Multiple sequence alignment - TraesCS2A01G136300

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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 TraesCS2A01G136300 chr2A 100.000 2516 0 0 1 2516 82188574 82186059 0.000000e+00 4647.0
1 TraesCS2A01G136300 chr1A 94.843 2036 45 16 420 2454 568054078 568056054 0.000000e+00 3123.0
2 TraesCS2A01G136300 chr1A 88.780 1533 126 24 861 2383 19516307 19514811 0.000000e+00 1836.0
3 TraesCS2A01G136300 chr1A 96.970 66 2 0 2451 2516 568056083 568056148 7.360000e-21 111.0
4 TraesCS2A01G136300 chr5A 95.194 1727 51 12 728 2454 687335159 687336853 0.000000e+00 2700.0
5 TraesCS2A01G136300 chr5A 90.625 320 16 14 385 693 687334843 687335159 1.800000e-111 412.0
6 TraesCS2A01G136300 chr5A 100.000 66 0 0 2451 2516 687336882 687336947 3.400000e-24 122.0
7 TraesCS2A01G136300 chr5A 93.617 47 2 1 434 479 345219730 345219684 4.490000e-08 69.4
8 TraesCS2A01G136300 chr5A 85.000 60 8 1 430 489 219236237 219236295 2.700000e-05 60.2
9 TraesCS2A01G136300 chr7B 87.778 1661 173 18 799 2454 341976058 341977693 0.000000e+00 1916.0
10 TraesCS2A01G136300 chr7B 96.782 435 10 4 1 431 348439873 348439439 0.000000e+00 723.0
11 TraesCS2A01G136300 chr5B 94.044 1276 47 13 1196 2461 166710248 166711504 0.000000e+00 1908.0
12 TraesCS2A01G136300 chr5B 96.056 431 15 2 4 432 656783287 656783717 0.000000e+00 701.0
13 TraesCS2A01G136300 chr5B 100.000 66 0 0 2451 2516 166711527 166711592 3.400000e-24 122.0
14 TraesCS2A01G136300 chr7A 92.438 767 54 4 1265 2028 134187532 134188297 0.000000e+00 1092.0
15 TraesCS2A01G136300 chr7A 93.784 370 21 2 2072 2441 134188302 134188669 2.830000e-154 555.0
16 TraesCS2A01G136300 chr7A 91.045 67 5 1 2451 2516 134188708 134188774 3.450000e-14 89.8
17 TraesCS2A01G136300 chr2D 88.986 917 52 19 1557 2454 21420586 21421472 0.000000e+00 1088.0
18 TraesCS2A01G136300 chr2D 90.230 348 34 0 1183 1530 21420245 21420592 2.950000e-124 455.0
19 TraesCS2A01G136300 chr2D 85.128 390 47 10 792 1175 21419702 21420086 3.040000e-104 388.0
20 TraesCS2A01G136300 chr6B 84.017 951 101 27 786 1706 680080684 680081613 0.000000e+00 867.0
21 TraesCS2A01G136300 chr6B 81.316 942 121 27 776 1706 679758403 679759300 0.000000e+00 713.0
22 TraesCS2A01G136300 chr6B 85.081 248 30 3 2074 2320 394006478 394006237 1.930000e-61 246.0
23 TraesCS2A01G136300 chr4A 87.795 762 62 15 1702 2454 200167046 200167785 0.000000e+00 863.0
24 TraesCS2A01G136300 chr4A 95.000 440 20 2 1 438 650164313 650164752 0.000000e+00 689.0
25 TraesCS2A01G136300 chr4A 98.485 66 1 0 2451 2516 200167814 200167879 1.580000e-22 117.0
26 TraesCS2A01G136300 chr4A 84.270 89 13 1 430 518 30970436 30970349 4.460000e-13 86.1
27 TraesCS2A01G136300 chr6D 84.145 883 91 24 776 1631 448691840 448692700 0.000000e+00 809.0
28 TraesCS2A01G136300 chr6D 82.743 226 32 4 787 1012 448656555 448656773 7.100000e-46 195.0
29 TraesCS2A01G136300 chr2B 85.601 757 60 21 1702 2454 106717042 106716331 0.000000e+00 749.0
30 TraesCS2A01G136300 chr2B 96.956 427 12 1 1 426 289639233 289638807 0.000000e+00 715.0
31 TraesCS2A01G136300 chr6A 81.668 971 89 38 786 1706 594728954 594729885 0.000000e+00 725.0
