Multiple sequence alignment - TraesCS5A01G340700

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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 TraesCS5A01G340700 chr5A 100.000 3457 0 0 1 3457 547174139 547170683 0.000000e+00 6384
1 TraesCS5A01G340700 chrUn 98.034 3255 61 3 136 3388 290086751 290090004 0.000000e+00 5653
2 TraesCS5A01G340700 chrUn 96.277 188 7 0 134 321 442211637 442211824 3.350000e-80 309
3 TraesCS5A01G340700 chr6A 97.244 3266 88 2 133 3397 563383310 563386574 0.000000e+00 5531
4 TraesCS5A01G340700 chr6A 91.722 2573 201 10 791 3357 61567964 61565398 0.000000e+00 3561
5 TraesCS5A01G340700 chr6A 96.257 187 6 1 134 320 563397242 563397427 4.330000e-79 305
6 TraesCS5A01G340700 chr4B 93.977 2889 157 10 496 3379 74326420 74323544 0.000000e+00 4355
7 TraesCS5A01G340700 chr4B 90.191 367 36 0 136 502 74328291 74327925 2.410000e-131 479
8 TraesCS5A01G340700 chr4B 91.351 185 16 0 136 320 74305041 74304857 1.590000e-63 254
9 TraesCS5A01G340700 chr4A 91.309 2612 204 18 795 3390 58508201 58510805 0.000000e+00 3544
10 TraesCS5A01G340700 chr6B 91.273 2624 192 24 795 3390 712152428 712155042 0.000000e+00 3542
11 TraesCS5A01G340700 chr2D 91.138 2618 201 19 804 3396 46693231 46690620 0.000000e+00 3520
12 TraesCS5A01G340700 chr7D 91.072 2621 200 21 795 3390 615779007 615781618 0.000000e+00 3513
13 TraesCS5A01G340700 chr3B 90.360 2614 215 23 795 3390 465858371 465860965 0.000000e+00 3397


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 TraesCS5A01G340700 chr5A 547170683 547174139 3456 True 6384 6384 100.000 1 3457 1 chr5A.!!$R1 3456
1 TraesCS5A01G340700 chrUn 290086751 290090004 3253 False 5653 5653 98.034 136 3388 1 chrUn.!!$F1 3252
2 TraesCS5A01G340700 chr6A 563383310 563386574 3264 False 5531 5531 97.244 133 3397 1 chr6A.!!$F1 3264
3 TraesCS5A01G340700 chr6A 61565398 61567964 2566 True 3561 3561 91.722 791 3357 1 chr6A.!!$R1 2566
4 TraesCS5A01G340700 chr4B 74323544 74328291 4747 True 2417 4355 92.084 136 3379 2 chr4B.!!$R2 3243
5 TraesCS5A01G340700 chr4A 58508201 58510805 2604 False 3544 3544 91.309 795 3390 1 chr4A.!!$F1 2595
6 TraesCS5A01G340700 chr6B 712152428 712155042 2614 False 3542 3542 91.273 795 3390 1 chr6B.!!$F1 2595
7 TraesCS5A01G340700 chr2D 46690620 46693231 2611 True 3520 3520 91.138 804 3396 1 chr2D.!!$R1 2592
8 TraesCS5A01G340700 chr7D 615779007 615781618 2611 False 3513 3513 91.072 795 3390 1 chr7D.!!$F1 2595
9 TraesCS5A01G340700 chr3B 465858371 465860965 2594 False 3397 3397 90.360 795 3390 1 chr3B.!!$F1 2595

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
105 106 0.036022 GCCTCTCAAGTTGCTCCACT 59.964 55.000 0.00 0.0 0.00 4.00 F
665 2177 0.305922 GCTGATTGATAGTGGTGCGC 59.694 55.000 0.00 0.0 0.00 6.09 F
714 2226 1.403647 CGTGAGATTTGGTCAGGCGTA 60.404 52.381 0.00 0.0 0.00 4.42 F
870 2386 1.763968 ATACTCTGCTCGTGCCTGTA 58.236 50.000 7.05 7.7 38.71 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 3452 3.288381 AGCTCCCTGACCTCCCCT 61.288 66.667 0.0 0.0 0.0 4.79 R
2331 3871 3.067833 GCTAACTGACAAGAGGTTGACC 58.932 50.000 0.0 0.0 37.1 4.02 R
2451 3991 7.727634 TCATCAAGATAGTAGAGTCCATCATGT 59.272 37.037 0.0 0.0 0.0 3.21 R
2761 4306 6.311723 AGCAATCGATAAAAGTTACAAACCG 58.688 36.000 0.0 0.0 0.0 4.44 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
27 28 3.509266 GCGCAACGGCTATTTACAG 57.491 52.632 0.30 0.00 38.10 2.74
