Multiple sequence alignment - TraesCS2B01G180100

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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 TraesCS2B01G180100 chr2B 100.000 2228 0 0 1 2228 154595806 154593579 0.000000e+00 4115.0
1 TraesCS2B01G180100 chr2B 93.007 429 17 2 1 417 154499847 154500274 4.070000e-172 614.0
2 TraesCS2B01G180100 chr2B 88.655 238 21 6 186 420 154490558 154490792 3.620000e-73 285.0
3 TraesCS2B01G180100 chr2B 88.235 238 24 4 184 419 154718661 154718426 4.680000e-72 281.0
4 TraesCS2B01G180100 chr2B 100.000 35 0 0 1 35 154527091 154527125 5.140000e-07 65.8
5 TraesCS2B01G180100 chr2B 88.462 52 4 2 3 52 154588790 154588841 6.640000e-06 62.1
6 TraesCS2B01G180100 chr2D 93.923 1629 76 8 602 2227 103129770 103128162 0.000000e+00 2438.0
7 TraesCS2B01G180100 chr2D 85.000 440 48 12 150 583 103130184 103129757 4.400000e-117 431.0
8 TraesCS2B01G180100 chr2D 87.160 257 24 6 169 420 106265627 106265375 1.300000e-72 283.0
9 TraesCS2B01G180100 chr2D 88.186 237 21 5 185 418 103147787 103147555 2.180000e-70 276.0
10 TraesCS2B01G180100 chr2D 86.765 68 9 0 1989 2056 11376293 11376226 2.370000e-10 76.8
11 TraesCS2B01G180100 chr2D 88.333 60 5 2 1 58 103124054 103124113 1.100000e-08 71.3
12 TraesCS2B01G180100 chr2D 97.059 34 1 0 1 34 103065555 103065588 8.590000e-05 58.4
13 TraesCS2B01G180100 chr2A 93.215 1577 94 10 639 2205 102133028 102131455 0.000000e+00 2307.0
14 TraesCS2B01G180100 chr2A 87.549 257 23 6 169 420 102679396 102679144 2.800000e-74 289.0
15 TraesCS2B01G180100 chr2A 84.564 298 34 8 170 464 102133405 102133117 3.620000e-73 285.0
16 TraesCS2B01G180100 chr2A 81.437 334 43 17 169 492 102043423 102043747 2.840000e-64 255.0
17 TraesCS2B01G180100 chr2A 100.000 33 0 0 1 33 102052084 102052116 6.640000e-06 62.1
18 TraesCS2B01G180100 chr2A 100.000 29 0 0 1 29 102100887 102100915 1.000000e-03 54.7
19 TraesCS2B01G180100 chr5A 88.186 237 24 4 186 420 10860503 10860737 1.680000e-71 279.0
20 TraesCS2B01G180100 chr4B 82.692 156 27 0 1989 2144 338361602 338361447 2.980000e-29 139.0
21 TraesCS2B01G180100 chr7B 81.410 156 29 0 1989 2144 610506769 610506924 6.460000e-26 128.0
22 TraesCS2B01G180100 chr3B 81.410 156 29 0 1989 2144 438117469 438117314 6.460000e-26 128.0
23 TraesCS2B01G180100 chr6A 94.595 37 2 0 2087 2123 234625489 234625453 8.590000e-05 58.4
24 TraesCS2B01G180100 chr1A 97.059 34 1 0 2087 2120 194526808 194526775 8.590000e-05 58.4


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 TraesCS2B01G180100 chr2B 154593579 154595806 2227 True 4115.0 4115 100.0000 1 2228 1 chr2B.!!$R1 2227
1 TraesCS2B01G180100 chr2D 103128162 103130184 2022 True 1434.5 2438 89.4615 150 2227 2 chr2D.!!$R4 2077
2 TraesCS2B01G180100 chr2A 102131455 102133405 1950 True 1296.0 2307 88.8895 170 2205 2 chr2A.!!$R2 2035

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
143 144 0.034896 GACCGCCACTTCTCCTTGAA 59.965 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1365 0.107703 TGGATTCATCGAAAGGCGCT 60.108 50.0 7.64 0.0 40.61 5.92 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
30 31 2.517321 GCGTTTCAGCTGATCTTGTC 57.483 50.000 19.04 1.45 0.00 3.18
31 32 1.201855 GCGTTTCAGCTGATCTTGTCG 60.202 52.381 19.04 15.66 0.00 4.35
