Multiple sequence alignment - TraesCS3A01G235700

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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 TraesCS3A01G235700 chr3A 100.000 4010 0 0 1 4010 439457439 439461448 0.000000e+00 7406.0
1 TraesCS3A01G235700 chr3D 94.247 3320 149 23 79 3380 325709676 325706381 0.000000e+00 5035.0
2 TraesCS3A01G235700 chr3D 87.758 629 63 9 3386 4010 213082523 213081905 0.000000e+00 723.0
3 TraesCS3A01G235700 chr3B 94.453 3263 150 15 127 3367 423180573 423177320 0.000000e+00 4994.0
4 TraesCS3A01G235700 chr3B 87.797 631 59 11 3385 4010 647942011 647941394 0.000000e+00 723.0
5 TraesCS3A01G235700 chr3B 85.377 212 30 1 503 713 18787258 18787047 6.750000e-53 219.0
6 TraesCS3A01G235700 chr2D 90.605 628 49 6 3385 4010 325986689 325987308 0.000000e+00 824.0
7 TraesCS3A01G235700 chr2D 79.747 237 42 5 504 737 503574882 503575115 2.480000e-37 167.0
8 TraesCS3A01G235700 chr4D 90.713 603 47 5 3408 4008 72432704 72433299 0.000000e+00 795.0
9 TraesCS3A01G235700 chr4D 91.791 268 19 3 84 349 305193677 305193943 1.760000e-98 370.0
10 TraesCS3A01G235700 chr4D 91.954 261 18 3 84 342 94508368 94508627 2.950000e-96 363.0
11 TraesCS3A01G235700 chr4D 91.538 260 21 1 84 342 294000426 294000685 1.370000e-94 357.0
12 TraesCS3A01G235700 chr4D 88.362 232 26 1 507 737 281304100 281303869 1.100000e-70 278.0
13 TraesCS3A01G235700 chr4D 100.000 33 0 0 47 79 285036414 285036382 1.200000e-05 62.1
14 TraesCS3A01G235700 chr7A 88.553 629 60 11 3386 4010 130455843 130456463 0.000000e+00 752.0
15 TraesCS3A01G235700 chr7A 88.357 627 60 12 3388 4010 649609597 649610214 0.000000e+00 741.0
16 TraesCS3A01G235700 chr1D 88.076 629 64 9 3386 4010 34987 35608 0.000000e+00 736.0
17 TraesCS3A01G235700 chr1D 91.353 266 18 5 84 345 305990281 305990017 3.810000e-95 359.0
18 TraesCS3A01G235700 chr1D 90.909 264 17 6 84 343 270483959 270484219 8.250000e-92 348.0
19 TraesCS3A01G235700 chr1D 100.000 46 0 0 1 46 350963791 350963836 7.140000e-13 86.1
20 TraesCS3A01G235700 chr1D 100.000 33 0 0 47 79 350957980 350958012 1.200000e-05 62.1
21 TraesCS3A01G235700 chr1D 100.000 33 0 0 47 79 461629683 461629651 1.200000e-05 62.1
22 TraesCS3A01G235700 chr5B 87.539 634 73 6 3380 4010 185545188 185544558 0.000000e+00 728.0
23 TraesCS3A01G235700 chr5B 79.186 221 28 9 507 726 675891102 675890899 1.940000e-28 137.0
24 TraesCS3A01G235700 chr5B 77.570 214 43 5 503 713 522354263 522354052 1.510000e-24 124.0
25 TraesCS3A01G235700 chr1A 87.559 635 68 11 3380 4010 307473848 307474475 0.000000e+00 725.0
26 TraesCS3A01G235700 chr7B 91.571 261 19 3 84 342 91754762 91754503 1.370000e-94 357.0
27 TraesCS3A01G235700 chr6D 90.000 270 21 6 84 348 295470802 295470534 1.070000e-90 344.0
28 TraesCS3A01G235700 chr6D 100.000 46 0 0 1 46 108499146 108499101 7.140000e-13 86.1
29 TraesCS3A01G235700 chr6D 100.000 33 0 0 47 79 108504986 108504954 1.200000e-05 62.1
30 TraesCS3A01G235700 chr6D 100.000 33 0 0 47 79 172752808 172752776 1.200000e-05 62.1
31 TraesCS3A01G235700 chr5A 80.000 245 41 8 503 743 9463046 9463286 1.480000e-39 174.0
32 TraesCS3A01G235700 chr5D 79.325 237 38 10 507 737 546034567 546034336 5.370000e-34 156.0
33 TraesCS3A01G235700 chr5D 77.083 240 47 8 503 738 513194163 513193928 9.040000e-27 132.0
34 TraesCS3A01G235700 chr5D 76.543 243 48 9 503 740 431695452 431695214 1.510000e-24 124.0
35 TraesCS3A01G235700 chr5D 76.471 238 48 7 503 737 433716708 433716940 5.440000e-24 122.0
36 TraesCS3A01G235700 chr2B 77.542 236 43 9 507 737 52898774 52898544 2.510000e-27 134.0
