTGGGCCTTTGTGGTTCTT 59.238 47.619 4.53 0.00 38.35 2.52
6551 6969 1.872773 TTGGGCCTTTGTGGTTCTTT 58.127 45.000 4.53 0.00 38.35 2.52
6552 6970 1.872773 TGGGCCTTTGTGGTTCTTTT 58.127 45.000 4.53 0.00 38.35 2.27
6553 6971 2.192263 TGGGCCTTTGTGGTTCTTTTT 58.808 42.857 4.53 0.00 38.35 1.94
6554 6972 2.093235 TGGGCCTTTGTGGTTCTTTTTG 60.093 45.455 4.53 0.00 38.35 2.44
6555 6973 2.169561 GGGCCTTTGTGGTTCTTTTTGA 59.830 45.455 0.84 0.00 38.35 2.69
6556 6974 3.369997 GGGCCTTTGTGGTTCTTTTTGAA 60.370 43.478 0.84 0.00 38.35 2.69
6557 6975 3.871006 GGCCTTTGTGGTTCTTTTTGAAG 59.129 43.478 0.00 0.00 38.35 3.02
6558 6976 4.382577 GGCCTTTGTGGTTCTTTTTGAAGA 60.383 41.667 0.00 0.00 38.35 2.87
6559 6977 5.175127 GCCTTTGTGGTTCTTTTTGAAGAA 58.825 37.500 0.00 0.00 38.35 2.52
6560 6978 5.641636 GCCTTTGTGGTTCTTTTTGAAGAAA 59.358 36.000 3.40 0.00 40.15 2.52
6561 6979 6.148645 GCCTTTGTGGTTCTTTTTGAAGAAAA 59.851 34.615 3.40 0.00 40.15 2.29
6562 6980 7.148255 GCCTTTGTGGTTCTTTTTGAAGAAAAT 60.148 33.333 3.40 0.00 40.15 1.82
6563 6981 8.177013 CCTTTGTGGTTCTTTTTGAAGAAAATG 58.823 33.333 3.40 0.00 40.15 2.32
6564 6982 7.608308 TTGTGGTTCTTTTTGAAGAAAATGG 57.392 32.000 3.40 0.00 40.15 3.16
6565 6983 6.706295 TGTGGTTCTTTTTGAAGAAAATGGT 58.294 32.000 3.40 0.00 40.15 3.55
6566 6984 7.841956 TGTGGTTCTTTTTGAAGAAAATGGTA 58.158 30.769 3.40 0.00 40.15 3.25
6567 6985 7.978975 TGTGGTTCTTTTTGAAGAAAATGGTAG 59.021 33.333 3.40 0.00 40.15 3.18
6568 6986 7.979537 GTGGTTCTTTTTGAAGAAAATGGTAGT 59.020 33.333 3.40 0.00 40.15 2.73
6569 6987 9.191479 TGGTTCTTTTTGAAGAAAATGGTAGTA 57.809 29.630 3.40 0.00 40.15 1.82
6570 6988 9.678941 GGTTCTTTTTGAAGAAAATGGTAGTAG 57.321 33.333 3.40 0.00 40.15 2.57
6571 6989 9.678941 GTTCTTTTTGAAGAAAATGGTAGTAGG 57.321 33.333 3.40 0.00 40.15 3.18
6572 6990 8.990163 TCTTTTTGAAGAAAATGGTAGTAGGT 57.010 30.769 0.00 0.00 31.07 3.08
6573 6991 8.846211 TCTTTTTGAAGAAAATGGTAGTAGGTG 58.154 33.333 0.00 0.00 31.07 4.00
6574 6992 8.528044 TTTTTGAAGAAAATGGTAGTAGGTGT 57.472 30.769 0.00 0.00 31.07 4.16
6575 6993 9.629878 TTTTTGAAGAAAATGGTAGTAGGTGTA 57.370 29.630 0.00 0.00 31.07 2.90
6576 6994 8.842358 TTTGAAGAAAATGGTAGTAGGTGTAG 57.158 34.615 0.00 0.00 0.00 2.74
6577 6995 6.403878 TGAAGAAAATGGTAGTAGGTGTAGC 58.596 40.000 0.00 0.00 0.00 3.58
6578 6996 5.354842 AGAAAATGGTAGTAGGTGTAGCC 57.645 43.478 0.00 0.00 37.58 3.93
6592 7010 4.636249 GGTGTAGCCTGATTTCTCTATGG 58.364 47.826 0.00 0.00 0.00 2.74
