Multiple sequence alignment - TraesCS1D01G204400

Loading Multiple Alignment...

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 TraesCS1D01G204400 chr1D 100.000 4747 0 0 1 4747 289601439 289596693 0.000000e+00 8767.0
1 TraesCS1D01G204400 chr1D 99.177 851 6 1 3897 4747 289575315 289574466 0.000000e+00 1531.0
2 TraesCS1D01G204400 chr1D 99.095 663 5 1 3897 4558 289532327 289531665 0.000000e+00 1190.0
3 TraesCS1D01G204400 chr1D 97.396 192 3 1 4556 4747 289519656 289519467 4.580000e-85 326.0
4 TraesCS1D01G204400 chr1B 96.277 1746 41 10 743 2477 390882603 390880871 0.000000e+00 2843.0
5 TraesCS1D01G204400 chr1B 93.964 1756 41 17 2472 4192 390880840 390879115 0.000000e+00 2595.0
6 TraesCS1D01G204400 chr1B 90.036 562 22 14 4188 4747 390878835 390878306 0.000000e+00 697.0
7 TraesCS1D01G204400 chr1B 86.292 569 59 12 119 684 390883288 390882736 6.800000e-168 601.0
8 TraesCS1D01G204400 chr1B 87.629 194 19 5 1 190 384503299 384503491 2.220000e-53 220.0
9 TraesCS1D01G204400 chr1B 98.387 62 1 0 686 747 390882692 390882631 5.020000e-20 110.0
10 TraesCS1D01G204400 chr1A 95.542 1660 46 9 825 2477 362063311 362061673 0.000000e+00 2630.0
11 TraesCS1D01G204400 chr1A 95.728 1381 28 6 2472 3848 362061642 362060289 0.000000e+00 2194.0
12 TraesCS1D01G204400 chr1A 96.008 501 13 4 3821 4314 362060241 362059741 0.000000e+00 808.0
13 TraesCS1D01G204400 chr1A 93.189 323 14 4 4430 4747 362059743 362059424 7.190000e-128 468.0
14 TraesCS1D01G204400 chr1A 83.948 461 65 6 119 577 362065836 362065383 2.620000e-117 433.0
15 TraesCS1D01G204400 chr1A 100.000 28 0 0 3821 3848 362060291 362060264 9.000000e-03 52.8
16 TraesCS1D01G204400 chr2D 82.938 674 47 20 2483 3151 107864357 107864967 3.230000e-151 545.0
17 TraesCS1D01G204400 chr2D 94.512 164 4 3 3952 4111 526525121 526524959 1.020000e-61 248.0
18 TraesCS1D01G204400 chr3B 92.941 170 7 3 3948 4113 428703827 428703659 4.750000e-60 243.0
19 TraesCS1D01G204400 chr3B 92.727 165 8 3 3949 4112 763799399 763799560 7.940000e-58 235.0
20 TraesCS1D01G204400 chr4D 89.062 192 18 3 1 190 22882882 22882692 7.940000e-58 235.0
21 TraesCS1D01G204400 chr4D 89.062 192 18 3 1 189 501031541 501031732 7.940000e-58 235.0
22 TraesCS1D01G204400 chr2B 92.814 167 5 5 3952 4112 769078169 769078004 7.940000e-58 235.0
23 TraesCS1D01G204400 chr6D 88.947 190 20 1 1 189 457524425 457524614 2.860000e-57 233.0
24 TraesCS1D01G204400 chr5D 88.718 195 16 5 1 190 200525468 200525275 2.860000e-57 233.0
25 TraesCS1D01G204400 chr5D 87.374 198 20 5 1 193 315161772 315161969 6.180000e-54 222.0
26 TraesCS1D01G204400 chr7B 88.205 195 18 3 1 190 223758843 223758649 1.330000e-55 228.0
27 TraesCS1D01G204400 chr6B 90.395 177 11 4 3949 4120 548811082 548811257 1.330000e-55 228.0
28 TraesCS1D01G204400 chr5A 88.144 194 19 3 1 190 174344179 174344372 1.330000e-55 228.0
29 TraesCS1D01G204400 chr3D 88.360 189 20 2 1 188 355298684 355298871 4.780000e-55 226.0
30 TraesCS1D01G204400 chr5B 94.444 36 2 0 3360 3395 582974081 582974116 6.640000e-04 56.5


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 TraesCS1D01G204400 chr1D 289596693 289601439 4746 True 8767.000000 8767 100.000000 1 4747 1 chr1D.!!$R4 4746
1 TraesCS1D01G204400 chr1D 289574466 289575315 849 True 1531.000000 1531 99.177000 3897 4747 1 chr1D.!!$R3 850
2 TraesCS1D01G204400 chr1D 289531665 289532327 662 True 1190.000000 1190 99.095000 3897 4558 1 chr1D.!!$R2 661
3 TraesCS1D01G204400 chr1B 390878306 390883288 4982 True 1369.200000 2843 92.991200 119 4747 5 chr1B.!!$R1 4628
