Multiple sequence alignment - TraesCS3B01G271700

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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 TraesCS3B01G271700 chr3B 100.000 2035 0 0 1 2035 437508973 437511007 0.000000e+00 3759.0
1 TraesCS3B01G271700 chr3B 100.000 695 0 0 2302 2996 437511274 437511968 0.000000e+00 1284.0
2 TraesCS3B01G271700 chr3B 87.903 620 68 4 2383 2996 51101037 51101655 0.000000e+00 723.0
3 TraesCS3B01G271700 chr3B 82.258 186 23 5 558 733 805434283 805434468 5.170000e-33 152.0
4 TraesCS3B01G271700 chr3B 90.909 66 6 0 6 71 502633441 502633376 4.110000e-14 89.8
5 TraesCS3B01G271700 chr3D 95.267 1310 48 8 732 2035 338945238 338946539 0.000000e+00 2063.0
6 TraesCS3B01G271700 chr3A 93.119 1308 42 6 732 2035 465822153 465820890 0.000000e+00 1873.0
7 TraesCS3B01G271700 chrUn 95.442 702 16 6 2302 2996 88389919 88390611 0.000000e+00 1105.0
8 TraesCS3B01G271700 chr7D 88.033 610 68 2 2392 2996 58046221 58045612 0.000000e+00 717.0
9 TraesCS3B01G271700 chr7D 79.623 530 99 8 2391 2914 598337983 598338509 3.650000e-99 372.0
10 TraesCS3B01G271700 chr7D 91.358 81 6 1 1 80 637396603 637396523 3.160000e-20 110.0
11 TraesCS3B01G271700 chr7D 89.041 73 8 0 1 73 135338005 135337933 1.140000e-14 91.6
12 TraesCS3B01G271700 chr6D 86.174 622 69 8 113 722 18024520 18025136 0.000000e+00 656.0
13 TraesCS3B01G271700 chr6D 86.013 622 69 9 113 722 18144800 18145415 0.000000e+00 651.0
14 TraesCS3B01G271700 chr6D 87.500 280 27 5 2356 2627 26459535 26459814 1.730000e-82 316.0
15 TraesCS3B01G271700 chr1D 86.134 613 65 10 113 710 402837836 402838443 0.000000e+00 643.0
16 TraesCS3B01G271700 chr1B 85.238 630 64 19 116 722 585245689 585246312 3.280000e-174 621.0
17 TraesCS3B01G271700 chr1B 84.628 631 78 12 116 733 495753737 495753113 7.100000e-171 610.0
18 TraesCS3B01G271700 chr1B 95.775 71 3 0 1 71 666250322 666250392 6.790000e-22 115.0
19 TraesCS3B01G271700 chr2D 84.590 610 77 11 113 710 563137593 563138197 9.250000e-165 590.0
20 TraesCS3B01G271700 chr2D 85.075 335 28 12 2302 2626 598110268 598110590 3.730000e-84 322.0
21 TraesCS3B01G271700 chr7B 83.699 638 82 12 113 733 632168336 632168968 1.550000e-162 582.0
22 TraesCS3B01G271700 chr7B 86.531 542 52 10 113 639 130516659 130517194 7.200000e-161 577.0
23 TraesCS3B01G271700 chr7B 94.286 70 3 1 1 69 628335319 628335388 4.080000e-19 106.0
24 TraesCS3B01G271700 chr6B 83.710 620 89 9 2386 2996 2406962 2407578 2.590000e-160 575.0
25 TraesCS3B01G271700 chr5A 92.250 400 31 0 2597 2996 692903882 692904281 4.330000e-158 568.0
26 TraesCS3B01G271700 chr5A 85.016 307 25 12 2304 2601 692899135 692899429 2.920000e-75 292.0
27 TraesCS3B01G271700 chr5A 86.957 69 9 0 5 73 827680 827748 8.900000e-11 78.7
28 TraesCS3B01G271700 chr1A 83.361 613 79 14 116 710 71409038 71409645 2.030000e-151 545.0
29 TraesCS3B01G271700 chr2B 74.856 521 120 10 2467 2981 9036660 9037175 3.000000e-55 226.0
