Multiple sequence alignment - TraesCS7B01G382500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G382500 chr7B 100.000 3270 0 0 1 3270 648377445 648380714 0.000000e+00 6039.0
1 TraesCS7B01G382500 chr7B 88.464 1439 89 27 845 2263 648434762 648436143 0.000000e+00 1666.0
2 TraesCS7B01G382500 chr7B 94.464 578 31 1 1718 2295 648436920 648436344 0.000000e+00 889.0
3 TraesCS7B01G382500 chr7B 90.941 287 26 0 975 1261 648389378 648389664 1.420000e-103 387.0
4 TraesCS7B01G382500 chr7B 86.047 129 15 3 2952 3079 648430663 648430789 5.690000e-28 135.0
5 TraesCS7B01G382500 chr7B 97.015 67 2 0 3097 3163 648437040 648437106 2.670000e-21 113.0
6 TraesCS7B01G382500 chr7B 88.462 78 6 2 3192 3266 648392648 648392725 1.250000e-14 91.6
7 TraesCS7B01G382500 chr7B 97.727 44 1 0 2245 2288 648436932 648436975 3.500000e-10 76.8
8 TraesCS7B01G382500 chr7D 92.191 2241 127 21 850 3058 580763325 580765549 0.000000e+00 3125.0
9 TraesCS7B01G382500 chr7D 82.603 1506 205 40 784 2262 580756502 580757977 0.000000e+00 1277.0
10 TraesCS7B01G382500 chr7D 81.588 1499 211 46 791 2262 580741553 580743013 0.000000e+00 1179.0
11 TraesCS7B01G382500 chr7D 79.512 1474 197 49 1729 3163 580758608 580760015 0.000000e+00 952.0
12 TraesCS7B01G382500 chr7D 74.504 1361 275 46 939 2262 581080593 581081918 2.890000e-145 525.0
13 TraesCS7B01G382500 chr7D 85.930 199 19 5 911 1109 580762668 580762857 1.540000e-48 204.0
14 TraesCS7B01G382500 chr7D 76.087 414 62 20 2314 2718 580757995 580758380 7.210000e-42 182.0
15 TraesCS7B01G382500 chr7D 91.228 114 4 4 3160 3270 580765668 580765778 2.030000e-32 150.0
16 TraesCS7B01G382500 chr7D 98.507 67 1 0 3097 3163 580765550 580765616 5.730000e-23 119.0
17 TraesCS7B01G382500 chr7D 86.364 110 12 2 3160 3266 580657410 580657519 2.060000e-22 117.0
18 TraesCS7B01G382500 chr7A 80.933 1757 281 37 756 2483 672311226 672312957 0.000000e+00 1339.0
19 TraesCS7B01G382500 chr7A 80.695 1497 230 41 791 2262 672315863 672317325 0.000000e+00 1109.0
20 TraesCS7B01G382500 chr7A 74.913 1156 234 36 1033 2168 673005101 673006220 8.210000e-131 477.0
21 TraesCS7B01G382500 chr7A 78.582 677 116 25 1080 1746 673028932 673029589 1.400000e-113 420.0
22 TraesCS7B01G382500 chr7A 82.073 357 56 7 1130 1482 673993700 673994052 6.860000e-77 298.0
23 TraesCS7B01G382500 chr7A 71.936 1183 268 41 1106 2252 672950161 672951315 1.480000e-73 287.0
24 TraesCS7B01G382500 chr7A 85.294 102 12 1 3160 3258 672318230 672318331 5.770000e-18 102.0
25 TraesCS7B01G382500 chr7A 87.209 86 7 3 3183 3266 672258521 672258604 9.660000e-16 95.3
26 TraesCS7B01G382500 chr7A 88.462 78 6 2 3192 3266 672305741 672305818 1.250000e-14 91.6
27 TraesCS7B01G382500 chr2B 96.965 593 16 2 138 729 118827084 118826493 0.000000e+00 994.0
28 TraesCS7B01G382500 chr2B 96.173 601 21 2 136 734 118609491 118608891 0.000000e+00 981.0
29 TraesCS7B01G382500 chr6B 96.807 595 18 1 136 729 67521144 67520550 0.000000e+00 992.0
30 TraesCS7B01G382500 chr6B 96.339 601 20 2 136 734 67946239 67945639 0.000000e+00 987.0
31 TraesCS7B01G382500 chr5A 96.807 595 16 2 138 729 664388867 664389461 0.000000e+00 990.0
32 TraesCS7B01G382500 chr4A 96.488 598 18 3 138 734 151958541 151959136 0.000000e+00 985.0
33 TraesCS7B01G382500 chr1B 96.339 601 19 3 136 734 295769569 295768970 0.000000e+00 985.0
34 TraesCS7B01G382500 chr2A 96.327 599 21 1 132 729 18195189 18195787 0.000000e+00 983.0
