Multiple sequence alignment - TraesCS3A01G246100

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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 TraesCS3A01G246100 chr3A 100.000 4458 0 0 1 4458 461842696 461838239 0.000000e+00 8233
1 TraesCS3A01G246100 chr3A 99.254 134 1 0 1 134 676815257 676815390 4.460000e-60 243
2 TraesCS3A01G246100 chr3A 97.761 134 3 0 1 134 727290165 727290298 9.640000e-57 231
3 TraesCS3A01G246100 chr3B 94.089 3434 155 24 135 3531 440227966 440231388 0.000000e+00 5173
4 TraesCS3A01G246100 chr3B 88.556 568 54 8 3532 4093 696677781 696678343 0.000000e+00 678
5 TraesCS3A01G246100 chr3B 88.065 553 54 9 3530 4076 99994151 99994697 0.000000e+00 645
6 TraesCS3A01G246100 chr3B 90.303 330 31 1 4124 4453 14051006 14050678 8.860000e-117 431
7 TraesCS3A01G246100 chr3B 95.588 136 6 0 1 136 285075 284940 7.510000e-53 219
8 TraesCS3A01G246100 chr3D 95.075 2599 110 9 944 3531 341493362 341495953 0.000000e+00 4074
9 TraesCS3A01G246100 chr3D 88.246 570 53 10 3530 4091 511682937 511682374 0.000000e+00 669
10 TraesCS3A01G246100 chr3D 90.287 453 27 9 190 626 341492019 341492470 1.080000e-160 577
11 TraesCS3A01G246100 chr3D 90.203 296 17 3 630 913 341492780 341493075 4.210000e-100 375
12 TraesCS3A01G246100 chr1D 85.543 2414 271 41 1066 3461 443552710 443555063 0.000000e+00 2453
13 TraesCS3A01G246100 chr1D 84.757 2388 299 34 1094 3461 443716412 443718754 0.000000e+00 2333
14 TraesCS3A01G246100 chr1D 84.883 2388 276 37 1094 3451 443467359 443465027 0.000000e+00 2331
15 TraesCS3A01G246100 chr1D 85.192 1695 204 29 1093 2768 443429533 443427867 0.000000e+00 1696
16 TraesCS3A01G246100 chr1A 85.188 2417 283 42 1066 3461 539616534 539614172 0.000000e+00 2410
17 TraesCS3A01G246100 chr1A 84.941 2384 296 34 1094 3461 539428196 539425860 0.000000e+00 2355
18 TraesCS3A01G246100 chr1A 96.129 930 28 5 3531 4458 239883589 239884512 0.000000e+00 1511
19 TraesCS3A01G246100 chr1A 81.682 1201 133 43 1990 3145 539721588 539722746 0.000000e+00 918
20 TraesCS3A01G246100 chr1A 97.794 136 3 0 1 136 406172693 406172558 7.450000e-58 235
21 TraesCS3A01G246100 chr1B 85.132 2381 297 30 1094 3461 603093688 603091352 0.000000e+00 2383
22 TraesCS3A01G246100 chr1B 85.137 2402 271 47 1079 3451 603149402 603147058 0.000000e+00 2379
23 TraesCS3A01G246100 chr1B 83.906 2504 311 39 989 3461 603261298 603263740 0.000000e+00 2307
24 TraesCS3A01G246100 chr1B 87.741 571 56 11 3530 4093 640549879 640549316 0.000000e+00 654
25 TraesCS3A01G246100 chr4B 85.006 2421 276 46 1054 3461 660197484 660195138 0.000000e+00 2379
26 TraesCS3A01G246100 chr5B 91.213 956 52 21 3530 4458 245598059 245597109 0.000000e+00 1271
27 TraesCS3A01G246100 chr5B 90.476 336 30 2 4124 4458 711282797 711282463 4.090000e-120 442
28 TraesCS3A01G246100 chr6B 90.957 951 59 18 3531 4458 51385952 51386898 0.000000e+00 1254
29 TraesCS3A01G246100 chr7B 90.870 942 70 12 3524 4458 603827928 603826996 0.000000e+00 1249
