Multiple sequence alignment - TraesCS7A01G094700

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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 TraesCS7A01G094700 chr7A 100.000 2384 0 0 1 2384 57865760 57863377 0.000000e+00 4403.0
1 TraesCS7A01G094700 chr7A 93.057 1253 73 6 251 1501 57804097 57802857 0.000000e+00 1820.0
2 TraesCS7A01G094700 chr7A 88.855 655 37 11 1625 2259 57802720 57802082 0.000000e+00 773.0
3 TraesCS7A01G094700 chr7A 95.455 44 2 0 1570 1613 95950801 95950844 1.180000e-08 71.3
4 TraesCS7A01G094700 chr7A 87.931 58 7 0 1498 1555 346972008 346972065 4.250000e-08 69.4
5 TraesCS7A01G094700 chr7A 91.837 49 4 0 1499 1547 713851239 713851287 4.250000e-08 69.4
6 TraesCS7A01G094700 chr7A 91.837 49 4 0 1499 1547 713868210 713868258 4.250000e-08 69.4
7 TraesCS7A01G094700 chr7A 97.143 35 1 0 2275 2309 57802082 57802048 2.560000e-05 60.2
8 TraesCS7A01G094700 chr7D 94.891 1096 49 4 354 1446 54320708 54319617 0.000000e+00 1707.0
9 TraesCS7A01G094700 chr7D 92.908 1114 51 4 354 1467 54354778 54353693 0.000000e+00 1594.0
10 TraesCS7A01G094700 chr7D 92.186 1139 61 5 346 1459 54311948 54310813 0.000000e+00 1585.0
11 TraesCS7A01G094700 chr7D 93.486 875 47 4 572 1446 54337396 54336532 0.000000e+00 1291.0
12 TraesCS7A01G094700 chr7D 93.963 762 40 4 1623 2384 54336338 54335583 0.000000e+00 1147.0
13 TraesCS7A01G094700 chr7D 93.247 770 37 7 1623 2384 54319427 54318665 0.000000e+00 1120.0
14 TraesCS7A01G094700 chr7D 86.697 436 42 8 1583 2005 54353547 54353115 9.980000e-129 470.0
15 TraesCS7A01G094700 chr7D 87.500 384 31 7 1643 2013 54310813 54310434 6.090000e-116 427.0
16 TraesCS7A01G094700 chr7D 79.615 260 40 13 2025 2280 54310383 54310133 8.760000e-40 174.0
17 TraesCS7A01G094700 chr7D 85.047 107 7 5 2278 2384 54309975 54309878 1.510000e-17 100.0
18 TraesCS7A01G094700 chr7D 100.000 32 0 0 251 282 54320776 54320745 2.560000e-05 60.2
19 TraesCS7A01G094700 chr7D 100.000 32 0 0 251 282 54354846 54354815 2.560000e-05 60.2
20 TraesCS7A01G094700 chrUn 92.688 889 58 3 572 1459 49140767 49139885 0.000000e+00 1275.0
21 TraesCS7A01G094700 chrUn 92.463 889 60 3 572 1459 49113928 49113046 0.000000e+00 1264.0
22 TraesCS7A01G094700 chrUn 92.551 886 59 3 569 1453 384623891 384624770 0.000000e+00 1264.0
23 TraesCS7A01G094700 chrUn 87.141 801 50 22 1612 2384 49113063 49112288 0.000000e+00 859.0
24 TraesCS7A01G094700 chrUn 87.141 801 50 22 1612 2384 49139902 49139127 0.000000e+00 859.0
25 TraesCS7A01G094700 chrUn 87.212 477 32 17 1612 2067 384624759 384625227 1.260000e-142 516.0
26 TraesCS7A01G094700 chrUn 86.503 489 32 18 1905 2384 329826066 329825603 7.600000e-140 507.0
27 TraesCS7A01G094700 chrUn 86.503 489 32 18 1905 2384 329829073 329829536 7.600000e-140 507.0
28 TraesCS7A01G094700 chrUn 91.837 49 4 0 1499 1547 358381511 358381559 4.250000e-08 69.4
29 TraesCS7A01G094700 chr4A 92.281 868 62 2 597 1462 669899039 669898175 0.000000e+00 1227.0
30 TraesCS7A01G094700 chr4A 87.141 801 50 22 1612 2384 669892317 669891542 0.000000e+00 859.0
31 TraesCS7A01G094700 chr4A 82.921 445 54 14 1573 2005 669898075 669897641 4.810000e-102 381.0
32 TraesCS7A01G094700 chr5A 92.793 222 16 0 1 222 591630309 591630530 2.960000e-84 322.0
33 TraesCS7A01G094700 chr3D 92.444 225 17 0 1 225 581391358 581391582 2.960000e-84 322.0
34 TraesCS7A01G094700 chr3D 92.000 225 17 1 1 225 581391292 581391069 4.950000e-82 315.0
35 TraesCS7A01G094700 chr3A 91.556 225 16 1 1 225 177108734 177108955 8.280000e-80 307.0
36 TraesCS7A01G094700 chr3A 90.222 225 22 0 1 225 717806062 717806286 6.440000e-76 294.0