4 TraesCS1D01G204400 chr1A 362059424 362065836 6412 True 1097.633333 2630 94.069167 119 4747 6 chr1A.!!$R1 4628
5 TraesCS1D01G204400 chr2D 107864357 107864967 610 False 545.000000 545 82.938000 2483 3151 1 chr2D.!!$F1 668

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
21 22 0.035439 TTGACAATCCTCTTCCCCGC 60.035 55.0 0.00 0.0 0.00 6.13 F
84 85 0.387929 TTTGTTCGCGTGAGTCTCCT 59.612 50.0 5.77 0.0 0.00 3.69 F
215 216 0.394216 CTGGCGATGGGAAATGACCA 60.394 55.0 0.00 0.0 43.22 4.02 F
448 451 0.403271 ACTGCTTGCCATGAAGAGGT 59.597 50.0 0.00 0.0 0.00 3.85 F
535 538 0.456312 GGAGATATAACCGGCGAGCG 60.456 60.0 9.30 0.0 0.00 5.03 F
1569 3586 0.478072 AGGAACATGGACCTGCACAA 59.522 50.0 11.28 0.0 34.99 3.33 F
2432 4452 0.663153 GATTCACCCTAACCATGCGC 59.337 55.0 0.00 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 3449 1.072965 GTTGATGGATGCCCCTAGAGG 59.927 57.143 0.00 0.00 35.38 3.69 R
1976 3995 1.135460 GCAGCTTTTCCTGATCAGTGC 60.135 52.381 21.11 17.29 34.77 4.40 R
2337 4357 5.613329 AGGAAGCAATCAAAAGCAAAATCA 58.387 33.333 0.00 0.00 0.00 2.57 R
2577 4634 0.772384 TTTTGGGCCGTTCCTCCTAA 59.228 50.000 0.00 0.00 34.39 2.69 R
2745 4802 1.550072 TCATCGGTCAGATCAGCAACA 59.450 47.619 0.00 0.00 37.52 3.33 R
3424 5488 2.026169 AGTCGATCCAGTCTCCACTACA 60.026 50.000 0.00 0.00 0.00 2.74 R
4510 6950 1.337447 TGTACAAGTCCGGCTGCTAAC 60.337 52.381 0.00 0.00 0.00 2.34 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
20 21 2.565841 GATTGACAATCCTCTTCCCCG 58.434 52.381 16.06 0.00 31.60 5.73
21 22 0.035439 TTGACAATCCTCTTCCCCGC 60.035 55.000 0.00 0.00 0.00 6.13
22 23 1.521681 GACAATCCTCTTCCCCGCG 60.522 63.158 0.00 0.00 0.00 6.46
23 24 2.240162 GACAATCCTCTTCCCCGCGT 62.240 60.000 4.92 0.00 0.00 6.01
24 25 1.078426 CAATCCTCTTCCCCGCGTT 60.078 57.895 4.92 0.00 0.00 4.84
25 26 1.078426 AATCCTCTTCCCCGCGTTG 60.078 57.895 4.92 0.00 0.00 4.10
26 27 2.536997 AATCCTCTTCCCCGCGTTGG 62.537 60.000 4.92 5.31 37.55 3.77
35 36 2.666862 CCGCGTTGGGTGCAAGTA 60.667 61.111 4.92 0.00 0.00 2.24
36 37 2.038269 CCGCGTTGGGTGCAAGTAT 61.038 57.895 4.92 0.00 0.00 2.12
37 38 1.582610 CCGCGTTGGGTGCAAGTATT 61.583 55.000 4.92 0.00 0.00 1.89
53 54 5.747565 CAAGTATTGTTGTGTGTGTGTAGG 58.252 41.667 0.00 0.00 42.34 3.18
54 55 5.031066 AGTATTGTTGTGTGTGTGTAGGT 57.969 39.130 0.00 0.00 0.00 3.08
55 56 6.164417 AGTATTGTTGTGTGTGTGTAGGTA 57.836 37.500 0.00 0.00 0.00 3.08
56 57 5.987347 AGTATTGTTGTGTGTGTGTAGGTAC 59.013 40.000 0.00 0.00 0.00 3.34
57 58 4.475051 TTGTTGTGTGTGTGTAGGTACT 57.525 40.909 0.00 0.00 46.37 2.73
58 59 3.787785 TGTTGTGTGTGTGTAGGTACTG 58.212 45.455 0.00 0.00 41.52 2.74
59 60 3.196039 TGTTGTGTGTGTGTAGGTACTGT 59.804 43.478 0.00 0.00 41.52 3.55
60 61 4.186159 GTTGTGTGTGTGTAGGTACTGTT 58.814 43.478 0.00 0.00 41.52 3.16
61 62 3.787785 TGTGTGTGTGTAGGTACTGTTG 58.212 45.455 0.00 0.00 41.52 3.33
62 63 3.447944 TGTGTGTGTGTAGGTACTGTTGA 59.552 43.478 0.00 0.00 41.52 3.18
63 64 3.800506 GTGTGTGTGTAGGTACTGTTGAC 59.199 47.826 0.00 0.00 41.52 3.18
64 65 3.447944 TGTGTGTGTAGGTACTGTTGACA 59.552 43.478 0.00 0.00 41.52 3.58
65 66 4.100344 TGTGTGTGTAGGTACTGTTGACAT 59.900 41.667 0.00 0.00 41.52 3.06
66 67 5.054477 GTGTGTGTAGGTACTGTTGACATT 58.946 41.667 0.00 0.00 41.52 2.71
67 68 5.526111 GTGTGTGTAGGTACTGTTGACATTT 59.474 40.000 0.00 0.00 41.52 2.32
68 69 5.525745 TGTGTGTAGGTACTGTTGACATTTG 59.474 40.000 0.00 0.00 41.52 2.32
69 70 5.526111 GTGTGTAGGTACTGTTGACATTTGT 59.474 40.000 0.00 0.00 41.52 2.83