37 TraesCS3A01G235700 chrUn 100.000 46 0 0 1 46 77787248 77787293 7.140000e-13 86.1
38 TraesCS3A01G235700 chrUn 100.000 46 0 0 1 46 231552244 231552289 7.140000e-13 86.1
39 TraesCS3A01G235700 chrUn 100.000 46 0 0 1 46 312172347 312172392 7.140000e-13 86.1
40 TraesCS3A01G235700 chrUn 100.000 46 0 0 1 46 385941773 385941818 7.140000e-13 86.1
41 TraesCS3A01G235700 chrUn 100.000 46 0 0 1 46 389107738 389107693 7.140000e-13 86.1
42 TraesCS3A01G235700 chrUn 100.000 33 0 0 47 79 45085763 45085795 1.200000e-05 62.1
43 TraesCS3A01G235700 chrUn 100.000 33 0 0 47 79 182460088 182460056 1.200000e-05 62.1
44 TraesCS3A01G235700 chrUn 100.000 33 0 0 47 79 186159623 186159655 1.200000e-05 62.1
45 TraesCS3A01G235700 chrUn 100.000 33 0 0 47 79 231546410 231546442 1.200000e-05 62.1
46 TraesCS3A01G235700 chr6A 100.000 46 0 0 1 46 338458371 338458416 7.140000e-13 86.1
47 TraesCS3A01G235700 chr4B 100.000 46 0 0 1 46 533729114 533729159 7.140000e-13 86.1


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 TraesCS3A01G235700 chr3A 439457439 439461448 4009 False 7406 7406 100.000 1 4010 1 chr3A.!!$F1 4009
1 TraesCS3A01G235700 chr3D 325706381 325709676 3295 True 5035 5035 94.247 79 3380 1 chr3D.!!$R2 3301
2 TraesCS3A01G235700 chr3D 213081905 213082523 618 True 723 723 87.758 3386 4010 1 chr3D.!!$R1 624
3 TraesCS3A01G235700 chr3B 423177320 423180573 3253 True 4994 4994 94.453 127 3367 1 chr3B.!!$R2 3240
4 TraesCS3A01G235700 chr3B 647941394 647942011 617 True 723 723 87.797 3385 4010 1 chr3B.!!$R3 625
5 TraesCS3A01G235700 chr2D 325986689 325987308 619 False 824 824 90.605 3385 4010 1 chr2D.!!$F1 625
6 TraesCS3A01G235700 chr4D 72432704 72433299 595 False 795 795 90.713 3408 4008 1 chr4D.!!$F1 600
7 TraesCS3A01G235700 chr7A 130455843 130456463 620 False 752 752 88.553 3386 4010 1 chr7A.!!$F1 624
8 TraesCS3A01G235700 chr7A 649609597 649610214 617 False 741 741 88.357 3388 4010 1 chr7A.!!$F2 622
9 TraesCS3A01G235700 chr1D 34987 35608 621 False 736 736 88.076 3386 4010 1 chr1D.!!$F1 624
10 TraesCS3A01G235700 chr5B 185544558 185545188 630 True 728 728 87.539 3380 4010 1 chr5B.!!$R1 630
11 TraesCS3A01G235700 chr1A 307473848 307474475 627 False 725 725 87.559 3380 4010 1 chr1A.!!$F1 630

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
869 876 0.039165 CTTTTGCTTTCGGCCACTCC 60.039 55.0 2.24 0.0 40.92 3.85 F
1296 1303 0.534203 ACCGCGTCACAAGGTTCATT 60.534 50.0 4.92 0.0 33.96 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2025 0.034863 TAAATGAGGACCGTTGGCCC 60.035 55.0 0.00 0.0 0.0 5.80 R
3227 3271 0.682292 TTACGGTGACACAGGCATCA 59.318 50.0 10.55 0.0 0.0 3.07 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
21 22 3.627395 ACCGGAGTCATTGATTAAGCA 57.373 42.857 9.46 0.00 0.00 3.91
22 23 3.535561 ACCGGAGTCATTGATTAAGCAG 58.464 45.455 9.46 0.00 0.00 4.24
23 24 2.874701 CCGGAGTCATTGATTAAGCAGG 59.125 50.000 0.00 0.00 0.00 4.85
24 25 3.535561 CGGAGTCATTGATTAAGCAGGT 58.464 45.455 0.00 0.00 0.00 4.00
25 26 3.557595 CGGAGTCATTGATTAAGCAGGTC 59.442 47.826 0.00 0.00 0.00 3.85
26 27 4.517285 GGAGTCATTGATTAAGCAGGTCA 58.483 43.478 0.00 0.00 0.00 4.02
27 28 4.574013 GGAGTCATTGATTAAGCAGGTCAG 59.426 45.833 0.00 0.00 0.00 3.51
28 29 5.423015 GAGTCATTGATTAAGCAGGTCAGA 58.577 41.667 0.00 0.00 0.00 3.27
29 30 5.999044 AGTCATTGATTAAGCAGGTCAGAT 58.001 37.500 0.00 0.00 0.00 2.90
30 31 5.821470 AGTCATTGATTAAGCAGGTCAGATG 59.179 40.000 0.00 0.00 0.00 2.90
31 32 5.008415 GTCATTGATTAAGCAGGTCAGATGG 59.992 44.000 0.00 0.00 0.00 3.51
32 33 3.565764 TGATTAAGCAGGTCAGATGGG 57.434 47.619 0.00 0.00 0.00 4.00