30 TraesCS3A01G246100 chr7B 96.350 137 5 0 1 137 641871046 641870910 4.490000e-55 226
31 TraesCS3A01G246100 chr6A 97.161 634 14 2 3826 4458 573337841 573338471 0.000000e+00 1068
32 TraesCS3A01G246100 chr6A 98.519 135 2 0 1 135 603304556 603304690 5.760000e-59 239
33 TraesCS3A01G246100 chr6A 97.761 134 3 0 1 134 562250153 562250020 9.640000e-57 231
34 TraesCS3A01G246100 chr6A 97.015 134 4 0 1 134 176999929 176999796 4.490000e-55 226
35 TraesCS3A01G246100 chr6D 88.348 575 53 10 3532 4099 5048832 5048265 0.000000e+00 678
36 TraesCS3A01G246100 chr6D 87.500 576 61 11 3532 4099 5232308 5232880 0.000000e+00 654
37 TraesCS3A01G246100 chr2A 83.143 350 46 10 4109 4449 688417252 688417597 1.560000e-79 307
38 TraesCS3A01G246100 chr2A 98.507 134 2 0 1 134 638304292 638304425 2.070000e-58 237
39 TraesCS3A01G246100 chr7A 81.989 372 54 12 4095 4458 85071033 85070667 2.010000e-78 303


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 TraesCS3A01G246100 chr3A 461838239 461842696 4457 True 8233.000000 8233 100.000 1 4458 1 chr3A.!!$R1 4457
1 TraesCS3A01G246100 chr3B 440227966 440231388 3422 False 5173.000000 5173 94.089 135 3531 1 chr3B.!!$F2 3396
2 TraesCS3A01G246100 chr3B 696677781 696678343 562 False 678.000000 678 88.556 3532 4093 1 chr3B.!!$F3 561
3 TraesCS3A01G246100 chr3B 99994151 99994697 546 False 645.000000 645 88.065 3530 4076 1 chr3B.!!$F1 546
4 TraesCS3A01G246100 chr3D 341492019 341495953 3934 False 1675.333333 4074 91.855 190 3531 3 chr3D.!!$F1 3341
5 TraesCS3A01G246100 chr3D 511682374 511682937 563 True 669.000000 669 88.246 3530 4091 1 chr3D.!!$R1 561
6 TraesCS3A01G246100 chr1D 443552710 443555063 2353 False 2453.000000 2453 85.543 1066 3461 1 chr1D.!!$F1 2395
7 TraesCS3A01G246100 chr1D 443716412 443718754 2342 False 2333.000000 2333 84.757 1094 3461 1 chr1D.!!$F2 2367
8 TraesCS3A01G246100 chr1D 443465027 443467359 2332 True 2331.000000 2331 84.883 1094 3451 1 chr1D.!!$R2 2357
9 TraesCS3A01G246100 chr1D 443427867 443429533 1666 True 1696.000000 1696 85.192 1093 2768 1 chr1D.!!$R1 1675
10 TraesCS3A01G246100 chr1A 539614172 539616534 2362 True 2410.000000 2410 85.188 1066 3461 1 chr1A.!!$R3 2395
11 TraesCS3A01G246100 chr1A 539425860 539428196 2336 True 2355.000000 2355 84.941 1094 3461 1 chr1A.!!$R2 2367
12 TraesCS3A01G246100 chr1A 239883589 239884512 923 False 1511.000000 1511 96.129 3531 4458 1 chr1A.!!$F1 927
13 TraesCS3A01G246100 chr1A 539721588 539722746 1158 False 918.000000 918 81.682 1990 3145 1 chr1A.!!$F2 1155
14 TraesCS3A01G246100 chr1B 603091352 603093688 2336 True 2383.000000 2383 85.132 1094 3461 1 chr1B.!!$R1 2367
15 TraesCS3A01G246100 chr1B 603147058 603149402 2344 True 2379.000000 2379 85.137 1079 3451 1 chr1B.!!$R2 2372
16 TraesCS3A01G246100 chr1B 603261298 603263740 2442 False 2307.000000 2307 83.906 989 3461 1 chr1B.!!$F1 2472
17 TraesCS3A01G246100 chr1B 640549316 640549879 563 True 654.000000 654 87.741 3530 4093 1 chr1B.!!$R3 563
