Multiple sequence alignment - TraesCS6A01G088400

Loading Multiple Alignment...

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 TraesCS6A01G088400 chr6A 100.000 2464 0 0 1 2464 57039562 57042025 0.000000e+00 4551.0
1 TraesCS6A01G088400 chr6A 100.000 1003 0 0 2778 3780 57042339 57043341 0.000000e+00 1853.0
2 TraesCS6A01G088400 chr6A 87.118 1048 89 33 889 1896 57652980 57651939 0.000000e+00 1146.0
3 TraesCS6A01G088400 chrUn 96.237 1887 58 8 565 2441 19854726 19852843 0.000000e+00 3079.0
4 TraesCS6A01G088400 chrUn 87.214 1048 91 25 886 1910 19736853 19737880 0.000000e+00 1153.0
5 TraesCS6A01G088400 chrUn 92.449 437 26 3 100 536 19855154 19854725 5.360000e-173 617.0
6 TraesCS6A01G088400 chrUn 81.963 438 33 20 3125 3548 88216894 88216489 2.810000e-86 329.0
7 TraesCS6A01G088400 chrUn 93.478 46 2 1 2778 2823 275707706 275707662 2.440000e-07 67.6
8 TraesCS6A01G088400 chr6B 93.441 1616 71 18 650 2247 92913417 92915015 0.000000e+00 2364.0
9 TraesCS6A01G088400 chr6B 85.042 1063 109 33 889 1910 93304219 93303166 0.000000e+00 1037.0
10 TraesCS6A01G088400 chr6B 91.983 237 15 2 337 573 92913183 92913415 2.810000e-86 329.0
11 TraesCS6A01G088400 chr6B 87.023 131 7 7 2320 2440 92915113 92915243 5.090000e-29 139.0
12 TraesCS6A01G088400 chr7D 83.846 650 44 24 3087 3682 570993532 570992890 2.550000e-156 562.0
13 TraesCS6A01G088400 chr7A 86.026 458 39 13 3087 3524 660088541 660088089 5.720000e-128 468.0
14 TraesCS6A01G088400 chr7A 90.625 320 20 4 3087 3396 668169386 668169705 2.100000e-112 416.0
15 TraesCS6A01G088400 chr7A 87.692 325 30 7 2779 3096 645938087 645937766 1.660000e-98 370.0
16 TraesCS6A01G088400 chr7A 89.316 234 17 4 3547 3780 668169784 668170009 1.720000e-73 287.0
17 TraesCS6A01G088400 chr4A 82.878 549 45 21 3259 3780 592219602 592220128 7.450000e-122 448.0
18 TraesCS6A01G088400 chr4A 85.315 429 60 1 1450 1875 82849 82421 1.250000e-119 440.0
19 TraesCS6A01G088400 chr4A 77.044 318 39 11 2779 3096 592219046 592219329 6.540000e-33 152.0
20 TraesCS6A01G088400 chr4A 83.077 65 7 3 2283 2343 731473535 731473599 5.270000e-04 56.5
21 TraesCS6A01G088400 chr4D 85.548 429 59 1 1450 1875 410884 410456 2.680000e-121 446.0
22 TraesCS6A01G088400 chr4D 86.744 347 45 1 2 347 183145120 183145466 5.920000e-103 385.0
23 TraesCS6A01G088400 chr4D 81.967 122 20 2 1216 1336 11165001 11164881 6.680000e-18 102.0
24 TraesCS6A01G088400 chr4D 100.000 28 0 0 2316 2343 60134690 60134663 7.000000e-03 52.8
25 TraesCS6A01G088400 chr1D 89.086 339 37 0 2 340 384898470 384898808 4.510000e-114 422.0
26 TraesCS6A01G088400 chr1D 88.596 342 39 0 3 344 294973728 294973387 2.100000e-112 416.0
27 TraesCS6A01G088400 chr1D 88.150 346 41 0 2 347 295048878 295048533 2.720000e-111 412.0
28 TraesCS6A01G088400 chr1D 87.791 344 41 1 2 344 157592410 157592067 5.880000e-108 401.0
29 TraesCS6A01G088400 chr1D 86.919 344 44 1 2 344 157587289 157586946 5.920000e-103 385.0
30 TraesCS6A01G088400 chr5D 88.393 336 38 1 10 344 327127623 327127288 1.640000e-108 403.0
31 TraesCS6A01G088400 chr5D 86.607 336 43 2 10 344 107144412 107144746 1.660000e-98 370.0
32 TraesCS6A01G088400 chr5D 83.333 78 11 2 2273 2349 405811662 405811738 1.880000e-08 71.3
33 TraesCS6A01G088400 chr5D 90.476 42 2 1 2302 2343 421173850 421173811 2.000000e-03 54.7