33 34 2.225467 GATTAAGCAGGTCAGATGGGC 58.775 52.381 0.00 0.00 0.00 5.36
34 35 1.289160 TTAAGCAGGTCAGATGGGCT 58.711 50.000 0.00 0.00 36.13 5.19
35 36 1.289160 TAAGCAGGTCAGATGGGCTT 58.711 50.000 0.00 0.00 45.78 4.35
36 37 1.289160 AAGCAGGTCAGATGGGCTTA 58.711 50.000 0.00 0.00 42.51 3.09
37 38 0.835941 AGCAGGTCAGATGGGCTTAG 59.164 55.000 0.00 0.00 0.00 2.18
38 39 0.543749 GCAGGTCAGATGGGCTTAGT 59.456 55.000 0.00 0.00 0.00 2.24
39 40 1.762957 GCAGGTCAGATGGGCTTAGTA 59.237 52.381 0.00 0.00 0.00 1.82
40 41 2.224161 GCAGGTCAGATGGGCTTAGTAG 60.224 54.545 0.00 0.00 0.00 2.57
41 42 2.366916 CAGGTCAGATGGGCTTAGTAGG 59.633 54.545 0.00 0.00 0.00 3.18
42 43 1.694696 GGTCAGATGGGCTTAGTAGGG 59.305 57.143 0.00 0.00 0.00 3.53
43 44 1.070914 GTCAGATGGGCTTAGTAGGGC 59.929 57.143 0.00 0.00 0.00 5.19
44 45 1.062121 TCAGATGGGCTTAGTAGGGCT 60.062 52.381 5.80 0.00 0.00 5.19
45 46 1.346068 CAGATGGGCTTAGTAGGGCTC 59.654 57.143 5.80 0.00 0.00 4.70
46 47 1.221781 AGATGGGCTTAGTAGGGCTCT 59.778 52.381 5.80 0.00 0.00 4.09
47 48 1.346068 GATGGGCTTAGTAGGGCTCTG 59.654 57.143 0.00 0.00 0.00 3.35
48 49 0.042731 TGGGCTTAGTAGGGCTCTGT 59.957 55.000 0.00 0.00 0.00 3.41
49 50 1.205055 GGGCTTAGTAGGGCTCTGTT 58.795 55.000 0.00 0.00 0.00 3.16
50 51 1.560146 GGGCTTAGTAGGGCTCTGTTT 59.440 52.381 0.00 0.00 0.00 2.83
51 52 2.633488 GGCTTAGTAGGGCTCTGTTTG 58.367 52.381 0.00 0.00 0.00 2.93
52 53 2.027100 GGCTTAGTAGGGCTCTGTTTGT 60.027 50.000 0.00 0.00 0.00 2.83
53 54 3.559384 GGCTTAGTAGGGCTCTGTTTGTT 60.559 47.826 0.00 0.00 0.00 2.83
54 55 3.437049 GCTTAGTAGGGCTCTGTTTGTTG 59.563 47.826 0.00 0.00 0.00 3.33
55 56 1.897560 AGTAGGGCTCTGTTTGTTGC 58.102 50.000 0.00 0.00 0.00 4.17
56 57 0.881796 GTAGGGCTCTGTTTGTTGCC 59.118 55.000 0.00 0.00 44.22 4.52
57 58 0.771127 TAGGGCTCTGTTTGTTGCCT 59.229 50.000 0.00 0.00 44.36 4.75
58 59 0.106015 AGGGCTCTGTTTGTTGCCTT 60.106 50.000 0.00 0.00 44.36 4.35
59 60 0.315251 GGGCTCTGTTTGTTGCCTTC 59.685 55.000 0.00 0.00 44.36 3.46
60 61 1.322442 GGCTCTGTTTGTTGCCTTCT 58.678 50.000 0.00 0.00 41.92 2.85
61 62 1.683385 GGCTCTGTTTGTTGCCTTCTT 59.317 47.619 0.00 0.00 41.92 2.52
62 63 2.287849 GGCTCTGTTTGTTGCCTTCTTC 60.288 50.000 0.00 0.00 41.92 2.87
63 64 2.603173 GCTCTGTTTGTTGCCTTCTTCG 60.603 50.000 0.00 0.00 0.00 3.79
64 65 2.872245 CTCTGTTTGTTGCCTTCTTCGA 59.128 45.455 0.00 0.00 0.00 3.71
65 66 2.612212 TCTGTTTGTTGCCTTCTTCGAC 59.388 45.455 0.00 0.00 0.00 4.20
66 67 1.673920 TGTTTGTTGCCTTCTTCGACC 59.326 47.619 0.00 0.00 0.00 4.79
67 68 0.941542 TTTGTTGCCTTCTTCGACCG 59.058 50.000 0.00 0.00 0.00 4.79
68 69 0.105224 TTGTTGCCTTCTTCGACCGA 59.895 50.000 0.00 0.00 0.00 4.69
69 70 0.599204 TGTTGCCTTCTTCGACCGAC 60.599 55.000 0.00 0.00 0.00 4.79
70 71 0.599204 GTTGCCTTCTTCGACCGACA 60.599 55.000 0.00 0.00 0.00 4.35
71 72 0.319555 TTGCCTTCTTCGACCGACAG 60.320 55.000 0.00 0.00 0.00 3.51
72 73 1.176619 TGCCTTCTTCGACCGACAGA 61.177 55.000 0.00 0.00 0.00 3.41
73 74 0.733223 GCCTTCTTCGACCGACAGAC 60.733 60.000 0.00 0.00 0.00 3.51
74 75 0.596577 CCTTCTTCGACCGACAGACA 59.403 55.000 0.00 0.00 0.00 3.41
75 76 1.000607 CCTTCTTCGACCGACAGACAA 60.001 52.381 0.00 0.00 0.00 3.18
76 77 2.320367 CTTCTTCGACCGACAGACAAG 58.680 52.381 0.00 0.00 0.00 3.16
77 78 0.596577 TCTTCGACCGACAGACAAGG 59.403 55.000 0.00 0.00 0.00 3.61
109 110 0.594602 TCCAAGTCACGTAGGTGTCG 59.405 55.000 14.78 3.14 44.68 4.35
111 112 1.269413 CCAAGTCACGTAGGTGTCGTT 60.269 52.381 14.78 5.05 44.68 3.85
112 113 2.049228 CAAGTCACGTAGGTGTCGTTC 58.951 52.381 14.78 3.33 44.68 3.95
121 122 1.111116 AGGTGTCGTTCGGTCCAAGA 61.111 55.000 0.00 0.00 0.00 3.02