30 TraesCS3B01G271700 chr4D 91.304 69 6 0 3 71 501671216 501671148 8.840000e-16 95.3
31 TraesCS3B01G271700 chr5D 88.732 71 8 0 1 71 463039688 463039758 1.480000e-13 87.9
32 TraesCS3B01G271700 chr5D 79.091 110 18 4 1417 1525 59215437 59215332 1.490000e-08 71.3
33 TraesCS3B01G271700 chr4B 86.486 74 9 1 1 73 649233859 649233932 2.480000e-11 80.5


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 TraesCS3B01G271700 chr3B 437508973 437511968 2995 False 2521.5 3759 100.000 1 2996 2 chr3B.!!$F3 2995
1 TraesCS3B01G271700 chr3B 51101037 51101655 618 False 723.0 723 87.903 2383 2996 1 chr3B.!!$F1 613
2 TraesCS3B01G271700 chr3D 338945238 338946539 1301 False 2063.0 2063 95.267 732 2035 1 chr3D.!!$F1 1303
3 TraesCS3B01G271700 chr3A 465820890 465822153 1263 True 1873.0 1873 93.119 732 2035 1 chr3A.!!$R1 1303
4 TraesCS3B01G271700 chrUn 88389919 88390611 692 False 1105.0 1105 95.442 2302 2996 1 chrUn.!!$F1 694
5 TraesCS3B01G271700 chr7D 58045612 58046221 609 True 717.0 717 88.033 2392 2996 1 chr7D.!!$R1 604
6 TraesCS3B01G271700 chr7D 598337983 598338509 526 False 372.0 372 79.623 2391 2914 1 chr7D.!!$F1 523
7 TraesCS3B01G271700 chr6D 18024520 18025136 616 False 656.0 656 86.174 113 722 1 chr6D.!!$F1 609
8 TraesCS3B01G271700 chr6D 18144800 18145415 615 False 651.0 651 86.013 113 722 1 chr6D.!!$F2 609
9 TraesCS3B01G271700 chr1D 402837836 402838443 607 False 643.0 643 86.134 113 710 1 chr1D.!!$F1 597
10 TraesCS3B01G271700 chr1B 585245689 585246312 623 False 621.0 621 85.238 116 722 1 chr1B.!!$F1 606
11 TraesCS3B01G271700 chr1B 495753113 495753737 624 True 610.0 610 84.628 116 733 1 chr1B.!!$R1 617
12 TraesCS3B01G271700 chr2D 563137593 563138197 604 False 590.0 590 84.590 113 710 1 chr2D.!!$F1 597
13 TraesCS3B01G271700 chr7B 632168336 632168968 632 False 582.0 582 83.699 113 733 1 chr7B.!!$F3 620
14 TraesCS3B01G271700 chr7B 130516659 130517194 535 False 577.0 577 86.531 113 639 1 chr7B.!!$F1 526
15 TraesCS3B01G271700 chr6B 2406962 2407578 616 False 575.0 575 83.710 2386 2996 1 chr6B.!!$F1 610
16 TraesCS3B01G271700 chr1A 71409038 71409645 607 False 545.0 545 83.361 116 710 1 chr1A.!!$F1 594
17 TraesCS3B01G271700 chr2B 9036660 9037175 515 False 226.0 226 74.856 2467 2981 1 chr2B.!!$F1 514

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
68 69 0.031716 TGGGGTCTGCTAGAGATGCT 60.032 55.0 0.0 0.0 31.63 3.79 F
287 293 0.032615 AGGGTTTGTGTTCTGCCCAA 60.033 50.0 0.0 0.0 41.67 4.12 F
1050 1084 0.040204 CTTGGCCCATCTGGAACCTT 59.960 55.0 0.0 0.0 37.39 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1111 0.040646 AGTCCACGTGGTCCCAGATA 59.959 55.0 32.74 9.47 36.34 1.98 R
1987 2021 1.315690 CGTCGCCCTATCTAGTTGGA 58.684 55.0 0.00 0.00 0.00 3.53 R
2753 2795 0.888736 CACATTGTTGAGGTGGCCGA 60.889 55.0 0.00 0.00 36.44 5.54 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 3.423996 TCGCCCAAAACTGTAAAACAC 57.576 42.857 0.00 0.00 0.00 3.32