35 TraesCS7B01G382500 chr3B 96.321 598 20 2 138 734 42860373 42859777 0.000000e+00 981.0


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 TraesCS7B01G382500 chr7B 648377445 648380714 3269 False 6039.000000 6039 100.000000 1 3270 1 chr7B.!!$F1 3269
1 TraesCS7B01G382500 chr7B 648436344 648436920 576 True 889.000000 889 94.464000 1718 2295 1 chr7B.!!$R1 577
2 TraesCS7B01G382500 chr7B 648430663 648437106 6443 False 497.700000 1666 92.313250 845 3163 4 chr7B.!!$F3 2318
3 TraesCS7B01G382500 chr7B 648389378 648392725 3347 False 239.300000 387 89.701500 975 3266 2 chr7B.!!$F2 2291
4 TraesCS7B01G382500 chr7D 580741553 580743013 1460 False 1179.000000 1179 81.588000 791 2262 1 chr7D.!!$F2 1471
5 TraesCS7B01G382500 chr7D 580756502 580765778 9276 False 858.428571 3125 86.579714 784 3270 7 chr7D.!!$F4 2486
6 TraesCS7B01G382500 chr7D 581080593 581081918 1325 False 525.000000 525 74.504000 939 2262 1 chr7D.!!$F3 1323
7 TraesCS7B01G382500 chr7A 672311226 672318331 7105 False 850.000000 1339 82.307333 756 3258 3 chr7A.!!$F7 2502
8 TraesCS7B01G382500 chr7A 673005101 673006220 1119 False 477.000000 477 74.913000 1033 2168 1 chr7A.!!$F4 1135
9 TraesCS7B01G382500 chr7A 673028932 673029589 657 False 420.000000 420 78.582000 1080 1746 1 chr7A.!!$F5 666
10 TraesCS7B01G382500 chr7A 672950161 672951315 1154 False 287.000000 287 71.936000 1106 2252 1 chr7A.!!$F3 1146
11 TraesCS7B01G382500 chr2B 118826493 118827084 591 True 994.000000 994 96.965000 138 729 1 chr2B.!!$R2 591
12 TraesCS7B01G382500 chr2B 118608891 118609491 600 True 981.000000 981 96.173000 136 734 1 chr2B.!!$R1 598
13 TraesCS7B01G382500 chr6B 67520550 67521144 594 True 992.000000 992 96.807000 136 729 1 chr6B.!!$R1 593
14 TraesCS7B01G382500 chr6B 67945639 67946239 600 True 987.000000 987 96.339000 136 734 1 chr6B.!!$R2 598
15 TraesCS7B01G382500 chr5A 664388867 664389461 594 False 990.000000 990 96.807000 138 729 1 chr5A.!!$F1 591
16 TraesCS7B01G382500 chr4A 151958541 151959136 595 False 985.000000 985 96.488000 138 734 1 chr4A.!!$F1 596
17 TraesCS7B01G382500 chr1B 295768970 295769569 599 True 985.000000 985 96.339000 136 734 1 chr1B.!!$R1 598
18 TraesCS7B01G382500 chr2A 18195189 18195787 598 False 983.000000 983 96.327000 132 729 1 chr2A.!!$F1 597
19 TraesCS7B01G382500 chr3B 42859777 42860373 596 True 981.000000 981 96.321000 138 734 1 chr3B.!!$R1 596

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
50 51 0.034337 GTACACGGTGGAAAGAGGCA 59.966 55.0 13.48 0.00 0.00 4.75 F
418 424 0.036590 TGCACTGCAGTTGCCATAGA 59.963 50.0 27.26 13.38 41.18 1.98 F
1377 4686 0.110486 AAATCAGCACCCCACTTCGT 59.890 50.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 5073 0.528033 CAGCAGTCCAGCAGATCGAG 60.528 60.0 0.0 0.0 36.85 4.04 R
1576 5219 0.687354 TGCTCACCTTCCTTGACTCC 59.313 55.0 0.0 0.0 0.00 3.85 R
2603 17010 0.595825 GCATTAGATGGCAAAGCGGC 60.596 55.0 0.0 0.0 41.67 6.53 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
27 28 4.884458 GCTCCAGTAGCCTTAATTTGAC 57.116 45.455 0.00 0.00 46.25 3.18
28 29 4.261801 GCTCCAGTAGCCTTAATTTGACA 58.738 43.478 0.00 0.00 46.25 3.58
30 31 6.055588 GCTCCAGTAGCCTTAATTTGACATA 58.944 40.000 0.00 0.00 46.25 2.29
33 34 8.313944 TCCAGTAGCCTTAATTTGACATAGTA 57.686 34.615 0.00 0.00 0.00 1.82
34 35 8.202137 TCCAGTAGCCTTAATTTGACATAGTAC 58.798 37.037 0.00 0.00 0.00 2.73
37 38 6.903883 AGCCTTAATTTGACATAGTACACG 57.096 37.500 0.00 0.00 0.00 4.49