37 TraesCS7A01G094700 chr3A 87.931 58 7 0 1498 1555 397456158 397456215 4.250000e-08 69.4
38 TraesCS7A01G094700 chr2B 91.111 225 20 0 1 225 651986499 651986723 2.980000e-79 305.0
39 TraesCS7A01G094700 chr2B 95.455 44 2 0 1570 1613 427299129 427299086 1.180000e-08 71.3
40 TraesCS7A01G094700 chr7B 90.667 225 21 0 1 225 539221580 539221356 1.390000e-77 300.0
41 TraesCS7A01G094700 chr2A 90.667 225 21 0 1 225 522245308 522245084 1.390000e-77 300.0
42 TraesCS7A01G094700 chr2A 87.931 58 7 0 1498 1555 534166077 534166134 4.250000e-08 69.4
43 TraesCS7A01G094700 chr5D 90.667 225 20 1 1 225 261281574 261281351 4.980000e-77 298.0
44 TraesCS7A01G094700 chr4B 89.655 58 6 0 1498 1555 123369768 123369711 9.140000e-10 75.0
45 TraesCS7A01G094700 chr1B 89.655 58 4 2 1499 1555 564270060 564270116 3.290000e-09 73.1
46 TraesCS7A01G094700 chr3B 95.455 44 2 0 1570 1613 379098258 379098301 1.180000e-08 71.3
47 TraesCS7A01G094700 chr6A 87.500 56 7 0 1500 1555 39504316 39504261 5.500000e-07 65.8


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 TraesCS7A01G094700 chr7A 57863377 57865760 2383 True 4403.000000 4403 100.000000 1 2384 1 chr7A.!!$R1 2383
1 TraesCS7A01G094700 chr7A 57802048 57804097 2049 True 884.400000 1820 93.018333 251 2309 3 chr7A.!!$R2 2058
2 TraesCS7A01G094700 chr7D 54335583 54337396 1813 True 1219.000000 1291 93.724500 572 2384 2 chr7D.!!$R3 1812
3 TraesCS7A01G094700 chr7D 54318665 54320776 2111 True 962.400000 1707 96.046000 251 2384 3 chr7D.!!$R2 2133
4 TraesCS7A01G094700 chr7D 54353115 54354846 1731 True 708.066667 1594 93.201667 251 2005 3 chr7D.!!$R4 1754
5 TraesCS7A01G094700 chr7D 54309878 54311948 2070 True 571.500000 1585 86.087000 346 2384 4 chr7D.!!$R1 2038
6 TraesCS7A01G094700 chrUn 49139127 49140767 1640 True 1067.000000 1275 89.914500 572 2384 2 chrUn.!!$R3 1812
7 TraesCS7A01G094700 chrUn 49112288 49113928 1640 True 1061.500000 1264 89.802000 572 2384 2 chrUn.!!$R2 1812
8 TraesCS7A01G094700 chrUn 384623891 384625227 1336 False 890.000000 1264 89.881500 569 2067 2 chrUn.!!$F3 1498
9 TraesCS7A01G094700 chr4A 669891542 669892317 775 True 859.000000 859 87.141000 1612 2384 1 chr4A.!!$R1 772
10 TraesCS7A01G094700 chr4A 669897641 669899039 1398 True 804.000000 1227 87.601000 597 2005 2 chr4A.!!$R2 1408

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
249 250 0.250295 TCTTTGACGAGTGCCTTGGG 60.25 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1955 0.250467 GGCTGTTGGTGCTGAGAAGA 60.25 55.0 0.0 0.0 0.0 2.87 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
28 29 8.766000 TTTAATGATGTTTTCTCGTAGTAGCA 57.234 30.769 0.00 0.00 0.00 3.49
29 30 8.766000 TTAATGATGTTTTCTCGTAGTAGCAA 57.234 30.769 0.00 0.00 0.00 3.91
30 31 6.648725 ATGATGTTTTCTCGTAGTAGCAAC 57.351 37.500 0.00 0.00 0.00 4.17
31 32 5.779922 TGATGTTTTCTCGTAGTAGCAACT 58.220 37.500 0.00 0.00 39.91 3.16
32 33 6.220930 TGATGTTTTCTCGTAGTAGCAACTT 58.779 36.000 0.00 0.00 37.15 2.66
33 34 5.900339 TGTTTTCTCGTAGTAGCAACTTG 57.100 39.130 0.00 0.00 37.15 3.16
34 35 5.353938 TGTTTTCTCGTAGTAGCAACTTGT 58.646 37.500 0.00 0.00 37.15 3.16
35 36 5.813672 TGTTTTCTCGTAGTAGCAACTTGTT 59.186 36.000 0.00 0.00 37.15 2.83
36 37 6.314400 TGTTTTCTCGTAGTAGCAACTTGTTT 59.686 34.615 0.00 0.00 37.15 2.83
37 38 7.492020 TGTTTTCTCGTAGTAGCAACTTGTTTA 59.508 33.333 0.00 0.00 37.15 2.01
38 39 8.330302 GTTTTCTCGTAGTAGCAACTTGTTTAA 58.670 33.333 0.00 0.00 37.15 1.52
39 40 8.597662 TTTCTCGTAGTAGCAACTTGTTTAAT 57.402 30.769 0.00 0.00 37.15 1.40
40 41 9.695526 TTTCTCGTAGTAGCAACTTGTTTAATA 57.304 29.630 0.00 0.00 37.15 0.98
41 42 9.865321 TTCTCGTAGTAGCAACTTGTTTAATAT 57.135 29.630 0.00 0.00 37.15 1.28
