Multiple sequence alignment - TraesCS4D01G168000

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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 TraesCS4D01G168000 chr4D 100.000 2987 0 0 1 2987 292275626 292272640 0.000000e+00 5517
1 TraesCS4D01G168000 chr4D 86.177 2778 315 49 188 2921 163413952 163411200 0.000000e+00 2939
2 TraesCS4D01G168000 chr6B 86.481 2759 313 48 145 2864 272298776 272296039 0.000000e+00 2974
3 TraesCS4D01G168000 chr4B 86.002 2729 314 42 183 2864 165971944 165969237 0.000000e+00 2861
4 TraesCS4D01G168000 chr4B 86.061 2676 319 41 219 2856 376027722 376030381 0.000000e+00 2826
5 TraesCS4D01G168000 chr6A 85.828 2759 308 60 164 2874 462850445 462853168 0.000000e+00 2852
6 TraesCS4D01G168000 chr6A 85.384 2333 276 37 164 2468 462854993 462857288 0.000000e+00 2359
7 TraesCS4D01G168000 chr6A 91.148 1220 82 19 1719 2918 333075155 333076368 0.000000e+00 1631
8 TraesCS4D01G168000 chr2D 89.020 2295 211 31 193 2460 323249141 323246861 0.000000e+00 2804
9 TraesCS4D01G168000 chr2D 87.588 1136 110 18 1809 2921 290209893 290208766 0.000000e+00 1288
10 TraesCS4D01G168000 chr2D 95.714 70 3 0 2918 2987 121461875 121461944 2.430000e-21 113
11 TraesCS4D01G168000 chr2D 95.714 70 3 0 2918 2987 194279494 194279425 2.430000e-21 113
12 TraesCS4D01G168000 chr2D 95.714 70 3 0 2918 2987 313056321 313056390 2.430000e-21 113
13 TraesCS4D01G168000 chr2A 84.696 2777 350 58 145 2874 266908645 266905897 0.000000e+00 2704
14 TraesCS4D01G168000 chr2A 91.581 1164 77 12 1775 2921 100898518 100897359 0.000000e+00 1587
15 TraesCS4D01G168000 chr3D 85.000 2720 324 55 159 2843 402309341 402306671 0.000000e+00 2686
16 TraesCS4D01G168000 chr3D 91.155 1221 77 16 1722 2921 213695538 213694328 0.000000e+00 1628
17 TraesCS4D01G168000 chr3D 92.733 344 22 3 1 343 304092805 304092464 7.440000e-136 494
18 TraesCS4D01G168000 chr3D 95.714 70 3 0 2918 2987 35084340 35084409 2.430000e-21 113
19 TraesCS4D01G168000 chr1D 91.557 1220 82 10 1719 2921 143121961 143120746 0.000000e+00 1663
20 TraesCS4D01G168000 chr1D 95.714 70 3 0 2918 2987 50524747 50524678 2.430000e-21 113
21 TraesCS4D01G168000 chr6D 89.289 1223 94 20 1722 2921 283634371 283633163 0.000000e+00 1498
22 TraesCS4D01G168000 chr6D 95.714 70 3 0 2918 2987 199769420 199769489 2.430000e-21 113
23 TraesCS4D01G168000 chr6D 95.714 70 3 0 2918 2987 337983022 337982953 2.430000e-21 113
24 TraesCS4D01G168000 chr2B 88.191 1194 96 23 1719 2874 550641798 550640612 0.000000e+00 1382
25 TraesCS4D01G168000 chr7B 87.310 1182 107 26 1719 2864 476086671 476085497 0.000000e+00 1312
26 TraesCS4D01G168000 chrUn 92.558 860 57 7 2068 2921 79018471 79017613 0.000000e+00 1227
27 TraesCS4D01G168000 chr1B 95.714 70 3 0 2918 2987 323215435 323215366 2.430000e-21 113
28 TraesCS4D01G168000 chr1A 95.714 70 3 0 2918 2987 498826121 498826190 2.430000e-21 113


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 TraesCS4D01G168000 chr4D 292272640 292275626 2986 True 5517.0 5517 100.000 1 2987 1 chr4D.!!$R2 2986
1 TraesCS4D01G168000 chr4D 163411200 163413952 2752 True 2939.0 2939 86.177 188 2921 1 chr4D.!!$R1 2733
2 TraesCS4D01G168000 chr6B 272296039 272298776 2737 True 2974.0 2974 86.481 145 2864 1 chr6B.!!$R1 2719
3 TraesCS4D01G168000 chr4B 165969237 165971944 2707 True 2861.0 2861 86.002 183 2864 1 chr4B.!!$R1 2681
4 TraesCS4D01G168000 chr4B 376027722 376030381 2659 False 2826.0 2826 86.061 219 2856 1 chr4B.!!$F1 2637