32 TraesCS2A01G136300 chr3B 97.190 427 11 1 1 426 583375296 583374870 0.000000e+00 721.0
33 TraesCS2A01G136300 chr1B 96.721 427 13 1 1 426 313489952 313489526 0.000000e+00 710.0
34 TraesCS2A01G136300 chr1B 96.934 424 12 1 1 423 591222259 591222682 0.000000e+00 710.0
35 TraesCS2A01G136300 chr4B 95.682 440 16 3 1 438 365087066 365086628 0.000000e+00 704.0
36 TraesCS2A01G136300 chr4B 95.455 440 17 3 1 438 258987867 258988305 0.000000e+00 699.0
37 TraesCS2A01G136300 chr3D 85.081 248 30 3 2074 2320 533890599 533890358 1.930000e-61 246.0
38 TraesCS2A01G136300 chr7D 100.000 40 0 0 1968 2007 33060897 33060858 9.650000e-10 75.0


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 TraesCS2A01G136300 chr2A 82186059 82188574 2515 True 4647.000000 4647 100.000000 1 2516 1 chr2A.!!$R1 2515
1 TraesCS2A01G136300 chr1A 19514811 19516307 1496 True 1836.000000 1836 88.780000 861 2383 1 chr1A.!!$R1 1522
2 TraesCS2A01G136300 chr1A 568054078 568056148 2070 False 1617.000000 3123 95.906500 420 2516 2 chr1A.!!$F1 2096
3 TraesCS2A01G136300 chr5A 687334843 687336947 2104 False 1078.000000 2700 95.273000 385 2516 3 chr5A.!!$F2 2131
4 TraesCS2A01G136300 chr7B 341976058 341977693 1635 False 1916.000000 1916 87.778000 799 2454 1 chr7B.!!$F1 1655
5 TraesCS2A01G136300 chr5B 166710248 166711592 1344 False 1015.000000 1908 97.022000 1196 2516 2 chr5B.!!$F2 1320
6 TraesCS2A01G136300 chr7A 134187532 134188774 1242 False 578.933333 1092 92.422333 1265 2516 3 chr7A.!!$F1 1251
7 TraesCS2A01G136300 chr2D 21419702 21421472 1770 False 643.666667 1088 88.114667 792 2454 3 chr2D.!!$F1 1662
8 TraesCS2A01G136300 chr6B 680080684 680081613 929 False 867.000000 867 84.017000 786 1706 1 chr6B.!!$F2 920
9 TraesCS2A01G136300 chr6B 679758403 679759300 897 False 713.000000 713 81.316000 776 1706 1 chr6B.!!$F1 930
10 TraesCS2A01G136300 chr4A 200167046 200167879 833 False 490.000000 863 93.140000 1702 2516 2 chr4A.!!$F2 814
11 TraesCS2A01G136300 chr6D 448691840 448692700 860 False 809.000000 809 84.145000 776 1631 1 chr6D.!!$F2 855
12 TraesCS2A01G136300 chr2B 106716331 106717042 711 True 749.000000 749 85.601000 1702 2454 1 chr2B.!!$R1 752
13 TraesCS2A01G136300 chr6A 594728954 594729885 931 False 725.000000 725 81.668000 786 1706 1 chr6A.!!$F1 920

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
459 467 0.532573 GCACGGATTGAGTCTCTGGA 59.467 55.0 0.65 0.0 0.0 3.86 F
1187 1423 0.179234 TTCGTGCAGTCCTGGTTCAA 59.821 50.0 0.00 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1648 1.228894 AGAGGAGAAGCACGGGACA 60.229 57.895 0.0 0.0 0.0 4.02 R
2057 2355 1.354031 TGTGTGTAATGGATGGGTGCT 59.646 47.619 0.0 0.0 0.0 4.40 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
43 44 3.259902 GCTACAAGCAGTGGTAGTTACC 58.740 50.000 0.00 1.25 43.08 2.85
44 45 3.306502 GCTACAAGCAGTGGTAGTTACCA 60.307 47.826 6.92 6.92 46.72 3.25
53 54 1.435577 GGTAGTTACCACCACTTGCG 58.564 55.000 3.45 0.00 45.73 4.85
54 55 1.270465 GGTAGTTACCACCACTTGCGT 60.270 52.381 3.45 0.00 45.73 5.24
55 56 2.486918 GTAGTTACCACCACTTGCGTT 58.513 47.619 0.00 0.00 0.00 4.84
