Multiple sequence alignment - TraesCS6D01G262100

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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 TraesCS6D01G262100 chr6D 100.000 3744 0 0 1 3744 370047579 370043836 0.000000e+00 6914.0
1 TraesCS6D01G262100 chr6D 88.260 477 44 8 1643 2115 370045761 370045293 9.080000e-156 560.0
2 TraesCS6D01G262100 chr6D 88.260 477 44 8 1819 2287 370045937 370045465 9.080000e-156 560.0
3 TraesCS6D01G262100 chr6B 93.819 2184 117 11 110 2287 555347306 555345135 0.000000e+00 3269.0
4 TraesCS6D01G262100 chr6B 91.266 1477 77 31 1638 3079 555345608 555344149 0.000000e+00 1965.0
5 TraesCS6D01G262100 chr6B 93.249 474 18 8 3279 3744 555343501 555343034 0.000000e+00 686.0
6 TraesCS6D01G262100 chr6B 87.421 477 48 10 1819 2287 555345779 555345307 4.260000e-149 538.0
7 TraesCS6D01G262100 chr6B 86.983 484 47 10 1637 2113 555345439 555344965 7.120000e-147 531.0
8 TraesCS6D01G262100 chr6B 83.706 313 37 11 1983 2287 555345785 555345479 2.200000e-72 283.0
9 TraesCS6D01G262100 chr6B 86.301 73 9 1 1034 1105 68219401 68219473 1.110000e-10 78.7
10 TraesCS6D01G262100 chr6A 89.789 1900 116 41 407 2287 511044517 511042677 0.000000e+00 2362.0
11 TraesCS6D01G262100 chr6A 94.814 1369 55 10 1637 3000 511043154 511041797 0.000000e+00 2121.0
12 TraesCS6D01G262100 chr6A 91.915 470 28 6 3279 3744 511041349 511040886 0.000000e+00 649.0
13 TraesCS6D01G262100 chr6A 87.866 478 43 11 1643 2115 511042972 511042505 7.070000e-152 547.0
14 TraesCS6D01G262100 chr6A 84.887 311 37 7 1981 2285 511043332 511043026 4.700000e-79 305.0
15 TraesCS6D01G262100 chr6A 89.610 77 7 1 224 300 486268134 486268059 3.080000e-16 97.1
16 TraesCS6D01G262100 chr5D 98.276 116 0 2 1 115 168063435 168063549 6.340000e-48 202.0
17 TraesCS6D01G262100 chr5D 96.610 118 2 2 1 117 168054933 168055049 1.060000e-45 195.0
18 TraesCS6D01G262100 chr4D 99.099 111 0 1 1 110 225370767 225370877 8.200000e-47 198.0
19 TraesCS6D01G262100 chr7D 99.091 110 0 1 1 109 322865976 322866085 2.950000e-46 196.0
20 TraesCS6D01G262100 chr7D 97.414 116 0 3 1 113 514276537 514276422 1.060000e-45 195.0
21 TraesCS6D01G262100 chr7D 95.833 120 2 3 1 117 257427668 257427549 1.370000e-44 191.0
22 TraesCS6D01G262100 chr7D 86.301 73 9 1 1034 1105 209825270 209825198 1.110000e-10 78.7
23 TraesCS6D01G262100 chr2D 98.230 113 1 1 1 112 270784031 270784143 2.950000e-46 196.0
24 TraesCS6D01G262100 chr2D 97.391 115 1 2 1 114 315651132 315651245 1.060000e-45 195.0
25 TraesCS6D01G262100 chr1D 97.368 114 1 2 1 112 178736286 178736399 3.820000e-45 193.0
26 TraesCS6D01G262100 chr7B 84.810 79 11 1 1028 1105 191727632 191727710 1.110000e-10 78.7
27 TraesCS6D01G262100 chr7A 94.231 52 2 1 1055 1105 920026 919975 1.110000e-10 78.7
28 TraesCS6D01G262100 chr7A 86.301 73 9 1 1034 1105 222505411 222505339 1.110000e-10 78.7
29 TraesCS6D01G262100 chr3A 86.957 69 9 0 1028 1096 373432410 373432478 1.110000e-10 78.7
30 TraesCS6D01G262100 chr2B 84.810 79 11 1 1028 1105 321106315 321106393 1.110000e-10 78.7


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 TraesCS6D01G262100 chr6D 370043836 370047579 3743 True 2678.0 6914 92.173333 1 3744 3 chr6D.!!$R1 3743
1 TraesCS6D01G262100 chr6B 555343034 555347306 4272 True 1212.0 3269 89.407333 110 3744 6 chr6B.!!$R1 3634
2 TraesCS6D01G262100 chr6A 511040886 511044517 3631 True 1196.8 2362 89.854200 407 3744 5 chr6A.!!$R2 3337

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
