Multiple sequence alignment - TraesCS4A01G469200

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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 TraesCS4A01G469200 chr4A 100.000 2339 0 0 1 2339 731061905 731059567 0.000000e+00 4320
1 TraesCS4A01G469200 chr4A 94.505 1201 53 6 1145 2339 729294198 729293005 0.000000e+00 1840
2 TraesCS4A01G469200 chr4A 93.611 1033 48 9 131 1154 729303207 729302184 0.000000e+00 1526
3 TraesCS4A01G469200 chr4A 84.989 473 52 11 912 1366 730358407 730357936 1.640000e-126 462
4 TraesCS4A01G469200 chr4A 79.825 456 83 8 865 1317 729280441 729279992 8.060000e-85 324
5 TraesCS4A01G469200 chr4A 77.460 559 96 12 953 1491 729582055 729582603 8.120000e-80 307
6 TraesCS4A01G469200 chr4A 77.536 414 79 9 1931 2339 729279199 729278795 1.080000e-58 237
7 TraesCS4A01G469200 chr4A 100.000 127 0 0 1 127 686728884 686728758 3.890000e-58 235
8 TraesCS4A01G469200 chr2D 89.082 403 25 2 126 509 596590866 596591268 1.260000e-132 483
9 TraesCS4A01G469200 chr2D 89.779 362 16 5 168 509 60771513 60771153 5.930000e-121 444
10 TraesCS4A01G469200 chr2D 85.753 365 41 6 156 509 646420322 646419958 2.190000e-100 375
11 TraesCS4A01G469200 chr2A 88.861 404 24 4 126 509 12184099 12184501 5.850000e-131 477
12 TraesCS4A01G469200 chr7D 88.614 404 25 4 126 508 249618701 249618298 2.720000e-129 472
13 TraesCS4A01G469200 chr7D 83.989 356 50 6 969 1320 10513309 10513661 3.720000e-88 335
14 TraesCS4A01G469200 chr5B 88.529 401 26 4 126 506 387899442 387899842 3.520000e-128 468
15 TraesCS4A01G469200 chr5B 100.000 127 0 0 1 127 610061788 610061914 3.890000e-58 235
16 TraesCS4A01G469200 chr5B 100.000 125 0 0 1 125 316254021 316254145 5.030000e-57 231
17 TraesCS4A01G469200 chr1B 88.148 405 27 4 126 509 231623947 231623543 1.640000e-126 462
18 TraesCS4A01G469200 chr1B 99.213 127 1 0 1 127 482884602 482884728 1.810000e-56 230
19 TraesCS4A01G469200 chr3A 87.042 409 32 4 122 511 688985128 688985534 2.130000e-120 442
20 TraesCS4A01G469200 chr3B 86.946 406 30 8 126 510 39354007 39353604 3.570000e-118 435
21 TraesCS4A01G469200 chr1A 87.565 386 27 4 134 499 129395979 129396363 5.970000e-116 427
22 TraesCS4A01G469200 chr5D 86.352 403 30 6 126 508 552631536 552631933 1.290000e-112 416
23 TraesCS4A01G469200 chr1D 87.580 314 20 5 126 420 70581314 70581001 1.720000e-91 346
24 TraesCS4A01G469200 chr6D 82.286 350 52 7 164 508 97866223 97865879 6.320000e-76 294
25 TraesCS4A01G469200 chrUn 99.213 127 1 0 1 127 17304330 17304456 1.810000e-56 230
26 TraesCS4A01G469200 chr7B 99.213 127 1 0 1 127 634191799 634191925 1.810000e-56 230
27 TraesCS4A01G469200 chr6B 99.213 127 1 0 1 127 18588964 18588838 1.810000e-56 230
28 TraesCS4A01G469200 chr6B 99.213 127 1 0 1 127 31328186 31328060 1.810000e-56 230
29 TraesCS4A01G469200 chr4B 99.213 127 1 0 1 127 380113350 380113476 1.810000e-56 230
30 TraesCS4A01G469200 chr7A 76.190 294 46 11 1212 1482 9661430 9661722 1.460000e-27 134


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 TraesCS4A01G469200 chr4A 731059567 731061905 2338 True 4320.0 4320 100.0000 1 2339 1 chr4A.!!$R5 2338
1 TraesCS4A01G469200 chr4A 729293005 729294198 1193 True 1840.0 1840 94.5050 1145 2339 1 chr4A.!!$R2 1194
2 TraesCS4A01G469200 chr4A 729302184 729303207 1023 True 1526.0 1526 93.6110 131 1154 1 chr4A.!!$R3 1023
