Multiple sequence alignment - TraesCS1D01G306000

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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 TraesCS1D01G306000 chr1D 100.000 5245 0 0 1 5245 403272875 403278119 0.000000e+00 9686.0
1 TraesCS1D01G306000 chr1D 86.166 253 31 4 2005 2255 367846123 367846373 2.410000e-68 270.0
2 TraesCS1D01G306000 chr1D 78.344 157 13 20 4589 4732 253071787 253071935 1.210000e-11 82.4
3 TraesCS1D01G306000 chr1A 95.545 3412 112 13 225 3616 498532452 498535843 0.000000e+00 5422.0
4 TraesCS1D01G306000 chr1A 97.082 377 7 2 4110 4482 498536440 498536816 2.670000e-177 632.0
5 TraesCS1D01G306000 chr1A 97.585 207 5 0 3611 3817 498535869 498536075 6.460000e-94 355.0
6 TraesCS1D01G306000 chr1A 90.037 271 13 5 3847 4103 498536075 498536345 6.510000e-89 339.0
7 TraesCS1D01G306000 chr1B 93.580 3536 140 27 103 3607 542134739 542138218 0.000000e+00 5192.0
8 TraesCS1D01G306000 chr1B 93.692 650 34 3 3611 4256 542138268 542138914 0.000000e+00 966.0
9 TraesCS1D01G306000 chr1B 83.938 193 10 9 4312 4500 542138912 542139087 1.170000e-36 165.0
10 TraesCS1D01G306000 chr1B 96.970 33 1 0 4328 4360 542138982 542139014 7.340000e-04 56.5
11 TraesCS1D01G306000 chr7D 94.805 770 19 5 4480 5245 559287493 559288245 0.000000e+00 1181.0
12 TraesCS1D01G306000 chr7D 86.056 251 28 5 2006 2252 37221805 37221558 4.030000e-66 263.0
13 TraesCS1D01G306000 chr4B 93.299 776 20 9 4478 5245 184602155 184601404 0.000000e+00 1116.0
14 TraesCS1D01G306000 chr4B 80.311 193 35 3 14 205 382202461 382202651 5.480000e-30 143.0
15 TraesCS1D01G306000 chr4B 92.500 40 3 0 4834 4873 81205634 81205673 2.040000e-04 58.4
16 TraesCS1D01G306000 chr2D 97.126 661 11 3 4589 5245 579179716 579179060 0.000000e+00 1109.0
17 TraesCS1D01G306000 chr2D 93.333 75 5 0 4480 4554 579184981 579184907 1.540000e-20 111.0
18 TraesCS1D01G306000 chr5A 92.290 441 18 7 4724 5160 615773238 615773666 3.470000e-171 612.0
19 TraesCS1D01G306000 chr5A 91.629 442 21 7 4723 5160 615832349 615832778 9.720000e-167 597.0
20 TraesCS1D01G306000 chr5A 87.451 255 25 7 2006 2257 130535256 130535506 2.390000e-73 287.0
21 TraesCS1D01G306000 chr3B 94.677 263 10 2 4687 4945 195340508 195340770 6.320000e-109 405.0
22 TraesCS1D01G306000 chr3B 98.667 75 1 0 4616 4690 195340459 195340533 3.300000e-27 134.0
23 TraesCS1D01G306000 chr6B 87.209 258 29 4 2000 2255 715838675 715838420 1.850000e-74 291.0
24 TraesCS1D01G306000 chr6B 92.771 83 6 0 5156 5238 82012380 82012462 2.570000e-23 121.0
25 TraesCS1D01G306000 chr5D 87.402 254 29 3 2005 2257 491433543 491433794 6.650000e-74 289.0
26 TraesCS1D01G306000 chr5D 86.454 251 25 7 2006 2252 66973793 66974038 3.110000e-67 267.0
27 TraesCS1D01G306000 chr7A 86.000 250 31 4 2005 2252 578444755 578444508 1.120000e-66 265.0
28 TraesCS1D01G306000 chrUn 82.258 186 28 4 20 203 48224468 48224286 7.030000e-34 156.0
29 TraesCS1D01G306000 chrUn 82.258 186 28 4 20 203 48225776 48225594 7.030000e-34 156.0
30 TraesCS1D01G306000 chrUn 82.258 186 28 4 20 203 421392429 421392247 7.030000e-34 156.0
31 TraesCS1D01G306000 chr2B 81.868 182 31 2 26 206 663142404 663142224 9.100000e-33 152.0
32 TraesCS1D01G306000 chr5B 80.303 198 33 5 11 206 655717705 655717898 1.520000e-30 145.0
33 TraesCS1D01G306000 chr5B 80.851 188 31 4 20 205 518809465 518809281 5.480000e-30 143.0
34 TraesCS1D01G306000 chr6D 80.105 191 34 4 14 203 448346083 448346270 7.080000e-29 139.0