102 103 0.034059 CTGTTTGAGGTCTGGTCGCT 59.966 55.0 0.0 0.0 0.00 4.93 F
357 360 0.251564 AAATCGGCACCCATCCACAA 60.252 50.0 0.0 0.0 0.00 3.33 F
885 894 0.740737 CCAGCAAGCCCTAATTTCCG 59.259 55.0 0.0 0.0 0.00 4.30 F
1235 1245 1.035923 TGGATTTGCTGGTGCGAAAA 58.964 45.0 0.0 0.0 44.77 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1277 1.210931 CAGGTGCAACAGCCATTCG 59.789 57.895 3.64 0.0 39.98 3.34 R
2063 2430 1.747355 GCATATGAAGGCAGCAAGTGT 59.253 47.619 6.97 0.0 31.14 3.55 R
2599 2967 0.989602 TCCTGACACGGACTCTCCTA 59.010 55.000 0.00 0.0 33.30 2.94 R
3111 3800 0.039618 TCCCCTCAATTGCTTGACCC 59.960 55.000 0.00 0.0 36.46 4.46 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 8.910351 GCTACTCTGTTATAAATCCTCCATTT 57.090 34.615 0.00 0.00 38.35 2.32
26 27 8.778358 GCTACTCTGTTATAAATCCTCCATTTG 58.222 37.037 0.00 0.00 35.34 2.32
27 28 9.838339 CTACTCTGTTATAAATCCTCCATTTGT 57.162 33.333 0.00 0.00 35.34 2.83
29 30 9.614792 ACTCTGTTATAAATCCTCCATTTGTAC 57.385 33.333 0.00 0.00 35.34 2.90
30 31 9.838339 CTCTGTTATAAATCCTCCATTTGTACT 57.162 33.333 0.00 0.00 35.34 2.73
31 32 9.613428 TCTGTTATAAATCCTCCATTTGTACTG 57.387 33.333 0.00 0.00 35.34 2.74
32 33 9.396022 CTGTTATAAATCCTCCATTTGTACTGT 57.604 33.333 0.00 0.00 35.34 3.55
33 34 9.173021 TGTTATAAATCCTCCATTTGTACTGTG 57.827 33.333 0.00 0.00 35.34 3.66
34 35 8.621286 GTTATAAATCCTCCATTTGTACTGTGG 58.379 37.037 0.00 0.00 35.34 4.17
35 36 4.657814 AATCCTCCATTTGTACTGTGGT 57.342 40.909 10.24 0.00 34.61 4.16
36 37 3.417069 TCCTCCATTTGTACTGTGGTG 57.583 47.619 10.24 8.43 34.61 4.17
37 38 2.708861 TCCTCCATTTGTACTGTGGTGT 59.291 45.455 10.24 0.00 34.61 4.16
38 39 3.074412 CCTCCATTTGTACTGTGGTGTC 58.926 50.000 10.24 0.00 34.61 3.67
39 40 3.495983 CCTCCATTTGTACTGTGGTGTCA 60.496 47.826 10.24 0.00 34.61 3.58
40 41 3.738982 TCCATTTGTACTGTGGTGTCAG 58.261 45.455 10.24 0.00 40.80 3.51
41 42 2.226437 CCATTTGTACTGTGGTGTCAGC 59.774 50.000 0.00 0.00 38.84 4.26
42 43 2.700722 TTTGTACTGTGGTGTCAGCA 57.299 45.000 0.00 0.00 38.84 4.41
43 44 2.928801 TTGTACTGTGGTGTCAGCAT 57.071 45.000 8.18 0.00 38.84 3.79
44 45 2.928801 TGTACTGTGGTGTCAGCATT 57.071 45.000 8.18 0.00 38.84 3.56
45 46 4.344359 TTGTACTGTGGTGTCAGCATTA 57.656 40.909 8.18 0.14 38.84 1.90
46 47 3.659786 TGTACTGTGGTGTCAGCATTAC 58.340 45.455 8.18 10.35 38.84 1.89
47 48 3.323691 TGTACTGTGGTGTCAGCATTACT 59.676 43.478 8.18 0.00 38.84 2.24
59 60 3.784511 AGCATTACTGATCCAGGGATG 57.215 47.619 5.35 0.00 35.51 3.51
60 61 3.321039 AGCATTACTGATCCAGGGATGA 58.679 45.455 5.35 0.00 35.51 2.92
61 62 3.072184 AGCATTACTGATCCAGGGATGAC 59.928 47.826 5.35 0.00 35.51 3.06
62 63 3.181451 GCATTACTGATCCAGGGATGACA 60.181 47.826 5.35 0.00 35.51 3.58
63 64 4.384056 CATTACTGATCCAGGGATGACAC 58.616 47.826 5.35 0.00 35.51 3.67
64 65 2.260639 ACTGATCCAGGGATGACACT 57.739 50.000 5.35 0.00 35.51 3.55
65 66 1.836166 ACTGATCCAGGGATGACACTG 59.164 52.381 5.35 0.00 46.15 3.66
69 70 4.308526 CAGGGATGACACTGGTGC 57.691 61.111 0.17 0.00 43.19 5.01
70 71 1.376086 CAGGGATGACACTGGTGCA 59.624 57.895 0.17 1.12 43.19 4.57
71 72 0.957395 CAGGGATGACACTGGTGCAC 60.957 60.000 8.80 8.80 43.19 4.57
72 73 1.073025 GGGATGACACTGGTGCACA 59.927 57.895 20.43 3.92 0.00 4.57
84 85 2.507452 TGCACAGCAGCACAGACT 59.493 55.556 0.00 0.00 40.11 3.24
85 86 1.890510 TGCACAGCAGCACAGACTG 60.891 57.895 0.00 0.00 40.11 3.51
86 87 1.890979 GCACAGCAGCACAGACTGT 60.891 57.895 1.07 1.07 45.25 3.55
87 88 1.442526 GCACAGCAGCACAGACTGTT 61.443 55.000 5.04 0.00 42.59 3.16
