Multiple sequence alignment - TraesCS1D01G225600

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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 TraesCS1D01G225600 chr1D 100.000 4849 0 0 1 4849 314125894 314121046 0.000000e+00 8955.0
1 TraesCS1D01G225600 chr1A 95.014 3450 124 22 814 4231 394328535 394325102 0.000000e+00 5374.0
2 TraesCS1D01G225600 chr1A 89.286 476 41 7 4 472 394329652 394329180 5.410000e-164 588.0
3 TraesCS1D01G225600 chr1A 95.410 305 6 4 511 812 394329184 394328885 3.390000e-131 479.0
4 TraesCS1D01G225600 chr1A 86.425 221 6 10 4233 4453 373760142 373760338 2.270000e-53 220.0
5 TraesCS1D01G225600 chr1B 94.372 3003 125 19 489 3460 424180510 424177521 0.000000e+00 4569.0
6 TraesCS1D01G225600 chr1B 89.310 870 58 11 3277 4140 424177525 424176685 0.000000e+00 1059.0
7 TraesCS1D01G225600 chr1B 94.395 339 18 1 4457 4795 550681051 550681388 2.000000e-143 520.0
8 TraesCS1D01G225600 chr1B 80.716 363 52 10 1352 1710 424179543 424179195 2.880000e-67 267.0
9 TraesCS1D01G225600 chr1B 79.339 363 57 12 1448 1794 424179641 424179281 6.270000e-59 239.0
10 TraesCS1D01G225600 chr1B 85.345 232 31 3 44 273 650441715 650441945 2.260000e-58 237.0
11 TraesCS1D01G225600 chr1B 85.973 221 7 7 4233 4453 550680506 550680702 1.060000e-51 215.0
12 TraesCS1D01G225600 chr1B 85.520 221 8 7 4233 4453 61319262 61319458 4.920000e-50 209.0
13 TraesCS1D01G225600 chr6B 95.000 340 15 2 4457 4795 136922116 136921778 2.570000e-147 532.0
14 TraesCS1D01G225600 chr6B 94.985 339 17 0 4457 4795 708042350 708042012 2.570000e-147 532.0
15 TraesCS1D01G225600 chr6B 94.395 339 19 0 4457 4795 412283169 412282831 5.560000e-144 521.0
16 TraesCS1D01G225600 chr6B 86.878 221 5 7 4233 4453 412283714 412283518 4.880000e-55 226.0
17 TraesCS1D01G225600 chr6B 86.878 221 5 13 4233 4453 708042895 708042699 4.880000e-55 226.0
18 TraesCS1D01G225600 chr6B 95.349 86 4 0 4368 4453 197230782 197230697 2.350000e-28 137.0
19 TraesCS1D01G225600 chr2B 94.706 340 16 2 4457 4796 609079990 609079653 1.200000e-145 527.0
20 TraesCS1D01G225600 chr2B 94.152 342 20 0 4454 4795 383361246 383361587 5.560000e-144 521.0
21 TraesCS1D01G225600 chr2B 86.878 221 5 7 4233 4453 383360703 383360899 4.880000e-55 226.0
22 TraesCS1D01G225600 chr2B 85.068 221 9 10 4233 4453 609091883 609091687 2.290000e-48 204.0
23 TraesCS1D01G225600 chr2B 80.114 176 20 7 2452 2614 784192836 784192663 3.070000e-22 117.0
24 TraesCS1D01G225600 chr4B 94.152 342 20 0 4454 4795 646926166 646926507 5.560000e-144 521.0
25 TraesCS1D01G225600 chr3A 94.152 342 20 0 4454 4795 11779448 11779789 5.560000e-144 521.0
26 TraesCS1D01G225600 chr3A 88.603 272 27 3 8 276 543726640 543726370 1.300000e-85 327.0
27 TraesCS1D01G225600 chr3A 84.889 225 6 11 4233 4453 11778902 11779102 8.230000e-48 202.0
28 TraesCS1D01G225600 chr2A 93.805 339 18 2 4457 4795 671342156 671341821 1.560000e-139 507.0
29 TraesCS1D01G225600 chr2A 85.973 221 7 8 4233 4453 671342701 671342505 1.060000e-51 215.0
30 TraesCS1D01G225600 chr2D 88.971 272 26 3 5 273 648451619 648451889 2.800000e-87 333.0
31 TraesCS1D01G225600 chr3B 91.000 200 18 0 76 275 735073367 735073168 2.220000e-68 270.0
32 TraesCS1D01G225600 chr3B 79.817 218 20 5 4235 4452 225233392 225233199 2.350000e-28 137.0
33 TraesCS1D01G225600 chr5B 84.937 239 35 1 1259 1497 217630673 217630910 1.740000e-59 241.0
34 TraesCS1D01G225600 chr5D 76.923 208 38 10 70 275 474703451 474703252 5.130000e-20 110.0
35 TraesCS1D01G225600 chr5D 89.744 78 8 0 329 406 543492029 543492106 3.090000e-17 100.0