32 33 2.328473 CGTTTCAGCTGATCTTGTCGA 58.672 47.619 19.04 0.00 0.00 4.20
33 34 2.926200 CGTTTCAGCTGATCTTGTCGAT 59.074 45.455 19.04 0.00 34.25 3.59
34 35 4.105486 CGTTTCAGCTGATCTTGTCGATA 58.895 43.478 19.04 0.00 30.84 2.92
35 36 4.742167 CGTTTCAGCTGATCTTGTCGATAT 59.258 41.667 19.04 0.00 30.84 1.63
36 37 5.915196 CGTTTCAGCTGATCTTGTCGATATA 59.085 40.000 19.04 0.00 30.84 0.86
37 38 6.417930 CGTTTCAGCTGATCTTGTCGATATAA 59.582 38.462 19.04 0.46 30.84 0.98
38 39 7.043391 CGTTTCAGCTGATCTTGTCGATATAAA 60.043 37.037 19.04 0.00 30.84 1.40
39 40 8.768955 GTTTCAGCTGATCTTGTCGATATAAAT 58.231 33.333 19.04 0.00 30.84 1.40
40 41 8.526218 TTCAGCTGATCTTGTCGATATAAATC 57.474 34.615 19.04 0.00 30.84 2.17
41 42 7.093354 TCAGCTGATCTTGTCGATATAAATCC 58.907 38.462 13.74 0.00 30.84 3.01
42 43 6.034363 CAGCTGATCTTGTCGATATAAATCCG 59.966 42.308 8.42 0.00 30.84 4.18
43 44 5.220303 GCTGATCTTGTCGATATAAATCCGC 60.220 44.000 0.00 0.00 30.84 5.54
44 45 5.168569 TGATCTTGTCGATATAAATCCGCC 58.831 41.667 0.00 0.00 30.84 6.13
45 46 4.866508 TCTTGTCGATATAAATCCGCCT 57.133 40.909 0.00 0.00 0.00 5.52
46 47 5.209818 TCTTGTCGATATAAATCCGCCTT 57.790 39.130 0.00 0.00 0.00 4.35
47 48 5.227908 TCTTGTCGATATAAATCCGCCTTC 58.772 41.667 0.00 0.00 0.00 3.46
48 49 4.594123 TGTCGATATAAATCCGCCTTCA 57.406 40.909 0.00 0.00 0.00 3.02
49 50 4.951254 TGTCGATATAAATCCGCCTTCAA 58.049 39.130 0.00 0.00 0.00 2.69
50 51 5.361427 TGTCGATATAAATCCGCCTTCAAA 58.639 37.500 0.00 0.00 0.00 2.69
51 52 5.818336 TGTCGATATAAATCCGCCTTCAAAA 59.182 36.000 0.00 0.00 0.00 2.44
52 53 6.316640 TGTCGATATAAATCCGCCTTCAAAAA 59.683 34.615 0.00 0.00 0.00 1.94
71 72 2.134201 AAAAAGTACGGCTGCTTTGC 57.866 45.000 0.00 0.00 35.40 3.68
72 73 1.318576 AAAAGTACGGCTGCTTTGCT 58.681 45.000 0.00 0.00 35.40 3.91
73 74 1.318576 AAAGTACGGCTGCTTTGCTT 58.681 45.000 0.00 0.00 34.11 3.91
74 75 0.593128 AAGTACGGCTGCTTTGCTTG 59.407 50.000 0.00 0.00 0.00 4.01
75 76 1.210155 GTACGGCTGCTTTGCTTGG 59.790 57.895 0.00 0.00 0.00 3.61
76 77 1.971167 TACGGCTGCTTTGCTTGGG 60.971 57.895 0.00 0.00 0.00 4.12
77 78 4.729856 CGGCTGCTTTGCTTGGGC 62.730 66.667 0.00 0.00 39.26 5.36
78 79 4.383861 GGCTGCTTTGCTTGGGCC 62.384 66.667 0.00 0.00 37.74 5.80
79 80 3.618750 GCTGCTTTGCTTGGGCCA 61.619 61.111 0.00 0.00 37.74 5.36
80 81 2.951101 GCTGCTTTGCTTGGGCCAT 61.951 57.895 7.26 0.00 37.74 4.40
81 82 1.675219 CTGCTTTGCTTGGGCCATT 59.325 52.632 7.26 0.00 37.74 3.16
82 83 0.672401 CTGCTTTGCTTGGGCCATTG 60.672 55.000 7.26 4.66 37.74 2.82
83 84 1.376295 GCTTTGCTTGGGCCATTGG 60.376 57.895 7.26 1.75 37.74 3.16
93 94 3.058160 GCCATTGGCGTCACTGCT 61.058 61.111 12.82 0.00 39.62 4.24
94 95 2.872557 CCATTGGCGTCACTGCTG 59.127 61.111 1.18 0.00 34.52 4.41
95 96 1.968017 CCATTGGCGTCACTGCTGT 60.968 57.895 1.18 0.00 34.52 4.40
96 97 1.208358 CATTGGCGTCACTGCTGTG 59.792 57.895 16.95 16.95 45.07 3.66
97 98 1.968017 ATTGGCGTCACTGCTGTGG 60.968 57.895 21.80 9.36 43.94 4.17
101 102 4.624364 CGTCACTGCTGTGGCCCA 62.624 66.667 20.82 0.93 45.29 5.36
102 103 2.034687 GTCACTGCTGTGGCCCAT 59.965 61.111 21.80 0.00 42.54 4.00
103 104 2.034532 TCACTGCTGTGGCCCATG 59.965 61.111 21.80 0.00 43.94 3.66
104 105 3.066190 CACTGCTGTGGCCCATGG 61.066 66.667 15.43 4.14 40.33 3.66
105 106 4.371417 ACTGCTGTGGCCCATGGG 62.371 66.667 27.87 27.87 37.74 4.00