28 29 1.003851 GCGCAACGGCTATTTACAGA 58.996 50.000 0.30 0.00 38.10 3.41
29 30 1.267383 GCGCAACGGCTATTTACAGAC 60.267 52.381 0.30 0.00 38.10 3.51
30 31 1.996898 CGCAACGGCTATTTACAGACA 59.003 47.619 0.00 0.00 38.10 3.41
31 32 2.413796 CGCAACGGCTATTTACAGACAA 59.586 45.455 0.00 0.00 38.10 3.18
32 33 3.483574 CGCAACGGCTATTTACAGACAAG 60.484 47.826 0.00 0.00 38.10 3.16
33 34 3.435671 GCAACGGCTATTTACAGACAAGT 59.564 43.478 0.00 0.00 36.96 3.16
34 35 4.083484 GCAACGGCTATTTACAGACAAGTT 60.083 41.667 0.00 0.00 36.96 2.66
35 36 5.382303 CAACGGCTATTTACAGACAAGTTG 58.618 41.667 0.00 0.00 0.00 3.16
36 37 4.000988 ACGGCTATTTACAGACAAGTTGG 58.999 43.478 7.96 0.00 0.00 3.77
37 38 3.374058 CGGCTATTTACAGACAAGTTGGG 59.626 47.826 7.96 0.00 0.00 4.12
38 39 4.585879 GGCTATTTACAGACAAGTTGGGA 58.414 43.478 7.96 0.00 0.00 4.37
39 40 4.395231 GGCTATTTACAGACAAGTTGGGAC 59.605 45.833 7.96 0.00 0.00 4.46
40 41 5.246307 GCTATTTACAGACAAGTTGGGACT 58.754 41.667 7.96 0.96 37.87 3.85
41 42 5.122396 GCTATTTACAGACAAGTTGGGACTG 59.878 44.000 18.48 18.48 35.91 3.51
42 43 3.485463 TTACAGACAAGTTGGGACTGG 57.515 47.619 21.67 10.63 35.91 4.00
43 44 1.213296 ACAGACAAGTTGGGACTGGT 58.787 50.000 21.67 11.05 42.87 4.00
44 45 1.564348 ACAGACAAGTTGGGACTGGTT 59.436 47.619 21.67 7.58 40.21 3.67
45 46 2.222027 CAGACAAGTTGGGACTGGTTC 58.778 52.381 7.96 0.00 40.21 3.62
46 47 1.202651 AGACAAGTTGGGACTGGTTCG 60.203 52.381 7.96 0.00 40.21 3.95
47 48 0.179029 ACAAGTTGGGACTGGTTCGG 60.179 55.000 7.96 0.00 36.64 4.30
48 49 1.228154 AAGTTGGGACTGGTTCGGC 60.228 57.895 0.00 0.00 35.91 5.54
49 50 2.671963 GTTGGGACTGGTTCGGCC 60.672 66.667 0.00 0.00 37.90 6.13
50 51 3.961414 TTGGGACTGGTTCGGCCC 61.961 66.667 0.00 0.00 41.08 5.80
53 54 4.452733 GGACTGGTTCGGCCCGAG 62.453 72.222 5.73 0.00 37.14 4.63
54 55 4.452733 GACTGGTTCGGCCCGAGG 62.453 72.222 5.73 0.92 37.14 4.63
56 57 4.148825 CTGGTTCGGCCCGAGGAG 62.149 72.222 5.73 0.00 37.14 3.69
59 60 4.452733 GTTCGGCCCGAGGAGGTG 62.453 72.222 5.73 0.00 37.14 4.00
60 61 4.689549 TTCGGCCCGAGGAGGTGA 62.690 66.667 5.73 0.00 37.14 4.02
61 62 3.976490 TTCGGCCCGAGGAGGTGAT 62.976 63.158 5.73 0.00 37.14 3.06
62 63 3.470888 CGGCCCGAGGAGGTGATT 61.471 66.667 0.00 0.00 38.74 2.57
63 64 2.506472 GGCCCGAGGAGGTGATTC 59.494 66.667 0.00 0.00 38.74 2.52
64 65 2.367202 GGCCCGAGGAGGTGATTCA 61.367 63.158 0.00 0.00 38.74 2.57
65 66 1.700042 GGCCCGAGGAGGTGATTCAT 61.700 60.000 0.00 0.00 38.74 2.57
66 67 0.533755 GCCCGAGGAGGTGATTCATG 60.534 60.000 0.00 0.00 38.74 3.07
67 68 0.533755 CCCGAGGAGGTGATTCATGC 60.534 60.000 0.00 0.00 38.74 4.06
68 69 0.877649 CCGAGGAGGTGATTCATGCG 60.878 60.000 0.00 0.00 34.51 4.73
69 70 0.877649 CGAGGAGGTGATTCATGCGG 60.878 60.000 0.00 0.00 0.00 5.69
70 71 0.465705 GAGGAGGTGATTCATGCGGA 59.534 55.000 0.00 0.00 0.00 5.54
71 72 1.071385 GAGGAGGTGATTCATGCGGAT 59.929 52.381 0.00 0.00 0.00 4.18
72 73 1.202734 AGGAGGTGATTCATGCGGATG 60.203 52.381 11.15 11.15 0.00 3.51
73 74 0.590195 GAGGTGATTCATGCGGATGC 59.410 55.000 12.67 0.00 43.20 3.91
74 75 0.182061 AGGTGATTCATGCGGATGCT 59.818 50.000 12.67 1.53 43.34 3.79
75 76 1.027357 GGTGATTCATGCGGATGCTT 58.973 50.000 12.67 1.33 43.34 3.91
76 77 1.406539 GGTGATTCATGCGGATGCTTT 59.593 47.619 12.67 0.00 43.34 3.51
77 78 2.456989 GTGATTCATGCGGATGCTTTG 58.543 47.619 12.67 0.00 43.34 2.77
78 79 2.093890 TGATTCATGCGGATGCTTTGT 58.906 42.857 12.67 0.00 43.34 2.83
