Multiple sequence alignment - TraesCS3A01G306500

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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 TraesCS3A01G306500 chr3A 100.000 3047 0 0 1 3047 544189835 544192881 0.000000e+00 5627.0
1 TraesCS3A01G306500 chr3A 100.000 843 0 0 2205 3047 634727316 634726474 0.000000e+00 1557.0
2 TraesCS3A01G306500 chr3A 99.405 840 5 0 2208 3047 742313761 742312922 0.000000e+00 1524.0
3 TraesCS3A01G306500 chr3A 97.938 97 1 1 1 97 737535293 737535388 1.880000e-37 167.0
4 TraesCS3A01G306500 chr3B 92.164 1391 47 32 832 2207 533454707 533453364 0.000000e+00 1908.0
5 TraesCS3A01G306500 chr3B 88.986 572 29 15 209 761 533455376 533454820 0.000000e+00 676.0
6 TraesCS3A01G306500 chr3B 83.415 205 22 6 2302 2503 680702332 680702527 2.410000e-41 180.0
7 TraesCS3A01G306500 chr3B 95.918 49 1 1 2207 2255 597499707 597499660 9.060000e-11 78.7
8 TraesCS3A01G306500 chr3B 97.143 35 1 0 175 209 533455426 533455392 3.280000e-05 60.2
9 TraesCS3A01G306500 chr3D 91.189 1430 59 45 797 2207 407748320 407746939 0.000000e+00 1881.0
10 TraesCS3A01G306500 chr3D 89.366 536 24 11 216 737 407749121 407748605 0.000000e+00 643.0
11 TraesCS3A01G306500 chr4B 100.000 842 0 0 2206 3047 522086642 522085801 0.000000e+00 1555.0
12 TraesCS3A01G306500 chr4B 91.775 462 18 2 2605 3047 146428351 146427891 2.580000e-175 625.0
13 TraesCS3A01G306500 chr4B 94.898 294 11 3 2274 2565 146428646 146428355 9.960000e-125 457.0
14 TraesCS3A01G306500 chr7B 99.762 840 2 0 2208 3047 605954266 605953427 0.000000e+00 1541.0
15 TraesCS3A01G306500 chr7B 97.959 49 1 0 2207 2255 4137203 4137155 5.410000e-13 86.1
16 TraesCS3A01G306500 chr5B 82.927 205 23 6 2302 2503 610498296 610498101 1.120000e-39 174.0
17 TraesCS3A01G306500 chr2D 82.843 204 21 8 2304 2503 39758256 39758063 1.450000e-38 171.0
18 TraesCS3A01G306500 chr2D 82.353 204 22 8 2304 2503 39759483 39759290 6.760000e-37 165.0
19 TraesCS3A01G306500 chr7A 97.938 97 2 0 1 97 22222117 22222213 5.220000e-38 169.0
20 TraesCS3A01G306500 chr7A 96.000 100 4 0 1 100 673254829 673254730 2.430000e-36 163.0
21 TraesCS3A01G306500 chr5A 97.030 101 2 1 1 100 5845416 5845316 5.220000e-38 169.0
22 TraesCS3A01G306500 chr6A 97.938 97 1 1 1 97 193968633 193968728 1.880000e-37 167.0
23 TraesCS3A01G306500 chr2A 96.970 99 3 0 2 100 188830772 188830674 1.880000e-37 167.0
24 TraesCS3A01G306500 chr4A 96.000 100 4 0 1 100 614180260 614180161 2.430000e-36 163.0
25 TraesCS3A01G306500 chr1A 96.000 100 4 0 1 100 372926880 372926781 2.430000e-36 163.0
26 TraesCS3A01G306500 chr1A 96.040 101 3 1 1 100 504111868 504111768 2.430000e-36 163.0
27 TraesCS3A01G306500 chr1A 96.154 52 2 0 2204 2255 172352474 172352525 5.410000e-13 86.1
28 TraesCS3A01G306500 chr2B 79.755 163 19 8 2557 2717 799736947 799737097 4.150000e-19 106.0
29 TraesCS3A01G306500 chr2B 94.231 52 2 1 2207 2258 24256644 24256594 9.060000e-11 78.7
30 TraesCS3A01G306500 chr7D 96.154 52 2 0 2207 2258 47870772 47870721 5.410000e-13 86.1


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 TraesCS3A01G306500 chr3A 544189835 544192881 3046 False 5627.0 5627 100.000000 1 3047 1 chr3A.!!$F1 3046
1 TraesCS3A01G306500 chr3A 634726474 634727316 842 True 1557.0 1557 100.000000 2205 3047 1 chr3A.!!$R1 842