38 39 5.815740 AGCCTTAATTTGACATAGTACACGG 59.184 40.000 0.00 0.00 0.00 4.94
40 41 6.456449 GCCTTAATTTGACATAGTACACGGTG 60.456 42.308 6.58 6.58 0.00 4.94
41 42 6.036735 CCTTAATTTGACATAGTACACGGTGG 59.963 42.308 13.48 0.00 0.00 4.61
42 43 4.811969 ATTTGACATAGTACACGGTGGA 57.188 40.909 13.48 0.00 0.00 4.02
43 44 4.603989 TTTGACATAGTACACGGTGGAA 57.396 40.909 13.48 0.00 0.00 3.53
44 45 4.603989 TTGACATAGTACACGGTGGAAA 57.396 40.909 13.48 0.00 0.00 3.13
45 46 4.182693 TGACATAGTACACGGTGGAAAG 57.817 45.455 13.48 0.00 0.00 2.62
46 47 3.827876 TGACATAGTACACGGTGGAAAGA 59.172 43.478 13.48 0.00 0.00 2.52
47 48 4.082408 TGACATAGTACACGGTGGAAAGAG 60.082 45.833 13.48 1.05 0.00 2.85
48 49 3.194968 ACATAGTACACGGTGGAAAGAGG 59.805 47.826 13.48 0.00 0.00 3.69
49 50 0.320697 AGTACACGGTGGAAAGAGGC 59.679 55.000 13.48 0.00 0.00 4.70
50 51 0.034337 GTACACGGTGGAAAGAGGCA 59.966 55.000 13.48 0.00 0.00 4.75
51 52 0.981183 TACACGGTGGAAAGAGGCAT 59.019 50.000 13.48 0.00 0.00 4.40
52 53 0.321653 ACACGGTGGAAAGAGGCATC 60.322 55.000 13.48 0.00 0.00 3.91
53 54 1.026718 CACGGTGGAAAGAGGCATCC 61.027 60.000 0.00 0.00 36.21 3.51
54 55 1.299648 CGGTGGAAAGAGGCATCCA 59.700 57.895 0.00 0.00 43.32 3.41
60 61 4.314522 TGGAAAGAGGCATCCACATTTA 57.685 40.909 0.00 0.00 40.74 1.40
61 62 4.272489 TGGAAAGAGGCATCCACATTTAG 58.728 43.478 0.00 0.00 40.74 1.85
63 64 3.659183 AAGAGGCATCCACATTTAGCT 57.341 42.857 0.00 0.00 0.00 3.32
65 66 3.973425 AGAGGCATCCACATTTAGCTTT 58.027 40.909 0.00 0.00 0.00 3.51
67 68 5.509498 AGAGGCATCCACATTTAGCTTTAA 58.491 37.500 0.00 0.00 0.00 1.52
71 72 6.155049 AGGCATCCACATTTAGCTTTAATTGT 59.845 34.615 0.00 0.00 0.00 2.71
73 74 6.476706 GCATCCACATTTAGCTTTAATTGTCC 59.523 38.462 0.00 0.00 0.00 4.02
74 75 7.631377 GCATCCACATTTAGCTTTAATTGTCCT 60.631 37.037 0.00 0.00 0.00 3.85
75 76 7.156876 TCCACATTTAGCTTTAATTGTCCTG 57.843 36.000 0.00 0.00 0.00 3.86
76 77 5.807011 CCACATTTAGCTTTAATTGTCCTGC 59.193 40.000 0.00 0.00 0.00 4.85
77 78 6.350445 CCACATTTAGCTTTAATTGTCCTGCT 60.350 38.462 0.00 0.00 34.92 4.24
78 79 7.148086 CCACATTTAGCTTTAATTGTCCTGCTA 60.148 37.037 0.00 0.00 32.72 3.49
79 80 8.243426 CACATTTAGCTTTAATTGTCCTGCTAA 58.757 33.333 0.00 0.00 40.00 3.09
91 92 1.909700 CCTGCTAAAGGTTTGCTCCA 58.090 50.000 0.00 0.00 41.74 3.86
92 93 2.450476 CCTGCTAAAGGTTTGCTCCAT 58.550 47.619 0.00 0.00 41.74 3.41
93 94 2.827921 CCTGCTAAAGGTTTGCTCCATT 59.172 45.455 0.00 0.00 41.74 3.16
94 95 3.259123 CCTGCTAAAGGTTTGCTCCATTT 59.741 43.478 0.00 0.00 41.74 2.32
97 98 6.321181 CCTGCTAAAGGTTTGCTCCATTTATA 59.679 38.462 0.00 0.00 41.74 0.98
98 99 7.147915 CCTGCTAAAGGTTTGCTCCATTTATAA 60.148 37.037 0.00 0.00 41.74 0.98
99 100 8.305046 TGCTAAAGGTTTGCTCCATTTATAAT 57.695 30.769 0.00 0.00 0.00 1.28
100 101 8.413229 TGCTAAAGGTTTGCTCCATTTATAATC 58.587 33.333 0.00 0.00 0.00 1.75
101 102 7.867909 GCTAAAGGTTTGCTCCATTTATAATCC 59.132 37.037 0.00 0.00 0.00 3.01
102 103 6.731292 AAGGTTTGCTCCATTTATAATCCC 57.269 37.500 0.00 0.00 0.00 3.85
103 104 5.147767 AGGTTTGCTCCATTTATAATCCCC 58.852 41.667 0.00 0.00 0.00 4.81
104 105 5.103086 AGGTTTGCTCCATTTATAATCCCCT 60.103 40.000 0.00 0.00 0.00 4.79
105 106 5.243954 GGTTTGCTCCATTTATAATCCCCTC 59.756 44.000 0.00 0.00 0.00 4.30
106 107 4.286297 TGCTCCATTTATAATCCCCTCG 57.714 45.455 0.00 0.00 0.00 4.63
109 110 4.579869 CTCCATTTATAATCCCCTCGTGG 58.420 47.826 0.00 0.00 0.00 4.94
113 114 4.847990 TTTATAATCCCCTCGTGGTGTT 57.152 40.909 2.33 0.00 0.00 3.32