88 89 1.019673 CACAGCAGCACAGACTGTTT 58.980 50.000 5.04 0.00 42.59 2.83
89 90 1.019673 ACAGCAGCACAGACTGTTTG 58.980 50.000 5.04 8.79 41.78 2.93
90 91 1.302366 CAGCAGCACAGACTGTTTGA 58.698 50.000 17.11 0.00 39.96 2.69
91 92 1.263484 CAGCAGCACAGACTGTTTGAG 59.737 52.381 17.11 4.12 39.96 3.02
92 93 0.590195 GCAGCACAGACTGTTTGAGG 59.410 55.000 17.11 3.80 39.96 3.86
93 94 1.959042 CAGCACAGACTGTTTGAGGT 58.041 50.000 5.04 0.00 32.78 3.85
94 95 1.869767 CAGCACAGACTGTTTGAGGTC 59.130 52.381 5.04 0.00 32.78 3.85
95 96 1.765314 AGCACAGACTGTTTGAGGTCT 59.235 47.619 5.04 0.00 42.67 3.85
100 101 1.341531 AGACTGTTTGAGGTCTGGTCG 59.658 52.381 0.00 0.00 40.71 4.79
101 102 0.249911 ACTGTTTGAGGTCTGGTCGC 60.250 55.000 0.00 0.00 0.00 5.19
102 103 0.034059 CTGTTTGAGGTCTGGTCGCT 59.966 55.000 0.00 0.00 0.00 4.93
103 104 1.272490 CTGTTTGAGGTCTGGTCGCTA 59.728 52.381 0.00 0.00 0.00 4.26
104 105 1.000506 TGTTTGAGGTCTGGTCGCTAC 59.999 52.381 0.00 0.00 0.00 3.58
105 106 1.000506 GTTTGAGGTCTGGTCGCTACA 59.999 52.381 0.00 0.00 0.00 2.74
106 107 1.557099 TTGAGGTCTGGTCGCTACAT 58.443 50.000 0.00 0.00 0.00 2.29
107 108 1.103803 TGAGGTCTGGTCGCTACATC 58.896 55.000 0.00 0.00 0.00 3.06
108 109 0.386113 GAGGTCTGGTCGCTACATCC 59.614 60.000 0.00 0.00 0.00 3.51
210 211 2.125766 AACTTCTCTCCCGCCAACCC 62.126 60.000 0.00 0.00 0.00 4.11
222 225 1.668237 CGCCAACCCTTTTTGTTTTGG 59.332 47.619 0.00 0.00 39.86 3.28
252 255 0.919710 AAAAAGAGGGAGGGATCCGG 59.080 55.000 5.45 0.00 0.00 5.14
270 273 3.335786 CGGTAGATATAGCGGATTCGG 57.664 52.381 10.96 0.00 37.31 4.30
291 294 0.319900 CCGAACTATGCAGGATCCCG 60.320 60.000 8.55 0.00 0.00 5.14
292 295 0.673985 CGAACTATGCAGGATCCCGA 59.326 55.000 8.55 0.00 0.00 5.14
336 339 1.866015 ACAGGATCTGTTCGGGATGA 58.134 50.000 0.00 0.00 42.59 2.92
350 353 1.181786 GGATGAAAAATCGGCACCCA 58.818 50.000 0.00 0.00 0.00 4.51
357 360 0.251564 AAATCGGCACCCATCCACAA 60.252 50.000 0.00 0.00 0.00 3.33
389 392 0.949588 TTATGAACCGGTTTGCGCGA 60.950 50.000 23.22 0.00 0.00 5.87
391 394 2.202298 GAACCGGTTTGCGCGATG 60.202 61.111 23.22 0.00 0.00 3.84
638 646 2.271800 CTATGCTCCTTGGTCAACGTC 58.728 52.381 0.00 0.00 0.00 4.34
695 703 5.782047 TGTGGAGGCAAACATTAATCAAAG 58.218 37.500 0.00 0.00 0.00 2.77
696 704 5.304101 TGTGGAGGCAAACATTAATCAAAGT 59.696 36.000 0.00 0.00 0.00 2.66
728 736 2.013400 GGCAACAAAGTTTTTGGTGGG 58.987 47.619 18.15 0.00 37.58 4.61
736 744 1.886542 AGTTTTTGGTGGGATTCGCTC 59.113 47.619 2.19 0.00 0.00 5.03
793 801 8.926715 AACAGATTCACCTACAAAAAGAAAAC 57.073 30.769 0.00 0.00 0.00 2.43
800 808 8.888579 TCACCTACAAAAAGAAAACAAAAACA 57.111 26.923 0.00 0.00 0.00 2.83
801 809 9.495572 TCACCTACAAAAAGAAAACAAAAACAT 57.504 25.926 0.00 0.00 0.00 2.71
847 856 2.322081 CGGGCCGTCACGAAACATT 61.322 57.895 19.97 0.00 0.00 2.71
885 894 0.740737 CCAGCAAGCCCTAATTTCCG 59.259 55.000 0.00 0.00 0.00 4.30
906 916 1.301479 CTATAAAGCCGCGACCCCC 60.301 63.158 8.23 0.00 0.00 5.40
1235 1245 1.035923 TGGATTTGCTGGTGCGAAAA 58.964 45.000 0.00 0.00 44.77 2.29
1279 1289 2.099062 GCTCGCGAATGGCTGTTG 59.901 61.111 11.33 0.00 40.44 3.33
1567 1582 3.568007 TCCATTTGGGCTGTATATTTCGC 59.432 43.478 0.00 0.00 36.21 4.70
1569 1584 4.022068 CCATTTGGGCTGTATATTTCGCAT 60.022 41.667 0.00 0.00 0.00 4.73
1579 1594 7.693951 GGCTGTATATTTCGCATTGATATTGTC 59.306 37.037 0.00 0.00 0.00 3.18
1591 1606 7.588854 CGCATTGATATTGTCTGTTATTTCTGG 59.411 37.037 0.00 0.00 0.00 3.86
1775 1794 5.005094 TGGGCGCTACATTAAAACTAAACT 58.995 37.500 7.64 0.00 0.00 2.66
1816 1835 4.640771 ATAATCTGCCCATTATGTCCGT 57.359 40.909 0.00 0.00 29.35 4.69