42 43 9.865321 TCTCGTAGTAGCAACTTGTTTAATATT 57.135 29.630 0.00 0.00 37.15 1.28
45 46 8.995906 CGTAGTAGCAACTTGTTTAATATTTGC 58.004 33.333 0.00 0.00 39.69 3.68
46 47 9.834628 GTAGTAGCAACTTGTTTAATATTTGCA 57.165 29.630 6.86 0.00 41.43 4.08
48 49 9.357652 AGTAGCAACTTGTTTAATATTTGCATG 57.642 29.630 6.86 0.00 41.43 4.06
49 50 7.064060 AGCAACTTGTTTAATATTTGCATGC 57.936 32.000 11.82 11.82 41.43 4.06
50 51 6.649973 AGCAACTTGTTTAATATTTGCATGCA 59.350 30.769 18.46 18.46 41.43 3.96
51 52 7.334921 AGCAACTTGTTTAATATTTGCATGCAT 59.665 29.630 23.37 10.46 41.43 3.96
52 53 7.427030 GCAACTTGTTTAATATTTGCATGCATG 59.573 33.333 23.37 22.70 39.30 4.06
53 54 8.444715 CAACTTGTTTAATATTTGCATGCATGT 58.555 29.630 26.79 15.47 0.00 3.21
54 55 7.966111 ACTTGTTTAATATTTGCATGCATGTG 58.034 30.769 26.79 5.68 0.00 3.21
55 56 7.818446 ACTTGTTTAATATTTGCATGCATGTGA 59.182 29.630 26.79 13.56 0.00 3.58
56 57 8.719560 TTGTTTAATATTTGCATGCATGTGAT 57.280 26.923 26.79 19.08 0.00 3.06
57 58 8.355272 TGTTTAATATTTGCATGCATGTGATC 57.645 30.769 26.79 11.44 0.00 2.92
58 59 7.980099 TGTTTAATATTTGCATGCATGTGATCA 59.020 29.630 26.79 13.94 0.00 2.92
59 60 8.984764 GTTTAATATTTGCATGCATGTGATCAT 58.015 29.630 26.79 14.32 34.21 2.45
63 64 8.702163 ATATTTGCATGCATGTGATCATAATG 57.298 30.769 26.79 14.11 33.82 1.90
64 65 5.776173 TTGCATGCATGTGATCATAATGA 57.224 34.783 26.79 0.00 33.13 2.57
65 66 5.116069 TGCATGCATGTGATCATAATGAC 57.884 39.130 26.79 6.83 33.13 3.06
66 67 4.580995 TGCATGCATGTGATCATAATGACA 59.419 37.500 26.79 16.97 33.37 3.58
67 68 5.242838 TGCATGCATGTGATCATAATGACAT 59.757 36.000 26.79 17.98 39.90 3.06
68 69 6.156519 GCATGCATGTGATCATAATGACATT 58.843 36.000 26.79 5.87 37.59 2.71
69 70 6.089417 GCATGCATGTGATCATAATGACATTG 59.911 38.462 26.79 16.11 37.59 2.82
70 71 6.702716 TGCATGTGATCATAATGACATTGT 57.297 33.333 19.97 0.81 37.59 2.71
71 72 6.500041 TGCATGTGATCATAATGACATTGTG 58.500 36.000 19.97 16.47 37.59 3.33
72 73 5.401376 GCATGTGATCATAATGACATTGTGC 59.599 40.000 19.97 8.72 37.59 4.57
73 74 6.734871 GCATGTGATCATAATGACATTGTGCT 60.735 38.462 19.97 9.96 37.59 4.40
74 75 7.520937 GCATGTGATCATAATGACATTGTGCTA 60.521 37.037 19.97 4.77 37.59 3.49
75 76 7.250445 TGTGATCATAATGACATTGTGCTAC 57.750 36.000 17.48 15.25 32.23 3.58
76 77 7.049754 TGTGATCATAATGACATTGTGCTACT 58.950 34.615 17.48 4.95 32.23 2.57
77 78 7.553760 TGTGATCATAATGACATTGTGCTACTT 59.446 33.333 17.48 3.08 32.23 2.24
78 79 8.066595 GTGATCATAATGACATTGTGCTACTTC 58.933 37.037 17.48 10.45 32.23 3.01
79 80 6.925610 TCATAATGACATTGTGCTACTTCC 57.074 37.500 17.48 0.00 32.23 3.46
80 81 6.653020 TCATAATGACATTGTGCTACTTCCT 58.347 36.000 17.48 0.00 32.23 3.36
81 82 7.112122 TCATAATGACATTGTGCTACTTCCTT 58.888 34.615 17.48 0.00 32.23 3.36
82 83 5.886960 AATGACATTGTGCTACTTCCTTC 57.113 39.130 0.00 0.00 0.00 3.46
83 84 4.623932 TGACATTGTGCTACTTCCTTCT 57.376 40.909 0.00 0.00 0.00 2.85
84 85 4.569943 TGACATTGTGCTACTTCCTTCTC 58.430 43.478 0.00 0.00 0.00 2.87
85 86 4.040339 TGACATTGTGCTACTTCCTTCTCA 59.960 41.667 0.00 0.00 0.00 3.27
86 87 5.171339 ACATTGTGCTACTTCCTTCTCAT 57.829 39.130 0.00 0.00 0.00 2.90
87 88 5.564550 ACATTGTGCTACTTCCTTCTCATT 58.435 37.500 0.00 0.00 0.00 2.57
88 89 5.413833 ACATTGTGCTACTTCCTTCTCATTG 59.586 40.000 0.00 0.00 0.00 2.82
89 90 3.338249 TGTGCTACTTCCTTCTCATTGC 58.662 45.455 0.00 0.00 0.00 3.56
90 91 3.008375 TGTGCTACTTCCTTCTCATTGCT 59.992 43.478 0.00 0.00 0.00 3.91
91 92 4.006319 GTGCTACTTCCTTCTCATTGCTT 58.994 43.478 0.00 0.00 0.00 3.91
92 93 4.457257 GTGCTACTTCCTTCTCATTGCTTT 59.543 41.667 0.00 0.00 0.00 3.51
93 94 4.697352 TGCTACTTCCTTCTCATTGCTTTC 59.303 41.667 0.00 0.00 0.00 2.62