79 80 2.492881 TGATTCATGCGGATGCTTTGTT 59.507 40.909 12.67 0.00 43.34 2.83
80 81 2.634982 TTCATGCGGATGCTTTGTTC 57.365 45.000 12.67 0.00 43.34 3.18
81 82 1.532523 TCATGCGGATGCTTTGTTCA 58.467 45.000 12.67 0.00 43.34 3.18
82 83 1.885233 TCATGCGGATGCTTTGTTCAA 59.115 42.857 12.67 0.00 43.34 2.69
83 84 2.492881 TCATGCGGATGCTTTGTTCAAT 59.507 40.909 12.67 0.00 43.34 2.57
84 85 2.350899 TGCGGATGCTTTGTTCAATG 57.649 45.000 0.00 0.00 43.34 2.82
85 86 0.994263 GCGGATGCTTTGTTCAATGC 59.006 50.000 13.85 13.85 38.39 3.56
86 87 1.261989 CGGATGCTTTGTTCAATGCG 58.738 50.000 15.11 2.37 0.00 4.73
87 88 0.994263 GGATGCTTTGTTCAATGCGC 59.006 50.000 0.00 0.00 0.00 6.09
88 89 0.994263 GATGCTTTGTTCAATGCGCC 59.006 50.000 4.18 8.22 0.00 6.53
89 90 0.604578 ATGCTTTGTTCAATGCGCCT 59.395 45.000 4.18 0.00 0.00 5.52
90 91 0.039256 TGCTTTGTTCAATGCGCCTC 60.039 50.000 4.18 0.00 0.00 4.70
91 92 0.242017 GCTTTGTTCAATGCGCCTCT 59.758 50.000 4.18 0.00 0.00 3.69
92 93 1.730446 GCTTTGTTCAATGCGCCTCTC 60.730 52.381 4.18 0.00 0.00 3.20
93 94 1.536766 CTTTGTTCAATGCGCCTCTCA 59.463 47.619 4.18 0.00 0.00 3.27
94 95 1.603456 TTGTTCAATGCGCCTCTCAA 58.397 45.000 4.18 0.12 0.00 3.02
95 96 1.159285 TGTTCAATGCGCCTCTCAAG 58.841 50.000 4.18 0.00 0.00 3.02
96 97 1.160137 GTTCAATGCGCCTCTCAAGT 58.840 50.000 4.18 0.00 0.00 3.16
97 98 1.537202 GTTCAATGCGCCTCTCAAGTT 59.463 47.619 4.18 0.00 0.00 2.66
98 99 1.159285 TCAATGCGCCTCTCAAGTTG 58.841 50.000 4.18 0.00 0.00 3.16
99 100 0.455633 CAATGCGCCTCTCAAGTTGC 60.456 55.000 4.18 0.00 0.00 4.17
100 101 0.607489 AATGCGCCTCTCAAGTTGCT 60.607 50.000 4.18 0.00 0.00 3.91
101 102 1.023513 ATGCGCCTCTCAAGTTGCTC 61.024 55.000 4.18 0.00 0.00 4.26
102 103 2.394563 GCGCCTCTCAAGTTGCTCC 61.395 63.158 0.00 0.00 0.00 4.70
103 104 1.004560 CGCCTCTCAAGTTGCTCCA 60.005 57.895 0.00 0.00 0.00 3.86
104 105 1.294659 CGCCTCTCAAGTTGCTCCAC 61.295 60.000 0.00 0.00 0.00 4.02
105 106 0.036022 GCCTCTCAAGTTGCTCCACT 59.964 55.000 0.00 0.00 0.00 4.00
106 107 1.544314 GCCTCTCAAGTTGCTCCACTT 60.544 52.381 0.00 0.00 37.49 3.16
111 112 1.392589 CAAGTTGCTCCACTTGTGGT 58.607 50.000 18.05 0.00 45.93 4.16
112 113 2.571212 CAAGTTGCTCCACTTGTGGTA 58.429 47.619 18.05 5.89 45.93 3.25
113 114 2.256117 AGTTGCTCCACTTGTGGTAC 57.744 50.000 18.05 12.24 0.00 3.34
114 115 1.768870 AGTTGCTCCACTTGTGGTACT 59.231 47.619 18.05 13.85 0.00 2.73
115 116 2.172717 AGTTGCTCCACTTGTGGTACTT 59.827 45.455 18.05 0.42 0.00 2.24
116 117 2.949644 GTTGCTCCACTTGTGGTACTTT 59.050 45.455 18.05 0.00 0.00 2.66
117 118 4.131596 GTTGCTCCACTTGTGGTACTTTA 58.868 43.478 18.05 0.00 0.00 1.85
118 119 4.002906 TGCTCCACTTGTGGTACTTTAG 57.997 45.455 18.05 9.09 0.00 1.85
119 120 3.389983 TGCTCCACTTGTGGTACTTTAGT 59.610 43.478 18.05 0.00 0.00 2.24
120 121 3.995048 GCTCCACTTGTGGTACTTTAGTC 59.005 47.826 18.05 2.46 0.00 2.59
121 122 4.502604 GCTCCACTTGTGGTACTTTAGTCA 60.503 45.833 18.05 0.00 0.00 3.41
122 123 4.952460 TCCACTTGTGGTACTTTAGTCAC 58.048 43.478 18.05 0.00 0.00 3.67
123 124 4.652421 TCCACTTGTGGTACTTTAGTCACT 59.348 41.667 18.05 0.00 0.00 3.41
124 125 4.750098 CCACTTGTGGTACTTTAGTCACTG 59.250 45.833 11.39 0.00 0.00 3.66
125 126 4.750098 CACTTGTGGTACTTTAGTCACTGG 59.250 45.833 0.00 0.00 0.00 4.00
126 127 4.652421 ACTTGTGGTACTTTAGTCACTGGA 59.348 41.667 0.00 0.00 0.00 3.86
127 128 5.307196 ACTTGTGGTACTTTAGTCACTGGAT 59.693 40.000 0.00 0.00 0.00 3.41