5 TraesCS4D01G168000 chr6A 462850445 462857288 6843 False 2605.5 2852 85.606 164 2874 2 chr6A.!!$F2 2710
6 TraesCS4D01G168000 chr6A 333075155 333076368 1213 False 1631.0 1631 91.148 1719 2918 1 chr6A.!!$F1 1199
7 TraesCS4D01G168000 chr2D 323246861 323249141 2280 True 2804.0 2804 89.020 193 2460 1 chr2D.!!$R3 2267
8 TraesCS4D01G168000 chr2D 290208766 290209893 1127 True 1288.0 1288 87.588 1809 2921 1 chr2D.!!$R2 1112
9 TraesCS4D01G168000 chr2A 266905897 266908645 2748 True 2704.0 2704 84.696 145 2874 1 chr2A.!!$R2 2729
10 TraesCS4D01G168000 chr2A 100897359 100898518 1159 True 1587.0 1587 91.581 1775 2921 1 chr2A.!!$R1 1146
11 TraesCS4D01G168000 chr3D 402306671 402309341 2670 True 2686.0 2686 85.000 159 2843 1 chr3D.!!$R3 2684
12 TraesCS4D01G168000 chr3D 213694328 213695538 1210 True 1628.0 1628 91.155 1722 2921 1 chr3D.!!$R1 1199
13 TraesCS4D01G168000 chr1D 143120746 143121961 1215 True 1663.0 1663 91.557 1719 2921 1 chr1D.!!$R2 1202
14 TraesCS4D01G168000 chr6D 283633163 283634371 1208 True 1498.0 1498 89.289 1722 2921 1 chr6D.!!$R1 1199
15 TraesCS4D01G168000 chr2B 550640612 550641798 1186 True 1382.0 1382 88.191 1719 2874 1 chr2B.!!$R1 1155
16 TraesCS4D01G168000 chr7B 476085497 476086671 1174 True 1312.0 1312 87.310 1719 2864 1 chr7B.!!$R1 1145
17 TraesCS4D01G168000 chrUn 79017613 79018471 858 True 1227.0 1227 92.558 2068 2921 1 chrUn.!!$R1 853

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
355 359 0.600557 TGATCATTTTGGCGCCGTTT 59.399 45.0 23.9 3.18 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2019 1.212688 CTCTTCCATATGTGTGGCCCA 59.787 52.381 0.0 0.0 39.19 5.36 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
24 25 7.195374 ACATATATGTAGGTGGTGTGAAACT 57.805 36.000 16.85 0.00 39.68 2.66
25 26 7.630082 ACATATATGTAGGTGGTGTGAAACTT 58.370 34.615 16.85 0.00 39.68 2.66
26 27 8.764558 ACATATATGTAGGTGGTGTGAAACTTA 58.235 33.333 16.85 0.00 39.68 2.24
27 28 9.778741 CATATATGTAGGTGGTGTGAAACTTAT 57.221 33.333 4.43 0.00 38.04 1.73
30 31 9.778741 ATATGTAGGTGGTGTGAAACTTATATG 57.221 33.333 0.00 0.00 38.04 1.78
31 32 7.011499 TGTAGGTGGTGTGAAACTTATATGT 57.989 36.000 0.00 0.00 38.04 2.29
32 33 7.101054 TGTAGGTGGTGTGAAACTTATATGTC 58.899 38.462 0.00 0.00 38.04 3.06
33 34 5.497474 AGGTGGTGTGAAACTTATATGTCC 58.503 41.667 0.00 0.00 38.04 4.02
34 35 4.638865 GGTGGTGTGAAACTTATATGTCCC 59.361 45.833 0.00 0.00 38.04 4.46
35 36 5.250200 GTGGTGTGAAACTTATATGTCCCA 58.750 41.667 0.00 0.00 38.04 4.37
36 37 5.354234 GTGGTGTGAAACTTATATGTCCCAG 59.646 44.000 0.00 0.00 38.04 4.45
37 38 5.013704 TGGTGTGAAACTTATATGTCCCAGT 59.986 40.000 0.00 0.00 38.04 4.00
38 39 6.213802 TGGTGTGAAACTTATATGTCCCAGTA 59.786 38.462 0.00 0.00 38.04 2.74
39 40 6.537660 GGTGTGAAACTTATATGTCCCAGTAC 59.462 42.308 0.00 0.00 38.04 2.73
40 41 6.537660 GTGTGAAACTTATATGTCCCAGTACC 59.462 42.308 0.00 0.00 38.04 3.34
41 42 6.213802 TGTGAAACTTATATGTCCCAGTACCA 59.786 38.462 0.00 0.00 38.04 3.25
42 43 7.092623 TGTGAAACTTATATGTCCCAGTACCAT 60.093 37.037 0.00 0.00 38.04 3.55
43 44 8.426489 GTGAAACTTATATGTCCCAGTACCATA 58.574 37.037 0.00 0.00 0.00 2.74
44 45 8.426489 TGAAACTTATATGTCCCAGTACCATAC 58.574 37.037 0.00 0.00 0.00 2.39
45 46 8.562949 AAACTTATATGTCCCAGTACCATACT 57.437 34.615 0.00 0.00 40.28 2.12
46 47 9.664777 AAACTTATATGTCCCAGTACCATACTA 57.335 33.333 0.00 0.00 37.23 1.82
47 48 8.647256 ACTTATATGTCCCAGTACCATACTAC 57.353 38.462 0.00 0.00 37.23 2.73
48 49 8.454494 ACTTATATGTCCCAGTACCATACTACT 58.546 37.037 0.00 0.00 37.23 2.57