36 TraesCS1D01G225600 chr5D 76.056 142 30 4 133 273 483022544 483022406 2.420000e-08 71.3
37 TraesCS1D01G225600 chr4A 89.412 85 9 0 322 406 251275385 251275469 1.850000e-19 108.0
38 TraesCS1D01G225600 chr7B 87.778 90 11 0 318 407 632107912 632108001 6.640000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G225600 chr1D 314121046 314125894 4848 True 8955.0 8955 100.000000 1 4849 1 chr1D.!!$R1 4848
1 TraesCS1D01G225600 chr1A 394325102 394329652 4550 True 2147.0 5374 93.236667 4 4231 3 chr1A.!!$R1 4227
2 TraesCS1D01G225600 chr1B 424176685 424180510 3825 True 1533.5 4569 85.934250 489 4140 4 chr1B.!!$R1 3651
3 TraesCS1D01G225600 chr1B 550680506 550681388 882 False 367.5 520 90.184000 4233 4795 2 chr1B.!!$F3 562
4 TraesCS1D01G225600 chr6B 708042012 708042895 883 True 379.0 532 90.931500 4233 4795 2 chr6B.!!$R4 562
5 TraesCS1D01G225600 chr6B 412282831 412283714 883 True 373.5 521 90.636500 4233 4795 2 chr6B.!!$R3 562
6 TraesCS1D01G225600 chr2B 383360703 383361587 884 False 373.5 521 90.515000 4233 4795 2 chr2B.!!$F1 562
7 TraesCS1D01G225600 chr3A 11778902 11779789 887 False 361.5 521 89.520500 4233 4795 2 chr3A.!!$F1 562
8 TraesCS1D01G225600 chr2A 671341821 671342701 880 True 361.0 507 89.889000 4233 4795 2 chr2A.!!$R1 562

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
245 246 0.179043 GAAAAGGCCGGGATCCTCTC 60.179 60.000 12.58 0.35 32.45 3.20 F
398 400 1.048601 TCCGCCAGGTGATCCTAATC 58.951 55.000 0.00 0.00 43.07 1.75 F
906 1270 1.076705 GGTGAGGAATTCCCAGGCC 60.077 63.158 21.22 13.93 37.41 5.19 F
1114 1479 1.343681 ACAGTAATCCCGCCTCCCTAA 60.344 52.381 0.00 0.00 0.00 2.69 F
2541 2926 0.038343 CCCATTGGTTGCCTTTCACG 60.038 55.000 1.20 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2159 0.533531 TCTCAGCACAAGCACACTGG 60.534 55.000 0.0 0.0 45.49 4.00 R
1794 2168 2.928801 TACAGCCTTTCTCAGCACAA 57.071 45.000 0.0 0.0 0.00 3.33 R
2410 2795 1.376812 CTTCCAGTAACCGGCCCAC 60.377 63.158 0.0 0.0 0.00 4.61 R
2805 3190 3.998913 TCATCCACCTTTGTATCAGCA 57.001 42.857 0.0 0.0 0.00 4.41 R
4113 4695 0.106268 AACACCAATCAGCCACACCA 60.106 50.000 0.0 0.0 0.00 4.17 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
19 20 1.427809 TCATACAGGGAGGCATGGAG 58.572 55.000 0.00 0.00 0.00 3.86
29 30 3.207669 GCATGGAGGCTCAAGGCG 61.208 66.667 13.38 0.00 46.23 5.52
30 31 2.515523 CATGGAGGCTCAAGGCGG 60.516 66.667 17.69 0.00 46.23 6.13
106 107 2.180017 CCTAACCCGTCGACACCG 59.820 66.667 17.16 1.07 37.07 4.94
110 111 1.300971 TAACCCGTCGACACCGAGAG 61.301 60.000 17.16 0.00 46.52 3.20
165 166 0.320050 GATCTTCTCCCCTCGCATCC 59.680 60.000 0.00 0.00 0.00 3.51
167 168 0.617535 TCTTCTCCCCTCGCATCCAA 60.618 55.000 0.00 0.00 0.00 3.53
169 170 2.202932 CTCCCCTCGCATCCAACG 60.203 66.667 0.00 0.00 0.00 4.10
170 171 2.682136 TCCCCTCGCATCCAACGA 60.682 61.111 0.00 0.00 38.02 3.85
177 178 1.226660 CGCATCCAACGAAATGGGC 60.227 57.895 0.00 0.00 41.05 5.36
185 186 2.643551 CAACGAAATGGGCCTGTCTAT 58.356 47.619 4.53 0.00 0.00 1.98
192 193 0.918983 TGGGCCTGTCTATTTCCCTG 59.081 55.000 4.53 0.00 37.83 4.45
206 207 2.616458 CCCTGGGCCCAACTTAGCT 61.616 63.158 28.29 0.00 0.00 3.32
245 246 0.179043 GAAAAGGCCGGGATCCTCTC 60.179 60.000 12.58 0.35 32.45 3.20
274 275 4.325030 CCCTTAGAACCAAATGAGGCCTAA 60.325 45.833 4.42 0.00 0.00 2.69
277 278 7.060421 CCTTAGAACCAAATGAGGCCTAATTA 58.940 38.462 16.30 0.00 31.27 1.40
293 294 3.382083 AATTATTGCGGGGAAAGACCT 57.618 42.857 0.00 0.00 38.98 3.85
301 302 1.617322 GGGGAAAGACCTCAACAACC 58.383 55.000 0.00 0.00 39.39 3.77
306 307 4.394729 GGAAAGACCTCAACAACCATACA 58.605 43.478 0.00 0.00 35.41 2.29
