Multiple sequence alignment - TraesCS6D01G097700

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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 TraesCS6D01G097700 chr6D 100.000 2585 0 0 1 2585 61344561 61347145 0.000000e+00 4774.0
1 TraesCS6D01G097700 chr6D 97.222 36 1 0 409 444 61344886 61344921 7.720000e-06 62.1
2 TraesCS6D01G097700 chr6D 97.222 36 1 0 326 361 61344969 61345004 7.720000e-06 62.1
3 TraesCS6D01G097700 chr6B 90.614 1172 48 25 559 1718 135311720 135312841 0.000000e+00 1498.0
4 TraesCS6D01G097700 chr6B 92.718 412 15 6 162 569 135310422 135310822 4.790000e-162 580.0
5 TraesCS6D01G097700 chr6B 85.124 484 26 17 1718 2200 135312893 135313331 1.090000e-123 453.0
6 TraesCS6D01G097700 chr6B 93.137 306 17 2 2281 2584 135313511 135313814 1.820000e-121 446.0
7 TraesCS6D01G097700 chr6B 97.222 36 1 0 326 361 135310665 135310700 7.720000e-06 62.1
8 TraesCS6D01G097700 chr6A 93.502 831 23 13 688 1514 78478119 78478922 0.000000e+00 1206.0
9 TraesCS6D01G097700 chr6A 90.235 553 32 8 157 696 78477373 78477916 0.000000e+00 702.0
10 TraesCS6D01G097700 chr6A 92.371 485 27 6 1718 2200 78479172 78479648 0.000000e+00 682.0
11 TraesCS6D01G097700 chr6A 81.452 496 44 23 1719 2200 77888680 77889141 1.890000e-96 363.0
12 TraesCS6D01G097700 chr6A 80.894 492 43 18 1719 2194 77988107 77988563 8.860000e-90 340.0
13 TraesCS6D01G097700 chr6A 80.400 500 47 17 1719 2200 78018193 78018659 1.480000e-87 333.0
14 TraesCS6D01G097700 chr6A 82.243 428 33 16 1781 2200 78136802 78137194 1.920000e-86 329.0
15 TraesCS6D01G097700 chr6A 91.379 232 18 1 2354 2585 78029267 78029496 1.490000e-82 316.0
16 TraesCS6D01G097700 chr6A 90.517 232 20 1 2354 2585 77988829 77989058 3.230000e-79 305.0
17 TraesCS6D01G097700 chr6A 92.593 162 10 1 1559 1718 78478932 78479093 5.560000e-57 231.0
18 TraesCS6D01G097700 chr6A 91.463 164 12 1 2354 2517 77894859 77895020 9.310000e-55 224.0
19 TraesCS6D01G097700 chr6A 93.706 143 9 0 2443 2585 78137990 78138132 5.600000e-52 215.0
20 TraesCS6D01G097700 chr6A 90.977 133 9 1 1 130 132770537 132770405 2.640000e-40 176.0
21 TraesCS6D01G097700 chr6A 90.977 133 9 1 1 130 175008402 175008270 2.640000e-40 176.0
22 TraesCS6D01G097700 chr6A 82.110 218 25 5 1468 1671 77888341 77888558 9.510000e-40 174.0
23 TraesCS6D01G097700 chr6A 93.976 83 4 1 2503 2585 78485729 78485810 9.710000e-25 124.0
24 TraesCS6D01G097700 chr6A 97.959 49 1 0 2465 2513 78479986 78480034 4.580000e-13 86.1
25 TraesCS6D01G097700 chr6A 97.222 36 1 0 326 361 78477618 78477653 7.720000e-06 62.1
26 TraesCS6D01G097700 chr5D 88.591 149 14 1 1 146 379807674 379807526 7.350000e-41 178.0