156 157 6.954487 AAAGTTTTATTCCGTTTGGACTCT 57.046 33.333 0.00 0.00 46.45 3.24
173 174 9.581289 TTTGGACTCTGTTTGATAATCCTTTTA 57.419 29.630 0.00 0.00 0.00 1.52
177 178 9.994432 GACTCTGTTTGATAATCCTTTTATGTG 57.006 33.333 0.00 0.00 0.00 3.21
371 375 2.029288 CAGCAGCGCGGGGTATATG 61.029 63.158 8.83 0.00 0.00 1.78
396 400 6.415206 ACCCGCACAACTATTACACTATAT 57.585 37.500 0.00 0.00 0.00 0.86
397 401 6.220930 ACCCGCACAACTATTACACTATATG 58.779 40.000 0.00 0.00 0.00 1.78
421 425 2.033448 GTGGGGTTGTGATCCGCA 59.967 61.111 0.00 0.00 43.75 5.69
438 442 8.562892 GTGATCCGCACTACTACTACTTAATAA 58.437 37.037 0.00 0.00 44.27 1.40
468 472 2.125106 CTTACCCCTCGCCAGTGC 60.125 66.667 0.00 0.00 0.00 4.40
485 489 5.927115 GCCAGTGCTATTTGTCTACCTATAC 59.073 44.000 0.00 0.00 33.53 1.47
493 497 9.533253 GCTATTTGTCTACCTATACGGTTTTTA 57.467 33.333 0.00 0.00 46.37 1.52
620 624 2.629051 GTTGGTCAACTATAGCCGCTT 58.371 47.619 0.00 0.00 38.25 4.68
623 627 1.202382 GGTCAACTATAGCCGCTTCGT 60.202 52.381 0.00 0.00 0.00 3.85
670 674 1.475280 CGGTTCCACCTTGTATCGAGA 59.525 52.381 0.00 0.00 35.66 4.04
678 682 4.935205 CCACCTTGTATCGAGAATTTGTGA 59.065 41.667 0.00 0.00 0.00 3.58
689 693 5.312120 GAGAATTTGTGACCTCTCGACTA 57.688 43.478 0.00 0.00 0.00 2.59
869 876 0.039165 CTTTTGCTTTCGGCCACTCC 60.039 55.000 2.24 0.00 40.92 3.85
886 893 3.977244 CCTGCACGTTGTTGGCCC 61.977 66.667 0.00 0.00 0.00 5.80
906 913 4.416738 GGGAGAGCTGGTGGCACC 62.417 72.222 29.75 29.75 44.79 5.01
936 943 7.359598 GCAGTGACATCCGTATTTATCTGAATC 60.360 40.741 0.00 0.00 0.00 2.52
945 952 4.825546 ATTTATCTGAATCGCAGCCTTG 57.174 40.909 0.00 0.00 44.52 3.61
951 958 0.727398 GAATCGCAGCCTTGTACCAC 59.273 55.000 0.00 0.00 0.00 4.16
1120 1127 2.696893 GCCTCCTAGACCCCCTCA 59.303 66.667 0.00 0.00 0.00 3.86
1247 1254 2.434359 CCCGGCCTCGTTCTTCAC 60.434 66.667 0.00 0.00 33.95 3.18
1296 1303 0.534203 ACCGCGTCACAAGGTTCATT 60.534 50.000 4.92 0.00 33.96 2.57
1308 1315 1.062258 GGTTCATTTACGCGACGTCA 58.938 50.000 15.93 0.00 41.54 4.35
1506 1513 2.571757 CTGGACTTCGCGCTGGTA 59.428 61.111 5.56 0.00 0.00 3.25
1509 1516 2.260434 GACTTCGCGCTGGTACCA 59.740 61.111 15.39 15.39 0.00 3.25
1711 1718 5.794894 AGTACTGTTCTGAGGGTGTTATTG 58.205 41.667 0.00 0.00 0.00 1.90
1913 1922 1.374758 CTGTCCCAGCGAGTTCACC 60.375 63.158 0.00 0.00 0.00 4.02
1955 1964 0.606401 CGTTCCCACTTCTGCATGGT 60.606 55.000 3.47 0.00 33.80 3.55
1965 1974 2.672651 TGCATGGTGCTTGGGTCG 60.673 61.111 3.41 0.00 45.31 4.79
2014 2025 4.151335 CCGAATCTGACTGAAGTTGACAAG 59.849 45.833 0.00 0.00 0.00 3.16
2023 2034 1.106944 AAGTTGACAAGGGCCAACGG 61.107 55.000 6.18 0.00 45.19 4.44
2227 2241 7.929785 GGATTTTGGAACATCTGCATTTCATAT 59.070 33.333 0.00 0.00 39.30 1.78
2261 2275 0.944311 CTCGAAGGTGTTCACGGGTG 60.944 60.000 0.00 0.00 32.36 4.61
2264 2278 2.047213 GAAGGTGTTCACGGGTGGGA 62.047 60.000 0.00 0.00 32.36 4.37
2265 2279 2.281276 GGTGTTCACGGGTGGGAC 60.281 66.667 0.00 0.00 0.00 4.46
2276 2290 2.098233 GGTGGGACGTGCGTGTATG 61.098 63.158 0.67 0.00 0.00 2.39
2282 2296 1.727880 GGACGTGCGTGTATGCTTTTA 59.272 47.619 0.67 0.00 35.36 1.52
2287 2301 3.799963 CGTGCGTGTATGCTTTTATAGGA 59.200 43.478 0.00 0.00 35.36 2.94
2400 2440 3.733443 AATTTTTGACAGGTGCTGACC 57.267 42.857 0.00 0.00 43.52 4.02
2411 2451 1.351153 GTGCTGACCGAAGTAAGAGC 58.649 55.000 0.00 0.00 0.00 4.09
2532 2572 3.861263 GGATTCAACGTCCGCGGC 61.861 66.667 23.51 15.21 43.45 6.53
2533 2573 2.813908 GATTCAACGTCCGCGGCT 60.814 61.111 23.51 1.28 43.45 5.52
2617 2657 2.031682 CAGTTCAAGAAGGCTTTCCACG 60.032 50.000 4.73 0.00 33.64 4.94
2877 2917 0.877071 ACTTGGCGCTCATCAACAAG 59.123 50.000 7.64 12.87 43.01 3.16