56 57 2.047002 AGTTACCACCACTTGCGTTT 57.953 45.000 0.00 0.00 0.00 3.60
57 58 2.371306 AGTTACCACCACTTGCGTTTT 58.629 42.857 0.00 0.00 0.00 2.43
58 59 2.098443 AGTTACCACCACTTGCGTTTTG 59.902 45.455 0.00 0.00 0.00 2.44
59 60 1.752683 TACCACCACTTGCGTTTTGT 58.247 45.000 0.00 0.00 0.00 2.83
60 61 1.752683 ACCACCACTTGCGTTTTGTA 58.247 45.000 0.00 0.00 0.00 2.41
61 62 2.303175 ACCACCACTTGCGTTTTGTAT 58.697 42.857 0.00 0.00 0.00 2.29
62 63 2.034053 ACCACCACTTGCGTTTTGTATG 59.966 45.455 0.00 0.00 0.00 2.39
63 64 2.034053 CCACCACTTGCGTTTTGTATGT 59.966 45.455 0.00 0.00 0.00 2.29
64 65 3.490078 CCACCACTTGCGTTTTGTATGTT 60.490 43.478 0.00 0.00 0.00 2.71
65 66 3.485378 CACCACTTGCGTTTTGTATGTTG 59.515 43.478 0.00 0.00 0.00 3.33
66 67 3.129638 ACCACTTGCGTTTTGTATGTTGT 59.870 39.130 0.00 0.00 0.00 3.32
67 68 4.335874 ACCACTTGCGTTTTGTATGTTGTA 59.664 37.500 0.00 0.00 0.00 2.41
68 69 5.009210 ACCACTTGCGTTTTGTATGTTGTAT 59.991 36.000 0.00 0.00 0.00 2.29
69 70 5.341993 CCACTTGCGTTTTGTATGTTGTATG 59.658 40.000 0.00 0.00 0.00 2.39
70 71 5.912396 CACTTGCGTTTTGTATGTTGTATGT 59.088 36.000 0.00 0.00 0.00 2.29
71 72 7.072647 CACTTGCGTTTTGTATGTTGTATGTA 58.927 34.615 0.00 0.00 0.00 2.29
72 73 7.268235 CACTTGCGTTTTGTATGTTGTATGTAG 59.732 37.037 0.00 0.00 0.00 2.74
73 74 6.788684 TGCGTTTTGTATGTTGTATGTAGT 57.211 33.333 0.00 0.00 0.00 2.73
74 75 7.886405 TGCGTTTTGTATGTTGTATGTAGTA 57.114 32.000 0.00 0.00 0.00 1.82
75 76 8.481974 TGCGTTTTGTATGTTGTATGTAGTAT 57.518 30.769 0.00 0.00 0.00 2.12
76 77 8.597227 TGCGTTTTGTATGTTGTATGTAGTATC 58.403 33.333 0.00 0.00 0.00 2.24
77 78 8.814235 GCGTTTTGTATGTTGTATGTAGTATCT 58.186 33.333 0.00 0.00 0.00 1.98
81 82 9.511144 TTTGTATGTTGTATGTAGTATCTGTCG 57.489 33.333 0.00 0.00 0.00 4.35
82 83 8.441312 TGTATGTTGTATGTAGTATCTGTCGA 57.559 34.615 0.00 0.00 0.00 4.20
83 84 8.895737 TGTATGTTGTATGTAGTATCTGTCGAA 58.104 33.333 0.00 0.00 0.00 3.71
84 85 9.726232 GTATGTTGTATGTAGTATCTGTCGAAA 57.274 33.333 0.00 0.00 0.00 3.46
85 86 8.630278 ATGTTGTATGTAGTATCTGTCGAAAC 57.370 34.615 0.00 0.00 0.00 2.78
86 87 7.031372 TGTTGTATGTAGTATCTGTCGAAACC 58.969 38.462 0.00 0.00 0.00 3.27
87 88 5.813717 TGTATGTAGTATCTGTCGAAACCG 58.186 41.667 0.00 0.00 0.00 4.44
88 89 5.585844 TGTATGTAGTATCTGTCGAAACCGA 59.414 40.000 0.00 0.00 0.00 4.69
89 90 4.611310 TGTAGTATCTGTCGAAACCGAG 57.389 45.455 0.00 0.00 36.66 4.63
90 91 4.256110 TGTAGTATCTGTCGAAACCGAGA 58.744 43.478 0.00 0.00 36.66 4.04
91 92 4.331992 TGTAGTATCTGTCGAAACCGAGAG 59.668 45.833 5.76 5.76 45.37 3.20
92 93 3.345414 AGTATCTGTCGAAACCGAGAGT 58.655 45.455 10.88 3.24 44.63 3.24
93 94 4.511527 AGTATCTGTCGAAACCGAGAGTA 58.488 43.478 10.88 2.48 44.63 2.59
94 95 5.124645 AGTATCTGTCGAAACCGAGAGTAT 58.875 41.667 10.88 6.90 44.63 2.12
95 96 3.759527 TCTGTCGAAACCGAGAGTATG 57.240 47.619 10.88 0.00 44.63 2.39
96 97 3.079578 TCTGTCGAAACCGAGAGTATGT 58.920 45.455 10.88 0.00 44.63 2.29
97 98 4.256110 TCTGTCGAAACCGAGAGTATGTA 58.744 43.478 10.88 0.00 44.63 2.29
98 99 4.093998 TCTGTCGAAACCGAGAGTATGTAC 59.906 45.833 10.88 0.00 44.63 2.90
99 100 3.181517 TGTCGAAACCGAGAGTATGTACG 60.182 47.826 0.00 0.00 36.66 3.67