27 TraesCS6D01G097700 chr5D 90.299 134 10 1 1 131 279960014 279960147 3.420000e-39 172.0
28 TraesCS6D01G097700 chr5A 90.977 133 9 1 1 130 82648459 82648591 2.640000e-40 176.0
29 TraesCS6D01G097700 chr3D 88.889 144 13 2 2 142 258224876 258224733 9.510000e-40 174.0
30 TraesCS6D01G097700 chr3D 90.741 54 5 0 402 455 12122167 12122220 3.570000e-09 73.1
31 TraesCS6D01G097700 chr1D 87.919 149 15 1 1 146 378551847 378551699 3.420000e-39 172.0
32 TraesCS6D01G097700 chr1B 87.919 149 15 1 1 146 350734465 350734613 3.420000e-39 172.0
33 TraesCS6D01G097700 chr4D 89.474 133 11 1 1 130 349216768 349216900 5.720000e-37 165.0
34 TraesCS6D01G097700 chr7B 78.358 134 21 3 395 522 73211657 73211788 2.130000e-11 80.5


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 TraesCS6D01G097700 chr6D 61344561 61347145 2584 False 1632.733333 4774 98.148000 1 2585 3 chr6D.!!$F1 2584
1 TraesCS6D01G097700 chr6B 135310422 135313814 3392 False 607.820000 1498 91.763000 162 2584 5 chr6B.!!$F1 2422
2 TraesCS6D01G097700 chr6A 78477373 78480034 2661 False 494.866667 1206 93.980333 157 2513 6 chr6A.!!$F8 2356
3 TraesCS6D01G097700 chr6A 77988107 77989058 951 False 322.500000 340 85.705500 1719 2585 2 chr6A.!!$F6 866
4 TraesCS6D01G097700 chr6A 78136802 78138132 1330 False 272.000000 329 87.974500 1781 2585 2 chr6A.!!$F7 804
5 TraesCS6D01G097700 chr6A 77888341 77889141 800 False 268.500000 363 81.781000 1468 2200 2 chr6A.!!$F5 732

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
71 72 0.034896 ACGTGAAAGGAGCGTCCAAT 59.965 50.000 6.78 0.0 39.61 3.16 F
72 73 0.443869 CGTGAAAGGAGCGTCCAATG 59.556 55.000 6.78 0.0 39.61 2.82 F
1120 2258 1.142748 CTGGCCATGTCGTCTCTCC 59.857 63.158 5.51 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 2170 1.539124 GAGGGTTGAGGAGGGGTGT 60.539 63.158 0.0 0.0 0.00 4.16 R
1437 2576 1.860950 CAATCATCCCGTGTCATCGTC 59.139 52.381 0.0 0.0 0.00 4.20 R
2216 3479 0.536233 TGTGGGCGTGCAACTGTAAT 60.536 50.000 0.0 0.0 31.75 1.89 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
36 37 8.504812 AATATATGACATGCAAGTTACACACA 57.495 30.769 0.00 0.00 0.00 3.72
37 38 8.681486 ATATATGACATGCAAGTTACACACAT 57.319 30.769 0.00 0.00 0.00 3.21
38 39 9.777297 ATATATGACATGCAAGTTACACACATA 57.223 29.630 0.00 0.00 0.00 2.29
39 40 5.605564 TGACATGCAAGTTACACACATAC 57.394 39.130 0.00 0.00 0.00 2.39
40 41 5.304778 TGACATGCAAGTTACACACATACT 58.695 37.500 0.00 0.00 0.00 2.12
41 42 5.179182 TGACATGCAAGTTACACACATACTG 59.821 40.000 0.00 0.00 0.00 2.74
42 43 5.063204 ACATGCAAGTTACACACATACTGT 58.937 37.500 0.00 0.00 0.00 3.55
