Multiple sequence alignment - TraesCS5A01G075700

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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 TraesCS5A01G075700 chr5A 100.000 4943 0 0 1 4943 91005725 91000783 0.000000e+00 9129
1 TraesCS5A01G075700 chr5A 97.917 3648 46 13 1322 4943 91056019 91052376 0.000000e+00 6288
2 TraesCS5A01G075700 chr5A 95.958 3340 103 12 1091 4399 554775659 554772321 0.000000e+00 5391
3 TraesCS5A01G075700 chr5A 96.702 2638 62 5 163 2778 14170058 14172692 0.000000e+00 4366
4 TraesCS5A01G075700 chr5A 92.216 167 13 0 1 167 414558585 414558751 2.300000e-58 237
5 TraesCS5A01G075700 chr5A 91.617 167 14 0 1 167 414546990 414547156 1.070000e-56 231
6 TraesCS5A01G075700 chr2A 96.811 4829 103 23 158 4943 771786371 771781551 0.000000e+00 8017
7 TraesCS5A01G075700 chr2A 96.078 4819 152 13 159 4943 374689315 374684500 0.000000e+00 7817
8 TraesCS5A01G075700 chr2A 96.480 3125 88 4 168 3270 611707730 611710854 0.000000e+00 5142
9 TraesCS5A01G075700 chr2A 92.216 167 13 0 1 167 220412138 220412304 2.300000e-58 237
10 TraesCS5A01G075700 chr7A 96.656 4815 121 14 166 4943 150188525 150193336 0.000000e+00 7963
11 TraesCS5A01G075700 chr7A 96.097 4817 117 21 168 4943 689988464 689993250 0.000000e+00 7788
12 TraesCS5A01G075700 chr6A 96.492 4818 123 18 163 4943 200086134 200081326 0.000000e+00 7919
13 TraesCS5A01G075700 chr6A 95.954 4746 159 13 222 4943 61532450 61537186 0.000000e+00 7670
14 TraesCS5A01G075700 chr6A 96.655 4036 101 11 941 4943 203513761 203517795 0.000000e+00 6674
15 TraesCS5A01G075700 chr6A 92.814 167 12 0 1 167 436799401 436799567 4.940000e-60 243
16 TraesCS5A01G075700 chr1A 96.366 4815 143 9 161 4943 71237522 71242336 0.000000e+00 7893
17 TraesCS5A01G075700 chr1A 96.010 4812 158 10 165 4943 581950208 581945398 0.000000e+00 7792
18 TraesCS5A01G075700 chr1A 95.485 4806 172 16 168 4943 462537398 462532608 0.000000e+00 7631
19 TraesCS5A01G075700 chr1A 92.814 167 12 0 1 167 221824457 221824291 4.940000e-60 243
20 TraesCS5A01G075700 chr1A 92.169 166 11 2 3 167 115613672 115613836 2.980000e-57 233
21 TraesCS5A01G075700 chr2B 95.640 4816 143 15 168 4943 757370637 757365849 0.000000e+00 7668
22 TraesCS5A01G075700 chr3A 95.285 4836 156 23 168 4943 8011629 8006806 0.000000e+00 7601
23 TraesCS5A01G075700 chr3A 96.389 4569 132 11 168 4704 747058496 747063063 0.000000e+00 7492
24 TraesCS5A01G075700 chr3A 96.307 2708 83 10 2249 4943 735561131 735558428 0.000000e+00 4431
25 TraesCS5A01G075700 chrUn 95.260 4831 160 20 166 4943 43121672 43126486 0.000000e+00 7589
26 TraesCS5A01G075700 chrUn 95.364 3710 107 19 1283 4943 284641584 284637891 0.000000e+00 5838
27 TraesCS5A01G075700 chrUn 95.460 2643 75 14 2330 4943 231578480 231575854 0.000000e+00 4174