2 TraesCS3A01G306500 chr3A 742312922 742313761 839 True 1524.0 1524 99.405000 2208 3047 1 chr3A.!!$R2 839
3 TraesCS3A01G306500 chr3B 533453364 533455426 2062 True 881.4 1908 92.764333 175 2207 3 chr3B.!!$R2 2032
4 TraesCS3A01G306500 chr3D 407746939 407749121 2182 True 1262.0 1881 90.277500 216 2207 2 chr3D.!!$R1 1991
5 TraesCS3A01G306500 chr4B 522085801 522086642 841 True 1555.0 1555 100.000000 2206 3047 1 chr4B.!!$R1 841
6 TraesCS3A01G306500 chr4B 146427891 146428646 755 True 541.0 625 93.336500 2274 3047 2 chr4B.!!$R2 773
7 TraesCS3A01G306500 chr7B 605953427 605954266 839 True 1541.0 1541 99.762000 2208 3047 1 chr7B.!!$R2 839

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 0.034059 GGGCAGATACTCATCGTGGG 59.966 60.0 0.0 0.0 36.20 4.61 F
820 1090 0.179045 ACTGTTGACTGGTGAGTGGC 60.179 55.0 0.0 0.0 30.16 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1710 0.866061 CTTCTGCACGACGATACCGG 60.866 60.0 0.0 0.0 40.78 5.28 R
2166 2462 0.756294 TGCACGTCTTTTCCTCTGGA 59.244 50.0 0.0 0.0 0.00 3.86 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
17 18 4.461119 TGAGAGGTTCGGGCAGAT 57.539 55.556 0.00 0.00 0.00 2.90
18 19 3.607871 TGAGAGGTTCGGGCAGATA 57.392 52.632 0.00 0.00 0.00 1.98
19 20 1.112113 TGAGAGGTTCGGGCAGATAC 58.888 55.000 0.00 0.00 0.00 2.24
20 21 1.342076 TGAGAGGTTCGGGCAGATACT 60.342 52.381 0.00 0.00 0.00 2.12
21 22 1.338655 GAGAGGTTCGGGCAGATACTC 59.661 57.143 9.82 9.82 34.28 2.59
22 23 1.112113 GAGGTTCGGGCAGATACTCA 58.888 55.000 11.98 0.00 34.26 3.41
23 24 1.689273 GAGGTTCGGGCAGATACTCAT 59.311 52.381 11.98 0.00 34.26 2.90
24 25 1.689273 AGGTTCGGGCAGATACTCATC 59.311 52.381 0.00 0.00 0.00 2.92
25 26 1.603172 GGTTCGGGCAGATACTCATCG 60.603 57.143 0.00 0.00 36.20 3.84
26 27 1.067212 GTTCGGGCAGATACTCATCGT 59.933 52.381 0.00 0.00 36.20 3.73
27 28 0.668535 TCGGGCAGATACTCATCGTG 59.331 55.000 0.00 0.00 36.20 4.35
28 29 0.319040 CGGGCAGATACTCATCGTGG 60.319 60.000 0.00 0.00 36.20 4.94
29 30 0.034059 GGGCAGATACTCATCGTGGG 59.966 60.000 0.00 0.00 36.20 4.61
30 31 0.034059 GGCAGATACTCATCGTGGGG 59.966 60.000 0.00 0.00 36.20 4.96
31 32 1.040646 GCAGATACTCATCGTGGGGA 58.959 55.000 0.00 0.00 36.20 4.81
32 33 1.269831 GCAGATACTCATCGTGGGGAC 60.270 57.143 0.00 0.00 36.20 4.46
33 34 1.001268 CAGATACTCATCGTGGGGACG 60.001 57.143 0.00 0.00 36.20 4.79
34 35 0.318784 GATACTCATCGTGGGGACGC 60.319 60.000 0.00 0.00 37.54 5.19
65 66 4.554363 CGCCCGTAGCTCCGTCAG 62.554 72.222 0.00 0.00 40.39 3.51
66 67 3.450115 GCCCGTAGCTCCGTCAGT 61.450 66.667 0.00 0.00 38.99 3.41
67 68 2.490217 CCCGTAGCTCCGTCAGTG 59.510 66.667 0.00 0.00 0.00 3.66
68 69 2.202623 CCGTAGCTCCGTCAGTGC 60.203 66.667 0.00 0.00 35.13 4.40
69 70 2.577112 CGTAGCTCCGTCAGTGCG 60.577 66.667 0.00 0.71 39.99 5.34
70 71 2.875485 GTAGCTCCGTCAGTGCGA 59.125 61.111 8.27 0.00 39.99 5.10
71 72 1.226435 GTAGCTCCGTCAGTGCGAG 60.226 63.158 8.27 3.53 39.99 5.03
72 73 2.407428 TAGCTCCGTCAGTGCGAGG 61.407 63.158 8.27 0.98 39.99 4.63
77 78 3.550656 CGTCAGTGCGAGGGAAAC 58.449 61.111 1.37 0.00 0.00 2.78
97 98 4.394712 GGGGGACTGTGTGCTCCG 62.395 72.222 0.00 0.00 34.23 4.63
98 99 3.626924 GGGGACTGTGTGCTCCGT 61.627 66.667 0.00 0.00 0.00 4.69
99 100 2.048127 GGGACTGTGTGCTCCGTC 60.048 66.667 0.00 0.00 0.00 4.79
