Multiple sequence alignment - TraesCS1B01G425100

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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 TraesCS1B01G425100 chr1B 100.000 2428 0 0 761 3188 649429258 649431685 0.000000e+00 4484
1 TraesCS1B01G425100 chr1B 97.735 2428 53 2 761 3188 594015142 594017567 0.000000e+00 4178
2 TraesCS1B01G425100 chr1B 94.169 1818 52 16 761 2528 673447019 673445206 0.000000e+00 2721
3 TraesCS1B01G425100 chr1B 95.208 1565 48 15 761 2299 438160091 438161654 0.000000e+00 2449
4 TraesCS1B01G425100 chr1B 93.226 1299 53 20 773 2040 61450497 61449203 0.000000e+00 1879
5 TraesCS1B01G425100 chr1B 96.624 859 28 1 2330 3188 438161647 438162504 0.000000e+00 1424
6 TraesCS1B01G425100 chr1B 100.000 456 0 0 1 456 649428498 649428953 0.000000e+00 843
7 TraesCS1B01G425100 chr1B 95.730 281 12 0 176 456 594014821 594015101 1.350000e-123 453
8 TraesCS1B01G425100 chr1B 94.662 281 15 0 176 456 438159773 438160053 1.360000e-118 436
9 TraesCS1B01G425100 chr7B 96.958 2433 58 11 761 3188 506549127 506551548 0.000000e+00 4069
10 TraesCS1B01G425100 chr7B 94.646 1046 32 2 2143 3188 145546443 145545422 0.000000e+00 1600
11 TraesCS1B01G425100 chr7B 95.730 281 12 0 176 456 145547177 145546897 1.350000e-123 453
12 TraesCS1B01G425100 chr3B 96.776 1768 43 2 761 2528 53026559 53028312 0.000000e+00 2937
13 TraesCS1B01G425100 chr3B 96.719 1768 44 2 761 2528 52631371 52629618 0.000000e+00 2931
14 TraesCS1B01G425100 chr3B 96.842 665 19 2 2525 3188 53028728 53029391 0.000000e+00 1110
15 TraesCS1B01G425100 chr3B 95.730 281 11 1 176 456 52631696 52631417 4.850000e-123 451
16 TraesCS1B01G425100 chr3B 95.730 281 10 1 176 456 53026235 53026513 4.850000e-123 451
17 TraesCS1B01G425100 chr2B 94.224 1818 52 16 761 2528 453819826 453821640 0.000000e+00 2726
18 TraesCS1B01G425100 chr2B 95.475 663 23 5 2531 3188 794529855 794530515 0.000000e+00 1051
19 TraesCS1B01G425100 chr2B 96.338 628 23 0 2561 3188 453822386 453823013 0.000000e+00 1033
20 TraesCS1B01G425100 chr5B 95.858 1690 33 3 1512 3188 578450926 578452591 0.000000e+00 2699
21 TraesCS1B01G425100 chr5B 95.680 1412 37 2 1777 3188 567004790 567003403 0.000000e+00 2248
22 TraesCS1B01G425100 chr5B 96.797 281 9 0 176 456 567014791 567014511 1.340000e-128 470
23 TraesCS1B01G425100 chr6B 93.812 1002 31 16 761 1734 169167514 169166516 0.000000e+00 1478
24 TraesCS1B01G425100 chr6B 97.778 855 19 0 1445 2299 558313354 558312500 0.000000e+00 1474
25 TraesCS1B01G425100 chr6B 96.740 859 27 1 2330 3188 558312507 558311650 0.000000e+00 1430
26 TraesCS1B01G425100 chr6B 97.249 836 23 0 761 1596 151206908 151206073 0.000000e+00 1417
27 TraesCS1B01G425100 chr6B 97.509 281 7 0 176 456 151205625 151205905 6.180000e-132 481
28 TraesCS1B01G425100 chr6B 95.374 281 13 0 176 456 169167830 169167550 6.270000e-122 448
29 TraesCS1B01G425100 chrUn 96.842 665 19 2 2525 3188 415919906 415919243 0.000000e+00 1110
30 TraesCS1B01G425100 chrUn 96.692 665 20 2 2525 3188 438247095 438247758 0.000000e+00 1105
31 TraesCS1B01G425100 chrUn 96.336 655 13 1 1874 2528 211278796 211279439 0.000000e+00 1066
32 TraesCS1B01G425100 chrUn 97.148 561 16 0 761 1321 211274627 211275187 0.000000e+00 948
33 TraesCS1B01G425100 chrUn 95.730 281 11 1 176 456 371388781 371389060 4.850000e-123 451


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 TraesCS1B01G425100 chr1B 649428498 649431685 3187 False 2663.500000 4484 100.000000 1 3188 2 chr1B.!!$F3 3187