28 TraesCS5A01G075700 chrUn 90.102 1081 61 20 3864 4943 20577470 20576435 0.000000e+00 1362
29 TraesCS5A01G075700 chrUn 94.976 836 32 3 4117 4943 428825781 428826615 0.000000e+00 1303
30 TraesCS5A01G075700 chr5D 94.912 1081 43 7 3873 4943 482327945 482329023 0.000000e+00 1681
31 TraesCS5A01G075700 chr1D 94.761 1088 41 11 3864 4943 17036572 17037651 0.000000e+00 1679
32 TraesCS5A01G075700 chr1D 92.466 969 62 10 3982 4943 446629520 446628556 0.000000e+00 1375
33 TraesCS5A01G075700 chr3D 94.128 1090 46 12 3864 4943 546490165 546489084 0.000000e+00 1642
34 TraesCS5A01G075700 chr4D 94.123 1089 47 10 3864 4943 43233089 43234169 0.000000e+00 1640
35 TraesCS5A01G075700 chr4D 93.169 1098 48 14 3864 4943 459089089 459090177 0.000000e+00 1587
36 TraesCS5A01G075700 chr4A 93.976 166 10 0 2 167 362874885 362874720 8.210000e-63 252
37 TraesCS5A01G075700 chr4A 92.216 167 13 0 1 167 71756468 71756634 2.300000e-58 237
38 TraesCS5A01G075700 chr2D 91.617 167 13 1 1 167 445407620 445407455 3.850000e-56 230


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 TraesCS5A01G075700 chr5A 91000783 91005725 4942 True 9129 9129 100.000 1 4943 1 chr5A.!!$R1 4942
1 TraesCS5A01G075700 chr5A 91052376 91056019 3643 True 6288 6288 97.917 1322 4943 1 chr5A.!!$R2 3621
2 TraesCS5A01G075700 chr5A 554772321 554775659 3338 True 5391 5391 95.958 1091 4399 1 chr5A.!!$R3 3308
3 TraesCS5A01G075700 chr5A 14170058 14172692 2634 False 4366 4366 96.702 163 2778 1 chr5A.!!$F1 2615
4 TraesCS5A01G075700 chr2A 771781551 771786371 4820 True 8017 8017 96.811 158 4943 1 chr2A.!!$R2 4785
5 TraesCS5A01G075700 chr2A 374684500 374689315 4815 True 7817 7817 96.078 159 4943 1 chr2A.!!$R1 4784
6 TraesCS5A01G075700 chr2A 611707730 611710854 3124 False 5142 5142 96.480 168 3270 1 chr2A.!!$F2 3102
7 TraesCS5A01G075700 chr7A 150188525 150193336 4811 False 7963 7963 96.656 166 4943 1 chr7A.!!$F1 4777
8 TraesCS5A01G075700 chr7A 689988464 689993250 4786 False 7788 7788 96.097 168 4943 1 chr7A.!!$F2 4775
9 TraesCS5A01G075700 chr6A 200081326 200086134 4808 True 7919 7919 96.492 163 4943 1 chr6A.!!$R1 4780
10 TraesCS5A01G075700 chr6A 61532450 61537186 4736 False 7670 7670 95.954 222 4943 1 chr6A.!!$F1 4721
11 TraesCS5A01G075700 chr6A 203513761 203517795 4034 False 6674 6674 96.655 941 4943 1 chr6A.!!$F2 4002
12 TraesCS5A01G075700 chr1A 71237522 71242336 4814 False 7893 7893 96.366 161 4943 1 chr1A.!!$F1 4782
13 TraesCS5A01G075700 chr1A 581945398 581950208 4810 True 7792 7792 96.010 165 4943 1 chr1A.!!$R3 4778
14 TraesCS5A01G075700 chr1A 462532608 462537398 4790 True 7631 7631 95.485 168 4943 1 chr1A.!!$R2 4775
15 TraesCS5A01G075700 chr2B 757365849 757370637 4788 True 7668 7668 95.640 168 4943 1 chr2B.!!$R1 4775
16 TraesCS5A01G075700 chr3A 8006806 8011629 4823 True 7601 7601 95.285 168 4943 1 chr3A.!!$R1 4775