307 308 4.825085 GGAAAGACCTCAACAACCATACAA 59.175 41.667 0.00 0.00 35.41 2.41
308 309 5.300792 GGAAAGACCTCAACAACCATACAAA 59.699 40.000 0.00 0.00 35.41 2.83
312 313 4.881920 ACCTCAACAACCATACAAATTGC 58.118 39.130 0.00 0.00 0.00 3.56
383 385 2.245532 GCACGCATCGTTATCCGC 59.754 61.111 0.00 0.00 38.32 5.54
384 386 2.928361 CACGCATCGTTATCCGCC 59.072 61.111 0.00 0.00 38.32 6.13
385 387 1.880796 CACGCATCGTTATCCGCCA 60.881 57.895 0.00 0.00 38.32 5.69
398 400 1.048601 TCCGCCAGGTGATCCTAATC 58.951 55.000 0.00 0.00 43.07 1.75
451 456 3.296322 TTGACGGGTGCATCATTTTTC 57.704 42.857 0.00 0.00 0.00 2.29
460 468 5.406477 GGGTGCATCATTTTTCTTTTGAGAC 59.594 40.000 0.00 0.00 0.00 3.36
469 477 9.533253 TCATTTTTCTTTTGAGACAAAGAATCC 57.467 29.630 8.94 0.00 42.49 3.01
470 478 8.768019 CATTTTTCTTTTGAGACAAAGAATCCC 58.232 33.333 8.94 0.00 42.49 3.85
471 479 7.660030 TTTTCTTTTGAGACAAAGAATCCCT 57.340 32.000 8.94 0.00 42.49 4.20
472 480 6.884280 TTCTTTTGAGACAAAGAATCCCTC 57.116 37.500 4.81 0.00 39.34 4.30
473 481 4.997395 TCTTTTGAGACAAAGAATCCCTCG 59.003 41.667 0.00 0.00 32.62 4.63
474 482 4.617253 TTTGAGACAAAGAATCCCTCGA 57.383 40.909 0.00 0.00 0.00 4.04
475 483 4.617253 TTGAGACAAAGAATCCCTCGAA 57.383 40.909 0.00 0.00 0.00 3.71
476 484 4.826274 TGAGACAAAGAATCCCTCGAAT 57.174 40.909 0.00 0.00 0.00 3.34
477 485 4.759782 TGAGACAAAGAATCCCTCGAATC 58.240 43.478 0.00 0.00 0.00 2.52
478 486 3.786635 AGACAAAGAATCCCTCGAATCG 58.213 45.455 0.00 0.00 0.00 3.34
479 487 2.280628 ACAAAGAATCCCTCGAATCGC 58.719 47.619 0.00 0.00 0.00 4.58
480 488 2.279741 CAAAGAATCCCTCGAATCGCA 58.720 47.619 0.00 0.00 0.00 5.10
481 489 2.231215 AAGAATCCCTCGAATCGCAG 57.769 50.000 0.00 0.00 0.00 5.18
482 490 1.403814 AGAATCCCTCGAATCGCAGA 58.596 50.000 0.00 0.00 45.75 4.26
483 491 1.339610 AGAATCCCTCGAATCGCAGAG 59.660 52.381 0.00 0.00 43.63 3.35
486 494 2.279784 CCTCGAATCGCAGAGGCC 60.280 66.667 0.00 0.00 46.23 5.19
487 495 2.656651 CTCGAATCGCAGAGGCCG 60.657 66.667 0.00 0.00 43.63 6.13
499 507 1.153349 GAGGCCGATCCAAGTGTCC 60.153 63.158 0.00 0.00 37.29 4.02
722 737 3.560251 CCACCGCCTATCCCCCAG 61.560 72.222 0.00 0.00 0.00 4.45
723 738 2.768344 CACCGCCTATCCCCCAGT 60.768 66.667 0.00 0.00 0.00 4.00
724 739 2.446036 ACCGCCTATCCCCCAGTC 60.446 66.667 0.00 0.00 0.00 3.51
861 1225 3.171388 CCGATTCCCCTCCCCAGG 61.171 72.222 0.00 0.00 39.98 4.45
863 1227 3.502875 GATTCCCCTCCCCAGGCC 61.503 72.222 0.00 0.00 38.72 5.19
906 1270 1.076705 GGTGAGGAATTCCCAGGCC 60.077 63.158 21.22 13.93 37.41 5.19
995 1359 2.898662 TCTAACCTTCTCGGGTCCTTT 58.101 47.619 0.00 0.00 38.87 3.11
1103 1468 3.743396 GCCGAGATCATCAACAGTAATCC 59.257 47.826 0.00 0.00 0.00 3.01
1114 1479 1.343681 ACAGTAATCCCGCCTCCCTAA 60.344 52.381 0.00 0.00 0.00 2.69
1236 1602 3.568007 TCGCTGAATTTAGCTGTTTGGTT 59.432 39.130 18.83 0.00 41.51 3.67
1260 1626 4.998033 AGTAGCTCTGCAAGTTTTAAGGAC 59.002 41.667 0.00 0.00 33.76 3.85
1262 1628 5.228945 AGCTCTGCAAGTTTTAAGGACTA 57.771 39.130 0.00 0.00 33.76 2.59
1318 1685 7.976135 ATTAACATGATTAGAGTCCTGATGC 57.024 36.000 0.00 0.00 0.00 3.91
1387 1754 7.433708 TTTGTTGGTGATGTTGTACTCTATG 57.566 36.000 0.00 0.00 0.00 2.23
1404 1773 6.102663 ACTCTATGCTGTTATGTTCACAGTC 58.897 40.000 2.24 0.00 43.21 3.51
1421 1790 3.440173 ACAGTCCGCCTTCATGTAATTTG 59.560 43.478 0.00 0.00 0.00 2.32
1570 1940 3.633525 TGCTCCATTTTGCTGGTGATATC 59.366 43.478 0.00 0.00 37.57 1.63
1574 1944 5.056480 TCCATTTTGCTGGTGATATCGTAG 58.944 41.667 0.00 0.00 37.57 3.51
1596 1966 5.725362 AGTCTACTTTGCTATGTTCACCTC 58.275 41.667 0.00 0.00 0.00 3.85
