Multiple sequence alignment - TraesCS7A01G032700

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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 TraesCS7A01G032700 chr7A 100.000 4246 0 0 1 4246 13831914 13836159 0.000000e+00 7841.0
1 TraesCS7A01G032700 chr7A 81.445 1509 229 38 1954 3447 63783733 63785205 0.000000e+00 1188.0
2 TraesCS7A01G032700 chr7A 81.756 877 148 7 366 1241 63781888 63782753 0.000000e+00 723.0
3 TraesCS7A01G032700 chr7A 85.149 202 26 3 1018 1216 20513108 20512908 2.000000e-48 204.0
4 TraesCS7A01G032700 chr7D 96.607 3861 114 10 1 3854 14590137 14593987 0.000000e+00 6388.0
5 TraesCS7A01G032700 chr7D 80.316 1138 175 34 2326 3447 59469035 59470139 0.000000e+00 815.0
6 TraesCS7A01G032700 chr7D 82.106 883 139 9 366 1241 59466873 59467743 0.000000e+00 737.0
7 TraesCS7A01G032700 chr7D 84.682 346 49 4 1954 2298 59468694 59469036 4.070000e-90 342.0
8 TraesCS7A01G032700 chr7D 92.424 198 14 1 4050 4246 103193819 103194016 8.990000e-72 281.0
9 TraesCS7A01G032700 chr7D 90.000 200 10 4 3847 4039 14594386 14594582 2.530000e-62 250.0
10 TraesCS7A01G032700 chrUn 93.649 2598 123 23 59 2627 335449095 335446511 0.000000e+00 3845.0
11 TraesCS7A01G032700 chrUn 94.493 1271 64 4 1 1269 307992954 307991688 0.000000e+00 1954.0
12 TraesCS7A01G032700 chrUn 92.839 796 42 3 2610 3405 348216588 348217368 0.000000e+00 1140.0
13 TraesCS7A01G032700 chrUn 76.285 253 45 12 1544 1790 15442220 15441977 2.070000e-23 121.0
14 TraesCS7A01G032700 chrUn 76.793 237 42 10 1544 1776 283167169 283167396 2.070000e-23 121.0
15 TraesCS7A01G032700 chrUn 76.991 226 40 9 1555 1776 15722629 15722846 7.460000e-23 119.0
16 TraesCS7A01G032700 chrUn 76.543 243 42 13 1555 1790 358520486 358520252 7.460000e-23 119.0
17 TraesCS7A01G032700 chrUn 78.767 146 28 2 1631 1776 357010893 357011035 1.260000e-15 95.3
18 TraesCS7A01G032700 chr4A 92.904 2297 105 28 59 2299 722295037 722292743 0.000000e+00 3286.0
19 TraesCS7A01G032700 chr4A 96.556 1568 44 4 2288 3854 722288449 722286891 0.000000e+00 2588.0
20 TraesCS7A01G032700 chr4A 94.414 1271 65 4 1 1269 722296447 722295181 0.000000e+00 1949.0
21 TraesCS7A01G032700 chr4A 78.342 1182 202 41 2270 3434 722331523 722330379 0.000000e+00 715.0
22 TraesCS7A01G032700 chr4A 77.117 874 158 24 2326 3179 611265102 611264251 6.430000e-128 468.0
23 TraesCS7A01G032700 chr4A 93.401 197 11 2 4050 4244 646253971 646253775 1.490000e-74 291.0
24 TraesCS7A01G032700 chr4A 77.174 460 89 8 1339 1787 722332408 722331954 1.960000e-63 254.0
25 TraesCS7A01G032700 chr4A 86.266 233 31 1 1955 2187 722331796 722331565 7.050000e-63 252.0
26 TraesCS7A01G032700 chr4A 87.000 200 18 2 3847 4039 722286311 722286113 7.150000e-53 219.0
27 TraesCS7A01G032700 chr4A 90.000 90 7 2 3248 3336 722320505 722320417 9.650000e-22 115.0
28 TraesCS7A01G032700 chr3B 79.298 826 135 21 2346 3157 22459124 22458321 2.890000e-151 545.0
29 TraesCS7A01G032700 chr3B 80.769 208 33 4 1016 1220 22322514 22322311 5.680000e-34 156.0
30 TraesCS7A01G032700 chr3D 79.545 616 99 15 2346 2947 15342004 15341402 8.490000e-112 414.0