17 TraesCS5A01G075700 chr3A 747058496 747063063 4567 False 7492 7492 96.389 168 4704 1 chr3A.!!$F1 4536
18 TraesCS5A01G075700 chr3A 735558428 735561131 2703 True 4431 4431 96.307 2249 4943 1 chr3A.!!$R2 2694
19 TraesCS5A01G075700 chrUn 43121672 43126486 4814 False 7589 7589 95.260 166 4943 1 chrUn.!!$F1 4777
20 TraesCS5A01G075700 chrUn 284637891 284641584 3693 True 5838 5838 95.364 1283 4943 1 chrUn.!!$R3 3660
21 TraesCS5A01G075700 chrUn 231575854 231578480 2626 True 4174 4174 95.460 2330 4943 1 chrUn.!!$R2 2613
22 TraesCS5A01G075700 chrUn 20576435 20577470 1035 True 1362 1362 90.102 3864 4943 1 chrUn.!!$R1 1079
23 TraesCS5A01G075700 chrUn 428825781 428826615 834 False 1303 1303 94.976 4117 4943 1 chrUn.!!$F2 826
24 TraesCS5A01G075700 chr5D 482327945 482329023 1078 False 1681 1681 94.912 3873 4943 1 chr5D.!!$F1 1070
25 TraesCS5A01G075700 chr1D 17036572 17037651 1079 False 1679 1679 94.761 3864 4943 1 chr1D.!!$F1 1079
26 TraesCS5A01G075700 chr1D 446628556 446629520 964 True 1375 1375 92.466 3982 4943 1 chr1D.!!$R1 961
27 TraesCS5A01G075700 chr3D 546489084 546490165 1081 True 1642 1642 94.128 3864 4943 1 chr3D.!!$R1 1079
28 TraesCS5A01G075700 chr4D 43233089 43234169 1080 False 1640 1640 94.123 3864 4943 1 chr4D.!!$F1 1079
29 TraesCS5A01G075700 chr4D 459089089 459090177 1088 False 1587 1587 93.169 3864 4943 1 chr4D.!!$F2 1079

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
70 71 0.034283 GGCCCCCACCACGTAATTAA 60.034 55.000 0.00 0.0 0.00 1.40 F
149 150 0.551396 GTGGGGCCCTACTGCTAATT 59.449 55.000 30.04 0.0 0.00 1.40 F
1335 1346 1.095228 CGACAAGTGTGGGCAACAGT 61.095 55.000 0.00 0.0 44.72 3.55 F
1696 1710 0.842030 AGGTTGTCCATGGAGGCTGA 60.842 55.000 16.81 0.0 37.29 4.26 F
1751 1766 5.130350 TCAGGTCAAAGTGAACCCTTTTAG 58.870 41.667 0.00 0.0 33.71 1.85 F
3288 3327 1.893137 ACACAGTAGATCCAGCGTTCA 59.107 47.619 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1323 2.031163 GCCCACACTTGTCGAGCT 59.969 61.111 0.00 0.00 0.00 4.09 R
1696 1710 5.009911 TGCTATTCCGCATTTTAGATGCAAT 59.990 36.000 8.41 4.04 44.75 3.56 R
3188 3227 0.979665 CTCCAAGTCCAGCTCCTTCA 59.020 55.000 0.00 0.00 0.00 3.02 R
3288 3327 4.906747 AGCCTTCATTGAAACTCTCTCT 57.093 40.909 0.01 0.00 0.00 3.10 R
3300 3339 5.649782 ACATTTTCATCGAAGCCTTCATT 57.350 34.783 5.14 0.00 0.00 2.57 R
4747 4923 1.471119 TCTACGACCCTTGATCGCTT 58.529 50.000 0.00 0.00 43.46 4.68 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 4.134623 TTGACCCAGTCAACGTGC 57.865 55.556 6.08 0.00 45.88 5.34
21 22 1.524961 TTGACCCAGTCAACGTGCT 59.475 52.632 6.08 0.00 45.88 4.40
22 23 0.813610 TTGACCCAGTCAACGTGCTG 60.814 55.000 6.08 7.74 45.88 4.41
23 24 1.069090 GACCCAGTCAACGTGCTGA 59.931 57.895 14.20 1.51 34.87 4.26
24 25 1.222115 GACCCAGTCAACGTGCTGAC 61.222 60.000 11.62 11.62 45.10 3.51