35 TraesCS1D01G306000 chr6A 75.000 264 41 19 4480 4732 21581812 21582061 1.200000e-16 99.0
36 TraesCS1D01G306000 chr3D 85.057 87 4 9 4650 4732 293860022 293860103 4.350000e-11 80.5
37 TraesCS1D01G306000 chr4A 95.122 41 2 0 3232 3272 485387797 485387757 1.220000e-06 65.8


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 TraesCS1D01G306000 chr1D 403272875 403278119 5244 False 9686.000 9686 100.00000 1 5245 1 chr1D.!!$F3 5244
1 TraesCS1D01G306000 chr1A 498532452 498536816 4364 False 1687.000 5422 95.06225 225 4482 4 chr1A.!!$F1 4257
2 TraesCS1D01G306000 chr1B 542134739 542139087 4348 False 1594.875 5192 92.04500 103 4500 4 chr1B.!!$F1 4397
3 TraesCS1D01G306000 chr7D 559287493 559288245 752 False 1181.000 1181 94.80500 4480 5245 1 chr7D.!!$F1 765
4 TraesCS1D01G306000 chr4B 184601404 184602155 751 True 1116.000 1116 93.29900 4478 5245 1 chr4B.!!$R1 767
5 TraesCS1D01G306000 chr2D 579179060 579179716 656 True 1109.000 1109 97.12600 4589 5245 1 chr2D.!!$R1 656

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
29 30 0.172127 GCACATCTGCGAGAGACTGA 59.828 55.0 0.00 0.0 32.44 3.41 F
73 74 0.240411 ACGAAGTCACTGTAGACGCC 59.760 55.0 0.00 0.0 43.24 5.68 F
952 968 0.256464 TTTGGACACCGTTGTTCCCT 59.744 50.0 0.00 0.0 35.47 4.20 F
1367 1386 0.784495 AGTGGTGAGGAGGGTAGTCA 59.216 55.0 0.00 0.0 0.00 3.41 F
2828 2858 0.393820 TGCTGACAGACACATGCAGA 59.606 50.0 6.65 0.0 30.63 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1597 0.322816 TGAAAGGACCTGCCATGCTC 60.323 55.000 0.0 0.0 40.02 4.26 R
1855 1875 2.224670 ACCAATGCGTAGGAAAACAGGA 60.225 45.455 0.0 0.0 0.00 3.86 R
2684 2713 2.452600 AATGAGTTGTGTGGGTGGTT 57.547 45.000 0.0 0.0 0.00 3.67 R
3148 3187 5.185442 TCACCATGCAAAATATTGAGAAGCA 59.815 36.000 0.0 0.0 38.94 3.91 R
4286 4487 1.485480 TGTTTCTACCACAACCACGGA 59.515 47.619 0.0 0.0 0.00 4.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.070076 AGGCATACACGCACATCTG 57.930 52.632 0.00 0.00 0.00 2.90
19 20 1.091771 AGGCATACACGCACATCTGC 61.092 55.000 0.00 0.00 40.38 4.26
28 29 2.663358 GCACATCTGCGAGAGACTG 58.337 57.895 0.00 0.00 32.44 3.51
29 30 0.172127 GCACATCTGCGAGAGACTGA 59.828 55.000 0.00 0.00 32.44 3.41
30 31 1.798446 GCACATCTGCGAGAGACTGAG 60.798 57.143 0.00 0.00 32.44 3.35
31 32 0.455410 ACATCTGCGAGAGACTGAGC 59.545 55.000 0.00 0.00 31.75 4.26
32 33 0.248990 CATCTGCGAGAGACTGAGCC 60.249 60.000 0.00 0.00 31.75 4.70
33 34 0.682532 ATCTGCGAGAGACTGAGCCA 60.683 55.000 0.00 0.00 31.75 4.75
34 35 0.682532 TCTGCGAGAGACTGAGCCAT 60.683 55.000 0.00 0.00 0.00 4.40
35 36 0.248990 CTGCGAGAGACTGAGCCATC 60.249 60.000 0.00 0.00 0.00 3.51
36 37 0.967380 TGCGAGAGACTGAGCCATCA 60.967 55.000 0.00 0.00 0.00 3.07
37 38 0.388659 GCGAGAGACTGAGCCATCAT 59.611 55.000 0.00 0.00 34.12 2.45
38 39 1.611006 GCGAGAGACTGAGCCATCATA 59.389 52.381 0.00 0.00 34.12 2.15
39 40 2.230992 GCGAGAGACTGAGCCATCATAT 59.769 50.000 0.00 0.00 34.12 1.78
40 41 3.673052 GCGAGAGACTGAGCCATCATATC 60.673 52.174 0.00 0.00 34.12 1.63
41 42 3.505293 CGAGAGACTGAGCCATCATATCA 59.495 47.826 0.00 0.00 34.12 2.15
42 43 4.158209 CGAGAGACTGAGCCATCATATCAT 59.842 45.833 0.00 0.00 34.12 2.45
43 44 5.356470 CGAGAGACTGAGCCATCATATCATA 59.644 44.000 0.00 0.00 34.12 2.15
44 45 6.039605 CGAGAGACTGAGCCATCATATCATAT 59.960 42.308 0.00 0.00 34.12 1.78
45 46 7.416551 CGAGAGACTGAGCCATCATATCATATT 60.417 40.741 0.00 0.00 34.12 1.28