3 TraesCS4A01G469200 chr4A 729582055 729582603 548 False 307.0 307 77.4600 953 1491 1 chr4A.!!$F1 538
4 TraesCS4A01G469200 chr4A 729278795 729280441 1646 True 280.5 324 78.6805 865 2339 2 chr4A.!!$R6 1474

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
106 107 0.038343 TTAGTACCGGTTCGTGCCAC 60.038 55.0 15.04 1.99 0.0 5.01 F
319 320 0.179059 TGCGCGTTATGTGGATGGAT 60.179 50.0 8.43 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1208 0.038159 GACCCTCCATTATCGCCTCG 60.038 60.0 0.0 0.0 0.0 4.63 R
2165 2508 0.824109 TCATCTCTGCCGGTTACCTG 59.176 55.0 1.9 0.0 0.0 4.00 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
34 35 1.577468 TAATGCGTCCATTAGTGCCG 58.423 50.000 0.00 0.00 41.68 5.69
35 36 1.095228 AATGCGTCCATTAGTGCCGG 61.095 55.000 0.00 0.00 39.81 6.13
36 37 2.125269 GCGTCCATTAGTGCCGGT 60.125 61.111 1.90 0.00 0.00 5.28
37 38 1.743995 GCGTCCATTAGTGCCGGTT 60.744 57.895 1.90 0.00 0.00 4.44
38 39 1.702491 GCGTCCATTAGTGCCGGTTC 61.702 60.000 1.90 0.00 0.00 3.62
39 40 0.390603 CGTCCATTAGTGCCGGTTCA 60.391 55.000 1.90 0.00 0.00 3.18
40 41 1.816074 GTCCATTAGTGCCGGTTCAA 58.184 50.000 1.90 0.00 0.00 2.69
41 42 2.156098 GTCCATTAGTGCCGGTTCAAA 58.844 47.619 1.90 0.00 0.00 2.69
42 43 2.752903 GTCCATTAGTGCCGGTTCAAAT 59.247 45.455 1.90 0.00 0.00 2.32
43 44 2.752354 TCCATTAGTGCCGGTTCAAATG 59.248 45.455 1.90 8.84 0.00 2.32
44 45 2.752354 CCATTAGTGCCGGTTCAAATGA 59.248 45.455 17.69 0.00 0.00 2.57
45 46 3.427503 CCATTAGTGCCGGTTCAAATGAC 60.428 47.826 17.69 0.00 0.00 3.06
46 47 2.851263 TAGTGCCGGTTCAAATGACT 57.149 45.000 1.90 0.00 0.00 3.41
47 48 2.851263 AGTGCCGGTTCAAATGACTA 57.149 45.000 1.90 0.00 0.00 2.59
48 49 2.699954 AGTGCCGGTTCAAATGACTAG 58.300 47.619 1.90 0.00 0.00 2.57
49 50 1.737793 GTGCCGGTTCAAATGACTAGG 59.262 52.381 1.90 0.00 0.00 3.02
50 51 0.733150 GCCGGTTCAAATGACTAGGC 59.267 55.000 1.90 0.00 36.32 3.93
51 52 1.006832 CCGGTTCAAATGACTAGGCG 58.993 55.000 0.00 0.00 0.00 5.52
52 53 1.006832 CGGTTCAAATGACTAGGCGG 58.993 55.000 0.00 0.00 0.00 6.13
53 54 1.379527 GGTTCAAATGACTAGGCGGG 58.620 55.000 0.00 0.00 0.00 6.13
54 55 1.065709 GGTTCAAATGACTAGGCGGGA 60.066 52.381 0.00 0.00 0.00 5.14
55 56 2.280628 GTTCAAATGACTAGGCGGGAG 58.719 52.381 0.00 0.00 0.00 4.30
56 57 0.830648 TCAAATGACTAGGCGGGAGG 59.169 55.000 0.00 0.00 0.00 4.30
57 58 0.830648 CAAATGACTAGGCGGGAGGA 59.169 55.000 0.00 0.00 0.00 3.71
58 59 1.123928 AAATGACTAGGCGGGAGGAG 58.876 55.000 0.00 0.00 0.00 3.69
59 60 0.261991 AATGACTAGGCGGGAGGAGA 59.738 55.000 0.00 0.00 0.00 3.71
60 61 0.468400 ATGACTAGGCGGGAGGAGAC 60.468 60.000 0.00 0.00 0.00 3.36
61 62 1.829096 GACTAGGCGGGAGGAGACC 60.829 68.421 0.00 0.00 0.00 3.85
62 63 2.287264 GACTAGGCGGGAGGAGACCT 62.287 65.000 0.00 0.00 36.03 3.85
63 64 1.075896 CTAGGCGGGAGGAGACCTT 60.076 63.158 0.00 0.00 31.76 3.50
64 65 0.688087 CTAGGCGGGAGGAGACCTTT 60.688 60.000 0.00 0.00 31.76 3.11
65 66 0.632835 TAGGCGGGAGGAGACCTTTA 59.367 55.000 0.00 0.00 31.76 1.85
66 67 0.252558 AGGCGGGAGGAGACCTTTAA 60.253 55.000 0.00 0.00 31.76 1.52
67 68 0.837940 GGCGGGAGGAGACCTTTAAT 59.162 55.000 0.00 0.00 31.76 1.40
68 69 2.044758 GGCGGGAGGAGACCTTTAATA 58.955 52.381 0.00 0.00 31.76 0.98
69 70 2.224233 GGCGGGAGGAGACCTTTAATAC 60.224 54.545 0.00 0.00 31.76 1.89
70 71 2.224233 GCGGGAGGAGACCTTTAATACC 60.224 54.545 0.00 0.00 31.76 2.73