34 TraesCS6A01G088400 chr5A 88.750 320 21 7 3087 3396 435800284 435800598 9.910000e-101 377.0
35 TraesCS6A01G088400 chr5A 84.615 299 43 3 2779 3075 435799823 435800120 1.030000e-75 294.0
36 TraesCS6A01G088400 chr3D 88.000 325 20 8 3087 3396 146400045 146399725 2.150000e-97 366.0
37 TraesCS6A01G088400 chr3D 88.462 234 22 3 3547 3780 146399644 146399416 1.030000e-70 278.0
38 TraesCS6A01G088400 chr3D 82.036 334 42 5 2780 3096 146400532 146400200 6.220000e-68 268.0
39 TraesCS6A01G088400 chr3D 84.416 77 6 3 2272 2342 312907517 312907593 1.880000e-08 71.3
40 TraesCS6A01G088400 chr4B 84.570 337 49 1 1472 1805 21153010 21152674 7.830000e-87 331.0
41 TraesCS6A01G088400 chr4B 84.273 337 50 1 1472 1805 21151349 21151013 3.640000e-85 326.0
42 TraesCS6A01G088400 chr4B 81.452 124 21 2 1216 1338 21158095 21157973 2.400000e-17 100.0
43 TraesCS6A01G088400 chr4B 100.000 28 0 0 2316 2343 89304631 89304604 7.000000e-03 52.8
44 TraesCS6A01G088400 chr4B 100.000 28 0 0 2274 2301 664200711 664200738 7.000000e-03 52.8
45 TraesCS6A01G088400 chr2D 85.135 74 5 3 2276 2343 138762752 138762679 1.880000e-08 71.3
46 TraesCS6A01G088400 chr5B 84.615 78 2 6 2273 2342 84883235 84883310 6.780000e-08 69.4
47 TraesCS6A01G088400 chr3B 93.478 46 2 1 2778 2823 231918589 231918545 2.440000e-07 67.6
48 TraesCS6A01G088400 chr3B 93.478 46 2 1 2778 2823 826420957 826420913 2.440000e-07 67.6
49 TraesCS6A01G088400 chr3B 93.478 46 2 1 2778 2823 826474286 826474242 2.440000e-07 67.6
50 TraesCS6A01G088400 chr3B 93.478 46 2 1 2778 2823 826535623 826535579 2.440000e-07 67.6
51 TraesCS6A01G088400 chr3B 81.579 76 4 4 2273 2340 441718279 441718206 2.000000e-03 54.7
52 TraesCS6A01G088400 chr6D 90.476 42 4 0 2302 2343 310399894 310399853 5.270000e-04 56.5
53 TraesCS6A01G088400 chr6D 88.000 50 1 3 2297 2343 342467252 342467205 2.000000e-03 54.7


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 TraesCS6A01G088400 chr6A 57039562 57043341 3779 False 3202.0 4551 100.000000 1 3780 2 chr6A.!!$F1 3779
1 TraesCS6A01G088400 chr6A 57651939 57652980 1041 True 1146.0 1146 87.118000 889 1896 1 chr6A.!!$R1 1007
2 TraesCS6A01G088400 chrUn 19852843 19855154 2311 True 1848.0 3079 94.343000 100 2441 2 chrUn.!!$R3 2341
3 TraesCS6A01G088400 chrUn 19736853 19737880 1027 False 1153.0 1153 87.214000 886 1910 1 chrUn.!!$F1 1024
4 TraesCS6A01G088400 chr6B 93303166 93304219 1053 True 1037.0 1037 85.042000 889 1910 1 chr6B.!!$R1 1021
5 TraesCS6A01G088400 chr6B 92913183 92915243 2060 False 944.0 2364 90.815667 337 2440 3 chr6B.!!$F1 2103
6 TraesCS6A01G088400 chr7D 570992890 570993532 642 True 562.0 562 83.846000 3087 3682 1 chr7D.!!$R1 595
7 TraesCS6A01G088400 chr7A 668169386 668170009 623 False 351.5 416 89.970500 3087 3780 2 chr7A.!!$F1 693
8 TraesCS6A01G088400 chr4A 592219046 592220128 1082 False 300.0 448 79.961000 2779 3780 2 chr4A.!!$F2 1001
9 TraesCS6A01G088400 chr5A 435799823 435800598 775 False 335.5 377 86.682500 2779 3396 2 chr5A.!!$F1 617
10 TraesCS6A01G088400 chr3D 146399416 146400532 1116 True 304.0 366 86.166000 2780 3780 3 chr3D.!!$R1 1000
11 TraesCS6A01G088400 chr4B 21151013 21153010 1997 True 328.5 331 84.421500 1472 1805 2 chr4B.!!$R3 333

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
450 454 0.036164 ACTCGCTGTGGGTATTGCAA 59.964 50.0 0.00 0.00 0.00 4.08 F