43 44 5.179368 ACATGCAAGTTACACACATACTGTC 59.821 40.000 0.00 0.00 0.00 3.51
44 45 3.738791 TGCAAGTTACACACATACTGTCG 59.261 43.478 0.00 0.00 0.00 4.35
45 46 3.985279 GCAAGTTACACACATACTGTCGA 59.015 43.478 0.00 0.00 0.00 4.20
46 47 4.446385 GCAAGTTACACACATACTGTCGAA 59.554 41.667 0.00 0.00 0.00 3.71
47 48 5.120208 GCAAGTTACACACATACTGTCGAAT 59.880 40.000 0.00 0.00 0.00 3.34
48 49 6.347402 GCAAGTTACACACATACTGTCGAATT 60.347 38.462 0.00 0.00 0.00 2.17
49 50 6.946229 AGTTACACACATACTGTCGAATTC 57.054 37.500 0.00 0.00 0.00 2.17
50 51 5.571741 AGTTACACACATACTGTCGAATTCG 59.428 40.000 21.78 21.78 41.45 3.34
51 52 3.909430 ACACACATACTGTCGAATTCGT 58.091 40.909 25.93 10.58 40.80 3.85
52 53 5.050644 ACACACATACTGTCGAATTCGTA 57.949 39.130 25.93 15.72 40.80 3.43
53 54 4.855388 ACACACATACTGTCGAATTCGTAC 59.145 41.667 25.93 21.23 40.80 3.67
54 55 4.028750 CACACATACTGTCGAATTCGTACG 60.029 45.833 25.93 9.53 40.80 3.67
55 56 4.093514 CACATACTGTCGAATTCGTACGT 58.906 43.478 25.93 20.92 40.80 3.57
56 57 4.028750 CACATACTGTCGAATTCGTACGTG 60.029 45.833 25.93 15.82 40.80 4.49
57 58 2.975410 ACTGTCGAATTCGTACGTGA 57.025 45.000 25.93 4.12 40.80 4.35
58 59 3.272439 ACTGTCGAATTCGTACGTGAA 57.728 42.857 25.93 3.23 40.80 3.18
59 60 3.631144 ACTGTCGAATTCGTACGTGAAA 58.369 40.909 25.93 2.41 40.80 2.69
60 61 3.667261 ACTGTCGAATTCGTACGTGAAAG 59.333 43.478 25.93 13.14 40.80 2.62
61 62 2.981805 TGTCGAATTCGTACGTGAAAGG 59.018 45.455 25.93 2.15 40.80 3.11
62 63 3.236816 GTCGAATTCGTACGTGAAAGGA 58.763 45.455 25.93 4.53 40.80 3.36
63 64 3.300066 GTCGAATTCGTACGTGAAAGGAG 59.700 47.826 25.93 1.26 40.80 3.69
64 65 2.027688 CGAATTCGTACGTGAAAGGAGC 59.972 50.000 19.67 0.00 34.11 4.70
65 66 1.625616 ATTCGTACGTGAAAGGAGCG 58.374 50.000 16.05 0.00 0.00 5.03
66 67 0.311790 TTCGTACGTGAAAGGAGCGT 59.688 50.000 16.05 0.00 41.86 5.07
67 68 0.110056 TCGTACGTGAAAGGAGCGTC 60.110 55.000 16.05 0.00 39.64 5.19
68 69 1.069378 CGTACGTGAAAGGAGCGTCC 61.069 60.000 7.22 0.00 39.64 4.79
69 70 0.038892 GTACGTGAAAGGAGCGTCCA 60.039 55.000 0.00 0.00 39.61 4.02
70 71 0.675083 TACGTGAAAGGAGCGTCCAA 59.325 50.000 0.00 0.00 39.61 3.53
71 72 0.034896 ACGTGAAAGGAGCGTCCAAT 59.965 50.000 6.78 0.00 39.61 3.16
72 73 0.443869 CGTGAAAGGAGCGTCCAATG 59.556 55.000 6.78 0.00 39.61 2.82
73 74 1.808411 GTGAAAGGAGCGTCCAATGA 58.192 50.000 6.78 0.00 39.61 2.57
74 75 2.359900 GTGAAAGGAGCGTCCAATGAT 58.640 47.619 6.78 0.00 39.61 2.45
75 76 3.531538 GTGAAAGGAGCGTCCAATGATA 58.468 45.455 6.78 0.00 39.61 2.15
76 77 4.130118 GTGAAAGGAGCGTCCAATGATAT 58.870 43.478 6.78 0.00 39.61 1.63
77 78 5.297547 GTGAAAGGAGCGTCCAATGATATA 58.702 41.667 6.78 0.00 39.61 0.86
