Multiple sequence alignment - TraesCS1D01G134700

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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 TraesCS1D01G134700 chr1D 100.000 6516 0 0 484 6999 174819508 174812993 0.000000e+00 12033.0
1 TraesCS1D01G134700 chr1D 100.000 236 0 0 1 236 174819991 174819756 3.000000e-118 436.0
2 TraesCS1D01G134700 chr1D 89.130 92 9 1 6214 6304 483435870 483435779 5.740000e-21 113.0
3 TraesCS1D01G134700 chr1D 87.000 100 11 2 6206 6304 95877510 95877608 2.060000e-20 111.0
4 TraesCS1D01G134700 chr1B 96.890 4694 102 17 551 5220 261840845 261845518 0.000000e+00 7819.0
5 TraesCS1D01G134700 chr1B 96.434 617 10 4 5590 6206 261845999 261846603 0.000000e+00 1007.0
6 TraesCS1D01G134700 chr1B 96.875 448 13 1 5148 5595 261845518 261845964 0.000000e+00 749.0
7 TraesCS1D01G134700 chr1B 96.861 223 3 3 2 220 261840623 261840845 3.080000e-98 370.0
8 TraesCS1D01G134700 chr1B 77.203 522 91 20 6331 6838 678074559 678074052 5.350000e-71 279.0
9 TraesCS1D01G134700 chr1A 95.581 4843 131 24 772 5595 218220163 218215385 0.000000e+00 7681.0
10 TraesCS1D01G134700 chr1A 97.083 617 18 0 5590 6206 218215351 218214735 0.000000e+00 1040.0
11 TraesCS1D01G134700 chr1A 97.500 240 6 0 484 723 218220401 218220162 1.820000e-110 411.0
12 TraesCS1D01G134700 chr1A 93.443 244 7 2 2 236 218220691 218220448 3.110000e-93 353.0
13 TraesCS1D01G134700 chr6D 81.057 681 110 13 6312 6984 95868277 95868946 6.220000e-145 525.0
14 TraesCS1D01G134700 chr6D 80.151 529 98 6 6312 6836 464750472 464750997 8.510000e-104 388.0
15 TraesCS1D01G134700 chr6D 87.912 91 10 1 6215 6304 357869268 357869358 9.600000e-19 106.0
16 TraesCS1D01G134700 chr7B 82.030 601 98 9 3434 4025 524058575 524057976 2.910000e-138 503.0
17 TraesCS1D01G134700 chr5D 79.495 673 134 4 6314 6985 478561207 478561876 6.350000e-130 475.0
18 TraesCS1D01G134700 chr5D 89.011 91 9 1 6215 6304 450045758 450045668 2.060000e-20 111.0
19 TraesCS1D01G134700 chr5D 100.000 33 0 0 3088 3120 339106849 339106817 2.110000e-05 62.1
20 TraesCS1D01G134700 chr6B 81.282 593 100 11 3431 4015 178740018 178739429 2.960000e-128 470.0
21 TraesCS1D01G134700 chr6B 79.500 600 106 16 3428 4015 696532231 696532825 1.820000e-110 411.0
22 TraesCS1D01G134700 chr2A 79.326 682 127 12 6312 6985 711519071 711518396 3.820000e-127 466.0
23 TraesCS1D01G134700 chr2A 80.414 531 95 6 6312 6835 25342299 25342827 5.090000e-106 396.0
24 TraesCS1D01G134700 chr2A 79.094 287 60 0 6699 6985 755855233 755855519 1.540000e-46 198.0
25 TraesCS1D01G134700 chr2A 87.912 91 10 1 6215 6304 65247532 65247442 9.600000e-19 106.0
26 TraesCS1D01G134700 chr7D 80.858 606 91 13 3428 4025 495831276 495830688 2.980000e-123 453.0
27 TraesCS1D01G134700 chr3A 80.672 595 106 8 3428 4015 694838129 694838721 2.980000e-123 453.0
28 TraesCS1D01G134700 chr3A 80.471 594 107 8 3428 4014 249067903 249068494 4.980000e-121 446.0
29 TraesCS1D01G134700 chr3A 79.966 594 110 8 3428 4014 521075071 521075662 5.020000e-116 429.0
30 TraesCS1D01G134700 chr3A 96.875 32 0 1 3084 3115 679696604 679696574 1.300000e-02 52.8
31 TraesCS1D01G134700 chr7A 80.235 597 107 10 3427 4015 663489267 663488674 8.330000e-119 438.0
32 TraesCS1D01G134700 chr3B 78.152 682 134 10 6312 6985 799977175 799976501 3.020000e-113 420.0
33 TraesCS1D01G134700 chr3B 78.413 630 102 17 6234 6835 167699419 167700042 5.120000e-101 379.0