1864 1883 7.994425 AATTGTGGTTGATACAGTTACATGA 57.006 32.000 0.00 0.00 0.00 3.07
1908 2103 3.188254 TCGTTACATGTGTTGCCATCAAG 59.812 43.478 9.11 0.00 31.93 3.02
2095 2462 4.497006 GCCTTCATATGCTGTCATGTGTTC 60.497 45.833 0.00 0.00 41.05 3.18
2099 2466 5.195185 TCATATGCTGTCATGTGTTCCATT 58.805 37.500 0.00 0.00 41.05 3.16
2126 2493 6.599638 GGGCTCTACATTGAAACTAGATTGTT 59.400 38.462 0.00 0.00 0.00 2.83
2128 2495 8.604890 GGCTCTACATTGAAACTAGATTGTTAC 58.395 37.037 0.00 0.00 0.00 2.50
2157 2524 6.264528 TCTTATAGCTAGTCCATTATGCCCT 58.735 40.000 0.00 0.00 0.00 5.19
2263 2630 3.473625 CTGCCTTCATATGCTGTCATGA 58.526 45.455 0.00 0.00 34.22 3.07
2293 2660 4.508551 TGGGCACTACATTGAGATGAAT 57.491 40.909 0.00 0.00 36.73 2.57
2332 2700 8.345565 ACAATTGCTTTGTTTTGTTTGTGTTTA 58.654 25.926 5.05 0.00 46.51 2.01
2333 2701 9.339492 CAATTGCTTTGTTTTGTTTGTGTTTAT 57.661 25.926 0.00 0.00 0.00 1.40
2383 2751 5.301551 TGCTTGTGTTGTAATGTTCCATCTT 59.698 36.000 0.00 0.00 0.00 2.40
2443 2811 9.593134 CCTCTATTTGTATCTATCACTAATGGC 57.407 37.037 0.00 0.00 0.00 4.40
2599 2967 2.362369 CGGCATCAGGAGTGTCCCT 61.362 63.158 0.00 0.00 37.19 4.20
2647 3015 0.256464 AGAGGAACGACGAGGAGGAT 59.744 55.000 0.00 0.00 0.00 3.24
2932 3300 2.684001 TGTTGTTTGACTCTGGTCGT 57.316 45.000 0.00 0.00 44.83 4.34
2960 3344 6.705825 CGTCATTCCTTGTGATGATATTACCA 59.294 38.462 0.00 0.00 35.16 3.25
3014 3412 6.936279 AGGTTTGAGAATTCTTGATCGTAGA 58.064 36.000 9.87 0.00 45.75 2.59
3061 3459 4.309933 CAATGAGTTGAGATATGCGCCTA 58.690 43.478 4.18 0.00 37.53 3.93
3067 3465 6.102897 AGTTGAGATATGCGCCTAGTAAAT 57.897 37.500 4.18 0.00 0.00 1.40
3068 3466 6.159988 AGTTGAGATATGCGCCTAGTAAATC 58.840 40.000 4.18 0.00 0.00 2.17
3069 3467 4.733850 TGAGATATGCGCCTAGTAAATCG 58.266 43.478 4.18 0.00 0.00 3.34
3070 3468 4.217767 TGAGATATGCGCCTAGTAAATCGT 59.782 41.667 4.18 0.00 0.00 3.73
3073 3471 3.720949 ATGCGCCTAGTAAATCGTGTA 57.279 42.857 4.18 0.00 0.00 2.90
3074 3472 3.074504 TGCGCCTAGTAAATCGTGTAG 57.925 47.619 4.18 0.00 0.00 2.74
3075 3473 2.424601 TGCGCCTAGTAAATCGTGTAGT 59.575 45.455 4.18 0.00 0.00 2.73
3077 3475 3.485013 GCGCCTAGTAAATCGTGTAGTTC 59.515 47.826 0.00 0.00 0.00 3.01
3097 3786 6.343703 AGTTCTTGAAAGCAAAAGCTGAAAT 58.656 32.000 0.00 0.00 32.73 2.17
3111 3800 0.332632 TGAAATCCCCAGCTTCCCAG 59.667 55.000 0.00 0.00 0.00 4.45
3116 3820 2.935481 CCCAGCTTCCCAGGGTCA 60.935 66.667 5.01 0.00 37.81 4.02
3134 3838 0.101759 CAAGCAATTGAGGGGATGCG 59.898 55.000 10.34 0.00 43.39 4.73
3137 3841 0.749454 GCAATTGAGGGGATGCGTCT 60.749 55.000 10.34 0.00 0.00 4.18
3200 3905 1.417517 TGTGGTCAATGTGCAGAGAGT 59.582 47.619 0.00 0.00 0.00 3.24
3204 3909 3.244665 TGGTCAATGTGCAGAGAGTGATT 60.245 43.478 0.00 0.00 0.00 2.57
3219 3924 7.986320 CAGAGAGTGATTATCTTCCTGTCAATT 59.014 37.037 0.00 0.00 0.00 2.32
3231 3936 8.284945 TCTTCCTGTCAATTCATTCATTAAGG 57.715 34.615 0.00 0.00 0.00 2.69
3235 3940 7.890127 TCCTGTCAATTCATTCATTAAGGAACT 59.110 33.333 4.42 0.00 38.14 3.01
3247 3952 8.777865 TTCATTAAGGAACTGTACTCATCTTG 57.222 34.615 0.00 0.00 40.86 3.02
3248 3953 8.134202 TCATTAAGGAACTGTACTCATCTTGA 57.866 34.615 0.00 0.00 40.86 3.02
3272 3977 8.563732 TGACGTCAATTCATTCATTAAGAAACA 58.436 29.630 17.62 0.00 40.22 2.83
3274 3979 7.538678 ACGTCAATTCATTCATTAAGAAACAGC 59.461 33.333 0.00 0.00 40.22 4.40
3277 4149 8.366401 TCAATTCATTCATTAAGAAACAGCCAA 58.634 29.630 0.00 0.00 40.22 4.52
3284 4156 6.738114 TCATTAAGAAACAGCCAAAAGACAG 58.262 36.000 0.00 0.00 0.00 3.51