100 101 2.734591 GGACTGTGTGCTCCGTCA 59.265 61.111 0.00 0.00 0.00 4.35
101 102 1.373497 GGACTGTGTGCTCCGTCAG 60.373 63.158 0.00 0.00 0.00 3.51
102 103 1.364171 GACTGTGTGCTCCGTCAGT 59.636 57.895 7.66 7.66 42.66 3.41
103 104 0.941463 GACTGTGTGCTCCGTCAGTG 60.941 60.000 11.16 0.00 40.53 3.66
104 105 1.068083 CTGTGTGCTCCGTCAGTGT 59.932 57.895 0.00 0.00 0.00 3.55
105 106 0.941463 CTGTGTGCTCCGTCAGTGTC 60.941 60.000 0.00 0.00 0.00 3.67
106 107 1.364171 GTGTGCTCCGTCAGTGTCT 59.636 57.895 0.00 0.00 0.00 3.41
107 108 0.249489 GTGTGCTCCGTCAGTGTCTT 60.249 55.000 0.00 0.00 0.00 3.01
108 109 1.000607 GTGTGCTCCGTCAGTGTCTTA 60.001 52.381 0.00 0.00 0.00 2.10
109 110 1.684450 TGTGCTCCGTCAGTGTCTTAA 59.316 47.619 0.00 0.00 0.00 1.85
110 111 2.299013 TGTGCTCCGTCAGTGTCTTAAT 59.701 45.455 0.00 0.00 0.00 1.40
111 112 3.244078 TGTGCTCCGTCAGTGTCTTAATT 60.244 43.478 0.00 0.00 0.00 1.40
112 113 3.746492 GTGCTCCGTCAGTGTCTTAATTT 59.254 43.478 0.00 0.00 0.00 1.82
113 114 4.213482 GTGCTCCGTCAGTGTCTTAATTTT 59.787 41.667 0.00 0.00 0.00 1.82
114 115 5.407387 GTGCTCCGTCAGTGTCTTAATTTTA 59.593 40.000 0.00 0.00 0.00 1.52
115 116 5.992829 TGCTCCGTCAGTGTCTTAATTTTAA 59.007 36.000 0.00 0.00 0.00 1.52
116 117 6.653320 TGCTCCGTCAGTGTCTTAATTTTAAT 59.347 34.615 0.00 0.00 0.00 1.40
117 118 6.961554 GCTCCGTCAGTGTCTTAATTTTAATG 59.038 38.462 0.00 0.00 0.00 1.90
118 119 7.360946 GCTCCGTCAGTGTCTTAATTTTAATGT 60.361 37.037 0.00 0.00 0.00 2.71
119 120 9.146984 CTCCGTCAGTGTCTTAATTTTAATGTA 57.853 33.333 0.00 0.00 0.00 2.29
120 121 9.491675 TCCGTCAGTGTCTTAATTTTAATGTAA 57.508 29.630 0.00 0.00 0.00 2.41
164 165 9.667107 ACTGAAATCGAGACATTTATTTTAGGA 57.333 29.630 0.00 0.00 32.31 2.94
165 166 9.922305 CTGAAATCGAGACATTTATTTTAGGAC 57.078 33.333 0.00 0.00 0.00 3.85
166 167 8.600625 TGAAATCGAGACATTTATTTTAGGACG 58.399 33.333 0.00 0.00 0.00 4.79
167 168 8.712285 AAATCGAGACATTTATTTTAGGACGA 57.288 30.769 0.00 0.00 0.00 4.20
168 169 8.712285 AATCGAGACATTTATTTTAGGACGAA 57.288 30.769 0.00 0.00 0.00 3.85
169 170 7.751047 TCGAGACATTTATTTTAGGACGAAG 57.249 36.000 0.00 0.00 0.00 3.79
170 171 6.755141 TCGAGACATTTATTTTAGGACGAAGG 59.245 38.462 0.00 0.00 0.00 3.46
171 172 6.755141 CGAGACATTTATTTTAGGACGAAGGA 59.245 38.462 0.00 0.00 0.00 3.36
172 173 7.438459 CGAGACATTTATTTTAGGACGAAGGAT 59.562 37.037 0.00 0.00 0.00 3.24
173 174 8.438676 AGACATTTATTTTAGGACGAAGGATG 57.561 34.615 0.00 0.00 0.00 3.51
179 180 8.712285 TTATTTTAGGACGAAGGATGTACAAG 57.288 34.615 0.00 0.00 0.00 3.16
264 281 3.334272 CGAGAGCTTTCGTTTTTGGTT 57.666 42.857 17.92 0.00 35.91 3.67
265 282 4.461992 CGAGAGCTTTCGTTTTTGGTTA 57.538 40.909 17.92 0.00 35.91 2.85
276 293 9.352163 CTTTCGTTTTTGGTTAAATTGAATTCG 57.648 29.630 0.04 0.00 0.00 3.34
277 294 7.988904 TCGTTTTTGGTTAAATTGAATTCGT 57.011 28.000 0.04 0.00 0.00 3.85
348 365 4.654091 ATTTGTCCCCTAATTGAATGCG 57.346 40.909 0.00 0.00 0.00 4.73
349 366 1.388547 TGTCCCCTAATTGAATGCGC 58.611 50.000 0.00 0.00 0.00 6.09
358 375 3.316071 AATTGAATGCGCATTTGTCCA 57.684 38.095 34.24 24.45 0.00 4.02
494 514 1.730612 GTACTACGTGCCTTCTTTGCC 59.269 52.381 0.00 0.00 0.00 4.52
495 515 0.396811 ACTACGTGCCTTCTTTGCCT 59.603 50.000 0.00 0.00 0.00 4.75
509 529 3.128589 TCTTTGCCTATTGAAATCACCGC 59.871 43.478 0.00 0.00 0.00 5.68