31 TraesCS7A01G032700 chr3D 91.919 198 15 1 4050 4246 378920359 378920556 4.180000e-70 276.0
32 TraesCS7A01G032700 chr2B 92.754 207 13 2 4040 4246 58277236 58277440 8.930000e-77 298.0
33 TraesCS7A01G032700 chr6B 93.333 195 12 1 4050 4244 686198391 686198584 1.930000e-73 287.0
34 TraesCS7A01G032700 chr6D 91.500 200 14 1 4050 4246 307520225 307520424 5.410000e-69 272.0
35 TraesCS7A01G032700 chr5A 91.282 195 17 0 4050 4244 482623513 482623707 2.520000e-67 267.0
36 TraesCS7A01G032700 chr6A 90.769 195 18 0 4050 4244 184791391 184791197 1.170000e-65 261.0
37 TraesCS7A01G032700 chr4B 90.256 195 19 0 4050 4244 472424867 472424673 5.450000e-64 255.0


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 TraesCS7A01G032700 chr7A 13831914 13836159 4245 False 7841.000000 7841 100.0000 1 4246 1 chr7A.!!$F1 4245
1 TraesCS7A01G032700 chr7A 63781888 63785205 3317 False 955.500000 1188 81.6005 366 3447 2 chr7A.!!$F2 3081
2 TraesCS7A01G032700 chr7D 14590137 14594582 4445 False 3319.000000 6388 93.3035 1 4039 2 chr7D.!!$F2 4038
3 TraesCS7A01G032700 chr7D 59466873 59470139 3266 False 631.333333 815 82.3680 366 3447 3 chr7D.!!$F3 3081
4 TraesCS7A01G032700 chrUn 335446511 335449095 2584 True 3845.000000 3845 93.6490 59 2627 1 chrUn.!!$R3 2568
5 TraesCS7A01G032700 chrUn 307991688 307992954 1266 True 1954.000000 1954 94.4930 1 1269 1 chrUn.!!$R2 1268
6 TraesCS7A01G032700 chrUn 348216588 348217368 780 False 1140.000000 1140 92.8390 2610 3405 1 chrUn.!!$F3 795
7 TraesCS7A01G032700 chr4A 722292743 722296447 3704 True 2617.500000 3286 93.6590 1 2299 2 chr4A.!!$R5 2298
8 TraesCS7A01G032700 chr4A 722286113 722288449 2336 True 1403.500000 2588 91.7780 2288 4039 2 chr4A.!!$R4 1751
9 TraesCS7A01G032700 chr4A 611264251 611265102 851 True 468.000000 468 77.1170 2326 3179 1 chr4A.!!$R1 853
10 TraesCS7A01G032700 chr4A 722330379 722332408 2029 True 407.000000 715 80.5940 1339 3434 3 chr4A.!!$R6 2095
11 TraesCS7A01G032700 chr3B 22458321 22459124 803 True 545.000000 545 79.2980 2346 3157 1 chr3B.!!$R2 811
12 TraesCS7A01G032700 chr3D 15341402 15342004 602 True 414.000000 414 79.5450 2346 2947 1 chr3D.!!$R1 601

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
840 845 1.821332 CAGCGATTTCCTCAGCCCC 60.821 63.158 0.0 0.0 0.0 5.80 F
1744 3445 0.035439 GAGAAGGTGGATTTGGCCGA 60.035 55.000 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3789 3.439857 TCCCTGAAGAAAATGTCCCTG 57.560 47.619 0.0 0.0 0.00 4.45 R
3605 5494 2.968574 TCTGATTACCAGATGGCTCTCC 59.031 50.000 0.0 0.0 46.38 3.71 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
54 55 7.827701 TGACACAAAAGTATGGTGTTGTAAAA 58.172 30.769 0.00 0.00 45.09 1.52
86 88 8.717821 GCAATATAATAGCCACGAAGTCATAAA 58.282 33.333 0.00 0.00 41.61 1.40
124 126 9.471702 AAAAGATGTTGTCCAATTGATAGATCT 57.528 29.630 7.12 0.00 0.00 2.75
135 137 7.835682 TCCAATTGATAGATCTTGTGTTGGAAT 59.164 33.333 18.80 0.00 39.48 3.01
147 149 5.867903 TGTGTTGGAATTTTCATTCAGGT 57.132 34.783 0.00 0.00 40.77 4.00