49 50 9.310449 CTTATATGTCCCAGTACCATACTACTT 57.690 37.037 0.00 0.00 37.23 2.24
50 51 9.664777 TTATATGTCCCAGTACCATACTACTTT 57.335 33.333 0.00 0.00 37.23 2.66
51 52 6.886178 ATGTCCCAGTACCATACTACTTTT 57.114 37.500 0.00 0.00 37.23 2.27
52 53 6.045072 TGTCCCAGTACCATACTACTTTTG 57.955 41.667 0.00 0.00 37.23 2.44
53 54 4.874396 GTCCCAGTACCATACTACTTTTGC 59.126 45.833 0.00 0.00 37.23 3.68
54 55 4.532916 TCCCAGTACCATACTACTTTTGCA 59.467 41.667 0.00 0.00 37.23 4.08
55 56 5.190925 TCCCAGTACCATACTACTTTTGCAT 59.809 40.000 0.00 0.00 37.23 3.96
56 57 5.296780 CCCAGTACCATACTACTTTTGCATG 59.703 44.000 0.00 0.00 37.23 4.06
57 58 5.880332 CCAGTACCATACTACTTTTGCATGT 59.120 40.000 0.00 0.00 37.23 3.21
58 59 6.374333 CCAGTACCATACTACTTTTGCATGTT 59.626 38.462 0.00 0.00 37.23 2.71
59 60 7.414098 CCAGTACCATACTACTTTTGCATGTTC 60.414 40.741 0.00 0.00 37.23 3.18
60 61 7.119116 CAGTACCATACTACTTTTGCATGTTCA 59.881 37.037 0.00 0.00 37.23 3.18
61 62 6.500684 ACCATACTACTTTTGCATGTTCAG 57.499 37.500 0.00 0.00 0.00 3.02
62 63 6.003950 ACCATACTACTTTTGCATGTTCAGT 58.996 36.000 0.00 0.00 0.00 3.41
63 64 7.165485 ACCATACTACTTTTGCATGTTCAGTA 58.835 34.615 0.00 0.00 0.00 2.74
64 65 7.119262 ACCATACTACTTTTGCATGTTCAGTAC 59.881 37.037 0.00 0.00 0.00 2.73
65 66 7.334421 CCATACTACTTTTGCATGTTCAGTACT 59.666 37.037 0.00 0.00 0.00 2.73
66 67 9.366216 CATACTACTTTTGCATGTTCAGTACTA 57.634 33.333 0.00 0.00 0.00 1.82
68 69 8.256611 ACTACTTTTGCATGTTCAGTACTATG 57.743 34.615 0.00 0.00 0.00 2.23
69 70 8.094548 ACTACTTTTGCATGTTCAGTACTATGA 58.905 33.333 7.42 0.00 0.00 2.15
70 71 7.928307 ACTTTTGCATGTTCAGTACTATGAT 57.072 32.000 7.42 0.00 0.00 2.45
72 73 8.883731 ACTTTTGCATGTTCAGTACTATGATAC 58.116 33.333 7.42 0.88 0.00 2.24
73 74 8.785329 TTTTGCATGTTCAGTACTATGATACA 57.215 30.769 7.42 5.48 0.00 2.29
74 75 8.962884 TTTGCATGTTCAGTACTATGATACAT 57.037 30.769 7.42 7.11 34.33 2.29
75 76 8.593492 TTGCATGTTCAGTACTATGATACATC 57.407 34.615 7.42 5.78 33.04 3.06
76 77 7.955918 TGCATGTTCAGTACTATGATACATCT 58.044 34.615 7.42 0.00 33.04 2.90
77 78 7.869429 TGCATGTTCAGTACTATGATACATCTG 59.131 37.037 7.42 3.62 33.04 2.90
78 79 7.869937 GCATGTTCAGTACTATGATACATCTGT 59.130 37.037 7.42 0.00 33.04 3.41
79 80 9.755804 CATGTTCAGTACTATGATACATCTGTT 57.244 33.333 0.00 0.00 33.04 3.16
102 103 9.886132 TGTTATTTCTAGTTCCTACATTCTTCC 57.114 33.333 0.00 0.00 0.00 3.46
106 107 6.939132 TCTAGTTCCTACATTCTTCCTACG 57.061 41.667 0.00 0.00 0.00 3.51
107 108 6.421485 TCTAGTTCCTACATTCTTCCTACGT 58.579 40.000 0.00 0.00 0.00 3.57
108 109 7.568349 TCTAGTTCCTACATTCTTCCTACGTA 58.432 38.462 0.00 0.00 0.00 3.57
109 110 6.448207 AGTTCCTACATTCTTCCTACGTAC 57.552 41.667 0.00 0.00 0.00 3.67
110 111 6.186234 AGTTCCTACATTCTTCCTACGTACT 58.814 40.000 0.00 0.00 0.00 2.73
111 112 6.662663 AGTTCCTACATTCTTCCTACGTACTT 59.337 38.462 0.00 0.00 0.00 2.24
112 113 6.446781 TCCTACATTCTTCCTACGTACTTG 57.553 41.667 0.00 0.00 0.00 3.16
113 114 5.948162 TCCTACATTCTTCCTACGTACTTGT 59.052 40.000 0.00 0.00 0.00 3.16
114 115 6.034591 CCTACATTCTTCCTACGTACTTGTG 58.965 44.000 0.00 0.00 0.00 3.33
115 116 5.717078 ACATTCTTCCTACGTACTTGTGA 57.283 39.130 0.00 0.00 0.00 3.58
116 117 6.282199 ACATTCTTCCTACGTACTTGTGAT 57.718 37.500 0.00 0.00 0.00 3.06
117 118 7.400599 ACATTCTTCCTACGTACTTGTGATA 57.599 36.000 0.00 0.00 0.00 2.15
118 119 8.008513 ACATTCTTCCTACGTACTTGTGATAT 57.991 34.615 0.00 0.00 0.00 1.63
119 120 9.128404 ACATTCTTCCTACGTACTTGTGATATA 57.872 33.333 0.00 0.00 0.00 0.86