29 30 2.446341 GTCAACGTGCTGACTAGGC 58.554 57.895 12.17 0.00 42.11 3.93
30 31 0.319555 GTCAACGTGCTGACTAGGCA 60.320 55.000 12.17 0.00 42.11 4.75
31 32 0.608130 TCAACGTGCTGACTAGGCAT 59.392 50.000 0.00 0.00 41.86 4.40
32 33 1.002366 CAACGTGCTGACTAGGCATC 58.998 55.000 0.00 0.00 41.86 3.91
33 34 0.108138 AACGTGCTGACTAGGCATCC 60.108 55.000 0.00 0.00 41.86 3.51
34 35 0.972983 ACGTGCTGACTAGGCATCCT 60.973 55.000 0.00 0.00 41.86 3.24
35 36 1.032794 CGTGCTGACTAGGCATCCTA 58.967 55.000 0.00 0.00 41.86 2.94
42 43 3.997672 CTAGGCATCCTAGTGGCAC 57.002 57.895 10.29 10.29 46.15 5.01
43 44 1.418334 CTAGGCATCCTAGTGGCACT 58.582 55.000 25.34 25.34 46.15 4.40
44 45 2.598565 CTAGGCATCCTAGTGGCACTA 58.401 52.381 24.84 24.84 46.15 2.74
45 46 1.879575 AGGCATCCTAGTGGCACTAA 58.120 50.000 26.12 14.42 46.19 2.24
46 47 1.486726 AGGCATCCTAGTGGCACTAAC 59.513 52.381 26.12 13.78 46.19 2.34
47 48 1.209504 GGCATCCTAGTGGCACTAACA 59.790 52.381 26.12 16.43 43.52 2.41
48 49 2.158755 GGCATCCTAGTGGCACTAACAT 60.159 50.000 26.12 17.79 43.52 2.71
49 50 2.874701 GCATCCTAGTGGCACTAACATG 59.125 50.000 26.12 26.45 29.00 3.21
50 51 2.691409 TCCTAGTGGCACTAACATGC 57.309 50.000 26.12 0.00 45.34 4.06
56 57 3.518068 GCACTAACATGCGGCCCC 61.518 66.667 0.00 0.00 35.50 5.80
57 58 2.828549 CACTAACATGCGGCCCCC 60.829 66.667 0.00 0.00 0.00 5.40
58 59 3.334891 ACTAACATGCGGCCCCCA 61.335 61.111 0.00 0.00 0.00 4.96
59 60 2.828549 CTAACATGCGGCCCCCAC 60.829 66.667 0.00 0.00 0.00 4.61
60 61 4.434354 TAACATGCGGCCCCCACC 62.434 66.667 0.00 0.00 0.00 4.61
67 68 4.104183 CGGCCCCCACCACGTAAT 62.104 66.667 0.00 0.00 0.00 1.89
68 69 2.357446 GGCCCCCACCACGTAATT 59.643 61.111 0.00 0.00 0.00 1.40
69 70 1.608696 GGCCCCCACCACGTAATTA 59.391 57.895 0.00 0.00 0.00 1.40
70 71 0.034283 GGCCCCCACCACGTAATTAA 60.034 55.000 0.00 0.00 0.00 1.40
71 72 1.616456 GGCCCCCACCACGTAATTAAA 60.616 52.381 0.00 0.00 0.00 1.52
72 73 1.473677 GCCCCCACCACGTAATTAAAC 59.526 52.381 0.00 0.00 0.00 2.01
73 74 2.880990 GCCCCCACCACGTAATTAAACT 60.881 50.000 0.00 0.00 0.00 2.66
74 75 3.621958 GCCCCCACCACGTAATTAAACTA 60.622 47.826 0.00 0.00 0.00 2.24
75 76 4.587891 CCCCCACCACGTAATTAAACTAA 58.412 43.478 0.00 0.00 0.00 2.24
76 77 5.195185 CCCCCACCACGTAATTAAACTAAT 58.805 41.667 0.00 0.00 0.00 1.73
77 78 5.653330 CCCCCACCACGTAATTAAACTAATT 59.347 40.000 0.00 0.00 41.06 1.40
78 79 6.827762 CCCCCACCACGTAATTAAACTAATTA 59.172 38.462 0.00 0.00 39.06 1.40
79 80 7.338957 CCCCCACCACGTAATTAAACTAATTAA 59.661 37.037 0.00 0.00 40.97 1.40
80 81 8.738106 CCCCACCACGTAATTAAACTAATTAAA 58.262 33.333 0.00 0.00 40.97 1.52
123 124 9.654663 AACTAATTAGTCAACCTAATCAGTCAC 57.345 33.333 18.28 0.00 41.76 3.67
124 125 9.036980 ACTAATTAGTCAACCTAATCAGTCACT 57.963 33.333 12.50 0.00 39.47 3.41
125 126 9.307121 CTAATTAGTCAACCTAATCAGTCACTG 57.693 37.037 0.00 0.00 43.99 3.66