220 222 9.424319 TGGATTAACTAATTGCTCTATTCGATC 57.576 33.333 0.00 0.00 0.00 3.69
241 244 4.715523 GCCGGTTGGTAGCTGCCA 62.716 66.667 20.78 20.78 37.67 4.92
266 269 2.611974 AATTGTTTCATCGACACCGC 57.388 45.000 0.00 0.00 35.37 5.68
446 451 3.737850 AGCTAGCTAACATGCTGATTCC 58.262 45.455 17.69 0.00 43.87 3.01
615 620 4.721111 CAGCAATTTGCCGCCGCA 62.721 61.111 17.51 0.00 46.52 5.69
819 824 2.344203 CGTCCTCGGCTTCTCTGGT 61.344 63.158 0.00 0.00 0.00 4.00
840 845 1.821332 CAGCGATTTCCTCAGCCCC 60.821 63.158 0.00 0.00 0.00 5.80
1029 1037 3.111939 CCGACGCTCTACTCCCTG 58.888 66.667 0.00 0.00 0.00 4.45
1074 1082 2.673523 GGAGACTGCCTGGCATGT 59.326 61.111 23.64 20.96 38.13 3.21
1134 1142 2.520982 CGCCAGGGAGGACGGATA 60.521 66.667 0.00 0.00 41.22 2.59
1220 2579 2.366590 TCAATCCATCCTCCATCACTCG 59.633 50.000 0.00 0.00 0.00 4.18
1226 2585 2.801631 CCTCCATCACTCGGGCTCC 61.802 68.421 0.00 0.00 0.00 4.70
1281 2897 9.621046 TGTTCGTTTTATTTAATTTTGTTTCGC 57.379 25.926 0.00 0.00 0.00 4.70
1334 2950 7.066163 TGTTGATCATGCTCTTGATAATTCGTT 59.934 33.333 0.00 0.00 36.48 3.85
1390 3007 7.868922 TCAAAGCATGGATAATTGCAATATGTC 59.131 33.333 13.39 10.72 41.35 3.06
1477 3097 4.457949 GGATCAGAAAACGTGGGTAAATGT 59.542 41.667 0.00 0.00 0.00 2.71
1596 3297 2.953466 TTGCGAGAAAGGCGTACTAT 57.047 45.000 0.00 0.00 0.00 2.12
1743 3444 1.032114 GGAGAAGGTGGATTTGGCCG 61.032 60.000 0.00 0.00 0.00 6.13
1744 3445 0.035439 GAGAAGGTGGATTTGGCCGA 60.035 55.000 0.00 0.00 0.00 5.54
1878 3654 3.764434 AGTATCCCACATATAGCCTCGTG 59.236 47.826 0.00 0.00 0.00 4.35
2035 3859 1.963515 ACATTCAGGACAAGGTTTGGC 59.036 47.619 0.00 0.00 38.21 4.52
3167 5055 5.190677 CCACCGTATTTCAATCTAAGGGTT 58.809 41.667 0.00 0.00 0.00 4.11
3512 5401 6.346096 GCTGTAGATAATCCCACAAACTACA 58.654 40.000 0.00 0.00 37.15 2.74
3572 5461 2.086869 AGCATCTTCATCAAACCACCG 58.913 47.619 0.00 0.00 0.00 4.94
3588 5477 1.069204 CACCGTGCATAGATAGCCAGT 59.931 52.381 0.00 0.00 0.00 4.00
3590 5479 2.170607 ACCGTGCATAGATAGCCAGTTT 59.829 45.455 0.00 0.00 0.00 2.66
3605 5494 6.932356 AGCCAGTTTATGATGATAAGTGTG 57.068 37.500 0.00 0.00 0.00 3.82
3742 5631 0.464452 GAGTAGGATCAACCGGGGTG 59.536 60.000 5.48 5.48 44.74 4.61
3899 6376 7.913674 AGAGATCAAAAGTGAATCCAACTAC 57.086 36.000 0.00 0.00 37.30 2.73
3900 6377 7.453393 AGAGATCAAAAGTGAATCCAACTACA 58.547 34.615 0.00 0.00 37.30 2.74
3977 6454 1.155889 GCGGGGCAAAAAGGAAAATG 58.844 50.000 0.00 0.00 0.00 2.32
3996 6480 9.083080 GGAAAATGTAAACCAACTATTGCATAC 57.917 33.333 0.00 0.00 32.61 2.39
4012 6496 7.928307 ATTGCATACATTACACAAGACTTCT 57.072 32.000 0.00 0.00 0.00 2.85
4028 6512 4.104738 AGACTTCTGGGACAAGGATGAAAA 59.895 41.667 0.00 0.00 38.70 2.29
4055 6539 5.961396 AGACTATAATACTACTGGGTGCG 57.039 43.478 0.00 0.00 0.00 5.34
4056 6540 5.383476 AGACTATAATACTACTGGGTGCGT 58.617 41.667 0.00 0.00 0.00 5.24
4057 6541 5.832060 AGACTATAATACTACTGGGTGCGTT 59.168 40.000 0.00 0.00 0.00 4.84
4058 6542 6.323225 AGACTATAATACTACTGGGTGCGTTT 59.677 38.462 0.00 0.00 0.00 3.60
4059 6543 6.278363 ACTATAATACTACTGGGTGCGTTTG 58.722 40.000 0.00 0.00 0.00 2.93