6593 7011 4.101741 GGTGTAGCCTGATTTCTCTATGGT 59.898 45.833 0.00 0.00 0.00 3.55
6594 7012 5.396884 GGTGTAGCCTGATTTCTCTATGGTT 60.397 44.000 0.00 0.00 0.00 3.67
6595 7013 6.116126 GTGTAGCCTGATTTCTCTATGGTTT 58.884 40.000 0.00 0.00 0.00 3.27
6596 7014 6.599638 GTGTAGCCTGATTTCTCTATGGTTTT 59.400 38.462 0.00 0.00 0.00 2.43
6597 7015 6.599244 TGTAGCCTGATTTCTCTATGGTTTTG 59.401 38.462 0.00 0.00 0.00 2.44
6598 7016 4.400567 AGCCTGATTTCTCTATGGTTTTGC 59.599 41.667 0.00 0.00 0.00 3.68
6655 7073 2.779430 TGATGGATGGTGGCACTAAGAT 59.221 45.455 18.45 5.08 0.00 2.40
6666 7369 7.047891 TGGTGGCACTAAGATGTATAAGAAAG 58.952 38.462 18.45 0.00 0.00 2.62
6741 7453 5.064962 TGACACAAATAACCGTTTTCTCGTT 59.935 36.000 0.00 0.00 0.00 3.85
6748 7460 3.672767 ACCGTTTTCTCGTTGTCCTAT 57.327 42.857 0.00 0.00 0.00 2.57
6755 7467 5.661056 TTTCTCGTTGTCCTATGTGATCT 57.339 39.130 0.00 0.00 0.00 2.75
6758 7470 4.950475 TCTCGTTGTCCTATGTGATCTTCT 59.050 41.667 0.00 0.00 0.00 2.85
6792 7504 8.243426 CCAAAGTGTTGTATATGTGTAGCATTT 58.757 33.333 0.00 0.00 34.65 2.32
6862 7574 8.859090 TCACAAATAGAACAACATTTGGATCTT 58.141 29.630 10.71 0.00 43.36 2.40
6948 7660 2.555732 ATGGTTGAAAGGGATGGCAT 57.444 45.000 0.00 0.00 0.00 4.40
6986 7698 9.788960 GCCCTTCAAACTAAGTTATTTAATGAG 57.211 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.731519 GATAATTCGAAAAGACTTGCAAAAATG 57.268 29.630 0.00 0.00 0.00 2.32
74 75 3.691609 CCAAATCTAAGCACTTCTCCCAC 59.308 47.826 0.00 0.00 0.00 4.61
91 92 1.691434 ACCGCAACATTGAACCCAAAT 59.309 42.857 0.00 0.00 35.67 2.32
104 105 3.195698 GGGATCGAGCACCGCAAC 61.196 66.667 1.84 0.00 38.37 4.17
196 197 8.038862 ACATGATGTAGAGGGATAAACTCAAT 57.961 34.615 0.00 0.00 37.43 2.57
252 253 6.865726 AGCATGCATCTAGAGTATTAAGTTCG 59.134 38.462 21.98 0.00 0.00 3.95
279 280 3.682696 ACTCCATACATCGACCGCTATA 58.317 45.455 0.00 0.00 0.00 1.31
294 295 8.941995 TTCTGCATCTACTACTATTACTCCAT 57.058 34.615 0.00 0.00 0.00 3.41
475 476 0.841961 GTAAAATAGACCCGGGGGCT 59.158 55.000 27.95 27.95 39.32 5.19
677 679 3.506067 GCCTAGTACCTGCACAAACAATT 59.494 43.478 0.00 0.00 0.00 2.32
709 711 9.303116 CAAGGTATCAATCCAGTAGTAGACTAT 57.697 37.037 0.00 0.00 35.64 2.12
716 718 6.440647 TGAGAACAAGGTATCAATCCAGTAGT 59.559 38.462 0.00 0.00 0.00 2.73
775 778 4.733077 TGGTTTTCAGGAAAGGGTGATA 57.267 40.909 0.00 0.00 0.00 2.15
811 823 1.221840 CCCTGTCGGTTGCTGCTAT 59.778 57.895 0.00 0.00 0.00 2.97
823 835 1.666872 CGGACGACCAAACCCTGTC 60.667 63.158 4.48 0.00 35.59 3.51