46 47 8.835550 AGAGACTGAGCCATCATATCATATTA 57.164 34.615 0.00 0.00 34.12 0.98
47 48 9.264653 AGAGACTGAGCCATCATATCATATTAA 57.735 33.333 0.00 0.00 34.12 1.40
48 49 9.531942 GAGACTGAGCCATCATATCATATTAAG 57.468 37.037 0.00 0.00 34.12 1.85
49 50 9.264653 AGACTGAGCCATCATATCATATTAAGA 57.735 33.333 0.00 0.00 34.12 2.10
50 51 9.531942 GACTGAGCCATCATATCATATTAAGAG 57.468 37.037 0.00 0.00 34.12 2.85
51 52 9.044646 ACTGAGCCATCATATCATATTAAGAGT 57.955 33.333 0.00 0.00 34.12 3.24
52 53 9.887629 CTGAGCCATCATATCATATTAAGAGTT 57.112 33.333 0.00 0.00 34.12 3.01
65 66 9.569167 TCATATTAAGAGTTTACGAAGTCACTG 57.431 33.333 0.00 0.00 43.93 3.66
66 67 9.355215 CATATTAAGAGTTTACGAAGTCACTGT 57.645 33.333 0.00 0.00 43.93 3.55
68 69 8.967552 ATTAAGAGTTTACGAAGTCACTGTAG 57.032 34.615 0.00 0.00 43.93 2.74
69 70 6.630444 AAGAGTTTACGAAGTCACTGTAGA 57.370 37.500 0.00 0.00 43.93 2.59
70 71 5.999721 AGAGTTTACGAAGTCACTGTAGAC 58.000 41.667 0.00 3.25 43.93 2.59
71 72 4.781071 AGTTTACGAAGTCACTGTAGACG 58.219 43.478 0.00 0.00 43.93 4.18
72 73 2.888513 TACGAAGTCACTGTAGACGC 57.111 50.000 0.00 0.00 43.93 5.19
73 74 0.240411 ACGAAGTCACTGTAGACGCC 59.760 55.000 0.00 0.00 43.24 5.68
74 75 0.522180 CGAAGTCACTGTAGACGCCT 59.478 55.000 0.00 0.00 43.24 5.52
75 76 1.466024 CGAAGTCACTGTAGACGCCTC 60.466 57.143 0.00 0.00 43.24 4.70
76 77 0.522180 AAGTCACTGTAGACGCCTCG 59.478 55.000 0.00 0.00 43.24 4.63
77 78 0.605860 AGTCACTGTAGACGCCTCGT 60.606 55.000 0.00 0.00 45.10 4.18
78 79 1.081892 GTCACTGTAGACGCCTCGTA 58.918 55.000 0.00 0.00 41.37 3.43
79 80 1.062294 GTCACTGTAGACGCCTCGTAG 59.938 57.143 0.00 0.00 41.37 3.51
80 81 1.085091 CACTGTAGACGCCTCGTAGT 58.915 55.000 0.00 0.00 41.37 2.73
81 82 1.062294 CACTGTAGACGCCTCGTAGTC 59.938 57.143 0.00 0.00 41.37 2.59
82 83 1.338484 ACTGTAGACGCCTCGTAGTCA 60.338 52.381 0.00 0.00 41.37 3.41
83 84 1.736126 CTGTAGACGCCTCGTAGTCAA 59.264 52.381 0.00 0.00 41.37 3.18
84 85 2.355132 CTGTAGACGCCTCGTAGTCAAT 59.645 50.000 0.00 0.00 41.37 2.57
85 86 2.096980 TGTAGACGCCTCGTAGTCAATG 59.903 50.000 0.00 0.00 41.37 2.82
86 87 1.460504 AGACGCCTCGTAGTCAATGA 58.539 50.000 0.00 0.00 41.37 2.57
87 88 1.816835 AGACGCCTCGTAGTCAATGAA 59.183 47.619 0.00 0.00 41.37 2.57
88 89 2.230508 AGACGCCTCGTAGTCAATGAAA 59.769 45.455 0.00 0.00 41.37 2.69
89 90 2.991190 GACGCCTCGTAGTCAATGAAAA 59.009 45.455 0.00 0.00 41.37 2.29
90 91 2.735134 ACGCCTCGTAGTCAATGAAAAC 59.265 45.455 0.00 0.00 38.73 2.43
91 92 2.222508 CGCCTCGTAGTCAATGAAAACG 60.223 50.000 11.06 11.06 34.99 3.60
92 93 2.474032 GCCTCGTAGTCAATGAAAACGC 60.474 50.000 12.11 0.00 33.75 4.84
93 94 2.093783 CCTCGTAGTCAATGAAAACGCC 59.906 50.000 12.11 0.00 33.75 5.68
94 95 2.993899 CTCGTAGTCAATGAAAACGCCT 59.006 45.455 12.11 0.00 33.75 5.52
95 96 2.991190 TCGTAGTCAATGAAAACGCCTC 59.009 45.455 12.11 0.00 33.75 4.70
96 97 2.093783 CGTAGTCAATGAAAACGCCTCC 59.906 50.000 5.84 0.00 0.00 4.30
97 98 2.568623 AGTCAATGAAAACGCCTCCT 57.431 45.000 0.00 0.00 0.00 3.69
98 99 2.427506 AGTCAATGAAAACGCCTCCTC 58.572 47.619 0.00 0.00 0.00 3.71
99 100 1.468914 GTCAATGAAAACGCCTCCTCC 59.531 52.381 0.00 0.00 0.00 4.30
100 101 0.811281 CAATGAAAACGCCTCCTCCC 59.189 55.000 0.00 0.00 0.00 4.30
101 102 0.698818 AATGAAAACGCCTCCTCCCT 59.301 50.000 0.00 0.00 0.00 4.20
107 108 0.903236 AACGCCTCCTCCCTCTAAAC 59.097 55.000 0.00 0.00 0.00 2.01
122 123 0.866427 TAAACGCACATCGCCGAAAA 59.134 45.000 0.00 0.00 43.23 2.29