21 22 2.753452 TCGCCCAAAACTGTAAAACACA 59.247 40.909 0.00 0.00 35.30 3.72
22 23 3.192844 TCGCCCAAAACTGTAAAACACAA 59.807 39.130 0.00 0.00 36.48 3.33
23 24 3.927142 CGCCCAAAACTGTAAAACACAAA 59.073 39.130 0.00 0.00 36.48 2.83
24 25 4.389077 CGCCCAAAACTGTAAAACACAAAA 59.611 37.500 0.00 0.00 36.48 2.44
25 26 5.107065 CGCCCAAAACTGTAAAACACAAAAA 60.107 36.000 0.00 0.00 36.48 1.94
44 45 4.486125 AAAATTTGCAGGTTTGACCACT 57.514 36.364 0.00 0.00 41.95 4.00
45 46 4.486125 AAATTTGCAGGTTTGACCACTT 57.514 36.364 0.00 0.00 41.95 3.16
46 47 5.606348 AAATTTGCAGGTTTGACCACTTA 57.394 34.783 0.00 0.00 41.95 2.24
47 48 5.806654 AATTTGCAGGTTTGACCACTTAT 57.193 34.783 0.00 0.00 41.95 1.73
48 49 4.582701 TTTGCAGGTTTGACCACTTATG 57.417 40.909 0.00 0.00 41.95 1.90
49 50 3.222173 TGCAGGTTTGACCACTTATGT 57.778 42.857 0.00 0.00 41.95 2.29
50 51 2.884012 TGCAGGTTTGACCACTTATGTG 59.116 45.455 1.78 1.78 41.95 3.21
61 62 3.185246 CACTTATGTGGGGTCTGCTAG 57.815 52.381 0.80 0.00 40.33 3.42
62 63 2.766263 CACTTATGTGGGGTCTGCTAGA 59.234 50.000 0.00 0.00 40.33 2.43
63 64 3.034635 ACTTATGTGGGGTCTGCTAGAG 58.965 50.000 0.00 0.00 0.00 2.43
64 65 3.300388 CTTATGTGGGGTCTGCTAGAGA 58.700 50.000 0.00 0.00 0.00 3.10
65 66 2.485966 ATGTGGGGTCTGCTAGAGAT 57.514 50.000 0.00 0.00 31.63 2.75
66 67 1.489481 TGTGGGGTCTGCTAGAGATG 58.511 55.000 0.00 0.00 31.63 2.90
67 68 0.105778 GTGGGGTCTGCTAGAGATGC 59.894 60.000 0.00 0.00 31.63 3.91
68 69 0.031716 TGGGGTCTGCTAGAGATGCT 60.032 55.000 0.00 0.00 31.63 3.79
69 70 0.678950 GGGGTCTGCTAGAGATGCTC 59.321 60.000 0.00 0.00 31.63 4.26
70 71 1.703411 GGGTCTGCTAGAGATGCTCT 58.297 55.000 0.00 2.22 43.83 4.09
71 72 2.489985 GGGGTCTGCTAGAGATGCTCTA 60.490 54.545 0.00 4.30 41.50 2.43
72 73 3.226777 GGGTCTGCTAGAGATGCTCTAA 58.773 50.000 5.75 0.00 41.74 2.10
73 74 3.005367 GGGTCTGCTAGAGATGCTCTAAC 59.995 52.174 5.75 2.48 41.74 2.34
74 75 3.634448 GGTCTGCTAGAGATGCTCTAACA 59.366 47.826 5.75 6.53 41.74 2.41
75 76 4.499019 GGTCTGCTAGAGATGCTCTAACAC 60.499 50.000 5.75 0.45 41.74 3.32
76 77 3.634448 TCTGCTAGAGATGCTCTAACACC 59.366 47.826 5.75 0.00 41.74 4.16
77 78 2.359214 TGCTAGAGATGCTCTAACACCG 59.641 50.000 5.75 0.00 41.74 4.94
78 79 2.860582 GCTAGAGATGCTCTAACACCGC 60.861 54.545 5.75 2.28 41.74 5.68
79 80 0.461961 AGAGATGCTCTAACACCGCC 59.538 55.000 0.00 0.00 39.28 6.13
80 81 0.461961 GAGATGCTCTAACACCGCCT 59.538 55.000 0.00 0.00 0.00 5.52
81 82 0.905357 AGATGCTCTAACACCGCCTT 59.095 50.000 0.00 0.00 0.00 4.35
82 83 1.134670 AGATGCTCTAACACCGCCTTC 60.135 52.381 0.00 0.00 0.00 3.46
83 84 0.107654 ATGCTCTAACACCGCCTTCC 60.108 55.000 0.00 0.00 0.00 3.46
84 85 1.295423 GCTCTAACACCGCCTTCCA 59.705 57.895 0.00 0.00 0.00 3.53
85 86 0.741221 GCTCTAACACCGCCTTCCAG 60.741 60.000 0.00 0.00 0.00 3.86
86 87 0.608640 CTCTAACACCGCCTTCCAGT 59.391 55.000 0.00 0.00 0.00 4.00
87 88 1.822990 CTCTAACACCGCCTTCCAGTA 59.177 52.381 0.00 0.00 0.00 2.74
88 89 2.431057 CTCTAACACCGCCTTCCAGTAT 59.569 50.000 0.00 0.00 0.00 2.12