1 TraesCS1B01G425100 chr1B 673445206 673447019 1813 True 2721.000000 2721 94.169000 761 2528 1 chr1B.!!$R2 1767
2 TraesCS1B01G425100 chr1B 594014821 594017567 2746 False 2315.500000 4178 96.732500 176 3188 2 chr1B.!!$F2 3012
3 TraesCS1B01G425100 chr1B 61449203 61450497 1294 True 1879.000000 1879 93.226000 773 2040 1 chr1B.!!$R1 1267
4 TraesCS1B01G425100 chr1B 438159773 438162504 2731 False 1436.333333 2449 95.498000 176 3188 3 chr1B.!!$F1 3012
5 TraesCS1B01G425100 chr7B 506549127 506551548 2421 False 4069.000000 4069 96.958000 761 3188 1 chr7B.!!$F1 2427
6 TraesCS1B01G425100 chr7B 145545422 145547177 1755 True 1026.500000 1600 95.188000 176 3188 2 chr7B.!!$R1 3012
7 TraesCS1B01G425100 chr3B 52629618 52631696 2078 True 1691.000000 2931 96.224500 176 2528 2 chr3B.!!$R1 2352
8 TraesCS1B01G425100 chr3B 53026235 53029391 3156 False 1499.333333 2937 96.449333 176 3188 3 chr3B.!!$F1 3012
9 TraesCS1B01G425100 chr2B 453819826 453823013 3187 False 1879.500000 2726 95.281000 761 3188 2 chr2B.!!$F2 2427
10 TraesCS1B01G425100 chr2B 794529855 794530515 660 False 1051.000000 1051 95.475000 2531 3188 1 chr2B.!!$F1 657
11 TraesCS1B01G425100 chr5B 578450926 578452591 1665 False 2699.000000 2699 95.858000 1512 3188 1 chr5B.!!$F1 1676
12 TraesCS1B01G425100 chr5B 567003403 567004790 1387 True 2248.000000 2248 95.680000 1777 3188 1 chr5B.!!$R1 1411
13 TraesCS1B01G425100 chr6B 558311650 558313354 1704 True 1452.000000 1474 97.259000 1445 3188 2 chr6B.!!$R3 1743
14 TraesCS1B01G425100 chr6B 151206073 151206908 835 True 1417.000000 1417 97.249000 761 1596 1 chr6B.!!$R1 835
15 TraesCS1B01G425100 chr6B 169166516 169167830 1314 True 963.000000 1478 94.593000 176 1734 2 chr6B.!!$R2 1558
16 TraesCS1B01G425100 chrUn 415919243 415919906 663 True 1110.000000 1110 96.842000 2525 3188 1 chrUn.!!$R1 663
17 TraesCS1B01G425100 chrUn 438247095 438247758 663 False 1105.000000 1105 96.692000 2525 3188 1 chrUn.!!$F2 663
18 TraesCS1B01G425100 chrUn 211274627 211279439 4812 False 1007.000000 1066 96.742000 761 2528 2 chrUn.!!$F3 1767

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
85 86 0.108709 AGTTATTTACACGCGGCCGA 60.109 50.0 33.48 5.99 38.29 5.54 F
151 152 0.111253 CCTTTGGGTTCAGCAGTCCT 59.889 55.0 0.00 0.00 0.00 3.85 F
172 173 0.313672 GCCAAATTCTTCACCGTGCA 59.686 50.0 0.00 0.00 0.00 4.57 F
1015 1017 0.906066 TACAATGCAGGCGAACCCTA 59.094 50.0 0.00 0.00 44.09 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1017 2.511218 AGGATGCATCTATGGTGGTGTT 59.489 45.455 25.28 0.00 0.00 3.32 R
2067 5150 3.081061 CTCTATCATCCAGTCCCTCTCG 58.919 54.545 0.00 0.00 0.00 4.04 R
2110 5193 4.016444 GCTTTCATAAGATCACCCACCAA 58.984 43.478 0.00 0.00 32.92 3.67 R
2999 6907 1.639635 ATTAGTCCTGCCCAGCCTGG 61.640 60.000 2.91 2.91 37.25 4.45 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
23 24 5.499004 TTTAGGGAGTTGTATGCTCTTGT 57.501 39.130 0.00 0.00 33.73 3.16
24 25 3.618690 AGGGAGTTGTATGCTCTTGTC 57.381 47.619 0.00 0.00 33.73 3.18
25 26 2.906389 AGGGAGTTGTATGCTCTTGTCA 59.094 45.455 0.00 0.00 33.73 3.58
26 27 3.327757 AGGGAGTTGTATGCTCTTGTCAA 59.672 43.478 0.00 0.00 33.73 3.18
27 28 4.072131 GGGAGTTGTATGCTCTTGTCAAA 58.928 43.478 0.00 0.00 33.73 2.69
28 29 4.083271 GGGAGTTGTATGCTCTTGTCAAAC 60.083 45.833 0.00 0.00 33.73 2.93
29 30 4.515191 GGAGTTGTATGCTCTTGTCAAACA 59.485 41.667 0.00 0.00 33.73 2.83