128 129 5.147330 TGTGGTACTTTAGTCACTGGATG 57.853 43.478 0.00 0.00 0.00 3.51
129 130 4.591498 TGTGGTACTTTAGTCACTGGATGT 59.409 41.667 0.00 0.00 0.00 3.06
130 131 5.169295 GTGGTACTTTAGTCACTGGATGTC 58.831 45.833 0.00 0.00 0.00 3.06
131 132 4.222145 TGGTACTTTAGTCACTGGATGTCC 59.778 45.833 0.00 0.00 0.00 4.02
138 139 3.093057 AGTCACTGGATGTCCTAGTGTC 58.907 50.000 20.73 17.59 41.55 3.67
280 281 2.103094 CCTCTTCGTGCCATCTCCAATA 59.897 50.000 0.00 0.00 0.00 1.90
299 300 6.102615 TCCAATACCTAGCCCAAATCTTACAT 59.897 38.462 0.00 0.00 0.00 2.29
555 2067 1.228228 GGATGCTGGATGCTTGGGA 59.772 57.895 0.00 0.00 43.37 4.37
634 2146 1.398390 GCTTGCTAAGTGTCCGATTGG 59.602 52.381 0.00 0.00 0.00 3.16
665 2177 0.305922 GCTGATTGATAGTGGTGCGC 59.694 55.000 0.00 0.00 0.00 6.09
714 2226 1.403647 CGTGAGATTTGGTCAGGCGTA 60.404 52.381 0.00 0.00 0.00 4.42
870 2386 1.763968 ATACTCTGCTCGTGCCTGTA 58.236 50.000 7.05 7.70 38.71 2.74
1232 2772 5.500234 TGGCTATGAAGAATTGCTTAGTGT 58.500 37.500 0.00 0.00 36.83 3.55
1464 3004 3.262420 GAAGCAAGGCTCGAAATCAGTA 58.738 45.455 0.00 0.00 38.25 2.74
1912 3452 3.636764 GGAAAAAGGAAAGTCTCAGCCAA 59.363 43.478 0.00 0.00 0.00 4.52
2176 3716 3.009473 AGGAGCTACAAACCACATGACAT 59.991 43.478 0.00 0.00 0.00 3.06
2320 3860 4.946157 CCTTATCTCCTGTCTTGCATGTTT 59.054 41.667 0.00 0.00 0.00 2.83
2331 3871 7.327761 CCTGTCTTGCATGTTTCTAATTTTCTG 59.672 37.037 0.00 0.00 0.00 3.02
2451 3991 0.339162 TATTGGGGACTGGGACCGTA 59.661 55.000 0.00 0.00 0.00 4.02
2761 4306 2.661195 CGTTCAATTTTTGGGCATCGAC 59.339 45.455 0.00 0.00 0.00 4.20
2900 4445 8.782137 ACATGGGGCAACTATTAAAATCTTAT 57.218 30.769 0.00 0.00 0.00 1.73
3066 4611 3.424433 GCACGCTCACTTATGTTTACCAC 60.424 47.826 0.00 0.00 0.00 4.16
3332 4878 0.838608 TACCGGTGTTGGTGTCCTTT 59.161 50.000 19.93 0.00 43.68 3.11
3364 4910 3.663995 TTTTTGTGAGCATGGATGTGG 57.336 42.857 0.00 0.00 0.00 4.17
3390 4936 8.075574 GCATTCCGTGAACATGAATCATATTAA 58.924 33.333 0.00 0.00 0.00 1.40
3392 4938 8.731275 TTCCGTGAACATGAATCATATTAAGT 57.269 30.769 0.00 0.00 0.00 2.24
3400 4946 9.896645 AACATGAATCATATTAAGTCTCAGTGT 57.103 29.630 0.00 0.00 0.00 3.55
3401 4947 9.896645 ACATGAATCATATTAAGTCTCAGTGTT 57.103 29.630 0.00 0.00 0.00 3.32
3404 4950 9.383519 TGAATCATATTAAGTCTCAGTGTTTCC 57.616 33.333 0.00 0.00 0.00 3.13
3405 4951 8.738645 AATCATATTAAGTCTCAGTGTTTCCC 57.261 34.615 0.00 0.00 0.00 3.97
3406 4952 7.496346 TCATATTAAGTCTCAGTGTTTCCCT 57.504 36.000 0.00 0.00 0.00 4.20
3407 4953 7.918076 TCATATTAAGTCTCAGTGTTTCCCTT 58.082 34.615 0.00 0.00 0.00 3.95
3408 4954 7.824289 TCATATTAAGTCTCAGTGTTTCCCTTG 59.176 37.037 0.00 0.00 0.00 3.61
3409 4955 5.623956 TTAAGTCTCAGTGTTTCCCTTGA 57.376 39.130 0.00 0.00 0.00 3.02
3410 4956 3.477210 AGTCTCAGTGTTTCCCTTGAC 57.523 47.619 0.00 0.00 0.00 3.18
3411 4957 2.135933 GTCTCAGTGTTTCCCTTGACG 58.864 52.381 0.00 0.00 0.00 4.35
3412 4958 0.868406 CTCAGTGTTTCCCTTGACGC 59.132 55.000 0.00 0.00 0.00 5.19
3413 4959 0.179234 TCAGTGTTTCCCTTGACGCA 59.821 50.000 0.00 0.00 0.00 5.24
3414 4960 1.021202 CAGTGTTTCCCTTGACGCAA 58.979 50.000 0.00 0.00 0.00 4.85
3415 4961 1.021968 AGTGTTTCCCTTGACGCAAC 58.978 50.000 0.00 0.00 0.00 4.17
3416 4962 0.316689 GTGTTTCCCTTGACGCAACG 60.317 55.000 0.00 0.00 0.00 4.10
3417 4963 1.281656 GTTTCCCTTGACGCAACGG 59.718 57.895 0.00 0.00 0.00 4.44
3418 4964 2.548295 TTTCCCTTGACGCAACGGC 61.548 57.895 0.00 0.00 34.27 5.68