2950 2990 2.614057 GAGAATAACAAGGGCATGGTCG 59.386 50.000 0.00 0.00 0.00 4.79
3066 3110 8.280497 AGGCTTTTTACGAAATATAATACTGCG 58.720 33.333 0.00 0.00 0.00 5.18
3123 3167 7.593644 ACTTTTTACCGTCAAATATTTCTGTGC 59.406 33.333 0.00 0.00 0.00 4.57
3209 3253 7.250569 ACAAGATATGTTTGCACCGAAATTAG 58.749 34.615 0.00 0.00 40.06 1.73
3256 3300 2.991866 GTGTCACCGTAAGTAAAGCCTC 59.008 50.000 0.00 0.00 0.00 4.70
3258 3302 1.888512 TCACCGTAAGTAAAGCCTCGT 59.111 47.619 0.00 0.00 0.00 4.18
3304 3348 2.287009 GGACAAAGTTGAACAAGCTCCG 60.287 50.000 0.00 0.00 0.00 4.63
3312 3356 1.134699 TGAACAAGCTCCGGCATAGAG 60.135 52.381 0.00 0.00 41.70 2.43
3355 3399 6.141527 GTCGACGAGACTATGATTTCTCATTG 59.858 42.308 0.00 0.00 46.13 2.82
3360 3404 6.129326 CGAGACTATGATTTCTCATTGTACGC 60.129 42.308 3.32 0.75 44.41 4.42
3369 3413 1.321743 CTCATTGTACGCTCTTGACGC 59.678 52.381 0.00 0.00 0.00 5.19
3370 3414 1.067693 CATTGTACGCTCTTGACGCA 58.932 50.000 0.00 0.00 0.00 5.24
3371 3415 1.059692 CATTGTACGCTCTTGACGCAG 59.940 52.381 0.00 0.00 0.00 5.18
3372 3416 0.666274 TTGTACGCTCTTGACGCAGG 60.666 55.000 0.00 0.00 0.00 4.85
3373 3417 1.211969 GTACGCTCTTGACGCAGGA 59.788 57.895 0.00 0.00 0.00 3.86
3374 3418 0.179134 GTACGCTCTTGACGCAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
3375 3419 0.100682 TACGCTCTTGACGCAGGATC 59.899 55.000 0.00 0.00 0.00 3.36
3376 3420 2.226896 CGCTCTTGACGCAGGATCG 61.227 63.158 2.23 2.23 0.00 3.69
3417 3461 4.523943 AGATTACTTTGGCAATGCAACTCA 59.476 37.500 7.79 0.00 0.00 3.41
3476 3521 0.541863 ATAAAGTGGGCCTCGACCTG 59.458 55.000 4.53 0.00 0.00 4.00
3501 3546 4.481280 ACTATACAAGGACTAGGAGGTGGA 59.519 45.833 0.00 0.00 0.00 4.02
3543 3589 5.574891 TGCACAACCATATATTCAACACC 57.425 39.130 0.00 0.00 0.00 4.16
3544 3590 5.012893 TGCACAACCATATATTCAACACCA 58.987 37.500 0.00 0.00 0.00 4.17
3545 3591 5.105957 TGCACAACCATATATTCAACACCAC 60.106 40.000 0.00 0.00 0.00 4.16
3546 3592 5.678616 GCACAACCATATATTCAACACCACC 60.679 44.000 0.00 0.00 0.00 4.61
3547 3593 4.953579 ACAACCATATATTCAACACCACCC 59.046 41.667 0.00 0.00 0.00 4.61
3548 3594 4.178956 ACCATATATTCAACACCACCCC 57.821 45.455 0.00 0.00 0.00 4.95
3603 3654 2.576615 GCAAAGACTGGACCTGAACTT 58.423 47.619 5.22 7.41 0.00 2.66
3693 3744 2.270205 CCAGATGCGCCCAAGAGT 59.730 61.111 4.18 0.00 0.00 3.24
3694 3745 2.110967 CCAGATGCGCCCAAGAGTG 61.111 63.158 4.18 0.00 0.00 3.51
3835 3886 1.134521 ACGTCACAAAGCAACTCCTGA 60.135 47.619 0.00 0.00 0.00 3.86
3972 4024 2.352421 CGACCCAAGGTACACACAGTAG 60.352 54.545 0.00 0.00 35.25 2.57
3984 4036 1.229082 ACAGTAGCCCGAGGTGGAA 60.229 57.895 0.00 0.00 42.00 3.53
3987 4039 2.036098 TAGCCCGAGGTGGAACGA 59.964 61.111 0.00 0.00 42.00 3.85
3989 4041 3.998672 GCCCGAGGTGGAACGACA 61.999 66.667 0.00 0.00 42.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.442893 CCTGCTTAATCAATGACTCCGGTA 60.443 45.833 0.00 0.00 0.00 4.02
1 2 3.535561 CTGCTTAATCAATGACTCCGGT 58.464 45.455 0.00 0.00 0.00 5.28
2 3 2.874701 CCTGCTTAATCAATGACTCCGG 59.125 50.000 0.00 0.00 0.00 5.14
3 4 3.535561 ACCTGCTTAATCAATGACTCCG 58.464 45.455 0.00 0.00 0.00 4.63
4 5 4.517285 TGACCTGCTTAATCAATGACTCC 58.483 43.478 0.00 0.00 0.00 3.85
5 6 5.423015 TCTGACCTGCTTAATCAATGACTC 58.577 41.667 0.00 0.00 0.00 3.36
6 7 5.426689 TCTGACCTGCTTAATCAATGACT 57.573 39.130 0.00 0.00 0.00 3.41
7 8 5.008415 CCATCTGACCTGCTTAATCAATGAC 59.992 44.000 0.00 0.00 0.00 3.06
8 9 5.128205 CCATCTGACCTGCTTAATCAATGA 58.872 41.667 0.00 0.00 0.00 2.57
9 10 4.277672 CCCATCTGACCTGCTTAATCAATG 59.722 45.833 0.00 0.00 0.00 2.82
10 11 4.467769 CCCATCTGACCTGCTTAATCAAT 58.532 43.478 0.00 0.00 0.00 2.57
