Multiple sequence alignment - TraesCS3B01G075100

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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 TraesCS3B01G075100 chr3B 100.000 3631 0 0 1 3631 46059044 46062674 0.000000e+00 6706.0
1 TraesCS3B01G075100 chr3B 82.618 2934 379 84 342 3228 46593036 46590187 0.000000e+00 2471.0
2 TraesCS3B01G075100 chr3B 84.029 2204 277 38 279 2437 46788833 46786660 0.000000e+00 2050.0
3 TraesCS3B01G075100 chr3B 84.076 628 67 22 2566 3166 46786611 46785990 3.140000e-160 575.0
4 TraesCS3B01G075100 chr3B 77.877 669 137 11 1163 1825 47257008 47257671 4.370000e-109 405.0
5 TraesCS3B01G075100 chr3B 84.412 340 46 5 3295 3631 46785743 46785408 9.720000e-86 327.0
6 TraesCS3B01G075100 chr3B 76.220 635 123 18 1166 1792 46586175 46586789 9.790000e-81 311.0
7 TraesCS3B01G075100 chr3B 84.191 272 31 6 3295 3554 46590165 46589894 1.670000e-63 254.0
8 TraesCS3B01G075100 chr3B 73.358 822 121 63 1903 2706 46041252 46041993 7.900000e-52 215.0
9 TraesCS3B01G075100 chr3B 82.160 213 32 6 279 487 46593035 46592825 1.040000e-40 178.0
10 TraesCS3B01G075100 chr3D 92.914 2272 121 12 99 2346 27559492 27561747 0.000000e+00 3267.0
11 TraesCS3B01G075100 chr3D 83.911 2250 286 43 279 2472 27940979 27938750 0.000000e+00 2080.0
12 TraesCS3B01G075100 chr3D 98.179 659 11 1 2582 3239 27561754 27562412 0.000000e+00 1149.0
13 TraesCS3B01G075100 chr3D 97.802 364 8 0 3268 3631 27562412 27562775 2.380000e-176 628.0
14 TraesCS3B01G075100 chr3D 86.774 499 47 11 2523 3006 27938741 27938247 4.130000e-149 538.0
15 TraesCS3B01G075100 chr3D 88.312 77 9 0 3301 3377 27937624 27937548 3.860000e-15 93.5
16 TraesCS3B01G075100 chr3A 84.282 1686 210 25 322 1956 37831711 37833392 0.000000e+00 1594.0
17 TraesCS3B01G075100 chr3A 83.958 1228 132 41 1973 3168 37817041 37815847 0.000000e+00 1116.0
18 TraesCS3B01G075100 chr3A 81.275 251 43 4 1308 1556 37675097 37675345 2.210000e-47 200.0
19 TraesCS3B01G075100 chr3A 81.720 186 30 4 621 804 10612663 10612846 6.280000e-33 152.0
20 TraesCS3B01G075100 chr3A 76.327 245 52 6 279 519 37831603 37831845 3.810000e-25 126.0
21 TraesCS3B01G075100 chr1D 75.229 436 97 9 1332 1764 444333868 444334295 2.860000e-46 196.0
22 TraesCS3B01G075100 chr1A 75.058 433 103 5 1332 1761 539963128 539963558 2.860000e-46 196.0
23 TraesCS3B01G075100 chrUn 82.178 202 34 2 604 804 35303424 35303224 4.820000e-39 172.0
24 TraesCS3B01G075100 chrUn 82.178 202 34 2 604 804 229353264 229353064 4.820000e-39 172.0
25 TraesCS3B01G075100 chrUn 81.081 185 33 2 621 804 35288806 35288623 2.920000e-31 147.0
26 TraesCS3B01G075100 chrUn 81.081 185 33 2 621 804 197210463 197210280 2.920000e-31 147.0
27 TraesCS3B01G075100 chrUn 79.500 200 39 2 606 804 307248283 307248085 1.360000e-29 141.0
28 TraesCS3B01G075100 chrUn 95.122 41 1 1 222 262 213716437 213716476 3.030000e-06 63.9
29 TraesCS3B01G075100 chrUn 100.000 32 0 0 231 262 265027486 265027455 3.920000e-05 60.2
30 TraesCS3B01G075100 chrUn 100.000 32 0 0 231 262 287937573 287937604 3.920000e-05 60.2
31 TraesCS3B01G075100 chrUn 100.000 29 0 0 1336 1364 95119731 95119759 2.000000e-03 54.7
32 TraesCS3B01G075100 chr5B 92.308 39 3 0 830 868 705535457 705535495 5.060000e-04 56.5
33 TraesCS3B01G075100 chr7B 100.000 29 0 0 1250 1278 745672452 745672424 2.000000e-03 54.7


