Multiple sequence alignment - TraesCS5D01G531300

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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 TraesCS5D01G531300 chr5D 100.000 4799 0 0 1 4799 546917580 546922378 0.000000e+00 8863.0
1 TraesCS5D01G531300 chr5D 89.172 471 37 7 1954 2424 388394945 388394489 4.170000e-160 575.0
2 TraesCS5D01G531300 chr5D 88.747 471 39 7 1954 2424 462802523 462802979 9.020000e-157 564.0
3 TraesCS5D01G531300 chr5B 93.498 4737 190 68 122 4798 690089749 690094427 0.000000e+00 6933.0
4 TraesCS5D01G531300 chr5B 83.108 444 67 6 4361 4798 576252523 576252082 9.680000e-107 398.0
5 TraesCS5D01G531300 chr4A 91.747 2690 133 45 117 2781 621820139 621817514 0.000000e+00 3655.0
6 TraesCS5D01G531300 chr4A 93.859 1954 97 14 2862 4798 621817512 621815565 0.000000e+00 2922.0
7 TraesCS5D01G531300 chr1B 88.723 470 39 6 1955 2424 629472376 629471921 3.240000e-156 562.0
8 TraesCS5D01G531300 chr3D 85.987 471 39 12 1954 2424 22231091 22231534 3.360000e-131 479.0
9 TraesCS5D01G531300 chr5A 83.269 520 63 17 4293 4798 589384137 589383628 1.570000e-124 457.0
10 TraesCS5D01G531300 chr4B 89.262 298 18 6 2127 2424 626627889 626627606 1.270000e-95 361.0
11 TraesCS5D01G531300 chr7D 76.961 204 45 2 3339 3542 393578449 393578650 1.090000e-21 115.0
12 TraesCS5D01G531300 chr7D 93.750 64 4 0 2781 2844 611816959 611816896 3.950000e-16 97.1
13 TraesCS5D01G531300 chr7D 90.411 73 6 1 2777 2849 87769815 87769886 1.420000e-15 95.3
14 TraesCS5D01G531300 chr7D 87.838 74 9 0 2777 2850 165657857 165657930 2.380000e-13 87.9
15 TraesCS5D01G531300 chr7B 77.184 206 41 5 3339 3542 393317404 393317605 1.090000e-21 115.0
16 TraesCS5D01G531300 chrUn 88.462 78 9 0 2778 2855 35292109 35292032 1.420000e-15 95.3
17 TraesCS5D01G531300 chrUn 88.462 78 9 0 2778 2855 319858024 319858101 1.420000e-15 95.3
18 TraesCS5D01G531300 chrUn 88.462 78 9 0 2778 2855 331092118 331092041 1.420000e-15 95.3
19 TraesCS5D01G531300 chr3A 87.179 78 10 0 2778 2855 10690880 10690957 6.620000e-14 89.8
20 TraesCS5D01G531300 chr2D 83.529 85 14 0 2771 2855 125724864 125724948 3.980000e-11 80.5


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 TraesCS5D01G531300 chr5D 546917580 546922378 4798 False 8863.0 8863 100.000 1 4799 1 chr5D.!!$F2 4798
1 TraesCS5D01G531300 chr5B 690089749 690094427 4678 False 6933.0 6933 93.498 122 4798 1 chr5B.!!$F1 4676
2 TraesCS5D01G531300 chr4A 621815565 621820139 4574 True 3288.5 3655 92.803 117 4798 2 chr4A.!!$R1 4681
3 TraesCS5D01G531300 chr5A 589383628 589384137 509 True 457.0 457 83.269 4293 4798 1 chr5A.!!$R1 505

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
80 81 0.176680 CCTGGGAGAGAACATGACGG 59.823 60.0 0.00 0.0 0.00 4.79 F
145 146 0.250234 AGCCTAGCATCGCACAAGAA 59.750 50.0 0.00 0.0 0.00 2.52 F
678 710 0.385098 CCTTTTTCGTTTCGGTCGCC 60.385 55.0 0.00 0.0 0.00 5.54 F
1882 1923 0.107703 TCATGGTTCATCGGCCAGTC 60.108 55.0 2.24 0.0 38.27 3.51 F
2743 2787 0.671472 TGCACGCAATCTCTGACTGG 60.671 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1695 0.249784 CAGGATCCATCACAGGCTCG 60.250 60.0 15.82 0.0 0.00 5.03 R
1675 1716 0.806868 CAATCTGCAAGTGCGACCAT 59.193 50.0 0.00 0.0 45.83 3.55 R