11 12 3.889815 CCCATCTGACCTGCTTAATCAA 58.110 45.455 0.00 0.00 0.00 2.57
12 13 2.421952 GCCCATCTGACCTGCTTAATCA 60.422 50.000 0.00 0.00 0.00 2.57
13 14 2.158696 AGCCCATCTGACCTGCTTAATC 60.159 50.000 0.00 0.00 0.00 1.75
14 15 1.849039 AGCCCATCTGACCTGCTTAAT 59.151 47.619 0.00 0.00 0.00 1.40
15 16 1.289160 AGCCCATCTGACCTGCTTAA 58.711 50.000 0.00 0.00 0.00 1.85
16 17 1.289160 AAGCCCATCTGACCTGCTTA 58.711 50.000 7.38 0.00 40.26 3.09
17 18 1.211457 CTAAGCCCATCTGACCTGCTT 59.789 52.381 12.19 12.19 43.97 3.91
18 19 0.835941 CTAAGCCCATCTGACCTGCT 59.164 55.000 0.00 0.00 0.00 4.24
19 20 0.543749 ACTAAGCCCATCTGACCTGC 59.456 55.000 0.00 0.00 0.00 4.85
20 21 2.366916 CCTACTAAGCCCATCTGACCTG 59.633 54.545 0.00 0.00 0.00 4.00
21 22 2.683768 CCTACTAAGCCCATCTGACCT 58.316 52.381 0.00 0.00 0.00 3.85
22 23 1.694696 CCCTACTAAGCCCATCTGACC 59.305 57.143 0.00 0.00 0.00 4.02
23 24 1.070914 GCCCTACTAAGCCCATCTGAC 59.929 57.143 0.00 0.00 0.00 3.51
24 25 1.062121 AGCCCTACTAAGCCCATCTGA 60.062 52.381 0.00 0.00 0.00 3.27
25 26 1.346068 GAGCCCTACTAAGCCCATCTG 59.654 57.143 0.00 0.00 0.00 2.90
26 27 1.221781 AGAGCCCTACTAAGCCCATCT 59.778 52.381 0.00 0.00 0.00 2.90
27 28 1.346068 CAGAGCCCTACTAAGCCCATC 59.654 57.143 0.00 0.00 0.00 3.51
28 29 1.344496 ACAGAGCCCTACTAAGCCCAT 60.344 52.381 0.00 0.00 0.00 4.00
29 30 0.042731 ACAGAGCCCTACTAAGCCCA 59.957 55.000 0.00 0.00 0.00 5.36
30 31 1.205055 AACAGAGCCCTACTAAGCCC 58.795 55.000 0.00 0.00 0.00 5.19
31 32 2.027100 ACAAACAGAGCCCTACTAAGCC 60.027 50.000 0.00 0.00 0.00 4.35
32 33 3.336138 ACAAACAGAGCCCTACTAAGC 57.664 47.619 0.00 0.00 0.00 3.09
33 34 3.437049 GCAACAAACAGAGCCCTACTAAG 59.563 47.826 0.00 0.00 0.00 2.18
34 35 3.408634 GCAACAAACAGAGCCCTACTAA 58.591 45.455 0.00 0.00 0.00 2.24
35 36 2.290071 GGCAACAAACAGAGCCCTACTA 60.290 50.000 0.00 0.00 41.25 1.82
36 37 1.545651 GGCAACAAACAGAGCCCTACT 60.546 52.381 0.00 0.00 41.25 2.57
37 38 0.881796 GGCAACAAACAGAGCCCTAC 59.118 55.000 0.00 0.00 41.25 3.18
38 39 3.339547 GGCAACAAACAGAGCCCTA 57.660 52.632 0.00 0.00 41.25 3.53
39 40 4.181051 GGCAACAAACAGAGCCCT 57.819 55.556 0.00 0.00 41.25 5.19
42 43 2.603173 CGAAGAAGGCAACAAACAGAGC 60.603 50.000 0.00 0.00 41.41 4.09
43 44 2.872245 TCGAAGAAGGCAACAAACAGAG 59.128 45.455 0.00 0.00 41.41 3.35
44 45 2.612212 GTCGAAGAAGGCAACAAACAGA 59.388 45.455 0.00 0.00 39.69 3.41
45 46 2.287009 GGTCGAAGAAGGCAACAAACAG 60.287 50.000 0.00 0.00 39.69 3.16
46 47 1.673920 GGTCGAAGAAGGCAACAAACA 59.326 47.619 0.00 0.00 39.69 2.83
47 48 1.333791 CGGTCGAAGAAGGCAACAAAC 60.334 52.381 0.00 0.00 39.69 2.93
48 49 0.941542 CGGTCGAAGAAGGCAACAAA 59.058 50.000 0.00 0.00 39.69 2.83
49 50 0.105224 TCGGTCGAAGAAGGCAACAA 59.895 50.000 0.00 0.00 39.69 2.83
50 51 0.599204 GTCGGTCGAAGAAGGCAACA 60.599 55.000 0.00 0.00 39.69 3.33
51 52 0.599204 TGTCGGTCGAAGAAGGCAAC 60.599 55.000 0.00 0.00 39.69 4.17
52 53 0.319555 CTGTCGGTCGAAGAAGGCAA 60.320 55.000 0.00 0.00 39.69 4.52
53 54 1.176619 TCTGTCGGTCGAAGAAGGCA 61.177 55.000 0.00 0.00 39.69 4.75
54 55 0.733223 GTCTGTCGGTCGAAGAAGGC 60.733 60.000 0.00 0.00 39.69 4.35
55 56 0.596577 TGTCTGTCGGTCGAAGAAGG 59.403 55.000 0.00 0.00 39.69 3.46
56 57 2.320367 CTTGTCTGTCGGTCGAAGAAG 58.680 52.381 0.00 0.00 39.69 2.85
57 58 1.000607 CCTTGTCTGTCGGTCGAAGAA 60.001 52.381 0.00 0.00 39.69 2.52
58 59 0.596577 CCTTGTCTGTCGGTCGAAGA 59.403 55.000 0.00 0.00 0.00 2.87
59 60 0.314302 ACCTTGTCTGTCGGTCGAAG 59.686 55.000 0.00 0.00 0.00 3.79
60 61 0.313043 GACCTTGTCTGTCGGTCGAA 59.687 55.000 0.00 0.00 38.00 3.71
61 62 1.954528 GACCTTGTCTGTCGGTCGA 59.045 57.895 0.00 0.00 38.00 4.20