114 115 5.954153 TTTATAATCCCCTCGTGGTGTTA 57.046 39.130 2.33 0.00 0.00 2.41
115 116 3.832615 ATAATCCCCTCGTGGTGTTAC 57.167 47.619 2.33 0.00 0.00 2.50
119 120 0.246635 CCCCTCGTGGTGTTACTCTG 59.753 60.000 2.33 0.00 0.00 3.35
122 123 1.254026 CTCGTGGTGTTACTCTGGGA 58.746 55.000 0.00 0.00 0.00 4.37
126 127 0.976641 TGGTGTTACTCTGGGAGCAG 59.023 55.000 0.00 0.00 32.04 4.24
129 130 1.002544 GTGTTACTCTGGGAGCAGCTT 59.997 52.381 0.00 0.00 32.04 3.74
131 132 2.903784 TGTTACTCTGGGAGCAGCTTTA 59.096 45.455 0.00 0.00 32.04 1.85
132 133 3.326588 TGTTACTCTGGGAGCAGCTTTAA 59.673 43.478 0.00 0.00 32.04 1.52
133 134 2.481289 ACTCTGGGAGCAGCTTTAAC 57.519 50.000 0.00 0.00 32.04 2.01
346 350 5.392165 CGACGAGATCTTCAAAACTAGACCT 60.392 44.000 0.00 0.00 0.00 3.85
400 406 2.605338 CCAGAAGTTGCCACGATGTTTG 60.605 50.000 0.00 0.00 0.00 2.93
418 424 0.036590 TGCACTGCAGTTGCCATAGA 59.963 50.000 27.26 13.38 41.18 1.98
667 674 9.178427 GAAGAAAATAGCTGAAACATATCATGC 57.822 33.333 0.00 0.00 0.00 4.06
730 738 7.716799 AGACATGGCAACTTTAATCCAAATA 57.283 32.000 0.00 0.00 37.61 1.40
763 771 8.774586 ACATAGACAGAATTGATAATTTACCGC 58.225 33.333 0.00 0.00 0.00 5.68
764 772 6.619801 AGACAGAATTGATAATTTACCGCC 57.380 37.500 0.00 0.00 0.00 6.13
765 773 5.531287 AGACAGAATTGATAATTTACCGCCC 59.469 40.000 0.00 0.00 0.00 6.13
766 774 5.197451 ACAGAATTGATAATTTACCGCCCA 58.803 37.500 0.00 0.00 0.00 5.36
767 775 5.067283 ACAGAATTGATAATTTACCGCCCAC 59.933 40.000 0.00 0.00 0.00 4.61
768 776 5.299279 CAGAATTGATAATTTACCGCCCACT 59.701 40.000 0.00 0.00 0.00 4.00
769 777 5.299279 AGAATTGATAATTTACCGCCCACTG 59.701 40.000 0.00 0.00 0.00 3.66
770 778 3.916359 TGATAATTTACCGCCCACTGA 57.084 42.857 0.00 0.00 0.00 3.41
771 779 4.431416 TGATAATTTACCGCCCACTGAT 57.569 40.909 0.00 0.00 0.00 2.90
772 780 4.133820 TGATAATTTACCGCCCACTGATG 58.866 43.478 0.00 0.00 0.00 3.07
773 781 2.507407 AATTTACCGCCCACTGATGT 57.493 45.000 0.00 0.00 0.00 3.06
774 782 1.750193 ATTTACCGCCCACTGATGTG 58.250 50.000 0.00 0.00 43.45 3.21
780 788 1.545582 CCGCCCACTGATGTGAAAAAT 59.454 47.619 0.00 0.00 46.55 1.82
848 856 2.347452 CGTGACTAACGCATTTACAGGG 59.653 50.000 0.00 0.00 46.99 4.45
877 4145 0.958822 CAACACAGTTTAGCCCACCC 59.041 55.000 0.00 0.00 0.00 4.61
898 4166 4.536765 CCAAGGCCCATTGATTTACTACT 58.463 43.478 0.00 0.00 31.55 2.57
899 4167 5.398581 CCCAAGGCCCATTGATTTACTACTA 60.399 44.000 0.00 0.00 31.55 1.82
1029 4310 1.306141 AGTTGATCGCTCTCCCCCA 60.306 57.895 0.00 0.00 0.00 4.96
1126 4415 1.687493 CCCCTCACCTCTCCTCCAC 60.687 68.421 0.00 0.00 0.00 4.02
1288 4583 2.297895 CCTCATCCACCACCCGGAA 61.298 63.158 0.73 0.00 35.77 4.30
1303 4598 0.934436 CGGAACACCGCAAAAAGCTG 60.934 55.000 0.00 0.00 42.61 4.24
1318 4613 4.305956 CTGCCCCAAACCCTGGCT 62.306 66.667 0.00 0.00 44.90 4.75
1377 4686 0.110486 AAATCAGCACCCCACTTCGT 59.890 50.000 0.00 0.00 0.00 3.85
1426 5054 4.160626 CCGATAGACACCTCTTTCTCCTTT 59.839 45.833 0.00 0.00 39.76 3.11
1441 5069 1.228124 CTTTCTGCCCAACCACCGA 60.228 57.895 0.00 0.00 0.00 4.69
1445 5073 4.612412 TGCCCAACCACCGACGAC 62.612 66.667 0.00 0.00 0.00 4.34
1565 5208 3.134127 GGGTCATGCTGCCGGAAC 61.134 66.667 5.05 0.00 0.00 3.62
1753 13556 2.158549 GGAAAGGGGATGGAATGAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
1771 13574 1.728490 GGATTGGACATCTTGGCGGC 61.728 60.000 0.00 0.00 0.00 6.53
2127 15445 3.444034 CCGGAGTGTGACTTGATCTTCTA 59.556 47.826 0.00 0.00 0.00 2.10