89 90 2.167693 TCTAACACCGCCTTCCAGTATG 59.832 50.000 0.00 0.00 0.00 2.39
90 91 0.981183 AACACCGCCTTCCAGTATGA 59.019 50.000 0.00 0.00 39.69 2.15
91 92 0.537188 ACACCGCCTTCCAGTATGAG 59.463 55.000 0.00 0.00 39.69 2.90
92 93 0.824109 CACCGCCTTCCAGTATGAGA 59.176 55.000 0.00 0.00 39.69 3.27
93 94 1.115467 ACCGCCTTCCAGTATGAGAG 58.885 55.000 0.00 0.00 39.69 3.20
94 95 1.115467 CCGCCTTCCAGTATGAGAGT 58.885 55.000 0.00 0.00 39.69 3.24
95 96 2.307768 CCGCCTTCCAGTATGAGAGTA 58.692 52.381 0.00 0.00 39.69 2.59
96 97 2.693591 CCGCCTTCCAGTATGAGAGTAA 59.306 50.000 0.00 0.00 39.69 2.24
97 98 3.322254 CCGCCTTCCAGTATGAGAGTAAT 59.678 47.826 0.00 0.00 39.69 1.89
98 99 4.523173 CCGCCTTCCAGTATGAGAGTAATA 59.477 45.833 0.00 0.00 39.69 0.98
99 100 5.010719 CCGCCTTCCAGTATGAGAGTAATAA 59.989 44.000 0.00 0.00 39.69 1.40
100 101 5.921408 CGCCTTCCAGTATGAGAGTAATAAC 59.079 44.000 0.00 0.00 39.69 1.89
101 102 6.224584 GCCTTCCAGTATGAGAGTAATAACC 58.775 44.000 0.00 0.00 39.69 2.85
102 103 6.183360 GCCTTCCAGTATGAGAGTAATAACCA 60.183 42.308 0.00 0.00 39.69 3.67
103 104 7.473511 GCCTTCCAGTATGAGAGTAATAACCAT 60.474 40.741 0.00 0.00 39.69 3.55
104 105 8.091449 CCTTCCAGTATGAGAGTAATAACCATC 58.909 40.741 0.00 0.00 39.69 3.51
105 106 7.540474 TCCAGTATGAGAGTAATAACCATCC 57.460 40.000 0.00 0.00 39.69 3.51
106 107 6.497259 TCCAGTATGAGAGTAATAACCATCCC 59.503 42.308 0.00 0.00 39.69 3.85
107 108 6.270000 CCAGTATGAGAGTAATAACCATCCCA 59.730 42.308 0.00 0.00 39.69 4.37
108 109 7.382110 CAGTATGAGAGTAATAACCATCCCAG 58.618 42.308 0.00 0.00 39.69 4.45
109 110 4.689612 TGAGAGTAATAACCATCCCAGC 57.310 45.455 0.00 0.00 0.00 4.85
110 111 4.037222 TGAGAGTAATAACCATCCCAGCA 58.963 43.478 0.00 0.00 0.00 4.41
111 112 4.101585 TGAGAGTAATAACCATCCCAGCAG 59.898 45.833 0.00 0.00 0.00 4.24
114 115 0.630673 AATAACCATCCCAGCAGCCA 59.369 50.000 0.00 0.00 0.00 4.75
121 122 3.655211 CCCAGCAGCCACCTCCTT 61.655 66.667 0.00 0.00 0.00 3.36
125 126 0.323178 CAGCAGCCACCTCCTTCAAT 60.323 55.000 0.00 0.00 0.00 2.57
153 154 1.538950 GTTAGGGTTCGTGTCTCTCGT 59.461 52.381 0.00 0.00 0.00 4.18
251 257 2.082231 GGAAGGGCTCCGTTTTTAGTC 58.918 52.381 0.00 0.00 33.37 2.59
279 285 6.783708 TTCAATCTTGTTAGGGTTTGTGTT 57.216 33.333 0.00 0.00 0.00 3.32
284 290 2.303175 TGTTAGGGTTTGTGTTCTGCC 58.697 47.619 0.00 0.00 0.00 4.85
287 293 0.032615 AGGGTTTGTGTTCTGCCCAA 60.033 50.000 0.00 0.00 41.67 4.12
326 332 5.513267 GGCGACTCCCTTAAGATGGAATAAT 60.513 44.000 3.36 0.00 0.00 1.28
332 338 6.841601 TCCCTTAAGATGGAATAATGGTCTG 58.158 40.000 3.36 0.00 0.00 3.51
333 339 5.474876 CCCTTAAGATGGAATAATGGTCTGC 59.525 44.000 3.36 0.00 0.00 4.26
334 340 5.474876 CCTTAAGATGGAATAATGGTCTGCC 59.525 44.000 3.36 0.00 0.00 4.85
335 341 3.515602 AGATGGAATAATGGTCTGCCC 57.484 47.619 0.00 0.00 0.00 5.36
336 342 2.154462 GATGGAATAATGGTCTGCCCG 58.846 52.381 0.00 0.00 35.15 6.13
413 419 0.674534 GTGTCTCCGGCGGATCTATT 59.325 55.000 31.23 0.00 0.00 1.73