62 63 4.554163 GACCTTGTCTGTCGGTCG 57.446 61.111 0.00 0.00 38.00 4.79
63 64 2.352519 GGTTAGACCTTGTCTGTCGGTC 60.353 54.545 7.00 0.00 43.30 4.79
64 65 1.617357 GGTTAGACCTTGTCTGTCGGT 59.383 52.381 7.00 0.00 43.30 4.69
65 66 1.067071 GGGTTAGACCTTGTCTGTCGG 60.067 57.143 7.00 0.00 43.30 4.79
66 67 1.893801 AGGGTTAGACCTTGTCTGTCG 59.106 52.381 7.00 0.00 43.30 4.35
67 68 3.166679 AGAGGGTTAGACCTTGTCTGTC 58.833 50.000 7.00 0.58 43.30 3.51
68 69 3.166679 GAGAGGGTTAGACCTTGTCTGT 58.833 50.000 7.00 0.00 43.30 3.41
69 70 3.436243 AGAGAGGGTTAGACCTTGTCTG 58.564 50.000 7.89 0.00 44.50 3.51
70 71 3.837399 AGAGAGGGTTAGACCTTGTCT 57.163 47.619 3.49 3.49 42.03 3.41
71 72 2.761767 GGAGAGAGGGTTAGACCTTGTC 59.238 54.545 0.00 0.00 42.10 3.18
72 73 2.111972 TGGAGAGAGGGTTAGACCTTGT 59.888 50.000 0.00 0.00 42.10 3.16
73 74 2.821437 TGGAGAGAGGGTTAGACCTTG 58.179 52.381 0.00 0.00 42.10 3.61
74 75 3.181405 ACTTGGAGAGAGGGTTAGACCTT 60.181 47.826 0.00 0.00 42.10 3.50
75 76 2.384029 ACTTGGAGAGAGGGTTAGACCT 59.616 50.000 0.00 0.00 45.57 3.85
76 77 2.761767 GACTTGGAGAGAGGGTTAGACC 59.238 54.545 0.00 0.00 37.60 3.85
77 78 3.193903 GTGACTTGGAGAGAGGGTTAGAC 59.806 52.174 0.00 0.00 0.00 2.59
81 82 0.969894 CGTGACTTGGAGAGAGGGTT 59.030 55.000 0.00 0.00 0.00 4.11
109 110 5.371115 TGATGATTTTTCTTGGACCGAAC 57.629 39.130 0.00 0.00 0.00 3.95
111 112 7.393234 ACTTTATGATGATTTTTCTTGGACCGA 59.607 33.333 0.00 0.00 0.00 4.69
112 113 7.538575 ACTTTATGATGATTTTTCTTGGACCG 58.461 34.615 0.00 0.00 0.00 4.79
200 204 4.710375 CCTAGAGCCCAGTGTTAGTTTCTA 59.290 45.833 0.00 0.00 0.00 2.10
208 212 4.409247 CCTATTAACCTAGAGCCCAGTGTT 59.591 45.833 0.00 0.00 0.00 3.32
319 323 7.299586 GTCTGATACGTCTCCAACATATCTAC 58.700 42.308 0.00 0.00 34.78 2.59
326 330 1.822990 GGGTCTGATACGTCTCCAACA 59.177 52.381 0.00 0.00 0.00 3.33
331 335 4.157289 TGTTAAGTGGGTCTGATACGTCTC 59.843 45.833 0.00 0.00 0.00 3.36
371 375 3.332034 AGTGTAATAGTTGTGCGGGTTC 58.668 45.455 0.00 0.00 0.00 3.62
396 400 1.227704 CACAACCCCACGCTACACA 60.228 57.895 0.00 0.00 0.00 3.72
397 401 0.321298 ATCACAACCCCACGCTACAC 60.321 55.000 0.00 0.00 0.00 2.90
421 425 7.604164 TCCGCGCTATTATTAAGTAGTAGTAGT 59.396 37.037 5.56 0.00 0.00 2.73
438 442 1.440476 GGTAAGTGGTCCGCGCTAT 59.560 57.895 5.56 0.00 0.00 2.97
485 489 6.202188 CCATATGCCACTACTAGTAAAAACCG 59.798 42.308 3.76 0.00 0.00 4.44
493 497 6.500589 AAATGACCATATGCCACTACTAGT 57.499 37.500 0.00 0.00 0.00 2.57
575 579 5.174035 CGATCGGCAACTCTATTTTGACTAG 59.826 44.000 7.38 0.00 28.82 2.57
620 624 3.490249 CCACACAACAGTAGTTCTCACGA 60.490 47.826 0.00 0.00 35.28 4.35
623 627 4.481368 AACCACACAACAGTAGTTCTCA 57.519 40.909 0.00 0.00 35.28 3.27
670 674 6.812160 GTGTTATAGTCGAGAGGTCACAAATT 59.188 38.462 0.00 0.00 0.00 1.82
678 682 8.977267 AAGTTATAGTGTTATAGTCGAGAGGT 57.023 34.615 0.00 0.00 0.00 3.85
869 876 3.977244 GGGCCAACAACGTGCAGG 61.977 66.667 4.39 4.53 0.00 4.85
886 893 4.767255 GCCACCAGCTCTCCCACG 62.767 72.222 0.00 0.00 38.99 4.94
906 913 0.179111 ATACGGATGTCACTGCCACG 60.179 55.000 0.00 0.00 0.00 4.94
936 943 1.577328 CTTGGTGGTACAAGGCTGCG 61.577 60.000 0.00 0.00 44.16 5.18
945 952 0.537653 GGAGGAGAGCTTGGTGGTAC 59.462 60.000 0.00 0.00 0.00 3.34
951 958 1.118838 AGAATCGGAGGAGAGCTTGG 58.881 55.000 0.00 0.00 0.00 3.61
1181 1188 2.511600 CGGGGTCCGTGATGAAGC 60.512 66.667 0.00 0.00 42.73 3.86
1247 1254 2.742372 CGGACGCCTGAACCTTGG 60.742 66.667 0.00 0.00 0.00 3.61
1641 1648 4.217754 TGTTAACCTGAAATGTCGCAAC 57.782 40.909 2.48 0.00 0.00 4.17
1694 1701 4.642429 ACTGTCAATAACACCCTCAGAAC 58.358 43.478 0.00 0.00 33.24 3.01
1724 1731 3.384467 AGGAGAGTGCAGATTAGAGAAGC 59.616 47.826 0.00 0.00 0.00 3.86