115 116 4.783418 CCCATGGGCCTTTTGCTA 57.217 55.556 20.41 0.00 40.92 3.49
116 117 2.201927 CCCATGGGCCTTTTGCTAC 58.798 57.895 20.41 0.00 40.92 3.58
117 118 0.324645 CCCATGGGCCTTTTGCTACT 60.325 55.000 20.41 0.00 40.92 2.57
118 119 0.819582 CCATGGGCCTTTTGCTACTG 59.180 55.000 2.85 0.00 40.92 2.74
119 120 0.174162 CATGGGCCTTTTGCTACTGC 59.826 55.000 4.53 0.00 40.92 4.40
120 121 1.315257 ATGGGCCTTTTGCTACTGCG 61.315 55.000 4.53 0.00 43.34 5.18
121 122 2.700773 GGGCCTTTTGCTACTGCGG 61.701 63.158 0.84 0.00 43.34 5.69
122 123 1.971695 GGCCTTTTGCTACTGCGGT 60.972 57.895 2.42 2.42 43.34 5.68
123 124 1.210155 GCCTTTTGCTACTGCGGTG 59.790 57.895 8.92 0.00 43.34 4.94
124 125 1.875963 CCTTTTGCTACTGCGGTGG 59.124 57.895 8.92 6.54 43.34 4.61
125 126 0.605319 CCTTTTGCTACTGCGGTGGA 60.605 55.000 14.03 0.00 43.34 4.02
126 127 0.517316 CTTTTGCTACTGCGGTGGAC 59.483 55.000 14.03 4.93 43.34 4.02
127 128 0.887387 TTTTGCTACTGCGGTGGACC 60.887 55.000 14.03 0.00 43.34 4.46
139 140 2.203788 TGGACCGCCACTTCTCCT 60.204 61.111 0.00 0.00 39.92 3.69
140 141 1.841556 TGGACCGCCACTTCTCCTT 60.842 57.895 0.00 0.00 39.92 3.36
141 142 1.376037 GGACCGCCACTTCTCCTTG 60.376 63.158 0.00 0.00 0.00 3.61
142 143 1.671742 GACCGCCACTTCTCCTTGA 59.328 57.895 0.00 0.00 0.00 3.02
143 144 0.034896 GACCGCCACTTCTCCTTGAA 59.965 55.000 0.00 0.00 0.00 2.69
144 145 0.472471 ACCGCCACTTCTCCTTGAAA 59.528 50.000 0.00 0.00 33.79 2.69
145 146 1.160137 CCGCCACTTCTCCTTGAAAG 58.840 55.000 0.00 0.00 33.79 2.62
157 158 0.606401 CTTGAAAGGAGGCAGCGGAA 60.606 55.000 0.00 0.00 0.00 4.30
205 206 0.395311 TCGATTAGTCCCACCTCGCT 60.395 55.000 0.00 0.00 0.00 4.93
215 219 1.258445 CCACCTCGCTTGGGTAGAGT 61.258 60.000 0.00 0.00 35.00 3.24
219 223 1.178276 CTCGCTTGGGTAGAGTGAGT 58.822 55.000 6.54 0.00 43.42 3.41
221 225 0.888619 CGCTTGGGTAGAGTGAGTGA 59.111 55.000 0.00 0.00 0.00 3.41
223 227 1.404851 GCTTGGGTAGAGTGAGTGAGC 60.405 57.143 0.00 0.00 0.00 4.26
293 297 3.720193 GCTGCGTGGTGAGCACAG 61.720 66.667 15.55 6.73 40.01 3.66
408 413 1.380380 GAAGGCCCCACCAATCCTG 60.380 63.158 0.00 0.00 43.14 3.86
411 416 1.380380 GGCCCCACCAATCCTGAAG 60.380 63.158 0.00 0.00 38.86 3.02
420 425 6.398095 CCCACCAATCCTGAAGTTAAAATTC 58.602 40.000 0.00 0.00 0.00 2.17
421 426 6.211384 CCCACCAATCCTGAAGTTAAAATTCT 59.789 38.462 3.98 0.00 0.00 2.40
423 428 8.150296 CCACCAATCCTGAAGTTAAAATTCTTT 58.850 33.333 3.98 0.00 0.00 2.52
424 429 9.546428 CACCAATCCTGAAGTTAAAATTCTTTT 57.454 29.630 3.98 0.00 36.67 2.27
460 465 7.174080 TGTGGACAAAATACGATGATCTTGAAA 59.826 33.333 0.00 0.00 0.00 2.69
465 470 7.538678 ACAAAATACGATGATCTTGAAAGTTGC 59.461 33.333 0.00 0.00 0.00 4.17
493 512 2.968574 TGTTTGAAGGCCCTGCAAATTA 59.031 40.909 19.90 9.73 40.59 1.40
494 513 3.006752 TGTTTGAAGGCCCTGCAAATTAG 59.993 43.478 19.90 0.00 40.59 1.73
506 525 6.348458 GCCCTGCAAATTAGGAATTTCAAAAC 60.348 38.462 0.00 0.00 38.97 2.43
510 529 7.638134 TGCAAATTAGGAATTTCAAAACTTGC 58.362 30.769 16.02 16.02 38.97 4.01
558 577 2.366916 AGGGTGTTGTCTCTGTGAGAAG 59.633 50.000 0.00 0.00 40.59 2.85
566 585 0.108424 CTCTGTGAGAAGAAGGCCCG 60.108 60.000 0.00 0.00 0.00 6.13
573 592 0.678048 AGAAGAAGGCCCGCACAATC 60.678 55.000 0.00 0.00 0.00 2.67
574 593 1.657751 GAAGAAGGCCCGCACAATCC 61.658 60.000 0.00 0.00 0.00 3.01
575 594 2.044946 GAAGGCCCGCACAATCCT 60.045 61.111 0.00 0.00 0.00 3.24
