Multiple sequence alignment - TraesCS2A01G134100

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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 TraesCS2A01G134100 chr2A 100.000 4451 0 0 1 4451 80596669 80592219 0.000000e+00 8220
1 TraesCS2A01G134100 chr2A 98.140 215 3 1 1 214 34974926 34975140 1.510000e-99 374
2 TraesCS2A01G134100 chr2A 96.460 226 8 0 1 226 126590659 126590434 1.510000e-99 374
3 TraesCS2A01G134100 chr2B 97.150 3579 86 7 874 4451 131576971 131573408 0.000000e+00 6030
4 TraesCS2A01G134100 chr2D 96.872 3580 100 2 874 4451 79990246 79986677 0.000000e+00 5980
5 TraesCS2A01G134100 chr4D 96.678 602 20 0 871 1472 30752063 30751462 0.000000e+00 1002
6 TraesCS2A01G134100 chr4D 80.172 348 41 16 532 873 484757975 484758300 7.440000e-58 235
7 TraesCS2A01G134100 chr5D 93.934 610 29 4 871 1472 425666142 425665533 0.000000e+00 915
8 TraesCS2A01G134100 chr5D 89.037 301 27 5 239 533 539692453 539692753 7.030000e-98 368
9 TraesCS2A01G134100 chr5D 85.470 351 32 4 527 873 539692786 539693121 9.160000e-92 348
10 TraesCS2A01G134100 chr1A 74.470 1320 308 26 1307 2613 432637534 432636231 1.090000e-150 544
11 TraesCS2A01G134100 chr1A 98.131 214 4 0 1 214 551973656 551973443 1.510000e-99 374
12 TraesCS2A01G134100 chr1D 96.552 319 10 1 215 532 416269426 416269108 1.100000e-145 527
13 TraesCS2A01G134100 chr1D 91.642 335 24 1 528 858 416269071 416268737 1.130000e-125 460
14 TraesCS2A01G134100 chr6A 97.285 221 6 0 1 221 252315469 252315249 4.200000e-100 375
15 TraesCS2A01G134100 chr6A 98.131 214 4 0 1 214 80669156 80668943 1.510000e-99 374
16 TraesCS2A01G134100 chr6A 96.018 226 9 0 1 226 574620217 574619992 7.030000e-98 368
17 TraesCS2A01G134100 chr6A 88.255 298 15 7 256 533 2789359 2789656 5.510000e-89 339
18 TraesCS2A01G134100 chr6A 82.000 350 43 5 528 873 2789690 2790023 3.390000e-71 279
19 TraesCS2A01G134100 chr3A 96.070 229 7 2 1 229 697805158 697805384 5.440000e-99 372
20 TraesCS2A01G134100 chr4A 96.413 223 7 1 1 223 620201542 620201321 2.530000e-97 366
21 TraesCS2A01G134100 chrUn 92.713 247 14 4 1 246 42506205 42506448 1.970000e-93 353
22 TraesCS2A01G134100 chr6D 88.079 302 20 6 239 533 90343233 90343525 1.190000e-90 344
23 TraesCS2A01G134100 chr6D 84.551 356 38 8 532 873 90343563 90343915 1.980000e-88 337
24 TraesCS2A01G134100 chr1B 87.960 299 23 6 239 533 678554081 678553792 1.530000e-89 340
25 TraesCS2A01G134100 chr7B 87.919 298 16 7 256 533 686969988 686969691 2.570000e-87 333
26 TraesCS2A01G134100 chr7B 81.714 350 44 5 528 873 686969657 686969324 1.580000e-69 274
27 TraesCS2A01G134100 chr5B 89.837 246 15 4 294 533 106961615 106961856 1.560000e-79 307
28 TraesCS2A01G134100 chr5B 81.143 350 46 6 528 873 106961890 106962223 3.410000e-66 263


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 TraesCS2A01G134100 chr2A 80592219 80596669 4450 True 8220.0 8220 100.0000 1 4451 1 chr2A.!!$R1 4450
1 TraesCS2A01G134100 chr2B 131573408 131576971 3563 True 6030.0 6030 97.1500 874 4451 1 chr2B.!!$R1 3577
2 TraesCS2A01G134100 chr2D 79986677 79990246 3569 True 5980.0 5980 96.8720 874 4451 1 chr2D.!!$R1 3577