2529 2572 0.114364 TCTAGACAGACCAGCCACCA 59.886 55.0 0.00 0.0 0.00 4.17 R
3034 3094 0.599558 CTTGTCAGGTGCCCATTGTG 59.400 55.0 0.00 0.0 0.00 3.33 R
3954 4015 0.608640 GAGGCTCAGGACCGAGAAAA 59.391 55.0 10.25 0.0 34.79 2.29 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
22 23 5.590530 TGATTCACTTCTTCTCTCTAGCC 57.409 43.478 0.00 0.00 0.00 3.93
23 24 4.404073 TGATTCACTTCTTCTCTCTAGCCC 59.596 45.833 0.00 0.00 0.00 5.19
24 25 3.458044 TCACTTCTTCTCTCTAGCCCA 57.542 47.619 0.00 0.00 0.00 5.36
25 26 3.093057 TCACTTCTTCTCTCTAGCCCAC 58.907 50.000 0.00 0.00 0.00 4.61
26 27 2.828520 CACTTCTTCTCTCTAGCCCACA 59.171 50.000 0.00 0.00 0.00 4.17
27 28 3.096092 ACTTCTTCTCTCTAGCCCACAG 58.904 50.000 0.00 0.00 0.00 3.66
28 29 1.479709 TCTTCTCTCTAGCCCACAGC 58.520 55.000 0.00 0.00 44.25 4.40
29 30 0.463620 CTTCTCTCTAGCCCACAGCC 59.536 60.000 0.00 0.00 45.47 4.85
30 31 0.252239 TTCTCTCTAGCCCACAGCCA 60.252 55.000 0.00 0.00 45.47 4.75
31 32 0.252239 TCTCTCTAGCCCACAGCCAA 60.252 55.000 0.00 0.00 45.47 4.52
32 33 0.835941 CTCTCTAGCCCACAGCCAAT 59.164 55.000 0.00 0.00 45.47 3.16
33 34 0.833287 TCTCTAGCCCACAGCCAATC 59.167 55.000 0.00 0.00 45.47 2.67
34 35 0.835941 CTCTAGCCCACAGCCAATCT 59.164 55.000 0.00 0.00 45.47 2.40
35 36 0.833287 TCTAGCCCACAGCCAATCTC 59.167 55.000 0.00 0.00 45.47 2.75
36 37 0.543277 CTAGCCCACAGCCAATCTCA 59.457 55.000 0.00 0.00 45.47 3.27
37 38 1.142465 CTAGCCCACAGCCAATCTCAT 59.858 52.381 0.00 0.00 45.47 2.90
38 39 0.395311 AGCCCACAGCCAATCTCATG 60.395 55.000 0.00 0.00 45.47 3.07
39 40 0.394762 GCCCACAGCCAATCTCATGA 60.395 55.000 0.00 0.00 34.35 3.07
40 41 1.386533 CCCACAGCCAATCTCATGAC 58.613 55.000 0.00 0.00 0.00 3.06
41 42 1.012086 CCACAGCCAATCTCATGACG 58.988 55.000 0.00 0.00 0.00 4.35
42 43 1.012086 CACAGCCAATCTCATGACGG 58.988 55.000 0.00 0.00 0.00 4.79
43 44 0.745845 ACAGCCAATCTCATGACGGC 60.746 55.000 11.13 11.13 41.76 5.68
44 45 1.910722 AGCCAATCTCATGACGGCT 59.089 52.632 14.52 14.52 44.78 5.52
45 46 0.254178 AGCCAATCTCATGACGGCTT 59.746 50.000 14.52 3.44 46.37 4.35
46 47 1.486310 AGCCAATCTCATGACGGCTTA 59.514 47.619 14.52 0.00 46.37 3.09
47 48 2.092968 AGCCAATCTCATGACGGCTTAA 60.093 45.455 14.52 0.00 46.37 1.85
48 49 2.682856 GCCAATCTCATGACGGCTTAAA 59.317 45.455 11.62 0.00 39.63 1.52
49 50 3.487544 GCCAATCTCATGACGGCTTAAAC 60.488 47.826 11.62 0.00 39.63 2.01
50 51 3.065371 CCAATCTCATGACGGCTTAAACC 59.935 47.826 0.00 0.00 0.00 3.27
51 52 3.914426 ATCTCATGACGGCTTAAACCT 57.086 42.857 0.00 0.00 0.00 3.50
52 53 3.695830 TCTCATGACGGCTTAAACCTT 57.304 42.857 0.00 0.00 0.00 3.50
53 54 4.015872 TCTCATGACGGCTTAAACCTTT 57.984 40.909 0.00 0.00 0.00 3.11
54 55 4.394729 TCTCATGACGGCTTAAACCTTTT 58.605 39.130 0.00 0.00 0.00 2.27
55 56 4.825085 TCTCATGACGGCTTAAACCTTTTT 59.175 37.500 0.00 0.00 0.00 1.94
77 78 4.722526 TTTTTCCTGGGAGAGAACATGA 57.277 40.909 0.00 0.00 0.00 3.07
78 79 3.703001 TTTCCTGGGAGAGAACATGAC 57.297 47.619 0.00 0.00 0.00 3.06
79 80 1.186200 TCCTGGGAGAGAACATGACG 58.814 55.000 0.00 0.00 0.00 4.35
80 81 0.176680 CCTGGGAGAGAACATGACGG 59.823 60.000 0.00 0.00 0.00 4.79
81 82 0.460987 CTGGGAGAGAACATGACGGC 60.461 60.000 0.00 0.00 0.00 5.68