4060 6544 2.396590 ATACTACTGGGTGCGTTTGG 57.603 50.000 0.00 0.00 0.00 3.28
4061 6545 1.340088 TACTACTGGGTGCGTTTGGA 58.660 50.000 0.00 0.00 0.00 3.53
4062 6546 0.690762 ACTACTGGGTGCGTTTGGAT 59.309 50.000 0.00 0.00 0.00 3.41
4063 6547 1.086696 CTACTGGGTGCGTTTGGATG 58.913 55.000 0.00 0.00 0.00 3.51
4064 6548 0.958382 TACTGGGTGCGTTTGGATGC 60.958 55.000 0.00 0.00 38.31 3.91
4065 6549 2.203408 TGGGTGCGTTTGGATGCA 60.203 55.556 0.00 0.00 45.21 3.96
4072 6556 3.932545 TGCGTTTGGATGCAAAGTATT 57.067 38.095 13.15 0.00 44.47 1.89
4073 6557 4.250116 TGCGTTTGGATGCAAAGTATTT 57.750 36.364 13.15 0.00 44.47 1.40
4074 6558 4.626042 TGCGTTTGGATGCAAAGTATTTT 58.374 34.783 13.15 0.00 44.47 1.82
4075 6559 5.053145 TGCGTTTGGATGCAAAGTATTTTT 58.947 33.333 13.15 0.00 44.47 1.94
4076 6560 5.050499 TGCGTTTGGATGCAAAGTATTTTTG 60.050 36.000 13.15 0.00 44.47 2.44
4077 6561 5.050431 GCGTTTGGATGCAAAGTATTTTTGT 60.050 36.000 13.15 0.00 35.03 2.83
4078 6562 6.144724 GCGTTTGGATGCAAAGTATTTTTGTA 59.855 34.615 13.15 0.00 35.03 2.41
4079 6563 7.619161 GCGTTTGGATGCAAAGTATTTTTGTAG 60.619 37.037 13.15 0.00 35.03 2.74
4080 6564 7.381139 CGTTTGGATGCAAAGTATTTTTGTAGT 59.619 33.333 13.15 0.00 35.03 2.73
4081 6565 9.040939 GTTTGGATGCAAAGTATTTTTGTAGTT 57.959 29.630 13.15 0.00 35.03 2.24
4082 6566 9.606631 TTTGGATGCAAAGTATTTTTGTAGTTT 57.393 25.926 8.47 0.00 35.03 2.66
4083 6567 9.606631 TTGGATGCAAAGTATTTTTGTAGTTTT 57.393 25.926 0.00 0.00 35.03 2.43
4084 6568 9.606631 TGGATGCAAAGTATTTTTGTAGTTTTT 57.393 25.926 0.00 0.00 35.03 1.94
4098 6582 7.894376 TTGTAGTTTTTCTAGAATACCGTGG 57.106 36.000 5.89 0.00 28.88 4.94
4099 6583 6.996509 TGTAGTTTTTCTAGAATACCGTGGT 58.003 36.000 5.89 0.00 0.00 4.16
4100 6584 7.444299 TGTAGTTTTTCTAGAATACCGTGGTT 58.556 34.615 5.89 0.00 0.00 3.67
4101 6585 7.933033 TGTAGTTTTTCTAGAATACCGTGGTTT 59.067 33.333 5.89 0.00 0.00 3.27
4102 6586 7.812690 AGTTTTTCTAGAATACCGTGGTTTT 57.187 32.000 5.89 0.00 0.00 2.43
4103 6587 8.229253 AGTTTTTCTAGAATACCGTGGTTTTT 57.771 30.769 5.89 0.00 0.00 1.94
4130 6614 8.716646 AGAAAACCTTGGTTTTGAATACTTTG 57.283 30.769 28.48 0.00 36.75 2.77
4131 6615 8.536175 AGAAAACCTTGGTTTTGAATACTTTGA 58.464 29.630 28.48 0.00 36.75 2.69
4132 6616 9.325198 GAAAACCTTGGTTTTGAATACTTTGAT 57.675 29.630 28.48 6.19 36.75 2.57
4133 6617 8.661352 AAACCTTGGTTTTGAATACTTTGATG 57.339 30.769 11.60 0.00 0.00 3.07
4134 6618 6.223120 ACCTTGGTTTTGAATACTTTGATGC 58.777 36.000 0.00 0.00 0.00 3.91
4135 6619 5.345741 CCTTGGTTTTGAATACTTTGATGCG 59.654 40.000 0.00 0.00 0.00 4.73
4136 6620 5.446143 TGGTTTTGAATACTTTGATGCGT 57.554 34.783 0.00 0.00 0.00 5.24
4137 6621 5.837437 TGGTTTTGAATACTTTGATGCGTT 58.163 33.333 0.00 0.00 0.00 4.84
4138 6622 6.276847 TGGTTTTGAATACTTTGATGCGTTT 58.723 32.000 0.00 0.00 0.00 3.60
4139 6623 6.199908 TGGTTTTGAATACTTTGATGCGTTTG 59.800 34.615 0.00 0.00 0.00 2.93
4140 6624 6.346518 GGTTTTGAATACTTTGATGCGTTTGG 60.347 38.462 0.00 0.00 0.00 3.28
4141 6625 3.832276 TGAATACTTTGATGCGTTTGGC 58.168 40.909 0.00 0.00 43.96 4.52
4142 6626 3.505680 TGAATACTTTGATGCGTTTGGCT 59.494 39.130 0.00 0.00 44.05 4.75