70 71 6.037830 GTGTGTAGGTACTGTTGACATTTGTT 59.962 38.462 0.00 0.00 41.52 2.83
71 72 6.259167 TGTGTAGGTACTGTTGACATTTGTTC 59.741 38.462 0.00 0.00 41.52 3.18
72 73 5.464057 TGTAGGTACTGTTGACATTTGTTCG 59.536 40.000 0.00 0.00 41.52 3.95
73 74 3.250040 AGGTACTGTTGACATTTGTTCGC 59.750 43.478 0.00 0.00 37.18 4.70
74 75 2.383298 ACTGTTGACATTTGTTCGCG 57.617 45.000 0.00 0.00 0.00 5.87
75 76 1.668751 ACTGTTGACATTTGTTCGCGT 59.331 42.857 5.77 0.00 0.00 6.01
76 77 2.036217 CTGTTGACATTTGTTCGCGTG 58.964 47.619 5.77 0.00 0.00 5.34
77 78 1.666189 TGTTGACATTTGTTCGCGTGA 59.334 42.857 5.77 0.00 0.00 4.35
78 79 2.286125 TGTTGACATTTGTTCGCGTGAG 60.286 45.455 5.77 0.00 0.00 3.51
79 80 1.577468 TGACATTTGTTCGCGTGAGT 58.423 45.000 5.77 0.00 0.00 3.41
80 81 1.525197 TGACATTTGTTCGCGTGAGTC 59.475 47.619 5.77 2.81 0.00 3.36
81 82 1.792949 GACATTTGTTCGCGTGAGTCT 59.207 47.619 5.77 0.00 0.00 3.24
82 83 1.792949 ACATTTGTTCGCGTGAGTCTC 59.207 47.619 5.77 0.00 0.00 3.36
83 84 1.126846 CATTTGTTCGCGTGAGTCTCC 59.873 52.381 5.77 0.00 0.00 3.71
84 85 0.387929 TTTGTTCGCGTGAGTCTCCT 59.612 50.000 5.77 0.00 0.00 3.69
85 86 1.241165 TTGTTCGCGTGAGTCTCCTA 58.759 50.000 5.77 0.00 0.00 2.94
86 87 0.520404 TGTTCGCGTGAGTCTCCTAC 59.480 55.000 5.77 0.00 0.00 3.18
87 88 0.803740 GTTCGCGTGAGTCTCCTACT 59.196 55.000 5.77 0.00 42.80 2.57
88 89 0.803117 TTCGCGTGAGTCTCCTACTG 59.197 55.000 5.77 0.00 39.07 2.74
89 90 1.025113 TCGCGTGAGTCTCCTACTGG 61.025 60.000 5.77 0.00 39.07 4.00
90 91 1.306642 CGCGTGAGTCTCCTACTGGT 61.307 60.000 0.00 0.00 39.07 4.00
91 92 0.889306 GCGTGAGTCTCCTACTGGTT 59.111 55.000 0.00 0.00 39.07 3.67
92 93 1.135344 GCGTGAGTCTCCTACTGGTTC 60.135 57.143 0.00 0.00 39.07 3.62
93 94 2.160205 CGTGAGTCTCCTACTGGTTCA 58.840 52.381 0.00 0.00 39.07 3.18
94 95 2.557056 CGTGAGTCTCCTACTGGTTCAA 59.443 50.000 0.00 0.00 39.07 2.69
95 96 3.193691 CGTGAGTCTCCTACTGGTTCAAT 59.806 47.826 0.00 0.00 39.07 2.57
96 97 4.398358 CGTGAGTCTCCTACTGGTTCAATA 59.602 45.833 0.00 0.00 39.07 1.90
97 98 5.449314 CGTGAGTCTCCTACTGGTTCAATAG 60.449 48.000 0.00 0.00 39.07 1.73
98 99 4.402793 TGAGTCTCCTACTGGTTCAATAGC 59.597 45.833 0.00 0.00 39.07 2.97
99 100 3.707102 AGTCTCCTACTGGTTCAATAGCC 59.293 47.826 0.00 0.00 36.93 3.93
100 101 3.707102 GTCTCCTACTGGTTCAATAGCCT 59.293 47.826 0.00 0.00 34.23 4.58
101 102 4.162509 GTCTCCTACTGGTTCAATAGCCTT 59.837 45.833 0.00 0.00 34.23 4.35
102 103 4.162320 TCTCCTACTGGTTCAATAGCCTTG 59.838 45.833 0.00 0.00 34.23 3.61
103 104 3.199946 TCCTACTGGTTCAATAGCCTTGG 59.800 47.826 0.00 0.00 34.23 3.61
104 105 3.054361 CCTACTGGTTCAATAGCCTTGGT 60.054 47.826 0.00 0.00 0.00 3.67
105 106 3.525800 ACTGGTTCAATAGCCTTGGTT 57.474 42.857 0.00 0.00 0.00 3.67
106 107 3.421844 ACTGGTTCAATAGCCTTGGTTC 58.578 45.455 0.00 0.00 0.00 3.62
107 108 3.074538 ACTGGTTCAATAGCCTTGGTTCT 59.925 43.478 0.00 0.00 0.00 3.01
108 109 4.082125 CTGGTTCAATAGCCTTGGTTCTT 58.918 43.478 0.00 0.00 0.00 2.52
109 110 5.222048 ACTGGTTCAATAGCCTTGGTTCTTA 60.222 40.000 0.00 0.00 0.00 2.10
110 111 5.636123 TGGTTCAATAGCCTTGGTTCTTAA 58.364 37.500 0.00 0.00 0.00 1.85
111 112 5.475564 TGGTTCAATAGCCTTGGTTCTTAAC 59.524 40.000 0.00 0.00 0.00 2.01
112 113 5.710567 GGTTCAATAGCCTTGGTTCTTAACT 59.289 40.000 0.00 0.00 0.00 2.24
113 114 6.349363 GGTTCAATAGCCTTGGTTCTTAACTG 60.349 42.308 0.00 0.00 0.00 3.16
114 115 6.121776 TCAATAGCCTTGGTTCTTAACTGA 57.878 37.500 0.00 0.00 0.00 3.41
115 116 6.173339 TCAATAGCCTTGGTTCTTAACTGAG 58.827 40.000 0.00 0.00 0.00 3.35
116 117 6.013725 TCAATAGCCTTGGTTCTTAACTGAGA 60.014 38.462 0.00 0.00 0.00 3.27