100 101 3.002791 TCGAAACCGAGAGTATGTACGT 58.997 45.455 0.00 0.00 0.00 3.57
101 102 3.096461 CGAAACCGAGAGTATGTACGTG 58.904 50.000 0.00 0.00 0.00 4.49
102 103 3.425359 CGAAACCGAGAGTATGTACGTGT 60.425 47.826 0.00 0.00 0.00 4.49
103 104 4.201714 CGAAACCGAGAGTATGTACGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
104 105 4.871993 AACCGAGAGTATGTACGTGTAG 57.128 45.455 0.00 0.00 0.00 2.74
105 106 3.866651 ACCGAGAGTATGTACGTGTAGT 58.133 45.455 0.00 0.00 0.00 2.73
106 107 5.011090 ACCGAGAGTATGTACGTGTAGTA 57.989 43.478 0.00 0.00 0.00 1.82
107 108 5.605534 ACCGAGAGTATGTACGTGTAGTAT 58.394 41.667 0.00 0.00 37.69 2.12
108 109 5.464722 ACCGAGAGTATGTACGTGTAGTATG 59.535 44.000 0.00 0.00 37.69 2.39
109 110 5.464722 CCGAGAGTATGTACGTGTAGTATGT 59.535 44.000 0.00 0.00 37.69 2.29
110 111 6.642540 CCGAGAGTATGTACGTGTAGTATGTA 59.357 42.308 0.00 0.00 37.69 2.29
233 234 9.646427 TTCACAAATATAACAAAAACTATGGGC 57.354 29.630 0.00 0.00 0.00 5.36
234 235 9.030452 TCACAAATATAACAAAAACTATGGGCT 57.970 29.630 0.00 0.00 0.00 5.19
235 236 9.301153 CACAAATATAACAAAAACTATGGGCTC 57.699 33.333 0.00 0.00 0.00 4.70
236 237 9.030452 ACAAATATAACAAAAACTATGGGCTCA 57.970 29.630 0.00 0.00 0.00 4.26
241 242 5.520376 ACAAAAACTATGGGCTCATATGC 57.480 39.130 6.77 0.00 35.53 3.14
242 243 4.955450 ACAAAAACTATGGGCTCATATGCA 59.045 37.500 6.77 0.00 35.53 3.96
243 244 5.421693 ACAAAAACTATGGGCTCATATGCAA 59.578 36.000 6.77 0.00 35.53 4.08
244 245 6.098695 ACAAAAACTATGGGCTCATATGCAAT 59.901 34.615 6.77 0.00 35.53 3.56
245 246 6.736110 AAAACTATGGGCTCATATGCAATT 57.264 33.333 6.77 0.00 35.53 2.32
246 247 6.736110 AAACTATGGGCTCATATGCAATTT 57.264 33.333 6.77 1.06 35.53 1.82
247 248 6.736110 AACTATGGGCTCATATGCAATTTT 57.264 33.333 6.77 0.00 35.53 1.82
248 249 6.736110 ACTATGGGCTCATATGCAATTTTT 57.264 33.333 6.77 0.00 35.53 1.94
344 345 9.908747 ATAGTACCACATCCTAGTATATGAGAC 57.091 37.037 4.49 0.00 0.00 3.36
345 346 7.756614 AGTACCACATCCTAGTATATGAGACA 58.243 38.462 4.49 0.00 0.00 3.41
346 347 8.394822 AGTACCACATCCTAGTATATGAGACAT 58.605 37.037 4.49 0.00 0.00 3.06
347 348 7.473735 ACCACATCCTAGTATATGAGACATG 57.526 40.000 0.00 0.00 0.00 3.21
348 349 7.013220 ACCACATCCTAGTATATGAGACATGT 58.987 38.462 0.00 0.00 0.00 3.21
349 350 7.039434 ACCACATCCTAGTATATGAGACATGTG 60.039 40.741 1.15 14.39 35.60 3.21
350 351 7.318893 CACATCCTAGTATATGAGACATGTGG 58.681 42.308 1.15 0.00 33.16 4.17
351 352 6.438741 ACATCCTAGTATATGAGACATGTGGG 59.561 42.308 1.15 0.00 0.00 4.61
352 353 5.333581 TCCTAGTATATGAGACATGTGGGG 58.666 45.833 1.15 0.00 0.00 4.96
353 354 5.087323 CCTAGTATATGAGACATGTGGGGT 58.913 45.833 1.15 0.00 0.00 4.95
354 355 6.046286 TCCTAGTATATGAGACATGTGGGGTA 59.954 42.308 1.15 0.00 0.00 3.69
355 356 6.724441 CCTAGTATATGAGACATGTGGGGTAA 59.276 42.308 1.15 0.00 0.00 2.85
356 357 6.420913 AGTATATGAGACATGTGGGGTAAC 57.579 41.667 1.15 0.00 0.00 2.50
357 358 6.143915 AGTATATGAGACATGTGGGGTAACT 58.856 40.000 1.15 0.00 0.00 2.24
358 359 7.302948 AGTATATGAGACATGTGGGGTAACTA 58.697 38.462 1.15 0.00 0.00 2.24
359 360 4.755266 ATGAGACATGTGGGGTAACTAC 57.245 45.455 1.15 0.00 0.00 2.73
360 361 2.835764 TGAGACATGTGGGGTAACTACC 59.164 50.000 1.15 0.00 45.71 3.18