30 31 5.182001 GGAGTTGTATGCTCTTGTCAAACAT 59.818 40.000 0.00 0.00 33.73 2.71
31 32 6.371548 GGAGTTGTATGCTCTTGTCAAACATA 59.628 38.462 0.00 0.00 33.73 2.29
32 33 7.066284 GGAGTTGTATGCTCTTGTCAAACATAT 59.934 37.037 6.11 0.00 33.73 1.78
33 34 7.755591 AGTTGTATGCTCTTGTCAAACATATG 58.244 34.615 0.00 0.00 0.00 1.78
34 35 6.122850 TGTATGCTCTTGTCAAACATATGC 57.877 37.500 1.58 0.00 0.00 3.14
35 36 5.647225 TGTATGCTCTTGTCAAACATATGCA 59.353 36.000 1.58 0.00 33.71 3.96
36 37 5.847111 ATGCTCTTGTCAAACATATGCAT 57.153 34.783 3.79 3.79 34.82 3.96
37 38 5.648178 TGCTCTTGTCAAACATATGCATT 57.352 34.783 3.54 0.00 0.00 3.56
38 39 5.643664 TGCTCTTGTCAAACATATGCATTC 58.356 37.500 3.54 0.00 0.00 2.67
39 40 5.183522 TGCTCTTGTCAAACATATGCATTCA 59.816 36.000 3.54 0.00 0.00 2.57
40 41 5.514204 GCTCTTGTCAAACATATGCATTCAC 59.486 40.000 3.54 0.00 0.00 3.18
41 42 6.572167 TCTTGTCAAACATATGCATTCACA 57.428 33.333 3.54 0.00 0.00 3.58
42 43 6.979465 TCTTGTCAAACATATGCATTCACAA 58.021 32.000 3.54 6.85 0.00 3.33
43 44 6.862608 TCTTGTCAAACATATGCATTCACAAC 59.137 34.615 3.54 0.00 0.00 3.32
44 45 5.468592 TGTCAAACATATGCATTCACAACC 58.531 37.500 3.54 0.00 0.00 3.77
45 46 5.010415 TGTCAAACATATGCATTCACAACCA 59.990 36.000 3.54 0.00 0.00 3.67
46 47 5.925397 GTCAAACATATGCATTCACAACCAA 59.075 36.000 3.54 0.00 0.00 3.67
47 48 6.423302 GTCAAACATATGCATTCACAACCAAA 59.577 34.615 3.54 0.00 0.00 3.28
48 49 6.988580 TCAAACATATGCATTCACAACCAAAA 59.011 30.769 3.54 0.00 0.00 2.44
49 50 7.496920 TCAAACATATGCATTCACAACCAAAAA 59.503 29.630 3.54 0.00 0.00 1.94
67 68 3.824414 AAAACGCCGGATGTTCTTAAG 57.176 42.857 5.05 0.00 0.00 1.85
68 69 2.467566 AACGCCGGATGTTCTTAAGT 57.532 45.000 5.05 0.00 0.00 2.24
69 70 2.467566 ACGCCGGATGTTCTTAAGTT 57.532 45.000 5.05 0.00 0.00 2.66
70 71 3.598019 ACGCCGGATGTTCTTAAGTTA 57.402 42.857 5.05 0.00 0.00 2.24
71 72 4.133013 ACGCCGGATGTTCTTAAGTTAT 57.867 40.909 5.05 0.00 0.00 1.89
72 73 4.510571 ACGCCGGATGTTCTTAAGTTATT 58.489 39.130 5.05 0.00 0.00 1.40
73 74 4.939439 ACGCCGGATGTTCTTAAGTTATTT 59.061 37.500 5.05 0.00 0.00 1.40
74 75 6.108015 ACGCCGGATGTTCTTAAGTTATTTA 58.892 36.000 5.05 0.00 0.00 1.40
75 76 6.036408 ACGCCGGATGTTCTTAAGTTATTTAC 59.964 38.462 5.05 0.00 0.00 2.01
76 77 6.036300 CGCCGGATGTTCTTAAGTTATTTACA 59.964 38.462 5.05 0.12 0.00 2.41
77 78 7.184779 GCCGGATGTTCTTAAGTTATTTACAC 58.815 38.462 5.05 0.00 0.00 2.90
78 79 7.396419 CCGGATGTTCTTAAGTTATTTACACG 58.604 38.462 0.00 0.00 0.00 4.49
79 80 6.898189 CGGATGTTCTTAAGTTATTTACACGC 59.102 38.462 1.63 0.00 0.00 5.34
80 81 6.898189 GGATGTTCTTAAGTTATTTACACGCG 59.102 38.462 3.53 3.53 0.00 6.01
81 82 6.155691 TGTTCTTAAGTTATTTACACGCGG 57.844 37.500 12.47 1.27 0.00 6.46
82 83 4.845621 TCTTAAGTTATTTACACGCGGC 57.154 40.909 12.47 0.00 0.00 6.53
83 84 3.618150 TCTTAAGTTATTTACACGCGGCC 59.382 43.478 12.47 0.00 0.00 6.13
84 85 0.722848 AAGTTATTTACACGCGGCCG 59.277 50.000 24.05 24.05 41.14 6.13
85 86 0.108709 AGTTATTTACACGCGGCCGA 60.109 50.000 33.48 5.99 38.29 5.54
86 87 0.932399 GTTATTTACACGCGGCCGAT 59.068 50.000 33.48 14.00 38.29 4.18
87 88 1.071041 GTTATTTACACGCGGCCGATC 60.071 52.381 33.48 11.71 38.29 3.69
88 89 0.386476 TATTTACACGCGGCCGATCT 59.614 50.000 33.48 10.00 38.29 2.75
89 90 0.874607 ATTTACACGCGGCCGATCTC 60.875 55.000 33.48 10.38 38.29 2.75
90 91 2.215465 TTTACACGCGGCCGATCTCA 62.215 55.000 33.48 7.29 38.29 3.27
91 92 2.215465 TTACACGCGGCCGATCTCAA 62.215 55.000 33.48 13.72 38.29 3.02
92 93 2.215465 TACACGCGGCCGATCTCAAA 62.215 55.000 33.48 3.85 38.29 2.69