3419 4965 2.951475 TTTCCCTTGACGCAACGGCT 62.951 55.000 0.00 0.00 35.04 5.52
3420 4966 3.726517 CCCTTGACGCAACGGCTG 61.727 66.667 0.00 0.00 35.04 4.85
3441 4987 1.426423 CATCCGATGGAAGATCAGCG 58.574 55.000 0.00 0.00 44.82 5.18
3442 4988 1.043816 ATCCGATGGAAGATCAGCGT 58.956 50.000 0.00 0.00 43.89 5.07
3443 4989 0.385751 TCCGATGGAAGATCAGCGTC 59.614 55.000 0.00 0.00 43.89 5.19
3444 4990 0.387202 CCGATGGAAGATCAGCGTCT 59.613 55.000 0.00 0.00 43.89 4.18
3445 4991 1.601663 CCGATGGAAGATCAGCGTCTC 60.602 57.143 0.00 0.00 43.89 3.36
3446 4992 1.336440 CGATGGAAGATCAGCGTCTCT 59.664 52.381 0.00 0.00 41.00 3.10
3447 4993 2.604373 CGATGGAAGATCAGCGTCTCTC 60.604 54.545 0.00 0.00 41.00 3.20
3448 4994 1.839424 TGGAAGATCAGCGTCTCTCA 58.161 50.000 0.00 0.00 0.00 3.27
3449 4995 1.747924 TGGAAGATCAGCGTCTCTCAG 59.252 52.381 0.00 0.00 0.00 3.35
3450 4996 1.535860 GGAAGATCAGCGTCTCTCAGC 60.536 57.143 0.00 0.00 0.00 4.26
3451 4997 1.133982 GAAGATCAGCGTCTCTCAGCA 59.866 52.381 0.00 0.00 35.48 4.41
3452 4998 0.740149 AGATCAGCGTCTCTCAGCAG 59.260 55.000 0.00 0.00 35.48 4.24
3453 4999 0.871163 GATCAGCGTCTCTCAGCAGC 60.871 60.000 0.00 0.00 35.48 5.25
3454 5000 1.321805 ATCAGCGTCTCTCAGCAGCT 61.322 55.000 0.00 0.00 38.90 4.24
3455 5001 2.572812 AGCGTCTCTCAGCAGCTG 59.427 61.111 17.10 17.10 36.73 4.24
3456 5002 3.187414 GCGTCTCTCAGCAGCTGC 61.187 66.667 31.53 31.53 42.49 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.819259 AGCCGTTGCGCCATATTGAT 60.819 50.000 4.18 0.00 44.33 2.57
1 2 0.179070 TAGCCGTTGCGCCATATTGA 60.179 50.000 4.18 0.00 44.33 2.57
2 3 0.874390 ATAGCCGTTGCGCCATATTG 59.126 50.000 4.18 0.00 44.33 1.90
3 4 1.604604 AATAGCCGTTGCGCCATATT 58.395 45.000 4.18 0.00 44.33 1.28
4 5 1.604604 AAATAGCCGTTGCGCCATAT 58.395 45.000 4.18 0.00 44.33 1.78
5 6 1.868498 GTAAATAGCCGTTGCGCCATA 59.132 47.619 4.18 0.00 44.33 2.74
6 7 0.661020 GTAAATAGCCGTTGCGCCAT 59.339 50.000 4.18 0.00 44.33 4.40
7 8 0.673956 TGTAAATAGCCGTTGCGCCA 60.674 50.000 4.18 0.00 44.33 5.69
8 9 0.027586 CTGTAAATAGCCGTTGCGCC 59.972 55.000 4.18 0.00 44.33 6.53
9 10 1.003851 TCTGTAAATAGCCGTTGCGC 58.996 50.000 0.00 0.00 44.33 6.09
10 11 1.996898 TGTCTGTAAATAGCCGTTGCG 59.003 47.619 0.00 0.00 44.33 4.85
11 12 3.435671 ACTTGTCTGTAAATAGCCGTTGC 59.564 43.478 0.00 0.00 37.95 4.17
12 13 5.382303 CAACTTGTCTGTAAATAGCCGTTG 58.618 41.667 0.00 0.00 0.00 4.10
13 14 4.454504 CCAACTTGTCTGTAAATAGCCGTT 59.545 41.667 0.00 0.00 0.00 4.44
14 15 4.000988 CCAACTTGTCTGTAAATAGCCGT 58.999 43.478 0.00 0.00 0.00 5.68
15 16 3.374058 CCCAACTTGTCTGTAAATAGCCG 59.626 47.826 0.00 0.00 0.00 5.52
16 17 4.395231 GTCCCAACTTGTCTGTAAATAGCC 59.605 45.833 0.00 0.00 0.00 3.93
17 18 5.122396 CAGTCCCAACTTGTCTGTAAATAGC 59.878 44.000 0.00 0.00 31.71 2.97
18 19 5.643777 CCAGTCCCAACTTGTCTGTAAATAG 59.356 44.000 0.00 0.00 31.71 1.73
19 20 5.072600 ACCAGTCCCAACTTGTCTGTAAATA 59.927 40.000 0.00 0.00 31.71 1.40
20 21 4.141251 ACCAGTCCCAACTTGTCTGTAAAT 60.141 41.667 0.00 0.00 31.71 1.40
21 22 3.201266 ACCAGTCCCAACTTGTCTGTAAA 59.799 43.478 0.00 0.00 31.71 2.01
22 23 2.775384 ACCAGTCCCAACTTGTCTGTAA 59.225 45.455 0.00 0.00 31.71 2.41
23 24 2.404559 ACCAGTCCCAACTTGTCTGTA 58.595 47.619 0.00 0.00 31.71 2.74
24 25 1.213296 ACCAGTCCCAACTTGTCTGT 58.787 50.000 0.00 0.00 31.71 3.41
25 26 2.222027 GAACCAGTCCCAACTTGTCTG 58.778 52.381 0.00 0.00 30.50 3.51