510 530 2.121291 TGCCTATTGAAATCACCGCA 57.879 45.000 0.00 0.00 0.00 5.69
511 531 2.653726 TGCCTATTGAAATCACCGCAT 58.346 42.857 0.00 0.00 0.00 4.73
512 532 2.358582 TGCCTATTGAAATCACCGCATG 59.641 45.455 0.00 0.00 0.00 4.06
524 544 1.881252 CCGCATGTACTACGGTGCC 60.881 63.158 11.95 0.00 42.01 5.01
551 571 1.451387 GCACCCCGATCGTTTGGAT 60.451 57.895 15.09 0.00 38.35 3.41
553 573 1.095228 CACCCCGATCGTTTGGATGG 61.095 60.000 15.09 5.85 34.82 3.51
555 575 0.814010 CCCCGATCGTTTGGATGGAC 60.814 60.000 15.09 0.00 34.82 4.02
592 612 3.293702 AGAGCCTTCCACTCTCGC 58.706 61.111 0.00 0.00 40.52 5.03
593 613 1.607756 AGAGCCTTCCACTCTCGCA 60.608 57.895 0.00 0.00 40.52 5.10
594 614 0.975040 AGAGCCTTCCACTCTCGCAT 60.975 55.000 0.00 0.00 40.52 4.73
595 615 0.809241 GAGCCTTCCACTCTCGCATG 60.809 60.000 0.00 0.00 0.00 4.06
596 616 1.817099 GCCTTCCACTCTCGCATGG 60.817 63.158 0.00 0.00 37.32 3.66
597 617 1.817099 CCTTCCACTCTCGCATGGC 60.817 63.158 0.00 0.00 35.81 4.40
598 618 1.078918 CTTCCACTCTCGCATGGCA 60.079 57.895 0.00 0.00 35.81 4.92
599 619 0.463295 CTTCCACTCTCGCATGGCAT 60.463 55.000 0.00 0.00 35.81 4.40
713 747 6.575162 AAGCCAAAACGATAAGAGAAATGT 57.425 33.333 0.00 0.00 0.00 2.71
714 748 7.681939 AAGCCAAAACGATAAGAGAAATGTA 57.318 32.000 0.00 0.00 0.00 2.29
761 806 5.582269 CACGCTCAATCCTAATTCTTCTTGA 59.418 40.000 0.00 0.00 0.00 3.02
762 807 6.092670 CACGCTCAATCCTAATTCTTCTTGAA 59.907 38.462 0.00 0.00 39.24 2.69
763 808 6.655003 ACGCTCAATCCTAATTCTTCTTGAAA 59.345 34.615 0.00 0.00 38.29 2.69
767 836 8.256611 TCAATCCTAATTCTTCTTGAAACTCG 57.743 34.615 0.00 0.00 38.29 4.18
782 851 4.515191 TGAAACTCGCTCTGCAAATTAAGT 59.485 37.500 0.00 0.00 0.00 2.24
787 856 2.160219 CGCTCTGCAAATTAAGTCAGCA 59.840 45.455 3.51 3.51 0.00 4.41
818 1088 0.940126 GCACTGTTGACTGGTGAGTG 59.060 55.000 0.00 0.00 37.65 3.51
819 1089 1.586422 CACTGTTGACTGGTGAGTGG 58.414 55.000 0.00 0.00 32.13 4.00
820 1090 0.179045 ACTGTTGACTGGTGAGTGGC 60.179 55.000 0.00 0.00 30.16 5.01
821 1091 0.179048 CTGTTGACTGGTGAGTGGCA 60.179 55.000 0.00 0.00 30.16 4.92
822 1092 0.179048 TGTTGACTGGTGAGTGGCAG 60.179 55.000 0.00 0.00 30.16 4.85
823 1093 0.886490 GTTGACTGGTGAGTGGCAGG 60.886 60.000 0.00 0.00 30.16 4.85
824 1094 1.053835 TTGACTGGTGAGTGGCAGGA 61.054 55.000 0.00 0.00 30.16 3.86
825 1095 1.053835 TGACTGGTGAGTGGCAGGAA 61.054 55.000 0.00 0.00 30.16 3.36
826 1096 0.326264 GACTGGTGAGTGGCAGGAAT 59.674 55.000 0.00 0.00 30.16 3.01
827 1097 0.326264 ACTGGTGAGTGGCAGGAATC 59.674 55.000 0.00 0.00 0.00 2.52
828 1098 0.325933 CTGGTGAGTGGCAGGAATCA 59.674 55.000 0.00 0.00 0.00 2.57
829 1099 0.325933 TGGTGAGTGGCAGGAATCAG 59.674 55.000 0.00 0.00 0.00 2.90
830 1100 0.615331 GGTGAGTGGCAGGAATCAGA 59.385 55.000 0.00 0.00 0.00 3.27
874 1144 2.286654 GCAGACACAGCAGAAAGAACAC 60.287 50.000 0.00 0.00 0.00 3.32
892 1162 0.608035 ACAACCAGTTGCCCCATACG 60.608 55.000 10.39 0.00 44.03 3.06
982 1261 6.710744 ACCCCTATATAAAAAGCTCGAACATG 59.289 38.462 0.00 0.00 0.00 3.21
1030 1309 3.412408 GGTTCTCCCCCAGCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
1031 1310 2.285743 GTTCTCCCCCAGCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
1032 1311 2.041265 TTCTCCCCCAGCTCCCTC 59.959 66.667 0.00 0.00 0.00 4.30
1033 1312 3.984186 TTCTCCCCCAGCTCCCTCG 62.984 68.421 0.00 0.00 0.00 4.63