4143 6627 4.022416 TGAATACTTTGATGCGTTTGGCTT 60.022 37.500 0.00 0.00 44.05 4.35
4144 6628 2.422276 ACTTTGATGCGTTTGGCTTC 57.578 45.000 0.00 0.00 43.98 3.86
4147 6631 4.465413 GATGCGTTTGGCTTCAGC 57.535 55.556 0.00 0.00 43.38 4.26
4148 6632 1.580942 GATGCGTTTGGCTTCAGCA 59.419 52.632 0.30 1.47 43.38 4.41
4149 6633 0.039256 GATGCGTTTGGCTTCAGCAA 60.039 50.000 0.30 0.00 43.38 3.91
4150 6634 0.388659 ATGCGTTTGGCTTCAGCAAA 59.611 45.000 0.30 0.00 44.36 3.68
4151 6635 0.174389 TGCGTTTGGCTTCAGCAAAA 59.826 45.000 0.30 0.00 41.32 2.44
4152 6636 1.285578 GCGTTTGGCTTCAGCAAAAA 58.714 45.000 2.79 0.00 44.68 1.94
4153 6637 1.005032 GCGTTTGGCTTCAGCAAAAAC 60.005 47.619 14.77 14.77 44.68 2.43
4154 6638 1.592543 CGTTTGGCTTCAGCAAAAACC 59.407 47.619 17.24 2.85 44.68 3.27
4155 6639 1.592543 GTTTGGCTTCAGCAAAAACCG 59.407 47.619 14.19 0.00 44.68 4.44
4156 6640 1.107114 TTGGCTTCAGCAAAAACCGA 58.893 45.000 0.30 0.00 44.36 4.69
4157 6641 1.107114 TGGCTTCAGCAAAAACCGAA 58.893 45.000 0.30 0.00 44.36 4.30
4158 6642 1.066908 TGGCTTCAGCAAAAACCGAAG 59.933 47.619 0.30 0.00 44.36 3.79
4159 6643 1.067060 GGCTTCAGCAAAAACCGAAGT 59.933 47.619 0.30 0.00 44.36 3.01
4160 6644 2.481276 GGCTTCAGCAAAAACCGAAGTT 60.481 45.455 0.30 0.00 44.36 2.66
4161 6645 3.186909 GCTTCAGCAAAAACCGAAGTTT 58.813 40.909 0.00 0.00 43.67 2.66
4162 6646 5.444416 GGCTTCAGCAAAAACCGAAGTTTT 61.444 41.667 0.30 0.00 46.31 2.43
4179 6663 9.511144 CCGAAGTTTTGTAAACCATAATATTCC 57.489 33.333 0.00 0.00 0.00 3.01
4188 6672 9.747898 TGTAAACCATAATATTCCAGAAACTGT 57.252 29.630 0.00 0.00 0.00 3.55
4190 6674 7.645058 AACCATAATATTCCAGAAACTGTGG 57.355 36.000 0.00 0.00 36.28 4.17
4191 6675 6.731467 ACCATAATATTCCAGAAACTGTGGT 58.269 36.000 0.00 0.00 36.37 4.16
4192 6676 7.867921 ACCATAATATTCCAGAAACTGTGGTA 58.132 34.615 0.00 0.00 36.37 3.25
4193 6677 8.502738 ACCATAATATTCCAGAAACTGTGGTAT 58.497 33.333 0.00 0.00 36.37 2.73
4194 6678 9.354673 CCATAATATTCCAGAAACTGTGGTATT 57.645 33.333 0.00 0.00 36.37 1.89
4200 6684 8.934023 ATTCCAGAAACTGTGGTATTTTAGAA 57.066 30.769 0.00 0.00 36.37 2.10
4201 6685 7.979444 TCCAGAAACTGTGGTATTTTAGAAG 57.021 36.000 0.00 0.00 36.37 2.85
4202 6686 7.514721 TCCAGAAACTGTGGTATTTTAGAAGT 58.485 34.615 0.00 0.00 36.37 3.01
4203 6687 8.653191 TCCAGAAACTGTGGTATTTTAGAAGTA 58.347 33.333 0.00 0.00 36.37 2.24
4204 6688 9.449719 CCAGAAACTGTGGTATTTTAGAAGTAT 57.550 33.333 0.00 0.00 0.00 2.12
4221 6705 5.352643 AAGTATTCGAAAAAGTGGTTCGG 57.647 39.130 0.00 0.00 46.11 4.30
4222 6706 4.634199 AGTATTCGAAAAAGTGGTTCGGA 58.366 39.130 0.00 0.00 46.11 4.55
4223 6707 3.891056 ATTCGAAAAAGTGGTTCGGAC 57.109 42.857 0.00 0.00 46.11 4.79
4224 6708 1.585297 TCGAAAAAGTGGTTCGGACC 58.415 50.000 5.70 5.70 46.11 4.46
4225 6709 1.139455 TCGAAAAAGTGGTTCGGACCT 59.861 47.619 15.59 0.00 46.11 3.85
4226 6710 1.529865 CGAAAAAGTGGTTCGGACCTC 59.470 52.381 15.59 11.10 46.66 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.030692 CACCATACTTTTGTGTCAAATCATCAT 58.969 33.333 0.00 0.00 0.00 2.45