71 72 2.035576 CGGGAGGAGACCTTTAATACCG 59.964 54.545 0.00 0.00 31.76 4.02
72 73 2.367894 GGGAGGAGACCTTTAATACCGG 59.632 54.545 0.00 0.00 31.76 5.28
73 74 3.036819 GGAGGAGACCTTTAATACCGGT 58.963 50.000 13.98 13.98 31.76 5.28
74 75 3.453717 GGAGGAGACCTTTAATACCGGTT 59.546 47.826 15.04 0.00 31.76 4.44
75 76 4.442612 GGAGGAGACCTTTAATACCGGTTC 60.443 50.000 15.04 0.30 31.76 3.62
76 77 4.098894 AGGAGACCTTTAATACCGGTTCA 58.901 43.478 15.04 0.00 0.00 3.18
77 78 4.720273 AGGAGACCTTTAATACCGGTTCAT 59.280 41.667 15.04 0.00 0.00 2.57
78 79 5.191124 AGGAGACCTTTAATACCGGTTCATT 59.809 40.000 15.04 10.50 0.00 2.57
79 80 5.296035 GGAGACCTTTAATACCGGTTCATTG 59.704 44.000 15.04 0.00 0.00 2.82
80 81 4.638865 AGACCTTTAATACCGGTTCATTGC 59.361 41.667 15.04 0.00 0.00 3.56
81 82 3.375922 ACCTTTAATACCGGTTCATTGCG 59.624 43.478 15.04 0.00 0.00 4.85
82 83 3.623960 CCTTTAATACCGGTTCATTGCGA 59.376 43.478 15.04 0.00 0.00 5.10
83 84 4.095185 CCTTTAATACCGGTTCATTGCGAA 59.905 41.667 15.04 4.10 0.00 4.70
84 85 5.220970 CCTTTAATACCGGTTCATTGCGAAT 60.221 40.000 15.04 0.00 35.63 3.34
85 86 3.963383 AATACCGGTTCATTGCGAATC 57.037 42.857 15.04 0.00 35.63 2.52
86 87 2.684001 TACCGGTTCATTGCGAATCT 57.316 45.000 15.04 0.00 35.63 2.40
87 88 1.821216 ACCGGTTCATTGCGAATCTT 58.179 45.000 0.00 0.00 35.63 2.40
88 89 2.159382 ACCGGTTCATTGCGAATCTTT 58.841 42.857 0.00 0.00 35.63 2.52
89 90 3.340034 ACCGGTTCATTGCGAATCTTTA 58.660 40.909 0.00 0.00 35.63 1.85
90 91 3.374058 ACCGGTTCATTGCGAATCTTTAG 59.626 43.478 0.00 0.00 35.63 1.85
91 92 3.374058 CCGGTTCATTGCGAATCTTTAGT 59.626 43.478 0.00 0.00 35.63 2.24
92 93 4.569162 CCGGTTCATTGCGAATCTTTAGTA 59.431 41.667 0.00 0.00 35.63 1.82
93 94 5.490213 CGGTTCATTGCGAATCTTTAGTAC 58.510 41.667 0.00 0.00 35.63 2.73
94 95 5.501897 CGGTTCATTGCGAATCTTTAGTACC 60.502 44.000 0.00 0.00 35.63 3.34
95 96 5.490213 GTTCATTGCGAATCTTTAGTACCG 58.510 41.667 0.00 0.00 35.63 4.02
96 97 4.116961 TCATTGCGAATCTTTAGTACCGG 58.883 43.478 0.00 0.00 0.00 5.28
97 98 3.598019 TTGCGAATCTTTAGTACCGGT 57.402 42.857 13.98 13.98 0.00 5.28
98 99 3.598019 TGCGAATCTTTAGTACCGGTT 57.402 42.857 15.04 0.00 0.00 4.44
99 100 3.514645 TGCGAATCTTTAGTACCGGTTC 58.485 45.455 15.04 8.12 0.00 3.62
100 101 2.533129 GCGAATCTTTAGTACCGGTTCG 59.467 50.000 15.04 14.16 39.71 3.95
101 102 3.762779 CGAATCTTTAGTACCGGTTCGT 58.237 45.455 15.04 0.00 34.14 3.85
102 103 3.545078 CGAATCTTTAGTACCGGTTCGTG 59.455 47.826 15.04 0.80 34.14 4.35
103 104 2.352503 TCTTTAGTACCGGTTCGTGC 57.647 50.000 15.04 0.00 0.00 5.34
104 105 1.067635 TCTTTAGTACCGGTTCGTGCC 60.068 52.381 15.04 0.00 0.00 5.01
105 106 0.678395 TTTAGTACCGGTTCGTGCCA 59.322 50.000 15.04 0.00 0.00 4.92
106 107 0.038343 TTAGTACCGGTTCGTGCCAC 60.038 55.000 15.04 1.99 0.00 5.01
107 108 2.198906 TAGTACCGGTTCGTGCCACG 62.199 60.000 15.04 11.80 44.19 4.94
116 117 3.107661 CGTGCCACGAACCGGTAC 61.108 66.667 12.85 0.00 46.05 3.34
117 118 2.341176 GTGCCACGAACCGGTACT 59.659 61.111 8.00 0.00 36.33 2.73
118 119 1.586028 GTGCCACGAACCGGTACTA 59.414 57.895 8.00 0.00 36.33 1.82
119 120 0.038343 GTGCCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 36.33 2.24
120 121 0.678395 TGCCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
121 122 1.337074 TGCCACGAACCGGTACTAAAG 60.337 52.381 8.00 0.00 0.00 1.85
122 123 1.067635 GCCACGAACCGGTACTAAAGA 60.068 52.381 8.00 0.00 0.00 2.52