34 TraesCS1D01G134700 chr3B 88.043 92 10 1 6214 6304 272749524 272749433 2.670000e-19 108.0
35 TraesCS1D01G134700 chr5B 79.813 535 97 8 6312 6839 626172425 626171895 5.120000e-101 379.0
36 TraesCS1D01G134700 chr5B 79.626 535 98 8 6312 6839 626184029 626183499 2.380000e-99 374.0
37 TraesCS1D01G134700 chr2D 79.550 533 99 6 6312 6837 380928897 380928368 8.570000e-99 372.0
38 TraesCS1D01G134700 chr5A 79.362 533 100 7 6312 6837 670233941 670233412 3.990000e-97 366.0
39 TraesCS1D01G134700 chr5A 100.000 34 0 0 3087 3120 267002062 267002029 5.860000e-06 63.9
40 TraesCS1D01G134700 chr5A 100.000 29 0 0 3087 3115 662352289 662352261 4.000000e-03 54.7
41 TraesCS1D01G134700 chr2B 76.147 654 113 25 6214 6828 708703264 708702615 3.170000e-78 303.0
42 TraesCS1D01G134700 chr2B 94.444 36 2 0 3083 3118 333029169 333029134 1.000000e-03 56.5


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 TraesCS1D01G134700 chr1D 174812993 174819991 6998 True 6234.50 12033 100.00000 1 6999 2 chr1D.!!$R2 6998
1 TraesCS1D01G134700 chr1B 261840623 261846603 5980 False 2486.25 7819 96.76500 2 6206 4 chr1B.!!$F1 6204
2 TraesCS1D01G134700 chr1B 678074052 678074559 507 True 279.00 279 77.20300 6331 6838 1 chr1B.!!$R1 507
3 TraesCS1D01G134700 chr1A 218214735 218220691 5956 True 2371.25 7681 95.90175 2 6206 4 chr1A.!!$R1 6204
4 TraesCS1D01G134700 chr6D 95868277 95868946 669 False 525.00 525 81.05700 6312 6984 1 chr6D.!!$F1 672
5 TraesCS1D01G134700 chr6D 464750472 464750997 525 False 388.00 388 80.15100 6312 6836 1 chr6D.!!$F3 524
6 TraesCS1D01G134700 chr7B 524057976 524058575 599 True 503.00 503 82.03000 3434 4025 1 chr7B.!!$R1 591
7 TraesCS1D01G134700 chr5D 478561207 478561876 669 False 475.00 475 79.49500 6314 6985 1 chr5D.!!$F1 671
8 TraesCS1D01G134700 chr6B 178739429 178740018 589 True 470.00 470 81.28200 3431 4015 1 chr6B.!!$R1 584
9 TraesCS1D01G134700 chr6B 696532231 696532825 594 False 411.00 411 79.50000 3428 4015 1 chr6B.!!$F1 587
10 TraesCS1D01G134700 chr2A 711518396 711519071 675 True 466.00 466 79.32600 6312 6985 1 chr2A.!!$R2 673
11 TraesCS1D01G134700 chr2A 25342299 25342827 528 False 396.00 396 80.41400 6312 6835 1 chr2A.!!$F1 523
12 TraesCS1D01G134700 chr7D 495830688 495831276 588 True 453.00 453 80.85800 3428 4025 1 chr7D.!!$R1 597
13 TraesCS1D01G134700 chr3A 694838129 694838721 592 False 453.00 453 80.67200 3428 4015 1 chr3A.!!$F3 587
14 TraesCS1D01G134700 chr3A 249067903 249068494 591 False 446.00 446 80.47100 3428 4014 1 chr3A.!!$F1 586
15 TraesCS1D01G134700 chr3A 521075071 521075662 591 False 429.00 429 79.96600 3428 4014 1 chr3A.!!$F2 586
16 TraesCS1D01G134700 chr7A 663488674 663489267 593 True 438.00 438 80.23500 3427 4015 1 chr7A.!!$R1 588
17 TraesCS1D01G134700 chr3B 799976501 799977175 674 True 420.00 420 78.15200 6312 6985 1 chr3B.!!$R2 673
18 TraesCS1D01G134700 chr3B 167699419 167700042 623 False 379.00 379 78.41300 6234 6835 1 chr3B.!!$F1 601
19 TraesCS1D01G134700 chr5B 626171895 626172425 530 True 379.00 379 79.81300 6312 6839 1 chr5B.!!$R1 527
20 TraesCS1D01G134700 chr5B 626183499 626184029 530 True 374.00 374 79.62600 6312 6839 1 chr5B.!!$R2 527
21 TraesCS1D01G134700 chr2D 380928368 380928897 529 True 372.00 372 79.55000 6312 6837 1 chr2D.!!$R1 525
22 TraesCS1D01G134700 chr5A 670233412 670233941 529 True 366.00 366 79.36200 6312 6837 1 chr5A.!!$R3 525
23 TraesCS1D01G134700 chr2B 708702615 708703264 649 True 303.00 303 76.14700 6214 6828 1 chr2B.!!$R2 614