576 595 1.678970 GAAGGCCCGCACAATCCTT 60.679 57.895 0.00 0.00 41.27 3.36
577 596 1.228862 AAGGCCCGCACAATCCTTT 60.229 52.632 0.00 0.00 35.54 3.11
578 597 0.831711 AAGGCCCGCACAATCCTTTT 60.832 50.000 0.00 0.00 35.54 2.27
579 598 0.831711 AGGCCCGCACAATCCTTTTT 60.832 50.000 0.00 0.00 0.00 1.94
598 617 3.041874 TTTTTGCGCATAATGCCCG 57.958 47.368 12.75 0.00 41.12 6.13
599 618 0.244994 TTTTTGCGCATAATGCCCGT 59.755 45.000 12.75 0.00 41.12 5.28
600 619 0.179150 TTTTGCGCATAATGCCCGTC 60.179 50.000 12.75 0.00 41.12 4.79
601 620 1.999071 TTTGCGCATAATGCCCGTCC 61.999 55.000 12.75 0.00 41.12 4.79
602 621 2.899838 GCGCATAATGCCCGTCCA 60.900 61.111 0.30 0.00 41.12 4.02
603 622 2.477176 GCGCATAATGCCCGTCCAA 61.477 57.895 0.30 0.00 41.12 3.53
604 623 1.795170 GCGCATAATGCCCGTCCAAT 61.795 55.000 0.30 0.00 41.12 3.16
605 624 0.238289 CGCATAATGCCCGTCCAATC 59.762 55.000 0.00 0.00 41.12 2.67
614 633 4.237976 TGCCCGTCCAATCCTTAATTTA 57.762 40.909 0.00 0.00 0.00 1.40
719 738 6.418101 TCTAAAGTTCCATTCCTTCTGATGG 58.582 40.000 3.27 3.27 35.58 3.51
733 752 5.163478 CCTTCTGATGGGAATGCCTTAAAAG 60.163 44.000 1.73 0.00 0.00 2.27
734 753 4.934356 TCTGATGGGAATGCCTTAAAAGT 58.066 39.130 0.00 0.00 0.00 2.66
735 754 5.332743 TCTGATGGGAATGCCTTAAAAGTT 58.667 37.500 0.00 0.00 0.00 2.66
736 755 6.489603 TCTGATGGGAATGCCTTAAAAGTTA 58.510 36.000 0.00 0.00 0.00 2.24
737 756 6.951198 TCTGATGGGAATGCCTTAAAAGTTAA 59.049 34.615 0.00 0.00 0.00 2.01
738 757 7.453126 TCTGATGGGAATGCCTTAAAAGTTAAA 59.547 33.333 0.00 0.00 0.00 1.52
739 758 7.967908 TGATGGGAATGCCTTAAAAGTTAAAA 58.032 30.769 0.00 0.00 0.00 1.52
745 764 7.598869 GGAATGCCTTAAAAGTTAAAACTCCAG 59.401 37.037 0.00 0.00 38.57 3.86
752 780 8.810990 TTAAAAGTTAAAACTCCAGGTTCTGA 57.189 30.769 0.00 0.00 38.57 3.27
754 782 7.898014 AAAGTTAAAACTCCAGGTTCTGAAT 57.102 32.000 0.00 0.00 38.57 2.57
853 881 7.173390 TGTGTCCAATTTGAACATCACGTATAA 59.827 33.333 0.00 0.00 0.00 0.98
883 913 5.105716 TCACTACAAGATCTACACAAGGAGC 60.106 44.000 0.00 0.00 0.00 4.70
956 988 6.148315 CACAACTGATGAACAAGAATAGCTCA 59.852 38.462 0.00 0.00 0.00 4.26
991 1023 2.408271 TCAGTAATCCTTGCTGCAGG 57.592 50.000 17.12 4.57 42.25 4.85
1234 1266 2.437281 CCCCAGCTGATATGAGTTGACT 59.563 50.000 17.39 0.00 0.00 3.41
1262 1294 0.462759 GATCTTCTCCCTTGGCACCG 60.463 60.000 0.00 0.00 0.00 4.94
1263 1295 0.909610 ATCTTCTCCCTTGGCACCGA 60.910 55.000 0.00 0.00 0.00 4.69
1264 1296 0.909610 TCTTCTCCCTTGGCACCGAT 60.910 55.000 0.00 0.00 0.00 4.18
1290 1322 5.444663 TGATCATCGTCACTATCTTCCTG 57.555 43.478 0.00 0.00 0.00 3.86
1310 1342 4.399219 CTGATGATCTTCAGGCATGGAAT 58.601 43.478 24.31 0.00 39.58 3.01
1360 1392 2.787473 TCGATGAATCCAGCCTTGTT 57.213 45.000 0.00 0.00 0.00 2.83
1423 1455 5.630121 AGTTGGATGACATTTTCAGGTGTA 58.370 37.500 0.00 0.00 37.77 2.90
1425 1457 4.009675 TGGATGACATTTTCAGGTGTAGC 58.990 43.478 0.00 0.00 37.77 3.58
1445 1477 1.459348 TCAGTGACCTGAGGTGCCA 60.459 57.895 9.89 0.00 42.80 4.92
1528 1560 1.805871 CGCTCAGAAGGGATGCTTCTC 60.806 57.143 0.00 0.00 38.93 2.87
1572 1604 2.768527 CCTCTTCAGTTGGGCTCATCTA 59.231 50.000 0.00 0.00 0.00 1.98
1579 1611 3.624861 CAGTTGGGCTCATCTACAATCAC 59.375 47.826 0.00 0.00 0.00 3.06
1587 1619 5.858581 GGCTCATCTACAATCACACAAAAAC 59.141 40.000 0.00 0.00 0.00 2.43