126 127 6.911250 TTAGTCAACCTAATCAGTCACTGA 57.089 37.500 10.71 10.71 44.99 3.41
127 128 5.140747 AGTCAACCTAATCAGTCACTGAC 57.859 43.478 10.48 0.38 43.63 3.51
128 129 4.588951 AGTCAACCTAATCAGTCACTGACA 59.411 41.667 10.48 0.00 43.63 3.58
129 130 5.247110 AGTCAACCTAATCAGTCACTGACAT 59.753 40.000 10.48 4.83 43.63 3.06
130 131 5.349817 GTCAACCTAATCAGTCACTGACATG 59.650 44.000 10.48 2.73 43.63 3.21
131 132 5.012046 TCAACCTAATCAGTCACTGACATGT 59.988 40.000 10.48 0.00 43.63 3.21
132 133 4.825422 ACCTAATCAGTCACTGACATGTG 58.175 43.478 10.48 0.61 43.63 3.21
133 134 4.186926 CCTAATCAGTCACTGACATGTGG 58.813 47.826 10.48 4.80 43.63 4.17
134 135 2.775911 ATCAGTCACTGACATGTGGG 57.224 50.000 10.48 0.00 43.63 4.61
135 136 0.686789 TCAGTCACTGACATGTGGGG 59.313 55.000 2.36 0.00 35.39 4.96
136 137 0.957395 CAGTCACTGACATGTGGGGC 60.957 60.000 1.15 0.00 38.40 5.80
137 138 1.675641 GTCACTGACATGTGGGGCC 60.676 63.158 1.15 0.00 38.40 5.80
138 139 2.361610 CACTGACATGTGGGGCCC 60.362 66.667 18.17 18.17 34.56 5.80
139 140 2.532715 ACTGACATGTGGGGCCCT 60.533 61.111 25.93 1.41 0.00 5.19
140 141 1.229820 ACTGACATGTGGGGCCCTA 60.230 57.895 25.93 14.71 0.00 3.53
141 142 1.224592 CTGACATGTGGGGCCCTAC 59.775 63.158 30.56 30.56 0.00 3.18
142 143 1.229820 TGACATGTGGGGCCCTACT 60.230 57.895 35.27 18.66 0.00 2.57
143 144 1.224592 GACATGTGGGGCCCTACTG 59.775 63.158 35.27 29.78 0.00 2.74
144 145 2.124151 CATGTGGGGCCCTACTGC 60.124 66.667 35.27 13.47 0.00 4.40
145 146 2.286425 ATGTGGGGCCCTACTGCT 60.286 61.111 35.27 19.20 0.00 4.24
146 147 1.004230 ATGTGGGGCCCTACTGCTA 59.996 57.895 35.27 18.48 0.00 3.49
147 148 0.623324 ATGTGGGGCCCTACTGCTAA 60.623 55.000 35.27 18.10 0.00 3.09
148 149 0.623324 TGTGGGGCCCTACTGCTAAT 60.623 55.000 35.27 0.00 0.00 1.73
149 150 0.551396 GTGGGGCCCTACTGCTAATT 59.449 55.000 30.04 0.00 0.00 1.40
150 151 1.772453 GTGGGGCCCTACTGCTAATTA 59.228 52.381 30.04 0.00 0.00 1.40
151 152 2.173996 GTGGGGCCCTACTGCTAATTAA 59.826 50.000 30.04 0.00 0.00 1.40
152 153 2.173996 TGGGGCCCTACTGCTAATTAAC 59.826 50.000 25.93 0.00 0.00 2.01
153 154 2.442126 GGGGCCCTACTGCTAATTAACT 59.558 50.000 24.38 0.00 0.00 2.24
154 155 3.496337 GGGGCCCTACTGCTAATTAACTC 60.496 52.174 24.38 0.00 0.00 3.01
155 156 3.391626 GGGCCCTACTGCTAATTAACTCT 59.608 47.826 17.04 0.00 0.00 3.24
156 157 4.381411 GGCCCTACTGCTAATTAACTCTG 58.619 47.826 0.00 0.00 0.00 3.35
157 158 4.141688 GGCCCTACTGCTAATTAACTCTGT 60.142 45.833 0.00 0.00 0.00 3.41
158 159 5.429130 GCCCTACTGCTAATTAACTCTGTT 58.571 41.667 0.00 0.00 0.00 3.16
159 160 5.880887 GCCCTACTGCTAATTAACTCTGTTT 59.119 40.000 0.00 0.00 0.00 2.83
160 161 7.046033 GCCCTACTGCTAATTAACTCTGTTTA 58.954 38.462 0.00 0.00 0.00 2.01
161 162 7.551617 GCCCTACTGCTAATTAACTCTGTTTAA 59.448 37.037 0.00 0.00 0.00 1.52