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
524 534 0.462581 TGCTCATGTTCTCCGATGCC 60.463 55.000 0.0 0.0 0.00 4.40 F
1019 1029 0.111061 ATGCTTCAGTGCTTGGTGGA 59.889 50.000 0.0 0.0 0.00 4.02 F
1679 1690 0.610174 TGTTGCACTCTAGCAGGGAG 59.390 55.000 0.0 0.0 46.54 4.30 F
2368 2387 0.679002 GCTTGGCATCTCTCTTGGCA 60.679 55.000 0.0 0.0 46.51 4.92 F
2833 2854 2.158769 AGATTGCCCATGAATGCTACGA 60.159 45.455 0.0 0.0 0.00 3.43 F
4159 4220 1.485066 CCCCCGCTTTACTACAGTGAT 59.515 52.381 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2206 2.338577 AGCAGTGGATGTGGATAAGC 57.661 50.000 0.0 0.0 0.00 3.09 R
2362 2381 3.249080 CCAAATTTCAGCTTTGTGCCAAG 59.751 43.478 0.0 0.0 44.23 3.61 R
3123 3149 1.920351 ACCCCAGAATAACCACCGAAT 59.080 47.619 0.0 0.0 0.00 3.34 R
4093 4154 0.173255 GACATTGGGGCATTTCCACG 59.827 55.000 0.0 0.0 42.91 4.94 R
4495 4556 0.250858 TCAGTGGATGTGCTTGGTGG 60.251 55.000 0.0 0.0 0.00 4.61 R
6076 6251 0.333312 AGGACCATCTCAGGACGAGT 59.667 55.000 0.0 0.0 42.88 4.18 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
66 67 2.226437 AGCATACAGTTTGGAAAGCACG 59.774 45.455 0.00 0.00 0.00 5.34
222 232 5.357032 GGGAATATCGTTCCATCTTGTGTTT 59.643 40.000 8.88 0.00 40.32 2.83
524 534 0.462581 TGCTCATGTTCTCCGATGCC 60.463 55.000 0.00 0.00 0.00 4.40
755 765 7.041107 CACCCCATATTTAAGTGTGGAAAATG 58.959 38.462 14.29 4.40 32.59 2.32
815 825 3.357079 CCACTCCTGTTGGCACGC 61.357 66.667 0.00 0.00 0.00 5.34
1019 1029 0.111061 ATGCTTCAGTGCTTGGTGGA 59.889 50.000 0.00 0.00 0.00 4.02
1074 1084 3.244770 GGTGGGTTACTCAAATGGTCAGA 60.245 47.826 0.00 0.00 0.00 3.27
1083 1093 8.734386 GTTACTCAAATGGTCAGAAAATCTCAT 58.266 33.333 0.00 0.00 0.00 2.90
1096 1106 7.046652 CAGAAAATCTCATAAGGAAGCTCTCA 58.953 38.462 0.00 0.00 0.00 3.27
1118 1128 2.028385 GGACTGTTACGGGACAAGACAT 60.028 50.000 0.00 0.00 0.00 3.06
1303 1313 7.719633 AGGAAACAAAAGCATGTATCCGTATAT 59.280 33.333 0.00 0.00 32.02 0.86
1679 1690 0.610174 TGTTGCACTCTAGCAGGGAG 59.390 55.000 0.00 0.00 46.54 4.30
2000 2011 6.236409 CCATGGATGCACTATTGAGAGTATT 58.764 40.000 5.56 0.00 0.00 1.89
2037 2048 3.298619 TGATGATGGCTTAAACATGGGG 58.701 45.455 0.00 0.00 0.00 4.96
2195 2206 2.366533 TCTGGTCTACCTGTAAGCTCG 58.633 52.381 0.02 0.00 36.48 5.03
2341 2360 6.151144 AGGAACATGAATTGTGGCTTAGTTAC 59.849 38.462 0.00 0.00 38.99 2.50
2362 2381 4.006319 ACTTAGTTTGCTTGGCATCTCTC 58.994 43.478 0.00 0.00 38.76 3.20
2368 2387 0.679002 GCTTGGCATCTCTCTTGGCA 60.679 55.000 0.00 0.00 46.51 4.92
2590 2609 4.997395 TGGAGAAATCAGTCAAGTTGCTAC 59.003 41.667 0.00 0.00 0.00 3.58
2591 2610 5.221722 TGGAGAAATCAGTCAAGTTGCTACT 60.222 40.000 0.00 0.00 35.68 2.57
2592 2611 5.121454 GGAGAAATCAGTCAAGTTGCTACTG 59.879 44.000 15.33 15.33 41.58 2.74
2619 2638 7.851228 TGAAGGCAGAAGAAGATAGTTCAATA 58.149 34.615 0.00 0.00 0.00 1.90
2638 2657 7.615582 TCAATAAATGTAGACCAAGAAGCTG 57.384 36.000 0.00 0.00 0.00 4.24
2755 2774 8.814235 CAATCATGTATCCTTTGATTTTTCTGC 58.186 33.333 0.00 0.00 37.86 4.26
2833 2854 2.158769 AGATTGCCCATGAATGCTACGA 60.159 45.455 0.00 0.00 0.00 3.43
3061 3082 5.620879 GCCATTCTTTCAGTTGATGTCCTTC 60.621 44.000 0.00 0.00 0.00 3.46
3120 3146 4.628333 CCACGTCACTTATTTATGAACGGT 59.372 41.667 0.00 0.00 0.00 4.83
3121 3147 5.121142 CCACGTCACTTATTTATGAACGGTT 59.879 40.000 0.00 0.00 0.00 4.44
3122 3148 6.347888 CCACGTCACTTATTTATGAACGGTTT 60.348 38.462 0.00 0.00 0.00 3.27
3123 3149 7.148606 CCACGTCACTTATTTATGAACGGTTTA 60.149 37.037 0.00 0.00 0.00 2.01