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 TraesCS3B01G075100 chr3B 46059044 46062674 3630 False 6706.000000 6706 100.000000 1 3631 1 chr3B.!!$F2 3630
1 TraesCS3B01G075100 chr3B 46785408 46788833 3425 True 984.000000 2050 84.172333 279 3631 3 chr3B.!!$R2 3352
2 TraesCS3B01G075100 chr3B 46589894 46593036 3142 True 967.666667 2471 82.989667 279 3554 3 chr3B.!!$R1 3275
3 TraesCS3B01G075100 chr3B 47257008 47257671 663 False 405.000000 405 77.877000 1163 1825 1 chr3B.!!$F4 662
4 TraesCS3B01G075100 chr3B 46586175 46586789 614 False 311.000000 311 76.220000 1166 1792 1 chr3B.!!$F3 626
5 TraesCS3B01G075100 chr3B 46041252 46041993 741 False 215.000000 215 73.358000 1903 2706 1 chr3B.!!$F1 803
6 TraesCS3B01G075100 chr3D 27559492 27562775 3283 False 1681.333333 3267 96.298333 99 3631 3 chr3D.!!$F1 3532
7 TraesCS3B01G075100 chr3D 27937548 27940979 3431 True 903.833333 2080 86.332333 279 3377 3 chr3D.!!$R1 3098
8 TraesCS3B01G075100 chr3A 37815847 37817041 1194 True 1116.000000 1116 83.958000 1973 3168 1 chr3A.!!$R1 1195
9 TraesCS3B01G075100 chr3A 37831603 37833392 1789 False 860.000000 1594 80.304500 279 1956 2 chr3A.!!$F3 1677

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
95 96 0.179012 GGACCGAACCTGGTTTTGGA 60.179 55.0 28.21 0.0 44.01 3.53 F
320 337 0.250901 CTCTCCCAAACCCACACCAG 60.251 60.0 0.00 0.0 0.00 4.00 F
1329 1383 0.811219 TGGATTTGGATGAGCTCGCG 60.811 55.0 9.64 0.0 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1626 0.902516 CCCCTCTCATCGATCCCTCC 60.903 65.000 0.00 0.0 0.0 4.30 R
1958 2066 1.719780 GCTTAGACGACAAAGACACCG 59.280 52.381 0.00 0.0 0.0 4.94 R
3266 3813 0.107654 AGTTTCGATGGGCCAGTAGC 60.108 55.000 13.78 0.0 42.6 3.58 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
25 26 8.782137 ACCCTATAAGGAACATGCAAAATTAT 57.218 30.769 0.00 0.00 37.67 1.28
26 27 8.641541 ACCCTATAAGGAACATGCAAAATTATG 58.358 33.333 0.00 0.00 37.67 1.90
27 28 8.641541 CCCTATAAGGAACATGCAAAATTATGT 58.358 33.333 0.00 0.00 37.67 2.29
31 32 5.883661 AGGAACATGCAAAATTATGTCTCG 58.116 37.500 0.00 0.00 36.56 4.04
34 35 6.403636 GGAACATGCAAAATTATGTCTCGTCT 60.404 38.462 0.00 0.00 36.56 4.18
36 37 7.609760 ACATGCAAAATTATGTCTCGTCTAA 57.390 32.000 0.00 0.00 32.32 2.10
38 39 8.511321 ACATGCAAAATTATGTCTCGTCTAAAA 58.489 29.630 0.00 0.00 32.32 1.52
39 40 9.340695 CATGCAAAATTATGTCTCGTCTAAAAA 57.659 29.630 0.00 0.00 0.00 1.94
40 41 8.722342 TGCAAAATTATGTCTCGTCTAAAAAC 57.278 30.769 0.00 0.00 0.00 2.43
41 42 8.346300 TGCAAAATTATGTCTCGTCTAAAAACA 58.654 29.630 0.00 0.00 0.00 2.83
42 43 9.176181 GCAAAATTATGTCTCGTCTAAAAACAA 57.824 29.630 0.00 0.00 0.00 2.83
47 48 6.937436 ATGTCTCGTCTAAAAACAAAAGGT 57.063 33.333 0.00 0.00 0.00 3.50
48 49 6.746745 TGTCTCGTCTAAAAACAAAAGGTT 57.253 33.333 0.00 0.00 42.98 3.50
50 51 5.454554 GTCTCGTCTAAAAACAAAAGGTTGC 59.545 40.000 0.00 0.00 40.35 4.17
51 52 4.344448 TCGTCTAAAAACAAAAGGTTGCG 58.656 39.130 0.00 0.00 40.35 4.85
52 53 4.094590 TCGTCTAAAAACAAAAGGTTGCGA 59.905 37.500 0.00 0.00 40.35 5.10
53 54 4.794246 CGTCTAAAAACAAAAGGTTGCGAA 59.206 37.500 0.00 0.00 40.35 4.70
54 55 5.286558 CGTCTAAAAACAAAAGGTTGCGAAA 59.713 36.000 0.00 0.00 40.35 3.46
55 56 6.020201 CGTCTAAAAACAAAAGGTTGCGAAAT 60.020 34.615 0.00 0.00 40.35 2.17
56 57 7.463515 CGTCTAAAAACAAAAGGTTGCGAAATT 60.464 33.333 0.00 0.00 40.35 1.82
57 58 8.809478 GTCTAAAAACAAAAGGTTGCGAAATTA 58.191 29.630 0.00 0.00 40.35 1.40
59 60 9.579610 CTAAAAACAAAAGGTTGCGAAATTATG 57.420 29.630 0.00 0.00 40.35 1.90