26 27 1.202651 CGAACCAGTCCCAACTTGTCT 60.203 52.381 0.00 0.00 30.50 3.41
27 28 1.226746 CGAACCAGTCCCAACTTGTC 58.773 55.000 0.00 0.00 30.50 3.18
28 29 0.179029 CCGAACCAGTCCCAACTTGT 60.179 55.000 0.00 0.00 33.01 3.16
29 30 1.515521 GCCGAACCAGTCCCAACTTG 61.516 60.000 0.00 0.00 31.71 3.16
30 31 1.228154 GCCGAACCAGTCCCAACTT 60.228 57.895 0.00 0.00 31.71 2.66
31 32 2.430367 GCCGAACCAGTCCCAACT 59.570 61.111 0.00 0.00 35.60 3.16
32 33 2.671963 GGCCGAACCAGTCCCAAC 60.672 66.667 0.00 0.00 38.86 3.77
33 34 3.961414 GGGCCGAACCAGTCCCAA 61.961 66.667 0.00 0.00 42.05 4.12
36 37 4.452733 CTCGGGCCGAACCAGTCC 62.453 72.222 30.59 0.00 42.05 3.85
37 38 4.452733 CCTCGGGCCGAACCAGTC 62.453 72.222 30.59 0.00 42.05 3.51
39 40 4.148825 CTCCTCGGGCCGAACCAG 62.149 72.222 30.59 20.36 42.05 4.00
42 43 4.452733 CACCTCCTCGGGCCGAAC 62.453 72.222 30.59 0.00 34.74 3.95
43 44 3.976490 ATCACCTCCTCGGGCCGAA 62.976 63.158 30.59 15.48 34.74 4.30
44 45 3.976490 AATCACCTCCTCGGGCCGA 62.976 63.158 29.14 29.14 36.97 5.54
45 46 3.447025 GAATCACCTCCTCGGGCCG 62.447 68.421 22.51 22.51 36.97 6.13
46 47 1.700042 ATGAATCACCTCCTCGGGCC 61.700 60.000 0.00 0.00 36.97 5.80
47 48 0.533755 CATGAATCACCTCCTCGGGC 60.534 60.000 0.00 0.00 36.97 6.13
48 49 0.533755 GCATGAATCACCTCCTCGGG 60.534 60.000 0.00 0.00 36.97 5.14
49 50 0.877649 CGCATGAATCACCTCCTCGG 60.878 60.000 0.00 0.00 39.35 4.63
50 51 0.877649 CCGCATGAATCACCTCCTCG 60.878 60.000 0.00 0.00 0.00 4.63
51 52 0.465705 TCCGCATGAATCACCTCCTC 59.534 55.000 0.00 0.00 0.00 3.71
52 53 1.135094 ATCCGCATGAATCACCTCCT 58.865 50.000 0.00 0.00 0.00 3.69
53 54 1.233019 CATCCGCATGAATCACCTCC 58.767 55.000 0.00 0.00 30.57 4.30
54 55 0.590195 GCATCCGCATGAATCACCTC 59.410 55.000 0.00 0.00 38.36 3.85
55 56 0.182061 AGCATCCGCATGAATCACCT 59.818 50.000 0.00 0.00 42.27 4.00
56 57 1.027357 AAGCATCCGCATGAATCACC 58.973 50.000 0.00 0.00 42.27 4.02
57 58 2.159338 ACAAAGCATCCGCATGAATCAC 60.159 45.455 0.00 0.00 42.27 3.06
58 59 2.093890 ACAAAGCATCCGCATGAATCA 58.906 42.857 0.00 0.00 42.27 2.57
59 60 2.857592 ACAAAGCATCCGCATGAATC 57.142 45.000 0.00 0.00 42.27 2.52
60 61 2.492881 TGAACAAAGCATCCGCATGAAT 59.507 40.909 0.00 0.00 42.27 2.57
61 62 1.885233 TGAACAAAGCATCCGCATGAA 59.115 42.857 0.00 0.00 42.27 2.57
62 63 1.532523 TGAACAAAGCATCCGCATGA 58.467 45.000 0.00 0.00 42.27 3.07
63 64 2.350899 TTGAACAAAGCATCCGCATG 57.649 45.000 0.00 0.00 42.27 4.06
64 65 2.883574 CATTGAACAAAGCATCCGCAT 58.116 42.857 0.00 0.00 42.27 4.73
65 66 1.669502 GCATTGAACAAAGCATCCGCA 60.670 47.619 9.36 0.00 42.27 5.69
66 67 0.994263 GCATTGAACAAAGCATCCGC 59.006 50.000 9.36 0.00 35.35 5.54
67 68 1.261989 CGCATTGAACAAAGCATCCG 58.738 50.000 13.55 0.00 34.99 4.18
68 69 0.994263 GCGCATTGAACAAAGCATCC 59.006 50.000 0.30 0.33 34.99 3.51
69 70 0.994263 GGCGCATTGAACAAAGCATC 59.006 50.000 10.83 5.80 34.99 3.91
70 71 0.604578 AGGCGCATTGAACAAAGCAT 59.395 45.000 10.83 5.35 34.99 3.79
71 72 0.039256 GAGGCGCATTGAACAAAGCA 60.039 50.000 10.83 0.00 34.99 3.91
72 73 0.242017 AGAGGCGCATTGAACAAAGC 59.758 50.000 10.83 4.94 0.00 3.51
73 74 1.536766 TGAGAGGCGCATTGAACAAAG 59.463 47.619 10.83 0.00 0.00 2.77
74 75 1.603456 TGAGAGGCGCATTGAACAAA 58.397 45.000 10.83 0.00 0.00 2.83
75 76 1.536766 CTTGAGAGGCGCATTGAACAA 59.463 47.619 10.83 6.84 0.00 2.83
76 77 1.159285 CTTGAGAGGCGCATTGAACA 58.841 50.000 10.83 0.00 0.00 3.18
77 78 1.160137 ACTTGAGAGGCGCATTGAAC 58.840 50.000 10.83 0.00 0.00 3.18