2169 15680 5.176406 CGGAAGTCATGTGCTACAATATGAG 59.824 44.000 0.00 0.00 30.86 2.90
2255 16575 5.006746 GTGCCACTATATGCAGAGTTACAAC 59.993 44.000 0.00 0.00 38.34 3.32
2298 16618 7.835682 TCAATATGAGATTGTTGGTTCCTTCAT 59.164 33.333 0.00 0.00 0.00 2.57
2395 16715 8.950210 TCTCATTTTCTTTTACTGATGATGTCC 58.050 33.333 0.00 0.00 0.00 4.02
2453 16774 8.017373 CAGTATTGTGGTAACTTGTCTGATTTG 58.983 37.037 0.00 0.00 37.61 2.32
2493 16814 7.841282 TGTGGTGTTTAAGGGAAAAATGATA 57.159 32.000 0.00 0.00 0.00 2.15
2494 16815 8.251383 TGTGGTGTTTAAGGGAAAAATGATAA 57.749 30.769 0.00 0.00 0.00 1.75
2603 17010 7.103641 TCTTACTGCAAAGACCTAGTAAATGG 58.896 38.462 0.00 0.00 35.80 3.16
2699 17108 6.434596 TGGTGAAACACTTTGAATGATTACG 58.565 36.000 0.00 0.00 39.98 3.18
2711 17120 2.754946 TGATTACGTTGTCACTCCCC 57.245 50.000 0.00 0.00 0.00 4.81
2718 17127 1.270839 CGTTGTCACTCCCCTTGATGT 60.271 52.381 0.00 0.00 0.00 3.06
2759 17168 6.014669 TGTTTAAATAGAAAATGGTGCTGGCT 60.015 34.615 0.00 0.00 0.00 4.75
2769 17178 2.344535 GTGCTGGCTGAACACCATT 58.655 52.632 0.00 0.00 36.36 3.16
2882 17292 5.506708 AGGTGTCCTCTTTGTTTGTAAGTT 58.493 37.500 0.00 0.00 0.00 2.66
2883 17293 5.949952 AGGTGTCCTCTTTGTTTGTAAGTTT 59.050 36.000 0.00 0.00 0.00 2.66
2912 17322 5.794894 TCATGTAGGAAGGTGAAAGAGTTC 58.205 41.667 0.00 0.00 0.00 3.01
2914 17324 6.724441 TCATGTAGGAAGGTGAAAGAGTTCTA 59.276 38.462 0.00 0.00 34.60 2.10
2939 17349 2.358247 GACGCCGTGTTCCATGGT 60.358 61.111 12.58 0.00 42.15 3.55
2948 17358 2.710377 GTGTTCCATGGTGATGCTACA 58.290 47.619 12.58 3.54 0.00 2.74
3033 17449 2.673200 ATCACTCGCCACCAGCCAT 61.673 57.895 0.00 0.00 38.78 4.40
3042 17458 1.454295 CACCAGCCATGCCAGCATA 60.454 57.895 4.52 0.00 34.91 3.14
3044 17460 1.454295 CCAGCCATGCCAGCATACA 60.454 57.895 4.52 0.00 34.91 2.29
3071 17487 2.479566 TGTGGATTGCTGTCCTTCTC 57.520 50.000 8.98 0.26 39.12 2.87
3079 17495 0.674895 GCTGTCCTTCTCGGTGCAAT 60.675 55.000 0.00 0.00 0.00 3.56
3093 17509 1.139095 GCAATTGGCTGAGCAGAGC 59.861 57.895 6.82 0.00 40.25 4.09
3128 17563 1.303309 CATCGGCATCTTCTGTTCCC 58.697 55.000 0.00 0.00 0.00 3.97
3181 17674 4.481463 GAGCACTAGAGTTGTTGTCTCTC 58.519 47.826 0.00 0.00 41.66 3.20
3253 17749 0.963962 CTTCCATGGCTGCACAAGTT 59.036 50.000 6.96 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.042925 CCGTGTACTATGTCAAATTAAGGCTAC 60.043 40.741 0.00 0.00 0.00 3.58
15 16 5.583457 ACCGTGTACTATGTCAAATTAAGGC 59.417 40.000 0.00 0.00 0.00 4.35
16 17 6.036735 CCACCGTGTACTATGTCAAATTAAGG 59.963 42.308 0.00 0.00 0.00 2.69
17 18 6.814644 TCCACCGTGTACTATGTCAAATTAAG 59.185 38.462 0.00 0.00 0.00 1.85
18 19 6.699366 TCCACCGTGTACTATGTCAAATTAA 58.301 36.000 0.00 0.00 0.00 1.40
19 20 6.283544 TCCACCGTGTACTATGTCAAATTA 57.716 37.500 0.00 0.00 0.00 1.40
20 21 5.155278 TCCACCGTGTACTATGTCAAATT 57.845 39.130 0.00 0.00 0.00 1.82
21 22 4.811969 TCCACCGTGTACTATGTCAAAT 57.188 40.909 0.00 0.00 0.00 2.32
23 24 4.281435 TCTTTCCACCGTGTACTATGTCAA 59.719 41.667 0.00 0.00 0.00 3.18
24 25 3.827876 TCTTTCCACCGTGTACTATGTCA 59.172 43.478 0.00 0.00 0.00 3.58
25 26 4.421948 CTCTTTCCACCGTGTACTATGTC 58.578 47.826 0.00 0.00 0.00 3.06
27 28 3.782046 CCTCTTTCCACCGTGTACTATG 58.218 50.000 0.00 0.00 0.00 2.23
28 29 2.167900 GCCTCTTTCCACCGTGTACTAT 59.832 50.000 0.00 0.00 0.00 2.12
30 31 0.320697 GCCTCTTTCCACCGTGTACT 59.679 55.000 0.00 0.00 0.00 2.73
33 34 0.321653 GATGCCTCTTTCCACCGTGT 60.322 55.000 0.00 0.00 0.00 4.49