93 94 2.173669 CACGCGGCCGATCTCAAAT 61.174 57.895 33.48 0.03 38.29 2.32
94 95 2.173669 ACGCGGCCGATCTCAAATG 61.174 57.895 33.48 8.23 38.29 2.32
95 96 2.173669 CGCGGCCGATCTCAAATGT 61.174 57.895 33.48 0.00 36.29 2.71
96 97 1.705337 CGCGGCCGATCTCAAATGTT 61.705 55.000 33.48 0.00 36.29 2.71
97 98 0.248215 GCGGCCGATCTCAAATGTTG 60.248 55.000 33.48 0.00 0.00 3.33
98 99 1.086696 CGGCCGATCTCAAATGTTGT 58.913 50.000 24.07 0.00 0.00 3.32
99 100 1.062587 CGGCCGATCTCAAATGTTGTC 59.937 52.381 24.07 0.00 0.00 3.18
100 101 1.062587 GGCCGATCTCAAATGTTGTCG 59.937 52.381 0.00 0.00 0.00 4.35
102 103 1.665679 CCGATCTCAAATGTTGTCGGG 59.334 52.381 9.47 0.00 43.47 5.14
103 104 1.062587 CGATCTCAAATGTTGTCGGGC 59.937 52.381 0.00 0.00 0.00 6.13
104 105 2.359900 GATCTCAAATGTTGTCGGGCT 58.640 47.619 0.00 0.00 0.00 5.19
105 106 1.522668 TCTCAAATGTTGTCGGGCTG 58.477 50.000 0.00 0.00 0.00 4.85
106 107 0.523072 CTCAAATGTTGTCGGGCTGG 59.477 55.000 0.00 0.00 0.00 4.85
107 108 0.179004 TCAAATGTTGTCGGGCTGGT 60.179 50.000 0.00 0.00 0.00 4.00
108 109 0.673437 CAAATGTTGTCGGGCTGGTT 59.327 50.000 0.00 0.00 0.00 3.67
109 110 0.673437 AAATGTTGTCGGGCTGGTTG 59.327 50.000 0.00 0.00 0.00 3.77
110 111 0.467290 AATGTTGTCGGGCTGGTTGT 60.467 50.000 0.00 0.00 0.00 3.32
111 112 0.889186 ATGTTGTCGGGCTGGTTGTC 60.889 55.000 0.00 0.00 0.00 3.18
112 113 2.112297 TTGTCGGGCTGGTTGTCC 59.888 61.111 0.00 0.00 37.00 4.02
113 114 2.747443 TTGTCGGGCTGGTTGTCCA 61.747 57.895 0.00 0.00 41.50 4.02
114 115 2.063015 TTGTCGGGCTGGTTGTCCAT 62.063 55.000 0.00 0.00 43.43 3.41
115 116 2.040544 GTCGGGCTGGTTGTCCATG 61.041 63.158 0.00 0.00 43.43 3.66
116 117 2.220586 TCGGGCTGGTTGTCCATGA 61.221 57.895 0.00 0.00 43.43 3.07
117 118 1.303236 CGGGCTGGTTGTCCATGAA 60.303 57.895 0.00 0.00 43.43 2.57
118 119 0.893270 CGGGCTGGTTGTCCATGAAA 60.893 55.000 0.00 0.00 43.43 2.69
119 120 1.337118 GGGCTGGTTGTCCATGAAAA 58.663 50.000 0.00 0.00 43.43 2.29
120 121 1.691434 GGGCTGGTTGTCCATGAAAAA 59.309 47.619 0.00 0.00 43.43 1.94
139 140 5.833406 AAAAACTCAATTTTGCCTTTGGG 57.167 34.783 0.00 0.00 39.70 4.12
140 141 4.502105 AAACTCAATTTTGCCTTTGGGT 57.498 36.364 0.00 0.00 38.16 4.51
141 142 4.502105 AACTCAATTTTGCCTTTGGGTT 57.498 36.364 0.00 0.00 40.73 4.11
142 143 4.071961 ACTCAATTTTGCCTTTGGGTTC 57.928 40.909 0.00 0.00 32.70 3.62
143 144 3.454082 ACTCAATTTTGCCTTTGGGTTCA 59.546 39.130 0.00 0.00 32.70 3.18
144 145 4.060205 CTCAATTTTGCCTTTGGGTTCAG 58.940 43.478 0.00 0.00 34.45 3.02
145 146 2.549064 ATTTTGCCTTTGGGTTCAGC 57.451 45.000 0.00 0.00 34.45 4.26
146 147 1.198713 TTTTGCCTTTGGGTTCAGCA 58.801 45.000 0.00 0.00 34.45 4.41
147 148 0.752054 TTTGCCTTTGGGTTCAGCAG 59.248 50.000 0.00 0.00 34.45 4.24
148 149 0.396974 TTGCCTTTGGGTTCAGCAGT 60.397 50.000 0.00 0.00 34.45 4.40
149 150 0.823356 TGCCTTTGGGTTCAGCAGTC 60.823 55.000 0.00 0.00 34.45 3.51
150 151 1.527433 GCCTTTGGGTTCAGCAGTCC 61.527 60.000 0.00 0.00 34.45 3.85
151 152 0.111253 CCTTTGGGTTCAGCAGTCCT 59.889 55.000 0.00 0.00 0.00 3.85
152 153 1.351017 CCTTTGGGTTCAGCAGTCCTA 59.649 52.381 0.00 0.00 0.00 2.94
153 154 2.616510 CCTTTGGGTTCAGCAGTCCTAG 60.617 54.545 0.00 0.00 0.00 3.02
154 155 0.324943 TTGGGTTCAGCAGTCCTAGC 59.675 55.000 0.00 0.00 0.00 3.42
155 156 1.222113 GGGTTCAGCAGTCCTAGCC 59.778 63.158 0.00 0.00 0.00 3.93
156 157 1.553690 GGGTTCAGCAGTCCTAGCCA 61.554 60.000 0.00 0.00 0.00 4.75
157 158 0.324943 GGTTCAGCAGTCCTAGCCAA 59.675 55.000 0.00 0.00 0.00 4.52