78 79 1.536766 CAACTTGAGAGGCGCATTGAA 59.463 47.619 10.83 0.00 0.00 2.69
79 80 1.159285 CAACTTGAGAGGCGCATTGA 58.841 50.000 10.83 0.00 0.00 2.57
80 81 0.455633 GCAACTTGAGAGGCGCATTG 60.456 55.000 10.83 0.00 0.00 2.82
81 82 0.607489 AGCAACTTGAGAGGCGCATT 60.607 50.000 10.83 0.00 0.00 3.56
82 83 1.002868 AGCAACTTGAGAGGCGCAT 60.003 52.632 10.83 0.00 0.00 4.73
83 84 1.669115 GAGCAACTTGAGAGGCGCA 60.669 57.895 10.83 0.00 0.00 6.09
84 85 2.394563 GGAGCAACTTGAGAGGCGC 61.395 63.158 0.00 0.00 0.00 6.53
85 86 1.004560 TGGAGCAACTTGAGAGGCG 60.005 57.895 0.00 0.00 0.00 5.52
86 87 0.036022 AGTGGAGCAACTTGAGAGGC 59.964 55.000 0.00 0.00 0.00 4.70
87 88 2.557920 AAGTGGAGCAACTTGAGAGG 57.442 50.000 0.00 0.00 38.95 3.69
102 103 4.750098 CCAGTGACTAAAGTACCACAAGTG 59.250 45.833 0.00 0.00 32.35 3.16
103 104 4.652421 TCCAGTGACTAAAGTACCACAAGT 59.348 41.667 0.00 0.00 32.35 3.16
104 105 5.209818 TCCAGTGACTAAAGTACCACAAG 57.790 43.478 0.00 0.00 32.35 3.16
105 106 5.071250 ACATCCAGTGACTAAAGTACCACAA 59.929 40.000 0.00 0.00 32.35 3.33
106 107 4.591498 ACATCCAGTGACTAAAGTACCACA 59.409 41.667 0.00 0.00 32.35 4.17
107 108 5.148651 ACATCCAGTGACTAAAGTACCAC 57.851 43.478 0.00 0.00 0.00 4.16
108 109 4.222145 GGACATCCAGTGACTAAAGTACCA 59.778 45.833 0.00 0.00 35.64 3.25
109 110 4.466726 AGGACATCCAGTGACTAAAGTACC 59.533 45.833 0.00 0.00 38.89 3.34
110 111 5.662674 AGGACATCCAGTGACTAAAGTAC 57.337 43.478 0.00 0.00 38.89 2.73
111 112 6.377429 CACTAGGACATCCAGTGACTAAAGTA 59.623 42.308 18.28 0.00 42.47 2.24
112 113 5.186021 CACTAGGACATCCAGTGACTAAAGT 59.814 44.000 18.28 0.00 42.47 2.66
113 114 5.186021 ACACTAGGACATCCAGTGACTAAAG 59.814 44.000 24.87 8.01 42.47 1.85
114 115 5.084519 ACACTAGGACATCCAGTGACTAAA 58.915 41.667 24.87 0.00 42.47 1.85
115 116 4.673968 ACACTAGGACATCCAGTGACTAA 58.326 43.478 24.87 0.00 42.47 2.24
116 117 4.270834 GACACTAGGACATCCAGTGACTA 58.729 47.826 24.87 4.58 42.47 2.59
117 118 3.093057 GACACTAGGACATCCAGTGACT 58.907 50.000 24.87 12.14 42.47 3.41
118 119 2.159366 CGACACTAGGACATCCAGTGAC 60.159 54.545 24.87 20.18 42.47 3.67
119 120 2.092323 CGACACTAGGACATCCAGTGA 58.908 52.381 24.87 1.30 42.47 3.41
120 121 1.135139 CCGACACTAGGACATCCAGTG 59.865 57.143 20.08 20.08 43.92 3.66
121 122 1.272536 ACCGACACTAGGACATCCAGT 60.273 52.381 0.00 0.00 38.89 4.00
122 123 1.135139 CACCGACACTAGGACATCCAG 59.865 57.143 0.00 0.00 38.89 3.86
123 124 1.182667 CACCGACACTAGGACATCCA 58.817 55.000 0.00 0.00 38.89 3.41
124 125 1.183549 ACACCGACACTAGGACATCC 58.816 55.000 0.00 0.00 0.00 3.51
125 126 5.762825 TTATACACCGACACTAGGACATC 57.237 43.478 0.00 0.00 0.00 3.06
126 127 6.726490 ATTTATACACCGACACTAGGACAT 57.274 37.500 0.00 0.00 0.00 3.06
127 128 7.643569 TTATTTATACACCGACACTAGGACA 57.356 36.000 0.00 0.00 0.00 4.02
128 129 8.139989 ACATTATTTATACACCGACACTAGGAC 58.860 37.037 0.00 0.00 0.00 3.85
129 130 8.241497 ACATTATTTATACACCGACACTAGGA 57.759 34.615 0.00 0.00 0.00 2.94
130 131 9.970395 TTACATTATTTATACACCGACACTAGG 57.030 33.333 0.00 0.00 0.00 3.02
167 168 6.996509 ACACTTTACATTTTAGACCCTACGA 58.003 36.000 0.00 0.00 0.00 3.43
280 281 5.014228 GGGATATGTAAGATTTGGGCTAGGT 59.986 44.000 0.00 0.00 0.00 3.08
379 380 1.078709 CAGAAATCACGGCGACACAT 58.921 50.000 16.62 0.00 0.00 3.21
460 461 2.743928 CGCTCCTTCCGCAGCTTT 60.744 61.111 0.00 0.00 33.09 3.51
555 2067 5.203528 CCAAGTAATTTCCTGATGGACCAT 58.796 41.667 6.71 6.71 43.06 3.55