427 433 5.394115 GCGGATCTATTTTTGGTGGATTTGT 60.394 40.000 0.00 0.00 0.00 2.83
430 436 7.576666 CGGATCTATTTTTGGTGGATTTGTTCA 60.577 37.037 0.00 0.00 0.00 3.18
443 459 5.221362 TGGATTTGTTCAGAGTTCGTCTACA 60.221 40.000 0.00 0.00 32.51 2.74
523 544 0.639943 TCTGGGGTGCTGGTCCTATA 59.360 55.000 0.00 0.00 0.00 1.31
544 565 1.084289 GGCCTTATCGCGACAACTTT 58.916 50.000 12.93 0.00 0.00 2.66
559 580 5.391736 CGACAACTTTCCGACTGTCTACTAT 60.392 44.000 6.21 0.00 36.80 2.12
600 621 1.371022 CGATGGAGGAGCGATGACG 60.371 63.158 0.00 0.00 34.57 4.35
639 661 2.135933 GCTTCAGTGCTTGTAGTCGTT 58.864 47.619 0.00 0.00 0.00 3.85
644 666 4.878439 TCAGTGCTTGTAGTCGTTGTTAT 58.122 39.130 0.00 0.00 0.00 1.89
658 686 5.515626 GTCGTTGTTATGTGGTCTACAGATC 59.484 44.000 0.00 0.00 43.80 2.75
711 739 7.658179 TGCTATGATCGAAAATGAATAGACC 57.342 36.000 0.00 0.00 0.00 3.85
716 744 8.915057 ATGATCGAAAATGAATAGACCAGAAT 57.085 30.769 0.00 0.00 0.00 2.40
754 782 3.435186 GCCTTCCAGTGCCGAAGC 61.435 66.667 4.16 0.00 36.26 3.86
787 815 4.563976 GCGCTATTACGTGTTCTTTCCTTA 59.436 41.667 0.00 0.00 34.88 2.69
796 824 3.055312 GTGTTCTTTCCTTAGACCGGGAT 60.055 47.826 6.32 0.00 0.00 3.85
814 842 0.911769 ATGAGGAATCCGAGTGCCAA 59.088 50.000 0.00 0.00 0.00 4.52
840 868 2.727392 CCCCGCCAGTCCGATAACA 61.727 63.158 0.00 0.00 0.00 2.41
864 893 3.334691 TCCAACTTGCCTCTTCAATACG 58.665 45.455 0.00 0.00 0.00 3.06
889 920 3.480470 AGTATACATGGGAAGTGCATGC 58.520 45.455 11.82 11.82 0.00 4.06
892 923 0.394762 ACATGGGAAGTGCATGCGAT 60.395 50.000 14.09 0.04 0.00 4.58
964 995 2.127869 CCCTCCTCGGCTCGATCAA 61.128 63.158 0.00 0.00 34.61 2.57
1050 1084 0.040204 CTTGGCCCATCTGGAACCTT 59.960 55.000 0.00 0.00 37.39 3.50
1091 1125 2.423898 CGCCTATCTGGGACCACGT 61.424 63.158 0.00 0.00 36.00 4.49
1328 1362 1.811266 CCATGTCCTTCGACCGCAG 60.811 63.158 0.00 0.00 38.32 5.18
1368 1402 2.363276 ATGGAGTACGTCGGGCCA 60.363 61.111 4.39 0.00 0.00 5.36
1422 1456 2.285368 TGCCCGTTCCAGGAGGAT 60.285 61.111 0.00 0.00 45.26 3.24
1425 1459 1.221840 CCCGTTCCAGGAGGATGTG 59.778 63.158 0.00 0.00 45.26 3.21
1433 1467 1.685765 AGGAGGATGTGGTGCGCTA 60.686 57.895 9.73 0.00 0.00 4.26
1522 1556 1.906824 AAGCCCGAGAACGTCCTCA 60.907 57.895 1.75 0.00 37.88 3.86
1576 1610 1.679977 GCCATGCACATGTCCCAGT 60.680 57.895 9.63 0.00 37.11 4.00
1708 1742 1.149627 GAGCTCCTCCTAGGCGAGA 59.850 63.158 23.05 11.15 34.61 4.04
1987 2021 0.036010 CGAGCTTCCATGGTTCACCT 60.036 55.000 12.58 2.34 36.82 4.00
2001 2035 3.388350 GGTTCACCTCCAACTAGATAGGG 59.612 52.174 0.00 0.00 33.16 3.53
2023 2057 1.404391 GACGCTCCGGAAACTCTGATA 59.596 52.381 5.23 0.00 0.00 2.15
2462 2498 1.155624 GGGTAGTAGGGAGGCGGAT 59.844 63.158 0.00 0.00 0.00 4.18
2721 2763 3.692406 GAGGTGGTCGGCCGTCTT 61.692 66.667 27.15 10.66 37.67 3.01
2836 2878 0.889186 GGAGCCAGGCAAAGAAACGA 60.889 55.000 15.80 0.00 0.00 3.85
2921 2964 0.179468 GCATAGCTGGTAAACCCCGA 59.821 55.000 0.00 0.00 34.29 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.753452 TGTGTTTTACAGTTTTGGGCGA 59.247 40.909 0.00 0.00 33.42 5.54