3 TraesCS2A01G134100 chr4D 30751462 30752063 601 True 1002.0 1002 96.6780 871 1472 1 chr4D.!!$R1 601
4 TraesCS2A01G134100 chr5D 425665533 425666142 609 True 915.0 915 93.9340 871 1472 1 chr5D.!!$R1 601
5 TraesCS2A01G134100 chr5D 539692453 539693121 668 False 358.0 368 87.2535 239 873 2 chr5D.!!$F1 634
6 TraesCS2A01G134100 chr1A 432636231 432637534 1303 True 544.0 544 74.4700 1307 2613 1 chr1A.!!$R1 1306
7 TraesCS2A01G134100 chr1D 416268737 416269426 689 True 493.5 527 94.0970 215 858 2 chr1D.!!$R1 643
8 TraesCS2A01G134100 chr6A 2789359 2790023 664 False 309.0 339 85.1275 256 873 2 chr6A.!!$F1 617
9 TraesCS2A01G134100 chr6D 90343233 90343915 682 False 340.5 344 86.3150 239 873 2 chr6D.!!$F1 634
10 TraesCS2A01G134100 chr7B 686969324 686969988 664 True 303.5 333 84.8165 256 873 2 chr7B.!!$R1 617
11 TraesCS2A01G134100 chr5B 106961615 106962223 608 False 285.0 307 85.4900 294 873 2 chr5B.!!$F1 579

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
801 871 0.107263 TGCTAGCGCAATCCAATCCA 60.107 50.0 11.47 0.00 44.62 3.41 F
2034 2116 0.178975 TTGGGGGCCAACTAGTTGTG 60.179 55.0 29.05 21.92 38.75 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 2445 0.622665 CCCAAGATGGACAGAAGGCT 59.377 55.00 0.0 0.0 40.96 4.58 R
3758 3840 4.640364 TGCTGTCACATGTTCATCTACAA 58.360 39.13 0.0 0.0 0.00 2.41 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 3.213206 GACATCCAATGCCCATAGTCA 57.787 47.619 0.00 0.00 0.00 3.41
21 22 3.144506 GACATCCAATGCCCATAGTCAG 58.855 50.000 0.00 0.00 0.00 3.51
22 23 2.158564 ACATCCAATGCCCATAGTCAGG 60.159 50.000 0.00 0.00 0.00 3.86
23 24 1.891933 TCCAATGCCCATAGTCAGGA 58.108 50.000 0.00 0.00 0.00 3.86
24 25 2.204463 TCCAATGCCCATAGTCAGGAA 58.796 47.619 0.00 0.00 0.00 3.36
25 26 2.580322 TCCAATGCCCATAGTCAGGAAA 59.420 45.455 0.00 0.00 0.00 3.13
26 27 2.689983 CCAATGCCCATAGTCAGGAAAC 59.310 50.000 0.00 0.00 0.00 2.78
27 28 2.689983 CAATGCCCATAGTCAGGAAACC 59.310 50.000 0.00 0.00 0.00 3.27
28 29 1.367346 TGCCCATAGTCAGGAAACCA 58.633 50.000 0.00 0.00 0.00 3.67
29 30 1.922447 TGCCCATAGTCAGGAAACCAT 59.078 47.619 0.00 0.00 0.00 3.55
30 31 2.301346 GCCCATAGTCAGGAAACCATG 58.699 52.381 0.00 0.00 0.00 3.66
31 32 2.092429 GCCCATAGTCAGGAAACCATGA 60.092 50.000 0.00 0.00 0.00 3.07
32 33 3.545703 CCCATAGTCAGGAAACCATGAC 58.454 50.000 0.00 2.44 44.97 3.06
39 40 5.091261 GTCAGGAAACCATGACTATCTGT 57.909 43.478 0.00 0.00 42.06 3.41
40 41 5.491982 GTCAGGAAACCATGACTATCTGTT 58.508 41.667 0.00 0.00 42.06 3.16
41 42 5.352569 GTCAGGAAACCATGACTATCTGTTG 59.647 44.000 0.00 0.00 42.06 3.33
42 43 5.248248 TCAGGAAACCATGACTATCTGTTGA 59.752 40.000 0.00 0.00 0.00 3.18
43 44 6.070021 TCAGGAAACCATGACTATCTGTTGAT 60.070 38.462 0.00 0.00 36.74 2.57
44 45 6.600822 CAGGAAACCATGACTATCTGTTGATT 59.399 38.462 0.00 0.00 34.32 2.57
45 46 7.770433 CAGGAAACCATGACTATCTGTTGATTA 59.230 37.037 0.00 0.00 34.32 1.75
46 47 8.328758 AGGAAACCATGACTATCTGTTGATTAA 58.671 33.333 0.00 0.00 34.32 1.40
47 48 8.398665 GGAAACCATGACTATCTGTTGATTAAC 58.601 37.037 0.00 0.00 37.32 2.01
48 49 8.862325 AAACCATGACTATCTGTTGATTAACA 57.138 30.769 2.77 2.77 44.17 2.41
49 50 8.862325 AACCATGACTATCTGTTGATTAACAA 57.138 30.769 4.47 0.00 45.53 2.83