137 138 7.504924 TCGCCGAAAATCCTGAAATAAATAT 57.495 32.000 0.00 0.00 0.00 1.28
171 172 2.092429 AGCACCAAGACTTGAACCTTGA 60.092 45.455 16.99 0.00 41.56 3.02
175 176 4.214971 CACCAAGACTTGAACCTTGATGAG 59.785 45.833 16.99 0.00 41.56 2.90
180 181 7.308229 CCAAGACTTGAACCTTGATGAGTTAAG 60.308 40.741 16.99 0.00 41.56 1.85
185 186 9.654663 ACTTGAACCTTGATGAGTTAAGTATAC 57.345 33.333 0.00 0.00 0.00 1.47
225 226 5.776173 TCCGTTGTATTTTGTCCACATTT 57.224 34.783 0.00 0.00 0.00 2.32
234 235 8.633561 TGTATTTTGTCCACATTTAACACATCA 58.366 29.630 0.00 0.00 0.00 3.07
320 322 1.691196 TGTTGGAAGCTCAAACTGGG 58.309 50.000 0.00 0.00 0.00 4.45
413 415 3.411517 CTCGGTGGGCCCATTCCT 61.412 66.667 31.45 0.00 0.00 3.36
483 487 0.838122 CCTCCACTTCCACTCCCACT 60.838 60.000 0.00 0.00 0.00 4.00
484 488 0.610687 CTCCACTTCCACTCCCACTC 59.389 60.000 0.00 0.00 0.00 3.51
485 489 0.836400 TCCACTTCCACTCCCACTCC 60.836 60.000 0.00 0.00 0.00 3.85
486 490 1.679898 CACTTCCACTCCCACTCCC 59.320 63.158 0.00 0.00 0.00 4.30
487 491 1.127567 CACTTCCACTCCCACTCCCA 61.128 60.000 0.00 0.00 0.00 4.37
488 492 1.128188 ACTTCCACTCCCACTCCCAC 61.128 60.000 0.00 0.00 0.00 4.61
651 661 2.681778 CAGCTGGGAGGTCGGAGT 60.682 66.667 5.57 0.00 0.00 3.85
652 662 1.379977 CAGCTGGGAGGTCGGAGTA 60.380 63.158 5.57 0.00 0.00 2.59
724 734 1.479323 CCGGGAGACAATTCGAGGTTA 59.521 52.381 0.00 0.00 0.00 2.85
765 775 2.165301 GTCCCGTATGTGCTCGTGC 61.165 63.158 1.71 1.71 40.20 5.34
780 790 1.133915 TCGTGCTTTCCTTCCCAAGTT 60.134 47.619 0.00 0.00 0.00 2.66
885 901 2.885861 GCGGTCTCGTGGATCTGT 59.114 61.111 0.00 0.00 38.89 3.41
938 954 1.228862 GAAAGGGGGCTGCTTTGGA 60.229 57.895 0.00 0.00 0.00 3.53
952 968 0.256464 TTTGGACACCGTTGTTCCCT 59.744 50.000 0.00 0.00 35.47 4.20
994 1010 1.882989 GACCAGTCCAAGAGAGCGCT 61.883 60.000 11.27 11.27 0.00 5.92
995 1011 1.294780 CCAGTCCAAGAGAGCGCTT 59.705 57.895 13.26 0.58 0.00 4.68
1367 1386 0.784495 AGTGGTGAGGAGGGTAGTCA 59.216 55.000 0.00 0.00 0.00 3.41
1463 1482 3.629087 CTGAAGGGCATTTGAAGGATCT 58.371 45.455 0.00 0.00 0.00 2.75
1500 1519 2.933287 ATGGGTGCGGTTGGGAGA 60.933 61.111 0.00 0.00 0.00 3.71
1855 1875 6.041069 GGTCTACAGCTATTGTCCTGTCTATT 59.959 42.308 0.00 0.00 41.13 1.73
1896 1916 9.950680 CATTGGTTATGTCCTGTTATAATGTTC 57.049 33.333 0.00 0.00 0.00 3.18
1937 1957 8.947055 AGCTTTGTGAAAAGTTATTGTTGAAT 57.053 26.923 0.64 0.00 32.52 2.57
1938 1958 9.034544 AGCTTTGTGAAAAGTTATTGTTGAATC 57.965 29.630 0.64 0.00 32.52 2.52
1939 1959 9.034544 GCTTTGTGAAAAGTTATTGTTGAATCT 57.965 29.630 0.64 0.00 32.52 2.40
1971 1991 9.503427 GTATTGATTTAGGCATTTCTGTTACAC 57.497 33.333 0.00 0.00 0.00 2.90
1979 1999 6.447162 AGGCATTTCTGTTACACTTTTTAGC 58.553 36.000 0.00 0.00 0.00 3.09
2264 2292 6.128526 GCAGAGTAAAAAGAAACGACTATGCT 60.129 38.462 11.52 0.00 46.59 3.79
2475 2503 2.742589 CTGTTACTTTTCGCCCCTTCTC 59.257 50.000 0.00 0.00 0.00 2.87
2478 2506 2.186532 ACTTTTCGCCCCTTCTCTTC 57.813 50.000 0.00 0.00 0.00 2.87
2479 2507 1.700186 ACTTTTCGCCCCTTCTCTTCT 59.300 47.619 0.00 0.00 0.00 2.85
2480 2508 2.106684 ACTTTTCGCCCCTTCTCTTCTT 59.893 45.455 0.00 0.00 0.00 2.52
2481 2509 2.951229 TTTCGCCCCTTCTCTTCTTT 57.049 45.000 0.00 0.00 0.00 2.52
2482 2510 2.951229 TTCGCCCCTTCTCTTCTTTT 57.049 45.000 0.00 0.00 0.00 2.27
2548 2576 5.578157 AGTGAACCCAGGTTATTGTAACT 57.422 39.130 1.09 0.00 38.60 2.24
2615 2644 8.482429 GTCGATCGTTCAACTTCTTTTTACTTA 58.518 33.333 15.94 0.00 0.00 2.24