126 127 8.456471 TCCTACGTACTTGTGATATATATGTGC 58.544 37.037 0.00 0.00 0.00 4.57
127 128 8.459635 CCTACGTACTTGTGATATATATGTGCT 58.540 37.037 0.00 0.00 0.00 4.40
128 129 9.841880 CTACGTACTTGTGATATATATGTGCTT 57.158 33.333 0.00 0.00 0.00 3.91
129 130 8.520835 ACGTACTTGTGATATATATGTGCTTG 57.479 34.615 0.00 0.00 0.00 4.01
130 131 8.141909 ACGTACTTGTGATATATATGTGCTTGT 58.858 33.333 0.00 0.00 0.00 3.16
131 132 8.427774 CGTACTTGTGATATATATGTGCTTGTG 58.572 37.037 0.00 0.00 0.00 3.33
132 133 9.476202 GTACTTGTGATATATATGTGCTTGTGA 57.524 33.333 0.00 0.00 0.00 3.58
134 135 8.996271 ACTTGTGATATATATGTGCTTGTGATG 58.004 33.333 0.00 0.00 0.00 3.07
135 136 8.907222 TTGTGATATATATGTGCTTGTGATGT 57.093 30.769 0.00 0.00 0.00 3.06
136 137 8.314143 TGTGATATATATGTGCTTGTGATGTG 57.686 34.615 0.00 0.00 0.00 3.21
137 138 8.149647 TGTGATATATATGTGCTTGTGATGTGA 58.850 33.333 0.00 0.00 0.00 3.58
138 139 8.992073 GTGATATATATGTGCTTGTGATGTGAA 58.008 33.333 0.00 0.00 0.00 3.18
139 140 9.729281 TGATATATATGTGCTTGTGATGTGAAT 57.271 29.630 0.00 0.00 0.00 2.57
141 142 9.729281 ATATATATGTGCTTGTGATGTGAATCA 57.271 29.630 0.00 0.00 0.00 2.57
154 155 8.715191 GTGATGTGAATCACTTCTTAATCTCT 57.285 34.615 23.65 0.00 45.48 3.10
203 204 5.718130 TCGATGACCCTTCTTAGTTTTAGGA 59.282 40.000 0.00 0.00 0.00 2.94
207 208 9.327628 GATGACCCTTCTTAGTTTTAGGATTAC 57.672 37.037 0.00 0.00 0.00 1.89
265 267 3.381045 CTTTAGCCGAGCACGATCATTA 58.619 45.455 4.70 0.00 42.66 1.90
280 282 3.926058 TCATTAACTTGCCTAGTCCCC 57.074 47.619 0.00 0.00 35.54 4.81
355 359 0.600557 TGATCATTTTGGCGCCGTTT 59.399 45.000 23.90 3.18 0.00 3.60
419 423 6.566197 AGGTTTTGCTTCTGTTTCTATCTG 57.434 37.500 0.00 0.00 0.00 2.90
508 516 9.883142 TTTCTTGTTCATTTGTAGGTTGAATTT 57.117 25.926 0.00 0.00 32.48 1.82
774 782 0.639392 ATGGCTACTCTCACCCTCCT 59.361 55.000 0.00 0.00 0.00 3.69
804 812 1.675310 CATGAGCTTCGCCCCACAA 60.675 57.895 0.00 0.00 0.00 3.33
844 852 4.663120 ACAATTACTCATATGGGTGGCCTA 59.337 41.667 18.87 0.00 0.00 3.93
890 898 2.550855 GCAACAACCCTGAGATCTCACA 60.551 50.000 21.67 2.42 35.46 3.58
896 904 2.304180 ACCCTGAGATCTCACAGTTTGG 59.696 50.000 21.67 18.40 35.46 3.28
913 921 9.599866 CACAGTTTGGTTCTAGTAATCATATGA 57.400 33.333 8.10 8.10 0.00 2.15
958 966 2.892852 AGCAACAACTATGCACCACAAT 59.107 40.909 0.00 0.00 46.22 2.71
973 981 7.675062 TGCACCACAATAATTTTATTCACCTT 58.325 30.769 0.00 0.00 31.28 3.50
1004 1012 0.617413 CCTCAGCACCAGGAGATGTT 59.383 55.000 1.78 0.00 31.91 2.71
1116 1124 9.270640 GATGACTTTGATGATATAGACAAGCTT 57.729 33.333 0.00 0.00 0.00 3.74
1151 1159 1.517242 GAGTTCACTTGGAGTGCTGG 58.483 55.000 3.26 0.00 45.54 4.85
1334 1346 1.588674 GTTCCAACACCGTCACATCA 58.411 50.000 0.00 0.00 0.00 3.07
1362 1374 2.486907 GCAAGATAGCAAGAGCCCAGAT 60.487 50.000 0.00 0.00 43.56 2.90
1369 1381 1.666054 CAAGAGCCCAGATGAAGAGC 58.334 55.000 0.00 0.00 0.00 4.09
1413 1431 6.459923 ACTAGAAGACAAGGAACAAGATGAC 58.540 40.000 0.00 0.00 0.00 3.06
1419 1437 4.792068 ACAAGGAACAAGATGACCAAGAA 58.208 39.130 0.00 0.00 0.00 2.52
1420 1438 5.200483 ACAAGGAACAAGATGACCAAGAAA 58.800 37.500 0.00 0.00 0.00 2.52
1434 1452 3.826729 ACCAAGAAATTGACTACCCAAGC 59.173 43.478 0.00 0.00 0.00 4.01
1443 1461 2.094182 TGACTACCCAAGCGATCAAGTC 60.094 50.000 0.00 0.00 34.00 3.01
1477 1495 8.567948 CAATCTCTATCTCTCCTGAAGAAGTAC 58.432 40.741 0.00 0.00 32.23 2.73
1487 1505 3.434984 CCTGAAGAAGTACAAGAAGCTGC 59.565 47.826 0.00 0.00 0.00 5.25
1527 1545 9.794685 GAAGAACCAGAAATTCATTTTCCTATC 57.205 33.333 0.00 0.00 44.06 2.08