50 51 8.862325 ACCATGACTATCTGTTGATTAACAAA 57.138 30.769 4.47 0.00 45.53 2.83
51 52 8.730680 ACCATGACTATCTGTTGATTAACAAAC 58.269 33.333 4.47 0.00 45.53 2.93
52 53 8.950210 CCATGACTATCTGTTGATTAACAAACT 58.050 33.333 4.47 0.00 45.53 2.66
60 61 8.958119 TCTGTTGATTAACAAACTAGTCAACT 57.042 30.769 16.23 0.00 45.53 3.16
65 66 9.706691 TTGATTAACAAACTAGTCAACTAGAGG 57.293 33.333 21.08 12.67 40.64 3.69
66 67 7.817962 TGATTAACAAACTAGTCAACTAGAGGC 59.182 37.037 21.08 0.00 46.80 4.70
67 68 5.810080 AACAAACTAGTCAACTAGAGGCT 57.190 39.130 21.08 0.00 46.80 4.58
68 69 5.810080 ACAAACTAGTCAACTAGAGGCTT 57.190 39.130 21.08 4.92 46.80 4.35
69 70 6.912951 ACAAACTAGTCAACTAGAGGCTTA 57.087 37.500 21.08 0.00 46.80 3.09
70 71 6.689554 ACAAACTAGTCAACTAGAGGCTTAC 58.310 40.000 21.08 0.00 46.80 2.34
71 72 6.494146 ACAAACTAGTCAACTAGAGGCTTACT 59.506 38.462 21.08 0.00 46.80 2.24
72 73 7.668886 ACAAACTAGTCAACTAGAGGCTTACTA 59.331 37.037 21.08 0.00 46.80 1.82
73 74 7.868906 AACTAGTCAACTAGAGGCTTACTAG 57.131 40.000 21.08 8.32 46.80 2.57
74 75 6.358991 ACTAGTCAACTAGAGGCTTACTAGG 58.641 44.000 21.08 0.00 46.80 3.02
75 76 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
76 77 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
77 78 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
78 79 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
79 80 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
80 81 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
81 82 3.406512 AGAGGCTTACTAGGGACATGT 57.593 47.619 0.00 0.00 0.00 3.21
82 83 3.725634 AGAGGCTTACTAGGGACATGTT 58.274 45.455 0.00 0.00 0.00 2.71
83 84 3.452627 AGAGGCTTACTAGGGACATGTTG 59.547 47.826 0.00 0.00 0.00 3.33
84 85 2.505819 AGGCTTACTAGGGACATGTTGG 59.494 50.000 0.00 0.00 0.00 3.77
85 86 2.238898 GGCTTACTAGGGACATGTTGGT 59.761 50.000 0.00 0.00 0.00 3.67
86 87 3.270877 GCTTACTAGGGACATGTTGGTG 58.729 50.000 0.00 0.00 0.00 4.17
87 88 3.307480 GCTTACTAGGGACATGTTGGTGT 60.307 47.826 0.00 0.00 34.39 4.16
88 89 4.504858 CTTACTAGGGACATGTTGGTGTC 58.495 47.826 0.00 0.00 46.04 3.67
89 90 2.621070 ACTAGGGACATGTTGGTGTCT 58.379 47.619 0.00 0.00 46.02 3.41
90 91 3.786553 ACTAGGGACATGTTGGTGTCTA 58.213 45.455 0.00 0.00 46.02 2.59
91 92 4.362677 ACTAGGGACATGTTGGTGTCTAT 58.637 43.478 0.00 0.00 46.02 1.98
92 93 4.783227 ACTAGGGACATGTTGGTGTCTATT 59.217 41.667 0.00 0.00 46.02 1.73
93 94 5.962031 ACTAGGGACATGTTGGTGTCTATTA 59.038 40.000 0.00 0.00 46.02 0.98
94 95 5.975988 AGGGACATGTTGGTGTCTATTAT 57.024 39.130 0.00 0.00 46.02 1.28
95 96 6.327386 AGGGACATGTTGGTGTCTATTATT 57.673 37.500 0.00 0.00 46.02 1.40
96 97 6.357367 AGGGACATGTTGGTGTCTATTATTC 58.643 40.000 0.00 0.00 46.02 1.75
97 98 6.069673 AGGGACATGTTGGTGTCTATTATTCA 60.070 38.462 0.00 0.00 46.02 2.57
98 99 6.038271 GGGACATGTTGGTGTCTATTATTCAC 59.962 42.308 0.00 0.00 46.02 3.18
99 100 6.597672 GGACATGTTGGTGTCTATTATTCACA 59.402 38.462 0.00 0.00 46.02 3.58
100 101 7.377766 ACATGTTGGTGTCTATTATTCACAC 57.622 36.000 0.00 0.00 39.84 3.82
101 102 6.939730 ACATGTTGGTGTCTATTATTCACACA 59.060 34.615 0.00 0.00 41.93 3.72
102 103 7.611467 ACATGTTGGTGTCTATTATTCACACAT 59.389 33.333 0.00 0.00 41.93 3.21