123 124 2.417787 GCCACGAACCGGTACTAAAGAT 60.418 50.000 8.00 0.00 0.00 2.40
124 125 3.184541 CCACGAACCGGTACTAAAGATG 58.815 50.000 8.00 0.00 0.00 2.90
125 126 2.601763 CACGAACCGGTACTAAAGATGC 59.398 50.000 8.00 0.00 0.00 3.91
126 127 2.494870 ACGAACCGGTACTAAAGATGCT 59.505 45.455 8.00 0.00 0.00 3.79
127 128 3.056322 ACGAACCGGTACTAAAGATGCTT 60.056 43.478 8.00 0.00 0.00 3.91
128 129 3.550678 CGAACCGGTACTAAAGATGCTTC 59.449 47.826 8.00 0.00 0.00 3.86
129 130 3.160777 ACCGGTACTAAAGATGCTTCG 57.839 47.619 4.49 0.00 0.00 3.79
138 139 2.590007 GATGCTTCGCGCCTGGAT 60.590 61.111 0.00 0.00 38.05 3.41
152 153 4.899239 GGATGGACGAGCGCAGGG 62.899 72.222 11.47 0.00 0.00 4.45
244 245 2.838202 TCCTGAAGATGGGTAAGTGGTC 59.162 50.000 0.00 0.00 0.00 4.02
246 247 2.571653 CTGAAGATGGGTAAGTGGTCCA 59.428 50.000 0.00 0.00 34.79 4.02
278 279 4.215399 GGCGGCTTCTAAAACATATGCATA 59.785 41.667 9.27 9.27 0.00 3.14
296 297 3.462982 CATATGGTGTGCGCTTTAGGTA 58.537 45.455 9.73 0.00 0.00 3.08
319 320 0.179059 TGCGCGTTATGTGGATGGAT 60.179 50.000 8.43 0.00 0.00 3.41
320 321 0.512952 GCGCGTTATGTGGATGGATC 59.487 55.000 8.43 0.00 0.00 3.36
348 349 3.431207 CGACACCGGTTTTAGATATGGGT 60.431 47.826 2.97 0.00 0.00 4.51
393 394 2.158813 AGTTTGTAGGTGTGAGTGGTGG 60.159 50.000 0.00 0.00 0.00 4.61
434 435 4.214986 TGTTCTTGTCAGACCTTTGTGA 57.785 40.909 0.00 0.00 0.00 3.58
436 437 5.007034 TGTTCTTGTCAGACCTTTGTGAAA 58.993 37.500 0.00 0.00 0.00 2.69
498 500 2.165167 CCGGGGTTTAACCTCCTTTTC 58.835 52.381 14.27 0.00 34.38 2.29
536 538 6.594937 CGATTTTTGGGAACATGAATGGAAAT 59.405 34.615 0.00 0.00 42.32 2.17
568 570 1.376037 GGAAGTCAACTGAGCCGGG 60.376 63.158 2.18 0.00 0.00 5.73
585 587 3.068307 GCCGGGGTAGATGCATACTATAG 59.932 52.174 2.18 0.00 0.00 1.31
593 595 7.453126 GGGTAGATGCATACTATAGCTCCATAT 59.547 40.741 0.00 0.00 0.00 1.78
636 638 2.887151 ACCAGTTCCCTCTCAATTGG 57.113 50.000 5.42 0.00 36.83 3.16
713 719 2.826979 TAAGCACGACTTAGAGCTCG 57.173 50.000 8.37 0.00 39.97 5.03
724 730 4.342359 ACTTAGAGCTCGGAAACTTCCTA 58.658 43.478 8.37 0.00 45.33 2.94
726 732 3.596310 AGAGCTCGGAAACTTCCTAAC 57.404 47.619 8.37 0.00 45.33 2.34
727 733 2.897969 AGAGCTCGGAAACTTCCTAACA 59.102 45.455 8.37 0.00 45.33 2.41
785 792 6.363357 CCTTTGCTTAATTTGACTTTCTTCCG 59.637 38.462 0.00 0.00 0.00 4.30
830 837 8.990163 TTATTAGATTATGGTTTCTGGTTCCC 57.010 34.615 0.00 0.00 0.00 3.97
859 866 8.840321 GCTTAATTATTGTACCTGTGATGATGT 58.160 33.333 0.00 0.00 0.00 3.06
872 879 4.216902 TGTGATGATGTCCAAAGCTTTCTG 59.783 41.667 9.23 3.72 0.00 3.02
892 899 1.153939 CTTCTCTGACCAGCGTCGG 60.154 63.158 0.00 0.00 45.43 4.79
930 937 4.771590 AGAACACACACATAGCCATTTG 57.228 40.909 0.00 0.00 0.00 2.32
964 971 3.025978 TCTGAAAAGCATGGCCTAATGG 58.974 45.455 3.32 0.00 0.00 3.16
1077 1085 7.952930 TCACCTATTATCTCCAAGCTTCTAGAT 59.047 37.037 19.11 19.11 33.42 1.98
1115 1123 5.471456 ACTGCAAATTCGACAAAGAAGAGAT 59.529 36.000 0.00 0.00 33.19 2.75
1128 1136 2.706339 AAGAGATGCTTCATCGCCTT 57.294 45.000 2.07 8.54 44.67 4.35
1149 1157 1.154073 GACGGACGTTCTTCCTCGG 60.154 63.158 0.00 0.00 32.88 4.63
1161 1169 2.202756 CCTCGGCTGACGCTTACC 60.203 66.667 0.00 0.00 43.86 2.85
1200 1208 5.293560 GCTGTCAGTCATAGGGTATTCTTC 58.706 45.833 0.93 0.00 0.00 2.87
1205 1213 3.574826 AGTCATAGGGTATTCTTCGAGGC 59.425 47.826 0.00 0.00 0.00 4.70