60 61 5.590104 AACAAAAGGTTGCGAAATTATGC 57.410 34.783 0.00 0.00 38.60 3.14
61 62 3.993736 ACAAAAGGTTGCGAAATTATGCC 59.006 39.130 0.00 0.00 38.39 4.40
62 63 3.951775 AAAGGTTGCGAAATTATGCCA 57.048 38.095 0.00 0.00 0.00 4.92
63 64 3.951775 AAGGTTGCGAAATTATGCCAA 57.048 38.095 0.00 0.00 0.00 4.52
64 65 3.951775 AGGTTGCGAAATTATGCCAAA 57.048 38.095 0.00 0.00 0.00 3.28
65 66 3.584834 AGGTTGCGAAATTATGCCAAAC 58.415 40.909 0.00 0.00 0.00 2.93
67 68 3.584834 GTTGCGAAATTATGCCAAACCT 58.415 40.909 0.00 0.00 0.00 3.50
68 69 3.229276 TGCGAAATTATGCCAAACCTG 57.771 42.857 0.00 0.00 0.00 4.00
69 70 2.094286 TGCGAAATTATGCCAAACCTGG 60.094 45.455 0.00 0.00 46.65 4.45
70 71 2.094234 GCGAAATTATGCCAAACCTGGT 60.094 45.455 0.00 0.00 45.53 4.00
71 72 3.616317 GCGAAATTATGCCAAACCTGGTT 60.616 43.478 6.18 6.18 45.53 3.67
72 73 3.925913 CGAAATTATGCCAAACCTGGTTG 59.074 43.478 13.79 7.38 45.53 3.77
73 74 3.333029 AATTATGCCAAACCTGGTTGC 57.667 42.857 13.79 13.54 45.53 4.17
74 75 2.008242 TTATGCCAAACCTGGTTGCT 57.992 45.000 13.79 6.07 45.53 3.91
75 76 2.008242 TATGCCAAACCTGGTTGCTT 57.992 45.000 13.79 13.12 45.53 3.91
76 77 0.393820 ATGCCAAACCTGGTTGCTTG 59.606 50.000 13.79 7.79 45.53 4.01
77 78 1.069596 GCCAAACCTGGTTGCTTGG 59.930 57.895 19.88 19.88 45.53 3.61
78 79 1.398958 GCCAAACCTGGTTGCTTGGA 61.399 55.000 25.78 0.00 45.53 3.53
79 80 0.389025 CCAAACCTGGTTGCTTGGAC 59.611 55.000 19.60 0.00 40.72 4.02
80 81 0.389025 CAAACCTGGTTGCTTGGACC 59.611 55.000 13.79 0.00 37.69 4.46
81 82 1.106944 AAACCTGGTTGCTTGGACCG 61.107 55.000 13.79 0.00 40.13 4.79
82 83 1.990160 AACCTGGTTGCTTGGACCGA 61.990 55.000 12.11 0.00 40.13 4.69
83 84 1.228124 CCTGGTTGCTTGGACCGAA 60.228 57.895 0.00 0.00 40.13 4.30
84 85 1.515521 CCTGGTTGCTTGGACCGAAC 61.516 60.000 0.00 0.00 40.13 3.95
85 86 1.515521 CTGGTTGCTTGGACCGAACC 61.516 60.000 7.33 7.33 40.13 3.62
86 87 1.228154 GGTTGCTTGGACCGAACCT 60.228 57.895 0.00 0.00 35.86 3.50
87 88 1.515521 GGTTGCTTGGACCGAACCTG 61.516 60.000 0.00 0.00 35.86 4.00
88 89 1.228124 TTGCTTGGACCGAACCTGG 60.228 57.895 0.00 0.00 0.00 4.45
90 91 1.228154 GCTTGGACCGAACCTGGTT 60.228 57.895 12.82 12.82 44.01 3.67
91 92 0.822121 GCTTGGACCGAACCTGGTTT 60.822 55.000 14.28 0.00 44.01 3.27
92 93 1.687563 CTTGGACCGAACCTGGTTTT 58.312 50.000 14.28 1.13 44.01 2.43
93 94 1.336755 CTTGGACCGAACCTGGTTTTG 59.663 52.381 14.28 10.30 44.01 2.44
94 95 0.466555 TGGACCGAACCTGGTTTTGG 60.467 55.000 22.83 22.83 44.01 3.28
95 96 0.179012 GGACCGAACCTGGTTTTGGA 60.179 55.000 28.21 0.00 44.01 3.53
96 97 0.949397 GACCGAACCTGGTTTTGGAC 59.051 55.000 28.21 21.43 44.01 4.02
97 98 0.549469 ACCGAACCTGGTTTTGGACT 59.451 50.000 28.21 11.90 39.99 3.85
119 120 7.283354 GGACTTAGGAATTTTCTTCCCAGTATG 59.717 40.741 0.44 0.00 39.39 2.39
122 123 5.583932 AGGAATTTTCTTCCCAGTATGCTT 58.416 37.500 0.44 0.00 39.39 3.91
128 129 2.906389 TCTTCCCAGTATGCTTGTCAGT 59.094 45.455 0.00 0.00 31.97 3.41
129 130 3.327757 TCTTCCCAGTATGCTTGTCAGTT 59.672 43.478 0.00 0.00 31.97 3.16
130 131 3.057969 TCCCAGTATGCTTGTCAGTTG 57.942 47.619 0.00 0.00 31.97 3.16
136 137 0.478072 ATGCTTGTCAGTTGGGTGGA 59.522 50.000 0.00 0.00 0.00 4.02
163 165 8.321650 AGTACGTTTTATTTTCGGAATTACCA 57.678 30.769 0.00 0.00 38.90 3.25
169 171 7.513371 TTTATTTTCGGAATTACCACTGTGT 57.487 32.000 7.08 0.00 38.90 3.72
173 175 3.135225 TCGGAATTACCACTGTGTTGTG 58.865 45.455 7.08 0.00 38.90 3.33