824 836 2.424302 CGGACGACCAAACCCTGT 59.576 61.111 4.48 0.00 35.59 4.00
825 837 3.047877 GCGGACGACCAAACCCTG 61.048 66.667 4.48 0.00 35.59 4.45
826 838 4.324991 GGCGGACGACCAAACCCT 62.325 66.667 4.48 0.00 35.59 4.34
844 856 4.314440 TGGAGCCCACACTCGTGC 62.314 66.667 0.00 0.00 42.17 5.34
853 865 2.930019 CCTGACCTGTGGAGCCCA 60.930 66.667 0.00 0.00 0.00 5.36
854 866 3.721706 CCCTGACCTGTGGAGCCC 61.722 72.222 0.00 0.00 0.00 5.19
855 867 2.529744 AACCCTGACCTGTGGAGCC 61.530 63.158 0.00 0.00 0.00 4.70
856 868 1.302832 CAACCCTGACCTGTGGAGC 60.303 63.158 0.00 0.00 0.00 4.70
857 869 1.376466 CCAACCCTGACCTGTGGAG 59.624 63.158 0.00 0.00 0.00 3.86
858 870 2.153401 CCCAACCCTGACCTGTGGA 61.153 63.158 0.00 0.00 0.00 4.02
859 871 2.129555 CTCCCAACCCTGACCTGTGG 62.130 65.000 0.00 0.00 0.00 4.17
860 872 1.376466 CTCCCAACCCTGACCTGTG 59.624 63.158 0.00 0.00 0.00 3.66
861 873 2.529744 GCTCCCAACCCTGACCTGT 61.530 63.158 0.00 0.00 0.00 4.00
862 874 2.352805 GCTCCCAACCCTGACCTG 59.647 66.667 0.00 0.00 0.00 4.00
863 875 2.121963 TGCTCCCAACCCTGACCT 60.122 61.111 0.00 0.00 0.00 3.85
864 876 1.779061 TTCTGCTCCCAACCCTGACC 61.779 60.000 0.00 0.00 0.00 4.02
865 877 0.322008 CTTCTGCTCCCAACCCTGAC 60.322 60.000 0.00 0.00 0.00 3.51
866 878 2.069776 CTTCTGCTCCCAACCCTGA 58.930 57.895 0.00 0.00 0.00 3.86
867 879 1.676967 GCTTCTGCTCCCAACCCTG 60.677 63.158 0.00 0.00 36.03 4.45
868 880 2.759795 GCTTCTGCTCCCAACCCT 59.240 61.111 0.00 0.00 36.03 4.34
923 937 1.804372 CGGCCTACATGTCAGCTTCTC 60.804 57.143 16.89 2.99 0.00 2.87
1105 1128 4.115199 GCCCGCATCCTGGTTCCT 62.115 66.667 0.00 0.00 0.00 3.36
1152 1175 2.530151 AGCTGGAGGAGGTTGGCA 60.530 61.111 0.00 0.00 0.00 4.92
1258 1295 2.505982 CCCGATCTGCCACCGAAT 59.494 61.111 0.00 0.00 0.00 3.34
1501 1538 4.320421 CGATCAAAAACAGTCCATCAGCAA 60.320 41.667 0.00 0.00 0.00 3.91
1629 1666 4.810730 GCACAAACTGCAGCAACA 57.189 50.000 15.27 0.00 46.29 3.33
1648 1685 1.399714 ATGTCCATGCCTGCTGATTG 58.600 50.000 0.00 0.00 0.00 2.67
1738 1878 1.003580 ACCAGTGCCACTACAGAATGG 59.996 52.381 0.00 0.00 43.62 3.16
2509 2649 4.307432 CTTCCTCAAGCTTAAGTTGACGA 58.693 43.478 0.00 12.31 30.69 4.20
2651 2793 0.538516 TGGGGTCATTTTGTGGGTCG 60.539 55.000 0.00 0.00 0.00 4.79
2992 3135 3.817647 GCTATATAAGGCAGCAAAGCAGT 59.182 43.478 0.00 0.00 35.35 4.40
2993 3136 4.416505 GCTATATAAGGCAGCAAAGCAG 57.583 45.455 0.00 0.00 35.35 4.24