2766 2795 5.073554 TGAACCCCATATGATCATTGCTACT 59.926 40.000 14.65 0.00 0.00 2.57
2828 2858 0.393820 TGCTGACAGACACATGCAGA 59.606 50.000 6.65 0.00 30.63 4.26
3005 3044 2.990740 AACCAACTGAATGGGGCTAA 57.009 45.000 8.63 0.00 45.18 3.09
3015 3054 7.309770 ACTGAATGGGGCTAATTTTTGTTAA 57.690 32.000 0.00 0.00 0.00 2.01
3052 3091 9.586435 GTAATTTTTGGAAATATAAGCAGCTGT 57.414 29.630 16.64 0.00 34.44 4.40
3148 3187 6.492429 TGTATTGACCGATGTACTTAGGCTAT 59.508 38.462 7.68 6.30 0.00 2.97
3151 3190 3.231818 ACCGATGTACTTAGGCTATGCT 58.768 45.455 7.68 0.00 0.00 3.79
3153 3192 4.238514 CCGATGTACTTAGGCTATGCTTC 58.761 47.826 7.29 0.00 0.00 3.86
3159 3198 7.597288 TGTACTTAGGCTATGCTTCTCAATA 57.403 36.000 7.29 0.00 0.00 1.90
3415 3467 7.701445 ACTGCAGCATTAATTCATAGAACTTC 58.299 34.615 15.27 0.00 0.00 3.01
3607 3659 4.036852 GCAGTGTAATAGAATTGCTTCCCC 59.963 45.833 0.00 0.00 31.27 4.81
3820 3918 5.218139 CAAAAGAAAACCACAGAGAGCATC 58.782 41.667 0.00 0.00 0.00 3.91
3845 3943 8.081633 TCTATGCTTGTGTTTTCTGTATTTTGG 58.918 33.333 0.00 0.00 0.00 3.28
3909 4007 4.271696 TCTGTTAAGACCACATCACCTG 57.728 45.455 0.00 0.00 0.00 4.00
4010 4122 9.739276 ACTGAGATTTCATTGGTCATTACTTTA 57.261 29.630 0.00 0.00 31.68 1.85
4023 4135 9.688091 TGGTCATTACTTTATGGCTGTAAATAA 57.312 29.630 0.00 0.00 30.90 1.40
4064 4176 9.552114 GATGTAATTGACTCTTGTTCTTCAATG 57.448 33.333 0.00 0.00 38.42 2.82
4067 4179 5.833406 TTGACTCTTGTTCTTCAATGCAA 57.167 34.783 0.00 0.00 35.35 4.08
4074 4186 6.339730 TCTTGTTCTTCAATGCAACAAACAT 58.660 32.000 0.00 0.00 39.04 2.71
4246 4446 2.262423 AGTTCTGCTCCTGTTTGACC 57.738 50.000 0.00 0.00 0.00 4.02
4283 4484 5.784578 TGTAGATTACACCGCTCATATGT 57.215 39.130 1.90 0.00 32.89 2.29
4286 4487 7.045416 TGTAGATTACACCGCTCATATGTTTT 58.955 34.615 1.90 0.00 32.89 2.43
4287 4488 6.604735 AGATTACACCGCTCATATGTTTTC 57.395 37.500 1.90 0.00 0.00 2.29
4493 4697 2.885616 TCTTTGTACTCCCTCCGTTCT 58.114 47.619 0.00 0.00 0.00 3.01
4502 4706 5.793030 ACTCCCTCCGTTCTGAAATATAG 57.207 43.478 0.00 0.00 0.00 1.31
4540 4745 0.535102 CCGACCAGGTGAAAAGCTGT 60.535 55.000 0.00 0.00 34.51 4.40
4579 4788 3.955551 CCTGGTTCTAGTCTTCTACCTCC 59.044 52.174 0.00 0.00 0.00 4.30
4581 4790 2.358582 GGTTCTAGTCTTCTACCTCCGC 59.641 54.545 0.00 0.00 0.00 5.54
4591 4800 2.664835 CTACCTCCGCCCCCATCTCT 62.665 65.000 0.00 0.00 0.00 3.10
5168 5380 6.702329 CCTGGAGTACTTAGACTGAAAATGT 58.298 40.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.091771 GCAGATGTGCGTGTATGCCT 61.092 55.000 0.00 0.00 40.71 4.75
1 2 1.353103 GCAGATGTGCGTGTATGCC 59.647 57.895 0.00 0.00 40.71 4.40
2 3 4.983090 GCAGATGTGCGTGTATGC 57.017 55.556 0.00 0.00 40.71 3.14
11 12 1.798446 GCTCAGTCTCTCGCAGATGTG 60.798 57.143 0.00 0.00 33.89 3.21
12 13 0.455410 GCTCAGTCTCTCGCAGATGT 59.545 55.000 0.00 0.00 33.89 3.06
13 14 0.248990 GGCTCAGTCTCTCGCAGATG 60.249 60.000 0.00 0.00 33.89 2.90
14 15 0.682532 TGGCTCAGTCTCTCGCAGAT 60.683 55.000 0.00 0.00 33.89 2.90
15 16 0.682532 ATGGCTCAGTCTCTCGCAGA 60.683 55.000 0.00 0.00 0.00 4.26
16 17 0.248990 GATGGCTCAGTCTCTCGCAG 60.249 60.000 0.00 0.00 0.00 5.18
17 18 0.967380 TGATGGCTCAGTCTCTCGCA 60.967 55.000 0.00 0.00 0.00 5.10
18 19 0.388659 ATGATGGCTCAGTCTCTCGC 59.611 55.000 0.00 0.00 34.12 5.03
19 20 3.505293 TGATATGATGGCTCAGTCTCTCG 59.495 47.826 0.00 0.00 34.12 4.04
20 21 5.664294 ATGATATGATGGCTCAGTCTCTC 57.336 43.478 0.00 0.00 34.12 3.20
21 22 7.736881 AATATGATATGATGGCTCAGTCTCT 57.263 36.000 0.00 0.00 34.12 3.10