34 35 1.026718 GGATGCCTCTTTCCACCGTG 61.027 60.000 0.00 0.00 31.99 4.94
40 41 3.067320 GCTAAATGTGGATGCCTCTTTCC 59.933 47.826 0.00 0.00 0.00 3.13
41 42 3.950395 AGCTAAATGTGGATGCCTCTTTC 59.050 43.478 0.00 0.00 0.00 2.62
42 43 3.973425 AGCTAAATGTGGATGCCTCTTT 58.027 40.909 0.00 0.00 0.00 2.52
43 44 3.659183 AGCTAAATGTGGATGCCTCTT 57.341 42.857 0.00 0.00 0.00 2.85
44 45 3.659183 AAGCTAAATGTGGATGCCTCT 57.341 42.857 0.00 0.00 0.00 3.69
45 46 5.835113 TTAAAGCTAAATGTGGATGCCTC 57.165 39.130 0.00 0.00 0.00 4.70
46 47 6.155049 ACAATTAAAGCTAAATGTGGATGCCT 59.845 34.615 0.00 0.00 31.30 4.75
47 48 6.340522 ACAATTAAAGCTAAATGTGGATGCC 58.659 36.000 0.00 0.00 31.30 4.40
48 49 6.476706 GGACAATTAAAGCTAAATGTGGATGC 59.523 38.462 0.00 0.00 32.41 3.91
49 50 7.703621 CAGGACAATTAAAGCTAAATGTGGATG 59.296 37.037 0.00 0.00 32.41 3.51
50 51 7.631377 GCAGGACAATTAAAGCTAAATGTGGAT 60.631 37.037 0.00 0.00 32.41 3.41
51 52 6.350110 GCAGGACAATTAAAGCTAAATGTGGA 60.350 38.462 0.00 0.00 32.41 4.02
52 53 5.807011 GCAGGACAATTAAAGCTAAATGTGG 59.193 40.000 0.00 0.00 32.41 4.17
53 54 6.624423 AGCAGGACAATTAAAGCTAAATGTG 58.376 36.000 0.00 0.56 32.41 3.21
54 55 6.840780 AGCAGGACAATTAAAGCTAAATGT 57.159 33.333 0.00 0.00 34.49 2.71
73 74 4.525912 AAATGGAGCAAACCTTTAGCAG 57.474 40.909 0.00 0.00 0.00 4.24
74 75 7.710676 TTATAAATGGAGCAAACCTTTAGCA 57.289 32.000 0.00 0.00 0.00 3.49
75 76 7.867909 GGATTATAAATGGAGCAAACCTTTAGC 59.132 37.037 0.00 0.00 0.00 3.09
76 77 8.360390 GGGATTATAAATGGAGCAAACCTTTAG 58.640 37.037 0.00 0.00 0.00 1.85
77 78 7.289084 GGGGATTATAAATGGAGCAAACCTTTA 59.711 37.037 0.00 0.00 0.00 1.85
78 79 6.099701 GGGGATTATAAATGGAGCAAACCTTT 59.900 38.462 0.00 0.00 0.00 3.11
79 80 5.602561 GGGGATTATAAATGGAGCAAACCTT 59.397 40.000 0.00 0.00 0.00 3.50
81 82 5.147767 AGGGGATTATAAATGGAGCAAACC 58.852 41.667 0.00 0.00 0.00 3.27
83 84 5.070001 CGAGGGGATTATAAATGGAGCAAA 58.930 41.667 0.00 0.00 0.00 3.68
84 85 4.104102 ACGAGGGGATTATAAATGGAGCAA 59.896 41.667 0.00 0.00 0.00 3.91
85 86 3.650942 ACGAGGGGATTATAAATGGAGCA 59.349 43.478 0.00 0.00 0.00 4.26
87 88 4.041691 ACCACGAGGGGATTATAAATGGAG 59.958 45.833 3.29 0.00 42.91 3.86
88 89 3.977999 ACCACGAGGGGATTATAAATGGA 59.022 43.478 3.29 0.00 42.91 3.41
89 90 4.072131 CACCACGAGGGGATTATAAATGG 58.928 47.826 3.29 0.00 42.79 3.16
91 92 5.382664 AACACCACGAGGGGATTATAAAT 57.617 39.130 8.60 0.00 42.79 1.40
92 93 4.847990 AACACCACGAGGGGATTATAAA 57.152 40.909 8.60 0.00 42.79 1.40
93 94 4.964262 AGTAACACCACGAGGGGATTATAA 59.036 41.667 8.60 0.00 42.79 0.98
94 95 4.549668 AGTAACACCACGAGGGGATTATA 58.450 43.478 8.60 0.00 42.79 0.98
97 98 1.553704 GAGTAACACCACGAGGGGATT 59.446 52.381 8.60 1.09 42.79 3.01
98 99 1.192428 GAGTAACACCACGAGGGGAT 58.808 55.000 8.60 0.00 42.79 3.85
99 100 0.113776 AGAGTAACACCACGAGGGGA 59.886 55.000 8.60 0.00 42.79 4.81
100 101 0.246635 CAGAGTAACACCACGAGGGG 59.753 60.000 0.00 0.00 46.87 4.79
101 102 0.246635 CCAGAGTAACACCACGAGGG 59.753 60.000 3.29 0.00 44.81 4.30
102 103 0.246635 CCCAGAGTAACACCACGAGG 59.753 60.000 0.00 0.00 42.21 4.63
103 104 1.202582 CTCCCAGAGTAACACCACGAG 59.797 57.143 0.00 0.00 0.00 4.18
104 105 1.254026 CTCCCAGAGTAACACCACGA 58.746 55.000 0.00 0.00 0.00 4.35
105 106 0.389948 GCTCCCAGAGTAACACCACG 60.390 60.000 0.00 0.00 31.39 4.94
106 107 0.685097 TGCTCCCAGAGTAACACCAC 59.315 55.000 0.00 0.00 31.39 4.16
109 110 0.610687 AGCTGCTCCCAGAGTAACAC 59.389 55.000 0.00 0.00 41.77 3.32