82 83 0.904865 TGGGAGAGAACATGACGGCT 60.905 55.000 0.00 0.00 0.00 5.52
83 84 0.250513 GGGAGAGAACATGACGGCTT 59.749 55.000 0.00 0.00 0.00 4.35
84 85 1.480954 GGGAGAGAACATGACGGCTTA 59.519 52.381 0.00 0.00 0.00 3.09
85 86 2.093658 GGGAGAGAACATGACGGCTTAA 60.094 50.000 0.00 0.00 0.00 1.85
86 87 2.930682 GGAGAGAACATGACGGCTTAAC 59.069 50.000 0.00 0.00 0.00 2.01
87 88 2.599082 GAGAGAACATGACGGCTTAACG 59.401 50.000 0.00 0.00 40.31 3.18
88 89 1.659098 GAGAACATGACGGCTTAACGG 59.341 52.381 0.00 0.00 38.39 4.44
89 90 1.274167 AGAACATGACGGCTTAACGGA 59.726 47.619 0.00 0.00 38.39 4.69
90 91 2.070783 GAACATGACGGCTTAACGGAA 58.929 47.619 0.00 0.00 38.39 4.30
91 92 1.722011 ACATGACGGCTTAACGGAAG 58.278 50.000 0.00 0.00 38.39 3.46
92 93 1.006832 CATGACGGCTTAACGGAAGG 58.993 55.000 0.00 0.00 38.39 3.46
93 94 0.899720 ATGACGGCTTAACGGAAGGA 59.100 50.000 0.00 0.00 38.39 3.36
94 95 0.680618 TGACGGCTTAACGGAAGGAA 59.319 50.000 0.00 0.00 38.39 3.36
95 96 1.337447 TGACGGCTTAACGGAAGGAAG 60.337 52.381 0.00 0.00 38.39 3.46
96 97 0.971386 ACGGCTTAACGGAAGGAAGA 59.029 50.000 2.03 0.00 38.39 2.87
97 98 1.067071 ACGGCTTAACGGAAGGAAGAG 60.067 52.381 2.03 0.00 38.39 2.85
98 99 1.203994 CGGCTTAACGGAAGGAAGAGA 59.796 52.381 2.03 0.00 35.49 3.10
99 100 2.735762 CGGCTTAACGGAAGGAAGAGAG 60.736 54.545 2.03 0.00 35.49 3.20
100 101 2.496470 GGCTTAACGGAAGGAAGAGAGA 59.504 50.000 2.03 0.00 35.49 3.10
101 102 3.429684 GGCTTAACGGAAGGAAGAGAGAG 60.430 52.174 2.03 0.00 35.49 3.20
102 103 3.444388 GCTTAACGGAAGGAAGAGAGAGA 59.556 47.826 2.03 0.00 35.49 3.10
103 104 4.439563 GCTTAACGGAAGGAAGAGAGAGAG 60.440 50.000 2.03 0.00 35.49 3.20
104 105 2.137810 ACGGAAGGAAGAGAGAGAGG 57.862 55.000 0.00 0.00 0.00 3.69
105 106 1.341581 ACGGAAGGAAGAGAGAGAGGG 60.342 57.143 0.00 0.00 0.00 4.30
106 107 1.788229 GGAAGGAAGAGAGAGAGGGG 58.212 60.000 0.00 0.00 0.00 4.79
107 108 1.691163 GGAAGGAAGAGAGAGAGGGGG 60.691 61.905 0.00 0.00 0.00 5.40
145 146 0.250234 AGCCTAGCATCGCACAAGAA 59.750 50.000 0.00 0.00 0.00 2.52
195 196 3.451894 CCCTGCCCACGGATTTGC 61.452 66.667 0.00 0.00 0.00 3.68
200 201 0.755686 TGCCCACGGATTTGCTTTTT 59.244 45.000 0.00 0.00 0.00 1.94
207 208 6.598525 CCCACGGATTTGCTTTTTATTTTTC 58.401 36.000 0.00 0.00 0.00 2.29
211 212 9.715123 CACGGATTTGCTTTTTATTTTTCTTTT 57.285 25.926 0.00 0.00 0.00 2.27
212 213 9.929722 ACGGATTTGCTTTTTATTTTTCTTTTC 57.070 25.926 0.00 0.00 0.00 2.29
214 215 9.929722 GGATTTGCTTTTTATTTTTCTTTTCGT 57.070 25.926 0.00 0.00 0.00 3.85
216 217 9.631639 ATTTGCTTTTTATTTTTCTTTTCGTCG 57.368 25.926 0.00 0.00 0.00 5.12
338 358 2.695970 CCGAGTCCTCCCTCCCTCT 61.696 68.421 0.00 0.00 0.00 3.69
362 382 2.764547 CCCCGTCTTCCTCCTCCC 60.765 72.222 0.00 0.00 0.00 4.30
363 383 2.364961 CCCGTCTTCCTCCTCCCT 59.635 66.667 0.00 0.00 0.00 4.20
364 384 1.758906 CCCGTCTTCCTCCTCCCTC 60.759 68.421 0.00 0.00 0.00 4.30
365 385 1.000486 CCGTCTTCCTCCTCCCTCA 60.000 63.158 0.00 0.00 0.00 3.86
506 528 4.865761 TCAGCGCCGTCGTATGCC 62.866 66.667 2.29 0.00 38.14 4.40
510 532 4.547905 CGCCGTCGTATGCCGTCT 62.548 66.667 0.00 0.00 37.94 4.18
511 533 2.654404 GCCGTCGTATGCCGTCTC 60.654 66.667 0.00 0.00 37.94 3.36
512 534 3.108343 CCGTCGTATGCCGTCTCT 58.892 61.111 0.00 0.00 37.94 3.10