54 55 8.413229 ACTTCGTGGCTATTATATTGCAATTTT 58.587 29.630 18.75 8.46 32.56 1.82
57 59 6.710295 TGACTTCGTGGCTATTATATTGCAAT 59.290 34.615 17.56 17.56 32.56 3.56
124 126 6.047870 CACCTGAATGAAAATTCCAACACAA 58.952 36.000 0.00 0.00 0.00 3.33
135 137 9.567776 TGAAATAACTACTCACCTGAATGAAAA 57.432 29.630 0.00 0.00 0.00 2.29
220 222 3.717294 AGCTACCAACCGGCAGGG 61.717 66.667 16.37 10.99 43.47 4.45
266 269 6.250527 GTCAATAAAATGGAAACCGTCAATCG 59.749 38.462 0.00 0.00 39.52 3.34
446 451 3.901797 AAAAGGAGCAGGACGCCGG 62.902 63.158 0.00 0.00 44.30 6.13
819 824 0.391661 GGCTGAGGAAATCGCTGTCA 60.392 55.000 0.00 0.00 0.00 3.58
1050 1058 3.073735 AGGCAGTCTCCCGCAGAG 61.074 66.667 0.00 0.00 44.75 3.35
1056 1064 2.124403 CATGCCAGGCAGTCTCCC 60.124 66.667 21.51 0.00 43.65 4.30
1059 1067 1.601171 GAGACATGCCAGGCAGTCT 59.399 57.895 31.06 31.06 43.65 3.24
1071 1079 1.445095 GATGAGCCGCTGGAGACAT 59.555 57.895 0.00 0.00 41.51 3.06
1074 1082 3.531207 CCGATGAGCCGCTGGAGA 61.531 66.667 0.00 0.00 0.00 3.71
1220 2579 3.210012 TTGCCTGTTGGAGGAGCCC 62.210 63.158 0.00 0.00 46.33 5.19
1226 2585 5.065218 GTGTACATAATCTTGCCTGTTGGAG 59.935 44.000 0.00 0.00 34.57 3.86
1281 2897 3.414700 GAACTGTCTGGGCACGCG 61.415 66.667 3.53 3.53 0.00 6.01
1369 2986 6.097356 CCAGACATATTGCAATTATCCATGC 58.903 40.000 18.75 10.41 42.86 4.06
1371 2988 6.014647 AGCCAGACATATTGCAATTATCCAT 58.985 36.000 18.75 1.06 0.00 3.41
1390 3007 2.281970 TGCCACAGCAGAAGCCAG 60.282 61.111 0.00 0.00 46.52 4.85
1477 3097 7.041372 GGAGTACAAAGTAGCATTTCAGAAACA 60.041 37.037 0.00 0.00 0.00 2.83
1596 3297 0.988832 ATCCCCTCCGTGCAACTTAA 59.011 50.000 0.00 0.00 31.75 1.85
1878 3654 9.622004 TCGATGTTCTTCGGAGTAATATTTATC 57.378 33.333 0.00 0.00 39.56 1.75
1965 3789 3.439857 TCCCTGAAGAAAATGTCCCTG 57.560 47.619 0.00 0.00 0.00 4.45
2035 3859 4.676924 GCTGAACTTCATTTTTGAACTCCG 59.323 41.667 0.00 0.00 0.00 4.63
2126 3950 6.661805 TCGGCATGTATTCATAGACCAGTATA 59.338 38.462 0.00 0.00 32.47 1.47
3167 5055 4.774124 CAGAAGTATCCTCTTCATTGCCA 58.226 43.478 8.73 0.00 44.18 4.92
3399 5288 3.566742 GGTTTTGATTGGTTACGTCCACT 59.433 43.478 0.00 0.00 37.20 4.00
3512 5401 7.154656 GTCATTGTCTTGCCTTATTTTTCCTT 58.845 34.615 0.00 0.00 0.00 3.36
3572 5461 6.875726 TCATCATAAACTGGCTATCTATGCAC 59.124 38.462 0.00 0.00 0.00 4.57
3588 5477 6.126796 TGGCTCTCCACACTTATCATCATAAA 60.127 38.462 0.00 0.00 37.47 1.40
3590 5479 4.901250 TGGCTCTCCACACTTATCATCATA 59.099 41.667 0.00 0.00 37.47 2.15
3605 5494 2.968574 TCTGATTACCAGATGGCTCTCC 59.031 50.000 0.00 0.00 46.38 3.71
3848 5737 0.106708 TGCCGGCTCAGGATTGATAC 59.893 55.000 29.70 0.00 31.68 2.24
3849 5738 0.836606 TTGCCGGCTCAGGATTGATA 59.163 50.000 29.70 0.00 31.68 2.15
3899 6376 3.653344 TCTCTTGTGGATCGACAACTTG 58.347 45.455 18.11 9.97 32.39 3.16
3900 6377 3.306364 CCTCTCTTGTGGATCGACAACTT 60.306 47.826 18.11 0.00 32.39 2.66
3906 6383 2.231716 TTCCCTCTCTTGTGGATCGA 57.768 50.000 0.00 0.00 0.00 3.59
3977 6454 9.498307 GTGTAATGTATGCAATAGTTGGTTTAC 57.502 33.333 0.00 0.00 0.00 2.01
3996 6480 4.641396 TGTCCCAGAAGTCTTGTGTAATG 58.359 43.478 8.76 0.00 0.00 1.90