117 118 4.278975 AGCCTTGGTTCTTAACTGAGAG 57.721 45.455 0.00 0.00 0.00 3.20
148 149 7.830201 ACTATCTGCTACTATACTACATCACCC 59.170 40.741 0.00 0.00 0.00 4.61
158 159 3.791320 ACTACATCACCCTTCCTCTTCA 58.209 45.455 0.00 0.00 0.00 3.02
159 160 4.168101 ACTACATCACCCTTCCTCTTCAA 58.832 43.478 0.00 0.00 0.00 2.69
206 207 3.866582 GGACTCCCTGGCGATGGG 61.867 72.222 3.95 3.95 45.90 4.00
215 216 0.394216 CTGGCGATGGGAAATGACCA 60.394 55.000 0.00 0.00 43.22 4.02
273 275 0.976641 ACGGAATCACAGAGGAGCAA 59.023 50.000 0.00 0.00 0.00 3.91
293 295 1.602237 GGGAGCAACGAGGGATTCA 59.398 57.895 0.00 0.00 0.00 2.57
302 304 1.619827 ACGAGGGATTCACACGGTTAA 59.380 47.619 10.46 0.00 0.00 2.01
307 309 4.466827 AGGGATTCACACGGTTAACTTTT 58.533 39.130 5.42 0.00 0.00 2.27
308 310 4.277423 AGGGATTCACACGGTTAACTTTTG 59.723 41.667 5.42 3.14 0.00 2.44
309 311 4.037089 GGGATTCACACGGTTAACTTTTGT 59.963 41.667 5.42 3.75 0.00 2.83
329 331 2.879462 GGCTACAAGGTCGACGCG 60.879 66.667 9.92 3.53 0.00 6.01
345 347 2.029518 CGATGGAGCGGCTGCATA 59.970 61.111 32.50 10.44 42.36 3.14
355 357 2.435693 GGCTGCATAGACTCCCGGT 61.436 63.158 0.00 0.00 0.00 5.28
406 409 4.368543 GTTTCGCCGGGGAGTCGT 62.369 66.667 21.47 0.00 0.00 4.34
407 410 3.618750 TTTCGCCGGGGAGTCGTT 61.619 61.111 21.47 0.00 0.00 3.85
431 434 2.781595 AATCGCCTCGCCGTTGAACT 62.782 55.000 0.00 0.00 0.00 3.01
434 437 2.357517 CCTCGCCGTTGAACTGCT 60.358 61.111 9.91 0.00 0.00 4.24
440 443 1.959085 CCGTTGAACTGCTTGCCAT 59.041 52.632 0.00 0.00 0.00 4.40
448 451 0.403271 ACTGCTTGCCATGAAGAGGT 59.597 50.000 0.00 0.00 0.00 3.85
473 476 1.488705 AACTGGAGTGGAATGCGGGA 61.489 55.000 0.00 0.00 0.00 5.14
518 521 0.611714 GGGAGAAAACGGCTACTGGA 59.388 55.000 0.00 0.00 0.00 3.86
519 522 1.405661 GGGAGAAAACGGCTACTGGAG 60.406 57.143 0.00 0.00 0.00 3.86
530 533 2.094130 GGCTACTGGAGATATAACCGGC 60.094 54.545 0.00 0.00 36.12 6.13
535 538 0.456312 GGAGATATAACCGGCGAGCG 60.456 60.000 9.30 0.00 0.00 5.03
560 563 2.530297 CGATAGTGACGAATGGTGTTCG 59.470 50.000 8.46 8.46 46.36 3.95
590 593 3.672447 TTCCACCGCACGTCGCTA 61.672 61.111 8.07 0.00 39.08 4.26
604 607 2.399611 GCTATGCGTTGACGTGGC 59.600 61.111 0.00 0.00 42.22 5.01
635 639 3.055530 CAGGAGGACTGCACTGTAGATTT 60.056 47.826 0.54 0.00 40.97 2.17
660 664 3.808726 GCAAAACAAATGAATGGTGCTCA 59.191 39.130 0.00 0.00 0.00 4.26
661 665 4.084223 GCAAAACAAATGAATGGTGCTCAG 60.084 41.667 0.00 0.00 0.00 3.35
671 675 0.955428 TGGTGCTCAGAACATTCGGC 60.955 55.000 0.00 0.00 0.00 5.54
684 688 0.539438 ATTCGGCCCAAGTTGCTTCA 60.539 50.000 0.00 0.00 0.00 3.02
700 746 3.039011 GCTTCATAGAGGGAGTTGGGTA 58.961 50.000 0.00 0.00 0.00 3.69
774 852 2.322355 ATCTGTCCAATGGCTCTTCG 57.678 50.000 0.00 0.00 0.00 3.79
789 867 1.001181 TCTTCGTGTAAACCTTCCCGG 59.999 52.381 0.00 0.00 39.35 5.73
1109 3124 4.250305 ACCACAGACCCGTGCCAC 62.250 66.667 0.00 0.00 35.47 5.01
1136 3151 0.753262 CCGTTATGGGGAGTCTCTGG 59.247 60.000 0.00 0.00 0.00 3.86
1280 3296 7.390996 TCACTCGTTTTCTACTTCTGATCTAGT 59.609 37.037 0.00 0.00 0.00 2.57
1342 3359 2.203625 ATTGCTTGGGGGTTGCGT 60.204 55.556 0.00 0.00 0.00 5.24
1422 3439 3.221771 TGGTAGATTGCAAGTTGCTTGT 58.778 40.909 27.17 15.81 45.31 3.16
1427 3444 3.636300 AGATTGCAAGTTGCTTGTTGGTA 59.364 39.130 27.17 2.72 45.31 3.25
1432 3449 3.796717 GCAAGTTGCTTGTTGGTAGAAAC 59.203 43.478 20.71 0.00 42.77 2.78
1435 3452 3.883489 AGTTGCTTGTTGGTAGAAACCTC 59.117 43.478 0.00 0.00 46.91 3.85
1524 3541 6.195600 TGGTTCTACTTATTGACCCTGTTT 57.804 37.500 0.00 0.00 0.00 2.83