158 159 1.271379 GGTTCAGCAGTCCTAGCCAAA 60.271 52.381 0.00 0.00 0.00 3.28
159 160 2.619074 GGTTCAGCAGTCCTAGCCAAAT 60.619 50.000 0.00 0.00 0.00 2.32
160 161 3.084786 GTTCAGCAGTCCTAGCCAAATT 58.915 45.455 0.00 0.00 0.00 1.82
161 162 2.991250 TCAGCAGTCCTAGCCAAATTC 58.009 47.619 0.00 0.00 0.00 2.17
162 163 2.573462 TCAGCAGTCCTAGCCAAATTCT 59.427 45.455 0.00 0.00 0.00 2.40
163 164 3.009473 TCAGCAGTCCTAGCCAAATTCTT 59.991 43.478 0.00 0.00 0.00 2.52
164 165 3.376546 CAGCAGTCCTAGCCAAATTCTTC 59.623 47.826 0.00 0.00 0.00 2.87
165 166 3.009473 AGCAGTCCTAGCCAAATTCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
166 167 3.127721 GCAGTCCTAGCCAAATTCTTCAC 59.872 47.826 0.00 0.00 0.00 3.18
167 168 3.691609 CAGTCCTAGCCAAATTCTTCACC 59.308 47.826 0.00 0.00 0.00 4.02
168 169 2.678336 GTCCTAGCCAAATTCTTCACCG 59.322 50.000 0.00 0.00 0.00 4.94
169 170 2.304761 TCCTAGCCAAATTCTTCACCGT 59.695 45.455 0.00 0.00 0.00 4.83
170 171 2.420022 CCTAGCCAAATTCTTCACCGTG 59.580 50.000 0.00 0.00 0.00 4.94
171 172 0.598065 AGCCAAATTCTTCACCGTGC 59.402 50.000 0.00 0.00 0.00 5.34
172 173 0.313672 GCCAAATTCTTCACCGTGCA 59.686 50.000 0.00 0.00 0.00 4.57
173 174 1.666888 GCCAAATTCTTCACCGTGCAG 60.667 52.381 0.00 0.00 0.00 4.41
174 175 1.608590 CCAAATTCTTCACCGTGCAGT 59.391 47.619 0.00 0.00 0.00 4.40
263 264 4.126437 GTCCCAAAAATCCACCACTTTTG 58.874 43.478 0.00 0.00 38.95 2.44
296 297 4.861210 TCGCAATAAAAACAAATGACCGT 58.139 34.783 0.00 0.00 0.00 4.83
841 842 1.000731 GGAATGATGGAGAGGAGAGCG 59.999 57.143 0.00 0.00 0.00 5.03
1015 1017 0.906066 TACAATGCAGGCGAACCCTA 59.094 50.000 0.00 0.00 44.09 3.53
1102 1104 3.539518 TGGCCCCATGCATGAAATATA 57.460 42.857 28.31 6.82 43.89 0.86
1498 1524 3.768757 CCCAAATTGAAGCATTGACCCTA 59.231 43.478 0.00 0.00 0.00 3.53
1540 1566 7.615403 ACTGTCTGTCTGTACATGATTTGTAT 58.385 34.615 0.00 0.00 42.63 2.29
2067 5150 2.637947 GAGAGGGATGGCTTCAAGAAC 58.362 52.381 2.60 0.00 0.00 3.01
2080 5163 1.203013 TCAAGAACGAGAGGGACTGGA 60.203 52.381 0.00 0.00 41.55 3.86
2110 5193 3.244735 GGAGAAGAAGAGGCTGGAGTTTT 60.245 47.826 0.00 0.00 0.00 2.43
2158 5241 2.350738 GGCAACAAGGGCAAGCTTA 58.649 52.632 0.00 0.00 0.00 3.09
2358 5441 7.680442 TGTATGTAATGACTAGCTGCAAAAA 57.320 32.000 1.02 0.00 0.00 1.94
2611 6519 7.271511 AGTTCTCAGCCATAATAGTTCTGAAG 58.728 38.462 0.00 0.00 33.93 3.02
2948 6856 3.181440 TGAACCTGAAGCTCTTGTGGAAT 60.181 43.478 0.00 0.00 0.00 3.01
2999 6907 2.185004 TCTTGGCCTTGTAGAAGCAC 57.815 50.000 3.32 0.00 0.00 4.40
3112 7020 1.589716 CCCTAGTTGTTGCAGCAGGC 61.590 60.000 2.72 1.26 45.13 4.85
3169 7077 4.986467 CCCCCAGCTTCATGGTAC 57.014 61.111 0.00 0.00 38.81 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.012664 TGACAAGAGCATACAACTCCCTAAA 59.987 40.000 0.00 0.00 34.56 1.85
2 3 4.530553 TGACAAGAGCATACAACTCCCTAA 59.469 41.667 0.00 0.00 34.56 2.69
3 4 4.093743 TGACAAGAGCATACAACTCCCTA 58.906 43.478 0.00 0.00 34.56 3.53
4 5 2.906389 TGACAAGAGCATACAACTCCCT 59.094 45.455 0.00 0.00 34.56 4.20
5 6 3.334583 TGACAAGAGCATACAACTCCC 57.665 47.619 0.00 0.00 34.56 4.30
6 7 4.515191 TGTTTGACAAGAGCATACAACTCC 59.485 41.667 0.00 0.00 34.56 3.85
7 8 5.673337 TGTTTGACAAGAGCATACAACTC 57.327 39.130 0.00 0.00 0.00 3.01
8 9 7.627088 GCATATGTTTGACAAGAGCATACAACT 60.627 37.037 4.29 0.00 32.48 3.16
9 10 6.470235 GCATATGTTTGACAAGAGCATACAAC 59.530 38.462 4.29 0.00 32.48 3.32
10 11 6.150809 TGCATATGTTTGACAAGAGCATACAA 59.849 34.615 4.29 0.00 32.48 2.41