18 TraesCS3A01G246100 chr4B 660195138 660197484 2346 True 2379.000000 2379 85.006 1054 3461 1 chr4B.!!$R1 2407
19 TraesCS3A01G246100 chr5B 245597109 245598059 950 True 1271.000000 1271 91.213 3530 4458 1 chr5B.!!$R1 928
20 TraesCS3A01G246100 chr6B 51385952 51386898 946 False 1254.000000 1254 90.957 3531 4458 1 chr6B.!!$F1 927
21 TraesCS3A01G246100 chr7B 603826996 603827928 932 True 1249.000000 1249 90.870 3524 4458 1 chr7B.!!$R1 934
22 TraesCS3A01G246100 chr6A 573337841 573338471 630 False 1068.000000 1068 97.161 3826 4458 1 chr6A.!!$F1 632
23 TraesCS3A01G246100 chr6D 5048265 5048832 567 True 678.000000 678 88.348 3532 4099 1 chr6D.!!$R1 567
24 TraesCS3A01G246100 chr6D 5232308 5232880 572 False 654.000000 654 87.500 3532 4099 1 chr6D.!!$F1 567

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
311 313 0.037882 ATCCATCGCTGTCGCCATAG 60.038 55.0 0.0 0.0 35.26 2.23 F
916 1254 0.101759 ACGCAACTGACACGTACTGT 59.898 50.0 0.0 0.0 38.45 3.55 F
2270 2928 0.321653 ATCTCAACCTCAACGCCACC 60.322 55.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 2520 0.398098 ATCGGAGGGACGGTTGGTAT 60.398 55.0 0.00 0.0 0.0 2.73 R
2555 3250 0.599204 TTGAAGTTCCCAGTCGCGTC 60.599 55.0 5.77 0.0 0.0 5.19 R
3819 4566 0.108992 AGTTCTCGCCGCGACAATTA 60.109 50.0 12.39 0.0 0.0 1.40 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
18 19 3.146783 CTTGCAACGGGTATTCGGA 57.853 52.632 0.00 0.00 0.00 4.55
19 20 1.444836 CTTGCAACGGGTATTCGGAA 58.555 50.000 0.00 0.00 0.00 4.30
20 21 2.014128 CTTGCAACGGGTATTCGGAAT 58.986 47.619 8.49 8.49 0.00 3.01
21 22 1.374560 TGCAACGGGTATTCGGAATG 58.625 50.000 13.37 0.00 0.00 2.67
22 23 1.339247 TGCAACGGGTATTCGGAATGT 60.339 47.619 13.37 0.00 0.00 2.71
23 24 1.063469 GCAACGGGTATTCGGAATGTG 59.937 52.381 13.37 3.22 0.00 3.21
24 25 2.352388 CAACGGGTATTCGGAATGTGT 58.648 47.619 13.37 3.79 0.00 3.72
25 26 3.523547 CAACGGGTATTCGGAATGTGTA 58.476 45.455 13.37 0.00 0.00 2.90
26 27 4.124238 CAACGGGTATTCGGAATGTGTAT 58.876 43.478 13.37 0.00 0.00 2.29
27 28 5.291178 CAACGGGTATTCGGAATGTGTATA 58.709 41.667 13.37 0.00 0.00 1.47
28 29 5.733620 ACGGGTATTCGGAATGTGTATAT 57.266 39.130 13.37 0.00 0.00 0.86
29 30 5.475719 ACGGGTATTCGGAATGTGTATATG 58.524 41.667 13.37 0.00 0.00 1.78
30 31 4.328983 CGGGTATTCGGAATGTGTATATGC 59.671 45.833 13.37 0.00 0.00 3.14
31 32 5.242434 GGGTATTCGGAATGTGTATATGCA 58.758 41.667 13.37 0.00 0.00 3.96
32 33 5.880332 GGGTATTCGGAATGTGTATATGCAT 59.120 40.000 13.37 3.79 0.00 3.96
33 34 6.037172 GGGTATTCGGAATGTGTATATGCATC 59.963 42.308 13.37 0.00 0.00 3.91
34 35 6.037172 GGTATTCGGAATGTGTATATGCATCC 59.963 42.308 13.37 0.00 0.00 3.51
35 36 3.937814 TCGGAATGTGTATATGCATCCC 58.062 45.455 0.19 0.00 0.00 3.85
36 37 2.672874 CGGAATGTGTATATGCATCCCG 59.327 50.000 0.19 8.35 0.00 5.14
37 38 3.009723 GGAATGTGTATATGCATCCCGG 58.990 50.000 0.19 0.00 0.00 5.73
38 39 2.787473 ATGTGTATATGCATCCCGGG 57.213 50.000 16.85 16.85 0.00 5.73