1531 1549 6.037172 ACCAGAAATTCATTTTCCTATCGTCG 59.963 38.462 0.00 0.00 44.06 5.12
1541 1559 2.915349 TCCTATCGTCGTACAAGAGCT 58.085 47.619 0.00 0.00 0.00 4.09
1546 1564 3.132629 TCGTCGTACAAGAGCTTGATC 57.867 47.619 16.47 7.92 42.93 2.92
1584 1602 2.092538 CCCTCTTGATGACATGCTTCCT 60.093 50.000 0.00 0.00 0.00 3.36
1590 1608 6.053650 TCTTGATGACATGCTTCCTTATGAG 58.946 40.000 0.00 0.00 0.00 2.90
1591 1609 5.619132 TGATGACATGCTTCCTTATGAGA 57.381 39.130 0.00 0.00 0.00 3.27
1600 1618 4.880120 TGCTTCCTTATGAGATCTTTGCTG 59.120 41.667 0.00 0.00 0.00 4.41
1615 1633 0.109643 TGCTGCTACTTTGCATTGCG 60.110 50.000 3.84 0.00 42.48 4.85
1617 1635 1.887320 CTGCTACTTTGCATTGCGTC 58.113 50.000 3.84 0.00 42.48 5.19
1678 1697 4.294347 TGGACATGATCATACACACCCTA 58.706 43.478 8.15 0.00 0.00 3.53
1701 1720 1.073177 GTGGCATTGCTCACATTTGC 58.927 50.000 19.13 0.00 35.58 3.68
1702 1721 2.758497 GGCATTGCTCACATTTGCC 58.242 52.632 8.82 0.00 43.84 4.52
1703 1722 1.079875 GGCATTGCTCACATTTGCCG 61.080 55.000 8.82 0.00 42.29 5.69
1707 1726 1.028130 TTGCTCACATTTGCCGTGAA 58.972 45.000 0.00 0.00 42.56 3.18
1711 1730 1.197721 CTCACATTTGCCGTGAAGACC 59.802 52.381 0.00 0.00 42.56 3.85
1712 1731 0.950836 CACATTTGCCGTGAAGACCA 59.049 50.000 0.00 0.00 36.43 4.02
1745 1764 5.798132 TCATGCTAGACCTATGCTTAATGG 58.202 41.667 0.00 0.00 0.00 3.16
1763 1782 8.680903 GCTTAATGGTAAATATCATCCTCATGG 58.319 37.037 0.00 0.00 0.00 3.66
1782 1801 7.417911 CCTCATGGTAGTATTGAGCTTACTGAA 60.418 40.741 6.80 0.00 36.41 3.02
1790 1809 8.312669 AGTATTGAGCTTACTGAATTCTACCT 57.687 34.615 7.05 0.00 31.68 3.08
1879 1898 1.376609 CCCTACCGCTTGCATTGTCC 61.377 60.000 0.00 0.00 0.00 4.02
1967 1986 1.540367 ACATTCCTTGGGACCCCGA 60.540 57.895 8.45 1.08 39.42 5.14
2000 2019 3.552875 CATGGTGATGAGGAGAAGCAAT 58.447 45.455 0.00 0.00 0.00 3.56
2004 2024 1.316651 GATGAGGAGAAGCAATGGGC 58.683 55.000 0.00 0.00 45.30 5.36
2132 2184 5.707298 CCCCAATCTGAATACCATCATACAC 59.293 44.000 0.00 0.00 0.00 2.90
2189 2241 9.034544 GTTGCTTGAGTCATTTCTTAAATGTTT 57.965 29.630 11.09 2.86 46.46 2.83
2625 2686 0.036858 TCGGTGGCATGTGAAATCGA 60.037 50.000 0.00 0.00 0.00 3.59
2786 2871 1.138266 CTCGGGATCGGTGGTATGTTT 59.862 52.381 0.00 0.00 36.95 2.83
2852 2940 8.986477 AATTCAATAAGTGCTTCAACCATAAC 57.014 30.769 0.00 0.00 0.00 1.89
2922 5210 0.734942 CCTTTGGCGCAATCAGCAAG 60.735 55.000 10.83 0.00 46.13 4.01
2926 5214 2.123428 GGCGCAATCAGCAAGGGAT 61.123 57.895 10.83 0.00 46.13 3.85
2928 5216 1.242076 GCGCAATCAGCAAGGGATAT 58.758 50.000 0.30 0.00 46.13 1.63
2929 5217 2.426522 GCGCAATCAGCAAGGGATATA 58.573 47.619 0.30 0.00 46.13 0.86
2930 5218 3.012518 GCGCAATCAGCAAGGGATATAT 58.987 45.455 0.30 0.00 46.13 0.86
2934 5222 5.413833 CGCAATCAGCAAGGGATATATTTCT 59.586 40.000 0.00 0.00 46.13 2.52
2935 5223 6.072286 CGCAATCAGCAAGGGATATATTTCTT 60.072 38.462 0.00 0.00 46.13 2.52
2939 5227 9.425248 AATCAGCAAGGGATATATTTCTTGAAA 57.575 29.630 22.42 12.57 38.96 2.69
2943 5231 9.425248 AGCAAGGGATATATTTCTTGAAATGAA 57.575 29.630 22.42 6.72 38.96 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.778741 ATAAGTTTCACACCACCTACATATATG 57.221 33.333 11.29 11.29 0.00 1.78
4 5 9.778741 CATATAAGTTTCACACCACCTACATAT 57.221 33.333 0.00 0.00 0.00 1.78
6 7 7.630082 ACATATAAGTTTCACACCACCTACAT 58.370 34.615 0.00 0.00 0.00 2.29
8 9 6.537660 GGACATATAAGTTTCACACCACCTAC 59.462 42.308 0.00 0.00 0.00 3.18
9 10 6.352394 GGGACATATAAGTTTCACACCACCTA 60.352 42.308 0.00 0.00 0.00 3.08