78 79 5.758296 GTGAAAGGAGCGTCCAATGATATAA 59.242 40.000 6.78 0.00 39.61 0.98
79 80 6.428159 GTGAAAGGAGCGTCCAATGATATAAT 59.572 38.462 6.78 0.00 39.61 1.28
80 81 6.998074 TGAAAGGAGCGTCCAATGATATAATT 59.002 34.615 6.78 0.00 39.61 1.40
81 82 7.502226 TGAAAGGAGCGTCCAATGATATAATTT 59.498 33.333 6.78 0.00 39.61 1.82
82 83 7.823745 AAGGAGCGTCCAATGATATAATTTT 57.176 32.000 6.78 0.00 39.61 1.82
83 84 7.440523 AGGAGCGTCCAATGATATAATTTTC 57.559 36.000 6.78 0.00 39.61 2.29
84 85 6.998074 AGGAGCGTCCAATGATATAATTTTCA 59.002 34.615 6.78 0.00 39.61 2.69
85 86 7.667219 AGGAGCGTCCAATGATATAATTTTCAT 59.333 33.333 6.78 0.00 39.61 2.57
86 87 8.946085 GGAGCGTCCAATGATATAATTTTCATA 58.054 33.333 0.00 0.00 36.28 2.15
129 130 9.346725 CTTTTAATCTTGTCAATAGTCAAAGGC 57.653 33.333 0.00 0.00 0.00 4.35
130 131 7.994425 TTAATCTTGTCAATAGTCAAAGGCA 57.006 32.000 0.00 0.00 0.00 4.75
131 132 6.899393 AATCTTGTCAATAGTCAAAGGCAA 57.101 33.333 0.00 0.00 0.00 4.52
132 133 7.472334 AATCTTGTCAATAGTCAAAGGCAAT 57.528 32.000 0.00 0.00 0.00 3.56
133 134 6.500684 TCTTGTCAATAGTCAAAGGCAATC 57.499 37.500 0.00 0.00 0.00 2.67
134 135 6.240894 TCTTGTCAATAGTCAAAGGCAATCT 58.759 36.000 0.00 0.00 0.00 2.40
135 136 6.372659 TCTTGTCAATAGTCAAAGGCAATCTC 59.627 38.462 0.00 0.00 0.00 2.75
136 137 4.943705 TGTCAATAGTCAAAGGCAATCTCC 59.056 41.667 0.00 0.00 0.00 3.71
137 138 4.943705 GTCAATAGTCAAAGGCAATCTCCA 59.056 41.667 0.00 0.00 0.00 3.86
138 139 5.415701 GTCAATAGTCAAAGGCAATCTCCAA 59.584 40.000 0.00 0.00 0.00 3.53
139 140 6.009589 TCAATAGTCAAAGGCAATCTCCAAA 58.990 36.000 0.00 0.00 0.00 3.28
140 141 6.493115 TCAATAGTCAAAGGCAATCTCCAAAA 59.507 34.615 0.00 0.00 0.00 2.44
141 142 6.916360 ATAGTCAAAGGCAATCTCCAAAAA 57.084 33.333 0.00 0.00 0.00 1.94
142 143 5.813513 AGTCAAAGGCAATCTCCAAAAAT 57.186 34.783 0.00 0.00 0.00 1.82
143 144 6.916360 AGTCAAAGGCAATCTCCAAAAATA 57.084 33.333 0.00 0.00 0.00 1.40
144 145 6.691508 AGTCAAAGGCAATCTCCAAAAATAC 58.308 36.000 0.00 0.00 0.00 1.89
145 146 6.267471 AGTCAAAGGCAATCTCCAAAAATACA 59.733 34.615 0.00 0.00 0.00 2.29
146 147 6.366061 GTCAAAGGCAATCTCCAAAAATACAC 59.634 38.462 0.00 0.00 0.00 2.90
147 148 5.405935 AAGGCAATCTCCAAAAATACACC 57.594 39.130 0.00 0.00 0.00 4.16
148 149 3.769300 AGGCAATCTCCAAAAATACACCC 59.231 43.478 0.00 0.00 0.00 4.61
149 150 3.513515 GGCAATCTCCAAAAATACACCCA 59.486 43.478 0.00 0.00 0.00 4.51
150 151 4.162131 GGCAATCTCCAAAAATACACCCAT 59.838 41.667 0.00 0.00 0.00 4.00
151 152 5.111293 GCAATCTCCAAAAATACACCCATG 58.889 41.667 0.00 0.00 0.00 3.66
152 153 5.111293 CAATCTCCAAAAATACACCCATGC 58.889 41.667 0.00 0.00 0.00 4.06
153 154 3.772387 TCTCCAAAAATACACCCATGCA 58.228 40.909 0.00 0.00 0.00 3.96