39 40 1.723288 TGTGTATATGCATCCCGGGA 58.277 50.000 29.18 29.18 0.00 5.14
40 41 2.050918 TGTGTATATGCATCCCGGGAA 58.949 47.619 30.84 12.52 0.00 3.97
41 42 2.439880 TGTGTATATGCATCCCGGGAAA 59.560 45.455 30.84 17.17 0.00 3.13
42 43 3.073798 TGTGTATATGCATCCCGGGAAAT 59.926 43.478 30.84 22.85 0.00 2.17
43 44 4.287326 TGTGTATATGCATCCCGGGAAATA 59.713 41.667 30.84 24.21 0.00 1.40
44 45 5.221945 TGTGTATATGCATCCCGGGAAATAA 60.222 40.000 30.84 14.32 0.00 1.40
45 46 5.885912 GTGTATATGCATCCCGGGAAATAAT 59.114 40.000 30.84 20.31 0.00 1.28
46 47 6.377146 GTGTATATGCATCCCGGGAAATAATT 59.623 38.462 30.84 14.15 0.00 1.40
47 48 6.951198 TGTATATGCATCCCGGGAAATAATTT 59.049 34.615 30.84 15.59 0.00 1.82
48 49 4.871933 ATGCATCCCGGGAAATAATTTC 57.128 40.909 30.84 4.48 38.94 2.17
49 50 3.636679 TGCATCCCGGGAAATAATTTCA 58.363 40.909 30.84 7.64 41.43 2.69
50 51 3.383185 TGCATCCCGGGAAATAATTTCAC 59.617 43.478 30.84 7.84 41.43 3.18
51 52 3.383185 GCATCCCGGGAAATAATTTCACA 59.617 43.478 30.84 0.00 43.25 3.58
52 53 4.039124 GCATCCCGGGAAATAATTTCACAT 59.961 41.667 30.84 2.13 43.25 3.21
53 54 5.453198 GCATCCCGGGAAATAATTTCACATT 60.453 40.000 30.84 1.57 43.25 2.71
54 55 6.581712 CATCCCGGGAAATAATTTCACATTT 58.418 36.000 30.84 0.76 43.25 2.32
55 56 6.613153 TCCCGGGAAATAATTTCACATTTT 57.387 33.333 24.50 0.00 43.25 1.82
56 57 7.010339 TCCCGGGAAATAATTTCACATTTTT 57.990 32.000 24.50 0.00 43.25 1.94
105 106 8.268850 TGAAAAAGTCAAATATAGAGAGCACC 57.731 34.615 0.00 0.00 31.51 5.01
106 107 6.910536 AAAAGTCAAATATAGAGAGCACCG 57.089 37.500 0.00 0.00 0.00 4.94
107 108 4.592485 AGTCAAATATAGAGAGCACCGG 57.408 45.455 0.00 0.00 0.00 5.28
108 109 3.961408 AGTCAAATATAGAGAGCACCGGT 59.039 43.478 0.00 0.00 0.00 5.28
109 110 4.051922 GTCAAATATAGAGAGCACCGGTG 58.948 47.826 30.66 30.66 0.00 4.94
156 157 1.506309 ATGACGCTTGCTTTGCACGA 61.506 50.000 9.00 0.00 38.71 4.35
160 161 1.648720 GCTTGCTTTGCACGACAGA 59.351 52.632 0.23 0.00 38.71 3.41
170 171 5.108254 GCTTTGCACGACAGAATTACAAAAG 60.108 40.000 0.00 0.00 0.00 2.27
176 177 5.907391 CACGACAGAATTACAAAAGGTCAAC 59.093 40.000 0.00 0.00 0.00 3.18
249 250 5.906073 TGATGATGCTACATACATATCCCG 58.094 41.667 0.00 0.00 0.00 5.14
250 251 5.656416 TGATGATGCTACATACATATCCCGA 59.344 40.000 0.00 0.00 0.00 5.14
305 307 3.384668 AGATAAACATCCATCGCTGTCG 58.615 45.455 0.00 0.00 0.00 4.35
311 313 0.037882 ATCCATCGCTGTCGCCATAG 60.038 55.000 0.00 0.00 35.26 2.23
360 362 1.408969 ATTTTGCCAACCGTTGACCT 58.591 45.000 13.04 0.00 0.00 3.85
385 398 0.890683 AACTGGCAAGCCAACATAGC 59.109 50.000 15.55 0.00 46.63 2.97
402 415 5.945310 ACATAGCCAGGATGTTCATATGTT 58.055 37.500 1.90 0.00 33.70 2.71
413 426 3.128415 TGTTCATATGTTGACGCCATTGG 59.872 43.478 1.90 0.00 32.84 3.16
431 444 7.319646 GCCATTGGAAGAACACAATAATAACA 58.680 34.615 6.95 0.00 35.67 2.41
445 458 7.008266 CACAATAATAACAACTAAAGCTTGCCG 59.992 37.037 0.00 0.00 0.00 5.69
451 464 4.944048 ACAACTAAAGCTTGCCGAAAAAT 58.056 34.783 0.00 0.00 0.00 1.82