94 95 4.940654 GCTACTTCCTTCTCATTGCTTTCT 59.059 41.667 0.00 0.00 0.00 2.52
95 96 5.414144 GCTACTTCCTTCTCATTGCTTTCTT 59.586 40.000 0.00 0.00 0.00 2.52
96 97 5.702349 ACTTCCTTCTCATTGCTTTCTTG 57.298 39.130 0.00 0.00 0.00 3.02
97 98 4.022503 ACTTCCTTCTCATTGCTTTCTTGC 60.023 41.667 0.00 0.00 0.00 4.01
98 99 3.489355 TCCTTCTCATTGCTTTCTTGCA 58.511 40.909 0.00 0.00 41.65 4.08
99 100 4.084287 TCCTTCTCATTGCTTTCTTGCAT 58.916 39.130 0.00 0.00 42.96 3.96
100 101 4.082408 TCCTTCTCATTGCTTTCTTGCATG 60.082 41.667 0.00 0.00 42.96 4.06
101 102 3.226346 TCTCATTGCTTTCTTGCATGC 57.774 42.857 11.82 11.82 42.96 4.06
102 103 2.559231 TCTCATTGCTTTCTTGCATGCA 59.441 40.909 18.46 18.46 42.96 3.96
103 104 3.194755 TCTCATTGCTTTCTTGCATGCAT 59.805 39.130 23.37 0.00 42.96 3.96
104 105 3.258228 TCATTGCTTTCTTGCATGCATG 58.742 40.909 23.37 23.63 42.96 4.06
121 122 5.247507 TGCATGCGGGCATATTAATAATC 57.752 39.130 14.09 0.00 39.25 1.75
122 123 4.097741 TGCATGCGGGCATATTAATAATCC 59.902 41.667 14.09 3.85 39.25 3.01
123 124 4.499696 GCATGCGGGCATATTAATAATCCC 60.500 45.833 18.59 18.59 34.91 3.85
130 131 7.092137 GGGCATATTAATAATCCCGGTTAAC 57.908 40.000 15.53 0.00 0.00 2.01
131 132 6.183360 GGGCATATTAATAATCCCGGTTAACG 60.183 42.308 15.53 0.00 43.80 3.18
147 148 6.782298 GGTTAACGAGAAGAAAAGTTAGCT 57.218 37.500 0.00 0.00 33.07 3.32
148 149 7.187244 GGTTAACGAGAAGAAAAGTTAGCTT 57.813 36.000 0.00 0.00 36.30 3.74
149 150 7.070183 GGTTAACGAGAAGAAAAGTTAGCTTG 58.930 38.462 0.00 0.00 34.71 4.01
150 151 4.733972 ACGAGAAGAAAAGTTAGCTTGC 57.266 40.909 0.00 0.00 34.71 4.01
151 152 4.127171 ACGAGAAGAAAAGTTAGCTTGCA 58.873 39.130 0.00 0.00 34.71 4.08
152 153 4.574828 ACGAGAAGAAAAGTTAGCTTGCAA 59.425 37.500 0.00 0.00 34.71 4.08
153 154 5.065988 ACGAGAAGAAAAGTTAGCTTGCAAA 59.934 36.000 0.00 0.00 34.71 3.68
201 202 8.879427 ATACCTTTAATTTGAGTTTGTAGCCT 57.121 30.769 0.00 0.00 0.00 4.58
202 203 7.597288 ACCTTTAATTTGAGTTTGTAGCCTT 57.403 32.000 0.00 0.00 0.00 4.35
203 204 7.433680 ACCTTTAATTTGAGTTTGTAGCCTTG 58.566 34.615 0.00 0.00 0.00 3.61
204 205 7.069455 ACCTTTAATTTGAGTTTGTAGCCTTGT 59.931 33.333 0.00 0.00 0.00 3.16
205 206 8.573035 CCTTTAATTTGAGTTTGTAGCCTTGTA 58.427 33.333 0.00 0.00 0.00 2.41
223 224 6.253946 CTTGTATAAGGGAATTGAGGGAGT 57.746 41.667 0.00 0.00 0.00 3.85
224 225 7.374975 CTTGTATAAGGGAATTGAGGGAGTA 57.625 40.000 0.00 0.00 0.00 2.59
225 226 6.996180 TGTATAAGGGAATTGAGGGAGTAG 57.004 41.667 0.00 0.00 0.00 2.57
226 227 5.844516 TGTATAAGGGAATTGAGGGAGTAGG 59.155 44.000 0.00 0.00 0.00 3.18
227 228 3.508952 AAGGGAATTGAGGGAGTAGGA 57.491 47.619 0.00 0.00 0.00 2.94
228 229 3.508952 AGGGAATTGAGGGAGTAGGAA 57.491 47.619 0.00 0.00 0.00 3.36
229 230 3.116174 AGGGAATTGAGGGAGTAGGAAC 58.884 50.000 0.00 0.00 0.00 3.62
230 231 3.116174 GGGAATTGAGGGAGTAGGAACT 58.884 50.000 0.00 0.00 46.37 3.01
242 243 4.506886 AGTAGGAACTCTTTGACGAGTG 57.493 45.455 0.00 0.00 43.14 3.51
243 244 2.156343 AGGAACTCTTTGACGAGTGC 57.844 50.000 0.00 0.00 43.14 4.40
245 246 2.156343 GAACTCTTTGACGAGTGCCT 57.844 50.000 0.00 0.00 43.14 4.75
246 247 2.484889 GAACTCTTTGACGAGTGCCTT 58.515 47.619 0.00 0.00 43.14 4.35
247 248 1.871080 ACTCTTTGACGAGTGCCTTG 58.129 50.000 0.00 0.00 42.39 3.61
248 249 1.151668 CTCTTTGACGAGTGCCTTGG 58.848 55.000 0.00 0.00 0.00 3.61
249 250 0.250295 TCTTTGACGAGTGCCTTGGG 60.250 55.000 0.00 0.00 0.00 4.12
314 315 2.719705 ACCAACTTTCCAGTAATGGGGA 59.280 45.455 9.77 0.00 35.79 4.81
465 466 3.664107 TGACGAGAATTGAACCAAGGAG 58.336 45.455 0.00 0.00 0.00 3.69
558 582 5.105635 GGATGAAAGCAAACAATGGAGATGA 60.106 40.000 0.00 0.00 0.00 2.92
765 793 2.902846 ATCCTCGCCGTCTCCTCG 60.903 66.667 0.00 0.00 0.00 4.63