113 114 2.094182 CGTTAAAGCTGCTCCCAGAGTA 60.094 50.000 1.00 0.00 41.77 2.59
114 115 1.338200 CGTTAAAGCTGCTCCCAGAGT 60.338 52.381 1.00 0.00 41.77 3.24
115 116 1.066858 TCGTTAAAGCTGCTCCCAGAG 60.067 52.381 1.00 0.00 41.77 3.35
119 120 1.136057 CGTTTCGTTAAAGCTGCTCCC 60.136 52.381 1.00 0.00 0.00 4.30
122 123 3.955771 TTTCGTTTCGTTAAAGCTGCT 57.044 38.095 0.00 0.00 0.00 4.24
126 127 6.986045 CGTTAACATTTTCGTTTCGTTAAAGC 59.014 34.615 6.39 0.00 34.75 3.51
129 130 5.394904 GGCGTTAACATTTTCGTTTCGTTAA 59.605 36.000 6.39 0.00 32.03 2.01
131 132 3.725245 GGCGTTAACATTTTCGTTTCGTT 59.275 39.130 6.39 0.00 32.03 3.85
132 133 3.290748 GGCGTTAACATTTTCGTTTCGT 58.709 40.909 6.39 0.00 32.03 3.85
133 134 2.653113 GGGCGTTAACATTTTCGTTTCG 59.347 45.455 6.39 0.00 0.00 3.46
245 248 8.760569 AGATACAACATTTTTAAGCCAAAAACG 58.239 29.630 8.31 4.15 46.19 3.60
251 255 8.871629 TTAGGAGATACAACATTTTTAAGCCA 57.128 30.769 0.00 0.00 0.00 4.75
400 406 0.731417 CTCTATGGCAACTGCAGTGC 59.269 55.000 22.49 23.67 44.36 4.40
418 424 5.278957 CCACATGGCAACTTTAGTTTAAGCT 60.279 40.000 0.00 0.00 35.83 3.74
667 674 5.702865 CCATGATGTTTACACTGAAGTTGG 58.297 41.667 0.00 0.00 0.00 3.77
737 745 8.774586 GCGGTAAATTATCAATTCTGTCTATGT 58.225 33.333 0.00 0.00 0.00 2.29
738 746 8.230486 GGCGGTAAATTATCAATTCTGTCTATG 58.770 37.037 0.00 0.00 0.00 2.23
739 747 7.390718 GGGCGGTAAATTATCAATTCTGTCTAT 59.609 37.037 0.00 0.00 0.00 1.98
740 748 6.708949 GGGCGGTAAATTATCAATTCTGTCTA 59.291 38.462 0.00 0.00 0.00 2.59
741 749 5.531287 GGGCGGTAAATTATCAATTCTGTCT 59.469 40.000 0.00 0.00 0.00 3.41
742 750 5.298276 TGGGCGGTAAATTATCAATTCTGTC 59.702 40.000 0.00 0.00 0.00 3.51
743 751 5.067283 GTGGGCGGTAAATTATCAATTCTGT 59.933 40.000 0.00 0.00 0.00 3.41
744 752 5.299279 AGTGGGCGGTAAATTATCAATTCTG 59.701 40.000 0.00 0.00 0.00 3.02
745 753 5.299279 CAGTGGGCGGTAAATTATCAATTCT 59.701 40.000 0.00 0.00 0.00 2.40
746 754 5.298276 TCAGTGGGCGGTAAATTATCAATTC 59.702 40.000 0.00 0.00 0.00 2.17
747 755 5.197451 TCAGTGGGCGGTAAATTATCAATT 58.803 37.500 0.00 0.00 0.00 2.32
748 756 4.787551 TCAGTGGGCGGTAAATTATCAAT 58.212 39.130 0.00 0.00 0.00 2.57
749 757 4.223556 TCAGTGGGCGGTAAATTATCAA 57.776 40.909 0.00 0.00 0.00 2.57
750 758 3.916359 TCAGTGGGCGGTAAATTATCA 57.084 42.857 0.00 0.00 0.00 2.15
751 759 4.024048 CACATCAGTGGGCGGTAAATTATC 60.024 45.833 0.00 0.00 42.13 1.75
752 760 3.882888 CACATCAGTGGGCGGTAAATTAT 59.117 43.478 0.00 0.00 42.13 1.28
753 761 3.055021 TCACATCAGTGGGCGGTAAATTA 60.055 43.478 0.00 0.00 45.91 1.40
754 762 2.091541 CACATCAGTGGGCGGTAAATT 58.908 47.619 0.00 0.00 42.13 1.82
755 763 1.280710 TCACATCAGTGGGCGGTAAAT 59.719 47.619 0.00 0.00 45.91 1.40
756 764 0.687920 TCACATCAGTGGGCGGTAAA 59.312 50.000 0.00 0.00 45.91 2.01
757 765 0.687920 TTCACATCAGTGGGCGGTAA 59.312 50.000 0.00 0.00 45.91 2.85
758 766 0.687920 TTTCACATCAGTGGGCGGTA 59.312 50.000 0.00 0.00 45.91 4.02
759 767 0.179004 TTTTCACATCAGTGGGCGGT 60.179 50.000 0.00 0.00 45.91 5.68
760 768 0.958091 TTTTTCACATCAGTGGGCGG 59.042 50.000 0.00 0.00 45.91 6.13
761 769 4.433186 TTATTTTTCACATCAGTGGGCG 57.567 40.909 0.00 0.00 45.91 6.13
762 770 5.408299 GGTTTTATTTTTCACATCAGTGGGC 59.592 40.000 0.00 0.00 45.91 5.36
763 771 6.758254 AGGTTTTATTTTTCACATCAGTGGG 58.242 36.000 0.00 0.00 45.91 4.61
764 772 8.661352 AAAGGTTTTATTTTTCACATCAGTGG 57.339 30.769 0.00 0.00 45.91 4.00
841 849 2.224744 TGTTGCATCTTCAGCCCTGTAA 60.225 45.455 0.00 0.00 0.00 2.41