1210 1218 3.228453 AGGGTATTCTTCGAGGCGATAA 58.772 45.455 0.00 0.00 35.23 1.75
1214 1222 4.321750 GGTATTCTTCGAGGCGATAATGGA 60.322 45.833 0.00 0.00 35.23 3.41
1338 1370 6.916360 AAGAGGACCAAAATTGCTTCATAA 57.084 33.333 0.00 0.00 0.00 1.90
1408 1450 6.296026 TGTAAATGCATACTTCCTCATACCC 58.704 40.000 0.00 0.00 0.00 3.69
1409 1451 5.387113 AAATGCATACTTCCTCATACCCA 57.613 39.130 0.00 0.00 0.00 4.51
1653 1707 5.859205 AAAGAGATTTGTTTCTGGTGCTT 57.141 34.783 0.00 0.00 0.00 3.91
1704 1990 8.842358 TTTCTCTATTGAAAAGTACAACCGAT 57.158 30.769 0.00 0.00 33.59 4.18
1838 2181 8.894409 TTTCTTACATGTATTTCGAATGCAAG 57.106 30.769 6.36 0.44 0.00 4.01
1852 2195 1.217244 GCAAGGCAAATGAGGCAGG 59.783 57.895 0.00 0.00 36.37 4.85
2019 2362 6.884295 ACTTTCACGGGAGATTTAAATCATCA 59.116 34.615 26.02 5.98 37.89 3.07
2120 2463 1.452145 GGGCGAAACTTCAACTGCCA 61.452 55.000 3.24 0.00 44.21 4.92
2121 2464 0.040067 GGCGAAACTTCAACTGCCAG 60.040 55.000 0.00 0.00 42.03 4.85
2122 2465 0.944386 GCGAAACTTCAACTGCCAGA 59.056 50.000 0.00 0.00 0.00 3.86
2123 2466 1.333619 GCGAAACTTCAACTGCCAGAA 59.666 47.619 0.00 0.00 0.00 3.02
2124 2467 2.223479 GCGAAACTTCAACTGCCAGAAA 60.223 45.455 0.00 0.00 0.00 2.52
2125 2468 3.550842 GCGAAACTTCAACTGCCAGAAAT 60.551 43.478 0.00 0.00 0.00 2.17
2165 2508 5.006746 CACACTACTTCAACTCCAACAGAAC 59.993 44.000 0.00 0.00 0.00 3.01
2188 2531 1.112113 TAACCGGCAGAGATGAGGAC 58.888 55.000 0.00 0.00 0.00 3.85
2194 2537 0.102120 GCAGAGATGAGGACCGTGAG 59.898 60.000 0.00 0.00 0.00 3.51
2261 2607 5.349817 AGCTCAAGTGACAATAGATGTTTCG 59.650 40.000 0.00 0.00 44.12 3.46
2302 2648 2.118403 TTTCAGGGTCTGGGAAGACT 57.882 50.000 5.89 0.00 38.74 3.24
2318 2664 1.204941 AGACTACCCTCGCACAACATC 59.795 52.381 0.00 0.00 0.00 3.06
2330 2676 3.058983 CGCACAACATCTTTGCAAGTCTA 60.059 43.478 0.00 0.00 35.93 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.466167 GCATTAGTGCCGGCTCATATG 59.534 52.381 29.70 27.22 45.76 1.78
1 2 1.813513 GCATTAGTGCCGGCTCATAT 58.186 50.000 29.70 17.62 45.76 1.78
2 3 3.305709 GCATTAGTGCCGGCTCATA 57.694 52.632 29.70 16.06 45.76 2.15
3 4 4.147701 GCATTAGTGCCGGCTCAT 57.852 55.556 29.70 15.76 45.76 2.90
14 15 1.526887 CGGCACTAATGGACGCATTAG 59.473 52.381 16.60 16.60 45.68 1.73
15 16 1.577468 CGGCACTAATGGACGCATTA 58.423 50.000 0.00 0.00 0.00 1.90
16 17 1.095228 CCGGCACTAATGGACGCATT 61.095 55.000 0.00 0.00 0.00 3.56
17 18 1.523711 CCGGCACTAATGGACGCAT 60.524 57.895 0.00 0.00 0.00 4.73
18 19 2.125310 CCGGCACTAATGGACGCA 60.125 61.111 0.00 0.00 0.00 5.24
19 20 1.702491 GAACCGGCACTAATGGACGC 61.702 60.000 0.00 0.00 0.00 5.19
20 21 0.390603 TGAACCGGCACTAATGGACG 60.391 55.000 0.00 0.00 0.00 4.79
21 22 1.816074 TTGAACCGGCACTAATGGAC 58.184 50.000 0.00 0.00 0.00 4.02
22 23 2.570415 TTTGAACCGGCACTAATGGA 57.430 45.000 0.00 0.00 0.00 3.41
23 24 2.752354 TCATTTGAACCGGCACTAATGG 59.248 45.455 23.44 12.73 32.98 3.16
24 25 3.440173 AGTCATTTGAACCGGCACTAATG 59.560 43.478 20.45 20.45 33.24 1.90
25 26 3.686016 AGTCATTTGAACCGGCACTAAT 58.314 40.909 0.00 1.61 0.00 1.73
26 27 3.134574 AGTCATTTGAACCGGCACTAA 57.865 42.857 0.00 0.00 0.00 2.24
27 28 2.851263 AGTCATTTGAACCGGCACTA 57.149 45.000 0.00 0.00 0.00 2.74
28 29 2.615493 CCTAGTCATTTGAACCGGCACT 60.615 50.000 0.00 0.00 0.00 4.40
29 30 1.737793 CCTAGTCATTTGAACCGGCAC 59.262 52.381 0.00 0.00 0.00 5.01
30 31 1.948611 GCCTAGTCATTTGAACCGGCA 60.949 52.381 0.00 0.00 34.11 5.69