3293 4165 3.882888 CAGCCAAAAGACAGGAAACACTA 59.117 43.478 0.00 0.00 0.00 2.74
3381 4257 7.016465 CCTTCCTAGATGATCTTGAGAATTCCT 59.984 40.741 0.00 0.00 0.00 3.36
3383 4259 5.933463 CCTAGATGATCTTGAGAATTCCTGC 59.067 44.000 0.00 0.00 0.00 4.85
3432 4308 9.965902 ATGATTAATAAAGTCCACAAAGAGACT 57.034 29.630 0.00 0.00 45.18 3.24
3444 4320 5.722021 ACAAAGAGACTTTTGTGTGGTTT 57.278 34.783 12.16 0.00 46.44 3.27
3445 4321 5.709966 ACAAAGAGACTTTTGTGTGGTTTC 58.290 37.500 12.16 0.00 46.44 2.78
3446 4322 5.242838 ACAAAGAGACTTTTGTGTGGTTTCA 59.757 36.000 12.16 0.00 46.44 2.69
3493 4369 6.346279 CGTCGTAAGCAAATGAGTCTACAAAA 60.346 38.462 0.00 0.00 37.18 2.44
3571 4447 5.113383 TGTTTGGTATAGCATCTAACGTGG 58.887 41.667 5.28 0.00 0.00 4.94
3672 4551 6.256053 TGGAAAAGAATTTAGCTCCAAGGAT 58.744 36.000 0.00 0.00 38.99 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.778358 CAAATGGAGGATTTATAACAGAGTAGC 58.222 37.037 0.00 0.00 32.65 3.58
1 2 9.838339 ACAAATGGAGGATTTATAACAGAGTAG 57.162 33.333 0.00 0.00 32.65 2.57
3 4 9.614792 GTACAAATGGAGGATTTATAACAGAGT 57.385 33.333 0.00 0.00 32.65 3.24
4 5 9.838339 AGTACAAATGGAGGATTTATAACAGAG 57.162 33.333 0.00 0.00 32.65 3.35
5 6 9.613428 CAGTACAAATGGAGGATTTATAACAGA 57.387 33.333 0.00 0.00 32.65 3.41
6 7 9.396022 ACAGTACAAATGGAGGATTTATAACAG 57.604 33.333 0.00 0.00 32.65 3.16
7 8 9.173021 CACAGTACAAATGGAGGATTTATAACA 57.827 33.333 0.00 0.00 32.65 2.41
8 9 8.621286 CCACAGTACAAATGGAGGATTTATAAC 58.379 37.037 4.47 0.00 35.33 1.89
9 10 8.333235 ACCACAGTACAAATGGAGGATTTATAA 58.667 33.333 14.90 0.00 36.94 0.98
10 11 7.773224 CACCACAGTACAAATGGAGGATTTATA 59.227 37.037 14.90 0.00 36.94 0.98
11 12 6.603201 CACCACAGTACAAATGGAGGATTTAT 59.397 38.462 14.90 0.00 36.94 1.40
12 13 5.943416 CACCACAGTACAAATGGAGGATTTA 59.057 40.000 14.90 0.00 36.94 1.40
13 14 4.766891 CACCACAGTACAAATGGAGGATTT 59.233 41.667 14.90 0.00 36.94 2.17
14 15 4.202567 ACACCACAGTACAAATGGAGGATT 60.203 41.667 14.90 0.00 36.94 3.01
15 16 3.330701 ACACCACAGTACAAATGGAGGAT 59.669 43.478 14.90 0.00 36.94 3.24
16 17 2.708861 ACACCACAGTACAAATGGAGGA 59.291 45.455 14.90 0.00 36.94 3.71
17 18 3.074412 GACACCACAGTACAAATGGAGG 58.926 50.000 14.90 9.68 36.94 4.30
18 19 3.738982 TGACACCACAGTACAAATGGAG 58.261 45.455 14.90 10.36 36.94 3.86
19 20 3.738982 CTGACACCACAGTACAAATGGA 58.261 45.455 14.90 0.00 36.94 3.41
20 21 2.226437 GCTGACACCACAGTACAAATGG 59.774 50.000 8.16 8.16 39.73 3.16
21 22 2.877786 TGCTGACACCACAGTACAAATG 59.122 45.455 0.00 0.00 39.73 2.32
22 23 3.207265 TGCTGACACCACAGTACAAAT 57.793 42.857 0.00 0.00 39.73 2.32
23 24 2.700722 TGCTGACACCACAGTACAAA 57.299 45.000 0.00 0.00 39.73 2.83
24 25 2.928801 ATGCTGACACCACAGTACAA 57.071 45.000 0.00 0.00 39.73 2.41
25 26 2.928801 AATGCTGACACCACAGTACA 57.071 45.000 0.00 0.00 39.73 2.90
26 27 3.926616 AGTAATGCTGACACCACAGTAC 58.073 45.455 0.00 0.00 39.73 2.73
38 39 3.072038 TCATCCCTGGATCAGTAATGCTG 59.928 47.826 0.00 0.00 46.34 4.41
39 40 3.072184 GTCATCCCTGGATCAGTAATGCT 59.928 47.826 0.00 0.00 31.62 3.79
40 41 3.181451 TGTCATCCCTGGATCAGTAATGC 60.181 47.826 0.00 0.00 31.62 3.56
41 42 4.102210 AGTGTCATCCCTGGATCAGTAATG 59.898 45.833 0.00 0.00 31.62 1.90
42 43 4.102210 CAGTGTCATCCCTGGATCAGTAAT 59.898 45.833 0.00 0.00 31.62 1.89
43 44 3.452264 CAGTGTCATCCCTGGATCAGTAA 59.548 47.826 0.00 0.00 31.62 2.24
44 45 3.033909 CAGTGTCATCCCTGGATCAGTA 58.966 50.000 0.00 0.00 31.62 2.74
45 46 1.836166 CAGTGTCATCCCTGGATCAGT 59.164 52.381 0.00 0.00 31.62 3.41