11 12 5.647225 TGCATATGTTTGACAAGAGCATACA 59.353 36.000 4.29 0.00 30.78 2.29
12 13 6.122850 TGCATATGTTTGACAAGAGCATAC 57.877 37.500 4.29 0.00 30.78 2.39
13 14 6.947644 ATGCATATGTTTGACAAGAGCATA 57.052 33.333 0.00 9.85 39.28 3.14
14 15 5.847111 ATGCATATGTTTGACAAGAGCAT 57.153 34.783 0.00 9.91 37.62 3.79
15 16 5.183522 TGAATGCATATGTTTGACAAGAGCA 59.816 36.000 0.00 0.00 36.75 4.26
16 17 5.514204 GTGAATGCATATGTTTGACAAGAGC 59.486 40.000 0.00 0.00 0.00 4.09
17 18 6.614160 TGTGAATGCATATGTTTGACAAGAG 58.386 36.000 0.00 0.00 0.00 2.85
18 19 6.572167 TGTGAATGCATATGTTTGACAAGA 57.428 33.333 0.00 0.00 0.00 3.02
19 20 6.089820 GGTTGTGAATGCATATGTTTGACAAG 59.910 38.462 18.43 0.00 0.00 3.16
20 21 5.925397 GGTTGTGAATGCATATGTTTGACAA 59.075 36.000 15.85 15.85 0.00 3.18
21 22 5.010415 TGGTTGTGAATGCATATGTTTGACA 59.990 36.000 0.00 6.65 0.00 3.58
22 23 5.468592 TGGTTGTGAATGCATATGTTTGAC 58.531 37.500 0.00 4.20 0.00 3.18
23 24 5.718724 TGGTTGTGAATGCATATGTTTGA 57.281 34.783 0.00 0.00 0.00 2.69
24 25 6.782298 TTTGGTTGTGAATGCATATGTTTG 57.218 33.333 0.00 0.00 0.00 2.93
25 26 7.798596 TTTTTGGTTGTGAATGCATATGTTT 57.201 28.000 0.00 0.00 0.00 2.83
46 47 3.566742 ACTTAAGAACATCCGGCGTTTTT 59.433 39.130 10.09 14.07 0.00 1.94
47 48 3.143728 ACTTAAGAACATCCGGCGTTTT 58.856 40.909 10.09 2.68 0.00 2.43
48 49 2.774687 ACTTAAGAACATCCGGCGTTT 58.225 42.857 10.09 0.00 0.00 3.60
49 50 2.467566 ACTTAAGAACATCCGGCGTT 57.532 45.000 10.09 8.63 0.00 4.84
50 51 2.467566 AACTTAAGAACATCCGGCGT 57.532 45.000 10.09 0.00 0.00 5.68
51 52 5.479716 AAATAACTTAAGAACATCCGGCG 57.520 39.130 10.09 0.00 0.00 6.46
52 53 7.184779 GTGTAAATAACTTAAGAACATCCGGC 58.815 38.462 10.09 0.00 0.00 6.13
53 54 7.396419 CGTGTAAATAACTTAAGAACATCCGG 58.604 38.462 10.09 0.00 0.00 5.14
54 55 6.898189 GCGTGTAAATAACTTAAGAACATCCG 59.102 38.462 10.09 5.76 0.00 4.18
55 56 6.898189 CGCGTGTAAATAACTTAAGAACATCC 59.102 38.462 10.09 0.00 0.00 3.51
56 57 6.898189 CCGCGTGTAAATAACTTAAGAACATC 59.102 38.462 10.09 0.00 0.00 3.06
57 58 6.673796 GCCGCGTGTAAATAACTTAAGAACAT 60.674 38.462 10.09 0.00 0.00 2.71
58 59 5.389725 GCCGCGTGTAAATAACTTAAGAACA 60.390 40.000 10.09 1.08 0.00 3.18
59 60 5.017612 GCCGCGTGTAAATAACTTAAGAAC 58.982 41.667 10.09 0.00 0.00 3.01
60 61 4.093261 GGCCGCGTGTAAATAACTTAAGAA 59.907 41.667 10.09 0.00 0.00 2.52
61 62 3.618150 GGCCGCGTGTAAATAACTTAAGA 59.382 43.478 10.09 0.00 0.00 2.10
62 63 3.542680 CGGCCGCGTGTAAATAACTTAAG 60.543 47.826 14.67 0.00 0.00 1.85
63 64 2.348059 CGGCCGCGTGTAAATAACTTAA 59.652 45.455 14.67 0.00 0.00 1.85
64 65 1.925847 CGGCCGCGTGTAAATAACTTA 59.074 47.619 14.67 0.00 0.00 2.24
65 66 0.722848 CGGCCGCGTGTAAATAACTT 59.277 50.000 14.67 0.00 0.00 2.66
66 67 0.108709 TCGGCCGCGTGTAAATAACT 60.109 50.000 23.51 0.00 0.00 2.24
67 68 0.932399 ATCGGCCGCGTGTAAATAAC 59.068 50.000 23.51 0.00 0.00 1.89
68 69 1.202440 AGATCGGCCGCGTGTAAATAA 60.202 47.619 23.51 0.00 0.00 1.40
69 70 0.386476 AGATCGGCCGCGTGTAAATA 59.614 50.000 23.51 0.00 0.00 1.40
70 71 0.874607 GAGATCGGCCGCGTGTAAAT 60.875 55.000 23.51 6.61 0.00 1.40
71 72 1.517694 GAGATCGGCCGCGTGTAAA 60.518 57.895 23.51 0.16 0.00 2.01
72 73 2.103538 GAGATCGGCCGCGTGTAA 59.896 61.111 23.51 1.11 0.00 2.41
73 74 2.215465 TTTGAGATCGGCCGCGTGTA 62.215 55.000 23.51 2.08 0.00 2.90
74 75 2.852495 ATTTGAGATCGGCCGCGTGT 62.852 55.000 23.51 10.36 0.00 4.49
75 76 2.173669 ATTTGAGATCGGCCGCGTG 61.174 57.895 23.51 0.00 0.00 5.34
76 77 2.173669 CATTTGAGATCGGCCGCGT 61.174 57.895 23.51 12.10 0.00 6.01