10 11 5.497474 GGACATATAAGTTTCACACCACCT 58.503 41.667 0.00 0.00 0.00 4.00
11 12 4.638865 GGGACATATAAGTTTCACACCACC 59.361 45.833 0.00 0.00 0.00 4.61
12 13 5.250200 TGGGACATATAAGTTTCACACCAC 58.750 41.667 0.00 0.00 0.00 4.16
13 14 5.013704 ACTGGGACATATAAGTTTCACACCA 59.986 40.000 0.00 0.00 38.20 4.17
14 15 5.497474 ACTGGGACATATAAGTTTCACACC 58.503 41.667 0.00 0.00 38.20 4.16
15 16 6.537660 GGTACTGGGACATATAAGTTTCACAC 59.462 42.308 0.00 0.00 38.20 3.82
16 17 6.213802 TGGTACTGGGACATATAAGTTTCACA 59.786 38.462 0.00 0.00 38.20 3.58
17 18 6.646267 TGGTACTGGGACATATAAGTTTCAC 58.354 40.000 0.00 0.00 38.20 3.18
18 19 6.877668 TGGTACTGGGACATATAAGTTTCA 57.122 37.500 0.00 0.00 38.20 2.69
19 20 8.648693 AGTATGGTACTGGGACATATAAGTTTC 58.351 37.037 0.00 0.00 38.20 2.78
20 21 8.562949 AGTATGGTACTGGGACATATAAGTTT 57.437 34.615 0.00 0.00 38.20 2.66
21 22 9.086758 GTAGTATGGTACTGGGACATATAAGTT 57.913 37.037 0.06 0.00 39.81 2.66
22 23 8.454494 AGTAGTATGGTACTGGGACATATAAGT 58.546 37.037 0.06 0.00 39.81 2.24
23 24 8.880991 AGTAGTATGGTACTGGGACATATAAG 57.119 38.462 0.06 0.00 39.81 1.73
24 25 9.664777 AAAGTAGTATGGTACTGGGACATATAA 57.335 33.333 0.06 0.00 39.81 0.98
25 26 9.664777 AAAAGTAGTATGGTACTGGGACATATA 57.335 33.333 0.06 0.00 39.81 0.86
26 27 8.429641 CAAAAGTAGTATGGTACTGGGACATAT 58.570 37.037 0.06 0.00 39.81 1.78
27 28 7.634210 GCAAAAGTAGTATGGTACTGGGACATA 60.634 40.741 0.06 0.00 39.81 2.29
28 29 6.650120 CAAAAGTAGTATGGTACTGGGACAT 58.350 40.000 0.06 0.00 39.81 3.06
29 30 5.570034 GCAAAAGTAGTATGGTACTGGGACA 60.570 44.000 0.06 0.00 39.81 4.02
30 31 4.874396 GCAAAAGTAGTATGGTACTGGGAC 59.126 45.833 0.06 0.00 39.81 4.46
31 32 4.532916 TGCAAAAGTAGTATGGTACTGGGA 59.467 41.667 0.06 0.00 39.81 4.37
32 33 4.839121 TGCAAAAGTAGTATGGTACTGGG 58.161 43.478 0.06 0.00 39.81 4.45
33 34 5.880332 ACATGCAAAAGTAGTATGGTACTGG 59.120 40.000 0.00 0.00 39.81 4.00
34 35 6.985188 ACATGCAAAAGTAGTATGGTACTG 57.015 37.500 0.00 0.00 39.81 2.74
35 36 7.165485 TGAACATGCAAAAGTAGTATGGTACT 58.835 34.615 0.00 0.00 42.68 2.73
36 37 7.119262 ACTGAACATGCAAAAGTAGTATGGTAC 59.881 37.037 0.00 0.00 34.02 3.34
37 38 7.165485 ACTGAACATGCAAAAGTAGTATGGTA 58.835 34.615 0.00 0.00 34.02 3.25
38 39 6.003950 ACTGAACATGCAAAAGTAGTATGGT 58.996 36.000 0.00 0.00 34.02 3.55
39 40 6.500684 ACTGAACATGCAAAAGTAGTATGG 57.499 37.500 0.00 0.00 34.02 2.74
40 41 8.256611 AGTACTGAACATGCAAAAGTAGTATG 57.743 34.615 0.00 0.00 35.56 2.39
42 43 9.366216 CATAGTACTGAACATGCAAAAGTAGTA 57.634 33.333 5.39 12.02 35.07 1.82
43 44 8.094548 TCATAGTACTGAACATGCAAAAGTAGT 58.905 33.333 5.39 2.19 32.97 2.73
44 45 8.479313 TCATAGTACTGAACATGCAAAAGTAG 57.521 34.615 5.39 0.00 0.00 2.57
46 47 7.928307 ATCATAGTACTGAACATGCAAAAGT 57.072 32.000 5.39 0.00 0.00 2.66
47 48 8.882736 TGTATCATAGTACTGAACATGCAAAAG 58.117 33.333 5.39 0.00 0.00 2.27
48 49 8.785329 TGTATCATAGTACTGAACATGCAAAA 57.215 30.769 5.39 0.00 0.00 2.44
49 50 8.962884 ATGTATCATAGTACTGAACATGCAAA 57.037 30.769 5.39 0.00 31.61 3.68
50 51 8.424133 AGATGTATCATAGTACTGAACATGCAA 58.576 33.333 5.39 0.00 32.28 4.08
51 52 7.869429 CAGATGTATCATAGTACTGAACATGCA 59.131 37.037 5.39 2.77 32.28 3.96
52 53 7.869937 ACAGATGTATCATAGTACTGAACATGC 59.130 37.037 5.39 0.00 32.28 4.06
53 54 9.755804 AACAGATGTATCATAGTACTGAACATG 57.244 33.333 5.39 1.01 32.28 3.21
76 77 9.886132 GGAAGAATGTAGGAACTAGAAATAACA 57.114 33.333 0.00 0.00 44.14 2.41
80 81 8.414778 CGTAGGAAGAATGTAGGAACTAGAAAT 58.585 37.037 0.00 0.00 44.14 2.17