197 199 2.838225 TAGCTAGGTCCAGGCGGC 60.838 66.667 0.00 0.00 0.00 6.53
211 213 3.508840 CGGCGCCTCCATTCCAAC 61.509 66.667 26.68 0.00 34.01 3.77
216 218 0.745845 CGCCTCCATTCCAACTCCAG 60.746 60.000 0.00 0.00 0.00 3.86
275 277 3.560251 CCAGATCCCGGCCGGAAT 61.560 66.667 45.44 34.54 46.47 3.01
277 279 3.560251 AGATCCCGGCCGGAATGG 61.560 66.667 45.44 28.13 46.47 3.16
311 328 2.436824 GCGGCTCCTCTCCCAAAC 60.437 66.667 0.00 0.00 0.00 2.93
312 329 2.269241 CGGCTCCTCTCCCAAACC 59.731 66.667 0.00 0.00 0.00 3.27
320 337 0.250901 CTCTCCCAAACCCACACCAG 60.251 60.000 0.00 0.00 0.00 4.00
386 403 1.142748 CTCAGATCCCCGTGAGTGC 59.857 63.158 2.31 0.00 36.27 4.40
455 472 3.314331 CTGCGTGGGTGAGGAGGT 61.314 66.667 0.00 0.00 0.00 3.85
459 476 1.304547 CGTGGGTGAGGAGGTCTCT 60.305 63.158 0.00 0.00 42.86 3.10
462 479 1.388531 GGGTGAGGAGGTCTCTGGA 59.611 63.158 0.00 0.00 42.86 3.86
841 885 1.544246 ACATCGTGTTCACCTCGATCA 59.456 47.619 0.00 0.00 41.35 2.92
869 913 4.096003 CAACCGCATCCCTCCCGT 62.096 66.667 0.00 0.00 0.00 5.28
972 1025 3.008923 TGGCAGACTGGTTCATTGTATGA 59.991 43.478 4.26 0.00 37.55 2.15
1030 1083 6.457663 CGTTCCACTAGTGTTTGAAATGTCAA 60.458 38.462 21.18 0.00 42.12 3.18
1055 1108 0.833287 TTCTATGGGGCTGTGCTCTC 59.167 55.000 0.00 0.00 0.00 3.20
1329 1383 0.811219 TGGATTTGGATGAGCTCGCG 60.811 55.000 9.64 0.00 0.00 5.87
1522 1576 1.064003 TGGTGGTGCTACATGGTTCT 58.936 50.000 0.00 0.00 0.00 3.01
1572 1626 3.086600 GGGCTCCCTCCTCAGGTG 61.087 72.222 0.00 0.00 38.30 4.00
1616 1673 4.351111 GGAAATACTGGGGTATGATGAGGT 59.649 45.833 0.00 0.00 38.50 3.85
1764 1845 2.022195 CCAGGTGAATGCTCATCCTTG 58.978 52.381 0.00 0.00 32.55 3.61
1865 1970 4.293415 CAGTGTTCAGCAATTGTTCCTTC 58.707 43.478 7.40 0.00 0.00 3.46
1958 2066 7.648142 TCAAATGTCAAATGAGTAACTCAACC 58.352 34.615 0.00 0.00 44.04 3.77
2039 2155 7.658982 TGATCTTGCTATTGATGTTATCTCCAC 59.341 37.037 0.00 0.00 0.00 4.02
2131 2248 2.364002 TGCAGCAAGTGACTAGTACACA 59.636 45.455 20.38 3.96 40.25 3.72
2139 2256 7.339721 AGCAAGTGACTAGTACACATGTATACT 59.660 37.037 20.02 20.02 38.59 2.12
2145 2262 9.452287 TGACTAGTACACATGTATACTACACAA 57.548 33.333 18.01 2.24 42.23 3.33
2179 2296 4.406003 TGGATTTCTTGTCTCTAGTAGGCC 59.594 45.833 0.00 0.00 0.00 5.19
2360 2483 1.472480 CCGGAATGGTCTCGCATTTTT 59.528 47.619 0.00 0.00 0.00 1.94
2366 2489 6.099341 GGAATGGTCTCGCATTTTTAAACAT 58.901 36.000 0.00 0.00 0.00 2.71
2371 2494 7.598278 TGGTCTCGCATTTTTAAACATATGTT 58.402 30.769 15.47 15.47 40.50 2.71
2440 2564 3.505835 AAAAACAGTGAGGGCCGAA 57.494 47.368 0.00 0.00 0.00 4.30
2441 2565 1.995376 AAAAACAGTGAGGGCCGAAT 58.005 45.000 0.00 0.00 0.00 3.34
2486 2617 9.077885 AGTTATGTTTGTTGGTTCATCTATGTT 57.922 29.630 0.00 0.00 0.00 2.71
2490 2621 8.402798 TGTTTGTTGGTTCATCTATGTTATGT 57.597 30.769 0.00 0.00 0.00 2.29
2491 2622 9.508642 TGTTTGTTGGTTCATCTATGTTATGTA 57.491 29.630 0.00 0.00 0.00 2.29
2497 2628 8.942338 TGGTTCATCTATGTTATGTAACTGAC 57.058 34.615 4.71 0.00 37.12 3.51
2514 2645 8.904834 TGTAACTGACTCACTATTATCTTCTCC 58.095 37.037 0.00 0.00 0.00 3.71
2515 2646 9.127277 GTAACTGACTCACTATTATCTTCTCCT 57.873 37.037 0.00 0.00 0.00 3.69
2518 2649 8.499406 ACTGACTCACTATTATCTTCTCCTACT 58.501 37.037 0.00 0.00 0.00 2.57
2519 2650 8.911918 TGACTCACTATTATCTTCTCCTACTC 57.088 38.462 0.00 0.00 0.00 2.59
2520 2651 8.719596 TGACTCACTATTATCTTCTCCTACTCT 58.280 37.037 0.00 0.00 0.00 3.24
2521 2652 8.918202 ACTCACTATTATCTTCTCCTACTCTG 57.082 38.462 0.00 0.00 0.00 3.35