4012 6496 7.872138 AGTCTATATTTTTCATCCTTGTCCCA 58.128 34.615 0.00 0.00 0.00 4.37
4039 6523 3.514706 TCCAAACGCACCCAGTAGTATTA 59.485 43.478 0.00 0.00 0.00 0.98
4040 6524 2.303600 TCCAAACGCACCCAGTAGTATT 59.696 45.455 0.00 0.00 0.00 1.89
4041 6525 1.903860 TCCAAACGCACCCAGTAGTAT 59.096 47.619 0.00 0.00 0.00 2.12
4042 6526 1.340088 TCCAAACGCACCCAGTAGTA 58.660 50.000 0.00 0.00 0.00 1.82
4043 6527 0.690762 ATCCAAACGCACCCAGTAGT 59.309 50.000 0.00 0.00 0.00 2.73
4044 6528 1.086696 CATCCAAACGCACCCAGTAG 58.913 55.000 0.00 0.00 0.00 2.57
4045 6529 0.958382 GCATCCAAACGCACCCAGTA 60.958 55.000 0.00 0.00 0.00 2.74
4046 6530 2.268076 GCATCCAAACGCACCCAGT 61.268 57.895 0.00 0.00 0.00 4.00
4047 6531 1.804396 TTGCATCCAAACGCACCCAG 61.804 55.000 0.00 0.00 38.00 4.45
4048 6532 1.395045 TTTGCATCCAAACGCACCCA 61.395 50.000 0.00 0.00 38.00 4.51
4049 6533 0.667184 CTTTGCATCCAAACGCACCC 60.667 55.000 0.00 0.00 38.00 4.61
4050 6534 0.031994 ACTTTGCATCCAAACGCACC 59.968 50.000 0.00 0.00 38.00 5.01
4051 6535 2.697431 TACTTTGCATCCAAACGCAC 57.303 45.000 0.00 0.00 38.00 5.34
4052 6536 3.932545 AATACTTTGCATCCAAACGCA 57.067 38.095 0.00 0.00 36.09 5.24
4053 6537 5.050431 ACAAAAATACTTTGCATCCAAACGC 60.050 36.000 0.00 0.00 36.09 4.84
4054 6538 6.523676 ACAAAAATACTTTGCATCCAAACG 57.476 33.333 0.00 0.00 36.09 3.60
4055 6539 8.587952 ACTACAAAAATACTTTGCATCCAAAC 57.412 30.769 0.00 0.00 36.09 2.93
4056 6540 9.606631 AAACTACAAAAATACTTTGCATCCAAA 57.393 25.926 0.00 0.00 38.56 3.28
4057 6541 9.606631 AAAACTACAAAAATACTTTGCATCCAA 57.393 25.926 0.00 0.00 32.93 3.53
4058 6542 9.606631 AAAAACTACAAAAATACTTTGCATCCA 57.393 25.926 0.00 0.00 32.93 3.41
4072 6556 8.776470 CCACGGTATTCTAGAAAAACTACAAAA 58.224 33.333 9.71 0.00 0.00 2.44
4073 6557 7.933033 ACCACGGTATTCTAGAAAAACTACAAA 59.067 33.333 9.71 0.00 0.00 2.83
4074 6558 7.444299 ACCACGGTATTCTAGAAAAACTACAA 58.556 34.615 9.71 0.00 0.00 2.41
4075 6559 6.996509 ACCACGGTATTCTAGAAAAACTACA 58.003 36.000 9.71 0.00 0.00 2.74
4076 6560 7.895975 AACCACGGTATTCTAGAAAAACTAC 57.104 36.000 9.71 7.29 0.00 2.73
4077 6561 8.907222 AAAACCACGGTATTCTAGAAAAACTA 57.093 30.769 9.71 0.00 0.00 2.24
4078 6562 7.812690 AAAACCACGGTATTCTAGAAAAACT 57.187 32.000 9.71 0.00 0.00 2.66
4109 6593 6.705825 GCATCAAAGTATTCAAAACCAAGGTT 59.294 34.615 0.00 0.00 40.45 3.50
4110 6594 6.223120 GCATCAAAGTATTCAAAACCAAGGT 58.777 36.000 0.00 0.00 0.00 3.50
4111 6595 5.345741 CGCATCAAAGTATTCAAAACCAAGG 59.654 40.000 0.00 0.00 0.00 3.61
4112 6596 5.920273 ACGCATCAAAGTATTCAAAACCAAG 59.080 36.000 0.00 0.00 0.00 3.61
4113 6597 5.837437 ACGCATCAAAGTATTCAAAACCAA 58.163 33.333 0.00 0.00 0.00 3.67
4114 6598 5.446143 ACGCATCAAAGTATTCAAAACCA 57.554 34.783 0.00 0.00 0.00 3.67
4115 6599 6.346518 CCAAACGCATCAAAGTATTCAAAACC 60.347 38.462 0.00 0.00 0.00 3.27
4116 6600 6.580476 CCAAACGCATCAAAGTATTCAAAAC 58.420 36.000 0.00 0.00 0.00 2.43
4117 6601 5.176590 GCCAAACGCATCAAAGTATTCAAAA 59.823 36.000 0.00 0.00 37.47 2.44
4118 6602 4.683781 GCCAAACGCATCAAAGTATTCAAA 59.316 37.500 0.00 0.00 37.47 2.69