1235 1515 1.474478 GATCGGCTCAGTTGAGTGAGA 59.526 52.381 17.73 5.49 46.02 3.27
1269 1549 4.471908 ATCCGGTGCTGCATCGCA 62.472 61.111 28.55 16.57 36.57 5.10
1343 1623 2.801631 GGGTGGAGGAGATCAGCGG 61.802 68.421 0.00 0.00 32.75 5.52
1908 2203 7.556733 TCGATTCTCTAGTTTACTTCCTCTC 57.443 40.000 0.00 0.00 0.00 3.20
1932 2227 0.748005 TAATTCCCTCTGCTTGCGCC 60.748 55.000 4.18 0.00 34.43 6.53
1946 2241 2.582436 CGCCTCGGCCCTCTTTTA 59.418 61.111 0.00 0.00 37.98 1.52
1947 2242 1.146263 CGCCTCGGCCCTCTTTTAT 59.854 57.895 0.00 0.00 37.98 1.40
2071 2366 8.991243 AGATACAATTTTTGCTAGTACGTACA 57.009 30.769 26.55 12.17 0.00 2.90
2072 2367 9.084164 AGATACAATTTTTGCTAGTACGTACAG 57.916 33.333 26.55 20.60 0.00 2.74
2073 2368 8.767478 ATACAATTTTTGCTAGTACGTACAGT 57.233 30.769 26.55 10.40 0.00 3.55
2074 2369 9.859427 ATACAATTTTTGCTAGTACGTACAGTA 57.141 29.630 26.55 17.35 0.00 2.74
2118 2413 8.004087 ACGATTTCCTAATTACAGTAGCTGTA 57.996 34.615 0.00 5.03 43.46 2.74
2120 2415 7.115095 CGATTTCCTAATTACAGTAGCTGTAGC 59.885 40.741 0.00 0.00 45.83 3.58
2140 2436 2.472909 GGTACAGGCAGCGCAATCC 61.473 63.158 11.47 7.40 0.00 3.01
2145 2441 4.166011 GGCAGCGCAATCCACGTC 62.166 66.667 11.47 0.00 0.00 4.34
2166 2462 3.702045 TCCCGATTTTGTTCAAACACCTT 59.298 39.130 0.00 0.00 38.92 3.50
2168 2464 4.048504 CCGATTTTGTTCAAACACCTTCC 58.951 43.478 0.00 0.00 38.92 3.46
2169 2465 4.440802 CCGATTTTGTTCAAACACCTTCCA 60.441 41.667 0.00 0.00 38.92 3.53
2171 2467 5.449862 CGATTTTGTTCAAACACCTTCCAGA 60.450 40.000 0.00 0.00 38.92 3.86
2172 2468 4.981806 TTTGTTCAAACACCTTCCAGAG 57.018 40.909 0.00 0.00 38.92 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.112113 GTATCTGCCCGAACCTCTCA 58.888 55.000 0.00 0.00 0.00 3.27
1 2 1.338655 GAGTATCTGCCCGAACCTCTC 59.661 57.143 0.00 0.00 0.00 3.20
2 3 1.342076 TGAGTATCTGCCCGAACCTCT 60.342 52.381 0.00 0.00 34.92 3.69
3 4 1.112113 TGAGTATCTGCCCGAACCTC 58.888 55.000 0.00 0.00 34.92 3.85
4 5 1.689273 GATGAGTATCTGCCCGAACCT 59.311 52.381 0.00 0.00 34.92 3.50
5 6 1.603172 CGATGAGTATCTGCCCGAACC 60.603 57.143 0.00 0.00 34.92 3.62
6 7 1.067212 ACGATGAGTATCTGCCCGAAC 59.933 52.381 0.00 0.00 34.92 3.95
7 8 1.067060 CACGATGAGTATCTGCCCGAA 59.933 52.381 0.00 0.00 34.92 4.30
8 9 0.668535 CACGATGAGTATCTGCCCGA 59.331 55.000 0.00 0.00 34.92 5.14
9 10 0.319040 CCACGATGAGTATCTGCCCG 60.319 60.000 0.00 0.00 34.92 6.13
10 11 0.034059 CCCACGATGAGTATCTGCCC 59.966 60.000 0.00 0.00 34.92 5.36
11 12 0.034059 CCCCACGATGAGTATCTGCC 59.966 60.000 0.00 0.00 34.92 4.85
12 13 1.040646 TCCCCACGATGAGTATCTGC 58.959 55.000 0.00 0.00 34.92 4.26
13 14 2.802787 GTCCCCACGATGAGTATCTG 57.197 55.000 0.00 0.00 34.92 2.90
49 50 3.450115 ACTGACGGAGCTACGGGC 61.450 66.667 24.83 14.91 42.19 6.13
50 51 2.490217 CACTGACGGAGCTACGGG 59.510 66.667 24.83 14.55 38.39 5.28
51 52 2.202623 GCACTGACGGAGCTACGG 60.203 66.667 24.83 7.49 38.39 4.02
52 53 2.577112 CGCACTGACGGAGCTACG 60.577 66.667 19.02 19.02 40.31 3.51
53 54 1.226435 CTCGCACTGACGGAGCTAC 60.226 63.158 2.13 0.00 0.00 3.58
54 55 2.407428 CCTCGCACTGACGGAGCTA 61.407 63.158 2.13 0.00 0.00 3.32
55 56 3.753434 CCTCGCACTGACGGAGCT 61.753 66.667 2.13 0.00 0.00 4.09
56 57 4.803426 CCCTCGCACTGACGGAGC 62.803 72.222 0.00 0.00 0.00 4.70