513 535 1.009900 CCGTCGTATGCCGTCTCTC 60.010 63.158 0.00 0.00 37.94 3.20
514 536 1.367782 CGTCGTATGCCGTCTCTCG 60.368 63.158 0.00 0.00 37.94 4.04
515 537 1.654743 GTCGTATGCCGTCTCTCGC 60.655 63.158 0.00 0.00 38.35 5.03
516 538 2.722548 CGTATGCCGTCTCTCGCG 60.723 66.667 0.00 0.00 38.35 5.87
517 539 3.025176 GTATGCCGTCTCTCGCGC 61.025 66.667 0.00 0.00 38.35 6.86
518 540 4.607606 TATGCCGTCTCTCGCGCG 62.608 66.667 26.76 26.76 38.10 6.86
610 642 2.051345 CGGTGGTTTGTTGCGCTC 60.051 61.111 9.73 2.14 0.00 5.03
613 645 1.654137 GTGGTTTGTTGCGCTCGTG 60.654 57.895 9.73 0.00 0.00 4.35
669 701 3.666253 CCCGCCGCCTTTTTCGTT 61.666 61.111 0.00 0.00 0.00 3.85
678 710 0.385098 CCTTTTTCGTTTCGGTCGCC 60.385 55.000 0.00 0.00 0.00 5.54
750 782 2.037251 TGGGATTTACTCTAGATGCCGC 59.963 50.000 0.00 0.00 34.38 6.53
768 800 0.744771 GCCGGGACTGTTCTCCATTC 60.745 60.000 2.18 0.00 30.97 2.67
799 831 0.526524 CTACTTCGCTTCAGCCCTCG 60.527 60.000 0.00 0.00 37.91 4.63
959 992 3.633094 CTGCGTGGGTCTCGGTGAG 62.633 68.421 0.00 0.00 0.00 3.51
1027 1065 8.163111 ACCTAGGGTTTACTGTTCATCAGCAA 62.163 42.308 14.81 0.00 39.33 3.91
1241 1279 3.522731 CGAGAGGCGTGGAGAGGG 61.523 72.222 0.00 0.00 34.64 4.30
1242 1280 3.844090 GAGAGGCGTGGAGAGGGC 61.844 72.222 0.00 0.00 0.00 5.19
1291 1332 1.754621 CTCTGGGCTCAGCTACGGA 60.755 63.158 9.36 0.00 40.69 4.69
1348 1389 3.303990 CGAGGGTCAATAATGGCAATTCG 60.304 47.826 0.00 0.00 30.82 3.34
1351 1392 3.380004 GGGTCAATAATGGCAATTCGTCA 59.620 43.478 0.00 0.00 30.82 4.35
1411 1452 3.056035 ACGCCGAGAAGAATAACCTCTTT 60.056 43.478 0.00 0.00 35.76 2.52
1471 1512 1.696832 GCGACCCGACAAAGAGCATC 61.697 60.000 0.00 0.00 0.00 3.91
1606 1647 1.115930 ACCTGTTCAGGACGCTGACT 61.116 55.000 23.45 0.00 32.47 3.41
1654 1695 4.070716 CAGCCTATGATTTGGATGAGGAC 58.929 47.826 0.00 0.00 41.78 3.85
1675 1716 1.225426 GCCTGTGATGGATCCTGCA 59.775 57.895 14.23 8.17 0.00 4.41
1777 1818 5.175859 AGGTACATCGATCATTCGTTTGTT 58.824 37.500 0.00 0.00 45.65 2.83
1882 1923 0.107703 TCATGGTTCATCGGCCAGTC 60.108 55.000 2.24 0.00 38.27 3.51
2206 2247 3.140144 AGGAGGTGATGTTTTTGGGAGAA 59.860 43.478 0.00 0.00 0.00 2.87
2392 2434 5.519206 GCTTGATGCTTCATTTCCATTTCTC 59.481 40.000 2.75 0.00 38.95 2.87
2448 2490 6.942576 CCCTGGATAGGTAACAAATGAATAGG 59.057 42.308 0.00 0.00 42.96 2.57
2502 2544 1.089920 CAAGGCATGGTAGTGCAGAC 58.910 55.000 0.00 0.00 46.81 3.51
2504 2546 1.866015 AGGCATGGTAGTGCAGACTA 58.134 50.000 0.00 0.00 46.81 2.59
2558 2601 5.724328 CTGGTCTGTCTAGAATTAGTGCAA 58.276 41.667 0.00 0.00 34.01 4.08
2560 2603 6.530120 TGGTCTGTCTAGAATTAGTGCAAAA 58.470 36.000 0.00 0.00 34.01 2.44
2619 2662 3.185594 TCACTGCTTTGTATTCGAAACGG 59.814 43.478 0.00 0.00 0.00 4.44
2679 2723 4.152580 CGTTTACTCTCAGGCTTCCTTTTC 59.847 45.833 0.00 0.00 0.00 2.29
2712 2756 5.277586 CCTGTTATTTTGTGCTAACGACACA 60.278 40.000 0.00 0.00 45.90 3.72
2741 2785 1.018226 GCTGCACGCAATCTCTGACT 61.018 55.000 0.00 0.00 38.92 3.41
2742 2786 0.720027 CTGCACGCAATCTCTGACTG 59.280 55.000 0.00 0.00 0.00 3.51
2743 2787 0.671472 TGCACGCAATCTCTGACTGG 60.671 55.000 0.00 0.00 0.00 4.00
2744 2788 1.975363 GCACGCAATCTCTGACTGGC 61.975 60.000 0.00 0.00 0.00 4.85
2888 2944 3.923017 AAGTTGTTATGAAGCACTGCC 57.077 42.857 0.00 0.00 0.00 4.85