4119 6603 4.022416 AGCCAAACGCATCAAAGTATTCAA 60.022 37.500 0.00 0.00 41.38 2.69
4120 6604 3.505680 AGCCAAACGCATCAAAGTATTCA 59.494 39.130 0.00 0.00 41.38 2.57
4121 6605 4.096732 AGCCAAACGCATCAAAGTATTC 57.903 40.909 0.00 0.00 41.38 1.75
4122 6606 4.022416 TGAAGCCAAACGCATCAAAGTATT 60.022 37.500 0.00 0.00 42.01 1.89
4123 6607 3.505680 TGAAGCCAAACGCATCAAAGTAT 59.494 39.130 0.00 0.00 42.01 2.12
4124 6608 2.881513 TGAAGCCAAACGCATCAAAGTA 59.118 40.909 0.00 0.00 42.01 2.24
4125 6609 1.680735 TGAAGCCAAACGCATCAAAGT 59.319 42.857 0.00 0.00 42.01 2.66
4126 6610 2.322161 CTGAAGCCAAACGCATCAAAG 58.678 47.619 0.00 0.00 44.14 2.77
4127 6611 1.602668 GCTGAAGCCAAACGCATCAAA 60.603 47.619 0.00 0.00 44.14 2.69
4128 6612 0.039256 GCTGAAGCCAAACGCATCAA 60.039 50.000 0.00 0.00 44.14 2.57
4129 6613 1.171549 TGCTGAAGCCAAACGCATCA 61.172 50.000 0.00 0.00 42.69 3.07
4130 6614 0.039256 TTGCTGAAGCCAAACGCATC 60.039 50.000 0.00 0.00 41.38 3.91
4131 6615 0.388659 TTTGCTGAAGCCAAACGCAT 59.611 45.000 0.00 0.00 41.38 4.73
4132 6616 0.174389 TTTTGCTGAAGCCAAACGCA 59.826 45.000 0.00 0.00 41.38 5.24
4133 6617 1.005032 GTTTTTGCTGAAGCCAAACGC 60.005 47.619 9.98 1.26 41.18 4.84
4134 6618 1.592543 GGTTTTTGCTGAAGCCAAACG 59.407 47.619 15.58 0.00 40.90 3.60
4135 6619 1.592543 CGGTTTTTGCTGAAGCCAAAC 59.407 47.619 14.49 14.49 40.05 2.93
4136 6620 1.478510 TCGGTTTTTGCTGAAGCCAAA 59.521 42.857 0.00 0.00 41.18 3.28
4137 6621 1.107114 TCGGTTTTTGCTGAAGCCAA 58.893 45.000 0.00 0.00 41.18 4.52
4138 6622 1.066908 CTTCGGTTTTTGCTGAAGCCA 59.933 47.619 0.00 0.00 42.63 4.75
4139 6623 1.770957 CTTCGGTTTTTGCTGAAGCC 58.229 50.000 0.00 0.00 42.63 4.35
4153 6637 9.511144 GGAATATTATGGTTTACAAAACTTCGG 57.489 33.333 2.84 0.00 0.00 4.30
4162 6646 9.747898 ACAGTTTCTGGAATATTATGGTTTACA 57.252 29.630 1.90 0.00 35.51 2.41
4164 6648 9.184523 CCACAGTTTCTGGAATATTATGGTTTA 57.815 33.333 1.90 0.00 35.51 2.01
4165 6649 7.673926 ACCACAGTTTCTGGAATATTATGGTTT 59.326 33.333 1.90 0.00 35.51 3.27
4166 6650 7.182060 ACCACAGTTTCTGGAATATTATGGTT 58.818 34.615 1.90 0.00 35.51 3.67
4167 6651 6.731467 ACCACAGTTTCTGGAATATTATGGT 58.269 36.000 1.90 0.00 35.51 3.55
4168 6652 8.924511 ATACCACAGTTTCTGGAATATTATGG 57.075 34.615 1.90 0.00 35.51 2.74
4175 6659 8.934023 TTCTAAAATACCACAGTTTCTGGAAT 57.066 30.769 1.90 0.00 35.51 3.01
4176 6660 7.996644 ACTTCTAAAATACCACAGTTTCTGGAA 59.003 33.333 1.90 0.00 35.51 3.53
4177 6661 7.514721 ACTTCTAAAATACCACAGTTTCTGGA 58.485 34.615 1.90 0.00 35.51 3.86
4178 6662 7.745620 ACTTCTAAAATACCACAGTTTCTGG 57.254 36.000 1.90 0.00 35.51 3.86
4181 6665 9.968743 CGAATACTTCTAAAATACCACAGTTTC 57.031 33.333 0.00 0.00 0.00 2.78
4182 6666 9.715121 TCGAATACTTCTAAAATACCACAGTTT 57.285 29.630 0.00 0.00 0.00 2.66
4183 6667 9.715121 TTCGAATACTTCTAAAATACCACAGTT 57.285 29.630 0.00 0.00 0.00 3.16
4184 6668 9.715121 TTTCGAATACTTCTAAAATACCACAGT 57.285 29.630 0.00 0.00 0.00 3.55
4193 6677 9.940166 GAACCACTTTTTCGAATACTTCTAAAA 57.060 29.630 0.00 0.00 34.00 1.52


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

AutoCloner maintained by Alex Coulton.