1614 1648 9.504708 AACAATTGAGAATGCAAATTGGATAAA 57.495 25.926 19.68 0.00 0.00 1.40
1615 1649 8.938906 ACAATTGAGAATGCAAATTGGATAAAC 58.061 29.630 19.68 0.00 0.00 2.01
1616 1650 8.392612 CAATTGAGAATGCAAATTGGATAAACC 58.607 33.333 11.38 0.00 39.54 3.27
1625 1659 7.546358 TGCAAATTGGATAAACCTATTGTCAG 58.454 34.615 0.00 0.00 41.69 3.51
1660 1695 7.012799 GGAACTTTCTCATTCTATCCCAATCAC 59.987 40.741 0.00 0.00 0.00 3.06
1668 1703 0.834612 TATCCCAATCACCGGTCACC 59.165 55.000 2.59 0.00 0.00 4.02
1804 1839 2.909006 AGCCTTCAGAACTCCATCTTCA 59.091 45.455 0.00 0.00 0.00 3.02
1904 1939 6.006759 GCAGAAAGCAGAGTTTTAGACAAT 57.993 37.500 0.00 0.00 44.79 2.71
1921 1956 9.904198 TTTAGACAATGTTAGATGATGATCCAA 57.096 29.630 0.00 0.00 0.00 3.53
2124 2159 5.061853 CCATCCTCAATCACAACCTCATAG 58.938 45.833 0.00 0.00 0.00 2.23
2146 2181 1.481772 CCTCTCTCTCTTTCTGCAGGG 59.518 57.143 15.13 4.92 0.00 4.45
2153 2188 1.876156 CTCTTTCTGCAGGGACAACAC 59.124 52.381 15.13 0.00 0.00 3.32
2155 2190 2.158623 TCTTTCTGCAGGGACAACACAT 60.159 45.455 15.13 0.00 0.00 3.21
2158 2193 4.835284 TTCTGCAGGGACAACACATATA 57.165 40.909 15.13 0.00 0.00 0.86
2196 2231 4.020662 AGTCTTTCTGAACTCTCATGGACC 60.021 45.833 0.00 0.00 0.00 4.46
2215 2250 3.312890 ACCTGCATTCTACTCCAGCTAT 58.687 45.455 0.00 0.00 0.00 2.97
2216 2251 3.323403 ACCTGCATTCTACTCCAGCTATC 59.677 47.826 0.00 0.00 0.00 2.08
2227 2262 3.261897 ACTCCAGCTATCCATTTATCCCG 59.738 47.826 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.664107 AGCTGAAACGCTGACTAATCAA 58.336 40.909 0.00 0.00 39.16 2.57
1 2 3.319137 AGCTGAAACGCTGACTAATCA 57.681 42.857 0.00 0.00 39.16 2.57
10 11 2.072298 GACAAGATCAGCTGAAACGCT 58.928 47.619 22.50 12.74 41.90 5.07
11 12 1.201855 CGACAAGATCAGCTGAAACGC 60.202 52.381 22.50 10.59 0.00 4.84
12 13 2.328473 TCGACAAGATCAGCTGAAACG 58.672 47.619 22.50 18.07 0.00 3.60
13 14 7.700322 TTATATCGACAAGATCAGCTGAAAC 57.300 36.000 22.50 17.39 40.66 2.78
14 15 8.893219 ATTTATATCGACAAGATCAGCTGAAA 57.107 30.769 22.50 5.30 40.66 2.69
15 16 7.600375 GGATTTATATCGACAAGATCAGCTGAA 59.400 37.037 22.50 4.23 40.66 3.02
16 17 7.093354 GGATTTATATCGACAAGATCAGCTGA 58.907 38.462 20.79 20.79 40.66 4.26
17 18 6.034363 CGGATTTATATCGACAAGATCAGCTG 59.966 42.308 7.63 7.63 40.66 4.24
18 19 6.096036 CGGATTTATATCGACAAGATCAGCT 58.904 40.000 0.00 0.00 40.66 4.24
19 20 5.220303 GCGGATTTATATCGACAAGATCAGC 60.220 44.000 0.00 0.00 40.66 4.26
20 21 5.289675 GGCGGATTTATATCGACAAGATCAG 59.710 44.000 0.00 0.00 40.66 2.90
21 22 5.047306 AGGCGGATTTATATCGACAAGATCA 60.047 40.000 0.00 0.00 40.66 2.92
22 23 5.411781 AGGCGGATTTATATCGACAAGATC 58.588 41.667 0.00 0.00 40.66 2.75
23 24 5.407407 AGGCGGATTTATATCGACAAGAT 57.593 39.130 0.00 0.00 43.19 2.40
24 25 4.866508 AGGCGGATTTATATCGACAAGA 57.133 40.909 0.00 0.00 0.00 3.02
25 26 4.988540 TGAAGGCGGATTTATATCGACAAG 59.011 41.667 0.00 0.00 0.00 3.16
26 27 4.951254 TGAAGGCGGATTTATATCGACAA 58.049 39.130 0.00 0.00 0.00 3.18
27 28 4.594123 TGAAGGCGGATTTATATCGACA 57.406 40.909 0.00 0.00 0.00 4.35
28 29 5.917541 TTTGAAGGCGGATTTATATCGAC 57.082 39.130 0.00 0.00 0.00 4.20
29 30 6.928979 TTTTTGAAGGCGGATTTATATCGA 57.071 33.333 0.00 0.00 0.00 3.59
52 53 1.681264 AGCAAAGCAGCCGTACTTTTT 59.319 42.857 0.00 0.00 33.92 1.94
53 54 1.318576 AGCAAAGCAGCCGTACTTTT 58.681 45.000 0.00 0.00 33.92 2.27