1695 2067 8.233868 TGTAATGTTCACCTTCATGTAATTTCG 58.766 33.333 0.00 0.00 0.00 3.46
1781 2155 5.460646 ACGTTCACCTTCATGCAATTTTAG 58.539 37.500 0.00 0.00 0.00 1.85
1785 2159 7.008628 CGTTCACCTTCATGCAATTTTAGAATC 59.991 37.037 0.00 0.00 0.00 2.52
1794 2168 4.523943 TGCAATTTTAGAATCCAGTGTGCT 59.476 37.500 0.00 0.00 0.00 4.40
2270 2655 7.830697 AGAAAATGACATGGTGAAGATGTATGA 59.169 33.333 0.00 0.00 34.10 2.15
2296 2681 4.157840 CCCTTTAACCTTTCTACCATGTGC 59.842 45.833 0.00 0.00 0.00 4.57
2410 2795 4.036027 GGCTCATACACATGTCATCAAAGG 59.964 45.833 0.00 0.00 33.57 3.11
2541 2926 0.038343 CCCATTGGTTGCCTTTCACG 60.038 55.000 1.20 0.00 0.00 4.35
2805 3190 8.288689 ACAAAGTGGTACTTAGTGTTTCAAAT 57.711 30.769 0.00 0.00 37.47 2.32
2898 3283 2.241176 TGGCGAGGGAAAGGTGATAATT 59.759 45.455 0.00 0.00 0.00 1.40
3345 3922 4.142038 GTCAAAGTCACTTGGGGTTGTAT 58.858 43.478 0.00 0.00 0.00 2.29
3356 3933 7.393234 TCACTTGGGGTTGTATATCTTTTGAAG 59.607 37.037 0.00 0.00 0.00 3.02
3393 3971 6.586868 TGTGTTCATTTGTCATTTTTGCTC 57.413 33.333 0.00 0.00 0.00 4.26
3435 4013 3.823304 AGTCTCCCTTTCATGCTTGTTTC 59.177 43.478 0.00 0.00 0.00 2.78
3464 4042 1.993956 TTGCTGGTGTTTATGCAGGT 58.006 45.000 0.00 0.00 36.75 4.00
3546 4124 4.292186 ACTTCACATCCACTACAGCAAT 57.708 40.909 0.00 0.00 0.00 3.56
3596 4174 1.380524 CTGAGATCAAGGCTTGGCTG 58.619 55.000 25.92 13.13 0.00 4.85
3662 4240 2.959507 AAGGTTTGCTTGGTTGACAC 57.040 45.000 0.00 0.00 0.00 3.67
3667 4245 4.760204 AGGTTTGCTTGGTTGACACTATAC 59.240 41.667 0.00 0.00 0.00 1.47
3672 4250 3.065371 GCTTGGTTGACACTATACATGCC 59.935 47.826 0.00 0.00 0.00 4.40
3737 4318 4.442375 AGACTGGTTTACATCTGTCTCG 57.558 45.455 0.00 0.00 37.55 4.04
3912 4494 3.159472 TCCTTTGCTGCATCTGATTGTT 58.841 40.909 1.84 0.00 0.00 2.83
3997 4579 2.705220 CTGGCGCACATCACATCG 59.295 61.111 10.83 0.00 0.00 3.84
4030 4612 5.707298 GCCTGATAATTATGTATGGTGTGCT 59.293 40.000 1.78 0.00 0.00 4.40
4067 4649 5.468746 GTCAGTAATGCTTATAAATCCGGCA 59.531 40.000 0.00 0.00 37.32 5.69
4108 4690 4.076394 TGATGTTTACCTGTGCTTTACCC 58.924 43.478 0.00 0.00 0.00 3.69
4113 4695 5.422650 TGTTTACCTGTGCTTTACCCTTTTT 59.577 36.000 0.00 0.00 0.00 1.94
4150 4732 5.589452 TGGTGTTCACCTACGTTATTTGTTT 59.411 36.000 20.48 0.00 0.00 2.83
4161 4743 4.513318 ACGTTATTTGTTTTGGGCAATTGG 59.487 37.500 7.72 0.00 0.00 3.16
4162 4744 4.083590 CGTTATTTGTTTTGGGCAATTGGG 60.084 41.667 7.72 0.00 0.00 4.12
4165 4747 0.769873 TGTTTTGGGCAATTGGGCAT 59.230 45.000 7.72 0.00 45.66 4.40
4176 4758 3.129871 CAATTGGGCATGAACGTTTTGT 58.870 40.909 0.46 0.00 0.00 2.83
4180 4762 2.034053 TGGGCATGAACGTTTTGTCTTC 59.966 45.455 0.46 0.00 0.00 2.87
4191 4773 6.920569 ACGTTTTGTCTTCTATGTCTGTTT 57.079 33.333 0.00 0.00 0.00 2.83
4198 4780 6.401394 TGTCTTCTATGTCTGTTTGAGGATG 58.599 40.000 0.00 0.00 0.00 3.51
4199 4781 6.014242 TGTCTTCTATGTCTGTTTGAGGATGT 60.014 38.462 0.00 0.00 0.00 3.06
4200 4782 6.876257 GTCTTCTATGTCTGTTTGAGGATGTT 59.124 38.462 0.00 0.00 0.00 2.71
4201 4783 7.064016 GTCTTCTATGTCTGTTTGAGGATGTTC 59.936 40.741 0.00 0.00 0.00 3.18
4228 4810 5.880332 TGGTGTTTCTCTATACAATCTTGCC 59.120 40.000 0.00 0.00 0.00 4.52
4231 4813 7.715249 GGTGTTTCTCTATACAATCTTGCCATA 59.285 37.037 0.00 0.00 0.00 2.74
4304 4889 5.529060 ACTTGTCGAAGAAGAAGAATTGCTT 59.471 36.000 11.45 0.00 39.69 3.91
4324 4909 0.674895 GGTTCGATTGGCTCTGCACT 60.675 55.000 0.00 0.00 0.00 4.40
4343 4928 4.081087 GCACTATAACTTCTGGACTTCCCA 60.081 45.833 0.00 0.00 44.25 4.37
4352 4937 2.352561 TGGACTTCCCAGGTGGATAA 57.647 50.000 0.00 0.00 44.66 1.75