453 466 5.462068 ACAACTAAAGCTTGCCGAAAAATTC 59.538 36.000 0.00 0.00 0.00 2.17
454 467 5.453567 ACTAAAGCTTGCCGAAAAATTCT 57.546 34.783 0.00 0.00 0.00 2.40
455 468 6.569179 ACTAAAGCTTGCCGAAAAATTCTA 57.431 33.333 0.00 0.00 0.00 2.10
456 469 6.612306 ACTAAAGCTTGCCGAAAAATTCTAG 58.388 36.000 0.00 0.00 0.00 2.43
457 470 5.453567 AAAGCTTGCCGAAAAATTCTAGT 57.546 34.783 0.00 0.00 0.00 2.57
549 564 6.570672 AGGTATCCGGAAAAGAAAAGAAAC 57.429 37.500 9.01 0.00 0.00 2.78
550 565 5.180680 AGGTATCCGGAAAAGAAAAGAAACG 59.819 40.000 9.01 0.00 0.00 3.60
685 1013 1.228124 GCCAAAAGCCCAAAACCCC 60.228 57.895 0.00 0.00 34.35 4.95
725 1061 0.983378 ACCCCTCCTGAAATCCTCCG 60.983 60.000 0.00 0.00 0.00 4.63
729 1065 1.471676 CCTCCTGAAATCCTCCGAACG 60.472 57.143 0.00 0.00 0.00 3.95
745 1081 4.932799 TCCGAACGTGATGTATTTTCATGT 59.067 37.500 0.00 0.00 43.42 3.21
800 1138 0.256464 TGAGGGGTCAACGGTGTTTT 59.744 50.000 0.00 0.00 0.00 2.43
801 1139 1.341187 TGAGGGGTCAACGGTGTTTTT 60.341 47.619 0.00 0.00 0.00 1.94
853 1191 0.390603 TAGTTGGGTCAATGCCGTCG 60.391 55.000 0.00 0.00 0.00 5.12
900 1238 3.802418 AACACCGGTGACCTGACGC 62.802 63.158 40.21 0.00 0.00 5.19
913 1251 0.776451 CTGACGCAACTGACACGTAC 59.224 55.000 0.00 0.00 40.69 3.67
914 1252 0.382873 TGACGCAACTGACACGTACT 59.617 50.000 0.00 0.00 40.69 2.73
915 1253 0.776451 GACGCAACTGACACGTACTG 59.224 55.000 0.00 0.00 40.69 2.74
916 1254 0.101759 ACGCAACTGACACGTACTGT 59.898 50.000 0.00 0.00 38.45 3.55
917 1255 1.334556 ACGCAACTGACACGTACTGTA 59.665 47.619 0.00 0.00 38.45 2.74
992 1591 6.483640 TCGATCGATCAACTAGAAGATCTCAA 59.516 38.462 24.40 10.42 39.90 3.02
1157 1768 2.110213 GCCGTTCCTGGTGTCACA 59.890 61.111 5.12 0.00 0.00 3.58
1173 1784 1.534235 ACAGGACGCCACCTTCTCT 60.534 57.895 0.00 0.00 38.32 3.10
1200 1820 4.473520 CTCCAGGCCGGCGACAAT 62.474 66.667 22.54 0.00 33.14 2.71
1434 2064 3.822192 CTCATCGCCGACCCGTCA 61.822 66.667 0.00 0.00 0.00 4.35
1988 2631 4.649705 TTCAGCCTCCCCACCGGA 62.650 66.667 9.46 0.00 38.83 5.14
2270 2928 0.321653 ATCTCAACCTCAACGCCACC 60.322 55.000 0.00 0.00 0.00 4.61
2291 2949 2.184322 CCGCAGCTGTCGGTACAT 59.816 61.111 29.69 0.00 41.85 2.29
2425 3096 1.135315 CGCGGTGCTTGGATTTCTG 59.865 57.895 0.00 0.00 0.00 3.02
2434 3111 3.264193 TGCTTGGATTTCTGGAGCTTCTA 59.736 43.478 0.00 0.00 34.56 2.10
2435 3118 4.263462 TGCTTGGATTTCTGGAGCTTCTAA 60.263 41.667 0.00 0.00 34.56 2.10
2444 3127 0.935366 GGAGCTTCTAATCGTCGCCG 60.935 60.000 0.00 0.00 0.00 6.46
2555 3250 2.348888 ACGTACCGGGAGCTCAAGG 61.349 63.158 20.92 20.92 0.00 3.61
2691 3386 1.682684 GCGAGGAGGAGTTCTGGGA 60.683 63.158 0.00 0.00 0.00 4.37
3016 3739 3.298958 CTAGCCAAGCTGTCCGGA 58.701 61.111 0.00 0.00 40.10 5.14
3023 3746 0.875059 CAAGCTGTCCGGAAGAAACC 59.125 55.000 5.23 0.00 0.00 3.27
3152 3875 4.552355 CAAGGTCGATGTGTACAGTTACA 58.448 43.478 0.00 0.00 35.75 2.41
3349 4072 2.767960 GGCCATGGAAATGGTGAAGATT 59.232 45.455 18.40 0.00 43.53 2.40
3433 4162 2.278857 GCGTGCGATGACGAGGAT 60.279 61.111 6.28 0.00 42.10 3.24