2539 2670 8.153550 CCTACTCTGCTATCCATATGTCTTTTT 58.846 37.037 1.24 0.00 0.00 1.94
2754 2895 4.858850 TGGAAATATCTGGCTGTCAACAT 58.141 39.130 0.00 0.00 0.00 2.71
2784 2925 4.142491 CGTGCATCCCAAAAACTATTGCTA 60.142 41.667 0.00 0.00 0.00 3.49
2982 3138 4.338118 CCTTGGTTTTGCTGTTTCAGAGTA 59.662 41.667 0.66 0.00 32.44 2.59
3118 3446 5.625150 AGCATAATACAGATTCCCCACTTC 58.375 41.667 0.00 0.00 0.00 3.01
3134 3466 3.426159 CCACTTCGACACCAAATATGTGC 60.426 47.826 0.00 0.00 37.22 4.57
3238 3785 5.391312 ACAAGTGGTTTATTGAAGCCATC 57.609 39.130 0.00 0.00 46.34 3.51
3240 3787 5.481473 ACAAGTGGTTTATTGAAGCCATCAT 59.519 36.000 0.00 0.00 46.34 2.45
3241 3788 5.841957 AGTGGTTTATTGAAGCCATCATC 57.158 39.130 0.00 0.00 46.34 2.92
3245 3792 5.951148 TGGTTTATTGAAGCCATCATCTTCA 59.049 36.000 1.72 1.72 45.62 3.02
3247 3794 7.144000 GGTTTATTGAAGCCATCATCTTCATC 58.856 38.462 6.31 0.00 46.26 2.92
3248 3795 7.014038 GGTTTATTGAAGCCATCATCTTCATCT 59.986 37.037 6.31 1.44 46.26 2.90
3249 3796 7.741027 TTATTGAAGCCATCATCTTCATCTC 57.259 36.000 6.31 0.00 46.26 2.75
3250 3797 4.082665 TGAAGCCATCATCTTCATCTCC 57.917 45.455 1.72 0.00 43.34 3.71
3251 3798 2.835580 AGCCATCATCTTCATCTCCG 57.164 50.000 0.00 0.00 0.00 4.63
3252 3799 2.323599 AGCCATCATCTTCATCTCCGA 58.676 47.619 0.00 0.00 0.00 4.55
3253 3800 2.702478 AGCCATCATCTTCATCTCCGAA 59.298 45.455 0.00 0.00 0.00 4.30
3254 3801 3.065655 GCCATCATCTTCATCTCCGAAG 58.934 50.000 0.00 0.00 43.17 3.79
3255 3802 3.065655 CCATCATCTTCATCTCCGAAGC 58.934 50.000 0.00 0.00 41.84 3.86
3256 3803 2.898729 TCATCTTCATCTCCGAAGCC 57.101 50.000 0.00 0.00 41.84 4.35
3257 3804 2.110578 TCATCTTCATCTCCGAAGCCA 58.889 47.619 0.00 0.00 41.84 4.75
3258 3805 2.702478 TCATCTTCATCTCCGAAGCCAT 59.298 45.455 0.00 0.00 41.84 4.40
3259 3806 2.898729 TCTTCATCTCCGAAGCCATC 57.101 50.000 0.00 0.00 41.84 3.51
3260 3807 2.110578 TCTTCATCTCCGAAGCCATCA 58.889 47.619 0.00 0.00 41.84 3.07
3261 3808 2.702478 TCTTCATCTCCGAAGCCATCAT 59.298 45.455 0.00 0.00 41.84 2.45
3262 3809 2.827800 TCATCTCCGAAGCCATCATC 57.172 50.000 0.00 0.00 0.00 2.92
3263 3810 2.323599 TCATCTCCGAAGCCATCATCT 58.676 47.619 0.00 0.00 0.00 2.90
3264 3811 2.702478 TCATCTCCGAAGCCATCATCTT 59.298 45.455 0.00 0.00 0.00 2.40
3265 3812 2.609427 TCTCCGAAGCCATCATCTTG 57.391 50.000 0.00 0.00 0.00 3.02
3266 3813 1.139654 TCTCCGAAGCCATCATCTTGG 59.860 52.381 0.00 0.00 39.94 3.61
3284 3831 2.394604 GCTACTGGCCCATCGAAAC 58.605 57.895 0.00 0.00 34.27 2.78
3430 3996 7.219726 GGTTAGATTTGTAGTTCGCACTAGTAC 59.780 40.741 0.00 0.00 36.09 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.641541 CATAATTTTGCATGTTCCTTATAGGGT 58.358 33.333 0.11 0.00 35.59 4.34
2 3 9.683069 GACATAATTTTGCATGTTCCTTATAGG 57.317 33.333 0.00 0.00 35.55 2.57
6 7 7.120579 ACGAGACATAATTTTGCATGTTCCTTA 59.879 33.333 0.00 0.00 35.55 2.69
7 8 6.071952 ACGAGACATAATTTTGCATGTTCCTT 60.072 34.615 0.00 0.00 35.55 3.36
8 9 5.415701 ACGAGACATAATTTTGCATGTTCCT 59.584 36.000 0.00 0.00 35.55 3.36
9 10 5.640732 ACGAGACATAATTTTGCATGTTCC 58.359 37.500 0.00 0.00 35.55 3.62
10 11 6.546395 AGACGAGACATAATTTTGCATGTTC 58.454 36.000 0.00 0.00 35.55 3.18
11 12 6.500684 AGACGAGACATAATTTTGCATGTT 57.499 33.333 0.00 0.00 35.55 2.71
12 13 7.609760 TTAGACGAGACATAATTTTGCATGT 57.390 32.000 0.00 0.00 38.08 3.21
13 14 8.894409 TTTTAGACGAGACATAATTTTGCATG 57.106 30.769 0.00 0.00 0.00 4.06
14 15 9.341899 GTTTTTAGACGAGACATAATTTTGCAT 57.658 29.630 0.00 0.00 0.00 3.96