22 23 9.531942 CTTAATATGATATGATGGCTCAGTCTC 57.468 37.037 0.00 0.00 34.12 3.36
23 24 9.264653 TCTTAATATGATATGATGGCTCAGTCT 57.735 33.333 0.00 0.00 34.12 3.24
24 25 9.531942 CTCTTAATATGATATGATGGCTCAGTC 57.468 37.037 0.00 0.00 34.12 3.51
25 26 9.044646 ACTCTTAATATGATATGATGGCTCAGT 57.955 33.333 0.00 0.00 34.12 3.41
26 27 9.887629 AACTCTTAATATGATATGATGGCTCAG 57.112 33.333 0.00 0.00 34.12 3.35
39 40 9.569167 CAGTGACTTCGTAAACTCTTAATATGA 57.431 33.333 0.00 0.00 0.00 2.15
40 41 9.355215 ACAGTGACTTCGTAAACTCTTAATATG 57.645 33.333 0.00 0.00 0.00 1.78
43 44 8.790718 TCTACAGTGACTTCGTAAACTCTTAAT 58.209 33.333 0.00 0.00 0.00 1.40
44 45 8.072567 GTCTACAGTGACTTCGTAAACTCTTAA 58.927 37.037 0.00 0.00 34.39 1.85
45 46 7.570140 CGTCTACAGTGACTTCGTAAACTCTTA 60.570 40.741 0.00 0.00 35.00 2.10
46 47 6.437094 GTCTACAGTGACTTCGTAAACTCTT 58.563 40.000 0.00 0.00 34.39 2.85
47 48 5.333952 CGTCTACAGTGACTTCGTAAACTCT 60.334 44.000 0.00 0.00 35.00 3.24
48 49 4.845060 CGTCTACAGTGACTTCGTAAACTC 59.155 45.833 0.00 0.00 35.00 3.01
49 50 4.781071 CGTCTACAGTGACTTCGTAAACT 58.219 43.478 0.00 0.00 35.00 2.66
50 51 3.360168 GCGTCTACAGTGACTTCGTAAAC 59.640 47.826 0.00 0.00 35.00 2.01
51 52 3.558505 GCGTCTACAGTGACTTCGTAAA 58.441 45.455 0.00 0.00 35.00 2.01
52 53 2.095567 GGCGTCTACAGTGACTTCGTAA 60.096 50.000 0.00 0.00 35.00 3.18
53 54 1.466167 GGCGTCTACAGTGACTTCGTA 59.534 52.381 0.00 0.00 35.00 3.43
54 55 0.240411 GGCGTCTACAGTGACTTCGT 59.760 55.000 0.00 0.00 35.00 3.85
55 56 0.522180 AGGCGTCTACAGTGACTTCG 59.478 55.000 0.00 0.00 35.00 3.79
56 57 1.466024 CGAGGCGTCTACAGTGACTTC 60.466 57.143 4.69 0.00 35.00 3.01
57 58 0.522180 CGAGGCGTCTACAGTGACTT 59.478 55.000 4.69 0.00 35.00 3.01
58 59 0.605860 ACGAGGCGTCTACAGTGACT 60.606 55.000 4.69 0.00 33.69 3.41
59 60 1.062294 CTACGAGGCGTCTACAGTGAC 59.938 57.143 4.69 0.00 41.54 3.67
60 61 1.338484 ACTACGAGGCGTCTACAGTGA 60.338 52.381 4.69 0.00 41.54 3.41
61 62 1.062294 GACTACGAGGCGTCTACAGTG 59.938 57.143 4.69 0.00 41.54 3.66
62 63 1.338484 TGACTACGAGGCGTCTACAGT 60.338 52.381 4.69 4.69 41.54 3.55
63 64 1.366679 TGACTACGAGGCGTCTACAG 58.633 55.000 4.69 1.56 41.54 2.74
64 65 1.812235 TTGACTACGAGGCGTCTACA 58.188 50.000 4.69 0.00 41.54 2.74
65 66 2.353889 TCATTGACTACGAGGCGTCTAC 59.646 50.000 4.69 0.00 41.54 2.59
66 67 2.635714 TCATTGACTACGAGGCGTCTA 58.364 47.619 4.69 0.00 41.54 2.59
67 68 1.460504 TCATTGACTACGAGGCGTCT 58.539 50.000 4.69 0.00 41.54 4.18
68 69 2.273370 TTCATTGACTACGAGGCGTC 57.727 50.000 0.00 0.00 41.54 5.19
69 70 2.735134 GTTTTCATTGACTACGAGGCGT 59.265 45.455 0.00 0.00 44.35 5.68
70 71 2.222508 CGTTTTCATTGACTACGAGGCG 60.223 50.000 12.12 0.00 34.36 5.52
71 72 2.474032 GCGTTTTCATTGACTACGAGGC 60.474 50.000 18.63 4.29 34.36 4.70
72 73 2.093783 GGCGTTTTCATTGACTACGAGG 59.906 50.000 18.63 0.00 34.36 4.63
73 74 2.993899 AGGCGTTTTCATTGACTACGAG 59.006 45.455 18.63 0.00 34.36 4.18
74 75 2.991190 GAGGCGTTTTCATTGACTACGA 59.009 45.455 18.63 0.00 34.36 3.43
75 76 2.093783 GGAGGCGTTTTCATTGACTACG 59.906 50.000 12.84 12.84 35.48 3.51
76 77 3.335579 AGGAGGCGTTTTCATTGACTAC 58.664 45.455 0.00 0.00 0.00 2.73
77 78 3.596214 GAGGAGGCGTTTTCATTGACTA 58.404 45.455 0.00 0.00 0.00 2.59
78 79 2.427506 GAGGAGGCGTTTTCATTGACT 58.572 47.619 0.00 0.00 0.00 3.41
79 80 1.468914 GGAGGAGGCGTTTTCATTGAC 59.531 52.381 0.00 0.00 0.00 3.18
80 81 1.613255 GGGAGGAGGCGTTTTCATTGA 60.613 52.381 0.00 0.00 0.00 2.57