3462 4191 4.439153 CCCTGCGTACTTATCGTGACTTTA 60.439 45.833 0.00 0.00 0.00 1.85
3467 4196 6.088483 TGCGTACTTATCGTGACTTTAGTTTG 59.912 38.462 0.00 0.00 0.00 2.93
3473 4202 7.387948 ACTTATCGTGACTTTAGTTTGATGCTT 59.612 33.333 0.00 0.00 0.00 3.91
3490 4219 1.538204 GCTTGATAGTCGATTCCCGCA 60.538 52.381 0.00 0.00 38.37 5.69
3501 4230 0.674534 ATTCCCGCATCTCTACCGTC 59.325 55.000 0.00 0.00 0.00 4.79
3502 4231 0.681887 TTCCCGCATCTCTACCGTCA 60.682 55.000 0.00 0.00 0.00 4.35
3550 4279 3.445008 AGGACAGTGCTATCTTCCAGAA 58.555 45.455 0.00 0.00 0.00 3.02
3572 4301 7.655328 CAGAAGTCCTGATTTTAGCGATAGATT 59.345 37.037 0.00 0.00 45.78 2.40
3600 4331 4.507710 GATTCACATGCAGTCCTTCTACA 58.492 43.478 0.00 0.00 0.00 2.74
3604 4335 2.159043 ACATGCAGTCCTTCTACATCGG 60.159 50.000 0.00 0.00 28.50 4.18
3632 4366 6.541907 TGCATGCAGTCCATTTTCCTATATA 58.458 36.000 18.46 0.00 29.71 0.86
3879 4627 5.119588 TGTTGATATGTTCCGACGACTTTTC 59.880 40.000 0.00 0.00 0.00 2.29
4213 4980 5.335348 GGCAAAGTTATCGTGGTGTTTGTAT 60.335 40.000 0.00 0.00 0.00 2.29
4231 4998 7.711772 TGTTTGTATCTAAGTTTTCAGGTTCGA 59.288 33.333 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.773993 ACACATTCCGAATACCCGTT 57.226 45.000 0.00 0.00 0.00 4.44
6 7 5.475719 CATATACACATTCCGAATACCCGT 58.524 41.667 0.00 0.00 0.00 5.28
8 9 5.242434 TGCATATACACATTCCGAATACCC 58.758 41.667 0.00 0.00 0.00 3.69
10 11 6.037172 GGGATGCATATACACATTCCGAATAC 59.963 42.308 0.00 0.00 32.29 1.89
11 12 6.112734 GGGATGCATATACACATTCCGAATA 58.887 40.000 0.00 0.00 32.29 1.75
12 13 4.943705 GGGATGCATATACACATTCCGAAT 59.056 41.667 0.00 0.00 32.29 3.34
13 14 4.323417 GGGATGCATATACACATTCCGAA 58.677 43.478 0.00 0.00 32.29 4.30
14 15 3.937814 GGGATGCATATACACATTCCGA 58.062 45.455 0.00 0.00 32.29 4.55
16 17 3.009723 CCGGGATGCATATACACATTCC 58.990 50.000 0.00 4.59 38.42 3.01
17 18 3.009723 CCCGGGATGCATATACACATTC 58.990 50.000 18.48 0.00 0.00 2.67
18 19 2.642311 TCCCGGGATGCATATACACATT 59.358 45.455 22.63 0.00 0.00 2.71
19 20 2.265367 TCCCGGGATGCATATACACAT 58.735 47.619 22.63 0.00 0.00 3.21
20 21 1.723288 TCCCGGGATGCATATACACA 58.277 50.000 22.63 0.00 0.00 3.72
21 22 2.851263 TTCCCGGGATGCATATACAC 57.149 50.000 27.48 0.00 0.00 2.90
22 23 5.506730 TTATTTCCCGGGATGCATATACA 57.493 39.130 27.48 1.92 0.00 2.29
23 24 7.122055 TGAAATTATTTCCCGGGATGCATATAC 59.878 37.037 27.48 13.90 38.90 1.47
24 25 7.122055 GTGAAATTATTTCCCGGGATGCATATA 59.878 37.037 27.48 13.88 38.90 0.86
25 26 6.015918 TGAAATTATTTCCCGGGATGCATAT 58.984 36.000 27.48 14.87 38.90 1.78
26 27 5.242838 GTGAAATTATTTCCCGGGATGCATA 59.757 40.000 27.48 17.82 38.90 3.14
27 28 4.039124 GTGAAATTATTTCCCGGGATGCAT 59.961 41.667 27.48 18.89 38.90 3.96
28 29 3.383185 GTGAAATTATTTCCCGGGATGCA 59.617 43.478 27.48 10.56 38.90 3.96
29 30 3.383185 TGTGAAATTATTTCCCGGGATGC 59.617 43.478 27.48 7.39 38.90 3.91
30 31 5.789643 ATGTGAAATTATTTCCCGGGATG 57.210 39.130 27.48 0.00 38.90 3.51
31 32 6.806668 AAATGTGAAATTATTTCCCGGGAT 57.193 33.333 27.48 13.83 38.90 3.85