15 16 8.346300 TGTTTTTAGACGAGACATAATTTTGCA 58.654 29.630 0.00 0.00 0.00 4.08
16 17 8.722342 TGTTTTTAGACGAGACATAATTTTGC 57.278 30.769 0.00 0.00 0.00 3.68
20 21 9.893305 CCTTTTGTTTTTAGACGAGACATAATT 57.107 29.630 0.00 0.00 0.00 1.40
21 22 9.063615 ACCTTTTGTTTTTAGACGAGACATAAT 57.936 29.630 0.00 0.00 0.00 1.28
22 23 8.441312 ACCTTTTGTTTTTAGACGAGACATAA 57.559 30.769 0.00 0.00 0.00 1.90
23 24 8.339714 CAACCTTTTGTTTTTAGACGAGACATA 58.660 33.333 0.00 0.00 34.00 2.29
24 25 6.937436 ACCTTTTGTTTTTAGACGAGACAT 57.063 33.333 0.00 0.00 0.00 3.06
25 26 6.548171 CAACCTTTTGTTTTTAGACGAGACA 58.452 36.000 0.00 0.00 34.00 3.41
26 27 5.454554 GCAACCTTTTGTTTTTAGACGAGAC 59.545 40.000 0.00 0.00 34.00 3.36
27 28 5.575019 GCAACCTTTTGTTTTTAGACGAGA 58.425 37.500 0.00 0.00 34.00 4.04
29 30 4.094590 TCGCAACCTTTTGTTTTTAGACGA 59.905 37.500 0.00 0.00 34.00 4.20
30 31 4.344448 TCGCAACCTTTTGTTTTTAGACG 58.656 39.130 0.00 0.00 34.00 4.18
31 32 6.635166 TTTCGCAACCTTTTGTTTTTAGAC 57.365 33.333 0.00 0.00 34.00 2.59
34 35 8.064814 GCATAATTTCGCAACCTTTTGTTTTTA 58.935 29.630 0.00 0.00 34.00 1.52
36 37 6.426327 GCATAATTTCGCAACCTTTTGTTTT 58.574 32.000 0.00 0.00 34.00 2.43
38 39 4.450757 GGCATAATTTCGCAACCTTTTGTT 59.549 37.500 1.76 0.00 37.80 2.83
39 40 3.993736 GGCATAATTTCGCAACCTTTTGT 59.006 39.130 1.76 0.00 34.90 2.83
40 41 3.993081 TGGCATAATTTCGCAACCTTTTG 59.007 39.130 1.76 0.00 35.62 2.44
41 42 4.264460 TGGCATAATTTCGCAACCTTTT 57.736 36.364 1.76 0.00 0.00 2.27
42 43 3.951775 TGGCATAATTTCGCAACCTTT 57.048 38.095 1.76 0.00 0.00 3.11
43 44 3.951775 TTGGCATAATTTCGCAACCTT 57.048 38.095 0.00 0.00 0.00 3.50
47 48 3.583806 CAGGTTTGGCATAATTTCGCAA 58.416 40.909 0.00 0.00 0.00 4.85
48 49 2.094286 CCAGGTTTGGCATAATTTCGCA 60.094 45.455 0.00 0.00 37.73 5.10
61 62 0.389025 GGTCCAAGCAACCAGGTTTG 59.611 55.000 0.44 0.00 35.33 2.93
62 63 1.106944 CGGTCCAAGCAACCAGGTTT 61.107 55.000 0.44 0.00 36.53 3.27
63 64 1.528309 CGGTCCAAGCAACCAGGTT 60.528 57.895 0.00 0.00 36.53 3.50
64 65 1.990160 TTCGGTCCAAGCAACCAGGT 61.990 55.000 0.00 0.00 36.53 4.00
65 66 1.228124 TTCGGTCCAAGCAACCAGG 60.228 57.895 0.00 0.00 36.53 4.45
67 68 1.527380 GGTTCGGTCCAAGCAACCA 60.527 57.895 4.76 0.00 38.57 3.67
68 69 1.228154 AGGTTCGGTCCAAGCAACC 60.228 57.895 0.00 0.00 38.94 3.77
69 70 1.515521 CCAGGTTCGGTCCAAGCAAC 61.516 60.000 6.18 0.00 0.00 4.17
70 71 1.228124 CCAGGTTCGGTCCAAGCAA 60.228 57.895 6.18 0.00 0.00 3.91
71 72 1.990160 AACCAGGTTCGGTCCAAGCA 61.990 55.000 0.00 0.00 38.76 3.91
72 73 0.822121 AAACCAGGTTCGGTCCAAGC 60.822 55.000 4.93 0.00 38.76 4.01
73 74 1.336755 CAAAACCAGGTTCGGTCCAAG 59.663 52.381 4.93 0.00 38.76 3.61
74 75 1.394618 CAAAACCAGGTTCGGTCCAA 58.605 50.000 4.93 0.00 38.76 3.53
75 76 0.466555 CCAAAACCAGGTTCGGTCCA 60.467 55.000 4.93 0.00 38.76 4.02
76 77 0.179012 TCCAAAACCAGGTTCGGTCC 60.179 55.000 16.87 0.00 38.76 4.46
77 78 0.949397 GTCCAAAACCAGGTTCGGTC 59.051 55.000 16.87 10.21 38.76 4.79
78 79 0.549469 AGTCCAAAACCAGGTTCGGT 59.451 50.000 16.87 0.00 42.71 4.69
79 80 1.687563 AAGTCCAAAACCAGGTTCGG 58.312 50.000 4.93 9.79 0.00 4.30
80 81 2.812011 CCTAAGTCCAAAACCAGGTTCG 59.188 50.000 4.93 0.00 0.00 3.95
81 82 4.094830 TCCTAAGTCCAAAACCAGGTTC 57.905 45.455 4.93 0.00 33.93 3.62
82 83 4.529716 TTCCTAAGTCCAAAACCAGGTT 57.470 40.909 0.00 0.00 33.93 3.50
83 84 4.741928 ATTCCTAAGTCCAAAACCAGGT 57.258 40.909 0.00 0.00 33.93 4.00