379 380 4.313523 CCGGGTGGTAGGATGGAT 57.686 61.111 0.00 0.00 0.00 3.41
380 381 2.539983 CCGGGTGGTAGGATGGATT 58.460 57.895 0.00 0.00 0.00 3.01
381 382 0.843984 CCGGGTGGTAGGATGGATTT 59.156 55.000 0.00 0.00 0.00 2.17
382 383 1.214424 CCGGGTGGTAGGATGGATTTT 59.786 52.381 0.00 0.00 0.00 1.82
383 384 2.572290 CGGGTGGTAGGATGGATTTTC 58.428 52.381 0.00 0.00 0.00 2.29
456 464 4.744795 ATAAAGCACGGATTGAGTCTCT 57.255 40.909 0.65 0.00 0.00 3.10
459 467 0.532573 GCACGGATTGAGTCTCTGGA 59.467 55.000 0.65 0.00 0.00 3.86
566 574 4.973055 CGTTTCGTGGCCGGTGGA 62.973 66.667 1.90 0.00 33.95 4.02
597 605 3.459232 TGGACTCGGAGCAGATTTATG 57.541 47.619 4.58 0.00 0.00 1.90
640 648 1.758936 TCTCCTCCTCGATGCGTAAA 58.241 50.000 0.00 0.00 0.00 2.01
724 733 1.078918 GTAAGGGTACGGTGCCACC 60.079 63.158 17.21 2.98 34.05 4.61
821 830 2.444256 GCAATCCCCGGCTCCTACT 61.444 63.158 0.00 0.00 0.00 2.57
829 838 2.363925 GGCTCCTACTGACCCCGT 60.364 66.667 0.00 0.00 0.00 5.28
839 848 0.824109 CTGACCCCGTAGCTTCATCA 59.176 55.000 0.00 0.00 0.00 3.07
996 1054 4.576463 AGCTGTTTGACGAAATTTCTCAGT 59.424 37.500 15.92 6.76 0.00 3.41
1080 1152 1.408702 GCCTTTTCTTGTTCCTGTGCA 59.591 47.619 0.00 0.00 0.00 4.57
1175 1411 4.024143 GCATGCGGTGTTCGTGCA 62.024 61.111 0.00 0.00 43.67 4.57
1178 1414 2.317609 ATGCGGTGTTCGTGCAGTC 61.318 57.895 0.00 0.00 42.65 3.51
1179 1415 3.712881 GCGGTGTTCGTGCAGTCC 61.713 66.667 0.00 0.00 41.72 3.85
1180 1416 2.029073 CGGTGTTCGTGCAGTCCT 59.971 61.111 0.00 0.00 0.00 3.85
1181 1417 2.310233 CGGTGTTCGTGCAGTCCTG 61.310 63.158 0.00 0.00 0.00 3.86
1182 1418 1.961277 GGTGTTCGTGCAGTCCTGG 60.961 63.158 0.00 0.00 0.00 4.45
1183 1419 1.227556 GTGTTCGTGCAGTCCTGGT 60.228 57.895 0.00 0.00 0.00 4.00
1187 1423 0.179234 TTCGTGCAGTCCTGGTTCAA 59.821 50.000 0.00 0.00 0.00 2.69
1404 1648 0.462581 CGCAGCCAGGTATGTCATGT 60.463 55.000 0.00 0.00 0.00 3.21
2030 2328 2.146342 CCACGAACTGAAACAGAGCAT 58.854 47.619 5.76 0.00 35.18 3.79
2052 2350 2.037251 TGGTGTTCAGTTAGACCAGAGC 59.963 50.000 0.00 0.00 33.44 4.09
2054 2352 3.307059 GGTGTTCAGTTAGACCAGAGCAT 60.307 47.826 0.00 0.00 0.00 3.79
2055 2353 4.081642 GGTGTTCAGTTAGACCAGAGCATA 60.082 45.833 0.00 0.00 0.00 3.14
2056 2354 5.105752 GTGTTCAGTTAGACCAGAGCATAG 58.894 45.833 0.00 0.00 0.00 2.23
2057 2355 5.016831 TGTTCAGTTAGACCAGAGCATAGA 58.983 41.667 0.00 0.00 0.00 1.98
2058 2356 5.126222 TGTTCAGTTAGACCAGAGCATAGAG 59.874 44.000 0.00 0.00 0.00 2.43
2059 2357 3.634448 TCAGTTAGACCAGAGCATAGAGC 59.366 47.826 0.00 0.00 46.19 4.09
2070 2368 2.283145 GCATAGAGCACCCATCCATT 57.717 50.000 0.00 0.00 44.79 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.306502 GGTAACTACCACTGCTTGTAGCA 60.307 47.826 0.98 0.98 46.72 3.49
22 23 3.259902 GGTAACTACCACTGCTTGTAGC 58.740 50.000 0.80 0.00 45.73 3.58
34 35 1.435577 CGCAAGTGGTGGTAACTACC 58.564 55.000 0.00 0.00 46.62 3.18
49 50 7.192148 ACTACATACAACATACAAAACGCAA 57.808 32.000 0.00 0.00 0.00 4.85
50 51 6.788684 ACTACATACAACATACAAAACGCA 57.211 33.333 0.00 0.00 0.00 5.24
51 52 8.814235 AGATACTACATACAACATACAAAACGC 58.186 33.333 0.00 0.00 0.00 4.84