81 82 7.395489 ACGTAGGAAGAATGTAGGAACTAGAAA 59.605 37.037 0.00 0.00 44.14 2.52
82 83 6.888632 ACGTAGGAAGAATGTAGGAACTAGAA 59.111 38.462 0.00 0.00 44.14 2.10
83 84 6.421485 ACGTAGGAAGAATGTAGGAACTAGA 58.579 40.000 0.00 0.00 44.14 2.43
84 85 6.696441 ACGTAGGAAGAATGTAGGAACTAG 57.304 41.667 0.00 0.00 44.14 2.57
85 86 7.341805 AGTACGTAGGAAGAATGTAGGAACTA 58.658 38.462 0.00 0.00 41.75 2.24
86 87 6.186234 AGTACGTAGGAAGAATGTAGGAACT 58.814 40.000 0.00 0.00 46.37 3.01
87 88 6.448207 AGTACGTAGGAAGAATGTAGGAAC 57.552 41.667 0.00 0.00 0.00 3.62
88 89 6.435277 ACAAGTACGTAGGAAGAATGTAGGAA 59.565 38.462 0.00 0.00 0.00 3.36
89 90 5.948162 ACAAGTACGTAGGAAGAATGTAGGA 59.052 40.000 0.00 0.00 0.00 2.94
90 91 6.034591 CACAAGTACGTAGGAAGAATGTAGG 58.965 44.000 0.00 0.00 0.00 3.18
91 92 6.849502 TCACAAGTACGTAGGAAGAATGTAG 58.150 40.000 0.00 0.00 0.00 2.74
92 93 6.822667 TCACAAGTACGTAGGAAGAATGTA 57.177 37.500 0.00 0.00 0.00 2.29
93 94 5.717078 TCACAAGTACGTAGGAAGAATGT 57.283 39.130 0.00 0.00 0.00 2.71
100 101 8.456471 GCACATATATATCACAAGTACGTAGGA 58.544 37.037 0.00 0.00 0.00 2.94
101 102 8.459635 AGCACATATATATCACAAGTACGTAGG 58.540 37.037 0.00 0.00 0.00 3.18
102 103 9.841880 AAGCACATATATATCACAAGTACGTAG 57.158 33.333 0.00 0.00 0.00 3.51
103 104 9.620660 CAAGCACATATATATCACAAGTACGTA 57.379 33.333 0.00 0.00 0.00 3.57
104 105 8.141909 ACAAGCACATATATATCACAAGTACGT 58.858 33.333 0.00 0.00 0.00 3.57
105 106 8.427774 CACAAGCACATATATATCACAAGTACG 58.572 37.037 0.00 0.00 0.00 3.67
106 107 9.476202 TCACAAGCACATATATATCACAAGTAC 57.524 33.333 0.00 0.00 0.00 2.73
108 109 8.996271 CATCACAAGCACATATATATCACAAGT 58.004 33.333 0.00 0.00 0.00 3.16
109 110 8.996271 ACATCACAAGCACATATATATCACAAG 58.004 33.333 0.00 0.00 0.00 3.16
110 111 8.776470 CACATCACAAGCACATATATATCACAA 58.224 33.333 0.00 0.00 0.00 3.33
111 112 8.149647 TCACATCACAAGCACATATATATCACA 58.850 33.333 0.00 0.00 0.00 3.58
112 113 8.538409 TCACATCACAAGCACATATATATCAC 57.462 34.615 0.00 0.00 0.00 3.06
113 114 9.729281 ATTCACATCACAAGCACATATATATCA 57.271 29.630 0.00 0.00 0.00 2.15
115 116 9.729281 TGATTCACATCACAAGCACATATATAT 57.271 29.630 0.00 0.00 34.22 0.86
130 131 8.756927 AGAGAGATTAAGAAGTGATTCACATCA 58.243 33.333 20.56 4.37 34.97 3.07
141 142 9.377312 GCAAACAGAATAGAGAGATTAAGAAGT 57.623 33.333 0.00 0.00 0.00 3.01
142 143 9.598517 AGCAAACAGAATAGAGAGATTAAGAAG 57.401 33.333 0.00 0.00 0.00 2.85
173 174 2.100605 AGAAGGGTCATCGACAAAGC 57.899 50.000 0.00 0.00 33.68 3.51
203 204 9.872684 ATTGGATGATGATTACAGGAAAGTAAT 57.127 29.630 0.00 0.00 44.90 1.89
207 208 8.663025 CGATATTGGATGATGATTACAGGAAAG 58.337 37.037 0.00 0.00 0.00 2.62
214 215 8.656849 GGTAACACGATATTGGATGATGATTAC 58.343 37.037 0.00 0.00 0.00 1.89
215 216 8.593679 AGGTAACACGATATTGGATGATGATTA 58.406 33.333 0.00 0.00 41.41 1.75
265 267 1.265454 CCTCGGGGACTAGGCAAGTT 61.265 60.000 0.00 0.00 39.07 2.66
280 282 0.452950 CGAGTGTCGTGTTCTCCTCG 60.453 60.000 0.00 0.00 34.72 4.63
355 359 4.415150 ACGACGCTAGTCCCCGGA 62.415 66.667 0.73 0.00 44.28 5.14
498 504 7.219322 CCATTTCCAAGAAGAAAATTCAACCT 58.781 34.615 0.00 0.00 39.11 3.50
508 516 6.248433 AGTAGAATGCCATTTCCAAGAAGAA 58.752 36.000 0.00 0.00 0.00 2.52
745 753 3.054875 TGAGAGTAGCCATGCTGACATTT 60.055 43.478 0.00 0.00 40.10 2.32
774 782 3.313249 CGAAGCTCATGCCATAACAATCA 59.687 43.478 0.00 0.00 40.80 2.57
804 812 7.402862 AGTAATTGTTTTGGTATGAGCTAGGT 58.597 34.615 0.00 0.00 0.00 3.08
844 852 9.289782 GCTCCTATATGACATATTCTGGTTTTT 57.710 33.333 13.09 0.00 0.00 1.94