3368 3403 6.128007 CCATTGTTTGACCCTCATGTAAGTAC 60.128 42.308 0.00 0.00 0.00 2.73
3420 3455 8.418662 TGTAACAGCCATCGAAAGTTATAGTAT 58.581 33.333 0.00 0.00 0.00 2.12
3665 3708 7.012799 GTGAGCTAATTTAAGCAATTCTAGCCT 59.987 37.037 3.15 0.00 45.30 4.58
3842 3890 6.476706 TGTCACATAGCTATTGACTCATTTCG 59.523 38.462 28.99 11.63 40.34 3.46
3862 3911 5.997732 TCGTTTAACTAATGCGTCACTAC 57.002 39.130 0.00 0.00 0.00 2.73
4093 4154 2.095919 GGTGCCTTTGTCGATGTTACAC 60.096 50.000 0.00 0.00 0.00 2.90
4159 4220 1.485066 CCCCCGCTTTACTACAGTGAT 59.515 52.381 0.00 0.00 0.00 3.06
4420 4481 3.244875 ACCACAACCTGACAGCATATGAA 60.245 43.478 6.97 0.00 0.00 2.57
4421 4482 3.949754 CCACAACCTGACAGCATATGAAT 59.050 43.478 6.97 0.00 0.00 2.57
4422 4483 4.400251 CCACAACCTGACAGCATATGAATT 59.600 41.667 6.97 0.00 0.00 2.17
4495 4556 3.341823 CTCCCTTATATCTGTGCATGGC 58.658 50.000 0.00 0.00 0.00 4.40
4580 4641 9.574577 ACCTGGGAATATCATTATATGGAAGTA 57.425 33.333 0.00 0.00 0.00 2.24
4749 4810 1.531602 GTGGCCCAGAAGCACCTTT 60.532 57.895 0.00 0.00 0.00 3.11
5232 5367 8.240682 TCAATGGTTGTGTATGTAAAGCATAAC 58.759 33.333 0.00 0.00 40.18 1.89
5254 5389 1.888512 TGCTGCTTCCAATCCTTTGTC 59.111 47.619 0.00 0.00 0.00 3.18
5396 5531 4.041198 TCTTCAAATCCTTACTGACCGGTT 59.959 41.667 9.42 0.00 0.00 4.44
5431 5566 1.125711 ACAGGCCCGGTGACTACTTT 61.126 55.000 0.00 0.00 0.00 2.66
5542 5677 7.411486 TCTCCACCTCTTTTGTTATCTCTAG 57.589 40.000 0.00 0.00 0.00 2.43
5544 5679 7.340743 TCTCCACCTCTTTTGTTATCTCTAGAG 59.659 40.741 13.98 13.98 0.00 2.43
5944 6119 6.806751 TCAACCTGATATTCTAAGGACTTCG 58.193 40.000 0.00 0.00 34.97 3.79
6072 6247 8.504005 CGTGAGAGTATATTCACCAAAAGTTTT 58.496 33.333 0.00 0.00 40.39 2.43
6073 6248 9.612620 GTGAGAGTATATTCACCAAAAGTTTTG 57.387 33.333 19.48 19.48 38.16 2.44
6074 6249 9.567776 TGAGAGTATATTCACCAAAAGTTTTGA 57.432 29.630 26.36 9.53 0.00 2.69
6081 6256 6.687081 TTCACCAAAAGTTTTGATACTCGT 57.313 33.333 26.36 13.34 0.00 4.18
6082 6257 6.295039 TCACCAAAAGTTTTGATACTCGTC 57.705 37.500 26.36 0.00 0.00 4.20
6083 6258 5.237779 TCACCAAAAGTTTTGATACTCGTCC 59.762 40.000 26.36 0.00 0.00 4.79
6148 6335 9.319143 GAATTGTATCTAAACTGTGTGCTATCT 57.681 33.333 0.00 0.00 0.00 1.98
6165 6352 3.498774 ATCTGTGAGTGGCAGAGTTTT 57.501 42.857 0.00 0.00 44.86 2.43
6201 6388 5.079643 AGACAGCTTGGTTAATTTGGATGT 58.920 37.500 0.00 0.00 0.00 3.06
6206 6393 7.132213 CAGCTTGGTTAATTTGGATGTATACG 58.868 38.462 0.00 0.00 0.00 3.06
6207 6394 5.912955 GCTTGGTTAATTTGGATGTATACGC 59.087 40.000 0.00 0.00 0.00 4.42
6208 6395 6.238648 GCTTGGTTAATTTGGATGTATACGCT 60.239 38.462 0.00 0.00 0.00 5.07
6209 6396 7.041644 GCTTGGTTAATTTGGATGTATACGCTA 60.042 37.037 0.00 0.00 0.00 4.26
6210 6397 8.734218 TTGGTTAATTTGGATGTATACGCTAA 57.266 30.769 0.00 0.00 0.00 3.09
6211 6398 8.911918 TGGTTAATTTGGATGTATACGCTAAT 57.088 30.769 0.00 0.00 0.00 1.73
6212 6399 9.999660 TGGTTAATTTGGATGTATACGCTAATA 57.000 29.630 0.00 0.00 0.00 0.98
6222 6409 6.340962 TGTATACGCTAATAGAAGTGCCAT 57.659 37.500 0.00 0.00 0.00 4.40
6226 6413 3.871594 ACGCTAATAGAAGTGCCATTGTC 59.128 43.478 0.00 0.00 0.00 3.18
6228 6415 4.199310 GCTAATAGAAGTGCCATTGTCCA 58.801 43.478 0.00 0.00 0.00 4.02
6231 6418 1.251251 AGAAGTGCCATTGTCCAAGC 58.749 50.000 0.00 0.00 0.00 4.01
6232 6419 0.961019 GAAGTGCCATTGTCCAAGCA 59.039 50.000 0.00 0.00 0.00 3.91
6293 6481 2.584608 CAGGCCCAACTACCCGAG 59.415 66.667 0.00 0.00 0.00 4.63
6297 6485 2.687566 CCCAACTACCCGAGGGCT 60.688 66.667 8.33 0.00 39.32 5.19