1 2 3.152261 TGTGTTTTACAGTTTTGGGCG 57.848 42.857 0.00 0.00 33.42 6.13
22 23 4.842574 AGTGGTCAAACCTGCAAATTTTT 58.157 34.783 0.00 0.00 39.58 1.94
23 24 4.486125 AGTGGTCAAACCTGCAAATTTT 57.514 36.364 0.00 0.00 39.58 1.82
24 25 4.486125 AAGTGGTCAAACCTGCAAATTT 57.514 36.364 0.00 0.00 39.58 1.82
25 26 5.070313 ACATAAGTGGTCAAACCTGCAAATT 59.930 36.000 0.00 0.00 39.58 1.82
26 27 4.588528 ACATAAGTGGTCAAACCTGCAAAT 59.411 37.500 0.00 0.00 39.58 2.32
27 28 3.957497 ACATAAGTGGTCAAACCTGCAAA 59.043 39.130 0.00 0.00 39.58 3.68
28 29 3.317711 CACATAAGTGGTCAAACCTGCAA 59.682 43.478 0.00 0.00 42.13 4.08
29 30 2.884012 CACATAAGTGGTCAAACCTGCA 59.116 45.455 0.00 0.00 42.13 4.41
30 31 3.559238 CACATAAGTGGTCAAACCTGC 57.441 47.619 0.00 0.00 42.13 4.85
41 42 2.766263 TCTAGCAGACCCCACATAAGTG 59.234 50.000 0.00 0.00 45.47 3.16
42 43 3.034635 CTCTAGCAGACCCCACATAAGT 58.965 50.000 0.00 0.00 0.00 2.24
43 44 3.300388 TCTCTAGCAGACCCCACATAAG 58.700 50.000 0.00 0.00 0.00 1.73
44 45 3.398318 TCTCTAGCAGACCCCACATAA 57.602 47.619 0.00 0.00 0.00 1.90
45 46 3.234353 CATCTCTAGCAGACCCCACATA 58.766 50.000 0.00 0.00 32.26 2.29
46 47 2.045524 CATCTCTAGCAGACCCCACAT 58.954 52.381 0.00 0.00 32.26 3.21
47 48 1.489481 CATCTCTAGCAGACCCCACA 58.511 55.000 0.00 0.00 32.26 4.17
48 49 0.105778 GCATCTCTAGCAGACCCCAC 59.894 60.000 0.00 0.00 32.26 4.61
49 50 0.031716 AGCATCTCTAGCAGACCCCA 60.032 55.000 0.00 0.00 32.26 4.96
50 51 0.678950 GAGCATCTCTAGCAGACCCC 59.321 60.000 0.00 0.00 32.26 4.95
63 64 1.291132 GAAGGCGGTGTTAGAGCATC 58.709 55.000 0.00 0.00 0.00 3.91
64 65 0.107654 GGAAGGCGGTGTTAGAGCAT 60.108 55.000 0.00 0.00 0.00 3.79
65 66 1.295423 GGAAGGCGGTGTTAGAGCA 59.705 57.895 0.00 0.00 0.00 4.26
66 67 0.741221 CTGGAAGGCGGTGTTAGAGC 60.741 60.000 0.00 0.00 0.00 4.09
67 68 0.608640 ACTGGAAGGCGGTGTTAGAG 59.391 55.000 0.00 0.00 39.30 2.43
68 69 1.927487 TACTGGAAGGCGGTGTTAGA 58.073 50.000 0.00 0.00 39.30 2.10
69 70 2.167693 TCATACTGGAAGGCGGTGTTAG 59.832 50.000 0.00 0.00 39.30 2.34
70 71 2.167693 CTCATACTGGAAGGCGGTGTTA 59.832 50.000 0.00 0.00 39.30 2.41
71 72 0.981183 TCATACTGGAAGGCGGTGTT 59.019 50.000 0.00 0.00 39.30 3.32
72 73 0.537188 CTCATACTGGAAGGCGGTGT 59.463 55.000 0.00 0.00 39.30 4.16
73 74 0.824109 TCTCATACTGGAAGGCGGTG 59.176 55.000 0.00 0.00 39.30 4.94
74 75 1.115467 CTCTCATACTGGAAGGCGGT 58.885 55.000 0.00 0.00 39.30 5.68
75 76 1.115467 ACTCTCATACTGGAAGGCGG 58.885 55.000 0.00 0.00 39.30 6.13
76 77 4.592485 ATTACTCTCATACTGGAAGGCG 57.408 45.455 0.00 0.00 39.30 5.52
77 78 6.183360 TGGTTATTACTCTCATACTGGAAGGC 60.183 42.308 0.00 0.00 39.30 4.35
78 79 7.361457 TGGTTATTACTCTCATACTGGAAGG 57.639 40.000 0.00 0.00 39.30 3.46
79 80 8.091449 GGATGGTTATTACTCTCATACTGGAAG 58.909 40.741 0.00 0.00 42.29 3.46
80 81 7.016268 GGGATGGTTATTACTCTCATACTGGAA 59.984 40.741 0.00 0.00 0.00 3.53