57 58 2.154798 TTTCCCTCGCACTGACGGAG 62.155 60.000 0.00 0.00 33.94 4.63
58 59 2.204461 TTTCCCTCGCACTGACGGA 61.204 57.895 0.00 0.00 30.90 4.69
59 60 2.027625 GTTTCCCTCGCACTGACGG 61.028 63.158 0.00 0.00 0.00 4.79
60 61 2.027625 GGTTTCCCTCGCACTGACG 61.028 63.158 0.00 0.00 0.00 4.35
61 62 2.027625 CGGTTTCCCTCGCACTGAC 61.028 63.158 0.00 0.00 0.00 3.51
62 63 2.342279 CGGTTTCCCTCGCACTGA 59.658 61.111 0.00 0.00 0.00 3.41
63 64 2.742372 CCGGTTTCCCTCGCACTG 60.742 66.667 0.00 0.00 0.00 3.66
64 65 4.016706 CCCGGTTTCCCTCGCACT 62.017 66.667 0.00 0.00 0.00 4.40
80 81 4.394712 CGGAGCACACAGTCCCCC 62.395 72.222 0.00 0.00 0.00 5.40
81 82 3.591254 GACGGAGCACACAGTCCCC 62.591 68.421 0.00 0.00 0.00 4.81
82 83 2.048127 GACGGAGCACACAGTCCC 60.048 66.667 0.00 0.00 0.00 4.46
83 84 1.373497 CTGACGGAGCACACAGTCC 60.373 63.158 0.00 0.00 34.94 3.85
84 85 0.941463 CACTGACGGAGCACACAGTC 60.941 60.000 0.00 0.00 40.84 3.51
85 86 1.068083 CACTGACGGAGCACACAGT 59.932 57.895 0.00 0.00 43.05 3.55
86 87 0.941463 GACACTGACGGAGCACACAG 60.941 60.000 0.00 0.00 36.58 3.66
87 88 1.067416 GACACTGACGGAGCACACA 59.933 57.895 0.00 0.00 0.00 3.72
88 89 0.249489 AAGACACTGACGGAGCACAC 60.249 55.000 0.00 0.00 0.00 3.82
89 90 1.324383 TAAGACACTGACGGAGCACA 58.676 50.000 0.00 0.00 0.00 4.57
90 91 2.433868 TTAAGACACTGACGGAGCAC 57.566 50.000 0.00 0.00 0.00 4.40
91 92 3.678056 AATTAAGACACTGACGGAGCA 57.322 42.857 0.00 0.00 0.00 4.26
92 93 6.476243 TTAAAATTAAGACACTGACGGAGC 57.524 37.500 0.00 0.00 0.00 4.70
93 94 8.029642 ACATTAAAATTAAGACACTGACGGAG 57.970 34.615 0.00 0.00 0.00 4.63
94 95 7.972832 ACATTAAAATTAAGACACTGACGGA 57.027 32.000 0.00 0.00 0.00 4.69
138 139 9.667107 TCCTAAAATAAATGTCTCGATTTCAGT 57.333 29.630 0.00 0.00 0.00 3.41
139 140 9.922305 GTCCTAAAATAAATGTCTCGATTTCAG 57.078 33.333 0.00 0.00 0.00 3.02
140 141 8.600625 CGTCCTAAAATAAATGTCTCGATTTCA 58.399 33.333 0.00 0.00 0.00 2.69
141 142 8.814235 TCGTCCTAAAATAAATGTCTCGATTTC 58.186 33.333 0.00 0.00 0.00 2.17
142 143 8.712285 TCGTCCTAAAATAAATGTCTCGATTT 57.288 30.769 0.00 0.00 0.00 2.17
143 144 8.712285 TTCGTCCTAAAATAAATGTCTCGATT 57.288 30.769 0.00 0.00 0.00 3.34
144 145 7.438459 CCTTCGTCCTAAAATAAATGTCTCGAT 59.562 37.037 0.00 0.00 0.00 3.59
145 146 6.755141 CCTTCGTCCTAAAATAAATGTCTCGA 59.245 38.462 0.00 0.00 0.00 4.04
146 147 6.755141 TCCTTCGTCCTAAAATAAATGTCTCG 59.245 38.462 0.00 0.00 0.00 4.04
147 148 8.552034 CATCCTTCGTCCTAAAATAAATGTCTC 58.448 37.037 0.00 0.00 0.00 3.36
148 149 8.047310 ACATCCTTCGTCCTAAAATAAATGTCT 58.953 33.333 0.00 0.00 0.00 3.41
149 150 8.209917 ACATCCTTCGTCCTAAAATAAATGTC 57.790 34.615 0.00 0.00 0.00 3.06
150 151 9.106070 GTACATCCTTCGTCCTAAAATAAATGT 57.894 33.333 0.00 0.00 0.00 2.71
151 152 9.104965 TGTACATCCTTCGTCCTAAAATAAATG 57.895 33.333 0.00 0.00 0.00 2.32
152 153 9.675464 TTGTACATCCTTCGTCCTAAAATAAAT 57.325 29.630 0.00 0.00 0.00 1.40
153 154 9.158233 CTTGTACATCCTTCGTCCTAAAATAAA 57.842 33.333 0.00 0.00 0.00 1.40
154 155 7.767198 CCTTGTACATCCTTCGTCCTAAAATAA 59.233 37.037 0.00 0.00 0.00 1.40
155 156 7.270047 CCTTGTACATCCTTCGTCCTAAAATA 58.730 38.462 0.00 0.00 0.00 1.40
156 157 6.113411 CCTTGTACATCCTTCGTCCTAAAAT 58.887 40.000 0.00 0.00 0.00 1.82
157 158 5.484715 CCTTGTACATCCTTCGTCCTAAAA 58.515 41.667 0.00 0.00 0.00 1.52