3093 3238 5.914033 TCTATCTTGGTATGAAAGGTTCCG 58.086 41.667 0.00 0.00 0.00 4.30
3126 3271 8.413229 ACAGCTTTAATTATGTTTTGTGTGTCT 58.587 29.630 0.00 0.00 0.00 3.41
3183 3329 1.279271 AGAACACATGCTGTACTCCCC 59.721 52.381 0.00 0.00 30.51 4.81
3186 3332 4.065088 TCCAAAGAACACATGCTGTACTC 58.935 43.478 0.00 0.00 30.51 2.59
3238 3384 9.807921 AAGAGTAAGGAAATAGAACATGGAAAA 57.192 29.630 0.00 0.00 0.00 2.29
3427 3574 9.249053 TGTTTAATTATCTACCAAGGAATGCAA 57.751 29.630 0.00 0.00 0.00 4.08
3615 3762 3.281727 TTGTTTGCTCTGTTCCTCACT 57.718 42.857 0.00 0.00 0.00 3.41
3868 4015 3.372954 CGCTAGTACCATAACAGCTCAC 58.627 50.000 0.00 0.00 0.00 3.51
4036 4183 8.620116 AACAAAATAGCCAAAGCAATTACATT 57.380 26.923 0.00 0.00 43.56 2.71
4524 4694 5.786311 ACATTGAGTTTGAATGACCAATGG 58.214 37.500 14.70 0.00 42.80 3.16
4942 5224 6.204688 CAGCTATACACAGAAACAGAACCAAA 59.795 38.462 0.00 0.00 0.00 3.28
5005 5287 1.416772 TGGAACATACGGTCAACACCA 59.583 47.619 0.00 0.00 44.02 4.17
5006 5288 2.172851 TGGAACATACGGTCAACACC 57.827 50.000 0.00 0.00 39.69 4.16
5023 5307 8.613060 AGCACAAGATACTAATTACATCATGG 57.387 34.615 10.20 3.97 0.00 3.66
5096 5380 0.820871 GCTCTTCTGATCTGGGTCGT 59.179 55.000 0.00 0.00 0.00 4.34
5270 5562 0.042448 GCGAGCGTTCACGAGTTTTT 60.042 50.000 2.87 0.00 43.02 1.94
5525 5817 2.528818 CCTGCCAGGGTCCTGTTCA 61.529 63.158 15.09 11.27 42.15 3.18
5615 5907 3.316308 GGTTATAGCCAAGCTCACCATTG 59.684 47.826 0.00 0.00 40.44 2.82
5887 6179 6.484643 AGCTGAAATGATGCGAATATTACTGT 59.515 34.615 0.00 0.00 0.00 3.55
5974 6266 4.862018 AGCATACAACAAACAAACACACAC 59.138 37.500 0.00 0.00 0.00 3.82
5975 6267 5.065704 AGCATACAACAAACAAACACACA 57.934 34.783 0.00 0.00 0.00 3.72
6364 6658 7.307632 CCTCTGACTTCTCAGTTTACAATGTTG 60.308 40.741 0.00 0.00 44.07 3.33
6507 6925 1.368374 TGACCAGTTCCCCCTAAAGG 58.632 55.000 0.00 0.00 0.00 3.11
6508 6926 2.880167 GCTTGACCAGTTCCCCCTAAAG 60.880 54.545 0.00 0.00 0.00 1.85
6509 6927 1.074889 GCTTGACCAGTTCCCCCTAAA 59.925 52.381 0.00 0.00 0.00 1.85
6510 6928 0.696501 GCTTGACCAGTTCCCCCTAA 59.303 55.000 0.00 0.00 0.00 2.69
6511 6929 1.205460 GGCTTGACCAGTTCCCCCTA 61.205 60.000 0.00 0.00 38.86 3.53
6512 6930 2.539081 GGCTTGACCAGTTCCCCCT 61.539 63.158 0.00 0.00 38.86 4.79
6513 6931 2.035783 GGCTTGACCAGTTCCCCC 59.964 66.667 0.00 0.00 38.86 5.40
6514 6932 0.178961 AAAGGCTTGACCAGTTCCCC 60.179 55.000 0.00 0.00 43.14 4.81
6515 6933 0.961753 CAAAGGCTTGACCAGTTCCC 59.038 55.000 0.00 0.00 43.14 3.97