1173 1201 0.250338 GCACCTCGAAGTCCACCTTT 60.250 55.000 0.00 0.00 32.03 3.11
1314 1342 2.087248 CAGGGAGGGATTGTTGGGT 58.913 57.895 0.00 0.00 0.00 4.51
1460 1491 8.076714 TGTTTGCATTGCGATTTAATTGTTTA 57.923 26.923 3.84 0.00 0.00 2.01
1465 1506 8.982685 TGCATTGCGATTTAATTGTTTAGAAAA 58.017 25.926 3.84 0.00 0.00 2.29
1479 1520 6.620678 TGTTTAGAAAATGGTAGATGCTTGC 58.379 36.000 0.00 0.00 0.00 4.01
1494 1535 1.896220 CTTGCTTGGCTGGTGAGTAA 58.104 50.000 0.00 0.00 0.00 2.24
1532 1629 2.027469 TCAGCTACTCGGTGACTCTACA 60.027 50.000 0.00 0.00 44.63 2.74
1538 1635 4.283363 ACTCGGTGACTCTACAAGTAGA 57.717 45.455 9.40 9.40 38.74 2.59
1553 1650 8.807118 TCTACAAGTAGAGATCAATTGACAAGT 58.193 33.333 11.07 0.00 37.28 3.16
1554 1651 9.429359 CTACAAGTAGAGATCAATTGACAAGTT 57.571 33.333 11.07 0.00 35.21 2.66
1555 1652 8.682936 ACAAGTAGAGATCAATTGACAAGTTT 57.317 30.769 11.07 0.00 0.00 2.66
1556 1653 9.125026 ACAAGTAGAGATCAATTGACAAGTTTT 57.875 29.630 11.07 0.00 0.00 2.43
1557 1654 9.956720 CAAGTAGAGATCAATTGACAAGTTTTT 57.043 29.630 11.07 0.00 0.00 1.94
1748 1853 2.579201 CTTGACGATGGCCTCCGT 59.421 61.111 19.92 19.92 42.17 4.69
1832 1943 2.050714 CAGCAAAGCACACGCCAG 60.051 61.111 0.00 0.00 39.83 4.85
1839 1950 2.665008 AAGCACACGCCAGCAGAAGA 62.665 55.000 0.00 0.00 39.83 2.87
1844 1955 1.208052 ACACGCCAGCAGAAGATACAT 59.792 47.619 0.00 0.00 0.00 2.29
1858 1969 5.426689 AAGATACATCTTCTCAGCACCAA 57.573 39.130 0.00 0.00 43.27 3.67
1873 1984 1.080569 CCAACAGCCGCCATTGTTC 60.081 57.895 4.09 0.00 35.46 3.18
1909 2035 7.603651 AGCTCGAGTTCTTGACTAAGATAAAA 58.396 34.615 15.13 0.00 42.25 1.52
1910 2036 7.757624 AGCTCGAGTTCTTGACTAAGATAAAAG 59.242 37.037 15.13 0.00 42.25 2.27
1925 2057 9.627123 CTAAGATAAAAGAGAGAGAGAAGAGGA 57.373 37.037 0.00 0.00 0.00 3.71
2053 2251 4.766404 TTTTCCGATCTTTCTTGCTTCC 57.234 40.909 0.00 0.00 0.00 3.46
2143 2341 0.469144 ACCCAGTGGCACCGAAAAAT 60.469 50.000 15.27 0.00 33.59 1.82
2151 2351 4.949856 AGTGGCACCGAAAAATAATCTCAT 59.050 37.500 15.27 0.00 0.00 2.90
2152 2352 5.036737 GTGGCACCGAAAAATAATCTCATG 58.963 41.667 6.29 0.00 0.00 3.07
2280 2667 2.002586 CGGTTGACTTGGCTGATGTAG 58.997 52.381 0.00 0.00 0.00 2.74
2321 2708 0.977395 GTAAGCTGGACCTGGACTGT 59.023 55.000 0.00 0.00 0.00 3.55
2373 2760 1.558294 AGATCAGGCAGCTGATTGACA 59.442 47.619 20.43 0.00 43.38 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.378551 TGCTACTACGAGAAAACATCATTAAAT 57.621 29.630 0.00 0.00 0.00 1.40
3 4 8.766000 TGCTACTACGAGAAAACATCATTAAA 57.234 30.769 0.00 0.00 0.00 1.52
4 5 8.653338 GTTGCTACTACGAGAAAACATCATTAA 58.347 33.333 0.00 0.00 0.00 1.40
5 6 8.033038 AGTTGCTACTACGAGAAAACATCATTA 58.967 33.333 0.00 0.00 31.21 1.90
6 7 6.874134 AGTTGCTACTACGAGAAAACATCATT 59.126 34.615 0.00 0.00 31.21 2.57
7 8 6.398918 AGTTGCTACTACGAGAAAACATCAT 58.601 36.000 0.00 0.00 31.21 2.45
8 9 5.779922 AGTTGCTACTACGAGAAAACATCA 58.220 37.500 0.00 0.00 31.21 3.07
9 10 6.145696 ACAAGTTGCTACTACGAGAAAACATC 59.854 38.462 1.81 0.00 33.17 3.06
10 11 5.989777 ACAAGTTGCTACTACGAGAAAACAT 59.010 36.000 1.81 0.00 33.17 2.71
11 12 5.353938 ACAAGTTGCTACTACGAGAAAACA 58.646 37.500 1.81 0.00 33.17 2.83
12 13 5.902051 ACAAGTTGCTACTACGAGAAAAC 57.098 39.130 1.81 0.00 33.17 2.43
13 14 6.913873 AAACAAGTTGCTACTACGAGAAAA 57.086 33.333 1.81 0.00 33.17 2.29
14 15 8.597662 ATTAAACAAGTTGCTACTACGAGAAA 57.402 30.769 1.81 0.00 33.17 2.52
15 16 9.865321 ATATTAAACAAGTTGCTACTACGAGAA 57.135 29.630 1.81 0.00 33.17 2.87
16 17 9.865321 AATATTAAACAAGTTGCTACTACGAGA 57.135 29.630 1.81 0.00 33.17 4.04
19 20 8.995906 GCAAATATTAAACAAGTTGCTACTACG 58.004 33.333 1.81 0.00 38.60 3.51
20 21 9.834628 TGCAAATATTAAACAAGTTGCTACTAC 57.165 29.630 16.59 0.00 41.43 2.73