533 537 0.388649 CGAGCTACATGTATCCGGGC 60.389 60.0 5.91 5.99 0.00 6.13 F
583 587 0.815095 TGCTAAATCTCAGCCGACGA 59.185 50.0 0.00 0.00 38.29 4.20 F
1442 1508 1.188219 TCTCCAGCAGCCTCGAACTT 61.188 55.0 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1478 0.112995 TGCTGGAGAGTTTGGCCATT 59.887 50.000 6.09 0.0 0.00 3.16 R
1442 1508 0.454600 CGTAGGCGAGCTTGTAGGAA 59.545 55.000 2.14 0.0 41.33 3.36 R
1882 3612 1.221840 GGCTTGGCATCCTTCTCGA 59.778 57.895 0.00 0.0 0.00 4.04 R
2835 4608 0.316204 ACACCGACGGACGAAAATCT 59.684 50.000 23.38 0.0 45.77 2.40 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
17 18 2.049526 TGCGTGACTACAGTGCCG 60.050 61.111 0.00 0.00 0.00 5.69
18 19 3.479269 GCGTGACTACAGTGCCGC 61.479 66.667 6.53 6.53 36.87 6.53
19 20 3.172575 CGTGACTACAGTGCCGCG 61.173 66.667 0.00 0.00 0.00 6.46
20 21 3.479269 GTGACTACAGTGCCGCGC 61.479 66.667 0.00 0.00 0.00 6.86
21 22 3.680786 TGACTACAGTGCCGCGCT 61.681 61.111 5.56 0.00 0.00 5.92
22 23 3.181967 GACTACAGTGCCGCGCTG 61.182 66.667 28.29 28.29 46.11 5.18
23 24 4.742201 ACTACAGTGCCGCGCTGG 62.742 66.667 31.75 20.02 45.11 4.85
49 50 4.814294 CGTCTGCCTGGTACGCCC 62.814 72.222 0.00 0.00 0.00 6.13
50 51 4.814294 GTCTGCCTGGTACGCCCG 62.814 72.222 0.00 0.00 35.15 6.13
56 57 4.373116 CTGGTACGCCCGCACTGT 62.373 66.667 0.00 0.00 35.15 3.55
57 58 4.673298 TGGTACGCCCGCACTGTG 62.673 66.667 2.76 2.76 35.15 3.66
64 65 4.373116 CCCGCACTGTGGCTACGT 62.373 66.667 10.21 0.00 0.00 3.57
65 66 2.357034 CCGCACTGTGGCTACGTT 60.357 61.111 10.21 0.00 0.00 3.99
66 67 2.380410 CCGCACTGTGGCTACGTTC 61.380 63.158 10.21 0.00 0.00 3.95
67 68 2.380410 CGCACTGTGGCTACGTTCC 61.380 63.158 10.21 0.00 0.00 3.62
68 69 1.004918 GCACTGTGGCTACGTTCCT 60.005 57.895 10.21 0.00 0.00 3.36
69 70 1.014564 GCACTGTGGCTACGTTCCTC 61.015 60.000 10.21 0.00 0.00 3.71
70 71 0.389948 CACTGTGGCTACGTTCCTCC 60.390 60.000 0.00 0.00 0.00 4.30
71 72 0.542232 ACTGTGGCTACGTTCCTCCT 60.542 55.000 0.00 0.00 0.00 3.69
72 73 0.108615 CTGTGGCTACGTTCCTCCTG 60.109 60.000 0.00 0.00 0.00 3.86
73 74 1.218316 GTGGCTACGTTCCTCCTGG 59.782 63.158 0.00 0.00 0.00 4.45
74 75 1.077805 TGGCTACGTTCCTCCTGGA 59.922 57.895 0.00 0.00 41.36 3.86
75 76 0.325296 TGGCTACGTTCCTCCTGGAT 60.325 55.000 0.00 0.00 42.81 3.41
76 77 0.831307 GGCTACGTTCCTCCTGGATT 59.169 55.000 0.00 0.00 42.81 3.01
77 78 1.202545 GGCTACGTTCCTCCTGGATTC 60.203 57.143 0.00 0.00 42.81 2.52
78 79 1.536284 GCTACGTTCCTCCTGGATTCG 60.536 57.143 0.00 2.85 42.81 3.34
79 80 1.067212 CTACGTTCCTCCTGGATTCGG 59.933 57.143 0.00 0.00 42.81 4.30
80 81 1.144057 CGTTCCTCCTGGATTCGGG 59.856 63.158 0.00 0.00 42.81 5.14
81 82 1.527370 GTTCCTCCTGGATTCGGGG 59.473 63.158 0.00 0.00 42.81 5.73
82 83 1.692749 TTCCTCCTGGATTCGGGGG 60.693 63.158 0.00 0.00 42.81 5.40
83 84 2.366972 CCTCCTGGATTCGGGGGT 60.367 66.667 0.00 0.00 38.27 4.95
84 85 2.746375 CCTCCTGGATTCGGGGGTG 61.746 68.421 0.00 0.00 38.27 4.61
85 86 2.690881 TCCTGGATTCGGGGGTGG 60.691 66.667 0.00 0.00 39.90 4.61
86 87 4.506255 CCTGGATTCGGGGGTGGC 62.506 72.222 0.00 0.00 35.76 5.01
87 88 3.727258 CTGGATTCGGGGGTGGCA 61.727 66.667 0.00 0.00 0.00 4.92
88 89 3.704231 CTGGATTCGGGGGTGGCAG 62.704 68.421 0.00 0.00 0.00 4.85
89 90 4.506255 GGATTCGGGGGTGGCAGG 62.506 72.222 0.00 0.00 0.00 4.85
90 91 3.728373 GATTCGGGGGTGGCAGGT 61.728 66.667 0.00 0.00 0.00 4.00