6516 6934 0.961753 CCAAAGGCTTGACCAGTTCC 59.038 55.000 0.00 0.00 43.14 3.62
6517 6935 0.961753 CCCAAAGGCTTGACCAGTTC 59.038 55.000 0.00 0.00 43.14 3.01
6518 6936 3.131850 CCCAAAGGCTTGACCAGTT 57.868 52.632 0.00 0.00 43.14 3.16
6519 6937 4.929807 CCCAAAGGCTTGACCAGT 57.070 55.556 0.00 0.00 43.14 4.00
6529 6947 0.392706 GAACCACAAAGGCCCAAAGG 59.607 55.000 0.00 0.00 43.14 3.11
6530 6948 1.413118 AGAACCACAAAGGCCCAAAG 58.587 50.000 0.00 0.00 43.14 2.77
6531 6949 1.872773 AAGAACCACAAAGGCCCAAA 58.127 45.000 0.00 0.00 43.14 3.28
6532 6950 1.872773 AAAGAACCACAAAGGCCCAA 58.127 45.000 0.00 0.00 43.14 4.12
6533 6951 1.872773 AAAAGAACCACAAAGGCCCA 58.127 45.000 0.00 0.00 43.14 5.36
6534 6952 2.169561 TCAAAAAGAACCACAAAGGCCC 59.830 45.455 0.00 0.00 43.14 5.80
6535 6953 3.535280 TCAAAAAGAACCACAAAGGCC 57.465 42.857 0.00 0.00 43.14 5.19
6536 6954 4.754322 TCTTCAAAAAGAACCACAAAGGC 58.246 39.130 0.00 0.00 38.58 4.35
6547 6965 8.846211 CACCTACTACCATTTTCTTCAAAAAGA 58.154 33.333 0.00 0.00 39.78 2.52
6548 6966 8.630037 ACACCTACTACCATTTTCTTCAAAAAG 58.370 33.333 0.00 0.00 35.10 2.27
6549 6967 8.528044 ACACCTACTACCATTTTCTTCAAAAA 57.472 30.769 0.00 0.00 35.10 1.94
6550 6968 9.280174 CTACACCTACTACCATTTTCTTCAAAA 57.720 33.333 0.00 0.00 35.92 2.44
6551 6969 7.389607 GCTACACCTACTACCATTTTCTTCAAA 59.610 37.037 0.00 0.00 0.00 2.69
6552 6970 6.877322 GCTACACCTACTACCATTTTCTTCAA 59.123 38.462 0.00 0.00 0.00 2.69
6553 6971 6.403878 GCTACACCTACTACCATTTTCTTCA 58.596 40.000 0.00 0.00 0.00 3.02
6554 6972 5.816258 GGCTACACCTACTACCATTTTCTTC 59.184 44.000 0.00 0.00 34.51 2.87
6555 6973 5.742063 GGCTACACCTACTACCATTTTCTT 58.258 41.667 0.00 0.00 34.51 2.52
6556 6974 5.354842 GGCTACACCTACTACCATTTTCT 57.645 43.478 0.00 0.00 34.51 2.52
6570 6988 4.101741 ACCATAGAGAAATCAGGCTACACC 59.898 45.833 0.00 0.00 39.61 4.16
6571 6989 5.283457 ACCATAGAGAAATCAGGCTACAC 57.717 43.478 0.00 0.00 0.00 2.90
6572 6990 5.957771 AACCATAGAGAAATCAGGCTACA 57.042 39.130 0.00 0.00 0.00 2.74
6573 6991 6.458888 GCAAAACCATAGAGAAATCAGGCTAC 60.459 42.308 0.00 0.00 0.00 3.58
6574 6992 5.590259 GCAAAACCATAGAGAAATCAGGCTA 59.410 40.000 0.00 0.00 0.00 3.93
6575 6993 4.400567 GCAAAACCATAGAGAAATCAGGCT 59.599 41.667 0.00 0.00 0.00 4.58
6576 6994 4.400567 AGCAAAACCATAGAGAAATCAGGC 59.599 41.667 0.00 0.00 0.00 4.85
6577 6995 5.649395 TCAGCAAAACCATAGAGAAATCAGG 59.351 40.000 0.00 0.00 0.00 3.86
6578 6996 6.748333 TCAGCAAAACCATAGAGAAATCAG 57.252 37.500 0.00 0.00 0.00 2.90