154 155 4.155709 TCTCCAAAAATACACCCATGCAA 58.844 39.130 0.00 0.00 0.00 4.08
155 156 4.021544 TCTCCAAAAATACACCCATGCAAC 60.022 41.667 0.00 0.00 0.00 4.17
184 185 9.868277 AAAAATCTCGAAAAATACATTATGCCA 57.132 25.926 0.00 0.00 0.00 4.92
357 360 3.589288 CCCTAGGCCATTAGCTAGGATTT 59.411 47.826 13.75 0.00 41.35 2.17
552 560 4.382291 CGTAAATCCCGTATCAAATCCCA 58.618 43.478 0.00 0.00 0.00 4.37
638 1561 4.062991 GTTTTCTAAGAGAGCGGTTGGAA 58.937 43.478 0.00 0.00 0.00 3.53
642 1565 2.568623 AAGAGAGCGGTTGGAATTGT 57.431 45.000 0.00 0.00 0.00 2.71
646 1569 2.416893 GAGAGCGGTTGGAATTGTTCTC 59.583 50.000 0.00 0.00 32.81 2.87
670 1593 1.278637 CCACGTTGCTTTGTCCGTC 59.721 57.895 0.00 0.00 0.00 4.79
697 1833 3.559171 CCGTATCAAATCCCCCATAGGTG 60.559 52.174 0.00 0.00 0.00 4.00
811 1948 5.534654 GGGCATCTGTATAATTAAACCAGCA 59.465 40.000 0.00 0.00 0.00 4.41
858 1995 3.524380 ACCATACCACCTCCCGAAAAATA 59.476 43.478 0.00 0.00 0.00 1.40
864 2001 8.688151 CATACCACCTCCCGAAAAATAAAAATA 58.312 33.333 0.00 0.00 0.00 1.40
911 2048 9.532494 TTCCTTCCTAAGAATTGATCATCAAAA 57.468 29.630 3.63 0.00 40.12 2.44
920 2057 8.420374 AGAATTGATCATCAAAAATGACATGC 57.580 30.769 3.63 0.00 40.12 4.06
921 2058 8.038351 AGAATTGATCATCAAAAATGACATGCA 58.962 29.630 3.63 0.00 40.12 3.96
922 2059 8.731275 AATTGATCATCAAAAATGACATGCAT 57.269 26.923 3.63 0.00 40.12 3.96
923 2060 9.825109 AATTGATCATCAAAAATGACATGCATA 57.175 25.926 3.63 0.00 40.12 3.14
924 2061 8.637281 TTGATCATCAAAAATGACATGCATAC 57.363 30.769 0.00 0.00 32.48 2.39
925 2062 7.204604 TGATCATCAAAAATGACATGCATACC 58.795 34.615 0.00 0.00 35.78 2.73
926 2063 6.527057 TCATCAAAAATGACATGCATACCA 57.473 33.333 0.00 0.07 35.78 3.25
927 2064 7.114866 TCATCAAAAATGACATGCATACCAT 57.885 32.000 0.00 2.84 35.78 3.55
928 2065 7.557724 TCATCAAAAATGACATGCATACCATT 58.442 30.769 15.82 15.82 35.78 3.16
929 2066 8.041919 TCATCAAAAATGACATGCATACCATTT 58.958 29.630 22.52 22.52 39.90 2.32
930 2067 7.598189 TCAAAAATGACATGCATACCATTTG 57.402 32.000 25.96 19.97 38.68 2.32
931 2068 6.594547 TCAAAAATGACATGCATACCATTTGG 59.405 34.615 25.96 22.14 38.68 3.28
932 2069 5.936187 AAATGACATGCATACCATTTGGA 57.064 34.783 25.24 0.00 37.69 3.53
933 2070 5.524971 AATGACATGCATACCATTTGGAG 57.475 39.130 15.82 0.00 35.78 3.86
934 2071 3.289836 TGACATGCATACCATTTGGAGG 58.710 45.455 0.00 0.00 38.94 4.30
935 2072 3.290710 GACATGCATACCATTTGGAGGT 58.709 45.455 0.00 0.00 43.14 3.85
936 2073 3.701040 GACATGCATACCATTTGGAGGTT 59.299 43.478 0.00 0.00 40.54 3.50
937 2074 3.701040 ACATGCATACCATTTGGAGGTTC 59.299 43.478 0.00 0.00 40.54 3.62
938 2075 2.364632 TGCATACCATTTGGAGGTTCG 58.635 47.619 3.01 0.00 40.54 3.95