4353 4938 1.913419 TGGACTTCCCAGGTGGATAAC 59.087 52.381 0.00 0.00 44.66 1.89
4354 4939 2.197465 GGACTTCCCAGGTGGATAACT 58.803 52.381 0.00 0.00 44.66 2.24
4355 4940 2.576648 GGACTTCCCAGGTGGATAACTT 59.423 50.000 0.00 0.00 44.66 2.66
4356 4941 3.370633 GGACTTCCCAGGTGGATAACTTC 60.371 52.174 0.00 0.00 44.66 3.01
4357 4942 3.519913 GACTTCCCAGGTGGATAACTTCT 59.480 47.826 0.00 0.00 44.66 2.85
4358 4943 3.264450 ACTTCCCAGGTGGATAACTTCTG 59.736 47.826 0.00 0.00 44.66 3.02
4359 4944 2.196595 TCCCAGGTGGATAACTTCTGG 58.803 52.381 0.00 0.00 43.26 3.86
4360 4945 2.196595 CCCAGGTGGATAACTTCTGGA 58.803 52.381 9.02 0.00 45.66 3.86
4361 4946 2.092914 CCCAGGTGGATAACTTCTGGAC 60.093 54.545 9.02 0.00 45.66 4.02
4362 4947 2.840651 CCAGGTGGATAACTTCTGGACT 59.159 50.000 0.00 0.00 45.66 3.85
4363 4948 3.264450 CCAGGTGGATAACTTCTGGACTT 59.736 47.826 0.00 0.00 45.66 3.01
4364 4949 4.508662 CAGGTGGATAACTTCTGGACTTC 58.491 47.826 0.00 0.00 0.00 3.01
4365 4950 3.519913 AGGTGGATAACTTCTGGACTTCC 59.480 47.826 0.00 0.00 0.00 3.46
4366 4951 3.519913 GGTGGATAACTTCTGGACTTCCT 59.480 47.826 0.00 0.00 36.82 3.36
4455 5387 2.301296 CTCACATGTCCACCTTGACTCT 59.699 50.000 0.00 0.00 36.21 3.24
4470 5402 0.247736 ACTCTGATTGGAGTGACGCC 59.752 55.000 0.00 0.00 43.89 5.68
4583 5515 5.104318 GGGAGTTATGGAAAGAGAGGAATGT 60.104 44.000 0.00 0.00 0.00 2.71
4627 5559 2.337532 CGGTGGGAGTCGTCGTTT 59.662 61.111 0.00 0.00 0.00 3.60
4643 5575 4.503370 CGTCGTTTCTAGGATTAAAGAGGC 59.497 45.833 0.00 0.00 0.00 4.70
4696 5628 7.116075 AGGCATTTGAATAACATAATGCTGT 57.884 32.000 15.57 4.23 43.59 4.40
4748 5680 6.183361 TGGCCTTAACCTCTAAAACTTCTCTT 60.183 38.462 3.32 0.00 0.00 2.85
4817 5749 9.540431 AAAACTTGAAATTTCGTCATTTTGTTG 57.460 25.926 13.34 0.00 0.00 3.33
4818 5750 8.472683 AACTTGAAATTTCGTCATTTTGTTGA 57.527 26.923 13.34 0.00 0.00 3.18
4819 5751 8.472683 ACTTGAAATTTCGTCATTTTGTTGAA 57.527 26.923 13.34 0.00 0.00 2.69
4820 5752 9.097257 ACTTGAAATTTCGTCATTTTGTTGAAT 57.903 25.926 13.34 0.00 0.00 2.57
4823 5755 9.521503 TGAAATTTCGTCATTTTGTTGAATACA 57.478 25.926 13.34 0.00 34.12 2.29
4826 5758 9.474920 AATTTCGTCATTTTGTTGAATACATGT 57.525 25.926 2.69 2.69 36.44 3.21
4827 5759 8.864069 TTTCGTCATTTTGTTGAATACATGTT 57.136 26.923 2.30 0.00 36.44 2.71
4828 5760 8.864069 TTCGTCATTTTGTTGAATACATGTTT 57.136 26.923 2.30 0.00 36.44 2.83
4829 5761 8.864069 TCGTCATTTTGTTGAATACATGTTTT 57.136 26.923 2.30 1.42 36.44 2.43
4830 5762 9.307121 TCGTCATTTTGTTGAATACATGTTTTT 57.693 25.926 2.30 0.00 36.44 1.94
4831 5763 9.566624 CGTCATTTTGTTGAATACATGTTTTTC 57.433 29.630 2.30 8.88 36.44 2.29
4832 5764 9.862585 GTCATTTTGTTGAATACATGTTTTTCC 57.137 29.630 2.30 0.00 36.44 3.13
4833 5765 9.605275 TCATTTTGTTGAATACATGTTTTTCCA 57.395 25.926 2.30 0.00 36.44 3.53
4834 5766 9.649024 CATTTTGTTGAATACATGTTTTTCCAC 57.351 29.630 2.30 10.47 36.44 4.02
4835 5767 9.612066 ATTTTGTTGAATACATGTTTTTCCACT 57.388 25.926 2.30 0.00 36.44 4.00
4836 5768 9.442047 TTTTGTTGAATACATGTTTTTCCACTT 57.558 25.926 2.30 0.00 36.44 3.16
4838 5770 9.743057 TTGTTGAATACATGTTTTTCCACTTAG 57.257 29.630 2.30 0.00 36.44 2.18
4839 5771 8.908903 TGTTGAATACATGTTTTTCCACTTAGT 58.091 29.630 2.30 0.00 0.00 2.24
4840 5772 9.744468 GTTGAATACATGTTTTTCCACTTAGTT 57.256 29.630 2.30 0.00 0.00 2.24
4842 5774 9.743057 TGAATACATGTTTTTCCACTTAGTTTG 57.257 29.630 2.30 0.00 0.00 2.93
4843 5775 9.959749 GAATACATGTTTTTCCACTTAGTTTGA 57.040 29.630 2.30 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.427809 CTCCATGCCTCCCTGTATGA 58.572 55.000 0.00 0.00 0.00 2.15
1 2 0.399454 CCTCCATGCCTCCCTGTATG 59.601 60.000 0.00 0.00 0.00 2.39