158 159 4.622220 GCCTTGTACATCCTTCGTCCTAAA 60.622 45.833 0.00 0.00 0.00 1.85
159 160 3.118884 GCCTTGTACATCCTTCGTCCTAA 60.119 47.826 0.00 0.00 0.00 2.69
160 161 2.429610 GCCTTGTACATCCTTCGTCCTA 59.570 50.000 0.00 0.00 0.00 2.94
161 162 1.207329 GCCTTGTACATCCTTCGTCCT 59.793 52.381 0.00 0.00 0.00 3.85
162 163 1.066430 TGCCTTGTACATCCTTCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
163 164 2.000447 GTGCCTTGTACATCCTTCGTC 59.000 52.381 0.00 0.00 0.00 4.20
164 165 1.346395 TGTGCCTTGTACATCCTTCGT 59.654 47.619 0.00 0.00 0.00 3.85
165 166 2.093306 TGTGCCTTGTACATCCTTCG 57.907 50.000 0.00 0.00 0.00 3.79
260 277 6.806249 GCATCTCAACGAATTCAATTTAACCA 59.194 34.615 6.22 0.00 0.00 3.67
262 279 6.523201 ACGCATCTCAACGAATTCAATTTAAC 59.477 34.615 6.22 0.00 0.00 2.01
264 281 6.176975 ACGCATCTCAACGAATTCAATTTA 57.823 33.333 6.22 0.00 0.00 1.40
265 282 5.046910 ACGCATCTCAACGAATTCAATTT 57.953 34.783 6.22 0.00 0.00 1.82
276 293 2.287188 CCATGCCAATACGCATCTCAAC 60.287 50.000 0.00 0.00 46.55 3.18
277 294 1.948834 CCATGCCAATACGCATCTCAA 59.051 47.619 0.00 0.00 46.55 3.02
299 316 1.006571 GAAGGAACCGTGTCTCGCA 60.007 57.895 0.00 0.00 38.35 5.10
348 365 1.084289 GACCCGTAGTGGACAAATGC 58.916 55.000 0.00 0.00 42.00 3.56
349 366 2.233922 AGAGACCCGTAGTGGACAAATG 59.766 50.000 0.00 0.00 42.00 2.32
494 514 5.991328 AGTACATGCGGTGATTTCAATAG 57.009 39.130 0.00 0.00 0.00 1.73
495 515 5.460748 CGTAGTACATGCGGTGATTTCAATA 59.539 40.000 0.38 0.00 32.81 1.90
509 529 1.355971 GTGTGGCACCGTAGTACATG 58.644 55.000 16.26 0.00 0.00 3.21
510 530 0.108992 CGTGTGGCACCGTAGTACAT 60.109 55.000 16.26 0.00 0.00 2.29
511 531 1.286570 CGTGTGGCACCGTAGTACA 59.713 57.895 16.26 0.00 0.00 2.90
512 532 2.090524 GCGTGTGGCACCGTAGTAC 61.091 63.158 22.92 10.85 42.87 2.73
577 597 1.220206 CATGCGAGAGTGGAAGGCT 59.780 57.895 0.00 0.00 0.00 4.58
591 611 0.391228 TCATCATGCCAATGCCATGC 59.609 50.000 0.00 0.00 36.33 4.06
592 612 1.605457 GCTCATCATGCCAATGCCATG 60.605 52.381 0.00 0.00 36.33 3.66
593 613 0.679505 GCTCATCATGCCAATGCCAT 59.320 50.000 0.00 0.00 36.33 4.40
594 614 2.120765 GCTCATCATGCCAATGCCA 58.879 52.632 0.00 0.00 36.33 4.92
686 720 5.371115 TCTCTTATCGTTTTGGCTTTTGG 57.629 39.130 0.00 0.00 0.00 3.28
724 769 3.766676 TGAGCGTGTCTCTACTCATTC 57.233 47.619 0.00 0.00 42.38 2.67
761 806 4.515191 TGACTTAATTTGCAGAGCGAGTTT 59.485 37.500 0.00 0.00 0.00 2.66
762 807 4.065088 TGACTTAATTTGCAGAGCGAGTT 58.935 39.130 0.00 0.00 0.00 3.01
763 808 3.664107 TGACTTAATTTGCAGAGCGAGT 58.336 40.909 0.00 0.00 0.00 4.18
767 836 3.837213 TGCTGACTTAATTTGCAGAGC 57.163 42.857 0.00 0.00 0.00 4.09
782 851 0.958822 TGCTACGACTCACTTGCTGA 59.041 50.000 0.00 0.00 0.00 4.26
787 856 2.361119 TCAACAGTGCTACGACTCACTT 59.639 45.455 0.00 0.00 41.19 3.16
818 1088 2.433604 TGATCACTCTCTGATTCCTGCC 59.566 50.000 0.00 0.00 39.96 4.85
819 1089 3.493002 CCTGATCACTCTCTGATTCCTGC 60.493 52.174 0.00 0.00 39.96 4.85
820 1090 3.959449 TCCTGATCACTCTCTGATTCCTG 59.041 47.826 0.00 0.00 39.96 3.86
821 1091 4.217510 CTCCTGATCACTCTCTGATTCCT 58.782 47.826 0.00 0.00 39.96 3.36
822 1092 3.243839 GCTCCTGATCACTCTCTGATTCC 60.244 52.174 0.00 0.00 39.96 3.01
823 1093 3.638160 AGCTCCTGATCACTCTCTGATTC 59.362 47.826 0.00 0.00 39.96 2.52
824 1094 3.645434 AGCTCCTGATCACTCTCTGATT 58.355 45.455 0.00 0.00 39.96 2.57