81 82 0.811281 GGGAGGAGGCGTTTTCATTG 59.189 55.000 0.00 0.00 0.00 2.82
82 83 0.698818 AGGGAGGAGGCGTTTTCATT 59.301 50.000 0.00 0.00 0.00 2.57
83 84 0.253327 GAGGGAGGAGGCGTTTTCAT 59.747 55.000 0.00 0.00 0.00 2.57
84 85 0.836400 AGAGGGAGGAGGCGTTTTCA 60.836 55.000 0.00 0.00 0.00 2.69
85 86 1.192428 TAGAGGGAGGAGGCGTTTTC 58.808 55.000 0.00 0.00 0.00 2.29
86 87 1.652947 TTAGAGGGAGGAGGCGTTTT 58.347 50.000 0.00 0.00 0.00 2.43
87 88 1.278413 GTTTAGAGGGAGGAGGCGTTT 59.722 52.381 0.00 0.00 0.00 3.60
88 89 0.903236 GTTTAGAGGGAGGAGGCGTT 59.097 55.000 0.00 0.00 0.00 4.84
89 90 1.321074 CGTTTAGAGGGAGGAGGCGT 61.321 60.000 0.00 0.00 0.00 5.68
90 91 1.437986 CGTTTAGAGGGAGGAGGCG 59.562 63.158 0.00 0.00 0.00 5.52
91 92 1.144276 GCGTTTAGAGGGAGGAGGC 59.856 63.158 0.00 0.00 0.00 4.70
92 93 0.175989 GTGCGTTTAGAGGGAGGAGG 59.824 60.000 0.00 0.00 0.00 4.30
93 94 0.895530 TGTGCGTTTAGAGGGAGGAG 59.104 55.000 0.00 0.00 0.00 3.69
94 95 1.480954 GATGTGCGTTTAGAGGGAGGA 59.519 52.381 0.00 0.00 0.00 3.71
95 96 1.802880 CGATGTGCGTTTAGAGGGAGG 60.803 57.143 0.00 0.00 34.64 4.30
96 97 1.560923 CGATGTGCGTTTAGAGGGAG 58.439 55.000 0.00 0.00 34.64 4.30
97 98 0.459585 GCGATGTGCGTTTAGAGGGA 60.460 55.000 0.00 0.00 43.41 4.20
98 99 2.006772 GCGATGTGCGTTTAGAGGG 58.993 57.895 0.00 0.00 43.41 4.30
137 138 6.711277 AGTCTTGGTGCTTGTATTTATCTCA 58.289 36.000 0.00 0.00 0.00 3.27
156 157 7.283329 ACTTAACTCATCAAGGTTCAAGTCTT 58.717 34.615 0.00 0.00 0.00 3.01
157 158 6.831976 ACTTAACTCATCAAGGTTCAAGTCT 58.168 36.000 0.00 0.00 0.00 3.24
180 181 7.980099 CGGATGGTTAGAAGGATAATGGTATAC 59.020 40.741 0.00 0.00 0.00 1.47
185 186 5.228945 ACGGATGGTTAGAAGGATAATGG 57.771 43.478 0.00 0.00 0.00 3.16
196 197 5.413213 TGGACAAAATACAACGGATGGTTAG 59.587 40.000 0.00 0.00 36.49 2.34
225 226 5.956642 TGCTAGTACGATGTTGATGTGTTA 58.043 37.500 0.00 0.00 0.00 2.41
234 235 2.100197 TGGAGCTGCTAGTACGATGTT 58.900 47.619 6.82 0.00 0.00 2.71
676 686 2.990479 GACCAGCGGATTGGAGGT 59.010 61.111 6.05 0.00 40.87 3.85
708 718 6.364435 ACGTTAAACTAACCTCGAATTGTCTC 59.636 38.462 0.00 0.00 35.27 3.36
715 725 5.200368 AGGAACGTTAAACTAACCTCGAA 57.800 39.130 0.00 0.00 35.27 3.71
724 734 0.233848 CGCGCAAGGAACGTTAAACT 59.766 50.000 8.75 0.00 38.28 2.66
765 775 4.974399 ACAGAGTAACTTGGGAAGGAAAG 58.026 43.478 0.00 0.00 0.00 2.62
780 790 2.631062 ACACCCGTTCATGAACAGAGTA 59.369 45.455 32.06 0.00 41.20 2.59
885 901 3.611674 TCACAAGTCGCCGAGCCA 61.612 61.111 0.00 0.00 0.00 4.75
918 934 1.228988 CAAAGCAGCCCCCTTTCCT 60.229 57.895 0.00 0.00 30.52 3.36
938 954 0.395312 CACCTAGGGAACAACGGTGT 59.605 55.000 14.81 0.00 40.75 4.16
994 1010 3.368635 GCCATTGCCTGAATCATGAACAA 60.369 43.478 0.00 0.00 0.00 2.83
995 1011 2.166870 GCCATTGCCTGAATCATGAACA 59.833 45.455 0.00 2.52 0.00 3.18
1463 1482 3.138884 TGTTAGCTGGCAAGTCAATCA 57.861 42.857 0.00 0.00 0.00 2.57
1500 1519 1.815003 GCAGCAGCCTCAATTACACTT 59.185 47.619 0.00 0.00 33.58 3.16
1578 1597 0.322816 TGAAAGGACCTGCCATGCTC 60.323 55.000 0.00 0.00 40.02 4.26
1855 1875 2.224670 ACCAATGCGTAGGAAAACAGGA 60.225 45.455 0.00 0.00 0.00 3.86
1896 1916 2.941453 AGCTTTGATGCTGCAATCAG 57.059 45.000 6.36 1.73 42.33 2.90
1939 1959 9.806203 CAGAAATGCCTAAATCAATACATTCAA 57.194 29.630 0.00 0.00 0.00 2.69
1940 1960 8.970020 ACAGAAATGCCTAAATCAATACATTCA 58.030 29.630 0.00 0.00 0.00 2.57
1941 1961 9.807649 AACAGAAATGCCTAAATCAATACATTC 57.192 29.630 0.00 0.00 0.00 2.67