103 104 7.376435 TGTTGGTGTCTATTATTCACACATG 57.624 36.000 4.00 0.00 41.93 3.21
104 105 6.939730 TGTTGGTGTCTATTATTCACACATGT 59.060 34.615 0.00 0.00 41.93 3.21
105 106 8.097662 TGTTGGTGTCTATTATTCACACATGTA 58.902 33.333 0.00 0.00 41.93 2.29
106 107 9.109393 GTTGGTGTCTATTATTCACACATGTAT 57.891 33.333 0.00 0.00 41.93 2.29
107 108 9.679661 TTGGTGTCTATTATTCACACATGTATT 57.320 29.630 0.00 0.00 41.93 1.89
117 118 5.959652 TCACACATGTATTACGATTTCCG 57.040 39.130 0.00 0.00 45.44 4.30
118 119 4.806775 TCACACATGTATTACGATTTCCGG 59.193 41.667 0.00 0.00 43.93 5.14
119 120 4.806775 CACACATGTATTACGATTTCCGGA 59.193 41.667 0.00 0.00 43.93 5.14
120 121 5.465390 CACACATGTATTACGATTTCCGGAT 59.535 40.000 4.15 0.00 43.93 4.18
121 122 6.643360 CACACATGTATTACGATTTCCGGATA 59.357 38.462 4.15 0.00 43.93 2.59
122 123 7.170151 CACACATGTATTACGATTTCCGGATAA 59.830 37.037 4.15 0.00 43.93 1.75
123 124 7.170320 ACACATGTATTACGATTTCCGGATAAC 59.830 37.037 4.15 0.00 43.93 1.89
124 125 7.170151 CACATGTATTACGATTTCCGGATAACA 59.830 37.037 4.15 0.00 43.93 2.41
125 126 7.170320 ACATGTATTACGATTTCCGGATAACAC 59.830 37.037 4.15 0.00 43.93 3.32
126 127 6.571605 TGTATTACGATTTCCGGATAACACA 58.428 36.000 4.15 3.08 43.93 3.72
127 128 7.040494 TGTATTACGATTTCCGGATAACACAA 58.960 34.615 4.15 0.00 43.93 3.33
128 129 7.711772 TGTATTACGATTTCCGGATAACACAAT 59.288 33.333 4.15 0.00 43.93 2.71
129 130 6.988622 TTACGATTTCCGGATAACACAATT 57.011 33.333 4.15 0.00 43.93 2.32
130 131 8.665643 ATTACGATTTCCGGATAACACAATTA 57.334 30.769 4.15 0.00 43.93 1.40
131 132 8.665643 TTACGATTTCCGGATAACACAATTAT 57.334 30.769 4.15 0.00 43.93 1.28
132 133 9.761504 TTACGATTTCCGGATAACACAATTATA 57.238 29.630 4.15 0.00 43.93 0.98
133 134 8.306680 ACGATTTCCGGATAACACAATTATAG 57.693 34.615 4.15 0.00 43.93 1.31
134 135 7.095355 ACGATTTCCGGATAACACAATTATAGC 60.095 37.037 4.15 0.00 43.93 2.97
135 136 7.095397 CGATTTCCGGATAACACAATTATAGCA 60.095 37.037 4.15 0.00 33.91 3.49
136 137 8.635765 ATTTCCGGATAACACAATTATAGCAT 57.364 30.769 4.15 0.00 0.00 3.79
137 138 7.433708 TTCCGGATAACACAATTATAGCATG 57.566 36.000 4.15 0.00 0.00 4.06
138 139 6.764379 TCCGGATAACACAATTATAGCATGA 58.236 36.000 0.00 0.00 0.00 3.07
139 140 7.220740 TCCGGATAACACAATTATAGCATGAA 58.779 34.615 0.00 0.00 0.00 2.57
140 141 7.882791 TCCGGATAACACAATTATAGCATGAAT 59.117 33.333 0.00 0.00 0.00 2.57
141 142 9.161629 CCGGATAACACAATTATAGCATGAATA 57.838 33.333 0.00 0.00 0.00 1.75
200 201 7.530426 AATGCTTTTATTATTGCCTCTAGGG 57.470 36.000 0.00 0.00 35.18 3.53
213 214 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
229 230 4.373527 TCCAACACGTATATGTGGTATGC 58.626 43.478 25.18 0.00 44.21 3.14
263 264 4.773323 ATTTTCTTGCAGGTGCTAACTC 57.227 40.909 3.18 0.00 42.66 3.01
461 482 6.291377 TGATGTATTTCTGTATGGCCTTCTC 58.709 40.000 3.32 0.00 0.00 2.87
650 720 2.512286 CCGCGGAGATGCATGTGT 60.512 61.111 24.07 0.00 34.15 3.72
703 773 1.024046 TGGGTCGCAACAATCCATCG 61.024 55.000 0.00 0.00 0.00 3.84
733 803 6.155737 AGCTGAAAATATCTTCCCAAATTGCT 59.844 34.615 0.00 0.00 0.00 3.91
756 826 2.152016 TGGATCTCGTATACTGCTCGG 58.848 52.381 0.56 0.00 0.00 4.63
757 827 2.224450 TGGATCTCGTATACTGCTCGGA 60.224 50.000 0.56 0.00 0.00 4.55