32 33 6.613153 AAAATGTGAAATTATTTCCCGGGA 57.387 33.333 22.63 22.63 38.90 5.14
79 80 8.730680 GGTGCTCTCTATATTTGACTTTTTCAA 58.269 33.333 0.00 0.00 42.83 2.69
80 81 7.064609 CGGTGCTCTCTATATTTGACTTTTTCA 59.935 37.037 0.00 0.00 0.00 2.69
81 82 7.402640 CGGTGCTCTCTATATTTGACTTTTTC 58.597 38.462 0.00 0.00 0.00 2.29
82 83 6.316390 CCGGTGCTCTCTATATTTGACTTTTT 59.684 38.462 0.00 0.00 0.00 1.94
83 84 5.817816 CCGGTGCTCTCTATATTTGACTTTT 59.182 40.000 0.00 0.00 0.00 2.27
84 85 5.104900 ACCGGTGCTCTCTATATTTGACTTT 60.105 40.000 6.12 0.00 0.00 2.66
85 86 4.406003 ACCGGTGCTCTCTATATTTGACTT 59.594 41.667 6.12 0.00 0.00 3.01
86 87 3.961408 ACCGGTGCTCTCTATATTTGACT 59.039 43.478 6.12 0.00 0.00 3.41
87 88 4.051922 CACCGGTGCTCTCTATATTTGAC 58.948 47.826 24.02 0.00 0.00 3.18
88 89 4.322080 CACCGGTGCTCTCTATATTTGA 57.678 45.455 24.02 0.00 0.00 2.69
121 122 1.392853 GTCATTCTGAGAGCAGCGTTG 59.607 52.381 0.00 0.00 42.01 4.10
122 123 1.719600 GTCATTCTGAGAGCAGCGTT 58.280 50.000 0.00 0.00 42.01 4.84
123 124 0.457509 CGTCATTCTGAGAGCAGCGT 60.458 55.000 0.00 0.00 42.01 5.07
124 125 1.750572 GCGTCATTCTGAGAGCAGCG 61.751 60.000 0.00 0.00 42.01 5.18
125 126 0.459934 AGCGTCATTCTGAGAGCAGC 60.460 55.000 7.11 0.00 42.01 5.25
126 127 1.659601 CAAGCGTCATTCTGAGAGCAG 59.340 52.381 7.11 0.00 43.67 4.24
127 128 1.718396 CAAGCGTCATTCTGAGAGCA 58.282 50.000 7.11 0.00 34.82 4.26
128 129 0.373024 GCAAGCGTCATTCTGAGAGC 59.627 55.000 0.00 0.00 33.26 4.09
129 130 2.007360 AGCAAGCGTCATTCTGAGAG 57.993 50.000 0.00 0.00 0.00 3.20
130 131 2.462456 AAGCAAGCGTCATTCTGAGA 57.538 45.000 0.00 0.00 0.00 3.27
131 132 2.847901 CAAAGCAAGCGTCATTCTGAG 58.152 47.619 0.00 0.00 0.00 3.35
132 133 1.069022 GCAAAGCAAGCGTCATTCTGA 60.069 47.619 0.00 0.00 0.00 3.27
133 134 1.334054 GCAAAGCAAGCGTCATTCTG 58.666 50.000 0.00 0.00 0.00 3.02
156 157 8.006298 TCATTGTTGACCTTTTGTAATTCTGT 57.994 30.769 0.00 0.00 0.00 3.41
170 171 8.607441 TGCTTGATACTATATCATTGTTGACC 57.393 34.615 0.00 0.00 33.85 4.02
217 218 2.216898 GTAGCATCATCAGGTTGCTCC 58.783 52.381 0.00 0.00 46.98 4.70
305 307 1.674221 GCCCTCATCGTCATCTATGGC 60.674 57.143 0.00 0.00 0.00 4.40
342 344 1.134965 CAAGGTCAACGGTTGGCAAAA 60.135 47.619 25.02 1.52 36.88 2.44
346 348 1.358759 CACAAGGTCAACGGTTGGC 59.641 57.895 19.91 18.41 33.62 4.52
375 377 1.678101 GAACATCCTGGCTATGTTGGC 59.322 52.381 15.99 2.51 45.24 4.52
380 382 5.999600 TCAACATATGAACATCCTGGCTATG 59.000 40.000 10.38 0.00 34.30 2.23
385 398 3.002656 GCGTCAACATATGAACATCCTGG 59.997 47.826 10.38 0.00 40.50 4.45
402 415 1.234821 GTGTTCTTCCAATGGCGTCA 58.765 50.000 0.00 0.00 0.00 4.35
431 444 5.842907 AGAATTTTTCGGCAAGCTTTAGTT 58.157 33.333 0.00 0.00 34.02 2.24
457 470 9.177671 TCTTATTCAAGGACATCGAGTGACGAA 62.178 40.741 0.00 0.00 42.09 3.85
712 1048 1.067142 TCACGTTCGGAGGATTTCAGG 60.067 52.381 0.00 0.00 0.00 3.86
725 1061 8.942669 TGTTTACATGAAAATACATCACGTTC 57.057 30.769 0.00 0.00 0.00 3.95