2919 2976 2.411547 GCACTGCGACTGACAACATTAC 60.412 50.000 0.00 0.00 0.00 1.89
3034 3094 3.942130 AGCTGTTTATGGCTTTTGTCC 57.058 42.857 0.00 0.00 34.96 4.02
3090 3150 1.732259 GTCTGTTTCGTGTGGGCTATG 59.268 52.381 0.00 0.00 0.00 2.23
3350 3410 4.818546 AGCTAATGGTGCTTATGCTACTTG 59.181 41.667 1.96 0.00 37.52 3.16
3351 3411 4.576463 GCTAATGGTGCTTATGCTACTTGT 59.424 41.667 1.96 0.00 40.48 3.16
3399 3459 3.809832 GTGGAACAATGACCATATCGAGG 59.190 47.826 7.09 0.00 44.16 4.63
3536 3596 3.599730 TTGTTCTCTGATCATGACGCT 57.400 42.857 0.00 0.00 0.00 5.07
3638 3698 1.683917 TGGAAGCGCCTAGAAGAGATC 59.316 52.381 2.29 0.00 37.63 2.75
3783 3843 1.278127 TCTGCTGGGTAGTTTGTAGCC 59.722 52.381 0.00 0.00 33.60 3.93
3784 3844 1.279271 CTGCTGGGTAGTTTGTAGCCT 59.721 52.381 2.22 0.00 36.16 4.58
3791 3851 2.225727 GGTAGTTTGTAGCCTGTGCAAC 59.774 50.000 0.00 0.00 41.13 4.17
3807 3867 4.213270 TGTGCAACTGTGTCTAATGTAAGC 59.787 41.667 0.00 0.00 38.04 3.09
3960 4021 3.861569 CGGGAGCGTCATAATTTTCTC 57.138 47.619 0.00 0.00 0.00 2.87
4033 4094 8.884323 TCATTGCTATATCCTTTATCCTTGTCT 58.116 33.333 0.00 0.00 0.00 3.41
4099 4163 1.209127 GCAAATGGTCGGTCGTTGG 59.791 57.895 0.00 0.00 0.00 3.77
4111 4178 1.005867 TCGTTGGCGGTGGTTAGAC 60.006 57.895 0.00 0.00 38.89 2.59
4216 4283 4.552166 TGGAAGCAGAGTTTTCTTTTCG 57.448 40.909 0.00 0.00 30.55 3.46
4269 4337 3.542712 ACGTGTGAGTTGCATTCATTC 57.457 42.857 4.91 1.98 0.00 2.67
4270 4338 2.226437 ACGTGTGAGTTGCATTCATTCC 59.774 45.455 4.91 0.00 0.00 3.01
4299 4369 1.076332 ATTACGGCGTTCTGTCTTGC 58.924 50.000 21.24 0.00 33.08 4.01
4310 4380 4.690748 CGTTCTGTCTTGCTGGAAGAAATA 59.309 41.667 13.37 0.00 42.56 1.40
4314 4384 6.111382 TCTGTCTTGCTGGAAGAAATATGAG 58.889 40.000 13.37 3.76 42.56 2.90
4381 4454 1.695893 CTGTTCGTGGCCATAGCGTG 61.696 60.000 9.72 0.00 41.24 5.34
4457 4540 4.024048 AGTTCAACTGAATTACAACAGCCG 60.024 41.667 0.00 0.00 37.61 5.52
4495 4584 5.182190 GCTGAATGCTGAAGATGATGATGAT 59.818 40.000 0.00 0.00 38.95 2.45
4618 4707 0.249120 CGACCTTGTACATGGCCTCA 59.751 55.000 23.97 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.404073 GGGCTAGAGAGAAGAAGTGAATCA 59.596 45.833 0.00 0.00 0.00 2.57
1 2 4.404073 TGGGCTAGAGAGAAGAAGTGAATC 59.596 45.833 0.00 0.00 0.00 2.52
2 3 4.161377 GTGGGCTAGAGAGAAGAAGTGAAT 59.839 45.833 0.00 0.00 0.00 2.57
3 4 3.511934 GTGGGCTAGAGAGAAGAAGTGAA 59.488 47.826 0.00 0.00 0.00 3.18
4 5 3.093057 GTGGGCTAGAGAGAAGAAGTGA 58.907 50.000 0.00 0.00 0.00 3.41
7 8 2.159114 GCTGTGGGCTAGAGAGAAGAAG 60.159 54.545 0.00 0.00 38.06 2.85
8 9 1.827969 GCTGTGGGCTAGAGAGAAGAA 59.172 52.381 0.00 0.00 38.06 2.52
9 10 1.479709 GCTGTGGGCTAGAGAGAAGA 58.520 55.000 0.00 0.00 38.06 2.87
10 11 0.463620 GGCTGTGGGCTAGAGAGAAG 59.536 60.000 0.00 0.00 41.46 2.85
11 12 0.252239 TGGCTGTGGGCTAGAGAGAA 60.252 55.000 0.00 0.00 41.46 2.87
12 13 0.252239 TTGGCTGTGGGCTAGAGAGA 60.252 55.000 0.00 0.00 41.46 3.10
13 14 0.835941 ATTGGCTGTGGGCTAGAGAG 59.164 55.000 0.00 0.00 41.46 3.20
14 15 0.833287 GATTGGCTGTGGGCTAGAGA 59.167 55.000 0.00 0.00 41.46 3.10
15 16 0.835941 AGATTGGCTGTGGGCTAGAG 59.164 55.000 0.00 0.00 41.46 2.43
16 17 0.833287 GAGATTGGCTGTGGGCTAGA 59.167 55.000 0.00 0.00 41.46 2.43