766 836 5.745294 TCGTATACTGCTCGGATTAAACAAC 59.255 40.000 0.56 0.00 0.00 3.32
787 857 0.109086 AGTGCACGCTGTACTGCTAG 60.109 55.000 20.65 14.06 41.73 3.42
800 870 2.706636 TGCTAGCGCAATCCAATCC 58.293 52.632 11.47 0.00 44.62 3.01
801 871 0.107263 TGCTAGCGCAATCCAATCCA 60.107 50.000 11.47 0.00 44.62 3.41
804 874 1.462283 CTAGCGCAATCCAATCCATCG 59.538 52.381 11.47 0.00 0.00 3.84
805 875 1.168407 AGCGCAATCCAATCCATCGG 61.168 55.000 11.47 0.00 0.00 4.18
836 910 7.046033 GGGACGTTAGATCTTCAGGAATAAAA 58.954 38.462 0.00 0.00 0.00 1.52
854 928 9.045223 GGAATAAAAGGCCAATATTCATTTCAC 57.955 33.333 24.56 11.27 37.63 3.18
1065 1139 1.451567 CGTCTACCTCCTCCTCGCA 60.452 63.158 0.00 0.00 0.00 5.10
1788 1870 0.674895 GCCTTCCAGATGTTGACGCT 60.675 55.000 0.00 0.00 0.00 5.07
1863 1945 2.345991 GCAGACGCACCCAAGGTA 59.654 61.111 0.00 0.00 38.36 3.08
1899 1981 1.375908 GATGGCGCCAGTCAACTCA 60.376 57.895 35.36 7.66 34.62 3.41
1902 1984 2.320587 GGCGCCAGTCAACTCACTG 61.321 63.158 24.80 0.00 43.13 3.66
2028 2110 1.286305 GGGAGATTGGGGGCCAACTA 61.286 60.000 4.39 0.00 46.95 2.24
2034 2116 0.178975 TTGGGGGCCAACTAGTTGTG 60.179 55.000 29.05 21.92 38.75 3.33
2187 2269 3.942829 TGAGCGGATTCTTGATTTGAGT 58.057 40.909 0.00 0.00 0.00 3.41
2363 2445 1.478654 GGAGTTTGTCCCCAAGAAGCA 60.479 52.381 0.00 0.00 39.88 3.91
2494 2576 1.304713 GGACCTGTGGACCGGACTA 60.305 63.158 9.46 0.00 0.00 2.59
2520 2602 2.092699 AGAGTGGAGGCTTCTTTATGGC 60.093 50.000 0.00 0.00 0.00 4.40
2640 2722 3.126514 CAGCTTGATCTGTAACCTTGCAG 59.873 47.826 0.00 0.00 41.49 4.41
3078 3160 3.486875 CGGTTGACAGTTTTCCAGTTCAC 60.487 47.826 0.00 0.00 0.00 3.18
3457 3539 1.280457 GGAGTTGGTCTGATCCAGGT 58.720 55.000 0.00 0.00 38.80 4.00
3744 3826 8.647143 AAACAGTTAAAAATGACACTCCATTG 57.353 30.769 0.00 0.00 36.90 2.82
3758 3840 8.758829 TGACACTCCATTGTCTGTTACTATATT 58.241 33.333 4.97 0.00 45.34 1.28
4121 4205 3.193479 GCTTCCTGAACGAATTGGGATTT 59.807 43.478 0.00 0.00 0.00 2.17
4169 4253 4.872124 TCTTCATCTTCGATGAATGTGGTG 59.128 41.667 16.84 7.14 37.40 4.17
4232 4316 3.609853 TGCACTCCATCCAACAGTATTC 58.390 45.455 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.144506 CTGACTATGGGCATTGGATGTC 58.855 50.000 0.00 0.00 0.00 3.06
1 2 2.158564 CCTGACTATGGGCATTGGATGT 60.159 50.000 0.00 0.00 0.00 3.06
2 3 2.107031 TCCTGACTATGGGCATTGGATG 59.893 50.000 0.00 0.00 0.00 3.51
3 4 2.421725 TCCTGACTATGGGCATTGGAT 58.578 47.619 0.00 0.00 0.00 3.41
4 5 1.891933 TCCTGACTATGGGCATTGGA 58.108 50.000 0.00 0.00 0.00 3.53
5 6 2.689983 GTTTCCTGACTATGGGCATTGG 59.310 50.000 0.00 0.00 0.00 3.16
6 7 2.689983 GGTTTCCTGACTATGGGCATTG 59.310 50.000 0.00 0.00 0.00 2.82
7 8 2.311542 TGGTTTCCTGACTATGGGCATT 59.688 45.455 0.00 0.00 0.00 3.56
8 9 1.922447 TGGTTTCCTGACTATGGGCAT 59.078 47.619 0.00 0.00 0.00 4.40
9 10 1.367346 TGGTTTCCTGACTATGGGCA 58.633 50.000 0.00 0.00 0.00 5.36
10 11 2.092429 TCATGGTTTCCTGACTATGGGC 60.092 50.000 0.00 0.00 38.56 5.36
11 12 3.545703 GTCATGGTTTCCTGACTATGGG 58.454 50.000 0.00 0.00 38.56 4.00
17 18 5.091261 ACAGATAGTCATGGTTTCCTGAC 57.909 43.478 10.65 8.96 41.65 3.51
18 19 5.248248 TCAACAGATAGTCATGGTTTCCTGA 59.752 40.000 10.65 0.00 0.00 3.86
19 20 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