825 1095 3.317455 AGCTCCTGATCACTCTCTGAT 57.683 47.619 0.00 0.00 42.84 2.90
826 1096 2.824689 AGCTCCTGATCACTCTCTGA 57.175 50.000 0.00 0.00 0.00 3.27
827 1097 2.886523 CCTAGCTCCTGATCACTCTCTG 59.113 54.545 0.00 0.00 0.00 3.35
828 1098 2.752829 GCCTAGCTCCTGATCACTCTCT 60.753 54.545 0.00 0.00 0.00 3.10
829 1099 1.613437 GCCTAGCTCCTGATCACTCTC 59.387 57.143 0.00 0.00 0.00 3.20
830 1100 1.703411 GCCTAGCTCCTGATCACTCT 58.297 55.000 0.00 0.00 0.00 3.24
874 1144 1.933115 GCGTATGGGGCAACTGGTTG 61.933 60.000 8.89 8.89 43.14 3.77
892 1162 5.445939 CGACTCTGTATTTGTGTACAATGGC 60.446 44.000 0.00 0.00 34.41 4.40
982 1261 3.680786 GGTCCTTTTGGTGCGGGC 61.681 66.667 0.00 0.00 41.38 6.13
1032 1311 4.156622 TACACCGACGAGCGAGCG 62.157 66.667 0.00 0.00 44.57 5.03
1033 1312 2.277373 CTACACCGACGAGCGAGC 60.277 66.667 0.00 0.00 44.57 5.03
1141 1420 1.964933 GCTATCCCTATCTATCCCCGC 59.035 57.143 0.00 0.00 0.00 6.13
1148 1427 3.010250 TGCTCTTCCGCTATCCCTATCTA 59.990 47.826 0.00 0.00 0.00 1.98
1235 1515 2.324541 GGATGGTCTCCATGACTAGCT 58.675 52.381 5.98 0.00 45.26 3.32
1237 1517 1.615883 CCGGATGGTCTCCATGACTAG 59.384 57.143 5.98 0.00 45.26 2.57
1238 1518 1.704641 CCGGATGGTCTCCATGACTA 58.295 55.000 5.98 0.00 45.26 2.59
1430 1710 0.866061 CTTCTGCACGACGATACCGG 60.866 60.000 0.00 0.00 40.78 5.28
1434 1714 1.141019 GGGCTTCTGCACGACGATA 59.859 57.895 0.00 0.00 41.91 2.92
1875 2168 9.425577 AGTAAACTAGAGAATCGAAAGGAAAAG 57.574 33.333 0.00 0.00 42.67 2.27
1908 2203 2.424956 GCAAGCAGAGGGAATTAACAGG 59.575 50.000 0.00 0.00 0.00 4.00
2071 2366 5.812642 CGTAAAGAGAAAGATGCATGGTACT 59.187 40.000 2.46 0.00 0.00 2.73
2072 2367 5.810587 TCGTAAAGAGAAAGATGCATGGTAC 59.189 40.000 2.46 0.00 0.00 3.34
2073 2368 5.972935 TCGTAAAGAGAAAGATGCATGGTA 58.027 37.500 2.46 0.00 0.00 3.25
2074 2369 4.832248 TCGTAAAGAGAAAGATGCATGGT 58.168 39.130 2.46 0.00 0.00 3.55
2075 2370 5.998454 ATCGTAAAGAGAAAGATGCATGG 57.002 39.130 2.46 0.00 0.00 3.66
2076 2371 6.909357 GGAAATCGTAAAGAGAAAGATGCATG 59.091 38.462 2.46 0.00 0.00 4.06
2120 2415 1.709147 GATTGCGCTGCCTGTACCAG 61.709 60.000 9.73 0.00 0.00 4.00
2121 2416 1.745115 GATTGCGCTGCCTGTACCA 60.745 57.895 9.73 0.00 0.00 3.25
2122 2417 2.472909 GGATTGCGCTGCCTGTACC 61.473 63.158 9.73 0.00 0.00 3.34
2123 2418 1.745115 TGGATTGCGCTGCCTGTAC 60.745 57.895 9.73 0.00 0.00 2.90
2124 2419 1.745115 GTGGATTGCGCTGCCTGTA 60.745 57.895 9.73 0.00 0.00 2.74
2126 2421 4.170062 CGTGGATTGCGCTGCCTG 62.170 66.667 9.73 0.90 0.00 4.85
2127 2422 4.704833 ACGTGGATTGCGCTGCCT 62.705 61.111 9.73 0.00 0.00 4.75
2128 2423 4.166011 GACGTGGATTGCGCTGCC 62.166 66.667 9.73 7.94 0.00 4.85
2140 2436 3.040099 GTTTGAACAAAATCGGGACGTG 58.960 45.455 0.00 0.00 42.15 4.49
2145 2441 3.726291 AGGTGTTTGAACAAAATCGGG 57.274 42.857 1.47 0.00 41.21 5.14
2166 2462 0.756294 TGCACGTCTTTTCCTCTGGA 59.244 50.000 0.00 0.00 0.00 3.86
2168 2464 3.665323 CGATTTGCACGTCTTTTCCTCTG 60.665 47.826 0.00 0.00 0.00 3.35
2169 2465 2.480419 CGATTTGCACGTCTTTTCCTCT 59.520 45.455 0.00 0.00 0.00 3.69
2171 2467 1.069227 GCGATTTGCACGTCTTTTCCT 60.069 47.619 0.00 0.00 45.45 3.36
2172 2468 1.327507 GCGATTTGCACGTCTTTTCC 58.672 50.000 0.00 0.00 45.45 3.13


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

AutoCloner maintained by Alex Coulton.