2 3 1.422161 GCCTCCATGCCTCCCTGTAT 61.422 60.000 0.00 0.00 0.00 2.29
11 12 2.832201 GCCTTGAGCCTCCATGCC 60.832 66.667 0.00 0.00 34.35 4.40
29 30 2.725008 CGAGAGTCGATGGCCTCC 59.275 66.667 3.32 0.00 43.74 4.30
30 31 2.065906 GACCGAGAGTCGATGGCCTC 62.066 65.000 3.32 0.00 43.74 4.70
51 52 2.529005 TTCGCTTGCGACTCTCCTCG 62.529 60.000 17.53 0.00 36.70 4.63
95 96 1.090625 AGATCTCTCGGTGTCGACGG 61.091 60.000 11.62 2.80 40.88 4.79
106 107 1.314730 GTCCCCGAGTCAGATCTCTC 58.685 60.000 0.00 0.00 32.83 3.20
110 111 2.491022 CCCGTCCCCGAGTCAGATC 61.491 68.421 0.00 0.00 35.63 2.75
151 152 2.721167 CGTTGGATGCGAGGGGAGA 61.721 63.158 0.00 0.00 0.00 3.71
165 166 2.107950 TAGACAGGCCCATTTCGTTG 57.892 50.000 0.00 0.00 0.00 4.10
167 168 3.279434 GAAATAGACAGGCCCATTTCGT 58.721 45.455 0.00 0.00 30.31 3.85
169 170 2.959030 GGGAAATAGACAGGCCCATTTC 59.041 50.000 0.00 7.40 38.68 2.17
170 171 2.587307 AGGGAAATAGACAGGCCCATTT 59.413 45.455 0.00 0.00 41.34 2.32
177 178 0.183731 GGCCCAGGGAAATAGACAGG 59.816 60.000 10.89 0.00 0.00 4.00
185 186 0.407918 CTAAGTTGGGCCCAGGGAAA 59.592 55.000 26.87 6.83 0.00 3.13
192 193 1.745489 CACGAGCTAAGTTGGGCCC 60.745 63.158 17.59 17.59 0.00 5.80
245 246 3.118038 TCATTTGGTTCTAAGGGATCCCG 60.118 47.826 25.48 11.55 41.95 5.14
274 275 2.241176 TGAGGTCTTTCCCCGCAATAAT 59.759 45.455 0.00 0.00 36.75 1.28
277 278 0.404040 TTGAGGTCTTTCCCCGCAAT 59.596 50.000 0.00 0.00 36.94 3.56
293 294 6.037610 GGTTTTGCAATTTGTATGGTTGTTGA 59.962 34.615 0.00 0.00 0.00 3.18
338 339 3.000819 TCCGTGGCCGTTGGATCT 61.001 61.111 6.33 0.00 0.00 2.75
385 387 5.937492 ATGGGAAATGATTAGGATCACCT 57.063 39.130 0.00 0.00 44.64 4.00
432 437 2.513753 AGAAAAATGATGCACCCGTCA 58.486 42.857 0.00 0.00 41.00 4.35
435 440 4.305769 TCAAAAGAAAAATGATGCACCCG 58.694 39.130 0.00 0.00 0.00 5.28
451 456 4.997395 TCGAGGGATTCTTTGTCTCAAAAG 59.003 41.667 0.00 0.00 38.31 2.27
460 468 2.279741 TGCGATTCGAGGGATTCTTTG 58.720 47.619 10.88 0.00 0.00 2.77
467 475 2.786495 GCCTCTGCGATTCGAGGGA 61.786 63.158 10.88 3.35 45.52 4.20
468 476 2.279784 GCCTCTGCGATTCGAGGG 60.280 66.667 10.88 4.48 45.52 4.30
470 478 2.413437 ATCGGCCTCTGCGATTCGAG 62.413 60.000 10.88 4.84 38.85 4.04
471 479 2.407846 GATCGGCCTCTGCGATTCGA 62.408 60.000 10.88 0.00 38.85 3.71
472 480 2.018866 GATCGGCCTCTGCGATTCG 61.019 63.158 0.00 0.62 38.85 3.34
473 481 1.666234 GGATCGGCCTCTGCGATTC 60.666 63.158 0.00 0.00 38.85 2.52
474 482 1.971505 TTGGATCGGCCTCTGCGATT 61.972 55.000 0.00 0.00 38.85 3.34
475 483 2.374830 CTTGGATCGGCCTCTGCGAT 62.375 60.000 0.00 0.00 38.85 4.58
476 484 3.074369 TTGGATCGGCCTCTGCGA 61.074 61.111 0.00 0.00 38.85 5.10
477 485 2.587194 CTTGGATCGGCCTCTGCG 60.587 66.667 0.00 0.00 38.85 5.18
478 486 1.817099 CACTTGGATCGGCCTCTGC 60.817 63.158 0.00 0.00 37.63 4.26
479 487 0.460987 GACACTTGGATCGGCCTCTG 60.461 60.000 0.00 0.00 37.63 3.35
480 488 1.617947 GGACACTTGGATCGGCCTCT 61.618 60.000 0.00 0.00 37.63 3.69
481 489 1.153349 GGACACTTGGATCGGCCTC 60.153 63.158 0.00 0.00 37.63 4.70
482 490 2.670148 GGGACACTTGGATCGGCCT 61.670 63.158 0.00 0.00 37.63 5.19
483 491 2.124695 GGGACACTTGGATCGGCC 60.125 66.667 0.00 0.00 37.10 6.13
484 492 2.668632 TGGGACACTTGGATCGGC 59.331 61.111 0.00 0.00 0.00 5.54
631 639 4.385405 AGACGCTGAGCTGTGGGC 62.385 66.667 1.78 0.00 42.19 5.36
637 645 1.366111 GAGACGAGAGACGCTGAGCT 61.366 60.000 1.78 0.00 46.94 4.09
971 1335 3.649502 AGGACCCGAGAAGGTTAGAAAAA 59.350 43.478 0.00 0.00 41.42 1.94
995 1359 1.399440 CCTCGTCGGACGACATCTAAA 59.601 52.381 27.66 6.63 46.73 1.85
1103 1468 0.747852 GAGAGAGTTTAGGGAGGCGG 59.252 60.000 0.00 0.00 0.00 6.13