20 21 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
21 22 8.398665 GTTAATCAACAGATAGTCATGGTTTCC 58.601 37.037 0.00 0.00 34.60 3.13
22 23 8.946085 TGTTAATCAACAGATAGTCATGGTTTC 58.054 33.333 0.00 0.00 39.75 2.78
23 24 8.862325 TGTTAATCAACAGATAGTCATGGTTT 57.138 30.769 0.00 0.00 39.75 3.27
24 25 8.862325 TTGTTAATCAACAGATAGTCATGGTT 57.138 30.769 0.00 0.00 45.17 3.67
25 26 8.730680 GTTTGTTAATCAACAGATAGTCATGGT 58.269 33.333 0.00 0.00 45.17 3.55
26 27 8.950210 AGTTTGTTAATCAACAGATAGTCATGG 58.050 33.333 0.00 0.00 45.17 3.66
34 35 9.561069 AGTTGACTAGTTTGTTAATCAACAGAT 57.439 29.630 17.15 0.70 45.17 2.90
35 36 8.958119 AGTTGACTAGTTTGTTAATCAACAGA 57.042 30.769 17.15 0.00 45.17 3.41
39 40 9.706691 CCTCTAGTTGACTAGTTTGTTAATCAA 57.293 33.333 15.67 0.00 44.74 2.57
40 41 7.817962 GCCTCTAGTTGACTAGTTTGTTAATCA 59.182 37.037 15.67 0.00 44.74 2.57
41 42 8.035984 AGCCTCTAGTTGACTAGTTTGTTAATC 58.964 37.037 15.67 0.00 44.74 1.75
42 43 7.908453 AGCCTCTAGTTGACTAGTTTGTTAAT 58.092 34.615 15.67 0.00 44.74 1.40
43 44 7.299246 AGCCTCTAGTTGACTAGTTTGTTAA 57.701 36.000 15.67 0.00 44.74 2.01
44 45 6.912951 AGCCTCTAGTTGACTAGTTTGTTA 57.087 37.500 15.67 0.00 44.74 2.41
45 46 5.810080 AGCCTCTAGTTGACTAGTTTGTT 57.190 39.130 15.67 3.96 44.74 2.83
46 47 5.810080 AAGCCTCTAGTTGACTAGTTTGT 57.190 39.130 15.67 0.80 44.74 2.83
47 48 6.926313 AGTAAGCCTCTAGTTGACTAGTTTG 58.074 40.000 15.67 8.33 44.74 2.93
48 49 7.339976 CCTAGTAAGCCTCTAGTTGACTAGTTT 59.660 40.741 15.67 9.94 44.74 2.66
49 50 6.829811 CCTAGTAAGCCTCTAGTTGACTAGTT 59.170 42.308 15.67 7.30 44.74 2.24
50 51 6.358991 CCTAGTAAGCCTCTAGTTGACTAGT 58.641 44.000 15.67 0.00 44.74 2.57
51 52 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
52 53 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
53 54 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
54 55 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
55 56 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
56 57 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
57 58 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
58 59 4.079096 ACATGTCCCTAGTAAGCCTCTAGT 60.079 45.833 0.00 0.00 34.72 2.57
59 60 4.475345 ACATGTCCCTAGTAAGCCTCTAG 58.525 47.826 0.00 0.00 35.86 2.43
60 61 4.537945 ACATGTCCCTAGTAAGCCTCTA 57.462 45.455 0.00 0.00 0.00 2.43
61 62 3.406512 ACATGTCCCTAGTAAGCCTCT 57.593 47.619 0.00 0.00 0.00 3.69
62 63 3.432326 CCAACATGTCCCTAGTAAGCCTC 60.432 52.174 0.00 0.00 0.00 4.70
63 64 2.505819 CCAACATGTCCCTAGTAAGCCT 59.494 50.000 0.00 0.00 0.00 4.58
64 65 2.238898 ACCAACATGTCCCTAGTAAGCC 59.761 50.000 0.00 0.00 0.00 4.35
65 66 3.270877 CACCAACATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
66 67 4.504858 GACACCAACATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 42.74 2.34
67 68 4.546829 GACACCAACATGTCCCTAGTAA 57.453 45.455 0.00 0.00 42.74 2.24
76 77 6.939730 TGTGTGAATAATAGACACCAACATGT 59.060 34.615 0.00 0.00 39.43 3.21
77 78 7.376435 TGTGTGAATAATAGACACCAACATG 57.624 36.000 0.00 0.00 39.43 3.21
78 79 7.611467 ACATGTGTGAATAATAGACACCAACAT 59.389 33.333 0.00 0.00 39.43 2.71
79 80 6.939730 ACATGTGTGAATAATAGACACCAACA 59.060 34.615 0.00 0.00 39.43 3.33