17 18 0.543277 TGAGATTGGCTGTGGGCTAG 59.457 55.000 0.00 0.00 41.46 3.42
18 19 1.134007 CATGAGATTGGCTGTGGGCTA 60.134 52.381 0.00 0.00 41.46 3.93
19 20 0.395311 CATGAGATTGGCTGTGGGCT 60.395 55.000 0.00 0.00 41.46 5.19
20 21 0.394762 TCATGAGATTGGCTGTGGGC 60.395 55.000 0.00 0.00 40.90 5.36
21 22 1.386533 GTCATGAGATTGGCTGTGGG 58.613 55.000 0.00 0.00 0.00 4.61
22 23 1.012086 CGTCATGAGATTGGCTGTGG 58.988 55.000 0.00 0.00 0.00 4.17
23 24 1.012086 CCGTCATGAGATTGGCTGTG 58.988 55.000 0.00 0.00 0.00 3.66
24 25 0.745845 GCCGTCATGAGATTGGCTGT 60.746 55.000 16.81 0.00 41.97 4.40
25 26 2.020131 GCCGTCATGAGATTGGCTG 58.980 57.895 16.81 0.00 41.97 4.85
26 27 4.547859 GCCGTCATGAGATTGGCT 57.452 55.556 16.81 0.00 41.97 4.75
27 28 1.953559 TAAGCCGTCATGAGATTGGC 58.046 50.000 16.50 16.50 44.17 4.52
28 29 3.065371 GGTTTAAGCCGTCATGAGATTGG 59.935 47.826 0.00 0.00 0.00 3.16
29 30 3.941483 AGGTTTAAGCCGTCATGAGATTG 59.059 43.478 0.00 0.00 0.00 2.67
30 31 4.222124 AGGTTTAAGCCGTCATGAGATT 57.778 40.909 0.00 0.00 0.00 2.40
31 32 3.914426 AGGTTTAAGCCGTCATGAGAT 57.086 42.857 0.00 0.00 0.00 2.75
32 33 3.695830 AAGGTTTAAGCCGTCATGAGA 57.304 42.857 0.00 0.00 0.00 3.27
33 34 4.766404 AAAAGGTTTAAGCCGTCATGAG 57.234 40.909 0.00 0.00 0.00 2.90
56 57 4.398319 GTCATGTTCTCTCCCAGGAAAAA 58.602 43.478 0.00 0.00 0.00 1.94
57 58 3.557054 CGTCATGTTCTCTCCCAGGAAAA 60.557 47.826 0.00 0.00 0.00 2.29
58 59 2.028112 CGTCATGTTCTCTCCCAGGAAA 60.028 50.000 0.00 0.00 0.00 3.13
59 60 1.550524 CGTCATGTTCTCTCCCAGGAA 59.449 52.381 0.00 0.00 0.00 3.36
60 61 1.186200 CGTCATGTTCTCTCCCAGGA 58.814 55.000 0.00 0.00 0.00 3.86
61 62 0.176680 CCGTCATGTTCTCTCCCAGG 59.823 60.000 0.00 0.00 0.00 4.45
62 63 0.460987 GCCGTCATGTTCTCTCCCAG 60.461 60.000 0.00 0.00 0.00 4.45
63 64 0.904865 AGCCGTCATGTTCTCTCCCA 60.905 55.000 0.00 0.00 0.00 4.37
64 65 0.250513 AAGCCGTCATGTTCTCTCCC 59.749 55.000 0.00 0.00 0.00 4.30
65 66 2.930682 GTTAAGCCGTCATGTTCTCTCC 59.069 50.000 0.00 0.00 0.00 3.71
66 67 2.599082 CGTTAAGCCGTCATGTTCTCTC 59.401 50.000 0.00 0.00 0.00 3.20
67 68 2.607187 CGTTAAGCCGTCATGTTCTCT 58.393 47.619 0.00 0.00 0.00 3.10
68 69 1.659098 CCGTTAAGCCGTCATGTTCTC 59.341 52.381 0.00 0.00 0.00 2.87
69 70 1.274167 TCCGTTAAGCCGTCATGTTCT 59.726 47.619 0.00 0.00 0.00 3.01
70 71 1.717194 TCCGTTAAGCCGTCATGTTC 58.283 50.000 0.00 0.00 0.00 3.18
71 72 2.073816 CTTCCGTTAAGCCGTCATGTT 58.926 47.619 0.00 0.00 0.00 2.71
72 73 1.674817 CCTTCCGTTAAGCCGTCATGT 60.675 52.381 0.00 0.00 33.49 3.21
73 74 1.006832 CCTTCCGTTAAGCCGTCATG 58.993 55.000 0.00 0.00 33.49 3.07
74 75 0.899720 TCCTTCCGTTAAGCCGTCAT 59.100 50.000 0.00 0.00 33.49 3.06
75 76 0.680618 TTCCTTCCGTTAAGCCGTCA 59.319 50.000 0.00 0.00 33.49 4.35
76 77 1.067354 TCTTCCTTCCGTTAAGCCGTC 60.067 52.381 0.00 0.00 33.49 4.79
77 78 0.971386 TCTTCCTTCCGTTAAGCCGT 59.029 50.000 0.00 0.00 33.49 5.68
78 79 1.203994 TCTCTTCCTTCCGTTAAGCCG 59.796 52.381 0.00 0.00 33.49 5.52
79 80 2.496470 TCTCTCTTCCTTCCGTTAAGCC 59.504 50.000 0.00 0.00 33.49 4.35
80 81 3.444388 TCTCTCTCTTCCTTCCGTTAAGC 59.556 47.826 0.00 0.00 33.49 3.09
81 82 4.097286 CCTCTCTCTCTTCCTTCCGTTAAG 59.903 50.000 0.00 0.00 34.73 1.85
82 83 4.017808 CCTCTCTCTCTTCCTTCCGTTAA 58.982 47.826 0.00 0.00 0.00 2.01