77 78 1.705337 AACATTTGAGATCGGCCGCG 61.705 55.000 23.51 0.00 0.00 6.46
78 79 0.248215 CAACATTTGAGATCGGCCGC 60.248 55.000 23.51 7.63 0.00 6.53
79 80 1.062587 GACAACATTTGAGATCGGCCG 59.937 52.381 22.12 22.12 0.00 6.13
80 81 1.062587 CGACAACATTTGAGATCGGCC 59.937 52.381 0.00 0.00 0.00 6.13
81 82 1.062587 CCGACAACATTTGAGATCGGC 59.937 52.381 0.00 0.00 42.23 5.54
82 83 1.665679 CCCGACAACATTTGAGATCGG 59.334 52.381 3.53 3.53 46.77 4.18
83 84 1.062587 GCCCGACAACATTTGAGATCG 59.937 52.381 0.00 0.00 0.00 3.69
84 85 2.096496 CAGCCCGACAACATTTGAGATC 59.904 50.000 0.00 0.00 0.00 2.75
85 86 2.086869 CAGCCCGACAACATTTGAGAT 58.913 47.619 0.00 0.00 0.00 2.75
86 87 1.522668 CAGCCCGACAACATTTGAGA 58.477 50.000 0.00 0.00 0.00 3.27
87 88 0.523072 CCAGCCCGACAACATTTGAG 59.477 55.000 0.00 0.00 0.00 3.02
88 89 0.179004 ACCAGCCCGACAACATTTGA 60.179 50.000 0.00 0.00 0.00 2.69
89 90 0.673437 AACCAGCCCGACAACATTTG 59.327 50.000 0.00 0.00 0.00 2.32
90 91 0.673437 CAACCAGCCCGACAACATTT 59.327 50.000 0.00 0.00 0.00 2.32
91 92 0.467290 ACAACCAGCCCGACAACATT 60.467 50.000 0.00 0.00 0.00 2.71
92 93 0.889186 GACAACCAGCCCGACAACAT 60.889 55.000 0.00 0.00 0.00 2.71
93 94 1.525077 GACAACCAGCCCGACAACA 60.525 57.895 0.00 0.00 0.00 3.33
94 95 2.258726 GGACAACCAGCCCGACAAC 61.259 63.158 0.00 0.00 35.97 3.32
95 96 2.112297 GGACAACCAGCCCGACAA 59.888 61.111 0.00 0.00 35.97 3.18
96 97 3.164977 TGGACAACCAGCCCGACA 61.165 61.111 0.00 0.00 41.77 4.35
117 118 5.260424 ACCCAAAGGCAAAATTGAGTTTTT 58.740 33.333 0.00 0.00 34.68 1.94
118 119 4.854173 ACCCAAAGGCAAAATTGAGTTTT 58.146 34.783 0.00 0.00 37.24 2.43
119 120 4.502105 ACCCAAAGGCAAAATTGAGTTT 57.498 36.364 0.00 0.00 36.11 2.66
120 121 4.080638 TGAACCCAAAGGCAAAATTGAGTT 60.081 37.500 0.00 0.00 36.11 3.01
121 122 3.454082 TGAACCCAAAGGCAAAATTGAGT 59.546 39.130 0.00 0.00 36.11 3.41
122 123 4.060205 CTGAACCCAAAGGCAAAATTGAG 58.940 43.478 0.00 0.00 36.11 3.02
123 124 3.743899 GCTGAACCCAAAGGCAAAATTGA 60.744 43.478 0.00 0.00 36.11 2.57
124 125 2.549329 GCTGAACCCAAAGGCAAAATTG 59.451 45.455 0.00 0.00 36.11 2.32
125 126 2.172293 TGCTGAACCCAAAGGCAAAATT 59.828 40.909 0.00 0.00 36.11 1.82
126 127 1.767681 TGCTGAACCCAAAGGCAAAAT 59.232 42.857 0.00 0.00 36.11 1.82
127 128 1.138661 CTGCTGAACCCAAAGGCAAAA 59.861 47.619 0.00 0.00 36.11 2.44
128 129 0.752054 CTGCTGAACCCAAAGGCAAA 59.248 50.000 0.00 0.00 36.11 3.68
129 130 0.396974 ACTGCTGAACCCAAAGGCAA 60.397 50.000 0.00 0.00 36.11 4.52
130 131 0.823356 GACTGCTGAACCCAAAGGCA 60.823 55.000 0.00 0.00 36.11 4.75
131 132 1.527433 GGACTGCTGAACCCAAAGGC 61.527 60.000 0.00 0.00 36.11 4.35
132 133 0.111253 AGGACTGCTGAACCCAAAGG 59.889 55.000 0.00 0.00 40.04 3.11
133 134 2.704572 CTAGGACTGCTGAACCCAAAG 58.295 52.381 0.00 0.00 0.00 2.77
134 135 1.271379 GCTAGGACTGCTGAACCCAAA 60.271 52.381 0.00 0.00 0.00 3.28
135 136 0.324943 GCTAGGACTGCTGAACCCAA 59.675 55.000 0.00 0.00 0.00 4.12
136 137 1.553690 GGCTAGGACTGCTGAACCCA 61.554 60.000 0.00 0.00 0.00 4.51
137 138 1.222113 GGCTAGGACTGCTGAACCC 59.778 63.158 0.00 0.00 0.00 4.11
138 139 0.324943 TTGGCTAGGACTGCTGAACC 59.675 55.000 0.00 0.64 0.00 3.62
139 140 2.185004 TTTGGCTAGGACTGCTGAAC 57.815 50.000 0.00 0.00 0.00 3.18
140 141 3.009473 AGAATTTGGCTAGGACTGCTGAA 59.991 43.478 0.00 0.00 0.00 3.02
141 142 2.573462 AGAATTTGGCTAGGACTGCTGA 59.427 45.455 0.00 0.00 0.00 4.26
142 143 2.996631 AGAATTTGGCTAGGACTGCTG 58.003 47.619 0.00 0.00 0.00 4.41
143 144 3.009473 TGAAGAATTTGGCTAGGACTGCT 59.991 43.478 0.00 0.00 0.00 4.24