1958 1978 7.648142 TGAGGCTAAAAAGTGTAACAGAAATG 58.352 34.615 0.00 0.00 41.43 2.32
1963 1983 7.096065 GCAATTTGAGGCTAAAAAGTGTAACAG 60.096 37.037 18.14 0.33 41.43 3.16
1971 1991 7.662604 ATTCTTGCAATTTGAGGCTAAAAAG 57.337 32.000 0.00 0.00 0.00 2.27
1979 1999 8.636213 ACCTAATGATATTCTTGCAATTTGAGG 58.364 33.333 0.00 0.00 0.00 3.86
2264 2292 8.005388 AGAATAAGTCAATAGGCTACTCCAGTA 58.995 37.037 0.00 0.00 37.29 2.74
2475 2503 2.675658 TCCCCTCCACCAAAAAGAAG 57.324 50.000 0.00 0.00 0.00 2.85
2478 2506 6.667848 AGTTAAATATCCCCTCCACCAAAAAG 59.332 38.462 0.00 0.00 0.00 2.27
2479 2507 6.566914 AGTTAAATATCCCCTCCACCAAAAA 58.433 36.000 0.00 0.00 0.00 1.94
2480 2508 6.160483 AGTTAAATATCCCCTCCACCAAAA 57.840 37.500 0.00 0.00 0.00 2.44
2481 2509 5.806955 AGTTAAATATCCCCTCCACCAAA 57.193 39.130 0.00 0.00 0.00 3.28
2482 2510 5.732170 TGTAGTTAAATATCCCCTCCACCAA 59.268 40.000 0.00 0.00 0.00 3.67
2615 2644 8.978874 TTGTTACACATGATATTATTGAGCCT 57.021 30.769 0.00 0.00 0.00 4.58
2638 2667 6.044682 TGATCACATCAGTATAGTGCACTTG 58.955 40.000 27.06 17.24 33.59 3.16
2684 2713 2.452600 AATGAGTTGTGTGGGTGGTT 57.547 45.000 0.00 0.00 0.00 3.67
2828 2858 9.252962 GAACATCAAAAACAAACAATGAGATCT 57.747 29.630 0.00 0.00 0.00 2.75
3148 3187 5.185442 TCACCATGCAAAATATTGAGAAGCA 59.815 36.000 0.00 0.00 38.94 3.91
3151 3190 7.230849 ACTTCACCATGCAAAATATTGAGAA 57.769 32.000 0.00 0.00 38.94 2.87
3153 3192 7.092079 TCAACTTCACCATGCAAAATATTGAG 58.908 34.615 0.00 0.00 38.94 3.02
3159 3198 6.814644 CACATATCAACTTCACCATGCAAAAT 59.185 34.615 0.00 0.00 0.00 1.82
3280 3327 7.494625 ACCGAAACAATAGAGTACAACATATGG 59.505 37.037 7.80 0.00 0.00 2.74
3415 3467 3.340814 ACACTGTAGAGAAGGGCAATG 57.659 47.619 0.00 0.00 0.00 2.82
3607 3659 8.173130 GGTTTGTCAATTGTATAAAGGACTACG 58.827 37.037 5.13 0.00 0.00 3.51
3797 3895 4.637483 TGCTCTCTGTGGTTTTCTTTTG 57.363 40.909 0.00 0.00 0.00 2.44
3820 3918 7.329226 CCCAAAATACAGAAAACACAAGCATAG 59.671 37.037 0.00 0.00 0.00 2.23
3822 3920 5.990996 CCCAAAATACAGAAAACACAAGCAT 59.009 36.000 0.00 0.00 0.00 3.79
3845 3943 1.901833 AGGACCAAATGGAATTGCACC 59.098 47.619 0.12 0.00 36.10 5.01
3909 4007 8.557592 TGATTAATATCACCAGCATCATCTTC 57.442 34.615 0.00 0.00 35.87 2.87
4064 4176 5.376854 AGTGTGAGGATAATGTTTGTTGC 57.623 39.130 0.00 0.00 0.00 4.17
4067 4179 7.823745 AAAGAAGTGTGAGGATAATGTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
4074 4186 5.415701 GCATCCAAAAGAAGTGTGAGGATAA 59.584 40.000 0.00 0.00 33.37 1.75
4235 4435 5.988310 TTTACTATCGAGGTCAAACAGGA 57.012 39.130 0.00 0.00 0.00 3.86
4283 4484 3.278668 TTCTACCACAACCACGGAAAA 57.721 42.857 0.00 0.00 0.00 2.29
4286 4487 1.485480 TGTTTCTACCACAACCACGGA 59.515 47.619 0.00 0.00 0.00 4.69
4287 4488 1.871039 CTGTTTCTACCACAACCACGG 59.129 52.381 0.00 0.00 0.00 4.94
4493 4697 4.411256 GTCCCCAACGACCTATATTTCA 57.589 45.455 0.00 0.00 0.00 2.69
4540 4745 5.168647 ACCAGGGTATTAACGTCATTTCA 57.831 39.130 0.00 0.00 0.00 2.69
4974 5186 5.159925 CAGTATTGCTCCATCAGTAGATCG 58.840 45.833 0.00 0.00 30.20 3.69
4975 5187 6.095432 ACAGTATTGCTCCATCAGTAGATC 57.905 41.667 0.00 0.00 30.20 2.75
4976 5188 6.491714 AACAGTATTGCTCCATCAGTAGAT 57.508 37.500 0.00 0.00 33.87 1.98
4977 5189 5.939764 AACAGTATTGCTCCATCAGTAGA 57.060 39.130 0.00 0.00 0.00 2.59
5168 5380 4.890158 ACATGTGTACTCCAGATGACAA 57.110 40.909 0.00 0.00 45.35 3.18


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

AutoCloner maintained by Alex Coulton.