800 1138 5.897050 ACGCAAAGTGTTTTATCAGGAAAA 58.103 33.333 0.00 0.00 0.00 2.29
801 1139 5.298276 AGACGCAAAGTGTTTTATCAGGAAA 59.702 36.000 0.00 0.00 0.00 3.13
802 1140 4.819630 AGACGCAAAGTGTTTTATCAGGAA 59.180 37.500 0.00 0.00 0.00 3.36
803 1141 4.385825 AGACGCAAAGTGTTTTATCAGGA 58.614 39.130 0.00 0.00 0.00 3.86
853 1191 0.461961 CTCCCACAGTAGCTACCTGC 59.538 60.000 20.31 0.00 43.29 4.85
900 1238 5.755813 ACTACTTACAGTACGTGTCAGTTG 58.244 41.667 13.72 13.75 40.12 3.16
992 1591 2.696989 TCTCGCCATCATGAATGTGT 57.303 45.000 0.00 0.00 33.13 3.72
1027 1635 9.246670 CAGTAGATGAGAGATCAGATAAAGGAT 57.753 37.037 0.00 0.00 0.00 3.24
1077 1688 1.079127 GTGCTGTACCGATGGTGCT 60.079 57.895 5.67 0.00 39.07 4.40
1157 1768 1.674057 CAAGAGAAGGTGGCGTCCT 59.326 57.895 0.00 0.00 39.84 3.85
1173 1784 4.722700 GCCTGGAGGAAGCCGCAA 62.723 66.667 0.00 0.00 37.39 4.85
1200 1820 1.819288 CAGACGGAGAAGTAGAAGGCA 59.181 52.381 0.00 0.00 0.00 4.75
1886 2520 0.398098 ATCGGAGGGACGGTTGGTAT 60.398 55.000 0.00 0.00 0.00 2.73
1967 2601 2.430367 GTGGGGAGGCTGAACGTT 59.570 61.111 0.00 0.00 0.00 3.99
1988 2631 1.447317 CTTCGCTGCAGTTGGTGGTT 61.447 55.000 16.64 0.00 0.00 3.67
2416 3087 4.162320 ACGATTAGAAGCTCCAGAAATCCA 59.838 41.667 0.00 0.00 0.00 3.41
2425 3096 2.888218 GGCGACGATTAGAAGCTCC 58.112 57.895 0.00 0.00 0.00 4.70
2500 3195 1.146930 CGCCATGACCAGCCTGTAT 59.853 57.895 0.00 0.00 0.00 2.29
2555 3250 0.599204 TTGAAGTTCCCAGTCGCGTC 60.599 55.000 5.77 0.00 0.00 5.19
2691 3386 1.605058 CCCGAACACCGTCATCTCCT 61.605 60.000 0.00 0.00 36.31 3.69
3001 3724 1.768684 TTCTTCCGGACAGCTTGGCT 61.769 55.000 1.83 0.00 40.77 4.75
3349 4072 2.103094 CTCCTCCATGCACGATAAGGAA 59.897 50.000 0.00 0.00 32.77 3.36
3433 4162 1.136305 GATAAGTACGCAGGGTGCTCA 59.864 52.381 8.71 0.00 41.05 4.26
3451 4180 5.700832 TCAAGCATCAAACTAAAGTCACGAT 59.299 36.000 0.00 0.00 0.00 3.73
3462 4191 5.525378 GGAATCGACTATCAAGCATCAAACT 59.475 40.000 0.00 0.00 0.00 2.66
3467 4196 2.989840 CGGGAATCGACTATCAAGCATC 59.010 50.000 0.00 0.00 42.43 3.91
3473 4202 2.229062 GAGATGCGGGAATCGACTATCA 59.771 50.000 0.00 0.00 42.43 2.15
3490 4219 2.753452 ACAACACGATGACGGTAGAGAT 59.247 45.455 0.00 0.00 44.46 2.75
3501 4230 5.232202 ACAATATAGCGAGAACAACACGATG 59.768 40.000 0.00 0.00 34.75 3.84
3502 4231 5.348986 ACAATATAGCGAGAACAACACGAT 58.651 37.500 0.00 0.00 34.75 3.73
3550 4279 6.153067 CGAATCTATCGCTAAAATCAGGACT 58.847 40.000 0.00 0.00 45.89 3.85
3572 4301 0.246360 ACTGCATGTGAATCGTCCGA 59.754 50.000 0.00 0.00 0.00 4.55
3600 4331 0.820891 GGACTGCATGCAATCCCGAT 60.821 55.000 32.99 8.32 36.44 4.18
3604 4335 2.973694 AAATGGACTGCATGCAATCC 57.026 45.000 35.39 35.39 42.15 3.01
3819 4566 0.108992 AGTTCTCGCCGCGACAATTA 60.109 50.000 12.39 0.00 0.00 1.40
3823 4570 2.430244 GAAGTTCTCGCCGCGACA 60.430 61.111 12.39 0.00 0.00 4.35
4213 4980 6.579865 AGTCTTTCGAACCTGAAAACTTAGA 58.420 36.000 0.00 0.00 37.40 2.10


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

AutoCloner maintained by Alex Coulton.