6304 6492 4.159879 CCAACTACCCGAGGGCTTATATAG 59.840 50.000 8.33 4.04 39.32 1.31
6323 6542 1.587054 CCGACACACTCACTCCCTC 59.413 63.158 0.00 0.00 0.00 4.30
6380 6599 0.877071 CTGTGCTGCTTCCAACGATT 59.123 50.000 0.00 0.00 0.00 3.34
6381 6600 2.076100 CTGTGCTGCTTCCAACGATTA 58.924 47.619 0.00 0.00 0.00 1.75
6418 6638 1.983224 CACGATTGGTGGGGAGAGT 59.017 57.895 0.00 0.00 43.16 3.24
6433 6653 0.032017 AGAGTAGGTGCCTCCGGAAT 60.032 55.000 5.23 0.00 41.99 3.01
6450 6670 2.436173 GGAATCCCGTCCTTCAAGATCT 59.564 50.000 0.00 0.00 34.56 2.75
6453 6673 2.257207 TCCCGTCCTTCAAGATCTTGT 58.743 47.619 29.80 0.00 41.16 3.16
6463 6683 2.497675 TCAAGATCTTGTCCGGGAGAAG 59.502 50.000 29.80 24.05 41.16 2.85
6474 6698 1.400737 CGGGAGAAGGACGATAAGGT 58.599 55.000 0.00 0.00 0.00 3.50
6513 6738 1.520342 GTGACTGCTCCCGATCTGC 60.520 63.158 0.00 0.00 0.00 4.26
6524 6749 2.764128 GATCTGCCCCCGTCTCCA 60.764 66.667 0.00 0.00 0.00 3.86
6539 6764 1.290431 TCTCCATCCTCCTCTGCTTCT 59.710 52.381 0.00 0.00 0.00 2.85
6556 6781 5.201243 TGCTTCTACTACTTCCTCTGCATA 58.799 41.667 0.00 0.00 0.00 3.14
6593 6824 1.611673 CCGTCAAGAAGAAGGCCACAT 60.612 52.381 5.01 0.00 39.05 3.21
6605 6836 0.035317 GGCCACATATGATGCCGAGA 59.965 55.000 19.43 0.00 33.59 4.04
6617 6848 4.079850 CCGAGACTGCTGCTGCCT 62.080 66.667 13.47 0.11 38.71 4.75
6638 6870 2.990967 CCGTGTTGCCTGGCCAAT 60.991 61.111 17.53 0.00 0.00 3.16
6642 6874 3.451894 GTTGCCTGGCCAATCGGG 61.452 66.667 17.53 5.47 40.85 5.14
6679 6911 7.556275 TGTTCATCCCCTATTTACTTGTTCATC 59.444 37.037 0.00 0.00 0.00 2.92
6683 6915 7.133133 TCCCCTATTTACTTGTTCATCTACC 57.867 40.000 0.00 0.00 0.00 3.18
6695 6927 3.868757 TCATCTACCAGCCGTATATGC 57.131 47.619 3.36 0.00 33.57 3.14
6721 6953 9.979270 CAATGTTCATAGATGTTTCAGTTCTAC 57.021 33.333 0.00 0.00 0.00 2.59
6725 6957 9.517609 GTTCATAGATGTTTCAGTTCTACGTAT 57.482 33.333 0.00 0.00 0.00 3.06
6731 6963 8.301720 AGATGTTTCAGTTCTACGTATTGTACA 58.698 33.333 0.00 0.00 0.00 2.90
6738 6970 6.530181 CAGTTCTACGTATTGTACATGCTCAA 59.470 38.462 0.00 5.79 0.00 3.02
6873 7105 6.554334 TTTAGTCACTTTTCGATTCAAGGG 57.446 37.500 0.00 0.00 0.00 3.95
6878 7110 4.642885 TCACTTTTCGATTCAAGGGTTTGT 59.357 37.500 0.00 0.00 35.73 2.83
6885 7117 2.623878 TTCAAGGGTTTGTCGCTACA 57.376 45.000 0.00 0.00 38.40 2.74
6886 7118 2.851263 TCAAGGGTTTGTCGCTACAT 57.149 45.000 0.00 0.00 38.40 2.29
6896 7128 0.645868 GTCGCTACATTGAAGCCGAC 59.354 55.000 0.00 0.00 36.60 4.79
6897 7129 0.459585 TCGCTACATTGAAGCCGACC 60.460 55.000 0.00 0.00 36.60 4.79
6898 7130 1.429148 CGCTACATTGAAGCCGACCC 61.429 60.000 0.00 0.00 36.60 4.46
6899 7131 1.095807 GCTACATTGAAGCCGACCCC 61.096 60.000 0.00 0.00 33.73 4.95
6906 7138 2.047939 AAGCCGACCCCGTTTACG 60.048 61.111 0.00 0.00 39.44 3.18
6907 7139 2.770132 GAAGCCGACCCCGTTTACGT 62.770 60.000 0.00 0.00 37.74 3.57
6917 7149 0.094046 CCGTTTACGTGGACGCATTC 59.906 55.000 16.87 0.00 44.43 2.67
6918 7150 0.094046 CGTTTACGTGGACGCATTCC 59.906 55.000 11.60 0.00 46.13 3.01
6941 7173 4.073293 AGTGTTGGTAGACAAAGACCAG 57.927 45.455 0.00 0.00 46.23 4.00
6985 7217 2.120312 TGTTCTGGGTTAGTGGTGTGA 58.880 47.619 0.00 0.00 0.00 3.58
6986 7218 2.708861 TGTTCTGGGTTAGTGGTGTGAT 59.291 45.455 0.00 0.00 0.00 3.06
6987 7219 3.137544 TGTTCTGGGTTAGTGGTGTGATT 59.862 43.478 0.00 0.00 0.00 2.57
6988 7220 3.695830 TCTGGGTTAGTGGTGTGATTC 57.304 47.619 0.00 0.00 0.00 2.52
6989 7221 2.304761 TCTGGGTTAGTGGTGTGATTCC 59.695 50.000 0.00 0.00 0.00 3.01