1114 1479 2.748605 CAGACAGCAAACGAGAGAGTT 58.251 47.619 0.00 0.00 35.59 3.01
1215 1581 3.559238 ACCAAACAGCTAAATTCAGCG 57.441 42.857 0.00 0.00 46.52 5.18
1236 1602 6.014499 AGTCCTTAAAACTTGCAGAGCTACTA 60.014 38.462 0.00 0.00 0.00 1.82
1260 1626 1.973515 TGCAGGGAGCTGTATGGATAG 59.026 52.381 0.00 0.00 45.94 2.08
1262 1628 0.763652 CTGCAGGGAGCTGTATGGAT 59.236 55.000 5.57 0.00 45.94 3.41
1318 1685 6.147821 CCAGTGTCATAAAACTACAACCAGAG 59.852 42.308 0.00 0.00 0.00 3.35
1404 1773 6.589523 TGAATTTTCAAATTACATGAAGGCGG 59.410 34.615 0.00 0.00 38.64 6.13
1421 1790 3.609103 AGACGTGCACACTGAATTTTC 57.391 42.857 18.64 0.00 0.00 2.29
1570 1940 5.515626 GGTGAACATAGCAAAGTAGACTACG 59.484 44.000 6.98 0.00 0.00 3.51
1574 1944 5.725362 AGAGGTGAACATAGCAAAGTAGAC 58.275 41.667 0.00 0.00 0.00 2.59
1596 1966 7.511965 CGTGCGCTGAATTTTGAAATTACATAG 60.512 37.037 9.73 1.54 38.64 2.23
1695 2067 7.647907 AAGAATGAATTGCACACTGAATTTC 57.352 32.000 0.00 0.00 0.00 2.17
1781 2155 1.068748 CAGCACAAGCACACTGGATTC 60.069 52.381 0.00 0.00 45.49 2.52
1785 2159 0.533531 TCTCAGCACAAGCACACTGG 60.534 55.000 0.00 0.00 45.49 4.00
1794 2168 2.928801 TACAGCCTTTCTCAGCACAA 57.071 45.000 0.00 0.00 0.00 3.33
1939 2313 3.173151 TCAGAGCCTCTGTTCCACAATA 58.827 45.455 20.67 0.00 44.58 1.90
2270 2655 5.312443 ACATGGTAGAAAGGTTAAAGGGAGT 59.688 40.000 0.00 0.00 0.00 3.85
2296 2681 9.071276 AGGCATGTGGTGAAATAATAAGATAAG 57.929 33.333 0.00 0.00 0.00 1.73
2410 2795 1.376812 CTTCCAGTAACCGGCCCAC 60.377 63.158 0.00 0.00 0.00 4.61
2541 2926 8.345565 TGCAGTGAAAGAAAAAGAAGATAACTC 58.654 33.333 0.00 0.00 0.00 3.01
2805 3190 3.998913 TCATCCACCTTTGTATCAGCA 57.001 42.857 0.00 0.00 0.00 4.41
2898 3283 9.699703 CAAAATATCATCATGCCAATAACATCA 57.300 29.630 0.00 0.00 0.00 3.07
3166 3565 2.879907 CGCCCTGCCACAATTCAG 59.120 61.111 0.00 0.00 0.00 3.02
3310 3709 4.511826 GTGACTTTGACAGAAGTTACAGGG 59.488 45.833 14.64 0.00 42.44 4.45
3321 3896 2.348411 ACCCCAAGTGACTTTGACAG 57.652 50.000 0.00 0.00 0.00 3.51
3345 3922 9.734620 CAAACAATTCAGACACTTCAAAAGATA 57.265 29.630 0.00 0.00 0.00 1.98
3356 3933 7.063308 ACAAATGAACACAAACAATTCAGACAC 59.937 33.333 0.00 0.00 35.89 3.67
3435 4013 4.749245 AAACACCAGCAATTAAGAGACG 57.251 40.909 0.00 0.00 0.00 4.18
3546 4124 2.738743 GATGGATTTTGAGGGCTCCAA 58.261 47.619 0.00 0.00 40.94 3.53
3662 4240 2.545526 CCAAACAGAGCGGCATGTATAG 59.454 50.000 10.67 5.00 0.00 1.31
3667 4245 0.387622 CAACCAAACAGAGCGGCATG 60.388 55.000 1.45 2.94 0.00 4.06
3672 4250 0.877071 ATCAGCAACCAAACAGAGCG 59.123 50.000 0.00 0.00 0.00 5.03
3737 4318 2.630580 ACTCTGTGAGTTCAAGGGACTC 59.369 50.000 0.00 0.00 40.28 3.36
3912 4494 6.905736 TCCCCACAGCTGAATGTAATATAAA 58.094 36.000 23.35 0.00 0.00 1.40
4030 4612 6.237901 AGCATTACTGACAGGTAAACATTCA 58.762 36.000 7.51 0.00 35.66 2.57
4108 4690 2.102925 ACCAATCAGCCACACCAAAAAG 59.897 45.455 0.00 0.00 0.00 2.27
4113 4695 0.106268 AACACCAATCAGCCACACCA 60.106 50.000 0.00 0.00 0.00 4.17
4150 4732 0.324285 GTTCATGCCCAATTGCCCAA 59.676 50.000 0.00 0.00 0.00 4.12
4161 4743 3.626028 AGAAGACAAAACGTTCATGCC 57.374 42.857 0.00 0.00 0.00 4.40
4162 4744 5.689819 ACATAGAAGACAAAACGTTCATGC 58.310 37.500 0.00 1.34 0.00 4.06
4165 4747 6.046593 ACAGACATAGAAGACAAAACGTTCA 58.953 36.000 0.00 0.00 0.00 3.18
4176 4758 6.611613 ACATCCTCAAACAGACATAGAAGA 57.388 37.500 0.00 0.00 0.00 2.87
4180 4762 6.534436 CAGAGAACATCCTCAAACAGACATAG 59.466 42.308 0.00 0.00 35.68 2.23
4191 4773 3.648067 AGAAACACCAGAGAACATCCTCA 59.352 43.478 0.00 0.00 35.68 3.86
4198 4780 8.254508 AGATTGTATAGAGAAACACCAGAGAAC 58.745 37.037 0.00 0.00 0.00 3.01