91 92 3.995506 GATTCGGGGGTGGCAGGTG 62.996 68.421 0.00 0.00 0.00 4.00
121 122 2.174107 CGCCACGTCTCGTCGTAA 59.826 61.111 0.00 0.00 42.27 3.18
144 145 2.086610 ATGGGTGCAAACTTTGAGGT 57.913 45.000 5.65 0.00 0.00 3.85
156 157 1.691195 TTTGAGGTGACGCAGGTCCA 61.691 55.000 0.00 0.00 42.58 4.02
178 179 3.082579 GCTAGGTGTCGGCTCCCTG 62.083 68.421 4.13 0.00 0.00 4.45
202 203 2.383527 GCCTTCTGAGAACACGCCG 61.384 63.158 0.00 0.00 0.00 6.46
277 278 1.382629 GGAGGTGCAAGGGGCTTTA 59.617 57.895 0.00 0.00 45.15 1.85
294 295 3.069158 GCTTTACTAGCCCCGATGTCTTA 59.931 47.826 0.00 0.00 44.48 2.10
299 300 4.451900 ACTAGCCCCGATGTCTTAAAATG 58.548 43.478 0.00 0.00 0.00 2.32
304 305 4.083271 GCCCCGATGTCTTAAAATGCTATC 60.083 45.833 0.00 0.00 0.00 2.08
312 313 5.054477 GTCTTAAAATGCTATCGGGTGCTA 58.946 41.667 0.00 0.00 0.00 3.49
319 320 1.344763 GCTATCGGGTGCTAATGAGGT 59.655 52.381 0.00 0.00 0.00 3.85
325 326 2.767505 GGGTGCTAATGAGGTTATCCG 58.232 52.381 0.00 0.00 39.05 4.18
380 381 8.481974 TTTGAAAAATGACATGAGCCATAATG 57.518 30.769 0.00 0.00 0.00 1.90
398 399 3.520862 GTCACCATGCATGCCCCG 61.521 66.667 21.69 10.04 0.00 5.73
410 411 0.105453 ATGCCCCGTGTAGAGAGGAT 60.105 55.000 0.00 0.00 0.00 3.24
423 424 7.416890 CGTGTAGAGAGGATGTATTCTTTCCTT 60.417 40.741 0.00 0.00 0.00 3.36
425 426 6.882768 AGAGAGGATGTATTCTTTCCTTGT 57.117 37.500 0.00 0.00 0.00 3.16
449 453 0.391130 GACTCGCTGTGGGTATTGCA 60.391 55.000 0.00 0.00 0.00 4.08
450 454 0.036164 ACTCGCTGTGGGTATTGCAA 59.964 50.000 0.00 0.00 0.00 4.08
451 455 0.447801 CTCGCTGTGGGTATTGCAAC 59.552 55.000 0.00 0.00 0.00 4.17
533 537 0.388649 CGAGCTACATGTATCCGGGC 60.389 60.000 5.91 5.99 0.00 6.13
577 581 3.258971 ACAGGACTGCTAAATCTCAGC 57.741 47.619 0.00 0.00 39.56 4.26
583 587 0.815095 TGCTAAATCTCAGCCGACGA 59.185 50.000 0.00 0.00 38.29 4.20
592 596 2.688446 TCTCAGCCGACGATGACTTAAT 59.312 45.455 0.00 0.00 0.00 1.40
632 636 2.969628 ATTCGTGAGCTCTTAGGTGG 57.030 50.000 16.19 0.00 0.00 4.61
648 652 1.808945 GGTGGAGATCTGTGCAAACTG 59.191 52.381 0.00 0.00 0.00 3.16
657 661 7.308830 GGAGATCTGTGCAAACTGTTCTTTTAT 60.309 37.037 0.00 0.00 0.00 1.40
714 721 3.034635 ACTAAGATCTAGCCACACCCAG 58.965 50.000 0.00 0.00 0.00 4.45
766 773 5.227805 GTGTGCAATTATTATGTGCTTCACG 59.772 40.000 0.00 0.00 39.09 4.35
832 839 4.081697 GTGTAGCATTTTTGCCCCTAACAT 60.082 41.667 0.00 0.00 34.90 2.71
1005 1035 4.929211 ACGTTCGCATGCATGTATGTATAT 59.071 37.500 26.79 4.81 31.75 0.86
1054 1086 2.571212 TCATCCTCACAACACAACACC 58.429 47.619 0.00 0.00 0.00 4.16
1259 1325 5.579753 AGCTGATGGAGGATATCAACAAT 57.420 39.130 4.83 0.00 34.41 2.71
1442 1508 1.188219 TCTCCAGCAGCCTCGAACTT 61.188 55.000 0.00 0.00 0.00 2.66
1882 3612 2.104967 CATCAATGCCATGACCCAAGT 58.895 47.619 0.00 0.00 30.82 3.16
1985 3715 0.465460 AAGCCTGAACTCGCCAACAA 60.465 50.000 0.00 0.00 0.00 2.83
2012 3742 8.437360 ACACATCGAATCAATGAGCTTTATTA 57.563 30.769 0.00 0.00 0.00 0.98
2039 3769 7.495901 TCAAAGGTTTTGATTACAATCTTGCA 58.504 30.769 0.36 0.00 36.39 4.08
2154 3889 2.804421 TGTATTCGTTTCATGCAGCG 57.196 45.000 0.00 0.00 0.00 5.18
2250 3987 4.220724 TGGCATATAGTACTTCCTCCGTT 58.779 43.478 0.00 0.00 0.00 4.44
2252 3989 4.523558 GGCATATAGTACTTCCTCCGTTCT 59.476 45.833 0.00 0.00 0.00 3.01
2265 4002 7.224167 ACTTCCTCCGTTCTTAATATAAAAGCG 59.776 37.037 0.00 0.00 0.00 4.68