84 85 6.267699 AGAAAATTCCTAAGTCCAAAACCAGG 59.732 38.462 0.00 0.00 33.65 4.45
85 86 7.290110 AGAAAATTCCTAAGTCCAAAACCAG 57.710 36.000 0.00 0.00 0.00 4.00
86 87 7.201965 GGAAGAAAATTCCTAAGTCCAAAACCA 60.202 37.037 0.00 0.00 35.73 3.67
87 88 7.152645 GGAAGAAAATTCCTAAGTCCAAAACC 58.847 38.462 0.00 0.00 35.73 3.27
88 89 7.152645 GGGAAGAAAATTCCTAAGTCCAAAAC 58.847 38.462 6.60 0.00 38.61 2.43
89 90 6.841755 TGGGAAGAAAATTCCTAAGTCCAAAA 59.158 34.615 6.60 0.00 38.61 2.44
90 91 6.377912 TGGGAAGAAAATTCCTAAGTCCAAA 58.622 36.000 6.60 0.00 38.61 3.28
91 92 5.959512 TGGGAAGAAAATTCCTAAGTCCAA 58.040 37.500 6.60 0.00 38.61 3.53
92 93 5.074515 ACTGGGAAGAAAATTCCTAAGTCCA 59.925 40.000 6.60 0.00 38.61 4.02
93 94 5.571285 ACTGGGAAGAAAATTCCTAAGTCC 58.429 41.667 6.60 0.00 38.61 3.85
94 95 7.201741 GCATACTGGGAAGAAAATTCCTAAGTC 60.202 40.741 14.57 3.40 37.03 3.01
95 96 6.603599 GCATACTGGGAAGAAAATTCCTAAGT 59.396 38.462 15.15 15.15 38.28 2.24
96 97 6.830838 AGCATACTGGGAAGAAAATTCCTAAG 59.169 38.462 6.60 7.28 38.61 2.18
97 98 6.731467 AGCATACTGGGAAGAAAATTCCTAA 58.269 36.000 6.60 0.00 38.61 2.69
119 120 0.108585 TCTCCACCCAACTGACAAGC 59.891 55.000 0.00 0.00 0.00 4.01
122 123 1.968493 GTACTCTCCACCCAACTGACA 59.032 52.381 0.00 0.00 0.00 3.58
128 129 4.895668 ATAAAACGTACTCTCCACCCAA 57.104 40.909 0.00 0.00 0.00 4.12
129 130 4.895668 AATAAAACGTACTCTCCACCCA 57.104 40.909 0.00 0.00 0.00 4.51
130 131 5.163923 CGAAAATAAAACGTACTCTCCACCC 60.164 44.000 0.00 0.00 0.00 4.61
136 137 8.659491 GGTAATTCCGAAAATAAAACGTACTCT 58.341 33.333 0.00 0.00 0.00 3.24
163 165 2.704065 AGCTAGGGTTACACAACACAGT 59.296 45.455 0.00 0.00 40.81 3.55
197 199 0.745845 CTGGAGTTGGAATGGAGGCG 60.746 60.000 0.00 0.00 0.00 5.52
199 201 0.257039 CCCTGGAGTTGGAATGGAGG 59.743 60.000 0.00 0.00 0.00 4.30
249 251 2.219875 CGGGATCTGGGGATGGAGG 61.220 68.421 0.00 0.00 31.46 4.30
311 328 2.124983 CATCCTCGCTGGTGTGGG 60.125 66.667 3.02 0.00 37.07 4.61
312 329 2.124983 CCATCCTCGCTGGTGTGG 60.125 66.667 0.00 0.00 36.75 4.17
433 450 0.036388 TCCTCACCCACGCAGATTTC 60.036 55.000 0.00 0.00 0.00 2.17
439 456 3.311110 GACCTCCTCACCCACGCA 61.311 66.667 0.00 0.00 0.00 5.24
455 472 0.680280 GCGGTAGGTCACTCCAGAGA 60.680 60.000 0.70 0.00 39.02 3.10
459 476 3.066190 CGGCGGTAGGTCACTCCA 61.066 66.667 0.00 0.00 39.02 3.86
462 479 3.760035 CTGCGGCGGTAGGTCACT 61.760 66.667 9.78 0.00 0.00 3.41
492 512 2.879233 GCTCGTGTGGAGTTGGGGA 61.879 63.158 0.00 0.00 45.03 4.81
539 568 3.256960 GGACTTGGGGGTGGAGCA 61.257 66.667 0.00 0.00 0.00 4.26
751 795 3.744941 CAGAGAAGCTGCTGAGGAG 57.255 57.895 0.00 0.00 37.90 3.69
841 885 3.728373 GCGGTTGGGAGGGTCCAT 61.728 66.667 0.00 0.00 38.64 3.41
869 913 2.028484 GCCGTGTGTCGAACCTCA 59.972 61.111 0.00 0.00 42.86 3.86
972 1025 0.326264 GCTCACTGGTGATTGGGTCT 59.674 55.000 3.80 0.00 39.13 3.85
1002 1055 3.102052 TCAAACACTAGTGGAACGTCC 57.898 47.619 26.12 0.00 45.86 4.79
1030 1083 2.092914 GCACAGCCCCATAGAAGTAGTT 60.093 50.000 0.00 0.00 0.00 2.24
1031 1084 1.486726 GCACAGCCCCATAGAAGTAGT 59.513 52.381 0.00 0.00 0.00 2.73
1329 1383 6.747280 CCAAATCAAACTCAATTATGTCGTCC 59.253 38.462 0.00 0.00 0.00 4.79
1522 1576 6.882610 ATGTATTTCAACAGTCTTCTGCAA 57.117 33.333 0.00 0.00 44.77 4.08
1572 1626 0.902516 CCCCTCTCATCGATCCCTCC 60.903 65.000 0.00 0.00 0.00 4.30
1764 1845 4.383444 GGTTACTACCACCATACAAGGACC 60.383 50.000 0.00 0.00 44.36 4.46
1896 2001 9.897744 CTGAAGAGCAAGATATAAAAACACAAA 57.102 29.630 0.00 0.00 0.00 2.83