80 81 7.377766 ACATGTGTGAATAATAGACACCAAC 57.622 36.000 0.00 0.00 39.43 3.77
81 82 9.679661 AATACATGTGTGAATAATAGACACCAA 57.320 29.630 9.11 0.00 39.43 3.67
91 92 8.544597 CGGAAATCGTAATACATGTGTGAATAA 58.455 33.333 9.11 0.00 0.00 1.40
92 93 7.170151 CCGGAAATCGTAATACATGTGTGAATA 59.830 37.037 9.11 0.00 37.11 1.75
93 94 6.018262 CCGGAAATCGTAATACATGTGTGAAT 60.018 38.462 9.11 0.00 37.11 2.57
94 95 5.292345 CCGGAAATCGTAATACATGTGTGAA 59.708 40.000 9.11 0.00 37.11 3.18
95 96 4.806775 CCGGAAATCGTAATACATGTGTGA 59.193 41.667 9.11 0.00 37.11 3.58
96 97 4.806775 TCCGGAAATCGTAATACATGTGTG 59.193 41.667 9.11 0.00 37.11 3.82
97 98 5.013568 TCCGGAAATCGTAATACATGTGT 57.986 39.130 9.11 0.00 37.11 3.72
98 99 7.170151 TGTTATCCGGAAATCGTAATACATGTG 59.830 37.037 9.01 0.00 37.11 3.21
99 100 7.170320 GTGTTATCCGGAAATCGTAATACATGT 59.830 37.037 9.01 2.69 37.11 3.21
100 101 7.170151 TGTGTTATCCGGAAATCGTAATACATG 59.830 37.037 9.01 0.00 31.67 3.21
101 102 7.211573 TGTGTTATCCGGAAATCGTAATACAT 58.788 34.615 9.01 0.00 31.67 2.29
102 103 6.571605 TGTGTTATCCGGAAATCGTAATACA 58.428 36.000 9.01 13.79 33.00 2.29
103 104 7.467557 TTGTGTTATCCGGAAATCGTAATAC 57.532 36.000 9.01 11.23 37.11 1.89
104 105 8.665643 AATTGTGTTATCCGGAAATCGTAATA 57.334 30.769 9.01 0.00 37.11 0.98
105 106 7.562454 AATTGTGTTATCCGGAAATCGTAAT 57.438 32.000 9.01 3.30 37.11 1.89
106 107 6.988622 AATTGTGTTATCCGGAAATCGTAA 57.011 33.333 9.01 0.00 37.11 3.18
107 108 9.414295 CTATAATTGTGTTATCCGGAAATCGTA 57.586 33.333 9.01 0.00 37.11 3.43
108 109 7.095355 GCTATAATTGTGTTATCCGGAAATCGT 60.095 37.037 9.01 0.00 37.11 3.73
109 110 7.095397 TGCTATAATTGTGTTATCCGGAAATCG 60.095 37.037 9.01 0.00 38.88 3.34
110 111 8.094798 TGCTATAATTGTGTTATCCGGAAATC 57.905 34.615 9.01 1.80 0.00 2.17
111 112 8.514594 CATGCTATAATTGTGTTATCCGGAAAT 58.485 33.333 9.01 0.00 0.00 2.17
112 113 7.717436 TCATGCTATAATTGTGTTATCCGGAAA 59.283 33.333 9.01 0.99 0.00 3.13
113 114 7.220740 TCATGCTATAATTGTGTTATCCGGAA 58.779 34.615 9.01 0.00 0.00 4.30
114 115 6.764379 TCATGCTATAATTGTGTTATCCGGA 58.236 36.000 6.61 6.61 0.00 5.14
115 116 7.433708 TTCATGCTATAATTGTGTTATCCGG 57.566 36.000 0.00 0.00 0.00 5.14
174 175 9.247861 CCCTAGAGGCAATAATAAAAGCATTAT 57.752 33.333 0.00 0.00 33.46 1.28
175 176 8.635765 CCCTAGAGGCAATAATAAAAGCATTA 57.364 34.615 0.00 0.00 0.00 1.90
176 177 7.530426 CCCTAGAGGCAATAATAAAAGCATT 57.470 36.000 0.00 0.00 0.00 3.56
192 193 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
193 194 3.809832 CGTGTTGGAAATATGCCCTAGAG 59.190 47.826 0.00 0.00 0.00 2.43
194 195 3.199071 ACGTGTTGGAAATATGCCCTAGA 59.801 43.478 0.00 0.00 0.00 2.43
195 196 3.541632 ACGTGTTGGAAATATGCCCTAG 58.458 45.455 0.00 0.00 0.00 3.02
196 197 3.637911 ACGTGTTGGAAATATGCCCTA 57.362 42.857 0.00 0.00 0.00 3.53
197 198 2.507407 ACGTGTTGGAAATATGCCCT 57.493 45.000 0.00 0.00 0.00 5.19
198 199 5.472137 ACATATACGTGTTGGAAATATGCCC 59.528 40.000 10.66 0.00 35.07 5.36
199 200 6.370593 CACATATACGTGTTGGAAATATGCC 58.629 40.000 10.66 0.00 35.07 4.40
200 201 6.017440 ACCACATATACGTGTTGGAAATATGC 60.017 38.462 8.33 0.00 35.07 3.14
201 202 7.490962 ACCACATATACGTGTTGGAAATATG 57.509 36.000 8.33 9.03 36.84 1.78