2288 4025 7.657761 AGCGTTTTGAGTCCCATAATATAAGAG 59.342 37.037 0.00 0.00 0.00 2.85
2303 4040 9.935682 ATAATATAAGAGCGTTTTGACATTGTG 57.064 29.630 0.00 0.00 0.00 3.33
2305 4042 4.370364 AAGAGCGTTTTGACATTGTGTT 57.630 36.364 0.00 0.00 0.00 3.32
2310 4047 6.472163 AGAGCGTTTTGACATTGTGTTAAAAG 59.528 34.615 11.47 8.21 43.35 2.27
2441 4214 6.165659 TGCAACGAACTAGAAGCTTTATTC 57.834 37.500 0.00 1.86 0.00 1.75
2442 4215 5.932303 TGCAACGAACTAGAAGCTTTATTCT 59.068 36.000 0.00 0.00 42.20 2.40
2443 4216 7.094631 TGCAACGAACTAGAAGCTTTATTCTA 58.905 34.615 0.00 0.00 40.08 2.10
2444 4217 7.764443 TGCAACGAACTAGAAGCTTTATTCTAT 59.236 33.333 0.00 0.00 40.18 1.98
2445 4218 9.245962 GCAACGAACTAGAAGCTTTATTCTATA 57.754 33.333 0.00 0.00 40.18 1.31
2823 4596 5.576447 ACCACCATTATTTTCATCCGTTC 57.424 39.130 0.00 0.00 0.00 3.95
2829 4602 2.483014 ATTTTCATCCGTTCGGTCCA 57.517 45.000 11.04 0.00 0.00 4.02
2835 4608 2.696187 TCATCCGTTCGGTCCATCATAA 59.304 45.455 11.04 0.00 0.00 1.90
2850 4623 4.085055 CCATCATAAGATTTTCGTCCGTCG 60.085 45.833 0.00 0.00 34.81 5.12
2890 4666 1.155424 TCGTGTTTGGCACTTCGTCC 61.155 55.000 0.00 0.00 45.57 4.79
2932 4720 1.620323 GAACAGCCCAGCCAAGAAAAT 59.380 47.619 0.00 0.00 0.00 1.82
2940 4728 5.706833 AGCCCAGCCAAGAAAATTATTTTTG 59.293 36.000 4.32 0.38 35.20 2.44
2946 4734 6.423604 AGCCAAGAAAATTATTTTTGTGTCCG 59.576 34.615 4.32 0.00 35.20 4.79
3038 4829 3.653836 TCAAAGTGAGCTTTAACCCCCTA 59.346 43.478 0.00 0.00 42.54 3.53
3042 4833 3.396611 AGTGAGCTTTAACCCCCTAAACA 59.603 43.478 0.00 0.00 0.00 2.83
3049 4840 6.005823 GCTTTAACCCCCTAAACAAACTAGA 58.994 40.000 0.00 0.00 0.00 2.43
3083 4874 7.133891 ACTTGTGATTACTAAATGCTGTGTC 57.866 36.000 0.00 0.00 0.00 3.67
3162 5132 1.400494 GAAATCGTGGGTGTATGTGGC 59.600 52.381 0.00 0.00 0.00 5.01
3188 5158 5.125417 TGCCTGGTATCTAAACTTTGCATTC 59.875 40.000 0.00 0.00 0.00 2.67
3214 5190 8.821147 TGCATATTATGAAAGGAAATGATTGC 57.179 30.769 7.87 0.00 0.00 3.56
3215 5191 7.874016 TGCATATTATGAAAGGAAATGATTGCC 59.126 33.333 7.87 0.00 0.00 4.52
3264 5258 3.686016 AGTACGGATTGTGGCTTTGATT 58.314 40.909 0.00 0.00 0.00 2.57
3280 5274 5.700373 GCTTTGATTAAAAATTGTGGGCTGA 59.300 36.000 0.00 0.00 0.00 4.26
3380 5375 4.273318 AGGAATGATTGTGGGCTAGAAAC 58.727 43.478 0.00 0.00 0.00 2.78
3390 5385 3.740832 GTGGGCTAGAAACAAAAATGCAC 59.259 43.478 0.00 0.00 0.00 4.57
3418 5417 5.652452 AGTAAGAATTGTGGGCTGGATTAAC 59.348 40.000 0.00 0.00 0.00 2.01
3422 5421 6.435164 AGAATTGTGGGCTGGATTAACTAAT 58.565 36.000 0.00 0.00 0.00 1.73
3488 5487 3.316308 GCGGACAATGCCTCAAATCTAAT 59.684 43.478 0.00 0.00 0.00 1.73
3491 5490 5.760253 CGGACAATGCCTCAAATCTAATACT 59.240 40.000 0.00 0.00 0.00 2.12
3519 5518 3.190535 CCTAGGCGAGAAGAAGATAGAGC 59.809 52.174 0.00 0.00 0.00 4.09
3531 5530 4.464597 AGAAGATAGAGCAAACGGAACTCT 59.535 41.667 0.00 0.00 43.12 3.24
3540 5539 3.771160 CGGAACTCTCCACCCCCG 61.771 72.222 0.00 0.00 42.58 5.73
3541 5540 2.606826 GGAACTCTCCACCCCCGT 60.607 66.667 0.00 0.00 41.96 5.28
3542 5541 2.663196 GAACTCTCCACCCCCGTG 59.337 66.667 0.00 0.00 39.91 4.94
3543 5542 1.911766 GAACTCTCCACCCCCGTGA 60.912 63.158 0.00 0.00 43.14 4.35
3544 5543 1.889530 GAACTCTCCACCCCCGTGAG 61.890 65.000 0.00 0.00 43.14 3.51
3545 5544 2.037367 CTCTCCACCCCCGTGAGA 59.963 66.667 0.00 0.00 43.14 3.27
3550 5578 0.042131 TCCACCCCCGTGAGATAAGT 59.958 55.000 0.00 0.00 43.14 2.24