83 84 3.622630 CCTCTCTCTCTTCCTTCCGTTA 58.377 50.000 0.00 0.00 0.00 3.18
84 85 2.452505 CCTCTCTCTCTTCCTTCCGTT 58.547 52.381 0.00 0.00 0.00 4.44
85 86 1.341581 CCCTCTCTCTCTTCCTTCCGT 60.342 57.143 0.00 0.00 0.00 4.69
86 87 1.398692 CCCTCTCTCTCTTCCTTCCG 58.601 60.000 0.00 0.00 0.00 4.30
87 88 1.691163 CCCCCTCTCTCTCTTCCTTCC 60.691 61.905 0.00 0.00 0.00 3.46
88 89 1.788229 CCCCCTCTCTCTCTTCCTTC 58.212 60.000 0.00 0.00 0.00 3.46
120 121 1.593750 GCGATGCTAGGCTGTCTGG 60.594 63.158 0.00 0.00 0.00 3.86
145 146 1.235724 CCGGGTCGCTTTTCTTTCTT 58.764 50.000 0.00 0.00 0.00 2.52
195 196 8.776680 TCTCCGACGAAAAGAAAAATAAAAAG 57.223 30.769 0.00 0.00 0.00 2.27
200 201 5.867716 CCTCTCTCCGACGAAAAGAAAAATA 59.132 40.000 0.00 0.00 0.00 1.40
207 208 0.173708 CCCCTCTCTCCGACGAAAAG 59.826 60.000 0.00 0.00 0.00 2.27
211 212 2.146146 TTTCCCCCTCTCTCCGACGA 62.146 60.000 0.00 0.00 0.00 4.20
212 213 1.255667 TTTTCCCCCTCTCTCCGACG 61.256 60.000 0.00 0.00 0.00 5.12
214 215 1.276622 CTTTTTCCCCCTCTCTCCGA 58.723 55.000 0.00 0.00 0.00 4.55
215 216 0.393132 GCTTTTTCCCCCTCTCTCCG 60.393 60.000 0.00 0.00 0.00 4.63
216 217 0.393132 CGCTTTTTCCCCCTCTCTCC 60.393 60.000 0.00 0.00 0.00 3.71
456 478 2.125912 CTGTGGTTCCGAGGAGCG 60.126 66.667 0.00 0.00 40.47 5.03
457 479 1.255667 TACCTGTGGTTCCGAGGAGC 61.256 60.000 12.01 0.00 37.09 4.70
458 480 0.531200 GTACCTGTGGTTCCGAGGAG 59.469 60.000 12.01 0.00 37.09 3.69
546 568 4.845580 ATGCTTCCGAGGCCGCAG 62.846 66.667 7.44 0.00 35.66 5.18
547 569 4.838152 GATGCTTCCGAGGCCGCA 62.838 66.667 7.44 5.10 36.75 5.69
678 710 1.553248 TCTGACAAATCCCCCACTACG 59.447 52.381 0.00 0.00 0.00 3.51
722 754 6.069963 GCATCTAGAGTAAATCCCACCCATAT 60.070 42.308 0.00 0.00 0.00 1.78
750 782 3.460648 GAATGGAGAACAGTCCCGG 57.539 57.895 0.00 0.00 38.20 5.73
788 820 0.103208 AATCTACGCGAGGGCTGAAG 59.897 55.000 15.93 0.00 36.88 3.02
790 822 1.035385 TCAATCTACGCGAGGGCTGA 61.035 55.000 15.93 7.01 36.88 4.26
792 824 0.753262 AATCAATCTACGCGAGGGCT 59.247 50.000 15.93 0.00 36.88 5.19
799 831 0.435008 CGCGGCTAATCAATCTACGC 59.565 55.000 0.00 0.00 41.84 4.42
839 871 1.876714 GTAAGATCGCGCGAGGCAA 60.877 57.895 36.99 19.96 43.84 4.52
945 977 1.939769 GAGCTCTCACCGAGACCCAC 61.940 65.000 6.43 0.00 42.62 4.61
1027 1065 3.958860 GCTGCCACCTCACCCTGT 61.959 66.667 0.00 0.00 0.00 4.00
1351 1392 4.774503 GGCAGCAGCTCGAAGGCT 62.775 66.667 0.00 0.00 44.10 4.58
1411 1452 2.682856 GCACAGGTTCAGTTTCTTGACA 59.317 45.455 0.00 0.00 0.00 3.58
1471 1512 5.054477 TGTCGTTTTACTTCCTTCTCCTTG 58.946 41.667 0.00 0.00 0.00 3.61
1606 1647 1.089978 TGTTCTCTCTGGGAGGGGTA 58.910 55.000 4.41 0.00 42.10 3.69
1654 1695 0.249784 CAGGATCCATCACAGGCTCG 60.250 60.000 15.82 0.00 0.00 5.03
1675 1716 0.806868 CAATCTGCAAGTGCGACCAT 59.193 50.000 0.00 0.00 45.83 3.55
1777 1818 5.019470 TCAAAGAGATCAAGTAGCCTGAGA 58.981 41.667 0.00 0.00 0.00 3.27
1882 1923 5.163513 GTGTTGTTGATGGCTTTCCTAATG 58.836 41.667 0.00 0.00 0.00 1.90
2029 2070 2.026262 GTGAAGTGGAATCAAGGCCCTA 60.026 50.000 0.00 0.00 0.00 3.53
2206 2247 9.854668 TGTGTAGCTTCTAGTATCTCTTCTAAT 57.145 33.333 0.00 0.00 0.00 1.73
2392 2434 6.207417 AGGACAGATGAAAATTACACAACAGG 59.793 38.462 0.00 0.00 0.00 4.00