622 2134 1.238439 CTTGCAACCAATCGGACACT 58.762 50.000 0.00 0.00 35.59 3.55
634 2146 2.086869 TCAATCAGCTAGCCTTGCAAC 58.913 47.619 12.13 0.00 0.00 4.17
714 2226 8.732746 AAGAAAAGTGAACTGTACTTGTATGT 57.267 30.769 0.00 0.00 38.32 2.29
870 2386 2.430465 ACGAGTTGCTCTCAAATGCAT 58.570 42.857 0.00 0.00 42.88 3.96
958 2495 2.300437 GGAGCTAGTCACACAGGACTTT 59.700 50.000 0.72 0.00 45.59 2.66
1232 2772 6.925165 GCCACTTTTCAATTTCTCTTCATCAA 59.075 34.615 0.00 0.00 0.00 2.57
1427 2967 5.277538 CCTTGCTTCAAGTTAGTCAACTCAC 60.278 44.000 5.92 0.00 44.41 3.51
1464 3004 3.771479 TCATCTCACCTGCATACTCAGTT 59.229 43.478 0.00 0.00 32.32 3.16
1874 3414 4.463050 TTTTCCCACCAAGTTGGATAGT 57.537 40.909 28.80 2.52 40.96 2.12
1912 3452 3.288381 AGCTCCCTGACCTCCCCT 61.288 66.667 0.00 0.00 0.00 4.79
2320 3860 6.601332 ACAAGAGGTTGACCAGAAAATTAGA 58.399 36.000 2.56 0.00 37.10 2.10
2331 3871 3.067833 GCTAACTGACAAGAGGTTGACC 58.932 50.000 0.00 0.00 37.10 4.02
2451 3991 7.727634 TCATCAAGATAGTAGAGTCCATCATGT 59.272 37.037 0.00 0.00 0.00 3.21
2761 4306 6.311723 AGCAATCGATAAAAGTTACAAACCG 58.688 36.000 0.00 0.00 0.00 4.44
2900 4445 1.634960 TCCGTACCATTGTCTGACCA 58.365 50.000 5.17 0.00 0.00 4.02
3066 4611 4.864247 CCCCAAAGAAATTTAGCACATTCG 59.136 41.667 0.00 0.00 0.00 3.34
3237 4783 7.148171 GGATCTAATTTTCCAACAGAGTTCCTG 60.148 40.741 0.00 0.00 39.08 3.86
3364 4910 3.763097 TGATTCATGTTCACGGAATGC 57.237 42.857 0.00 0.00 31.77 3.56
3390 4936 2.224066 CGTCAAGGGAAACACTGAGACT 60.224 50.000 0.00 0.00 0.00 3.24
3392 4938 1.540363 GCGTCAAGGGAAACACTGAGA 60.540 52.381 0.00 0.00 0.00 3.27
3397 4943 0.316689 CGTTGCGTCAAGGGAAACAC 60.317 55.000 4.92 0.00 0.00 3.32
3398 4944 2.018544 CGTTGCGTCAAGGGAAACA 58.981 52.632 4.92 0.00 0.00 2.83
3399 4945 4.914291 CGTTGCGTCAAGGGAAAC 57.086 55.556 4.92 0.00 0.00 2.78
3404 4950 4.389576 GCAGCCGTTGCGTCAAGG 62.390 66.667 0.00 5.62 44.09 3.61
3422 4968 1.269988 ACGCTGATCTTCCATCGGATG 60.270 52.381 11.07 11.07 30.86 3.51
3423 4969 1.000283 GACGCTGATCTTCCATCGGAT 60.000 52.381 0.00 0.00 30.86 4.18
3424 4970 0.385751 GACGCTGATCTTCCATCGGA 59.614 55.000 0.00 0.00 30.86 4.55
3425 4971 0.387202 AGACGCTGATCTTCCATCGG 59.613 55.000 0.00 0.00 30.86 4.18
3426 4972 1.336440 AGAGACGCTGATCTTCCATCG 59.664 52.381 0.00 0.00 0.00 3.84
3427 4973 2.360483 TGAGAGACGCTGATCTTCCATC 59.640 50.000 0.00 0.00 0.00 3.51
3428 4974 2.361757 CTGAGAGACGCTGATCTTCCAT 59.638 50.000 0.00 0.00 0.00 3.41
3429 4975 1.747924 CTGAGAGACGCTGATCTTCCA 59.252 52.381 0.00 0.00 0.00 3.53
3430 4976 1.535860 GCTGAGAGACGCTGATCTTCC 60.536 57.143 0.00 0.00 0.00 3.46
3431 4977 1.133982 TGCTGAGAGACGCTGATCTTC 59.866 52.381 0.00 0.00 0.00 2.87
3432 4978 1.134753 CTGCTGAGAGACGCTGATCTT 59.865 52.381 0.00 0.00 0.00 2.40
3433 4979 0.740149 CTGCTGAGAGACGCTGATCT 59.260 55.000 0.00 0.00 0.00 2.75
3434 4980 0.871163 GCTGCTGAGAGACGCTGATC 60.871 60.000 0.00 0.00 0.00 2.92
3435 4981 1.141449 GCTGCTGAGAGACGCTGAT 59.859 57.895 0.00 0.00 0.00 2.90
3436 4982 1.975940 AGCTGCTGAGAGACGCTGA 60.976 57.895 0.00 0.00 0.00 4.26
3437 4983 1.806351 CAGCTGCTGAGAGACGCTG 60.806 63.158 24.88 0.00 41.57 5.18
3438 4984 2.572812 CAGCTGCTGAGAGACGCT 59.427 61.111 24.88 0.00 32.44 5.07
3439 4985 3.187414 GCAGCTGCTGAGAGACGC 61.187 66.667 32.30 11.90 38.21 5.19


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

AutoCloner maintained by Alex Coulton.