81 82 6.497259 GGGATGGTTATTACTCTCATACTGGA 59.503 42.308 0.00 0.00 0.00 3.86
82 83 6.270000 TGGGATGGTTATTACTCTCATACTGG 59.730 42.308 0.00 0.00 0.00 4.00
83 84 7.303182 TGGGATGGTTATTACTCTCATACTG 57.697 40.000 0.00 0.00 0.00 2.74
84 85 6.014156 GCTGGGATGGTTATTACTCTCATACT 60.014 42.308 0.00 0.00 0.00 2.12
85 86 6.166982 GCTGGGATGGTTATTACTCTCATAC 58.833 44.000 0.00 0.00 0.00 2.39
86 87 5.843969 TGCTGGGATGGTTATTACTCTCATA 59.156 40.000 0.00 0.00 0.00 2.15
87 88 4.660303 TGCTGGGATGGTTATTACTCTCAT 59.340 41.667 0.00 0.00 0.00 2.90
88 89 4.037222 TGCTGGGATGGTTATTACTCTCA 58.963 43.478 0.00 0.00 0.00 3.27
89 90 4.636249 CTGCTGGGATGGTTATTACTCTC 58.364 47.826 0.00 0.00 0.00 3.20
90 91 3.181450 GCTGCTGGGATGGTTATTACTCT 60.181 47.826 0.00 0.00 0.00 3.24
91 92 3.142174 GCTGCTGGGATGGTTATTACTC 58.858 50.000 0.00 0.00 0.00 2.59
92 93 2.158608 GGCTGCTGGGATGGTTATTACT 60.159 50.000 0.00 0.00 0.00 2.24
93 94 2.230660 GGCTGCTGGGATGGTTATTAC 58.769 52.381 0.00 0.00 0.00 1.89
94 95 1.849692 TGGCTGCTGGGATGGTTATTA 59.150 47.619 0.00 0.00 0.00 0.98
95 96 0.630673 TGGCTGCTGGGATGGTTATT 59.369 50.000 0.00 0.00 0.00 1.40
96 97 0.106519 GTGGCTGCTGGGATGGTTAT 60.107 55.000 0.00 0.00 0.00 1.89
97 98 1.302949 GTGGCTGCTGGGATGGTTA 59.697 57.895 0.00 0.00 0.00 2.85
98 99 2.036256 GTGGCTGCTGGGATGGTT 59.964 61.111 0.00 0.00 0.00 3.67
99 100 4.052518 GGTGGCTGCTGGGATGGT 62.053 66.667 0.00 0.00 0.00 3.55
100 101 3.711059 GAGGTGGCTGCTGGGATGG 62.711 68.421 0.00 0.00 0.00 3.51
101 102 2.124403 GAGGTGGCTGCTGGGATG 60.124 66.667 0.00 0.00 0.00 3.51
102 103 3.415087 GGAGGTGGCTGCTGGGAT 61.415 66.667 0.00 0.00 0.00 3.85
103 104 4.664267 AGGAGGTGGCTGCTGGGA 62.664 66.667 0.00 0.00 0.00 4.37
104 105 3.635268 GAAGGAGGTGGCTGCTGGG 62.635 68.421 0.00 0.00 0.00 4.45
105 106 2.045536 GAAGGAGGTGGCTGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
106 107 0.323178 ATTGAAGGAGGTGGCTGCTG 60.323 55.000 0.00 0.00 0.00 4.41
107 108 1.289160 TATTGAAGGAGGTGGCTGCT 58.711 50.000 0.00 0.00 0.00 4.24
108 109 2.128771 TTATTGAAGGAGGTGGCTGC 57.871 50.000 0.00 0.00 0.00 5.25
109 110 3.955471 TCTTTATTGAAGGAGGTGGCTG 58.045 45.455 0.00 0.00 35.98 4.85
110 111 4.657814 TTCTTTATTGAAGGAGGTGGCT 57.342 40.909 0.00 0.00 35.98 4.75
111 112 4.767409 ACTTTCTTTATTGAAGGAGGTGGC 59.233 41.667 0.00 0.00 32.29 5.01
114 115 7.175797 CCCTAACTTTCTTTATTGAAGGAGGT 58.824 38.462 0.00 0.00 34.82 3.85
121 122 6.993902 ACACGAACCCTAACTTTCTTTATTGA 59.006 34.615 0.00 0.00 0.00 2.57
125 126 6.041296 AGAGACACGAACCCTAACTTTCTTTA 59.959 38.462 0.00 0.00 0.00 1.85
233 234 3.503800 AAGACTAAAAACGGAGCCCTT 57.496 42.857 0.00 0.00 0.00 3.95
279 285 1.872237 CGTCTCGTCTTTTTGGGCAGA 60.872 52.381 0.00 0.00 0.00 4.26
284 290 1.491563 CGCCGTCTCGTCTTTTTGG 59.508 57.895 0.00 0.00 0.00 3.28
287 293 2.737376 GCCGCCGTCTCGTCTTTT 60.737 61.111 0.00 0.00 0.00 2.27
306 312 6.621514 AGACCATTATTCCATCTTAAGGGAGT 59.378 38.462 1.85 2.09 36.55 3.85
313 319 4.504864 CGGGCAGACCATTATTCCATCTTA 60.505 45.833 0.00 0.00 40.22 2.10