22 23 9.357652 CATGCAAATATTAAACAAGTTGCTACT 57.642 29.630 16.59 0.00 41.43 2.57
23 24 8.110002 GCATGCAAATATTAAACAAGTTGCTAC 58.890 33.333 14.21 0.00 41.43 3.58
24 25 7.816513 TGCATGCAAATATTAAACAAGTTGCTA 59.183 29.630 20.30 8.12 41.43 3.49
25 26 6.649973 TGCATGCAAATATTAAACAAGTTGCT 59.350 30.769 20.30 0.00 41.43 3.91
26 27 6.829703 TGCATGCAAATATTAAACAAGTTGC 58.170 32.000 20.30 11.67 41.28 4.17
27 28 8.444715 ACATGCATGCAAATATTAAACAAGTTG 58.555 29.630 26.68 14.36 0.00 3.16
28 29 8.444715 CACATGCATGCAAATATTAAACAAGTT 58.555 29.630 26.68 0.00 0.00 2.66
29 30 7.818446 TCACATGCATGCAAATATTAAACAAGT 59.182 29.630 26.68 0.00 0.00 3.16
30 31 8.187354 TCACATGCATGCAAATATTAAACAAG 57.813 30.769 26.68 0.78 0.00 3.16
31 32 8.719560 ATCACATGCATGCAAATATTAAACAA 57.280 26.923 26.68 0.00 0.00 2.83
32 33 7.980099 TGATCACATGCATGCAAATATTAAACA 59.020 29.630 26.68 13.40 0.00 2.83
33 34 8.355272 TGATCACATGCATGCAAATATTAAAC 57.645 30.769 26.68 11.07 0.00 2.01
37 38 9.150348 CATTATGATCACATGCATGCAAATATT 57.850 29.630 26.68 10.03 37.87 1.28
38 39 8.527810 TCATTATGATCACATGCATGCAAATAT 58.472 29.630 26.68 15.48 37.87 1.28
39 40 7.810759 GTCATTATGATCACATGCATGCAAATA 59.189 33.333 26.68 11.09 37.87 1.40
40 41 6.645003 GTCATTATGATCACATGCATGCAAAT 59.355 34.615 26.68 16.50 37.87 2.32
41 42 5.980715 GTCATTATGATCACATGCATGCAAA 59.019 36.000 26.68 11.38 37.87 3.68
42 43 5.067936 TGTCATTATGATCACATGCATGCAA 59.932 36.000 26.68 14.95 37.87 4.08
43 44 4.580995 TGTCATTATGATCACATGCATGCA 59.419 37.500 26.53 25.04 37.87 3.96
44 45 5.116069 TGTCATTATGATCACATGCATGC 57.884 39.130 26.53 11.82 37.87 4.06
45 46 7.114811 CACAATGTCATTATGATCACATGCATG 59.885 37.037 25.09 25.09 37.87 4.06
46 47 7.145323 CACAATGTCATTATGATCACATGCAT 58.855 34.615 0.00 8.71 37.87 3.96
47 48 6.500041 CACAATGTCATTATGATCACATGCA 58.500 36.000 0.00 6.88 37.87 3.96
48 49 5.401376 GCACAATGTCATTATGATCACATGC 59.599 40.000 8.04 3.40 37.87 4.06
49 50 6.735130 AGCACAATGTCATTATGATCACATG 58.265 36.000 8.04 3.83 37.87 3.21
50 51 6.954487 AGCACAATGTCATTATGATCACAT 57.046 33.333 8.04 0.00 40.16 3.21
51 52 7.049754 AGTAGCACAATGTCATTATGATCACA 58.950 34.615 8.04 0.00 0.00 3.58
52 53 7.488187 AGTAGCACAATGTCATTATGATCAC 57.512 36.000 8.04 2.21 0.00 3.06
53 54 7.227314 GGAAGTAGCACAATGTCATTATGATCA 59.773 37.037 8.04 0.00 0.00 2.92
54 55 7.443575 AGGAAGTAGCACAATGTCATTATGATC 59.556 37.037 8.04 0.00 0.00 2.92
55 56 7.285566 AGGAAGTAGCACAATGTCATTATGAT 58.714 34.615 8.04 3.87 0.00 2.45
56 57 6.653020 AGGAAGTAGCACAATGTCATTATGA 58.347 36.000 8.04 0.00 0.00 2.15
57 58 6.932356 AGGAAGTAGCACAATGTCATTATG 57.068 37.500 0.00 0.00 0.00 1.90
58 59 7.341805 AGAAGGAAGTAGCACAATGTCATTAT 58.658 34.615 0.00 0.00 0.00 1.28
59 60 6.711277 AGAAGGAAGTAGCACAATGTCATTA 58.289 36.000 0.00 0.00 0.00 1.90
60 61 5.564550 AGAAGGAAGTAGCACAATGTCATT 58.435 37.500 0.00 0.00 0.00 2.57
61 62 5.171339 AGAAGGAAGTAGCACAATGTCAT 57.829 39.130 0.00 0.00 0.00 3.06
62 63 4.040339 TGAGAAGGAAGTAGCACAATGTCA 59.960 41.667 0.00 0.00 0.00 3.58
63 64 4.569943 TGAGAAGGAAGTAGCACAATGTC 58.430 43.478 0.00 0.00 0.00 3.06
64 65 4.623932 TGAGAAGGAAGTAGCACAATGT 57.376 40.909 0.00 0.00 0.00 2.71
65 66 5.675575 GCAATGAGAAGGAAGTAGCACAATG 60.676 44.000 0.00 0.00 0.00 2.82
66 67 4.397417 GCAATGAGAAGGAAGTAGCACAAT 59.603 41.667 0.00 0.00 0.00 2.71
67 68 3.753272 GCAATGAGAAGGAAGTAGCACAA 59.247 43.478 0.00 0.00 0.00 3.33
68 69 3.008375 AGCAATGAGAAGGAAGTAGCACA 59.992 43.478 0.00 0.00 0.00 4.57
69 70 3.604582 AGCAATGAGAAGGAAGTAGCAC 58.395 45.455 0.00 0.00 0.00 4.40
70 71 3.988976 AGCAATGAGAAGGAAGTAGCA 57.011 42.857 0.00 0.00 0.00 3.49