54 55 1.001378 CAAGCAAAGCAGCCGTACTTT 60.001 47.619 0.00 0.00 36.56 2.66
55 56 0.593128 CAAGCAAAGCAGCCGTACTT 59.407 50.000 0.00 0.00 34.23 2.24
56 57 1.237285 CCAAGCAAAGCAGCCGTACT 61.237 55.000 0.00 0.00 34.23 2.73
57 58 1.210155 CCAAGCAAAGCAGCCGTAC 59.790 57.895 0.00 0.00 34.23 3.67
58 59 1.971167 CCCAAGCAAAGCAGCCGTA 60.971 57.895 0.00 0.00 34.23 4.02
59 60 3.297620 CCCAAGCAAAGCAGCCGT 61.298 61.111 0.00 0.00 34.23 5.68
60 61 4.729856 GCCCAAGCAAAGCAGCCG 62.730 66.667 0.00 0.00 39.53 5.52
61 62 4.383861 GGCCCAAGCAAAGCAGCC 62.384 66.667 0.00 0.00 42.56 4.85
62 63 2.459202 AATGGCCCAAGCAAAGCAGC 62.459 55.000 0.00 0.00 42.56 5.25
63 64 0.672401 CAATGGCCCAAGCAAAGCAG 60.672 55.000 0.00 0.00 42.56 4.24
64 65 1.371932 CAATGGCCCAAGCAAAGCA 59.628 52.632 0.00 0.00 42.56 3.91
65 66 1.376295 CCAATGGCCCAAGCAAAGC 60.376 57.895 0.00 0.00 42.56 3.51
66 67 1.376295 GCCAATGGCCCAAGCAAAG 60.376 57.895 14.47 0.00 44.06 2.77
67 68 2.749016 GCCAATGGCCCAAGCAAA 59.251 55.556 14.47 0.00 44.06 3.68
76 77 3.058160 AGCAGTGACGCCAATGGC 61.058 61.111 15.52 15.52 46.75 4.40
77 78 1.968017 ACAGCAGTGACGCCAATGG 60.968 57.895 0.48 0.00 38.67 3.16
78 79 3.659334 ACAGCAGTGACGCCAATG 58.341 55.556 0.00 0.00 40.97 2.82
87 88 3.066190 CCATGGGCCACAGCAGTG 61.066 66.667 9.28 0.94 45.47 3.66
88 89 4.371417 CCCATGGGCCACAGCAGT 62.371 66.667 20.41 0.00 42.56 4.40
98 99 0.324645 AGTAGCAAAAGGCCCATGGG 60.325 55.000 27.87 27.87 46.50 4.00
99 100 0.819582 CAGTAGCAAAAGGCCCATGG 59.180 55.000 4.14 4.14 46.50 3.66
100 101 0.174162 GCAGTAGCAAAAGGCCCATG 59.826 55.000 0.00 0.00 46.50 3.66
101 102 1.315257 CGCAGTAGCAAAAGGCCCAT 61.315 55.000 0.00 0.00 46.50 4.00
102 103 1.971167 CGCAGTAGCAAAAGGCCCA 60.971 57.895 0.00 0.00 46.50 5.36
103 104 2.700773 CCGCAGTAGCAAAAGGCCC 61.701 63.158 0.00 0.00 46.50 5.80
104 105 1.971695 ACCGCAGTAGCAAAAGGCC 60.972 57.895 0.00 0.00 46.50 5.19
105 106 1.210155 CACCGCAGTAGCAAAAGGC 59.790 57.895 0.00 0.00 42.27 4.35
106 107 0.605319 TCCACCGCAGTAGCAAAAGG 60.605 55.000 0.00 0.00 42.27 3.11
107 108 0.517316 GTCCACCGCAGTAGCAAAAG 59.483 55.000 0.00 0.00 42.27 2.27
108 109 0.887387 GGTCCACCGCAGTAGCAAAA 60.887 55.000 0.00 0.00 42.27 2.44
109 110 1.302192 GGTCCACCGCAGTAGCAAA 60.302 57.895 0.00 0.00 42.27 3.68
110 111 2.345991 GGTCCACCGCAGTAGCAA 59.654 61.111 0.00 0.00 42.27 3.91
122 123 1.841556 AAGGAGAAGTGGCGGTCCA 60.842 57.895 0.00 0.00 40.85 4.02
123 124 1.376037 CAAGGAGAAGTGGCGGTCC 60.376 63.158 0.00 0.00 0.00 4.46
124 125 0.034896 TTCAAGGAGAAGTGGCGGTC 59.965 55.000 0.00 0.00 0.00 4.79
125 126 0.472471 TTTCAAGGAGAAGTGGCGGT 59.528 50.000 0.00 0.00 37.57 5.68
126 127 1.160137 CTTTCAAGGAGAAGTGGCGG 58.840 55.000 0.00 0.00 37.57 6.13
138 139 0.606401 TTCCGCTGCCTCCTTTCAAG 60.606 55.000 0.00 0.00 0.00 3.02
139 140 0.606401 CTTCCGCTGCCTCCTTTCAA 60.606 55.000 0.00 0.00 0.00 2.69
140 141 1.003355 CTTCCGCTGCCTCCTTTCA 60.003 57.895 0.00 0.00 0.00 2.69
141 142 0.321653 TTCTTCCGCTGCCTCCTTTC 60.322 55.000 0.00 0.00 0.00 2.62
142 143 0.322008 CTTCTTCCGCTGCCTCCTTT 60.322 55.000 0.00 0.00 0.00 3.11
143 144 1.298014 CTTCTTCCGCTGCCTCCTT 59.702 57.895 0.00 0.00 0.00 3.36
144 145 2.985456 CTTCTTCCGCTGCCTCCT 59.015 61.111 0.00 0.00 0.00 3.69
145 146 2.821810 GCTTCTTCCGCTGCCTCC 60.822 66.667 0.00 0.00 0.00 4.30