362 368 1.134401 CCCACCAACGATGCTAGACAT 60.134 52.381 0.00 0.00 43.54 3.06
413 419 5.449862 CGAACTCTGAACAAATCCACCAAAA 60.450 40.000 0.00 0.00 0.00 2.44
427 433 4.023450 ACACGAATGTAGACGAACTCTGAA 60.023 41.667 0.00 0.00 37.26 3.02
430 436 3.252701 ACACACGAATGTAGACGAACTCT 59.747 43.478 0.00 0.00 36.72 3.24
443 459 1.871039 CCAAACCGAAGACACACGAAT 59.129 47.619 0.00 0.00 0.00 3.34
523 544 1.153429 GTTGTCGCGATAAGGCCCT 60.153 57.895 19.08 0.00 0.00 5.19
532 553 0.937699 CAGTCGGAAAGTTGTCGCGA 60.938 55.000 3.71 3.71 0.00 5.87
534 555 0.507358 GACAGTCGGAAAGTTGTCGC 59.493 55.000 0.00 0.00 31.72 5.19
544 565 6.432162 ACAACTTGTTATAGTAGACAGTCGGA 59.568 38.462 0.00 0.00 0.00 4.55
559 580 1.541670 GGAGTCGGGCACAACTTGTTA 60.542 52.381 0.00 0.00 0.00 2.41
679 707 8.207521 TCATTTTCGATCATAGCAATACAACA 57.792 30.769 0.00 0.00 0.00 3.33
686 714 7.714813 TGGTCTATTCATTTTCGATCATAGCAA 59.285 33.333 0.00 0.00 0.00 3.91
787 815 2.841595 GGATTCCTCATCCCGGTCT 58.158 57.895 0.00 0.00 45.71 3.85
796 824 0.036388 GTTGGCACTCGGATTCCTCA 60.036 55.000 0.30 0.00 0.00 3.86
814 842 2.528378 ACTGGCGGGGTACAAGGT 60.528 61.111 0.00 0.00 0.00 3.50
840 868 3.297134 TTGAAGAGGCAAGTTGGAGTT 57.703 42.857 4.75 0.00 0.00 3.01
864 893 5.531122 TGCACTTCCCATGTATACTACTC 57.469 43.478 4.17 0.00 0.00 2.59
889 920 2.107141 GGGGAGAAGGTCGCATCG 59.893 66.667 0.00 0.00 39.95 3.84
892 923 1.682684 GAGAGGGGAGAAGGTCGCA 60.683 63.158 0.00 0.00 39.95 5.10
964 995 3.426615 AGAAGATGGACAGAGAACGAGT 58.573 45.455 0.00 0.00 0.00 4.18
974 1005 0.687757 CGGAGGGGAGAAGATGGACA 60.688 60.000 0.00 0.00 0.00 4.02
1050 1084 2.036098 TCGACCCCGTAGCCTTGA 59.964 61.111 0.00 0.00 37.05 3.02
1073 1107 2.417516 CGTGGTCCCAGATAGGCG 59.582 66.667 0.00 0.00 35.39 5.52
1077 1111 0.040646 AGTCCACGTGGTCCCAGATA 59.959 55.000 32.74 9.47 36.34 1.98
1079 1113 2.200370 AGTCCACGTGGTCCCAGA 59.800 61.111 32.74 11.09 36.34 3.86
1368 1402 2.600769 AGGACGTCGTGGAGGCTT 60.601 61.111 10.45 0.00 0.00 4.35
1433 1467 2.437359 GAAGCTGCCGCATGAGGT 60.437 61.111 17.41 0.00 39.10 3.85
1564 1598 2.268920 CGGGGACTGGGACATGTG 59.731 66.667 1.15 0.00 38.20 3.21
1565 1599 3.717294 GCGGGGACTGGGACATGT 61.717 66.667 0.00 0.00 38.20 3.21
1987 2021 1.315690 CGTCGCCCTATCTAGTTGGA 58.684 55.000 0.00 0.00 0.00 3.53
2001 2035 3.179939 GAGTTTCCGGAGCGTCGC 61.180 66.667 9.80 9.80 0.00 5.19
2673 2715 2.278330 CCCTTTGCCCAGCAGTTCC 61.278 63.158 0.00 0.00 40.61 3.62
2721 2763 2.127869 ATCTGCTCGGCTCCGCTTA 61.128 57.895 2.96 0.00 39.59 3.09
2753 2795 0.888736 CACATTGTTGAGGTGGCCGA 60.889 55.000 0.00 0.00 36.44 5.54
2827 2869 1.681264 CCAAGCAGGGTTCGTTTCTTT 59.319 47.619 0.00 0.00 0.00 2.52
2836 2878 1.296715 CTACGCTCCAAGCAGGGTT 59.703 57.895 0.00 0.00 42.58 4.11
2921 2964 1.000646 GGACCGACCTCTCCTCTGT 60.001 63.158 0.00 0.00 35.41 3.41


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

AutoCloner maintained by Alex Coulton.