202 203 9.214957 CATACCACATATACGTGTTGGAAATAT 57.785 33.333 8.33 0.00 34.98 1.28
203 204 7.171848 GCATACCACATATACGTGTTGGAAATA 59.828 37.037 8.33 0.00 34.98 1.40
204 205 6.017440 GCATACCACATATACGTGTTGGAAAT 60.017 38.462 8.33 0.03 34.98 2.17
205 206 5.294799 GCATACCACATATACGTGTTGGAAA 59.705 40.000 8.33 0.00 34.98 3.13
206 207 4.812091 GCATACCACATATACGTGTTGGAA 59.188 41.667 8.33 0.00 34.98 3.53
207 208 4.100344 AGCATACCACATATACGTGTTGGA 59.900 41.667 8.33 0.00 34.98 3.53
208 209 4.377021 AGCATACCACATATACGTGTTGG 58.623 43.478 0.00 0.00 34.98 3.77
209 210 5.737353 CAAGCATACCACATATACGTGTTG 58.263 41.667 0.00 0.00 34.98 3.33
210 211 4.272504 GCAAGCATACCACATATACGTGTT 59.727 41.667 0.00 0.00 34.98 3.32
211 212 3.807622 GCAAGCATACCACATATACGTGT 59.192 43.478 0.00 0.00 34.98 4.49
212 213 3.807071 TGCAAGCATACCACATATACGTG 59.193 43.478 0.00 0.00 36.61 4.49
213 214 4.066646 TGCAAGCATACCACATATACGT 57.933 40.909 0.00 0.00 0.00 3.57
229 230 7.118680 ACCTGCAAGAAAATTTTATGATGCAAG 59.881 33.333 19.74 17.19 41.44 4.01
263 264 1.270147 CGGTTATTTCCTAGGAGCGGG 60.270 57.143 12.26 0.00 0.00 6.13
290 291 0.445436 CAGTCTGTTGGCAATCGAGC 59.555 55.000 1.92 0.00 0.00 5.03
650 720 3.583276 ATTCTGTTCCGCCGTCGCA 62.583 57.895 0.00 0.00 34.03 5.10
703 773 3.810386 GGGAAGATATTTTCAGCTCGTCC 59.190 47.826 8.15 0.00 36.09 4.79
733 803 3.498777 CGAGCAGTATACGAGATCCAAGA 59.501 47.826 9.86 0.00 0.00 3.02
756 826 2.031157 AGCGTGCACTGGTTGTTTAATC 60.031 45.455 16.19 0.00 0.00 1.75
757 827 1.953686 AGCGTGCACTGGTTGTTTAAT 59.046 42.857 16.19 0.00 0.00 1.40
766 836 2.671177 GCAGTACAGCGTGCACTGG 61.671 63.158 16.19 6.50 41.03 4.00
787 857 1.283793 CCGATGGATTGGATTGCGC 59.716 57.895 0.00 0.00 32.77 6.09
789 859 0.825010 AGGCCGATGGATTGGATTGC 60.825 55.000 0.00 0.00 32.77 3.56
798 868 2.674754 GTCCCAAAGGCCGATGGA 59.325 61.111 26.13 15.21 39.12 3.41
800 870 0.391927 TAACGTCCCAAAGGCCGATG 60.392 55.000 0.00 0.00 0.00 3.84
801 871 0.107848 CTAACGTCCCAAAGGCCGAT 60.108 55.000 0.00 0.00 0.00 4.18
804 874 1.209747 AGATCTAACGTCCCAAAGGCC 59.790 52.381 0.00 0.00 0.00 5.19
805 875 2.693267 AGATCTAACGTCCCAAAGGC 57.307 50.000 0.00 0.00 0.00 4.35
836 910 3.631250 ACCGTGAAATGAATATTGGCCT 58.369 40.909 3.32 0.00 0.00 5.19
854 928 2.835027 GGGAGCTCTTTTATGGTACCG 58.165 52.381 14.64 0.00 0.00 4.02
1522 1604 2.203294 GGTGAGGTTGTTGCCGGT 60.203 61.111 1.90 0.00 0.00 5.28
1788 1870 3.131577 ACTTTCGTGTGAGGTAGAACACA 59.868 43.478 6.73 0.00 45.61 3.72
2187 2269 0.673985 CCTCCTCCGTCATCGCATAA 59.326 55.000 0.00 0.00 35.54 1.90
2363 2445 0.622665 CCCAAGATGGACAGAAGGCT 59.377 55.000 0.00 0.00 40.96 4.58
2494 2576 2.614134 AGAAGCCTCCACTCTAGTGT 57.386 50.000 9.17 0.00 44.21 3.55
2893 2975 5.667539 TCACAAATTTCACAAACCAGGAA 57.332 34.783 0.00 0.00 0.00 3.36
2934 3016 9.213799 GAGAAGTTAGTTTTGACAGATCAGAAT 57.786 33.333 0.00 0.00 35.83 2.40
3078 3160 5.349543 GCTTCTTTTGTAATTGGCTTGATGG 59.650 40.000 0.00 0.00 0.00 3.51
3758 3840 4.640364 TGCTGTCACATGTTCATCTACAA 58.360 39.130 0.00 0.00 0.00 2.41
4121 4205 0.615331 GGAAGAGGCTGATGGACACA 59.385 55.000 0.00 0.00 0.00 3.72
4169 4253 2.223745 TGGGTTTACGAGGAAGCAAAC 58.776 47.619 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.