1909 2014 5.946942 TTGGTATCTCTGAAGAGCAAGAT 57.053 39.130 2.26 0.00 41.80 2.40
1958 2066 1.719780 GCTTAGACGACAAAGACACCG 59.280 52.381 0.00 0.00 0.00 4.94
2080 2197 4.683129 GCCTTCAACAGGTGACCAAAAATT 60.683 41.667 3.63 0.00 46.07 1.82
2081 2198 3.181466 GCCTTCAACAGGTGACCAAAAAT 60.181 43.478 3.63 0.00 46.07 1.82
2383 2506 4.037923 ACCCACTTTTGATGCTAACAACAG 59.962 41.667 0.00 0.00 33.17 3.16
2434 2558 4.918583 TGAAAAACAAATCGTTATTCGGCC 59.081 37.500 0.00 0.00 36.59 6.13
2437 2561 8.488979 ACTTCTGAAAAACAAATCGTTATTCG 57.511 30.769 0.00 0.00 36.59 3.34
2489 2620 9.127277 AGGAGAAGATAATAGTGAGTCAGTTAC 57.873 37.037 5.63 0.00 0.00 2.50
2491 2622 9.127277 GTAGGAGAAGATAATAGTGAGTCAGTT 57.873 37.037 5.63 0.00 0.00 3.16
2492 2623 8.499406 AGTAGGAGAAGATAATAGTGAGTCAGT 58.501 37.037 5.64 5.64 0.00 3.41
2493 2624 8.918202 AGTAGGAGAAGATAATAGTGAGTCAG 57.082 38.462 0.00 0.00 0.00 3.51
2497 2628 7.665559 AGCAGAGTAGGAGAAGATAATAGTGAG 59.334 40.741 0.00 0.00 0.00 3.51
2506 2637 5.332106 TGGATAGCAGAGTAGGAGAAGAT 57.668 43.478 0.00 0.00 0.00 2.40
2507 2638 4.797912 TGGATAGCAGAGTAGGAGAAGA 57.202 45.455 0.00 0.00 0.00 2.87
2514 2645 9.202273 GAAAAAGACATATGGATAGCAGAGTAG 57.798 37.037 7.80 0.00 0.00 2.57
2515 2646 8.928448 AGAAAAAGACATATGGATAGCAGAGTA 58.072 33.333 7.80 0.00 0.00 2.59
2516 2647 7.800092 AGAAAAAGACATATGGATAGCAGAGT 58.200 34.615 7.80 0.00 0.00 3.24
2518 2649 6.925718 CGAGAAAAAGACATATGGATAGCAGA 59.074 38.462 7.80 0.00 0.00 4.26
2519 2650 6.703607 ACGAGAAAAAGACATATGGATAGCAG 59.296 38.462 7.80 0.00 0.00 4.24
2520 2651 6.582636 ACGAGAAAAAGACATATGGATAGCA 58.417 36.000 7.80 0.00 0.00 3.49
2521 2652 7.148722 GCTACGAGAAAAAGACATATGGATAGC 60.149 40.741 7.80 0.00 0.00 2.97
2539 2670 9.525409 GTCAGGTAATAAATAAAAGCTACGAGA 57.475 33.333 0.00 0.00 0.00 4.04
2561 2692 1.293924 CGCCCAGAAGCATAAGTCAG 58.706 55.000 0.00 0.00 0.00 3.51
2564 2695 1.473434 GCTACGCCCAGAAGCATAAGT 60.473 52.381 0.00 0.00 36.26 2.24
2754 2895 2.476852 TTTGGGATGCACGCTGCCTA 62.477 55.000 7.38 0.00 44.23 3.93
2784 2925 6.222038 TGAAACAATCTCTATAGCCGAGTT 57.778 37.500 0.00 0.00 0.00 3.01
2982 3138 3.131709 TGTCTTGCTTTCAGCTAGCTT 57.868 42.857 16.46 0.00 42.46 3.74
3118 3446 2.415357 GGTTGGCACATATTTGGTGTCG 60.415 50.000 0.00 0.00 43.60 4.35
3134 3466 4.852134 TCAAACACATCTGATTGGTTGG 57.148 40.909 20.30 12.04 40.27 3.77
3238 3785 2.609427 TGGCTTCGGAGATGAAGATG 57.391 50.000 7.63 0.00 46.64 2.90
3240 3787 2.110578 TGATGGCTTCGGAGATGAAGA 58.889 47.619 7.63 0.00 46.64 2.87
3241 3788 2.609427 TGATGGCTTCGGAGATGAAG 57.391 50.000 0.00 0.00 46.47 3.02
3245 3792 2.224475 CCAAGATGATGGCTTCGGAGAT 60.224 50.000 0.00 0.00 31.49 2.75
3247 3794 1.590932 CCAAGATGATGGCTTCGGAG 58.409 55.000 0.00 0.00 32.78 4.63
3248 3795 3.786656 CCAAGATGATGGCTTCGGA 57.213 52.632 0.00 0.00 32.78 4.55
3255 3802 1.602311 GCCAGTAGCCAAGATGATGG 58.398 55.000 0.00 0.00 43.70 3.51
3266 3813 0.107654 AGTTTCGATGGGCCAGTAGC 60.108 55.000 13.78 0.00 42.60 3.58
3284 3831 1.760613 TGGGCGGAAGTTATCACCTAG 59.239 52.381 0.00 0.00 0.00 3.02
3398 3964 5.006746 GCGAACTACAAATCTAACCTCCATG 59.993 44.000 0.00 0.00 0.00 3.66
3430 3996 2.162608 TGGACAAAATGGTTATTCGGCG 59.837 45.455 0.00 0.00 0.00 6.46
3549 4117 7.554118 TGTGAAGATTCTCTTTTTCTGTGTTCT 59.446 33.333 0.00 0.00 36.73 3.01


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

AutoCloner maintained by Alex Coulton.