71 72 4.940654 AGAAAGCAATGAGAAGGAAGTAGC 59.059 41.667 0.00 0.00 0.00 3.58
72 73 6.622462 GCAAGAAAGCAATGAGAAGGAAGTAG 60.622 42.308 0.00 0.00 0.00 2.57
73 74 5.182001 GCAAGAAAGCAATGAGAAGGAAGTA 59.818 40.000 0.00 0.00 0.00 2.24
74 75 4.022503 GCAAGAAAGCAATGAGAAGGAAGT 60.023 41.667 0.00 0.00 0.00 3.01
75 76 4.022589 TGCAAGAAAGCAATGAGAAGGAAG 60.023 41.667 0.00 0.00 42.46 3.46
76 77 3.890756 TGCAAGAAAGCAATGAGAAGGAA 59.109 39.130 0.00 0.00 42.46 3.36
77 78 3.489355 TGCAAGAAAGCAATGAGAAGGA 58.511 40.909 0.00 0.00 42.46 3.36
78 79 3.928727 TGCAAGAAAGCAATGAGAAGG 57.071 42.857 0.00 0.00 42.46 3.46
99 100 4.097741 GGATTATTAATATGCCCGCATGCA 59.902 41.667 19.57 0.00 46.94 3.96
100 101 4.499696 GGGATTATTAATATGCCCGCATGC 60.500 45.833 7.91 7.91 37.82 4.06
101 102 5.186996 GGGATTATTAATATGCCCGCATG 57.813 43.478 12.42 0.00 37.82 4.06
106 107 6.183360 CGTTAACCGGGATTATTAATATGCCC 60.183 42.308 17.37 17.37 0.00 5.36
107 108 6.594937 TCGTTAACCGGGATTATTAATATGCC 59.405 38.462 6.32 1.26 37.11 4.40
108 109 7.546667 TCTCGTTAACCGGGATTATTAATATGC 59.453 37.037 6.32 0.00 42.36 3.14
109 110 8.991243 TCTCGTTAACCGGGATTATTAATATG 57.009 34.615 6.32 0.00 42.36 1.78
120 121 3.070015 ACTTTTCTTCTCGTTAACCGGGA 59.930 43.478 6.32 0.00 46.54 5.14
121 122 3.396560 ACTTTTCTTCTCGTTAACCGGG 58.603 45.455 6.32 0.00 38.86 5.73
122 123 5.389202 GCTAACTTTTCTTCTCGTTAACCGG 60.389 44.000 0.00 0.00 37.11 5.28
123 124 5.404667 AGCTAACTTTTCTTCTCGTTAACCG 59.595 40.000 0.00 0.00 38.13 4.44
124 125 6.782298 AGCTAACTTTTCTTCTCGTTAACC 57.218 37.500 0.00 0.00 0.00 2.85
125 126 6.574093 GCAAGCTAACTTTTCTTCTCGTTAAC 59.426 38.462 0.00 0.00 32.29 2.01
126 127 6.259167 TGCAAGCTAACTTTTCTTCTCGTTAA 59.741 34.615 0.00 0.00 32.29 2.01
127 128 5.756347 TGCAAGCTAACTTTTCTTCTCGTTA 59.244 36.000 0.00 0.00 32.29 3.18
128 129 4.574828 TGCAAGCTAACTTTTCTTCTCGTT 59.425 37.500 0.00 0.00 32.29 3.85
129 130 4.127171 TGCAAGCTAACTTTTCTTCTCGT 58.873 39.130 0.00 0.00 32.29 4.18
130 131 4.732285 TGCAAGCTAACTTTTCTTCTCG 57.268 40.909 0.00 0.00 32.29 4.04
131 132 6.983059 CTTTGCAAGCTAACTTTTCTTCTC 57.017 37.500 0.00 0.00 32.29 2.87
175 176 9.309224 AGGCTACAAACTCAAATTAAAGGTATT 57.691 29.630 0.00 0.00 0.00 1.89
176 177 8.879427 AGGCTACAAACTCAAATTAAAGGTAT 57.121 30.769 0.00 0.00 0.00 2.73
177 178 8.573035 CAAGGCTACAAACTCAAATTAAAGGTA 58.427 33.333 0.00 0.00 0.00 3.08
178 179 7.069455 ACAAGGCTACAAACTCAAATTAAAGGT 59.931 33.333 0.00 0.00 0.00 3.50
179 180 7.433680 ACAAGGCTACAAACTCAAATTAAAGG 58.566 34.615 0.00 0.00 0.00 3.11
184 185 8.739972 CCTTATACAAGGCTACAAACTCAAATT 58.260 33.333 0.00 0.00 44.90 1.82
185 186 8.281212 CCTTATACAAGGCTACAAACTCAAAT 57.719 34.615 0.00 0.00 44.90 2.32
186 187 7.681939 CCTTATACAAGGCTACAAACTCAAA 57.318 36.000 0.00 0.00 44.90 2.69
200 201 6.253946 ACTCCCTCAATTCCCTTATACAAG 57.746 41.667 0.00 0.00 0.00 3.16
201 202 6.329197 CCTACTCCCTCAATTCCCTTATACAA 59.671 42.308 0.00 0.00 0.00 2.41
202 203 5.844516 CCTACTCCCTCAATTCCCTTATACA 59.155 44.000 0.00 0.00 0.00 2.29
203 204 6.082707 TCCTACTCCCTCAATTCCCTTATAC 58.917 44.000 0.00 0.00 0.00 1.47
204 205 6.303427 TCCTACTCCCTCAATTCCCTTATA 57.697 41.667 0.00 0.00 0.00 0.98
205 206 5.171541 TCCTACTCCCTCAATTCCCTTAT 57.828 43.478 0.00 0.00 0.00 1.73
206 207 4.637288 TCCTACTCCCTCAATTCCCTTA 57.363 45.455 0.00 0.00 0.00 2.69
207 208 3.508952 TCCTACTCCCTCAATTCCCTT 57.491 47.619 0.00 0.00 0.00 3.95
208 209 3.116174 GTTCCTACTCCCTCAATTCCCT 58.884 50.000 0.00 0.00 0.00 4.20
209 210 3.116174 AGTTCCTACTCCCTCAATTCCC 58.884 50.000 0.00 0.00 0.00 3.97
210 211 4.409718 GAGTTCCTACTCCCTCAATTCC 57.590 50.000 0.00 0.00 44.15 3.01
229 230 1.151668 CCAAGGCACTCGTCAAAGAG 58.848 55.000 0.00 0.00 38.49 2.85