55 56 9.511144 CGACAGATACTACATACAACATACAAA 57.489 33.333 0.00 0.00 0.00 2.83
56 57 8.895737 TCGACAGATACTACATACAACATACAA 58.104 33.333 0.00 0.00 0.00 2.41
57 58 8.441312 TCGACAGATACTACATACAACATACA 57.559 34.615 0.00 0.00 0.00 2.29
58 59 9.726232 TTTCGACAGATACTACATACAACATAC 57.274 33.333 0.00 0.00 0.00 2.39
59 60 9.726232 GTTTCGACAGATACTACATACAACATA 57.274 33.333 0.00 0.00 0.00 2.29
60 61 7.705325 GGTTTCGACAGATACTACATACAACAT 59.295 37.037 0.00 0.00 0.00 2.71
61 62 7.031372 GGTTTCGACAGATACTACATACAACA 58.969 38.462 0.00 0.00 0.00 3.33
62 63 6.195983 CGGTTTCGACAGATACTACATACAAC 59.804 42.308 0.00 0.00 39.00 3.32
63 64 6.093909 TCGGTTTCGACAGATACTACATACAA 59.906 38.462 0.00 0.00 40.88 2.41
64 65 5.585844 TCGGTTTCGACAGATACTACATACA 59.414 40.000 0.00 0.00 40.88 2.29
65 66 6.018425 TCTCGGTTTCGACAGATACTACATAC 60.018 42.308 0.00 0.00 40.88 2.39
66 67 6.051074 TCTCGGTTTCGACAGATACTACATA 58.949 40.000 0.00 0.00 40.88 2.29
67 68 4.880120 TCTCGGTTTCGACAGATACTACAT 59.120 41.667 0.00 0.00 40.88 2.29
68 69 4.256110 TCTCGGTTTCGACAGATACTACA 58.744 43.478 0.00 0.00 40.88 2.74
69 70 4.332268 ACTCTCGGTTTCGACAGATACTAC 59.668 45.833 0.00 0.00 40.88 2.73
70 71 4.511527 ACTCTCGGTTTCGACAGATACTA 58.488 43.478 0.00 0.00 40.88 1.82
71 72 3.345414 ACTCTCGGTTTCGACAGATACT 58.655 45.455 0.00 0.00 40.88 2.12
72 73 3.761311 ACTCTCGGTTTCGACAGATAC 57.239 47.619 0.00 0.00 40.88 2.24
73 74 4.880120 ACATACTCTCGGTTTCGACAGATA 59.120 41.667 0.00 0.00 40.88 1.98
74 75 3.695060 ACATACTCTCGGTTTCGACAGAT 59.305 43.478 0.00 0.00 40.88 2.90
75 76 3.079578 ACATACTCTCGGTTTCGACAGA 58.920 45.455 0.00 0.00 40.88 3.41
76 77 3.489180 ACATACTCTCGGTTTCGACAG 57.511 47.619 0.00 0.00 40.88 3.51
77 78 3.181517 CGTACATACTCTCGGTTTCGACA 60.182 47.826 0.00 0.00 40.88 4.35
78 79 3.181516 ACGTACATACTCTCGGTTTCGAC 60.182 47.826 0.00 0.00 40.88 4.20
79 80 3.002791 ACGTACATACTCTCGGTTTCGA 58.997 45.455 0.00 0.00 43.86 3.71
80 81 3.096461 CACGTACATACTCTCGGTTTCG 58.904 50.000 0.00 0.00 37.82 3.46
81 82 4.088823 ACACGTACATACTCTCGGTTTC 57.911 45.455 0.00 0.00 0.00 2.78
82 83 4.697352 ACTACACGTACATACTCTCGGTTT 59.303 41.667 0.00 0.00 0.00 3.27
83 84 4.256920 ACTACACGTACATACTCTCGGTT 58.743 43.478 0.00 0.00 0.00 4.44
84 85 3.866651 ACTACACGTACATACTCTCGGT 58.133 45.455 0.00 0.00 0.00 4.69
85 86 5.464722 ACATACTACACGTACATACTCTCGG 59.535 44.000 0.00 0.00 0.00 4.63
86 87 6.522233 ACATACTACACGTACATACTCTCG 57.478 41.667 0.00 0.00 0.00 4.04
87 88 8.586570 AGTACATACTACACGTACATACTCTC 57.413 38.462 0.00 0.00 38.35 3.20
207 208 9.646427 GCCCATAGTTTTTGTTATATTTGTGAA 57.354 29.630 0.00 0.00 0.00 3.18
208 209 9.030452 AGCCCATAGTTTTTGTTATATTTGTGA 57.970 29.630 0.00 0.00 0.00 3.58
209 210 9.301153 GAGCCCATAGTTTTTGTTATATTTGTG 57.699 33.333 0.00 0.00 0.00 3.33
210 211 9.030452 TGAGCCCATAGTTTTTGTTATATTTGT 57.970 29.630 0.00 0.00 0.00 2.83
215 216 8.792633 GCATATGAGCCCATAGTTTTTGTTATA 58.207 33.333 6.97 0.00 38.53 0.98
216 217 7.287466 TGCATATGAGCCCATAGTTTTTGTTAT 59.713 33.333 6.97 0.00 38.53 1.89
217 218 6.605194 TGCATATGAGCCCATAGTTTTTGTTA 59.395 34.615 6.97 0.00 38.53 2.41
218 219 5.421693 TGCATATGAGCCCATAGTTTTTGTT 59.578 36.000 6.97 0.00 38.53 2.83