31 32 0.733150 GCCTAGTCATTTGAACCGGC 59.267 55.000 0.00 0.00 0.00 6.13
32 33 1.006832 CGCCTAGTCATTTGAACCGG 58.993 55.000 0.00 0.00 0.00 5.28
33 34 1.006832 CCGCCTAGTCATTTGAACCG 58.993 55.000 0.00 0.00 0.00 4.44
34 35 1.065709 TCCCGCCTAGTCATTTGAACC 60.066 52.381 0.00 0.00 0.00 3.62
35 36 2.280628 CTCCCGCCTAGTCATTTGAAC 58.719 52.381 0.00 0.00 0.00 3.18
36 37 1.209504 CCTCCCGCCTAGTCATTTGAA 59.790 52.381 0.00 0.00 0.00 2.69
37 38 0.830648 CCTCCCGCCTAGTCATTTGA 59.169 55.000 0.00 0.00 0.00 2.69
38 39 0.830648 TCCTCCCGCCTAGTCATTTG 59.169 55.000 0.00 0.00 0.00 2.32
39 40 1.123928 CTCCTCCCGCCTAGTCATTT 58.876 55.000 0.00 0.00 0.00 2.32
40 41 0.261991 TCTCCTCCCGCCTAGTCATT 59.738 55.000 0.00 0.00 0.00 2.57
41 42 0.468400 GTCTCCTCCCGCCTAGTCAT 60.468 60.000 0.00 0.00 0.00 3.06
42 43 1.076923 GTCTCCTCCCGCCTAGTCA 60.077 63.158 0.00 0.00 0.00 3.41
43 44 1.829096 GGTCTCCTCCCGCCTAGTC 60.829 68.421 0.00 0.00 0.00 2.59
44 45 1.876546 AAGGTCTCCTCCCGCCTAGT 61.877 60.000 0.00 0.00 30.89 2.57
45 46 0.688087 AAAGGTCTCCTCCCGCCTAG 60.688 60.000 0.00 0.00 30.89 3.02
46 47 0.632835 TAAAGGTCTCCTCCCGCCTA 59.367 55.000 0.00 0.00 30.89 3.93
47 48 0.252558 TTAAAGGTCTCCTCCCGCCT 60.253 55.000 0.00 0.00 30.89 5.52
48 49 0.837940 ATTAAAGGTCTCCTCCCGCC 59.162 55.000 0.00 0.00 30.89 6.13
49 50 2.224233 GGTATTAAAGGTCTCCTCCCGC 60.224 54.545 0.00 0.00 30.89 6.13
50 51 2.035576 CGGTATTAAAGGTCTCCTCCCG 59.964 54.545 0.00 0.00 30.89 5.14
51 52 2.367894 CCGGTATTAAAGGTCTCCTCCC 59.632 54.545 0.00 0.00 30.89 4.30
52 53 3.036819 ACCGGTATTAAAGGTCTCCTCC 58.963 50.000 4.49 0.00 31.69 4.30
53 54 4.161001 TGAACCGGTATTAAAGGTCTCCTC 59.839 45.833 8.00 0.00 37.26 3.71
54 55 4.098894 TGAACCGGTATTAAAGGTCTCCT 58.901 43.478 8.00 0.00 37.26 3.69
55 56 4.476628 TGAACCGGTATTAAAGGTCTCC 57.523 45.455 8.00 0.00 37.26 3.71
56 57 5.220796 GCAATGAACCGGTATTAAAGGTCTC 60.221 44.000 8.00 0.00 37.26 3.36
57 58 4.638865 GCAATGAACCGGTATTAAAGGTCT 59.361 41.667 8.00 0.00 37.26 3.85
58 59 4.495184 CGCAATGAACCGGTATTAAAGGTC 60.495 45.833 8.00 0.00 37.26 3.85
59 60 3.375922 CGCAATGAACCGGTATTAAAGGT 59.624 43.478 8.00 0.00 40.50 3.50
60 61 3.623960 TCGCAATGAACCGGTATTAAAGG 59.376 43.478 8.00 0.00 0.00 3.11
61 62 4.868450 TCGCAATGAACCGGTATTAAAG 57.132 40.909 8.00 0.00 0.00 1.85
62 63 5.587043 AGATTCGCAATGAACCGGTATTAAA 59.413 36.000 8.00 1.12 40.00 1.52
63 64 5.120399 AGATTCGCAATGAACCGGTATTAA 58.880 37.500 8.00 0.00 40.00 1.40
64 65 4.699637 AGATTCGCAATGAACCGGTATTA 58.300 39.130 8.00 0.00 40.00 0.98
65 66 3.541632 AGATTCGCAATGAACCGGTATT 58.458 40.909 8.00 1.06 40.00 1.89
66 67 3.194005 AGATTCGCAATGAACCGGTAT 57.806 42.857 8.00 0.00 40.00 2.73
67 68 2.684001 AGATTCGCAATGAACCGGTA 57.316 45.000 8.00 0.00 40.00 4.02
68 69 1.821216 AAGATTCGCAATGAACCGGT 58.179 45.000 0.00 0.00 40.00 5.28
69 70 2.919666 AAAGATTCGCAATGAACCGG 57.080 45.000 0.00 0.00 40.00 5.28
70 71 4.600012 ACTAAAGATTCGCAATGAACCG 57.400 40.909 0.00 0.00 40.00 4.44
71 72 5.501897 CGGTACTAAAGATTCGCAATGAACC 60.502 44.000 0.00 0.00 40.00 3.62
72 73 5.490213 CGGTACTAAAGATTCGCAATGAAC 58.510 41.667 0.00 0.00 40.00 3.18
73 74 4.569162 CCGGTACTAAAGATTCGCAATGAA 59.431 41.667 0.00 0.00 41.81 2.57
74 75 4.116961 CCGGTACTAAAGATTCGCAATGA 58.883 43.478 0.00 0.00 0.00 2.57
75 76 3.869246 ACCGGTACTAAAGATTCGCAATG 59.131 43.478 4.49 0.00 0.00 2.82