1809 1817 1.959985 CCCTACAGCAGATCATCGACT 59.040 52.381 0.00 0.00 0.00 4.18
1896 1905 2.741092 GGTGAACTCGCTGGGACA 59.259 61.111 0.00 0.00 0.00 4.02
1965 1974 1.728672 GACGAGATGTCCCGGTCTC 59.271 63.158 9.27 9.27 42.04 3.36
2014 2025 0.034863 TAAATGAGGACCGTTGGCCC 60.035 55.000 0.00 0.00 0.00 5.80
2023 2034 5.934935 TTTCGTTGGTCTTAAATGAGGAC 57.065 39.130 0.00 0.00 0.00 3.85
2261 2275 1.296056 AAAGCATACACGCACGTCCC 61.296 55.000 0.00 0.00 0.00 4.46
2264 2278 3.554324 CCTATAAAAGCATACACGCACGT 59.446 43.478 0.00 0.00 0.00 4.49
2265 2279 3.799963 TCCTATAAAAGCATACACGCACG 59.200 43.478 0.00 0.00 0.00 5.34
2357 2396 2.618816 GGAGCATGTGATGGTTCCTTCA 60.619 50.000 3.75 3.75 41.77 3.02
2400 2440 4.485554 AGCAGCGCTCTTACTTCG 57.514 55.556 7.13 0.00 30.62 3.79
2411 2451 1.113253 CTTGTACGTATCGAGCAGCG 58.887 55.000 0.00 0.00 42.69 5.18
2469 2509 4.035102 GTGGACAGTGCCCCTCCC 62.035 72.222 0.00 0.00 0.00 4.30
2475 2515 2.280797 TTGAGCGTGGACAGTGCC 60.281 61.111 0.00 0.00 0.00 5.01
2877 2917 2.202676 CTGAGCGCGTCCTCTTCC 60.203 66.667 8.43 0.00 33.02 3.46
2950 2990 0.946221 CAGTGTCCAGTGGCGTTCTC 60.946 60.000 3.51 0.00 0.00 2.87
3020 3060 4.672801 GCCTTTCAACGATCTTAGGCAAAG 60.673 45.833 14.51 0.60 45.73 2.77
3066 3110 6.663944 ACCAGCTTACATTTTCGATAAGAC 57.336 37.500 6.87 0.03 0.00 3.01
3187 3231 6.183360 CCACTAATTTCGGTGCAAACATATCT 60.183 38.462 0.00 0.00 32.68 1.98
3209 3253 6.488006 AGGCATCACTATCATATTTTGACCAC 59.512 38.462 0.00 0.00 37.11 4.16
3227 3271 0.682292 TTACGGTGACACAGGCATCA 59.318 50.000 10.55 0.00 0.00 3.07
3228 3272 1.337823 ACTTACGGTGACACAGGCATC 60.338 52.381 10.55 0.00 0.00 3.91
3304 3348 2.621055 AGAGACGACATGACTCTATGCC 59.379 50.000 0.00 0.00 45.84 4.40
3312 3356 2.338500 GACCCAAAGAGACGACATGAC 58.662 52.381 0.00 0.00 0.00 3.06
3355 3399 0.179134 ATCCTGCGTCAAGAGCGTAC 60.179 55.000 0.00 0.00 37.44 3.67
3360 3404 1.227089 CCCGATCCTGCGTCAAGAG 60.227 63.158 0.00 0.00 0.00 2.85
3369 3413 0.107508 AACACTGATGCCCGATCCTG 60.108 55.000 0.00 0.00 0.00 3.86
3370 3414 0.107508 CAACACTGATGCCCGATCCT 60.108 55.000 0.00 0.00 0.00 3.24
3371 3415 1.097547 CCAACACTGATGCCCGATCC 61.098 60.000 0.00 0.00 0.00 3.36
3372 3416 0.107703 TCCAACACTGATGCCCGATC 60.108 55.000 0.00 0.00 0.00 3.69
3373 3417 0.327924 TTCCAACACTGATGCCCGAT 59.672 50.000 0.00 0.00 0.00 4.18
3374 3418 0.321564 CTTCCAACACTGATGCCCGA 60.322 55.000 0.00 0.00 0.00 5.14
3375 3419 0.321564 TCTTCCAACACTGATGCCCG 60.322 55.000 0.00 0.00 0.00 6.13
3376 3420 1.003580 TCTCTTCCAACACTGATGCCC 59.996 52.381 0.00 0.00 0.00 5.36
3417 3461 6.060028 GTGTTATGCACCGATCAATACATT 57.940 37.500 0.00 0.00 42.10 2.71
3476 3521 5.302313 CCACCTCCTAGTCCTTGTATAGTTC 59.698 48.000 0.00 0.00 0.00 3.01
3501 3546 9.791801 TTGTGCATGTATATTGTATATCTTGGT 57.208 29.630 0.00 0.00 0.00 3.67
3603 3654 2.231478 CTGCCTACTTCCGTCTTTGAGA 59.769 50.000 0.00 0.00 0.00 3.27
3673 3724 1.971505 CTCTTGGGCGCATCTGGGTA 61.972 60.000 10.83 0.00 0.00 3.69
3678 3729 1.078848 GTCACTCTTGGGCGCATCT 60.079 57.895 10.83 0.00 0.00 2.90
3693 3744 1.221466 CTTTGTTCGCGAGCAGGTCA 61.221 55.000 24.49 8.36 0.00 4.02
3694 3745 1.222115 ACTTTGTTCGCGAGCAGGTC 61.222 55.000 24.49 6.21 0.00 3.85
3972 4024 3.310860 ATGTCGTTCCACCTCGGGC 62.311 63.158 0.00 0.00 34.36 6.13
3984 4036 3.171828 TTGCCCGGACACATGTCGT 62.172 57.895 0.73 0.00 45.65 4.34
3987 4039 2.282180 GGTTGCCCGGACACATGT 60.282 61.111 0.73 0.00 0.00 3.21
3989 4041 2.034066 CTGGTTGCCCGGACACAT 59.966 61.111 0.73 0.00 39.78 3.21


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

AutoCloner maintained by Alex Coulton.