219 220 4.955450 TGCATATGAGCCCATAGTTTTTGT 59.045 37.500 6.97 0.00 38.53 2.83
220 221 5.518848 TGCATATGAGCCCATAGTTTTTG 57.481 39.130 6.97 0.00 38.53 2.44
221 222 6.736110 ATTGCATATGAGCCCATAGTTTTT 57.264 33.333 6.97 0.00 38.53 1.94
222 223 6.736110 AATTGCATATGAGCCCATAGTTTT 57.264 33.333 6.97 0.00 38.53 2.43
223 224 6.736110 AAATTGCATATGAGCCCATAGTTT 57.264 33.333 6.97 0.00 38.53 2.66
224 225 6.736110 AAAATTGCATATGAGCCCATAGTT 57.264 33.333 6.97 0.00 38.53 2.24
225 226 6.736110 AAAAATTGCATATGAGCCCATAGT 57.264 33.333 6.97 0.00 38.53 2.12
318 319 9.908747 GTCTCATATACTAGGATGTGGTACTAT 57.091 37.037 11.46 0.00 0.00 2.12
319 320 8.887393 TGTCTCATATACTAGGATGTGGTACTA 58.113 37.037 11.46 0.00 0.00 1.82
320 321 7.756614 TGTCTCATATACTAGGATGTGGTACT 58.243 38.462 11.46 0.00 0.00 2.73
321 322 7.997773 TGTCTCATATACTAGGATGTGGTAC 57.002 40.000 11.46 10.11 0.00 3.34
322 323 8.170730 ACATGTCTCATATACTAGGATGTGGTA 58.829 37.037 11.46 0.00 0.00 3.25
323 324 7.013220 ACATGTCTCATATACTAGGATGTGGT 58.987 38.462 11.46 0.00 0.00 4.16
324 325 7.318893 CACATGTCTCATATACTAGGATGTGG 58.681 42.308 11.46 3.41 34.13 4.17
325 326 7.318893 CCACATGTCTCATATACTAGGATGTG 58.681 42.308 5.34 5.34 35.70 3.21
326 327 6.438741 CCCACATGTCTCATATACTAGGATGT 59.561 42.308 0.00 0.00 0.00 3.06
327 328 6.127225 CCCCACATGTCTCATATACTAGGATG 60.127 46.154 0.00 0.00 0.00 3.51
328 329 5.960811 CCCCACATGTCTCATATACTAGGAT 59.039 44.000 0.00 0.00 0.00 3.24
329 330 5.162870 ACCCCACATGTCTCATATACTAGGA 60.163 44.000 0.00 0.00 0.00 2.94
330 331 5.087323 ACCCCACATGTCTCATATACTAGG 58.913 45.833 0.00 0.00 0.00 3.02
331 332 7.451877 AGTTACCCCACATGTCTCATATACTAG 59.548 40.741 0.00 0.00 0.00 2.57
332 333 7.302948 AGTTACCCCACATGTCTCATATACTA 58.697 38.462 0.00 0.00 0.00 1.82
333 334 6.143915 AGTTACCCCACATGTCTCATATACT 58.856 40.000 0.00 0.00 0.00 2.12
334 335 6.420913 AGTTACCCCACATGTCTCATATAC 57.579 41.667 0.00 0.00 0.00 1.47
335 336 6.495872 GGTAGTTACCCCACATGTCTCATATA 59.504 42.308 0.00 0.00 40.53 0.86
336 337 5.307196 GGTAGTTACCCCACATGTCTCATAT 59.693 44.000 0.00 0.00 40.53 1.78
337 338 4.652421 GGTAGTTACCCCACATGTCTCATA 59.348 45.833 0.00 0.00 40.53 2.15
338 339 3.454812 GGTAGTTACCCCACATGTCTCAT 59.545 47.826 0.00 0.00 40.53 2.90
339 340 2.835764 GGTAGTTACCCCACATGTCTCA 59.164 50.000 0.00 0.00 40.53 3.27
340 341 2.835764 TGGTAGTTACCCCACATGTCTC 59.164 50.000 0.00 0.00 45.87 3.36
341 342 2.910544 TGGTAGTTACCCCACATGTCT 58.089 47.619 0.00 0.00 45.87 3.41
348 349 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
349 350 1.613332 ACCCGGTGGTAGTTACCCC 60.613 63.158 0.00 5.97 45.45 4.95
350 351 1.598517 CACCCGGTGGTAGTTACCC 59.401 63.158 9.99 0.00 45.57 3.69
362 363 0.843984 AAATCCATCCTACCACCCGG 59.156 55.000 0.00 0.00 38.77 5.73
363 364 2.572290 GAAAATCCATCCTACCACCCG 58.428 52.381 0.00 0.00 0.00 5.28
364 365 2.424379 GGGAAAATCCATCCTACCACCC 60.424 54.545 0.00 0.00 38.64 4.61
365 366 2.514160 AGGGAAAATCCATCCTACCACC 59.486 50.000 0.00 0.00 38.64 4.61
366 367 3.953542 AGGGAAAATCCATCCTACCAC 57.046 47.619 0.00 0.00 38.64 4.16
430 438 7.770897 AGAGACTCAATCCGTGCTTTATTTATT 59.229 33.333 5.02 0.00 0.00 1.40