1569 3586 0.478072 AGGAACATGGACCTGCACAA 59.522 50.000 11.28 0.00 34.99 3.33
1735 3752 4.263506 GGGGGTCTTTCCATACATATCCTG 60.264 50.000 0.00 0.00 38.11 3.86
1976 3995 9.528018 AACAAAACCTAATCACAATTTGTACAG 57.472 29.630 0.86 0.00 39.34 2.74
2046 4066 4.606210 ACAAGTTTGAAAAGGGTACTGGT 58.394 39.130 0.00 0.00 0.00 4.00
2256 4276 3.505464 ACAGTACGATAAGAGCACACC 57.495 47.619 0.00 0.00 0.00 4.16
2357 4377 7.136119 CACATTGATTTTGCTTTTGATTGCTT 58.864 30.769 0.00 0.00 0.00 3.91
2403 4423 1.772453 GGTAGCTGTTTGGCCCCTATA 59.228 52.381 0.00 0.00 0.00 1.31
2432 4452 0.663153 GATTCACCCTAACCATGCGC 59.337 55.000 0.00 0.00 0.00 6.09
2444 4464 2.898840 ATGCGCTGGCCTGATTCG 60.899 61.111 14.77 8.73 38.85 3.34
2646 4703 7.871853 AGTGAAATGCGTTTATTAGTTCAAGT 58.128 30.769 3.32 0.00 31.41 3.16
2745 4802 7.780271 TGTCCTACTACAGATTATCATGTCACT 59.220 37.037 0.00 0.00 0.00 3.41
2769 4830 4.446994 TGCTGATCTGACCGATGATATC 57.553 45.455 3.42 0.00 30.84 1.63
3217 5280 7.754924 ACATTTGCAATATCTTAAACTGGTTCG 59.245 33.333 0.00 0.00 0.00 3.95
3225 5288 0.941542 TAAACTGGTTCGTGCACAGC 59.058 50.000 18.64 8.58 35.70 4.40
3393 5457 2.042259 TGCTGCTGCATACACTGGC 61.042 57.895 14.93 1.34 45.31 4.85
3424 5488 3.196254 GGATTTGCCATCTGGATGTTGTT 59.804 43.478 0.00 0.00 37.11 2.83
3425 5489 3.663995 TTTGCCATCTGGATGTTGTTG 57.336 42.857 0.00 0.00 37.11 3.33
3426 5490 2.291209 TGCCATCTGGATGTTGTTGT 57.709 45.000 0.00 0.00 37.11 3.32
3475 5539 6.605594 TGAGGATGTATGGTGTTTTATTTCCC 59.394 38.462 0.00 0.00 0.00 3.97
3642 5706 7.765307 ACATGATGTTGGTTACTTGATTCATC 58.235 34.615 0.00 0.00 0.00 2.92
3722 5786 5.514834 CCTGAAGGAATTCTTAACACTCCCA 60.515 44.000 5.23 0.00 35.50 4.37
3895 6034 6.126863 TGGTCTAAGATGGGCCTATTTATG 57.873 41.667 1.86 0.00 0.00 1.90
3899 6039 7.890655 GGTCTAAGATGGGCCTATTTATGAAAT 59.109 37.037 1.86 0.00 34.90 2.17
4263 6696 8.854614 ATGCAATTTAACTTGTCTCTCTAGTT 57.145 30.769 7.31 0.00 42.63 2.24
4435 6870 4.326826 CAGCAGGAGTTGAATTGGTCTAA 58.673 43.478 0.00 0.00 0.00 2.10
4510 6950 1.027357 ACTGAAGCACTTTGCCACAG 58.973 50.000 15.74 15.74 46.52 3.66
4639 7079 6.442952 CAACGTAAAATGATGAGGGTGAAAA 58.557 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.565841 CGGGGAAGAGGATTGTCAATC 58.434 52.381 16.00 16.00 37.17 2.67
1 2 1.408822 GCGGGGAAGAGGATTGTCAAT 60.409 52.381 0.00 0.00 0.00 2.57
2 3 0.035439 GCGGGGAAGAGGATTGTCAA 60.035 55.000 0.00 0.00 0.00 3.18
3 4 1.602237 GCGGGGAAGAGGATTGTCA 59.398 57.895 0.00 0.00 0.00 3.58
4 5 1.521681 CGCGGGGAAGAGGATTGTC 60.522 63.158 0.00 0.00 0.00 3.18
5 6 1.838073 AACGCGGGGAAGAGGATTGT 61.838 55.000 12.47 0.00 0.00 2.71
6 7 1.078426 AACGCGGGGAAGAGGATTG 60.078 57.895 12.47 0.00 0.00 2.67
7 8 1.078426 CAACGCGGGGAAGAGGATT 60.078 57.895 12.47 0.00 0.00 3.01
8 9 2.584608 CAACGCGGGGAAGAGGAT 59.415 61.111 12.47 0.00 0.00 3.24
9 10 3.702048 CCAACGCGGGGAAGAGGA 61.702 66.667 12.47 0.00 0.00 3.71
18 19 1.582610 AATACTTGCACCCAACGCGG 61.583 55.000 12.47 0.00 0.00 6.46
19 20 0.454285 CAATACTTGCACCCAACGCG 60.454 55.000 3.53 3.53 0.00 6.01
20 21 0.596082 ACAATACTTGCACCCAACGC 59.404 50.000 0.00 0.00 0.00 4.84
21 22 2.034053 ACAACAATACTTGCACCCAACG 59.966 45.455 0.00 0.00 0.00 4.10
22 23 3.181480 ACACAACAATACTTGCACCCAAC 60.181 43.478 0.00 0.00 0.00 3.77
23 24 3.027412 ACACAACAATACTTGCACCCAA 58.973 40.909 0.00 0.00 0.00 4.12
24 25 2.360483 CACACAACAATACTTGCACCCA 59.640 45.455 0.00 0.00 0.00 4.51
25 26 2.360801 ACACACAACAATACTTGCACCC 59.639 45.455 0.00 0.00 0.00 4.61
26 27 3.181491 ACACACACAACAATACTTGCACC 60.181 43.478 0.00 0.00 0.00 5.01