46 47 2.616634 CAGTGTCATCCCTGGATCAG 57.383 55.000 0.00 0.00 31.62 2.90
52 53 0.957395 GTGCACCAGTGTCATCCCTG 60.957 60.000 5.22 0.00 0.00 4.45
53 54 1.376466 GTGCACCAGTGTCATCCCT 59.624 57.895 5.22 0.00 0.00 4.20
54 55 0.957395 CTGTGCACCAGTGTCATCCC 60.957 60.000 15.69 0.00 36.37 3.85
55 56 1.580845 GCTGTGCACCAGTGTCATCC 61.581 60.000 15.69 0.00 43.55 3.51
56 57 0.886043 TGCTGTGCACCAGTGTCATC 60.886 55.000 15.69 0.00 43.55 2.92
57 58 0.887836 CTGCTGTGCACCAGTGTCAT 60.888 55.000 15.69 0.00 43.55 3.06
58 59 1.524393 CTGCTGTGCACCAGTGTCA 60.524 57.895 15.69 4.95 43.55 3.58
59 60 2.901292 GCTGCTGTGCACCAGTGTC 61.901 63.158 19.98 4.77 43.55 3.67
60 61 2.903855 GCTGCTGTGCACCAGTGT 60.904 61.111 19.98 0.00 43.55 3.55
61 62 2.903350 TGCTGCTGTGCACCAGTG 60.903 61.111 19.98 12.80 43.55 3.66
67 68 1.890510 CAGTCTGTGCTGCTGTGCA 60.891 57.895 0.00 0.00 41.05 4.57
68 69 1.442526 AACAGTCTGTGCTGCTGTGC 61.443 55.000 6.18 0.00 41.94 4.57
69 70 1.019673 AAACAGTCTGTGCTGCTGTG 58.980 50.000 6.18 0.00 41.94 3.66
70 71 1.019673 CAAACAGTCTGTGCTGCTGT 58.980 50.000 6.18 0.00 44.31 4.40
71 72 1.263484 CTCAAACAGTCTGTGCTGCTG 59.737 52.381 6.18 0.18 39.96 4.41
72 73 1.590932 CTCAAACAGTCTGTGCTGCT 58.409 50.000 6.18 0.00 39.96 4.24
73 74 0.590195 CCTCAAACAGTCTGTGCTGC 59.410 55.000 6.18 0.00 39.96 5.25
74 75 1.869767 GACCTCAAACAGTCTGTGCTG 59.130 52.381 6.18 7.57 41.92 4.41
75 76 1.765314 AGACCTCAAACAGTCTGTGCT 59.235 47.619 6.18 0.00 41.74 4.40
76 77 2.246719 AGACCTCAAACAGTCTGTGC 57.753 50.000 6.18 0.00 41.74 4.57
80 81 1.341531 CGACCAGACCTCAAACAGTCT 59.658 52.381 0.00 0.00 44.12 3.24
81 82 1.784525 CGACCAGACCTCAAACAGTC 58.215 55.000 0.00 0.00 0.00 3.51
82 83 0.249911 GCGACCAGACCTCAAACAGT 60.250 55.000 0.00 0.00 0.00 3.55
83 84 0.034059 AGCGACCAGACCTCAAACAG 59.966 55.000 0.00 0.00 0.00 3.16
84 85 1.000506 GTAGCGACCAGACCTCAAACA 59.999 52.381 0.00 0.00 0.00 2.83
85 86 1.000506 TGTAGCGACCAGACCTCAAAC 59.999 52.381 0.00 0.00 0.00 2.93
86 87 1.334160 TGTAGCGACCAGACCTCAAA 58.666 50.000 0.00 0.00 0.00 2.69
87 88 1.476891 GATGTAGCGACCAGACCTCAA 59.523 52.381 0.00 0.00 0.00 3.02
88 89 1.103803 GATGTAGCGACCAGACCTCA 58.896 55.000 0.00 0.00 0.00 3.86
89 90 0.386113 GGATGTAGCGACCAGACCTC 59.614 60.000 0.00 0.00 0.00 3.85
90 91 1.043673 GGGATGTAGCGACCAGACCT 61.044 60.000 0.00 0.00 0.00 3.85
91 92 1.327690 TGGGATGTAGCGACCAGACC 61.328 60.000 0.00 0.00 0.00 3.85
92 93 0.753262 ATGGGATGTAGCGACCAGAC 59.247 55.000 0.00 0.00 36.27 3.51
93 94 0.752658 CATGGGATGTAGCGACCAGA 59.247 55.000 0.00 0.00 36.27 3.86
94 95 0.250038 CCATGGGATGTAGCGACCAG 60.250 60.000 2.85 0.00 36.27 4.00
95 96 0.980754 ACCATGGGATGTAGCGACCA 60.981 55.000 18.09 0.00 37.41 4.02
96 97 1.045407 TACCATGGGATGTAGCGACC 58.955 55.000 18.09 0.00 0.00 4.79
97 98 2.612972 CCATACCATGGGATGTAGCGAC 60.613 54.545 31.15 0.00 46.86 5.19
98 99 1.623311 CCATACCATGGGATGTAGCGA 59.377 52.381 31.15 0.00 46.86 4.93
99 100 2.099141 CCATACCATGGGATGTAGCG 57.901 55.000 31.15 15.15 46.86 4.26
119 120 2.667481 CCGCCGTACTCGAAAATGTTTA 59.333 45.455 6.05 0.00 39.71 2.01
170 171 2.507324 GCTCTCGCCACGGACTTC 60.507 66.667 0.00 0.00 0.00 3.01
193 194 1.842381 AAGGGTTGGCGGGAGAGAAG 61.842 60.000 0.00 0.00 0.00 2.85
197 198 0.825840 CAAAAAGGGTTGGCGGGAGA 60.826 55.000 0.00 0.00 0.00 3.71
210 211 3.741075 GCAGGGTCCTCCAAAACAAAAAG 60.741 47.826 0.00 0.00 38.24 2.27
222 225 1.539157 CCTCTTTTTGCAGGGTCCTC 58.461 55.000 0.00 0.00 0.00 3.71
252 255 2.223758 GGGCCGAATCCGCTATATCTAC 60.224 54.545 0.00 0.00 0.00 2.59