6579 6997 6.716628 AGTTCAGCAAAACCATAGAGAAATCA 59.283 34.615 0.00 0.00 0.00 2.57
6580 6998 7.150783 AGTTCAGCAAAACCATAGAGAAATC 57.849 36.000 0.00 0.00 0.00 2.17
6581 6999 7.231317 TGAAGTTCAGCAAAACCATAGAGAAAT 59.769 33.333 0.08 0.00 0.00 2.17
6582 7000 6.545666 TGAAGTTCAGCAAAACCATAGAGAAA 59.454 34.615 0.08 0.00 0.00 2.52
6583 7001 6.061441 TGAAGTTCAGCAAAACCATAGAGAA 58.939 36.000 0.08 0.00 0.00 2.87
6584 7002 5.620206 TGAAGTTCAGCAAAACCATAGAGA 58.380 37.500 0.08 0.00 0.00 3.10
6585 7003 5.947228 TGAAGTTCAGCAAAACCATAGAG 57.053 39.130 0.08 0.00 0.00 2.43
6586 7004 5.278463 GCTTGAAGTTCAGCAAAACCATAGA 60.278 40.000 17.22 0.00 0.00 1.98
6587 7005 4.919754 GCTTGAAGTTCAGCAAAACCATAG 59.080 41.667 17.22 6.13 0.00 2.23
6588 7006 4.261994 GGCTTGAAGTTCAGCAAAACCATA 60.262 41.667 21.15 0.00 0.00 2.74
6589 7007 3.493176 GGCTTGAAGTTCAGCAAAACCAT 60.493 43.478 21.15 0.00 0.00 3.55
6590 7008 2.159114 GGCTTGAAGTTCAGCAAAACCA 60.159 45.455 21.15 0.90 0.00 3.67
6591 7009 2.101415 AGGCTTGAAGTTCAGCAAAACC 59.899 45.455 21.15 12.03 0.00 3.27
6592 7010 3.443099 AGGCTTGAAGTTCAGCAAAAC 57.557 42.857 21.15 9.69 0.00 2.43
6593 7011 4.183101 CAAAGGCTTGAAGTTCAGCAAAA 58.817 39.130 21.15 2.73 34.14 2.44
6594 7012 3.430651 CCAAAGGCTTGAAGTTCAGCAAA 60.431 43.478 21.15 3.04 34.14 3.68
6595 7013 2.101249 CCAAAGGCTTGAAGTTCAGCAA 59.899 45.455 21.15 3.34 34.14 3.91
6596 7014 1.682854 CCAAAGGCTTGAAGTTCAGCA 59.317 47.619 21.15 3.96 34.14 4.41
6597 7015 1.000171 CCCAAAGGCTTGAAGTTCAGC 60.000 52.381 15.03 15.03 34.14 4.26
6598 7016 1.615392 CCCCAAAGGCTTGAAGTTCAG 59.385 52.381 5.56 2.17 34.14 3.02
6655 7073 8.590204 TGTTGGAGATGTACACTTTCTTATACA 58.410 33.333 0.00 1.05 32.38 2.29
6666 7369 2.076863 GGCTGTGTTGGAGATGTACAC 58.923 52.381 0.00 0.00 41.85 2.90
6741 7453 4.020307 TGTTGCAGAAGATCACATAGGACA 60.020 41.667 0.00 0.00 0.00 4.02
6748 7460 2.929641 TGGTTGTTGCAGAAGATCACA 58.070 42.857 0.00 0.00 0.00 3.58
6755 7467 3.583806 CAACACTTTGGTTGTTGCAGAA 58.416 40.909 2.50 0.00 42.43 3.02
6782 7494 5.233902 TGAAATGCAACAACAAATGCTACAC 59.766 36.000 0.00 0.00 42.97 2.90
6792 7504 1.068895 CAGCCCTGAAATGCAACAACA 59.931 47.619 0.00 0.00 0.00 3.33
6862 7574 3.118445 CCCCACTTTTCAAGCCAAAAAGA 60.118 43.478 17.71 0.00 43.32 2.52
6948 7660 2.204029 AAGGGCCCGAAGTACCCA 60.204 61.111 18.44 0.00 46.88 4.51


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

AutoCloner maintained by Alex Coulton.