188 189 4.295201 AGGGTTAATTATCCTTTTGCCCC 58.705 43.478 11.51 0.00 34.34 5.80
195 196 1.442886 ATCCTTTTGCCCCCAGTGGA 61.443 55.000 11.95 0.00 35.39 4.02
225 226 2.787994 CTCAGTTTTGCCCTCAGATGT 58.212 47.619 0.00 0.00 0.00 3.06
376 377 2.525629 TGGGTCCGGAGCTGACAA 60.526 61.111 31.09 10.89 34.36 3.18
678 689 5.675538 CTGCTGGAGCTATTTAAACTAGGT 58.324 41.667 0.00 0.00 42.66 3.08
759 770 3.531207 CGAGCTGGAGATCCGCCA 61.531 66.667 0.00 4.95 39.43 5.69
865 876 1.337728 GGTTTGCCCAATTAGTGTGCC 60.338 52.381 0.00 0.00 27.78 5.01
937 948 2.578021 ATGGTGCACATTAGAAGGGACT 59.422 45.455 20.43 0.00 36.79 3.85
1117 1128 2.969262 GGGGAAAAGAATTGGGTGACAA 59.031 45.455 0.00 0.00 44.54 3.18
1335 1346 1.095228 CGACAAGTGTGGGCAACAGT 61.095 55.000 0.00 0.00 44.72 3.55
1395 1408 4.934797 TTCTGGGGTTGATGAAGAGAAT 57.065 40.909 0.00 0.00 0.00 2.40
1696 1710 0.842030 AGGTTGTCCATGGAGGCTGA 60.842 55.000 16.81 0.00 37.29 4.26
1751 1766 5.130350 TCAGGTCAAAGTGAACCCTTTTAG 58.870 41.667 0.00 0.00 33.71 1.85
3188 3227 5.559148 AGAGTTGAATCAGACCTCAAAGT 57.441 39.130 8.60 0.00 33.52 2.66
3288 3327 1.893137 ACACAGTAGATCCAGCGTTCA 59.107 47.619 0.00 0.00 0.00 3.18
3300 3339 2.288457 CCAGCGTTCAGAGAGAGTTTCA 60.288 50.000 0.00 0.00 0.00 2.69
4259 4412 4.693566 TCAGCCAAATAACTTTCCTACACG 59.306 41.667 0.00 0.00 0.00 4.49
4747 4923 3.053095 AGGACCGTTCATCTAACCCTAGA 60.053 47.826 0.00 0.00 38.54 2.43
4764 4940 1.471119 AGAAGCGATCAAGGGTCGTA 58.529 50.000 0.57 0.00 40.98 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.069090 TCAGCACGTTGACTGGGTC 59.931 57.895 9.44 0.00 34.57 4.46
7 8 3.642755 GTCAGCACGTTGACTGGG 58.357 61.111 12.17 0.00 43.23 4.45
11 12 0.319555 TGCCTAGTCAGCACGTTGAC 60.320 55.000 11.62 11.62 46.14 3.18
12 13 0.608130 ATGCCTAGTCAGCACGTTGA 59.392 50.000 0.00 0.00 44.40 3.18
13 14 1.002366 GATGCCTAGTCAGCACGTTG 58.998 55.000 0.00 0.00 44.40 4.10
14 15 0.108138 GGATGCCTAGTCAGCACGTT 60.108 55.000 0.00 0.00 44.40 3.99
15 16 0.972983 AGGATGCCTAGTCAGCACGT 60.973 55.000 0.00 0.00 44.40 4.49
16 17 1.000827 CTAGGATGCCTAGTCAGCACG 60.001 57.143 11.50 0.00 46.15 5.34
17 18 2.810439 CTAGGATGCCTAGTCAGCAC 57.190 55.000 11.50 0.00 46.15 4.40
25 26 2.698797 GTTAGTGCCACTAGGATGCCTA 59.301 50.000 4.51 0.00 36.89 3.93
26 27 1.486726 GTTAGTGCCACTAGGATGCCT 59.513 52.381 4.51 0.00 36.89 4.75
27 28 1.209504 TGTTAGTGCCACTAGGATGCC 59.790 52.381 4.51 0.00 36.89 4.40
28 29 2.691409 TGTTAGTGCCACTAGGATGC 57.309 50.000 4.51 0.00 36.89 3.91
29 30 2.874701 GCATGTTAGTGCCACTAGGATG 59.125 50.000 15.70 15.70 39.18 3.51
30 31 2.483714 CGCATGTTAGTGCCACTAGGAT 60.484 50.000 4.51 0.00 42.06 3.24
31 32 1.134818 CGCATGTTAGTGCCACTAGGA 60.135 52.381 4.51 0.00 42.06 2.94
32 33 1.290203 CGCATGTTAGTGCCACTAGG 58.710 55.000 4.51 0.00 42.06 3.02
33 34 1.290203 CCGCATGTTAGTGCCACTAG 58.710 55.000 4.51 0.00 42.06 2.57