4199 4781 8.367660 AGATTGTATAGAGAAACACCAGAGAA 57.632 34.615 0.00 0.00 0.00 2.87
4200 4782 7.962995 AGATTGTATAGAGAAACACCAGAGA 57.037 36.000 0.00 0.00 0.00 3.10
4201 4783 7.010923 GCAAGATTGTATAGAGAAACACCAGAG 59.989 40.741 0.00 0.00 0.00 3.35
4228 4810 4.763793 CCTAATCCCATCAAGCCAAGTATG 59.236 45.833 0.00 0.00 0.00 2.39
4231 4813 2.687914 GCCTAATCCCATCAAGCCAAGT 60.688 50.000 0.00 0.00 0.00 3.16
4304 4889 0.955428 GTGCAGAGCCAATCGAACCA 60.955 55.000 0.00 0.00 0.00 3.67
4343 4928 3.519913 GGAAGTCCAGAAGTTATCCACCT 59.480 47.826 0.00 0.00 35.64 4.00
4344 4929 3.519913 AGGAAGTCCAGAAGTTATCCACC 59.480 47.826 0.00 0.00 38.89 4.61
4345 4930 4.828072 AGGAAGTCCAGAAGTTATCCAC 57.172 45.455 0.00 0.00 38.89 4.02
4346 4931 4.962995 CCTAGGAAGTCCAGAAGTTATCCA 59.037 45.833 1.05 0.00 38.89 3.41
4347 4932 4.963628 ACCTAGGAAGTCCAGAAGTTATCC 59.036 45.833 17.98 0.00 38.89 2.59
4348 4933 5.163395 CCACCTAGGAAGTCCAGAAGTTATC 60.163 48.000 17.98 0.00 41.22 1.75
4349 4934 4.717280 CCACCTAGGAAGTCCAGAAGTTAT 59.283 45.833 17.98 0.00 41.22 1.89
4350 4935 4.094476 CCACCTAGGAAGTCCAGAAGTTA 58.906 47.826 17.98 0.00 41.22 2.24
4351 4936 2.907042 CCACCTAGGAAGTCCAGAAGTT 59.093 50.000 17.98 0.00 41.22 2.66
4352 4937 2.111972 TCCACCTAGGAAGTCCAGAAGT 59.888 50.000 17.98 0.00 45.65 3.01
4353 4938 2.821437 TCCACCTAGGAAGTCCAGAAG 58.179 52.381 17.98 0.00 45.65 2.85
4363 4948 3.107601 CCTGAAGAATGTCCACCTAGGA 58.892 50.000 17.98 0.00 46.75 2.94
4364 4949 2.171448 CCCTGAAGAATGTCCACCTAGG 59.829 54.545 7.41 7.41 39.47 3.02
4365 4950 2.420687 GCCCTGAAGAATGTCCACCTAG 60.421 54.545 0.00 0.00 0.00 3.02
4366 4951 1.559682 GCCCTGAAGAATGTCCACCTA 59.440 52.381 0.00 0.00 0.00 3.08
4455 5387 4.693532 GTGGCGTCACTCCAATCA 57.306 55.556 14.12 0.00 40.58 2.57
4627 5559 3.890147 GAGGTCGCCTCTTTAATCCTAGA 59.110 47.826 15.90 0.00 46.41 2.43
4643 5575 1.466167 CAATGCTCCAAAGTGAGGTCG 59.534 52.381 0.00 0.00 32.81 4.79
4696 5628 4.391830 GCCGAATTACAACAATCACTCTCA 59.608 41.667 0.00 0.00 0.00 3.27
4797 5729 9.521503 TGTATTCAACAAAATGACGAAATTTCA 57.478 25.926 17.99 0.00 34.29 2.69
4800 5732 9.474920 ACATGTATTCAACAAAATGACGAAATT 57.525 25.926 0.00 0.00 42.70 1.82
4801 5733 9.474920 AACATGTATTCAACAAAATGACGAAAT 57.525 25.926 0.00 0.00 42.70 2.17
4802 5734 8.864069 AACATGTATTCAACAAAATGACGAAA 57.136 26.923 0.00 0.00 42.70 3.46
4803 5735 8.864069 AAACATGTATTCAACAAAATGACGAA 57.136 26.923 0.00 0.00 42.70 3.85
4804 5736 8.864069 AAAACATGTATTCAACAAAATGACGA 57.136 26.923 0.00 0.00 42.70 4.20
4805 5737 9.566624 GAAAAACATGTATTCAACAAAATGACG 57.433 29.630 15.71 0.00 42.70 4.35
4806 5738 9.862585 GGAAAAACATGTATTCAACAAAATGAC 57.137 29.630 19.96 2.30 42.70 3.06
4807 5739 9.605275 TGGAAAAACATGTATTCAACAAAATGA 57.395 25.926 19.96 0.00 42.70 2.57
4808 5740 9.649024 GTGGAAAAACATGTATTCAACAAAATG 57.351 29.630 19.60 0.00 42.70 2.32
4809 5741 9.612066 AGTGGAAAAACATGTATTCAACAAAAT 57.388 25.926 23.56 8.86 42.70 1.82
4810 5742 9.442047 AAGTGGAAAAACATGTATTCAACAAAA 57.558 25.926 23.56 5.44 42.70 2.44
4812 5744 9.743057 CTAAGTGGAAAAACATGTATTCAACAA 57.257 29.630 23.56 14.94 42.70 2.83
4813 5745 8.908903 ACTAAGTGGAAAAACATGTATTCAACA 58.091 29.630 23.56 13.14 43.86 3.33
4814 5746 9.744468 AACTAAGTGGAAAAACATGTATTCAAC 57.256 29.630 17.93 17.93 0.00 3.18
4816 5748 9.743057 CAAACTAAGTGGAAAAACATGTATTCA 57.257 29.630 19.96 5.21 0.00 2.57
4817 5749 9.959749 TCAAACTAAGTGGAAAAACATGTATTC 57.040 29.630 13.33 13.33 0.00 1.75


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

AutoCloner maintained by Alex Coulton.