27 28 3.790820 CACACACACAACAATACTTGCAC 59.209 43.478 0.00 0.00 0.00 4.57
28 29 3.441922 ACACACACACAACAATACTTGCA 59.558 39.130 0.00 0.00 0.00 4.08
29 30 4.027572 ACACACACACAACAATACTTGC 57.972 40.909 0.00 0.00 0.00 4.01
30 31 5.295787 ACCTACACACACACAACAATACTTG 59.704 40.000 0.00 0.00 0.00 3.16
31 32 5.433526 ACCTACACACACACAACAATACTT 58.566 37.500 0.00 0.00 0.00 2.24
32 33 5.031066 ACCTACACACACACAACAATACT 57.969 39.130 0.00 0.00 0.00 2.12
33 34 5.987347 AGTACCTACACACACACAACAATAC 59.013 40.000 0.00 0.00 0.00 1.89
34 35 5.986741 CAGTACCTACACACACACAACAATA 59.013 40.000 0.00 0.00 0.00 1.90
35 36 4.814234 CAGTACCTACACACACACAACAAT 59.186 41.667 0.00 0.00 0.00 2.71
36 37 4.185394 CAGTACCTACACACACACAACAA 58.815 43.478 0.00 0.00 0.00 2.83
37 38 3.196039 ACAGTACCTACACACACACAACA 59.804 43.478 0.00 0.00 0.00 3.33
38 39 3.788937 ACAGTACCTACACACACACAAC 58.211 45.455 0.00 0.00 0.00 3.32
39 40 4.081586 TCAACAGTACCTACACACACACAA 60.082 41.667 0.00 0.00 0.00 3.33
40 41 3.447944 TCAACAGTACCTACACACACACA 59.552 43.478 0.00 0.00 0.00 3.72
41 42 3.800506 GTCAACAGTACCTACACACACAC 59.199 47.826 0.00 0.00 0.00 3.82
42 43 3.447944 TGTCAACAGTACCTACACACACA 59.552 43.478 0.00 0.00 0.00 3.72
43 44 4.049546 TGTCAACAGTACCTACACACAC 57.950 45.455 0.00 0.00 0.00 3.82
44 45 4.948341 ATGTCAACAGTACCTACACACA 57.052 40.909 0.00 0.00 0.00 3.72
45 46 5.526111 ACAAATGTCAACAGTACCTACACAC 59.474 40.000 0.00 0.00 0.00 3.82
46 47 5.676552 ACAAATGTCAACAGTACCTACACA 58.323 37.500 0.00 0.00 0.00 3.72
47 48 6.563381 CGAACAAATGTCAACAGTACCTACAC 60.563 42.308 0.00 0.00 0.00 2.90
48 49 5.464057 CGAACAAATGTCAACAGTACCTACA 59.536 40.000 0.00 0.00 0.00 2.74
49 50 5.614013 GCGAACAAATGTCAACAGTACCTAC 60.614 44.000 0.00 0.00 0.00 3.18
50 51 4.449743 GCGAACAAATGTCAACAGTACCTA 59.550 41.667 0.00 0.00 0.00 3.08
51 52 3.250040 GCGAACAAATGTCAACAGTACCT 59.750 43.478 0.00 0.00 0.00 3.08
52 53 3.551551 GCGAACAAATGTCAACAGTACC 58.448 45.455 0.00 0.00 0.00 3.34
53 54 3.215244 CGCGAACAAATGTCAACAGTAC 58.785 45.455 0.00 0.00 0.00 2.73
54 55 2.867368 ACGCGAACAAATGTCAACAGTA 59.133 40.909 15.93 0.00 0.00 2.74
55 56 1.668751 ACGCGAACAAATGTCAACAGT 59.331 42.857 15.93 0.00 0.00 3.55
56 57 2.036217 CACGCGAACAAATGTCAACAG 58.964 47.619 15.93 0.00 0.00 3.16
57 58 1.666189 TCACGCGAACAAATGTCAACA 59.334 42.857 15.93 0.00 0.00 3.33
58 59 2.286184 ACTCACGCGAACAAATGTCAAC 60.286 45.455 15.93 0.00 0.00 3.18
59 60 1.937223 ACTCACGCGAACAAATGTCAA 59.063 42.857 15.93 0.00 0.00 3.18
60 61 1.525197 GACTCACGCGAACAAATGTCA 59.475 47.619 15.93 0.00 0.00 3.58
61 62 1.792949 AGACTCACGCGAACAAATGTC 59.207 47.619 15.93 10.67 0.00 3.06
62 63 1.792949 GAGACTCACGCGAACAAATGT 59.207 47.619 15.93 0.87 0.00 2.71
63 64 1.126846 GGAGACTCACGCGAACAAATG 59.873 52.381 15.93 0.00 0.00 2.32
64 65 1.000955 AGGAGACTCACGCGAACAAAT 59.999 47.619 15.93 0.00 32.90 2.32
65 66 0.387929 AGGAGACTCACGCGAACAAA 59.612 50.000 15.93 0.00 32.90 2.83
66 67 1.068748 GTAGGAGACTCACGCGAACAA 60.069 52.381 15.93 0.00 43.67 2.83
67 68 0.520404 GTAGGAGACTCACGCGAACA 59.480 55.000 15.93 0.00 43.67 3.18
68 69 0.803740 AGTAGGAGACTCACGCGAAC 59.196 55.000 15.93 0.00 43.67 3.95
69 70 0.803117 CAGTAGGAGACTCACGCGAA 59.197 55.000 15.93 0.00 43.67 4.70
70 71 1.025113 CCAGTAGGAGACTCACGCGA 61.025 60.000 15.93 0.00 43.67 5.87
71 72 1.306642 ACCAGTAGGAGACTCACGCG 61.307 60.000 3.53 3.53 43.67 6.01
72 73 0.889306 AACCAGTAGGAGACTCACGC 59.111 55.000 4.53 0.00 43.67 5.34