848 856 3.360249 AAACTGTGTTGCATCTTCAGC 57.640 42.857 15.26 0.00 0.00 4.26
877 4145 6.260936 CACTAGTAGTAAATCAATGGGCCTTG 59.739 42.308 4.53 7.24 0.00 3.61
898 4166 2.573462 AGATTTTCCTGCTCCTGCACTA 59.427 45.455 0.00 0.00 45.31 2.74
899 4167 1.353694 AGATTTTCCTGCTCCTGCACT 59.646 47.619 0.00 0.00 45.31 4.40
1013 4294 1.699054 CCATGGGGGAGAGCGATCAA 61.699 60.000 2.85 0.00 40.01 2.57
1045 4326 4.227134 CCTGATGCGGACCGAGGG 62.227 72.222 20.50 7.33 0.00 4.30
1318 4613 1.295423 GCCGGTGTAGAAGAAGCCA 59.705 57.895 1.90 0.00 0.00 4.75
1377 4686 0.537188 GCTTCTCCCCGAGACATTGA 59.463 55.000 0.00 0.00 38.51 2.57
1426 5054 4.308458 CGTCGGTGGTTGGGCAGA 62.308 66.667 0.00 0.00 0.00 4.26
1441 5069 0.678366 AGTCCAGCAGATCGAGTCGT 60.678 55.000 13.12 0.00 0.00 4.34
1445 5073 0.528033 CAGCAGTCCAGCAGATCGAG 60.528 60.000 0.00 0.00 36.85 4.04
1546 5189 2.982643 TTCCGGCAGCATGACCCAT 61.983 57.895 0.00 0.00 46.22 4.00
1571 5214 1.078848 CCTTCCTTGACTCCGCCTG 60.079 63.158 0.00 0.00 0.00 4.85
1573 5216 1.376037 CACCTTCCTTGACTCCGCC 60.376 63.158 0.00 0.00 0.00 6.13
1576 5219 0.687354 TGCTCACCTTCCTTGACTCC 59.313 55.000 0.00 0.00 0.00 3.85
1580 13368 2.957402 ACAATGCTCACCTTCCTTGA 57.043 45.000 0.00 0.00 0.00 3.02
1582 13370 2.038557 ACGTACAATGCTCACCTTCCTT 59.961 45.455 0.00 0.00 0.00 3.36
1632 13420 5.048782 TCCATCAACACAAACACATAGAAGC 60.049 40.000 0.00 0.00 0.00 3.86
1753 13556 1.728490 GGCCGCCAAGATGTCCAATC 61.728 60.000 3.91 0.00 0.00 2.67
1834 13637 1.200020 GCAGCTACACAAATGGGTGAC 59.800 52.381 0.00 0.00 41.32 3.67
2169 15680 5.963594 AGATCACTTTTACTTCCCGACTAC 58.036 41.667 0.00 0.00 0.00 2.73
2298 16618 4.025040 TCGACTACTAACCCACTTCTCA 57.975 45.455 0.00 0.00 0.00 3.27
2310 16630 6.548251 TCCATGGTATGAACAATCGACTACTA 59.452 38.462 12.58 0.00 0.00 1.82
2365 16685 8.110860 TCATCAGTAAAAGAAAATGAGAACCC 57.889 34.615 0.00 0.00 0.00 4.11
2395 16715 3.600388 ACTTCCAGACTTAAAGGATGCG 58.400 45.455 0.00 0.00 31.71 4.73
2405 16725 4.104102 TGAACCACCATAACTTCCAGACTT 59.896 41.667 0.00 0.00 0.00 3.01
2407 16727 4.003648 CTGAACCACCATAACTTCCAGAC 58.996 47.826 0.00 0.00 0.00 3.51
2453 16774 6.992063 ACACCACATGAACTAATCTCATTC 57.008 37.500 0.00 0.00 30.99 2.67
2603 17010 0.595825 GCATTAGATGGCAAAGCGGC 60.596 55.000 0.00 0.00 41.67 6.53
2652 17059 9.851686 ACCATCAGAAATAAATGTCTAGCATTA 57.148 29.630 11.24 3.64 46.29 1.90
2699 17108 2.568623 ACATCAAGGGGAGTGACAAC 57.431 50.000 0.00 0.00 0.00 3.32
2711 17120 3.440173 AGGCACGGTCAATTAACATCAAG 59.560 43.478 0.00 0.00 0.00 3.02
2718 17127 5.769484 TTAAACAAGGCACGGTCAATTAA 57.231 34.783 0.00 0.00 0.00 1.40
2912 17322 1.076533 ACACGGCGTCGCTCAATTAG 61.077 55.000 18.11 0.00 40.63 1.73
2914 17324 1.897398 GAACACGGCGTCGCTCAATT 61.897 55.000 18.11 7.09 40.63 2.32
2967 17377 5.977129 ACTTGTAAACAAACTGCTACATTGC 59.023 36.000 0.00 0.00 35.15 3.56
3033 17449 2.158914 ACATCGATTCTGTATGCTGGCA 60.159 45.455 0.00 0.00 0.00 4.92
3042 17458 2.941064 CAGCAATCCACATCGATTCTGT 59.059 45.455 0.00 0.00 29.85 3.41
3044 17460 3.201290 GACAGCAATCCACATCGATTCT 58.799 45.455 0.00 0.00 29.85 2.40
3071 17487 2.180017 GCTCAGCCAATTGCACCG 59.820 61.111 0.00 0.00 44.83 4.94
3093 17509 0.750911 GATGCCCCTTCTTCCAGCAG 60.751 60.000 0.00 0.00 36.80 4.24
3128 17563 1.734359 GAGTTGCGAGCGCTTCTACG 61.734 60.000 13.26 12.18 42.51 3.51
3181 17674 0.600057 GGAGGAACAAGCCAAGCAAG 59.400 55.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.