34 35 0.742990 GCCGCATGTTAGTGCCACTA 60.743 55.000 0.00 0.00 42.06 2.74
35 36 2.040544 GCCGCATGTTAGTGCCACT 61.041 57.895 1.54 1.54 42.06 4.00
36 37 2.485122 GCCGCATGTTAGTGCCAC 59.515 61.111 0.00 0.00 42.06 5.01
37 38 2.749839 GGCCGCATGTTAGTGCCA 60.750 61.111 0.00 0.00 42.06 4.92
38 39 3.518068 GGGCCGCATGTTAGTGCC 61.518 66.667 0.00 0.00 42.06 5.01
39 40 3.518068 GGGGCCGCATGTTAGTGC 61.518 66.667 16.21 0.00 41.65 4.40
40 41 2.828549 GGGGGCCGCATGTTAGTG 60.829 66.667 22.80 0.00 0.00 2.74
41 42 3.334891 TGGGGGCCGCATGTTAGT 61.335 61.111 20.63 0.00 0.00 2.24
42 43 2.828549 GTGGGGGCCGCATGTTAG 60.829 66.667 27.04 0.00 33.65 2.34
43 44 4.434354 GGTGGGGGCCGCATGTTA 62.434 66.667 27.04 0.00 35.42 2.41
50 51 2.254737 TAATTACGTGGTGGGGGCCG 62.255 60.000 0.00 0.00 0.00 6.13
51 52 0.034283 TTAATTACGTGGTGGGGGCC 60.034 55.000 0.00 0.00 0.00 5.80
52 53 1.473677 GTTTAATTACGTGGTGGGGGC 59.526 52.381 0.00 0.00 0.00 5.80
53 54 3.076079 AGTTTAATTACGTGGTGGGGG 57.924 47.619 0.00 0.00 0.00 5.40
54 55 6.762702 AATTAGTTTAATTACGTGGTGGGG 57.237 37.500 0.00 0.00 36.66 4.96
102 103 7.039011 TGTCAGTGACTGATTAGGTTGACTAAT 60.039 37.037 19.31 0.00 42.73 1.73
103 104 6.266786 TGTCAGTGACTGATTAGGTTGACTAA 59.733 38.462 19.31 0.00 42.73 2.24
104 105 5.773176 TGTCAGTGACTGATTAGGTTGACTA 59.227 40.000 19.31 0.00 42.73 2.59
105 106 4.588951 TGTCAGTGACTGATTAGGTTGACT 59.411 41.667 19.31 0.00 42.73 3.41
106 107 4.883083 TGTCAGTGACTGATTAGGTTGAC 58.117 43.478 19.31 3.79 42.73 3.18
107 108 5.012046 ACATGTCAGTGACTGATTAGGTTGA 59.988 40.000 19.31 0.00 42.73 3.18
108 109 5.121298 CACATGTCAGTGACTGATTAGGTTG 59.879 44.000 19.31 11.87 42.73 3.77
109 110 5.240891 CACATGTCAGTGACTGATTAGGTT 58.759 41.667 19.31 0.00 42.73 3.50
110 111 4.323028 CCACATGTCAGTGACTGATTAGGT 60.323 45.833 19.31 15.10 42.73 3.08
111 112 4.186926 CCACATGTCAGTGACTGATTAGG 58.813 47.826 19.31 14.48 42.73 2.69
112 113 4.186926 CCCACATGTCAGTGACTGATTAG 58.813 47.826 19.31 13.09 42.73 1.73
113 114 3.055167 CCCCACATGTCAGTGACTGATTA 60.055 47.826 19.31 11.44 42.73 1.75
114 115 2.290514 CCCCACATGTCAGTGACTGATT 60.291 50.000 19.31 6.87 42.73 2.57
115 116 1.280133 CCCCACATGTCAGTGACTGAT 59.720 52.381 19.31 7.51 42.73 2.90
116 117 0.686789 CCCCACATGTCAGTGACTGA 59.313 55.000 23.29 11.93 42.05 3.41
117 118 0.957395 GCCCCACATGTCAGTGACTG 60.957 60.000 23.29 19.34 42.05 3.51
118 119 1.376466 GCCCCACATGTCAGTGACT 59.624 57.895 23.29 7.08 42.05 3.41
119 120 1.675641 GGCCCCACATGTCAGTGAC 60.676 63.158 16.68 16.68 42.05 3.67
120 121 2.756400 GGCCCCACATGTCAGTGA 59.244 61.111 0.00 0.00 42.05 3.41
121 122 1.561769 TAGGGCCCCACATGTCAGTG 61.562 60.000 21.43 0.00 39.21 3.66
122 123 1.229820 TAGGGCCCCACATGTCAGT 60.230 57.895 21.43 0.00 0.00 3.41
123 124 1.224592 GTAGGGCCCCACATGTCAG 59.775 63.158 21.43 0.00 0.00 3.51