432 440 6.535150 CAGAGACTCAATCCGTGCTTTATTTA 59.465 38.462 5.02 0.00 0.00 1.40
433 441 5.352569 CAGAGACTCAATCCGTGCTTTATTT 59.647 40.000 5.02 0.00 0.00 1.40
466 474 4.885325 ACCTTTGTGTAAAAAGTCCACGAT 59.115 37.500 0.00 0.00 35.73 3.73
566 574 0.107508 CCGAGTCCATGAGGCACAAT 60.108 55.000 0.00 0.00 33.74 2.71
597 605 4.102649 CCCAAGTTCGTGTGTTCTTTTTC 58.897 43.478 0.00 0.00 0.00 2.29
821 830 1.412710 GATGATGAAGCTACGGGGTCA 59.587 52.381 0.00 0.00 0.00 4.02
829 838 1.865655 GCGACTGCGATGATGAAGCTA 60.866 52.381 0.00 0.00 40.82 3.32
839 848 4.760047 GGTGGTGGCGACTGCGAT 62.760 66.667 0.00 0.00 44.10 4.58
996 1054 3.798380 CGAACCATGCGCATCTCA 58.202 55.556 22.51 0.00 0.00 3.27
1080 1152 3.010420 GAGCTCGGCTTAGTTTTCCATT 58.990 45.455 0.00 0.00 39.88 3.16
1121 1198 3.314331 CTCCGCCAGTCCACCTGT 61.314 66.667 0.00 0.00 39.74 4.00
1175 1411 2.907892 TGATCTCCTTGAACCAGGACT 58.092 47.619 0.00 0.00 38.11 3.85
1178 1414 2.356535 CCCTTGATCTCCTTGAACCAGG 60.357 54.545 0.00 0.00 32.45 4.45
1179 1415 2.943199 GCCCTTGATCTCCTTGAACCAG 60.943 54.545 0.00 0.00 0.00 4.00
1180 1416 1.004745 GCCCTTGATCTCCTTGAACCA 59.995 52.381 0.00 0.00 0.00 3.67
1181 1417 1.756430 GCCCTTGATCTCCTTGAACC 58.244 55.000 0.00 0.00 0.00 3.62
1182 1418 1.339151 ACGCCCTTGATCTCCTTGAAC 60.339 52.381 0.00 0.00 0.00 3.18
1183 1419 0.984230 ACGCCCTTGATCTCCTTGAA 59.016 50.000 0.00 0.00 0.00 2.69
1187 1423 0.539051 CTTGACGCCCTTGATCTCCT 59.461 55.000 0.00 0.00 0.00 3.69
1404 1648 1.228894 AGAGGAGAAGCACGGGACA 60.229 57.895 0.00 0.00 0.00 4.02
2030 2328 3.494398 GCTCTGGTCTAACTGAACACCAA 60.494 47.826 0.00 0.00 37.49 3.67
2052 2350 4.067896 GTGTAATGGATGGGTGCTCTATG 58.932 47.826 0.00 0.00 0.00 2.23
2054 2352 3.111484 TGTGTAATGGATGGGTGCTCTA 58.889 45.455 0.00 0.00 0.00 2.43
2055 2353 1.915489 TGTGTAATGGATGGGTGCTCT 59.085 47.619 0.00 0.00 0.00 4.09
2056 2354 2.017049 GTGTGTAATGGATGGGTGCTC 58.983 52.381 0.00 0.00 0.00 4.26
2057 2355 1.354031 TGTGTGTAATGGATGGGTGCT 59.646 47.619 0.00 0.00 0.00 4.40
2058 2356 1.472480 GTGTGTGTAATGGATGGGTGC 59.528 52.381 0.00 0.00 0.00 5.01
2059 2357 1.737236 CGTGTGTGTAATGGATGGGTG 59.263 52.381 0.00 0.00 0.00 4.61
2060 2358 1.626321 TCGTGTGTGTAATGGATGGGT 59.374 47.619 0.00 0.00 0.00 4.51
2061 2359 2.394930 TCGTGTGTGTAATGGATGGG 57.605 50.000 0.00 0.00 0.00 4.00
2062 2360 3.530535 TGATCGTGTGTGTAATGGATGG 58.469 45.455 0.00 0.00 0.00 3.51
2063 2361 4.571984 ACATGATCGTGTGTGTAATGGATG 59.428 41.667 19.76 0.00 0.00 3.51
2064 2362 4.769688 ACATGATCGTGTGTGTAATGGAT 58.230 39.130 19.76 0.00 0.00 3.41
2065 2363 4.200838 ACATGATCGTGTGTGTAATGGA 57.799 40.909 19.76 0.00 0.00 3.41
2066 2364 4.944962 AACATGATCGTGTGTGTAATGG 57.055 40.909 21.05 0.00 31.49 3.16
2067 2365 5.015108 CGAAACATGATCGTGTGTGTAATG 58.985 41.667 21.05 1.97 35.64 1.90
2068 2366 4.092821 CCGAAACATGATCGTGTGTGTAAT 59.907 41.667 21.05 1.53 38.60 1.89
2069 2367 3.430556 CCGAAACATGATCGTGTGTGTAA 59.569 43.478 21.05 0.00 38.60 2.41
2070 2368 2.990514 CCGAAACATGATCGTGTGTGTA 59.009 45.455 21.05 0.00 38.60 2.90


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

AutoCloner maintained by Alex Coulton.