3552 5580 1.191535 CACCCCCGTGAGATAAGTGA 58.808 55.000 0.00 0.00 43.14 3.41
3570 5598 8.746922 ATAAGTGACACATTTTTGTTGCTATG 57.253 30.769 8.59 0.00 0.00 2.23
3626 5654 5.220739 GCTTGATCTACATGCAACTTCGATT 60.221 40.000 0.00 0.00 45.19 3.34
3640 5668 1.922570 TCGATTAACCTTCGCTCTGC 58.077 50.000 0.00 0.00 36.56 4.26
3715 5743 2.094906 TGACACCGATGTAAAGTCGAGG 60.095 50.000 0.00 0.00 39.95 4.63
3720 5748 1.202382 CGATGTAAAGTCGAGGTCCCC 60.202 57.143 0.00 0.00 41.40 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.049526 CGGCACTGTAGTCACGCA 60.050 61.111 0.00 0.00 0.00 5.24
1 2 3.479269 GCGGCACTGTAGTCACGC 61.479 66.667 12.13 12.13 40.92 5.34
2 3 3.172575 CGCGGCACTGTAGTCACG 61.173 66.667 0.00 0.00 0.00 4.35
3 4 3.479269 GCGCGGCACTGTAGTCAC 61.479 66.667 8.83 0.00 0.00 3.67
4 5 3.680786 AGCGCGGCACTGTAGTCA 61.681 61.111 8.83 0.00 0.00 3.41
5 6 3.181967 CAGCGCGGCACTGTAGTC 61.182 66.667 8.83 0.00 0.00 2.59
6 7 4.742201 CCAGCGCGGCACTGTAGT 62.742 66.667 16.05 0.00 33.09 2.73
32 33 4.814294 GGGCGTACCAGGCAGACG 62.814 72.222 5.03 5.03 39.85 4.18
33 34 4.814294 CGGGCGTACCAGGCAGAC 62.814 72.222 0.00 0.00 40.22 3.51
39 40 4.373116 ACAGTGCGGGCGTACCAG 62.373 66.667 0.00 0.00 40.22 4.00
40 41 4.673298 CACAGTGCGGGCGTACCA 62.673 66.667 0.00 0.00 40.22 3.25
47 48 3.876589 AACGTAGCCACAGTGCGGG 62.877 63.158 0.00 0.00 36.02 6.13
48 49 2.357034 AACGTAGCCACAGTGCGG 60.357 61.111 0.00 0.00 36.02 5.69
49 50 2.380410 GGAACGTAGCCACAGTGCG 61.380 63.158 0.00 0.00 36.02 5.34
50 51 1.004918 AGGAACGTAGCCACAGTGC 60.005 57.895 9.72 0.00 0.00 4.40
51 52 0.389948 GGAGGAACGTAGCCACAGTG 60.390 60.000 9.72 0.00 0.00 3.66
52 53 0.542232 AGGAGGAACGTAGCCACAGT 60.542 55.000 9.72 0.00 0.00 3.55
53 54 0.108615 CAGGAGGAACGTAGCCACAG 60.109 60.000 9.72 0.00 0.00 3.66
54 55 1.541310 CCAGGAGGAACGTAGCCACA 61.541 60.000 9.72 0.00 36.89 4.17
55 56 1.218316 CCAGGAGGAACGTAGCCAC 59.782 63.158 9.72 3.61 36.89 5.01
56 57 1.077805 TCCAGGAGGAACGTAGCCA 59.922 57.895 9.72 0.00 42.23 4.75
57 58 4.029472 TCCAGGAGGAACGTAGCC 57.971 61.111 0.00 0.00 42.23 3.93
66 67 2.366972 ACCCCCGAATCCAGGAGG 60.367 66.667 0.00 0.00 0.00 4.30
67 68 2.746375 CCACCCCCGAATCCAGGAG 61.746 68.421 0.00 0.00 0.00 3.69
68 69 2.690881 CCACCCCCGAATCCAGGA 60.691 66.667 0.00 0.00 0.00 3.86
69 70 4.506255 GCCACCCCCGAATCCAGG 62.506 72.222 0.00 0.00 0.00 4.45
70 71 3.704231 CTGCCACCCCCGAATCCAG 62.704 68.421 0.00 0.00 0.00 3.86
71 72 3.727258 CTGCCACCCCCGAATCCA 61.727 66.667 0.00 0.00 0.00 3.41
72 73 4.506255 CCTGCCACCCCCGAATCC 62.506 72.222 0.00 0.00 0.00 3.01
73 74 3.728373 ACCTGCCACCCCCGAATC 61.728 66.667 0.00 0.00 0.00 2.52
74 75 4.047125 CACCTGCCACCCCCGAAT 62.047 66.667 0.00 0.00 0.00 3.34
90 91 3.702048 GGCGTGGCTACAGGACCA 61.702 66.667 0.00 0.00 34.44 4.02
91 92 3.702048 TGGCGTGGCTACAGGACC 61.702 66.667 0.00 0.00 39.76 4.46
92 93 2.434359 GTGGCGTGGCTACAGGAC 60.434 66.667 0.00 0.00 39.80 3.85
93 94 4.063967 CGTGGCGTGGCTACAGGA 62.064 66.667 0.00 0.00 40.02 3.86
94 95 4.373116 ACGTGGCGTGGCTACAGG 62.373 66.667 0.00 0.00 40.02 4.00
95 96 2.809601 GACGTGGCGTGGCTACAG 60.810 66.667 0.00 0.00 41.37 2.74
96 97 3.277211 GAGACGTGGCGTGGCTACA 62.277 63.158 0.00 0.00 41.37 2.74
97 98 2.506438 GAGACGTGGCGTGGCTAC 60.506 66.667 0.00 0.00 41.37 3.58
98 99 4.111016 CGAGACGTGGCGTGGCTA 62.111 66.667 0.00 0.00 41.37 3.93