6990 7222 2.305927 CTGGGTTAGTGGTGTGATTCCT 59.694 50.000 0.00 0.00 0.00 3.36
6991 7223 3.517901 CTGGGTTAGTGGTGTGATTCCTA 59.482 47.826 0.00 0.00 0.00 2.94
6992 7224 3.517901 TGGGTTAGTGGTGTGATTCCTAG 59.482 47.826 0.00 0.00 0.00 3.02
6993 7225 3.518303 GGGTTAGTGGTGTGATTCCTAGT 59.482 47.826 0.00 0.00 0.00 2.57
6994 7226 4.504858 GGTTAGTGGTGTGATTCCTAGTG 58.495 47.826 0.00 0.00 0.00 2.74
6995 7227 4.222145 GGTTAGTGGTGTGATTCCTAGTGA 59.778 45.833 0.00 0.00 0.00 3.41
6996 7228 5.279809 GGTTAGTGGTGTGATTCCTAGTGAA 60.280 44.000 0.00 0.00 37.38 3.18
6997 7229 4.974645 AGTGGTGTGATTCCTAGTGAAA 57.025 40.909 0.00 0.00 36.33 2.69
6998 7230 4.642429 AGTGGTGTGATTCCTAGTGAAAC 58.358 43.478 0.00 0.00 36.33 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.936584 AGATCGAGTAGGTATCTTCAAAAGAG 58.063 38.462 0.00 0.00 41.61 2.85
66 67 3.056322 ACAATTTGGAAAGCTGGATCTGC 60.056 43.478 0.78 0.00 0.00 4.26
524 534 5.998454 ATCTTTGCATGATTAGGTTCGAG 57.002 39.130 0.00 0.00 0.00 4.04
682 692 7.416664 GCATATAGCAAGGAAATTTCTTGGACA 60.417 37.037 15.20 0.26 44.79 4.02
755 765 5.237815 TGGTGTCTCACATGTAAATCACTC 58.762 41.667 16.83 10.97 35.86 3.51
815 825 4.634004 TGTATTGGACCAATAACAAGAGCG 59.366 41.667 25.28 0.00 37.94 5.03
860 870 4.931601 TCATGTTGCTGATCAAGTCACTAC 59.068 41.667 0.00 0.00 34.91 2.73
1019 1029 6.657966 TGAATTTCTCTGCATCTCAGTCATTT 59.342 34.615 0.00 0.00 43.32 2.32
1074 1084 6.157645 TCCTGAGAGCTTCCTTATGAGATTTT 59.842 38.462 0.00 0.00 0.00 1.82
1083 1093 3.176924 ACAGTCCTGAGAGCTTCCTTA 57.823 47.619 0.40 0.00 0.00 2.69
1096 1106 1.617357 GTCTTGTCCCGTAACAGTCCT 59.383 52.381 0.00 0.00 0.00 3.85
1118 1128 2.705658 CCAGGGCCTACATCATCAGTAA 59.294 50.000 5.28 0.00 0.00 2.24
1235 1245 7.338710 CCTCTCTCCTTTGTAACCAATTATCA 58.661 38.462 0.00 0.00 0.00 2.15
1303 1313 0.251916 CCCGCAAGATGACCACCTAA 59.748 55.000 0.00 0.00 43.02 2.69
1559 1569 3.365472 ACAGATGGGGCCAGAAATTTAC 58.635 45.455 4.39 0.00 0.00 2.01
1679 1690 2.386661 TTAAGTCTGTAGCAGCCAGC 57.613 50.000 0.00 0.00 46.19 4.85
2000 2011 7.231925 AGCCATCATCATAAATTATGTGCTGAA 59.768 33.333 12.18 0.00 37.45 3.02
2037 2048 3.927142 GTGCCACAACTGTACTATCAGAC 59.073 47.826 0.00 0.00 38.63 3.51
2195 2206 2.338577 AGCAGTGGATGTGGATAAGC 57.661 50.000 0.00 0.00 0.00 3.09
2280 2291 9.569122 ACATTAACAGTTTAACTCCATAAGTGT 57.431 29.630 0.00 0.00 38.58 3.55
2341 2360 4.260170 AGAGAGATGCCAAGCAAACTAAG 58.740 43.478 0.00 0.00 43.62 2.18
2362 2381 3.249080 CCAAATTTCAGCTTTGTGCCAAG 59.751 43.478 0.00 0.00 44.23 3.61
2368 2387 8.776470 CATATGTTTTCCAAATTTCAGCTTTGT 58.224 29.630 0.00 0.00 32.83 2.83
2468 2487 5.928839 ACTACAGCTACACAACATTTCAGAG 59.071 40.000 0.00 0.00 0.00 3.35
2592 2611 4.135747 ACTATCTTCTTCTGCCTTCAGC 57.864 45.455 0.00 0.00 40.13 4.26
2619 2638 4.026356 AGCAGCTTCTTGGTCTACATTT 57.974 40.909 0.00 0.00 0.00 2.32
2705 2724 6.056236 GGATGGTTGGTAGGACTTAGAATTC 58.944 44.000 0.00 0.00 0.00 2.17
2755 2774 4.501559 CACACAAGTCAAGCAAATCAGTTG 59.498 41.667 0.00 0.00 40.50 3.16
3120 3146 4.018233 ACCCCAGAATAACCACCGAATAAA 60.018 41.667 0.00 0.00 0.00 1.40
3121 3147 3.524380 ACCCCAGAATAACCACCGAATAA 59.476 43.478 0.00 0.00 0.00 1.40
3122 3148 3.116959 ACCCCAGAATAACCACCGAATA 58.883 45.455 0.00 0.00 0.00 1.75
3123 3149 1.920351 ACCCCAGAATAACCACCGAAT 59.080 47.619 0.00 0.00 0.00 3.34
3368 3403 5.591099 AGTAATGTTCAAAACAGTGGCAAG 58.409 37.500 3.28 0.00 45.95 4.01
3420 3455 4.604490 ACCACTTCCCACCCTTAAAGAATA 59.396 41.667 0.00 0.00 0.00 1.75