144 145 3.127721 GTGAAGAATTTGGCTAGGACTGC 59.872 47.826 0.00 0.00 0.00 4.40
145 146 3.691609 GGTGAAGAATTTGGCTAGGACTG 59.308 47.826 0.00 0.00 0.00 3.51
146 147 3.619979 CGGTGAAGAATTTGGCTAGGACT 60.620 47.826 0.00 0.00 0.00 3.85
147 148 2.678336 CGGTGAAGAATTTGGCTAGGAC 59.322 50.000 0.00 0.00 0.00 3.85
148 149 2.304761 ACGGTGAAGAATTTGGCTAGGA 59.695 45.455 0.00 0.00 0.00 2.94
149 150 2.420022 CACGGTGAAGAATTTGGCTAGG 59.580 50.000 0.74 0.00 0.00 3.02
150 151 2.159517 GCACGGTGAAGAATTTGGCTAG 60.160 50.000 13.29 0.00 0.00 3.42
151 152 1.810151 GCACGGTGAAGAATTTGGCTA 59.190 47.619 13.29 0.00 0.00 3.93
152 153 0.598065 GCACGGTGAAGAATTTGGCT 59.402 50.000 13.29 0.00 0.00 4.75
153 154 0.313672 TGCACGGTGAAGAATTTGGC 59.686 50.000 13.29 0.00 0.00 4.52
154 155 1.608590 ACTGCACGGTGAAGAATTTGG 59.391 47.619 22.86 0.00 0.00 3.28
155 156 2.290367 TCACTGCACGGTGAAGAATTTG 59.710 45.455 22.86 10.29 42.35 2.32
156 157 2.549754 CTCACTGCACGGTGAAGAATTT 59.450 45.455 22.86 0.00 44.24 1.82
157 158 2.146342 CTCACTGCACGGTGAAGAATT 58.854 47.619 22.86 0.00 44.24 2.17
158 159 1.070758 ACTCACTGCACGGTGAAGAAT 59.929 47.619 22.86 0.00 44.24 2.40
159 160 0.464036 ACTCACTGCACGGTGAAGAA 59.536 50.000 22.86 9.14 44.24 2.52
160 161 0.249447 CACTCACTGCACGGTGAAGA 60.249 55.000 22.86 7.48 44.24 2.87
161 162 0.249447 TCACTCACTGCACGGTGAAG 60.249 55.000 14.72 14.72 44.24 3.02
162 163 0.176910 TTCACTCACTGCACGGTGAA 59.823 50.000 13.29 11.10 44.24 3.18
163 164 0.392706 ATTCACTCACTGCACGGTGA 59.607 50.000 13.29 11.63 42.96 4.02
164 165 1.069703 CAATTCACTCACTGCACGGTG 60.070 52.381 3.15 3.15 38.44 4.94
165 166 1.229428 CAATTCACTCACTGCACGGT 58.771 50.000 0.00 0.00 0.00 4.83
166 167 0.110056 GCAATTCACTCACTGCACGG 60.110 55.000 0.00 0.00 34.87 4.94
167 168 0.587768 TGCAATTCACTCACTGCACG 59.412 50.000 0.00 0.00 39.77 5.34
168 169 2.780065 TTGCAATTCACTCACTGCAC 57.220 45.000 0.00 0.00 44.08 4.57
169 170 3.797451 TTTTGCAATTCACTCACTGCA 57.203 38.095 0.00 0.00 42.79 4.41
296 297 0.818445 TCGGGTTAACTGCGGCAAAA 60.818 50.000 3.44 0.00 0.00 2.44
411 412 4.473520 CGGCGAGTGGAGGGCAAT 62.474 66.667 0.00 0.00 0.00 3.56
841 842 3.844090 GACCAGCTCCTCCTCGCC 61.844 72.222 0.00 0.00 0.00 5.54
1015 1017 2.511218 AGGATGCATCTATGGTGGTGTT 59.489 45.455 25.28 0.00 0.00 3.32
1102 1104 4.590222 AGTGTCCTTTCCTTCAAATGCAAT 59.410 37.500 0.00 0.00 0.00 3.56
1498 1524 9.155975 GACAGACAGTACAAATATCAGAACAAT 57.844 33.333 0.00 0.00 0.00 2.71
1561 1621 5.183904 GCTTCAAACTTTCAGATACCACCAT 59.816 40.000 0.00 0.00 0.00 3.55
2067 5150 3.081061 CTCTATCATCCAGTCCCTCTCG 58.919 54.545 0.00 0.00 0.00 4.04
2080 5163 4.834496 CAGCCTCTTCTTCTCCTCTATCAT 59.166 45.833 0.00 0.00 0.00 2.45
2110 5193 4.016444 GCTTTCATAAGATCACCCACCAA 58.984 43.478 0.00 0.00 32.92 3.67
2150 5233 5.869753 TGACTTGATCTTCTTAAGCTTGC 57.130 39.130 9.86 0.00 0.00 4.01
2358 5441 9.803507 GCTAACAACCTTAAATAATAGGGGTAT 57.196 33.333 0.00 0.00 35.79 2.73
2558 6427 9.313118 GTATGGTTCAGAACTTGTTTGATTTTT 57.687 29.630 13.13 0.00 0.00 1.94
2660 6568 9.120538 TCAGTATTTAGCTTGAGAACTTGTTTT 57.879 29.630 0.00 0.00 0.00 2.43
2852 6760 3.679389 CAACTACAACAGAGGGAGCAAT 58.321 45.455 0.00 0.00 0.00 3.56
2923 6831 3.470709 CACAAGAGCTTCAGGTTCAAGA 58.529 45.455 0.00 0.00 0.00 3.02
2999 6907 1.639635 ATTAGTCCTGCCCAGCCTGG 61.640 60.000 2.91 2.91 37.25 4.45


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

AutoCloner maintained by Alex Coulton.