146 147 1.237285 TTTGCTTCTTCCGCTGCCTC 61.237 55.000 0.00 0.00 0.00 4.70
147 148 0.823356 TTTTGCTTCTTCCGCTGCCT 60.823 50.000 0.00 0.00 0.00 4.75
148 149 0.664466 GTTTTGCTTCTTCCGCTGCC 60.664 55.000 0.00 0.00 0.00 4.85
154 155 0.110192 CGCCTCGTTTTGCTTCTTCC 60.110 55.000 0.00 0.00 0.00 3.46
157 158 0.951040 CTCCGCCTCGTTTTGCTTCT 60.951 55.000 0.00 0.00 0.00 2.85
181 182 1.897802 AGGTGGGACTAATCGAAACGT 59.102 47.619 0.00 0.00 0.00 3.99
187 188 0.460311 AAGCGAGGTGGGACTAATCG 59.540 55.000 0.00 0.00 36.51 3.34
205 206 0.888619 CGCTCACTCACTCTACCCAA 59.111 55.000 0.00 0.00 0.00 4.12
210 211 0.394488 CTCCCCGCTCACTCACTCTA 60.394 60.000 0.00 0.00 0.00 2.43
223 227 0.395311 TATATAGCCCTCGCTCCCCG 60.395 60.000 0.00 0.00 43.95 5.73
231 235 2.166664 CACCCGCTCTTATATAGCCCTC 59.833 54.545 2.85 0.00 36.60 4.30
232 236 2.180276 CACCCGCTCTTATATAGCCCT 58.820 52.381 2.85 0.00 36.60 5.19
239 243 1.038681 TCGCACCACCCGCTCTTATA 61.039 55.000 0.00 0.00 0.00 0.98
340 345 6.494666 AATTAGGGTATGCTGCTTAGTGTA 57.505 37.500 0.00 0.00 0.00 2.90
380 385 0.401738 TGGGGCCTTCTCACAAAGAG 59.598 55.000 0.84 0.00 46.14 2.85
420 425 4.566545 TGTCCACATGTGCAACTAAAAG 57.433 40.909 20.81 3.52 38.04 2.27
421 426 4.991153 TTGTCCACATGTGCAACTAAAA 57.009 36.364 20.81 8.19 38.04 1.52
423 428 4.991153 TTTTGTCCACATGTGCAACTAA 57.009 36.364 20.81 18.14 38.04 2.24
424 429 5.334491 CGTATTTTGTCCACATGTGCAACTA 60.334 40.000 20.81 13.70 38.04 2.24
425 430 4.556501 CGTATTTTGTCCACATGTGCAACT 60.557 41.667 20.81 11.57 38.04 3.16
428 433 3.142174 TCGTATTTTGTCCACATGTGCA 58.858 40.909 20.81 11.08 0.00 4.57
435 440 6.662414 TCAAGATCATCGTATTTTGTCCAC 57.338 37.500 0.00 0.00 0.00 4.02
493 512 4.405116 TGCTGCAAGTTTTGAAATTCCT 57.595 36.364 0.00 0.00 35.30 3.36
494 513 5.678132 AATGCTGCAAGTTTTGAAATTCC 57.322 34.783 6.36 0.00 35.30 3.01
531 550 5.502079 TCACAGAGACAACACCCTTAAAAA 58.498 37.500 0.00 0.00 0.00 1.94
535 554 3.572642 TCTCACAGAGACAACACCCTTA 58.427 45.455 0.00 0.00 33.35 2.69
544 563 1.620819 GGCCTTCTTCTCACAGAGACA 59.379 52.381 0.00 0.00 38.51 3.41
545 564 1.066502 GGGCCTTCTTCTCACAGAGAC 60.067 57.143 0.84 0.00 38.51 3.36
558 577 1.250840 AAAGGATTGTGCGGGCCTTC 61.251 55.000 0.84 0.00 39.71 3.46
586 605 0.238289 GATTGGACGGGCATTATGCG 59.762 55.000 11.28 0.74 46.21 4.73
587 606 0.598065 GGATTGGACGGGCATTATGC 59.402 55.000 8.93 8.93 44.08 3.14
588 607 2.276732 AGGATTGGACGGGCATTATG 57.723 50.000 0.00 0.00 0.00 1.90
589 608 4.447138 TTAAGGATTGGACGGGCATTAT 57.553 40.909 0.00 0.00 0.00 1.28
590 609 3.935818 TTAAGGATTGGACGGGCATTA 57.064 42.857 0.00 0.00 0.00 1.90
591 610 2.818751 TTAAGGATTGGACGGGCATT 57.181 45.000 0.00 0.00 0.00 3.56
592 611 3.312736 AATTAAGGATTGGACGGGCAT 57.687 42.857 0.00 0.00 0.00 4.40
593 612 2.818751 AATTAAGGATTGGACGGGCA 57.181 45.000 0.00 0.00 0.00 5.36
594 613 4.643334 AGTTAAATTAAGGATTGGACGGGC 59.357 41.667 0.00 0.00 0.00 6.13
595 614 6.769134 AAGTTAAATTAAGGATTGGACGGG 57.231 37.500 0.00 0.00 0.00 5.28
596 615 8.301002 TCAAAAGTTAAATTAAGGATTGGACGG 58.699 33.333 0.00 0.00 0.00 4.79
597 616 9.855021 ATCAAAAGTTAAATTAAGGATTGGACG 57.145 29.630 0.00 0.00 0.00 4.79
719 738 7.438564 TGGAGTTTTAACTTTTAAGGCATTCC 58.561 34.615 0.00 0.00 39.88 3.01
733 752 6.923508 CCAAATTCAGAACCTGGAGTTTTAAC 59.076 38.462 0.00 0.00 39.40 2.01