890 898 9.838339 CCTTCATATGATTACTAGAACCAAACT 57.162 33.333 6.17 0.00 0.00 2.66
913 921 5.970640 TCTCCTCATTGTACCTAAATCCCTT 59.029 40.000 0.00 0.00 0.00 3.95
973 981 5.061721 TGGTGCTGAGGTATATGAGTAGA 57.938 43.478 0.00 0.00 0.00 2.59
1004 1012 5.261216 GAGGACCATTTAACTCCATTGGAA 58.739 41.667 6.88 0.00 0.00 3.53
1116 1124 5.183331 AGTGAACTCGAGACTAAGCAATGTA 59.817 40.000 21.68 0.00 0.00 2.29
1151 1159 2.039084 ACCGGCCTAATTGGATCATCTC 59.961 50.000 0.00 0.00 38.35 2.75
1334 1346 3.533547 CTCTTGCTATCTTGCTCAGCTT 58.466 45.455 0.00 0.00 36.26 3.74
1413 1431 3.119849 CGCTTGGGTAGTCAATTTCTTGG 60.120 47.826 0.00 0.00 32.95 3.61
1419 1437 3.627395 TGATCGCTTGGGTAGTCAATT 57.373 42.857 0.00 0.00 0.00 2.32
1420 1438 3.055094 ACTTGATCGCTTGGGTAGTCAAT 60.055 43.478 0.00 0.00 0.00 2.57
1434 1452 4.264145 GAGATTGTGTCTTCGACTTGATCG 59.736 45.833 0.00 0.00 44.56 3.69
1443 1461 5.530915 AGGAGAGATAGAGATTGTGTCTTCG 59.469 44.000 0.00 0.00 37.29 3.79
1455 1473 7.773224 TCTTGTACTTCTTCAGGAGAGATAGAG 59.227 40.741 0.00 0.00 35.37 2.43
1477 1495 3.812053 AGTTCAACTACAGCAGCTTCTTG 59.188 43.478 0.00 0.00 0.00 3.02
1487 1505 6.049149 TCTGGTTCTTCAAGTTCAACTACAG 58.951 40.000 0.00 0.00 0.00 2.74
1527 1545 3.138205 AGATCAAGCTCTTGTACGACG 57.862 47.619 9.20 0.00 41.16 5.12
1531 1549 4.142049 ACCTGCTAGATCAAGCTCTTGTAC 60.142 45.833 9.20 5.45 43.19 2.90
1584 1602 6.183360 GCAAAGTAGCAGCAAAGATCTCATAA 60.183 38.462 0.00 0.00 0.00 1.90
1590 1608 3.837213 TGCAAAGTAGCAGCAAAGATC 57.163 42.857 0.00 0.00 40.11 2.75
1600 1618 2.549633 ATGACGCAATGCAAAGTAGC 57.450 45.000 5.91 0.00 0.00 3.58
1615 1633 8.768955 CAAGTCTAGCTTAATTGATGGTATGAC 58.231 37.037 0.00 0.00 35.27 3.06
1617 1635 8.893219 TCAAGTCTAGCTTAATTGATGGTATG 57.107 34.615 7.35 0.00 35.27 2.39
1678 1697 4.751060 CAAATGTGAGCAATGCCACTAAT 58.249 39.130 21.16 9.73 33.31 1.73
1701 1720 4.941263 TGAGGAAAATAATGGTCTTCACGG 59.059 41.667 0.00 0.00 0.00 4.94
1702 1721 6.489675 CATGAGGAAAATAATGGTCTTCACG 58.510 40.000 0.00 0.00 31.18 4.35
1703 1722 6.096001 AGCATGAGGAAAATAATGGTCTTCAC 59.904 38.462 0.00 0.00 31.18 3.18
1707 1726 6.995091 GTCTAGCATGAGGAAAATAATGGTCT 59.005 38.462 0.00 0.00 33.21 3.85
1711 1730 8.944029 CATAGGTCTAGCATGAGGAAAATAATG 58.056 37.037 0.00 0.00 0.00 1.90
1712 1731 7.609532 GCATAGGTCTAGCATGAGGAAAATAAT 59.390 37.037 0.00 0.00 0.00 1.28
1763 1782 9.465985 GGTAGAATTCAGTAAGCTCAATACTAC 57.534 37.037 8.44 0.00 32.47 2.73
1782 1801 6.067217 AGCACATGTTTAGGAAGGTAGAAT 57.933 37.500 0.00 0.00 0.00 2.40
1922 1941 3.449377 TCGAACCTGGTCAGCATGTATTA 59.551 43.478 0.00 0.00 37.40 0.98
1967 1986 1.576577 TCACCATGCTCTGAGTCCAT 58.423 50.000 6.53 0.00 0.00 3.41
2000 2019 1.212688 CTCTTCCATATGTGTGGCCCA 59.787 52.381 0.00 0.00 39.19 5.36
2004 2024 4.125703 GCTTCTCTCTTCCATATGTGTGG 58.874 47.826 1.24 0.00 40.76 4.17
2038 2058 3.749226 CTCTTCTCCTTTTGCTTCCACT 58.251 45.455 0.00 0.00 0.00 4.00
2132 2184 6.504398 AGCAAATGATTTCAGCATGTATCAG 58.496 36.000 3.55 0.00 39.89 2.90
2189 2241 4.340950 GTCAAAGGTGAAATTCAGTGGGAA 59.659 41.667 0.00 0.00 36.17 3.97
2573 2629 6.127101 ACATGACATGCTACTGTAGGTAGTA 58.873 40.000 15.49 1.17 46.99 1.82
2625 2686 8.996651 ATTATTAATTACTGCCCAAGCTAACT 57.003 30.769 0.00 0.00 40.80 2.24
2740 2825 0.388294 GTATACACCTGGCTCGACCC 59.612 60.000 0.00 0.00 37.83 4.46
2888 3014 3.874193 GCCAAAGGGTTCCTAAAGAGAGG 60.874 52.174 0.00 0.00 35.58 3.69


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

AutoCloner maintained by Alex Coulton.