121 122 4.592778 ACCTCAAAGTTTGCACCCATTTAT 59.407 37.500 10.90 0.00 0.00 1.40
178 179 1.448717 GTTCTCAGAAGGCGGCCTC 60.449 63.158 24.08 15.52 30.89 4.70
202 203 2.202946 GGCCGGCTGCTAGAAGAC 60.203 66.667 28.56 0.00 40.92 3.01
264 265 3.569873 GCTAGTAAAGCCCCTTGCA 57.430 52.632 0.00 0.00 46.25 4.08
277 278 4.451900 CATTTTAAGACATCGGGGCTAGT 58.548 43.478 0.00 0.00 0.00 2.57
284 285 5.269459 CCGATAGCATTTTAAGACATCGG 57.731 43.478 5.79 5.79 45.00 4.18
294 295 4.460263 TCATTAGCACCCGATAGCATTTT 58.540 39.130 0.00 0.00 0.00 1.82
299 300 1.344763 ACCTCATTAGCACCCGATAGC 59.655 52.381 0.00 0.00 0.00 2.97
304 305 2.767505 GGATAACCTCATTAGCACCCG 58.232 52.381 0.00 0.00 30.27 5.28
312 313 3.992943 TTGACCACGGATAACCTCATT 57.007 42.857 0.00 0.00 0.00 2.57
319 320 1.766496 GGAGGGATTGACCACGGATAA 59.234 52.381 0.00 0.00 41.20 1.75
325 326 1.073923 AGTGTTGGAGGGATTGACCAC 59.926 52.381 0.00 0.00 41.20 4.16
380 381 3.149648 GGGGCATGCATGGTGACC 61.150 66.667 27.34 18.90 44.43 4.02
398 399 7.354751 AGGAAAGAATACATCCTCTCTACAC 57.645 40.000 0.00 0.00 39.36 2.90
410 411 6.126863 AGTCATGGACAAGGAAAGAATACA 57.873 37.500 0.00 0.00 34.60 2.29
423 424 1.293179 CCACAGCGAGTCATGGACA 59.707 57.895 0.00 0.00 34.60 4.02
425 426 0.613572 TACCCACAGCGAGTCATGGA 60.614 55.000 0.00 0.00 33.80 3.41
449 453 7.868415 GTCAGACTATTTATATTCAGCCTCGTT 59.132 37.037 0.00 0.00 0.00 3.85
450 454 7.014326 TGTCAGACTATTTATATTCAGCCTCGT 59.986 37.037 1.31 0.00 0.00 4.18
451 455 7.371159 TGTCAGACTATTTATATTCAGCCTCG 58.629 38.462 1.31 0.00 0.00 4.63
533 537 8.467598 TGTTAAGTCTTATAGTAGACAAGCCAG 58.532 37.037 7.21 0.00 45.57 4.85
577 581 2.540101 GGCTTCATTAAGTCATCGTCGG 59.460 50.000 0.00 0.00 37.28 4.79
583 587 3.197766 TGACCGAGGCTTCATTAAGTCAT 59.802 43.478 0.00 0.00 39.94 3.06
592 596 1.860641 TAGGATTGACCGAGGCTTCA 58.139 50.000 0.00 0.00 44.74 3.02
632 636 5.429957 AAAGAACAGTTTGCACAGATCTC 57.570 39.130 0.00 0.00 0.00 2.75
766 773 2.158549 AGCCAGGATTAGAAATGAGGGC 60.159 50.000 0.00 0.00 39.14 5.19
832 839 8.669055 TTTACACTAACCTCTTACTAATCCCA 57.331 34.615 0.00 0.00 0.00 4.37
1005 1035 3.685272 CGTGGCTCTCGCTTATCTCTATA 59.315 47.826 0.00 0.00 36.09 1.31
1054 1086 3.117550 TCTTGGAGAGGAGAGGAGAGATG 60.118 52.174 0.00 0.00 0.00 2.90
1259 1325 4.269523 ACAGCCGCCTTGAAGCCA 62.270 61.111 0.00 0.00 0.00 4.75
1412 1478 0.112995 TGCTGGAGAGTTTGGCCATT 59.887 50.000 6.09 0.00 0.00 3.16
1442 1508 0.454600 CGTAGGCGAGCTTGTAGGAA 59.545 55.000 2.14 0.00 41.33 3.36
1882 3612 1.221840 GGCTTGGCATCCTTCTCGA 59.778 57.895 0.00 0.00 0.00 4.04
1985 3715 6.932356 AAAGCTCATTGATTCGATGTGTAT 57.068 33.333 12.61 3.01 0.00 2.29
2012 3742 8.992073 GCAAGATTGTAATCAAAACCTTTGATT 58.008 29.630 23.52 23.52 46.97 2.57
2039 3769 4.402474 CCCTTTCCTTGCCGATTTTCTAAT 59.598 41.667 0.00 0.00 0.00 1.73
2089 3820 4.742201 GCCGAGCGAGTCAAGGCA 62.742 66.667 9.43 0.00 46.48 4.75
2113 3844 5.541484 ACAAAGAAGGAAGCATCAGGAAAAT 59.459 36.000 0.00 0.00 0.00 1.82
2242 3979 6.576185 ACGCTTTTATATTAAGAACGGAGGA 58.424 36.000 0.00 0.00 0.00 3.71
2250 3987 8.671028 GGGACTCAAAACGCTTTTATATTAAGA 58.329 33.333 0.00 0.00 0.00 2.10
2252 3989 8.338072 TGGGACTCAAAACGCTTTTATATTAA 57.662 30.769 0.00 0.00 0.00 1.40
2261 3998 7.990886 TCTTATATTATGGGACTCAAAACGCTT 59.009 33.333 0.00 0.00 0.00 4.68
2265 4002 7.441458 ACGCTCTTATATTATGGGACTCAAAAC 59.559 37.037 0.00 0.00 0.00 2.43