270 273 0.603975 GGATCCTGCATAGTTCGGGC 60.604 60.000 3.84 0.00 0.00 6.13
306 309 5.869344 CGAACAGATCCTGTAAAATCACTCA 59.131 40.000 0.00 0.00 44.62 3.41
336 339 0.894835 GTGGATGGGTGCCGATTTTT 59.105 50.000 0.00 0.00 0.00 1.94
431 434 7.973388 CGTCCAATTTGCTATTATTCTTTTCCA 59.027 33.333 0.00 0.00 0.00 3.53
432 435 8.188139 TCGTCCAATTTGCTATTATTCTTTTCC 58.812 33.333 0.00 0.00 0.00 3.13
433 436 9.736023 ATCGTCCAATTTGCTATTATTCTTTTC 57.264 29.630 0.00 0.00 0.00 2.29
638 646 2.517959 TCTGGCTGGAAAAATGGAGTG 58.482 47.619 0.00 0.00 0.00 3.51
695 703 4.214758 ACTTTGTTGCCGGTAGTTTGATAC 59.785 41.667 1.90 0.00 0.00 2.24
696 704 4.391155 ACTTTGTTGCCGGTAGTTTGATA 58.609 39.130 1.90 0.00 0.00 2.15
728 736 2.043980 TTTTGGGCCCGAGCGAATC 61.044 57.895 19.37 0.00 41.24 2.52
736 744 1.227409 GTGTTTGGTTTTGGGCCCG 60.227 57.895 19.37 0.00 0.00 6.13
792 800 5.759506 TCGTCCATGTGTTATGTTTTTGT 57.240 34.783 0.00 0.00 0.00 2.83
793 801 5.629020 CCTTCGTCCATGTGTTATGTTTTTG 59.371 40.000 0.00 0.00 0.00 2.44
799 807 1.670811 GCCCTTCGTCCATGTGTTATG 59.329 52.381 0.00 0.00 0.00 1.90
800 808 1.408266 GGCCCTTCGTCCATGTGTTAT 60.408 52.381 0.00 0.00 0.00 1.89
801 809 0.035820 GGCCCTTCGTCCATGTGTTA 60.036 55.000 0.00 0.00 0.00 2.41
802 810 1.303317 GGCCCTTCGTCCATGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
804 812 0.462047 GTAGGCCCTTCGTCCATGTG 60.462 60.000 0.00 0.00 0.00 3.21
805 813 0.617820 AGTAGGCCCTTCGTCCATGT 60.618 55.000 0.00 0.00 0.00 3.21
806 814 0.541863 AAGTAGGCCCTTCGTCCATG 59.458 55.000 0.00 0.00 0.00 3.66
847 856 3.965026 CTGACTGGGCCTCTCCGGA 62.965 68.421 2.93 2.93 36.97 5.14
885 894 1.959738 GGTCGCGGCTTTATAGGGC 60.960 63.158 11.94 0.00 0.00 5.19
906 916 4.785453 GGGAAGGCCAGGTCGCAG 62.785 72.222 5.01 0.00 35.15 5.18
1098 1108 2.689034 GTGGGTGAGGAGGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
1144 1154 4.076394 GGAATCTGACTAGCGGATCTACT 58.924 47.826 8.38 0.00 41.80 2.57
1267 1277 1.210931 CAGGTGCAACAGCCATTCG 59.789 57.895 3.64 0.00 39.98 3.34
1279 1289 2.808543 GGATTTCGATCCATACAGGTGC 59.191 50.000 0.00 0.00 40.43 5.01
1356 1366 4.471025 TGGGATCAGATACAAGAGCAGAAA 59.529 41.667 0.00 0.00 0.00 2.52
1388 1399 2.492088 ACAGATCGAAGATCCACGTGAA 59.508 45.455 19.30 0.00 45.12 3.18
1389 1400 2.092323 ACAGATCGAAGATCCACGTGA 58.908 47.619 19.30 3.36 45.12 4.35
1611 1630 8.466798 GGTACAATTGCTCAATAAACTTACCAT 58.533 33.333 5.05 0.00 0.00 3.55
1613 1632 7.255569 GGGTACAATTGCTCAATAAACTTACC 58.744 38.462 5.05 5.26 0.00 2.85
1627 1646 2.870411 GACTATGTCCGGGTACAATTGC 59.130 50.000 5.05 0.00 32.02 3.56
1630 1649 2.698797 CCTGACTATGTCCGGGTACAAT 59.301 50.000 0.00 0.00 34.10 2.71
1793 1812 5.488341 ACGGACATAATGGGCAGATTATAC 58.512 41.667 1.86 1.09 29.16 1.47
1864 1883 4.481368 TGAGCAACATCTATTTACCGGT 57.519 40.909 13.98 13.98 0.00 5.28
1908 2103 4.762825 TGGAACACGTGGTAGCAC 57.237 55.556 21.57 15.12 0.00 4.40
1965 2160 2.553028 CCGGGCATAATGGACAAGCTAT 60.553 50.000 0.00 0.00 0.00 2.97
2063 2430 1.747355 GCATATGAAGGCAGCAAGTGT 59.253 47.619 6.97 0.00 31.14 3.55
2095 2462 4.463891 AGTTTCAATGTAGAGCCCAAATGG 59.536 41.667 0.00 0.00 37.09 3.16
2099 2466 5.755409 TCTAGTTTCAATGTAGAGCCCAA 57.245 39.130 0.00 0.00 0.00 4.12
2128 2495 9.311916 GCATAATGGACTAGCTATAAGATCAAG 57.688 37.037 0.00 0.00 0.00 3.02
2157 2524 8.589701 TTAAAGACAGATACCTGACTATGACA 57.410 34.615 0.00 0.00 42.87 3.58
2263 2630 2.969821 TGTAGTGCCCAAATGGAACT 57.030 45.000 0.00 6.96 37.39 3.01
2383 2751 5.360714 ACCACAAAGAAAGCATGAGAAAGAA 59.639 36.000 0.00 0.00 0.00 2.52