124 125 1.229820 AGTAGGGCCCCACATGTCA 60.230 57.895 23.21 0.00 0.00 3.58
125 126 1.224592 CAGTAGGGCCCCACATGTC 59.775 63.158 23.21 3.88 0.00 3.06
126 127 2.983879 GCAGTAGGGCCCCACATGT 61.984 63.158 23.21 3.30 0.00 3.21
127 128 1.344953 TAGCAGTAGGGCCCCACATG 61.345 60.000 23.21 17.28 0.00 3.21
128 129 0.623324 TTAGCAGTAGGGCCCCACAT 60.623 55.000 23.21 10.30 0.00 3.21
129 130 0.623324 ATTAGCAGTAGGGCCCCACA 60.623 55.000 23.21 3.34 0.00 4.17
130 131 0.551396 AATTAGCAGTAGGGCCCCAC 59.449 55.000 21.43 17.12 0.00 4.61
131 132 2.173996 GTTAATTAGCAGTAGGGCCCCA 59.826 50.000 21.43 0.00 0.00 4.96
132 133 2.442126 AGTTAATTAGCAGTAGGGCCCC 59.558 50.000 21.43 3.37 0.00 5.80
133 134 3.391626 AGAGTTAATTAGCAGTAGGGCCC 59.608 47.826 16.46 16.46 0.00 5.80
134 135 4.141688 ACAGAGTTAATTAGCAGTAGGGCC 60.142 45.833 0.00 0.00 0.00 5.80
135 136 5.024785 ACAGAGTTAATTAGCAGTAGGGC 57.975 43.478 1.97 0.00 0.00 5.19
136 137 9.614792 ATTAAACAGAGTTAATTAGCAGTAGGG 57.385 33.333 1.97 0.00 31.07 3.53
160 161 9.899661 GGCAAAAGGATAATTAACCCTTTAATT 57.100 29.630 24.01 13.38 46.29 1.40
161 162 8.491134 GGGCAAAAGGATAATTAACCCTTTAAT 58.509 33.333 24.01 13.85 46.29 1.40
188 189 0.392193 GAGCACATGGACTCCACTGG 60.392 60.000 0.00 0.00 35.80 4.00
195 196 1.610522 GCAAAACTGAGCACATGGACT 59.389 47.619 0.00 0.00 0.00 3.85
225 226 2.627699 GGGCAAAACTGAGGACAATTCA 59.372 45.455 0.00 0.00 0.00 2.57
376 377 0.688487 TTTAGTTGCACGGGCCTACT 59.312 50.000 17.21 17.21 40.13 2.57
633 644 3.764466 CCACCTTCGAGCGCTCCT 61.764 66.667 30.66 6.12 0.00 3.69
678 689 0.545787 TTCGCCCTAGGGTTCTTCCA 60.546 55.000 28.96 3.90 38.11 3.53
744 755 3.842923 CGTGGCGGATCTCCAGCT 61.843 66.667 7.37 0.00 36.36 4.24
865 876 2.160285 GCGAAAAACAAAGACGCAATCG 60.160 45.455 0.00 0.00 46.75 3.34
937 948 4.512484 TCCTTTGCATCGAACATGTATCA 58.488 39.130 0.00 0.00 0.00 2.15
1117 1128 8.527810 GGTAGCTAGCTCTTCATCATTACTAAT 58.472 37.037 23.26 0.00 0.00 1.73
1312 1323 2.031163 GCCCACACTTGTCGAGCT 59.969 61.111 0.00 0.00 0.00 4.09
1696 1710 5.009911 TGCTATTCCGCATTTTAGATGCAAT 59.990 36.000 8.41 4.04 44.75 3.56
2184 2201 3.300765 ACAAGCTTGCAGCCTGCC 61.301 61.111 26.27 0.00 43.77 4.85
2185 2202 2.049433 CACAAGCTTGCAGCCTGC 60.049 61.111 26.27 10.45 43.77 4.85
2186 2203 2.049433 GCACAAGCTTGCAGCCTG 60.049 61.111 26.27 16.88 43.77 4.85
3138 3177 2.232452 GTCTACCTGCTGCTCTCTTCAA 59.768 50.000 0.00 0.00 0.00 2.69
3188 3227 0.979665 CTCCAAGTCCAGCTCCTTCA 59.020 55.000 0.00 0.00 0.00 3.02
3288 3327 4.906747 AGCCTTCATTGAAACTCTCTCT 57.093 40.909 0.01 0.00 0.00 3.10
3300 3339 5.649782 ACATTTTCATCGAAGCCTTCATT 57.350 34.783 5.14 0.00 0.00 2.57
4747 4923 1.471119 TCTACGACCCTTGATCGCTT 58.529 50.000 0.00 0.00 43.46 4.68


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

AutoCloner maintained by Alex Coulton.