76 77 4.133013 ACCGGTACTAAAGATTCGCAAT 57.867 40.909 4.49 0.00 0.00 3.56
77 78 3.598019 ACCGGTACTAAAGATTCGCAA 57.402 42.857 4.49 0.00 0.00 4.85
78 79 3.514645 GAACCGGTACTAAAGATTCGCA 58.485 45.455 8.00 0.00 0.00 5.10
79 80 2.533129 CGAACCGGTACTAAAGATTCGC 59.467 50.000 8.00 0.00 32.18 4.70
80 81 3.545078 CACGAACCGGTACTAAAGATTCG 59.455 47.826 8.00 13.08 42.26 3.34
81 82 3.305361 GCACGAACCGGTACTAAAGATTC 59.695 47.826 8.00 0.00 0.00 2.52
82 83 3.256558 GCACGAACCGGTACTAAAGATT 58.743 45.455 8.00 0.00 0.00 2.40
83 84 2.417787 GGCACGAACCGGTACTAAAGAT 60.418 50.000 8.00 0.00 0.00 2.40
84 85 1.067635 GGCACGAACCGGTACTAAAGA 60.068 52.381 8.00 0.00 0.00 2.52
85 86 1.337074 TGGCACGAACCGGTACTAAAG 60.337 52.381 8.00 0.00 0.00 1.85
86 87 0.678395 TGGCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
87 88 0.038343 GTGGCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 0.00 2.24
88 89 1.586028 GTGGCACGAACCGGTACTA 59.414 57.895 8.00 0.00 0.00 1.82
89 90 2.341176 GTGGCACGAACCGGTACT 59.659 61.111 8.00 0.00 0.00 2.73
90 91 3.107661 CGTGGCACGAACCGGTAC 61.108 66.667 34.85 0.00 46.05 3.34
99 100 2.198906 TAGTACCGGTTCGTGGCACG 62.199 60.000 32.75 32.75 44.19 5.34
100 101 0.038343 TTAGTACCGGTTCGTGGCAC 60.038 55.000 15.04 7.79 0.00 5.01
101 102 0.678395 TTTAGTACCGGTTCGTGGCA 59.322 50.000 15.04 0.00 0.00 4.92
102 103 1.067635 TCTTTAGTACCGGTTCGTGGC 60.068 52.381 15.04 0.00 0.00 5.01
103 104 3.184541 CATCTTTAGTACCGGTTCGTGG 58.815 50.000 15.04 1.20 0.00 4.94
104 105 2.601763 GCATCTTTAGTACCGGTTCGTG 59.398 50.000 15.04 4.09 0.00 4.35
105 106 2.494870 AGCATCTTTAGTACCGGTTCGT 59.505 45.455 15.04 0.00 0.00 3.85
106 107 3.160777 AGCATCTTTAGTACCGGTTCG 57.839 47.619 15.04 0.00 0.00 3.95
107 108 3.550678 CGAAGCATCTTTAGTACCGGTTC 59.449 47.826 15.04 8.12 0.00 3.62
108 109 3.518590 CGAAGCATCTTTAGTACCGGTT 58.481 45.455 15.04 0.00 0.00 4.44
109 110 3.160777 CGAAGCATCTTTAGTACCGGT 57.839 47.619 13.98 13.98 0.00 5.28
124 125 4.838152 TCCATCCAGGCGCGAAGC 62.838 66.667 12.10 0.00 44.51 3.86
125 126 2.892425 GTCCATCCAGGCGCGAAG 60.892 66.667 12.10 0.00 37.29 3.79
126 127 4.812476 CGTCCATCCAGGCGCGAA 62.812 66.667 12.10 0.00 37.58 4.70
173 174 2.173669 CATCCGTCGATGCCACCAC 61.174 63.158 0.00 0.00 39.59 4.16
196 197 1.069204 TCCGCATCATCCTTGCTAGTC 59.931 52.381 0.00 0.00 37.96 2.59
200 201 0.763652 AGATCCGCATCATCCTTGCT 59.236 50.000 0.00 0.00 37.96 3.91
244 245 0.313043 GAAGCCGCCATCATCATTGG 59.687 55.000 0.00 0.00 37.31 3.16
246 247 2.936919 TAGAAGCCGCCATCATCATT 57.063 45.000 0.00 0.00 0.00 2.57
278 279 1.406887 CCTACCTAAAGCGCACACCAT 60.407 52.381 11.47 0.00 0.00 3.55
393 394 2.325583 TACATCAATCCACCCGAAGC 57.674 50.000 0.00 0.00 0.00 3.86
434 435 7.386848 GCATGCAGCCATCTTTATTGATTATTT 59.613 33.333 14.21 0.00 37.23 1.40
436 437 6.014925 TGCATGCAGCCATCTTTATTGATTAT 60.015 34.615 18.46 0.00 44.83 1.28
507 509 5.782893 TTCATGTTCCCAAAAATCGAGTT 57.217 34.783 0.00 0.00 0.00 3.01
508 510 5.336690 CCATTCATGTTCCCAAAAATCGAGT 60.337 40.000 0.00 0.00 0.00 4.18
512 514 7.926674 ATTTCCATTCATGTTCCCAAAAATC 57.073 32.000 0.00 0.00 0.00 2.17
536 538 2.901192 TGACTTCCGTCATGGTAGGAAA 59.099 45.455 14.94 2.77 44.85 3.13
549 551 1.738099 CCGGCTCAGTTGACTTCCG 60.738 63.158 0.00 8.44 36.90 4.30
568 570 6.723298 ATGGAGCTATAGTATGCATCTACC 57.277 41.667 0.19 3.17 0.00 3.18