734 753 6.836527 TCCAAATTCAGAACCTGGAGTTTTAA 59.163 34.615 10.00 0.00 39.40 1.52
735 754 6.369629 TCCAAATTCAGAACCTGGAGTTTTA 58.630 36.000 10.00 0.00 39.40 1.52
736 755 5.208121 TCCAAATTCAGAACCTGGAGTTTT 58.792 37.500 10.00 0.00 39.40 2.43
737 756 4.803452 TCCAAATTCAGAACCTGGAGTTT 58.197 39.130 10.00 0.00 39.40 2.66
738 757 4.453480 TCCAAATTCAGAACCTGGAGTT 57.547 40.909 10.00 0.00 43.07 3.01
739 758 4.453480 TTCCAAATTCAGAACCTGGAGT 57.547 40.909 12.72 0.00 37.48 3.85
745 764 6.652062 AGAATGCAATTTCCAAATTCAGAACC 59.348 34.615 0.00 0.00 36.07 3.62
752 780 5.185635 TCCGAGAGAATGCAATTTCCAAATT 59.814 36.000 0.00 0.00 36.07 1.82
754 782 4.078537 TCCGAGAGAATGCAATTTCCAAA 58.921 39.130 0.00 0.00 36.07 3.28
818 846 6.545666 TGTTCAAATTGGACACAAGTACAGAT 59.454 34.615 2.39 0.00 40.39 2.90
853 881 9.809096 CTTGTGTAGATCTTGTAGTGATGTATT 57.191 33.333 0.00 0.00 0.00 1.89
894 924 6.906901 AGGAATAAAGTCACCTATTGGGAGTA 59.093 38.462 0.00 0.00 38.76 2.59
1234 1266 3.428063 AGGGAGAAGATCATTGGGAGA 57.572 47.619 0.00 0.00 0.00 3.71
1263 1295 7.039152 AGGAAGATAGTGACGATGATCATTCAT 60.039 37.037 10.14 0.00 45.39 2.57
1264 1296 6.266330 AGGAAGATAGTGACGATGATCATTCA 59.734 38.462 10.14 7.82 36.00 2.57
1276 1308 7.048629 TGAAGATCATCAGGAAGATAGTGAC 57.951 40.000 0.00 0.00 34.43 3.67
1290 1322 5.068723 ACAAATTCCATGCCTGAAGATCATC 59.931 40.000 0.00 0.00 0.00 2.92
1310 1342 7.305705 CGCTGTAAACATCGAAAAATCAACAAA 60.306 33.333 0.24 0.00 37.65 2.83
1333 1365 0.107703 TGGATTCATCGAAAGGCGCT 60.108 50.000 7.64 0.00 40.61 5.92
1360 1392 5.958380 AGATCATAGCCAACCGGAGATATTA 59.042 40.000 9.46 0.00 0.00 0.98
1445 1477 0.613012 GCAGAAACCATCCCTTGCCT 60.613 55.000 0.00 0.00 0.00 4.75
1528 1560 0.251077 AGGAGTTTTGGAGCAGGCTG 60.251 55.000 10.94 10.94 0.00 4.85
1572 1604 7.601886 TCTCAATTGTTGTTTTTGTGTGATTGT 59.398 29.630 5.13 0.00 0.00 2.71
1579 1611 6.773080 TGCATTCTCAATTGTTGTTTTTGTG 58.227 32.000 5.13 0.00 0.00 3.33
1587 1619 6.788684 TCCAATTTGCATTCTCAATTGTTG 57.211 33.333 15.93 5.74 0.00 3.33
1614 1648 3.091545 CCCAAATGTGCTGACAATAGGT 58.908 45.455 0.00 0.00 35.11 3.08
1615 1649 3.355378 TCCCAAATGTGCTGACAATAGG 58.645 45.455 0.00 0.00 35.11 2.57
1616 1650 4.460382 AGTTCCCAAATGTGCTGACAATAG 59.540 41.667 0.00 0.00 35.11 1.73
1625 1659 4.525912 ATGAGAAAGTTCCCAAATGTGC 57.474 40.909 0.00 0.00 0.00 4.57
1804 1839 2.047560 GCGGGGCGACTAGTTGTT 60.048 61.111 11.83 0.00 0.00 2.83
1898 1933 9.499479 GTATTGGATCATCATCTAACATTGTCT 57.501 33.333 0.00 0.00 32.70 3.41
1904 1939 9.933723 CTATGTGTATTGGATCATCATCTAACA 57.066 33.333 0.00 0.00 32.70 2.41
1921 1956 6.936900 GCATTTGACCTATCACCTATGTGTAT 59.063 38.462 0.00 0.00 43.26 2.29
1941 1976 6.514947 ACTATCAACACACAACATTGCATTT 58.485 32.000 0.00 0.00 0.00 2.32
2058 2093 1.269102 AGGCAAATCCTCGATACGTCG 60.269 52.381 0.00 0.00 43.20 5.12
2064 2099 0.254178 ACAGCAGGCAAATCCTCGAT 59.746 50.000 0.00 0.00 45.52 3.59
2124 2159 2.166254 CCTGCAGAAAGAGAGAGAGGAC 59.834 54.545 17.39 0.00 0.00 3.85
2158 2193 8.908786 TCAGAAAGACTAATGATTCAAACTGT 57.091 30.769 0.00 0.00 0.00 3.55
2177 2212 3.557898 GCAGGTCCATGAGAGTTCAGAAA 60.558 47.826 0.00 0.00 36.61 2.52
2196 2231 3.323115 TGGATAGCTGGAGTAGAATGCAG 59.677 47.826 0.00 0.00 41.22 4.41


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

AutoCloner maintained by Alex Coulton.