2529 2572 0.114364 TCTAGACAGACCAGCCACCA 59.886 55.000 0.00 0.00 0.00 4.17
2619 2662 9.548208 GAATAGAGAAAACTATCACAAAAGTGC 57.452 33.333 0.00 0.00 32.72 4.40
2679 2723 3.063997 CACAAAATAACAGGGCGCTCTAG 59.936 47.826 10.89 7.41 0.00 2.43
2888 2944 4.514577 CGCAGTGCTAGGACCCCG 62.515 72.222 14.33 10.08 0.00 5.73
2919 2976 5.499139 TTGACTTTAGCACTTTGTTCTGG 57.501 39.130 0.00 0.00 0.00 3.86
3034 3094 0.599558 CTTGTCAGGTGCCCATTGTG 59.400 55.000 0.00 0.00 0.00 3.33
3090 3150 3.904339 TCCCTGAATTAGGTCATAGGCTC 59.096 47.826 0.00 0.00 45.80 4.70
3117 3177 6.158598 GCTTTTGATGGAATAAAGTGCAAGA 58.841 36.000 0.00 0.00 32.75 3.02
3326 3386 5.808366 AGTAGCATAAGCACCATTAGCTA 57.192 39.130 0.00 0.00 42.53 3.32
3327 3387 4.696479 AGTAGCATAAGCACCATTAGCT 57.304 40.909 0.00 0.00 45.97 3.32
3350 3410 4.764172 ACAATGATCTCTCAGCAACCTAC 58.236 43.478 0.00 0.00 34.12 3.18
3351 3411 5.426689 AACAATGATCTCTCAGCAACCTA 57.573 39.130 0.00 0.00 34.12 3.08
3536 3596 3.120796 ACACTCGGTGTACAGTCCA 57.879 52.632 7.76 0.00 45.56 4.02
3623 3683 1.727723 CGCGATCTCTTCTAGGCGC 60.728 63.158 0.00 0.00 42.27 6.53
3638 3698 1.291184 TGGTTGCTCTTGATGACGCG 61.291 55.000 3.53 3.53 0.00 6.01
3727 3787 5.959618 AGAAAAGGGAAACATCTTTACCG 57.040 39.130 0.00 0.00 44.53 4.02
3740 3800 9.435688 CAGAAAAAGAAAAGAAAAGAAAAGGGA 57.564 29.630 0.00 0.00 0.00 4.20
3783 3843 5.615544 GCTTACATTAGACACAGTTGCACAG 60.616 44.000 0.00 0.00 0.00 3.66
3784 3844 4.213270 GCTTACATTAGACACAGTTGCACA 59.787 41.667 0.00 0.00 0.00 4.57
3791 3851 8.032952 TCAAGAAATGCTTACATTAGACACAG 57.967 34.615 0.00 0.00 45.90 3.66
3807 3867 4.884164 GGACCCCTACTGATTCAAGAAATG 59.116 45.833 0.00 0.00 0.00 2.32
3888 3949 1.622607 ATCTCCCGTCGATTTGCCCA 61.623 55.000 0.00 0.00 0.00 5.36
3947 4008 4.271291 GCTCAGGACCGAGAAAATTATGAC 59.729 45.833 14.93 0.00 34.79 3.06
3952 4013 1.630878 AGGCTCAGGACCGAGAAAATT 59.369 47.619 14.93 0.00 34.79 1.82
3954 4015 0.608640 GAGGCTCAGGACCGAGAAAA 59.391 55.000 10.25 0.00 34.79 2.29
4033 4094 4.039973 AGGAACAGACTGTAACCGAATTCA 59.960 41.667 8.91 0.00 34.01 2.57
4099 4163 1.472188 ACTAGAGGTCTAACCACCGC 58.528 55.000 0.00 0.00 41.95 5.68
4135 4202 3.249080 TCGTTTTGAAATGAAGACCGACC 59.751 43.478 0.00 0.00 31.38 4.79
4269 4337 8.025243 ACAGAACGCCGTAATAATAATAATGG 57.975 34.615 0.00 0.00 0.00 3.16
4270 4338 8.922676 AGACAGAACGCCGTAATAATAATAATG 58.077 33.333 0.00 0.00 0.00 1.90
4282 4352 0.666274 CAGCAAGACAGAACGCCGTA 60.666 55.000 0.00 0.00 0.00 4.02
4284 4354 2.671177 CCAGCAAGACAGAACGCCG 61.671 63.158 0.00 0.00 0.00 6.46
4299 4369 4.272489 TGGCCAACTCATATTTCTTCCAG 58.728 43.478 0.61 0.00 0.00 3.86
4310 4380 4.415596 TCAGGTTAAAATGGCCAACTCAT 58.584 39.130 10.96 0.00 0.00 2.90
4314 4384 4.956085 AGTTTCAGGTTAAAATGGCCAAC 58.044 39.130 10.96 1.76 0.00 3.77
4381 4454 5.578727 GTGATTTGTGAGACAGATGTAGTCC 59.421 44.000 0.00 0.00 36.68 3.85
4382 4455 6.090088 GTGTGATTTGTGAGACAGATGTAGTC 59.910 42.308 0.00 0.00 36.26 2.59
4457 4540 1.168407 TTCAGCAGCAGTCTTGTGGC 61.168 55.000 0.00 0.00 0.00 5.01
4618 4707 2.261671 GACGGCGTCCACATGACT 59.738 61.111 28.72 0.00 42.13 3.41


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

AutoCloner maintained by Alex Coulton.