73 74 2.160205 TGAACCAGTAGGAGACTCACG 58.840 52.381 4.53 0.00 43.67 4.35
74 75 4.810191 ATTGAACCAGTAGGAGACTCAC 57.190 45.455 4.53 0.00 43.67 3.51
75 76 4.402793 GCTATTGAACCAGTAGGAGACTCA 59.597 45.833 4.53 0.00 43.67 3.41
76 77 4.202172 GGCTATTGAACCAGTAGGAGACTC 60.202 50.000 0.00 0.00 43.67 3.36
78 79 3.707102 AGGCTATTGAACCAGTAGGAGAC 59.293 47.826 0.00 0.00 38.69 3.36
79 80 3.995636 AGGCTATTGAACCAGTAGGAGA 58.004 45.455 0.00 0.00 38.69 3.71
80 81 4.446371 CAAGGCTATTGAACCAGTAGGAG 58.554 47.826 0.00 0.00 38.69 3.69
81 82 3.199946 CCAAGGCTATTGAACCAGTAGGA 59.800 47.826 4.09 0.00 38.69 2.94
82 83 3.054361 ACCAAGGCTATTGAACCAGTAGG 60.054 47.826 4.09 0.00 42.21 3.18
83 84 4.222124 ACCAAGGCTATTGAACCAGTAG 57.778 45.455 4.09 0.00 0.00 2.57
84 85 4.288626 AGAACCAAGGCTATTGAACCAGTA 59.711 41.667 4.09 0.00 0.00 2.74
85 86 3.074538 AGAACCAAGGCTATTGAACCAGT 59.925 43.478 4.09 0.00 0.00 4.00
86 87 3.690460 AGAACCAAGGCTATTGAACCAG 58.310 45.455 4.09 0.00 0.00 4.00
87 88 3.806949 AGAACCAAGGCTATTGAACCA 57.193 42.857 4.09 0.00 0.00 3.67
88 89 5.710567 AGTTAAGAACCAAGGCTATTGAACC 59.289 40.000 4.09 0.00 0.00 3.62
89 90 6.430000 TCAGTTAAGAACCAAGGCTATTGAAC 59.570 38.462 4.09 0.76 0.00 3.18
90 91 6.539173 TCAGTTAAGAACCAAGGCTATTGAA 58.461 36.000 4.09 0.00 0.00 2.69
91 92 6.013725 TCTCAGTTAAGAACCAAGGCTATTGA 60.014 38.462 4.09 0.00 0.00 2.57
92 93 6.173339 TCTCAGTTAAGAACCAAGGCTATTG 58.827 40.000 0.00 0.00 0.00 1.90
93 94 6.213600 TCTCTCAGTTAAGAACCAAGGCTATT 59.786 38.462 0.00 0.00 0.00 1.73
94 95 5.721960 TCTCTCAGTTAAGAACCAAGGCTAT 59.278 40.000 0.00 0.00 0.00 2.97
95 96 5.084519 TCTCTCAGTTAAGAACCAAGGCTA 58.915 41.667 0.00 0.00 0.00 3.93
96 97 3.904339 TCTCTCAGTTAAGAACCAAGGCT 59.096 43.478 0.00 0.00 0.00 4.58
97 98 4.273148 TCTCTCAGTTAAGAACCAAGGC 57.727 45.455 0.00 0.00 0.00 4.35
98 99 8.097662 AGTATTTCTCTCAGTTAAGAACCAAGG 58.902 37.037 0.00 0.00 31.46 3.61
105 106 9.415008 AGCAGATAGTATTTCTCTCAGTTAAGA 57.585 33.333 0.00 0.00 0.00 2.10
108 109 9.854668 AGTAGCAGATAGTATTTCTCTCAGTTA 57.145 33.333 0.00 0.00 0.00 2.24
109 110 8.760980 AGTAGCAGATAGTATTTCTCTCAGTT 57.239 34.615 0.00 0.00 0.00 3.16
129 130 6.011481 AGGAAGGGTGATGTAGTATAGTAGC 58.989 44.000 0.00 0.00 0.00 3.58
158 159 2.241176 TGATAGGCGTTGGGATTTCCTT 59.759 45.455 0.00 0.00 36.20 3.36
159 160 1.843851 TGATAGGCGTTGGGATTTCCT 59.156 47.619 0.00 0.00 36.20 3.36
198 199 1.384222 GGTGGTCATTTCCCATCGCC 61.384 60.000 0.00 0.00 33.76 5.54
203 204 0.325602 GTACGGGTGGTCATTTCCCA 59.674 55.000 0.00 0.00 41.12 4.37
206 207 0.616891 AGGGTACGGGTGGTCATTTC 59.383 55.000 0.00 0.00 0.00 2.17
210 211 1.914764 GGAAGGGTACGGGTGGTCA 60.915 63.158 0.00 0.00 0.00 4.02
251 252 0.460987 CTCCTCTGTGATTCCGTGGC 60.461 60.000 0.00 0.00 0.00 5.01
273 275 1.616628 AATCCCTCGTTGCTCCCCT 60.617 57.895 0.00 0.00 0.00 4.79
293 295 1.064357 CCGCACAAAAGTTAACCGTGT 59.936 47.619 0.88 1.32 0.00 4.49
302 304 0.951558 CCTTGTAGCCGCACAAAAGT 59.048 50.000 8.90 0.00 37.93 2.66
307 309 2.048597 CGACCTTGTAGCCGCACA 60.049 61.111 0.00 0.00 0.00 4.57
308 310 2.092882 GTCGACCTTGTAGCCGCAC 61.093 63.158 3.51 0.00 0.00 5.34
309 311 2.260434 GTCGACCTTGTAGCCGCA 59.740 61.111 3.51 0.00 0.00 5.69
329 331 0.948141 GTCTATGCAGCCGCTCCATC 60.948 60.000 0.00 0.00 39.64 3.51
431 434 1.065199 CCTACCTCTTCATGGCAAGCA 60.065 52.381 0.00 0.00 0.00 3.91
434 437 2.832838 TCTCCTACCTCTTCATGGCAA 58.167 47.619 0.00 0.00 0.00 4.52
440 443 3.076182 ACTCCAGTTCTCCTACCTCTTCA 59.924 47.826 0.00 0.00 0.00 3.02
448 451 2.501723 GCATTCCACTCCAGTTCTCCTA 59.498 50.000 0.00 0.00 0.00 2.94