230 231 0.250295 CCCAAGGCACTCGTCAAAGA 60.250 55.000 0.00 0.00 38.49 2.52
231 232 0.535102 ACCCAAGGCACTCGTCAAAG 60.535 55.000 0.00 0.00 38.49 2.77
232 233 0.106918 AACCCAAGGCACTCGTCAAA 60.107 50.000 0.00 0.00 38.49 2.69
233 234 0.817634 CAACCCAAGGCACTCGTCAA 60.818 55.000 0.00 0.00 38.49 3.18
234 235 1.227823 CAACCCAAGGCACTCGTCA 60.228 57.895 0.00 0.00 38.49 4.35
235 236 1.227853 ACAACCCAAGGCACTCGTC 60.228 57.895 0.00 0.00 38.49 4.20
236 237 1.227853 GACAACCCAAGGCACTCGT 60.228 57.895 0.00 0.00 38.49 4.18
237 238 2.317609 CGACAACCCAAGGCACTCG 61.318 63.158 0.00 0.00 38.49 4.18
238 239 0.951040 CTCGACAACCCAAGGCACTC 60.951 60.000 0.00 0.00 38.49 3.51
240 241 2.617274 GCTCGACAACCCAAGGCAC 61.617 63.158 0.00 0.00 0.00 5.01
241 242 2.281484 GCTCGACAACCCAAGGCA 60.281 61.111 0.00 0.00 0.00 4.75
242 243 1.578206 GAAGCTCGACAACCCAAGGC 61.578 60.000 0.00 0.00 0.00 4.35
243 244 0.035458 AGAAGCTCGACAACCCAAGG 59.965 55.000 0.00 0.00 0.00 3.61
244 245 1.151668 CAGAAGCTCGACAACCCAAG 58.848 55.000 0.00 0.00 0.00 3.61
245 246 0.468226 ACAGAAGCTCGACAACCCAA 59.532 50.000 0.00 0.00 0.00 4.12
246 247 0.249868 CACAGAAGCTCGACAACCCA 60.250 55.000 0.00 0.00 0.00 4.51
247 248 0.033504 TCACAGAAGCTCGACAACCC 59.966 55.000 0.00 0.00 0.00 4.11
248 249 2.086054 ATCACAGAAGCTCGACAACC 57.914 50.000 0.00 0.00 0.00 3.77
249 250 3.494626 TCAAATCACAGAAGCTCGACAAC 59.505 43.478 0.00 0.00 0.00 3.32
283 284 1.068541 GGAAAGTTGGTCGTTGGCATC 60.069 52.381 0.00 0.00 0.00 3.91
285 286 0.394488 TGGAAAGTTGGTCGTTGGCA 60.394 50.000 0.00 0.00 0.00 4.92
314 315 5.067413 GCATCTTCCAACATGACATCTCAAT 59.933 40.000 0.00 0.00 0.00 2.57
1252 1280 2.856039 ATCAAGGACGCCCTCGAGGA 62.856 60.000 33.39 9.76 43.48 3.71
1314 1342 4.441695 CCGGAGAAGCTCAGCGCA 62.442 66.667 11.47 0.00 42.61 6.09
1365 1393 0.320374 CCTAGGGTTGTGACGCTTCA 59.680 55.000 0.00 0.00 45.75 3.02
1453 1484 7.761249 GCAAGCATCTACCATTTTCTAAACAAT 59.239 33.333 0.00 0.00 0.00 2.71
1460 1491 4.159135 CCAAGCAAGCATCTACCATTTTCT 59.841 41.667 0.00 0.00 0.00 2.52
1465 1506 1.064166 AGCCAAGCAAGCATCTACCAT 60.064 47.619 0.00 0.00 0.00 3.55
1472 1513 1.228644 TCACCAGCCAAGCAAGCAT 60.229 52.632 0.00 0.00 0.00 3.79
1479 1520 0.984230 TCCCTTACTCACCAGCCAAG 59.016 55.000 0.00 0.00 0.00 3.61
1494 1535 8.268878 AGTAGCTGATAAACTGATAAATCCCT 57.731 34.615 0.00 0.00 0.00 4.20
1571 1668 9.165035 CCAATTAACCAGTTAACTTACCGATTA 57.835 33.333 5.07 0.00 37.80 1.75
1572 1669 7.884354 TCCAATTAACCAGTTAACTTACCGATT 59.116 33.333 5.07 1.86 37.80 3.34
1573 1670 7.396418 TCCAATTAACCAGTTAACTTACCGAT 58.604 34.615 5.07 0.00 37.80 4.18
1574 1671 6.767456 TCCAATTAACCAGTTAACTTACCGA 58.233 36.000 5.07 0.00 37.80 4.69
1725 1830 2.746277 GCCATCGTCAAGGGCGTT 60.746 61.111 0.00 0.00 38.04 4.84
1748 1853 4.954118 ACGACAGGTGCCCCCAGA 62.954 66.667 0.00 0.00 34.66 3.86
1839 1950 4.511527 CTGTTGGTGCTGAGAAGATGTAT 58.488 43.478 0.00 0.00 0.00 2.29
1844 1955 0.250467 GGCTGTTGGTGCTGAGAAGA 60.250 55.000 0.00 0.00 0.00 2.87
1858 1969 2.115052 TGGAACAATGGCGGCTGT 59.885 55.556 11.43 3.94 31.92 4.40
1909 2035 3.591527 TCACCTTCCTCTTCTCTCTCTCT 59.408 47.826 0.00 0.00 0.00 3.10
1910 2036 3.963129 TCACCTTCCTCTTCTCTCTCTC 58.037 50.000 0.00 0.00 0.00 3.20
1925 2057 0.807667 GCGCACTGATCGATCACCTT 60.808 55.000 23.99 8.66 32.50 3.50
2053 2251 2.331194 CCGGTGTAGTAACGTTCCAAG 58.669 52.381 2.82 0.00 0.00 3.61
2143 2341 1.046472 ACCGACGCCCCATGAGATTA 61.046 55.000 0.00 0.00 0.00 1.75
2151 2351 1.118965 ATATCATCACCGACGCCCCA 61.119 55.000 0.00 0.00 0.00 4.96
2152 2352 0.670546 CATATCATCACCGACGCCCC 60.671 60.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.