3504 3539 5.074115 TCCATTTTAGTTTGGACGTGGATT 58.926 37.500 0.00 0.00 37.10 3.01
3842 3890 9.298774 AGAATAGTAGTGACGCATTAGTTAAAC 57.701 33.333 0.00 0.00 0.00 2.01
4093 4154 0.173255 GACATTGGGGCATTTCCACG 59.827 55.000 0.00 0.00 42.91 4.94
4159 4220 1.076559 TAGACGGCCTTCGGGATGA 60.077 57.895 3.18 0.00 44.45 2.92
4177 4238 3.951775 CAGAGTGGACTAACTGCTTCT 57.048 47.619 0.00 0.00 0.00 2.85
4272 4333 6.610020 TCGATATCTTCCAAAAGAGGTAGGAA 59.390 38.462 0.34 0.00 44.53 3.36
4329 4390 5.163854 GGTGAAGATGTTTCTTGTCCATACG 60.164 44.000 0.00 0.00 42.34 3.06
4420 4481 6.238103 CGATTGGTGAAGTTGCTCGTAATAAT 60.238 38.462 0.00 0.00 0.00 1.28
4421 4482 5.062934 CGATTGGTGAAGTTGCTCGTAATAA 59.937 40.000 0.00 0.00 0.00 1.40
4422 4483 4.565166 CGATTGGTGAAGTTGCTCGTAATA 59.435 41.667 0.00 0.00 0.00 0.98
4495 4556 0.250858 TCAGTGGATGTGCTTGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
4693 4754 3.118038 AGTGCAGAAGGTTTTCCACAGTA 60.118 43.478 0.00 0.00 43.73 2.74
4749 4810 3.356267 GACGCACAGGCACATGCA 61.356 61.111 6.15 0.00 41.88 3.96
4758 4819 6.533723 TGATTTACTAGTTAATGGACGCACAG 59.466 38.462 11.65 0.00 0.00 3.66
5165 5229 5.964477 TCCCTACCATAACAAGATGAAGTCT 59.036 40.000 0.00 0.00 39.43 3.24
5232 5367 0.883833 AAAGGATTGGAAGCAGCACG 59.116 50.000 0.00 0.00 0.00 5.34
5254 5389 8.862550 AGAAGTAATTTTCAGTTTTTCAGCAG 57.137 30.769 0.00 0.00 0.00 4.24
5396 5531 2.094078 GCCTGTTTAGCCATGCATTCAA 60.094 45.455 0.00 0.00 0.00 2.69
5562 5697 4.144297 AGTGGAAAAGCATAGCTGAAACA 58.856 39.130 0.00 0.00 39.62 2.83
5944 6119 6.430451 CACACCACTTTCTTTCTCAATGTAC 58.570 40.000 0.00 0.00 0.00 2.90
6072 6247 3.215151 GACCATCTCAGGACGAGTATCA 58.785 50.000 0.00 0.00 42.88 2.15
6073 6248 2.554893 GGACCATCTCAGGACGAGTATC 59.445 54.545 0.00 0.00 42.88 2.24
6074 6249 2.175931 AGGACCATCTCAGGACGAGTAT 59.824 50.000 0.00 0.00 42.88 2.12
6075 6250 1.564818 AGGACCATCTCAGGACGAGTA 59.435 52.381 0.00 0.00 42.88 2.59
6076 6251 0.333312 AGGACCATCTCAGGACGAGT 59.667 55.000 0.00 0.00 42.88 4.18
6077 6252 2.350057 TAGGACCATCTCAGGACGAG 57.650 55.000 0.00 0.00 43.80 4.18
6078 6253 3.314307 AATAGGACCATCTCAGGACGA 57.686 47.619 0.00 0.00 0.00 4.20
6079 6254 4.408182 AAAATAGGACCATCTCAGGACG 57.592 45.455 0.00 0.00 0.00 4.79
6080 6255 5.104318 AGGAAAAATAGGACCATCTCAGGAC 60.104 44.000 0.00 0.00 0.00 3.85
6081 6256 5.039645 AGGAAAAATAGGACCATCTCAGGA 58.960 41.667 0.00 0.00 0.00 3.86
6082 6257 5.379706 AGGAAAAATAGGACCATCTCAGG 57.620 43.478 0.00 0.00 0.00 3.86
6083 6258 5.825151 GGAAGGAAAAATAGGACCATCTCAG 59.175 44.000 0.00 0.00 0.00 3.35
6087 6262 4.777463 TCGGAAGGAAAAATAGGACCATC 58.223 43.478 0.00 0.00 0.00 3.51
6091 6278 5.234543 CGAATCTCGGAAGGAAAAATAGGAC 59.765 44.000 0.00 0.00 36.00 3.85
6148 6335 1.405105 GCAAAAACTCTGCCACTCACA 59.595 47.619 0.00 0.00 33.51 3.58
6165 6352 2.808919 AGCTGTCTAGTCCTGTAGCAA 58.191 47.619 0.00 0.00 33.81 3.91
6171 6358 4.537135 TTAACCAAGCTGTCTAGTCCTG 57.463 45.455 0.00 0.00 0.00 3.86
6201 6388 6.755206 ACAATGGCACTTCTATTAGCGTATA 58.245 36.000 0.00 0.00 0.00 1.47
6206 6393 4.199310 TGGACAATGGCACTTCTATTAGC 58.801 43.478 0.00 0.00 0.00 3.09
6207 6394 5.220931 GCTTGGACAATGGCACTTCTATTAG 60.221 44.000 0.00 0.00 0.00 1.73
6208 6395 4.640201 GCTTGGACAATGGCACTTCTATTA 59.360 41.667 0.00 0.00 0.00 0.98
6209 6396 3.445096 GCTTGGACAATGGCACTTCTATT 59.555 43.478 0.00 0.00 0.00 1.73
6210 6397 3.019564 GCTTGGACAATGGCACTTCTAT 58.980 45.455 0.00 0.00 0.00 1.98