585 587 7.906199 AGAGTAATATACTGGGATATGGAGC 57.094 40.000 0.00 0.00 39.59 4.70
606 608 6.070767 TGAGAGGGAACTGGTTTGTATTAGAG 60.071 42.308 0.00 0.00 44.43 2.43
700 706 2.923605 AGTTTCCGAGCTCTAAGTCG 57.076 50.000 12.85 0.00 35.91 4.18
701 707 3.513662 GGAAGTTTCCGAGCTCTAAGTC 58.486 50.000 12.85 5.21 37.65 3.01
724 730 8.289618 GGCATGTATAATATCACGTGAATTGTT 58.710 33.333 24.13 13.84 34.26 2.83
726 732 7.805700 TGGCATGTATAATATCACGTGAATTG 58.194 34.615 24.13 7.90 34.26 2.32
727 733 7.977789 TGGCATGTATAATATCACGTGAATT 57.022 32.000 24.13 22.32 34.26 2.17
830 837 7.498900 TCATCACAGGTACAATAATTAAGCCAG 59.501 37.037 0.00 0.00 0.00 4.85
859 866 4.101585 TCAGAGAAGACAGAAAGCTTTGGA 59.898 41.667 18.30 0.00 0.00 3.53
872 879 0.455295 CGACGCTGGTCAGAGAAGAC 60.455 60.000 8.62 0.00 43.61 3.01
896 903 1.270625 TGTGTTCTAAGAACCAGGCCG 60.271 52.381 0.00 0.00 0.00 6.13
897 904 2.152016 GTGTGTTCTAAGAACCAGGCC 58.848 52.381 0.00 0.00 0.00 5.19
930 937 3.502595 GCTTTTCAGAGAACCAACCTACC 59.497 47.826 0.00 0.00 0.00 3.18
964 971 3.964031 AGGTAGGATGGAAGACATGAGAC 59.036 47.826 0.00 0.00 40.72 3.36
1077 1085 6.147164 CGAATTTGCAGTAGGACAAGACTTTA 59.853 38.462 0.00 0.00 0.00 1.85
1115 1123 0.516877 CGTCAAAAGGCGATGAAGCA 59.483 50.000 0.00 0.00 39.27 3.91
1122 1130 1.216941 GAACGTCCGTCAAAAGGCGA 61.217 55.000 0.00 0.00 34.26 5.54
1126 1134 2.475487 GAGGAAGAACGTCCGTCAAAAG 59.525 50.000 0.00 0.00 43.03 2.27
1128 1136 1.601162 CGAGGAAGAACGTCCGTCAAA 60.601 52.381 0.00 0.00 43.03 2.69
1149 1157 1.803252 GCTTCTAGGGTAAGCGTCAGC 60.803 57.143 0.00 0.00 39.92 4.26
1161 1169 4.852962 GCCTCTGCTGCTTCTAGG 57.147 61.111 0.00 3.66 33.53 3.02
1180 1188 5.278561 CCTCGAAGAATACCCTATGACTGAC 60.279 48.000 0.00 0.00 34.09 3.51
1184 1192 3.612004 CGCCTCGAAGAATACCCTATGAC 60.612 52.174 0.00 0.00 34.09 3.06
1200 1208 0.038159 GACCCTCCATTATCGCCTCG 60.038 60.000 0.00 0.00 0.00 4.63
1205 1213 4.993584 CAGATTTGAGACCCTCCATTATCG 59.006 45.833 0.00 0.00 0.00 2.92
1210 1218 2.203584 AGCAGATTTGAGACCCTCCAT 58.796 47.619 0.00 0.00 0.00 3.41
1214 1222 5.190528 TCATAGAAAGCAGATTTGAGACCCT 59.809 40.000 0.00 0.00 0.00 4.34
1408 1450 9.886132 ATTTACTAGGATAAAAGGTACTGTGTG 57.114 33.333 0.00 0.00 40.86 3.82
1454 1496 5.545588 ACATGACCCAATCTATCAGATTCG 58.454 41.667 0.00 0.00 42.67 3.34
1511 1557 6.041409 TGAATTACTTTGGGCAAATGTCTTCA 59.959 34.615 11.43 11.43 0.00 3.02
1552 1599 6.433716 TCATGATAGCCTTTGTGACATTTCAA 59.566 34.615 0.00 0.00 31.90 2.69
1682 1968 6.456988 GGCATCGGTTGTACTTTTCAATAGAG 60.457 42.308 0.00 0.00 0.00 2.43
1701 1987 1.595093 GGACCCCTTTGTTGGCATCG 61.595 60.000 0.00 0.00 0.00 3.84
1704 1990 2.200092 GGGACCCCTTTGTTGGCA 59.800 61.111 0.00 0.00 0.00 4.92
1830 2173 1.066716 TGCCTCATTTGCCTTGCATTC 60.067 47.619 0.00 0.00 38.76 2.67
1838 2181 1.065126 AGTAGACCTGCCTCATTTGCC 60.065 52.381 0.00 0.00 0.00 4.52
1852 2195 5.922053 ACGATGGGGGTAAAAATAGTAGAC 58.078 41.667 0.00 0.00 0.00 2.59
2165 2508 0.824109 TCATCTCTGCCGGTTACCTG 59.176 55.000 1.90 0.00 0.00 4.00
2188 2531 3.127548 ACATTTTTGCTATCTGCTCACGG 59.872 43.478 0.00 0.00 43.37 4.94
2194 2537 9.734620 TTATCATGTAACATTTTTGCTATCTGC 57.265 29.630 0.00 0.00 43.25 4.26
2261 2607 2.158928 TGCCATAAATCCCAATTGCAGC 60.159 45.455 0.00 0.00 0.00 5.25
2302 2648 2.422597 CAAAGATGTTGTGCGAGGGTA 58.577 47.619 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.