473 476 4.011517 ATTCACCCGCGTTCCCGT 62.012 61.111 4.92 0.00 36.15 5.28
498 501 0.739813 CCAGTAGCCGTTTTCTCCCG 60.740 60.000 0.00 0.00 0.00 5.14
518 521 0.039437 CACGCTCGCCGGTTATATCT 60.039 55.000 1.90 0.00 42.52 1.98
519 522 0.039798 TCACGCTCGCCGGTTATATC 60.040 55.000 1.90 0.00 42.52 1.63
530 533 0.919873 CGTCACTATCGTCACGCTCG 60.920 60.000 0.00 0.00 0.00 5.03
535 538 2.852413 CACCATTCGTCACTATCGTCAC 59.148 50.000 0.00 0.00 0.00 3.67
546 549 2.736682 CGCCCGAACACCATTCGTC 61.737 63.158 8.12 0.00 40.04 4.20
547 550 2.740826 CGCCCGAACACCATTCGT 60.741 61.111 8.12 0.00 40.04 3.85
548 551 2.433491 TCGCCCGAACACCATTCG 60.433 61.111 2.12 2.12 41.21 3.34
549 552 2.750888 GCTCGCCCGAACACCATTC 61.751 63.158 0.00 0.00 0.00 2.67
550 553 2.746277 GCTCGCCCGAACACCATT 60.746 61.111 0.00 0.00 0.00 3.16
604 607 2.125350 GTCCTCCTGGCTTGAGCG 60.125 66.667 0.00 0.00 43.26 5.03
635 639 3.311871 GCACCATTCATTTGTTTTGCACA 59.688 39.130 0.00 0.00 0.00 4.57
644 648 4.508461 TGTTCTGAGCACCATTCATTTG 57.492 40.909 0.00 0.00 0.00 2.32
660 664 1.247567 CAACTTGGGCCGAATGTTCT 58.752 50.000 0.00 0.00 0.00 3.01
661 665 0.388520 GCAACTTGGGCCGAATGTTC 60.389 55.000 0.00 0.17 0.00 3.18
671 675 2.239654 TCCCTCTATGAAGCAACTTGGG 59.760 50.000 0.00 0.00 0.00 4.12
774 852 1.293963 GCGTCCGGGAAGGTTTACAC 61.294 60.000 11.95 0.00 41.99 2.90
1280 3296 2.545952 GCCTTTTCTGTCAGACAGTCGA 60.546 50.000 26.65 13.48 46.03 4.20
1303 3319 5.506686 TCGACAAACAACAATTCAATCCA 57.493 34.783 0.00 0.00 0.00 3.41
1342 3359 2.816411 ACGAGAACCATCCCTCACTAA 58.184 47.619 0.00 0.00 0.00 2.24
1427 3444 1.274416 TGGATGCCCCTAGAGGTTTCT 60.274 52.381 0.00 0.00 37.46 2.52
1432 3449 1.072965 GTTGATGGATGCCCCTAGAGG 59.927 57.143 0.00 0.00 35.38 3.69
1435 3452 1.143813 AGGTTGATGGATGCCCCTAG 58.856 55.000 0.00 0.00 35.38 3.02
1524 3541 6.068010 ACACCTGAATTAAGTGGAACAATCA 58.932 36.000 6.85 0.00 44.16 2.57
1976 3995 1.135460 GCAGCTTTTCCTGATCAGTGC 60.135 52.381 21.11 17.29 34.77 4.40
2337 4357 5.613329 AGGAAGCAATCAAAAGCAAAATCA 58.387 33.333 0.00 0.00 0.00 2.57
2338 4358 6.203338 TCAAGGAAGCAATCAAAAGCAAAATC 59.797 34.615 0.00 0.00 0.00 2.17
2357 4377 2.368548 TGCTTCTAACACAGCTCAAGGA 59.631 45.455 0.00 0.00 36.92 3.36
2403 4423 5.010282 GGTTAGGGTGAATCAGTTTCATGT 58.990 41.667 0.00 0.00 45.77 3.21
2432 4452 1.737838 TTGCTAACGAATCAGGCCAG 58.262 50.000 5.01 0.00 0.00 4.85
2436 4456 3.600388 AGGACTTTGCTAACGAATCAGG 58.400 45.455 0.00 0.00 0.00 3.86
2577 4634 0.772384 TTTTGGGCCGTTCCTCCTAA 59.228 50.000 0.00 0.00 34.39 2.69
2745 4802 1.550072 TCATCGGTCAGATCAGCAACA 59.450 47.619 0.00 0.00 37.52 3.33
2769 4830 6.154203 TCAGTTCATGTGCTAGATCCTAAG 57.846 41.667 0.00 0.00 0.00 2.18
3393 5457 2.639970 TGGCAAATCCAAGTGACCG 58.360 52.632 0.00 0.00 43.21 4.79
3424 5488 2.026169 AGTCGATCCAGTCTCCACTACA 60.026 50.000 0.00 0.00 0.00 2.74
3425 5489 2.645802 AGTCGATCCAGTCTCCACTAC 58.354 52.381 0.00 0.00 0.00 2.73
3426 5490 3.740452 CGTAGTCGATCCAGTCTCCACTA 60.740 52.174 0.00 0.00 39.71 2.74
3475 5539 5.345741 CACCAAAAGAATTTAATGCTCACCG 59.654 40.000 0.00 0.00 37.28 4.94
3642 5706 3.996825 GCACAGGCAAGGATTAACG 57.003 52.632 0.00 0.00 40.72 3.18
3876 6015 8.641498 ACATTTCATAAATAGGCCCATCTTAG 57.359 34.615 0.00 0.00 0.00 2.18
4263 6696 3.333680 AGGGAAAGTGGGAAAGCTAATGA 59.666 43.478 0.00 0.00 0.00 2.57
4435 6870 5.116084 TGCTTGGGAAGAGCTATAAACAT 57.884 39.130 0.00 0.00 40.75 2.71
4510 6950 1.337447 TGTACAAGTCCGGCTGCTAAC 60.337 52.381 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.