6211 6398 2.224744 TGCTTGGACAATGGCACTTCTA 60.225 45.455 0.00 0.00 0.00 2.10
6212 6399 1.251251 GCTTGGACAATGGCACTTCT 58.749 50.000 0.00 0.00 0.00 2.85
6228 6415 2.676471 GCCCACGGTCCAATGCTT 60.676 61.111 0.00 0.00 0.00 3.91
6231 6418 1.586154 GAACAGCCCACGGTCCAATG 61.586 60.000 0.00 0.00 0.00 2.82
6232 6419 1.303317 GAACAGCCCACGGTCCAAT 60.303 57.895 0.00 0.00 0.00 3.16
6284 6472 3.363627 GCTATATAAGCCCTCGGGTAGT 58.636 50.000 3.54 0.00 46.25 2.73
6297 6485 4.277672 GGAGTGAGTGTGTCGGCTATATAA 59.722 45.833 0.00 0.00 0.00 0.98
6304 6492 2.048127 GGGAGTGAGTGTGTCGGC 60.048 66.667 0.00 0.00 0.00 5.54
6307 6521 0.892063 GAGGAGGGAGTGAGTGTGTC 59.108 60.000 0.00 0.00 0.00 3.67
6310 6524 0.896019 CACGAGGAGGGAGTGAGTGT 60.896 60.000 0.00 0.00 38.06 3.55
6323 6542 2.125106 GGCTAGGGTTGCACGAGG 60.125 66.667 0.00 0.00 0.00 4.63
6380 6599 4.777781 CGCGGTCGTCTGAATGTA 57.222 55.556 0.00 0.00 0.00 2.29
6404 6624 1.584724 CACCTACTCTCCCCACCAAT 58.415 55.000 0.00 0.00 0.00 3.16
6410 6630 1.762858 GGAGGCACCTACTCTCCCC 60.763 68.421 0.00 0.00 40.76 4.81
6433 6653 2.233922 GACAAGATCTTGAAGGACGGGA 59.766 50.000 36.15 0.00 42.93 5.14
6440 6660 2.497675 TCTCCCGGACAAGATCTTGAAG 59.502 50.000 36.15 25.12 42.93 3.02
6453 6673 1.688772 CTTATCGTCCTTCTCCCGGA 58.311 55.000 0.73 0.00 0.00 5.14
6513 6738 2.844839 GGAGGATGGAGACGGGGG 60.845 72.222 0.00 0.00 0.00 5.40
6524 6749 4.806952 AGTAGTAGAAGCAGAGGAGGAT 57.193 45.455 0.00 0.00 0.00 3.24
6539 6764 4.471548 GGGTCTATGCAGAGGAAGTAGTA 58.528 47.826 8.78 0.00 0.00 1.82
6576 6807 4.842531 TCATATGTGGCCTTCTTCTTGA 57.157 40.909 3.32 0.00 0.00 3.02
6593 6824 0.249615 GCAGCAGTCTCGGCATCATA 60.250 55.000 0.00 0.00 0.00 2.15
6624 6855 2.676121 CCGATTGGCCAGGCAACA 60.676 61.111 15.19 0.00 41.41 3.33
6679 6911 3.664107 ACATTGCATATACGGCTGGTAG 58.336 45.455 0.00 0.00 33.84 3.18
6683 6915 4.754372 ATGAACATTGCATATACGGCTG 57.246 40.909 0.00 0.00 0.00 4.85
6695 6927 9.979270 GTAGAACTGAAACATCTATGAACATTG 57.021 33.333 0.00 0.00 0.00 2.82
6721 6953 5.160699 AGCATTTGAGCATGTACAATACG 57.839 39.130 0.00 0.00 36.85 3.06
6725 6957 5.009631 ACCTAAGCATTTGAGCATGTACAA 58.990 37.500 0.00 0.00 36.85 2.41
6731 6963 5.203528 ACCAATACCTAAGCATTTGAGCAT 58.796 37.500 0.00 0.00 36.85 3.79
6738 6970 7.777910 TGCAACTTATACCAATACCTAAGCATT 59.222 33.333 0.00 0.00 0.00 3.56
6770 7002 6.470556 CGAGTAGATAATAGACATGGCAATCG 59.529 42.308 0.00 0.00 0.00 3.34
6855 7087 4.642885 ACAAACCCTTGAATCGAAAAGTGA 59.357 37.500 0.00 0.00 36.33 3.41
6873 7105 2.724839 CGGCTTCAATGTAGCGACAAAC 60.725 50.000 3.04 0.00 39.59 2.93
6878 7110 0.459585 GGTCGGCTTCAATGTAGCGA 60.460 55.000 5.80 4.43 39.54 4.93
6885 7117 0.325602 TAAACGGGGTCGGCTTCAAT 59.674 50.000 0.00 0.00 41.39 2.57
6886 7118 0.603439 GTAAACGGGGTCGGCTTCAA 60.603 55.000 0.00 0.00 41.39 2.69
6897 7129 1.293267 AATGCGTCCACGTAAACGGG 61.293 55.000 19.51 2.11 44.95 5.28
6898 7130 0.094046 GAATGCGTCCACGTAAACGG 59.906 55.000 19.51 3.86 44.95 4.44
6899 7131 0.094046 GGAATGCGTCCACGTAAACG 59.906 55.000 15.31 15.31 46.97 3.60
6918 7150 4.196193 TGGTCTTTGTCTACCAACACTTG 58.804 43.478 0.00 0.00 42.74 3.16
6922 7154 2.438021 AGCTGGTCTTTGTCTACCAACA 59.562 45.455 0.00 0.00 44.92 3.33
6941 7173 3.117491 TCATAGCTATGAGCCACAAGC 57.883 47.619 28.69 0.00 43.77 4.01
6957 7189 4.561938 CCACTAACCCAGAACACGTTCATA 60.562 45.833 12.21 0.00 41.84 2.15


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

AutoCloner maintained by Alex Coulton.