2275 4012 9.385902 CAATGTCAAAACGCTCTTATATTATGG 57.614 33.333 0.00 0.00 0.00 2.74
2288 4025 5.187480 GCTTTTAACACAATGTCAAAACGC 58.813 37.500 0.00 0.00 29.96 4.84
2303 4040 9.908152 GTCCCATAATATATGGTTGCTTTTAAC 57.092 33.333 13.78 0.00 37.48 2.01
2305 4042 7.392113 CCGTCCCATAATATATGGTTGCTTTTA 59.608 37.037 13.78 0.00 37.48 1.52
2310 4047 4.839121 TCCGTCCCATAATATATGGTTGC 58.161 43.478 13.78 4.58 37.48 4.17
2386 4153 9.503427 AAATGCTTTATGCTAGTATTTCGAAAC 57.497 29.630 13.81 1.78 43.37 2.78
2416 4189 4.474226 AAAGCTTCTAGTTCGTTGCAAG 57.526 40.909 0.00 0.00 0.00 4.01
2777 4550 7.504574 GGTAAGAAGCAATAGCCCCTTTATTAA 59.495 37.037 0.00 0.00 43.56 1.40
2823 4596 4.211374 GGACGAAAATCTTATGATGGACCG 59.789 45.833 0.00 0.00 32.44 4.79
2829 4602 4.049186 CCGACGGACGAAAATCTTATGAT 58.951 43.478 8.64 0.00 45.77 2.45
2835 4608 0.316204 ACACCGACGGACGAAAATCT 59.684 50.000 23.38 0.00 45.77 2.40
2861 4634 3.067833 TGCCAAACACGACGAATCATTA 58.932 40.909 0.00 0.00 0.00 1.90
2862 4635 1.876799 TGCCAAACACGACGAATCATT 59.123 42.857 0.00 0.00 0.00 2.57
2864 4637 0.584396 GTGCCAAACACGACGAATCA 59.416 50.000 0.00 0.00 40.07 2.57
2865 4638 3.361443 GTGCCAAACACGACGAATC 57.639 52.632 0.00 0.00 40.07 2.52
2932 4720 4.069304 CTGAGGGACGGACACAAAAATAA 58.931 43.478 0.00 0.00 0.00 1.40
2987 4775 1.267806 GTTCGAGTCCGACTGGTGTTA 59.732 52.381 5.57 0.00 45.50 2.41
3033 4824 4.635699 AGTGGTCTAGTTTGTTTAGGGG 57.364 45.455 0.00 0.00 0.00 4.79
3038 4829 9.623000 ACAAGTTTATAGTGGTCTAGTTTGTTT 57.377 29.630 0.00 0.00 0.00 2.83
3105 5061 2.088423 CCTAGCTCACGACAGAGAACT 58.912 52.381 0.00 0.00 37.87 3.01
3109 5065 2.548057 GAGATCCTAGCTCACGACAGAG 59.452 54.545 0.00 0.00 38.68 3.35
3162 5132 3.378427 GCAAAGTTTAGATACCAGGCAGG 59.622 47.826 0.00 0.00 45.67 4.85
3188 5158 8.922676 GCAATCATTTCCTTTCATAATATGCAG 58.077 33.333 0.00 0.00 0.00 4.41
3380 5375 7.847078 CACAATTCTTACTGTTGTGCATTTTTG 59.153 33.333 4.76 0.00 44.00 2.44
3390 5385 3.057315 CCAGCCCACAATTCTTACTGTTG 60.057 47.826 0.00 0.00 0.00 3.33
3422 5421 8.877864 AACTCAATTTACTCCAACCATAATCA 57.122 30.769 0.00 0.00 0.00 2.57
3488 5487 0.837940 TCTCGCCTAGGAGCTGAGTA 59.162 55.000 14.75 1.72 35.94 2.59
3491 5490 0.256177 TCTTCTCGCCTAGGAGCTGA 59.744 55.000 14.75 8.43 33.98 4.26
3531 5530 0.042131 ACTTATCTCACGGGGGTGGA 59.958 55.000 0.00 0.00 0.00 4.02
3540 5539 7.096477 GCAACAAAAATGTGTCACTTATCTCAC 60.096 37.037 4.27 0.00 0.00 3.51
3541 5540 6.917477 GCAACAAAAATGTGTCACTTATCTCA 59.083 34.615 4.27 0.00 0.00 3.27
3542 5541 7.141363 AGCAACAAAAATGTGTCACTTATCTC 58.859 34.615 4.27 0.00 0.00 2.75
3543 5542 7.042797 AGCAACAAAAATGTGTCACTTATCT 57.957 32.000 4.27 0.00 0.00 1.98
3544 5543 8.853345 CATAGCAACAAAAATGTGTCACTTATC 58.147 33.333 4.27 0.00 0.00 1.75
3545 5544 8.575589 TCATAGCAACAAAAATGTGTCACTTAT 58.424 29.630 4.27 0.00 0.00 1.73
3550 5578 8.484641 TTTTTCATAGCAACAAAAATGTGTCA 57.515 26.923 0.00 0.00 0.00 3.58
3593 5621 7.480760 TGCATGTAGATCAAGCAGGTATATA 57.519 36.000 0.00 0.00 44.16 0.86
3626 5654 1.877443 GTTTTGGCAGAGCGAAGGTTA 59.123 47.619 0.00 0.00 39.88 2.85
3640 5668 1.399089 ACTGTCGTGTTTCCGTTTTGG 59.601 47.619 0.00 0.00 40.09 3.28
3720 5748 1.512156 AAAGTTAAGGGCCACGCACG 61.512 55.000 6.18 0.00 36.86 5.34


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

AutoCloner maintained by Alex Coulton.