2431 2799 9.851686 AATAGAATGAAGTTGCCATTAGTGATA 57.148 29.630 0.00 0.00 34.67 2.15
2443 2811 6.072286 AGGTGCTGTTCAATAGAATGAAGTTG 60.072 38.462 0.00 0.00 39.84 3.16
2445 2813 5.564550 AGGTGCTGTTCAATAGAATGAAGT 58.435 37.500 0.00 0.00 39.84 3.01
2599 2967 0.989602 TCCTGACACGGACTCTCCTA 59.010 55.000 0.00 0.00 33.30 2.94
2647 3015 2.024846 AGAGTACAGCTCCTCCTTAGCA 60.025 50.000 0.00 0.00 45.21 3.49
2932 3300 3.694043 TCATCACAAGGAATGACGGAA 57.306 42.857 0.00 0.00 0.00 4.30
2960 3344 4.678256 TCCTAGAGTTCACCAGTCTCAAT 58.322 43.478 0.00 0.00 36.49 2.57
3014 3412 6.176183 CCACAAGTGAGTTCCTCATTAAGAT 58.824 40.000 0.94 0.00 42.73 2.40
3032 3430 5.732528 GCATATCTCAACTCATTGCCACAAG 60.733 44.000 0.00 0.00 35.63 3.16
3061 3459 6.704493 TGCTTTCAAGAACTACACGATTTACT 59.296 34.615 0.00 0.00 0.00 2.24
3067 3465 5.729454 GCTTTTGCTTTCAAGAACTACACGA 60.729 40.000 0.00 0.00 43.35 4.35
3068 3466 4.437820 GCTTTTGCTTTCAAGAACTACACG 59.562 41.667 0.00 0.00 43.35 4.49
3069 3467 5.873211 GCTTTTGCTTTCAAGAACTACAC 57.127 39.130 0.00 0.00 43.35 2.90
3097 3786 4.285790 ACCCTGGGAAGCTGGGGA 62.286 66.667 22.23 0.00 44.97 4.81
3111 3800 0.039618 TCCCCTCAATTGCTTGACCC 59.960 55.000 0.00 0.00 36.46 4.46
3116 3820 0.323725 ACGCATCCCCTCAATTGCTT 60.324 50.000 0.00 0.00 32.97 3.91
3134 3838 4.454678 TGATCATCCACATTTGGCTAGAC 58.545 43.478 0.00 0.00 43.56 2.59
3137 3841 6.545567 ACATATGATCATCCACATTTGGCTA 58.454 36.000 12.53 0.00 43.56 3.93
3142 3846 7.389884 GCTGTCTACATATGATCATCCACATTT 59.610 37.037 12.53 0.00 0.00 2.32
3165 3870 2.164219 GACCACAATTGTACCATGGCTG 59.836 50.000 13.04 2.40 33.46 4.85
3188 3893 5.366186 AGGAAGATAATCACTCTCTGCACAT 59.634 40.000 0.00 0.00 0.00 3.21
3189 3894 4.713814 AGGAAGATAATCACTCTCTGCACA 59.286 41.667 0.00 0.00 0.00 4.57
3190 3895 5.049167 CAGGAAGATAATCACTCTCTGCAC 58.951 45.833 0.00 0.00 0.00 4.57
3200 3905 9.636789 ATGAATGAATTGACAGGAAGATAATCA 57.363 29.630 0.00 0.00 0.00 2.57
3219 3924 8.762645 AGATGAGTACAGTTCCTTAATGAATGA 58.237 33.333 0.00 0.00 0.00 2.57
3228 3933 4.281182 ACGTCAAGATGAGTACAGTTCCTT 59.719 41.667 0.00 0.00 0.00 3.36
3231 3936 4.795268 TGACGTCAAGATGAGTACAGTTC 58.205 43.478 17.62 0.00 0.00 3.01
3235 3940 5.778862 TGAATTGACGTCAAGATGAGTACA 58.221 37.500 32.19 19.41 39.47 2.90
3247 3952 8.948853 TGTTTCTTAATGAATGAATTGACGTC 57.051 30.769 9.11 9.11 34.24 4.34
3248 3953 7.538678 GCTGTTTCTTAATGAATGAATTGACGT 59.461 33.333 0.00 0.00 34.24 4.34
3272 3977 3.018423 AGTGTTTCCTGTCTTTTGGCT 57.982 42.857 0.00 0.00 0.00 4.75
3274 3979 6.391227 ACATTAGTGTTTCCTGTCTTTTGG 57.609 37.500 0.00 0.00 34.01 3.28
3293 4165 3.462021 GCTAGAAGCTCATCCGAACATT 58.538 45.455 0.00 0.00 38.45 2.71
3381 4257 5.804639 AGGAATATTATAATCTGCCACGCA 58.195 37.500 9.89 0.00 36.92 5.24
3383 4259 9.599866 TCATTAGGAATATTATAATCTGCCACG 57.400 33.333 9.89 0.00 0.00 4.94
3437 4313 4.219725 TCGATGATAGAGTGTGAAACCACA 59.780 41.667 0.00 0.00 41.81 4.17
3438 4314 4.744570 TCGATGATAGAGTGTGAAACCAC 58.255 43.478 0.00 0.00 34.36 4.16
3439 4315 4.462834 ACTCGATGATAGAGTGTGAAACCA 59.537 41.667 7.42 0.00 46.12 3.67
3450 4326 3.246936 CGACGGTGTAACTCGATGATAGA 59.753 47.826 0.00 0.00 36.74 1.98
3493 4369 4.022242 CCGAGGTCGATATGATTACCACTT 60.022 45.833 0.00 0.00 43.02 3.16
3571 4447 6.293955 CCATTCGAATTGGATGTTATACCACC 60.294 42.308 8.21 0.00 35.81 4.61
3694 4573 4.322057 AACCTGGCTGATTTTCCAGTAT 57.678 40.909 7.41 0.00 46.43 2.12


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

AutoCloner maintained by Alex Coulton.