939 2076 2.026729 TGCATACCATTTGGAGGTTCGA 60.027 45.455 3.01 0.00 40.54 3.71
940 2077 2.614057 GCATACCATTTGGAGGTTCGAG 59.386 50.000 3.01 0.00 40.54 4.04
941 2078 3.681594 GCATACCATTTGGAGGTTCGAGA 60.682 47.826 3.01 0.00 40.54 4.04
942 2079 4.708177 CATACCATTTGGAGGTTCGAGAT 58.292 43.478 3.01 0.00 40.54 2.75
1032 2170 9.771534 CAAAGAAAAACCATAGGATTAACCAAA 57.228 29.630 0.00 0.00 42.04 3.28
1120 2258 1.142748 CTGGCCATGTCGTCTCTCC 59.857 63.158 5.51 0.00 0.00 3.71
1182 2320 2.173964 CTTCGCCCGCTAAAAATTTCG 58.826 47.619 0.00 0.00 0.00 3.46
1437 2576 2.551270 GCGTGAAGCCGTGAAGTG 59.449 61.111 0.00 0.00 40.81 3.16
1533 2674 4.518217 GACGATAGGTCATTGATTTTGCG 58.482 43.478 0.00 0.00 45.36 4.85
1534 2675 4.188462 ACGATAGGTCATTGATTTTGCGA 58.812 39.130 0.00 0.00 43.77 5.10
1710 2869 1.873591 GATACATCGGTGAACATGGGC 59.126 52.381 0.65 0.00 0.00 5.36
1711 2870 0.615850 TACATCGGTGAACATGGGCA 59.384 50.000 0.65 0.00 0.00 5.36
1728 2969 3.202906 GGGCAGATATTGTAGTTTCGCA 58.797 45.455 0.00 0.00 0.00 5.10
1874 3125 3.937814 ACTTTGCACCTCGATCATGTTA 58.062 40.909 0.00 0.00 0.00 2.41
1969 3226 6.475076 TGCACACATGTTTGAAAAATCTACAC 59.525 34.615 16.10 0.00 0.00 2.90
1970 3227 6.074356 GCACACATGTTTGAAAAATCTACACC 60.074 38.462 16.10 0.00 0.00 4.16
2135 3392 7.654520 GGGGTTTCACTTTTCATTTTTAGTACC 59.345 37.037 0.00 0.00 0.00 3.34
2137 3394 9.244799 GGTTTCACTTTTCATTTTTAGTACCTG 57.755 33.333 0.00 0.00 0.00 4.00
2200 3463 1.522668 TGCGCTCAATTACAGTTGCT 58.477 45.000 9.73 0.00 0.00 3.91
2201 3464 1.464608 TGCGCTCAATTACAGTTGCTC 59.535 47.619 9.73 0.00 0.00 4.26
2202 3465 1.734465 GCGCTCAATTACAGTTGCTCT 59.266 47.619 0.00 0.00 0.00 4.09
2203 3466 2.160417 GCGCTCAATTACAGTTGCTCTT 59.840 45.455 0.00 0.00 0.00 2.85
2204 3467 3.726190 GCGCTCAATTACAGTTGCTCTTC 60.726 47.826 0.00 0.00 0.00 2.87
2205 3468 3.482598 CGCTCAATTACAGTTGCTCTTCG 60.483 47.826 0.00 0.00 0.00 3.79
2206 3469 3.433615 GCTCAATTACAGTTGCTCTTCGT 59.566 43.478 0.00 0.00 0.00 3.85
2207 3470 4.083802 GCTCAATTACAGTTGCTCTTCGTT 60.084 41.667 0.00 0.00 0.00 3.85
2208 3471 5.591643 TCAATTACAGTTGCTCTTCGTTC 57.408 39.130 0.00 0.00 0.00 3.95
2209 3472 4.451096 TCAATTACAGTTGCTCTTCGTTCC 59.549 41.667 0.00 0.00 0.00 3.62
2210 3473 3.462483 TTACAGTTGCTCTTCGTTCCA 57.538 42.857 0.00 0.00 0.00 3.53
2211 3474 2.325583 ACAGTTGCTCTTCGTTCCAA 57.674 45.000 0.00 0.00 0.00 3.53
2212 3475 2.639065 ACAGTTGCTCTTCGTTCCAAA 58.361 42.857 0.00 0.00 0.00 3.28
2213 3476 3.013921 ACAGTTGCTCTTCGTTCCAAAA 58.986 40.909 0.00 0.00 0.00 2.44
2214 3477 3.442273 ACAGTTGCTCTTCGTTCCAAAAA 59.558 39.130 0.00 0.00 0.00 1.94
2261 3571 5.833082 CGGAGAGCAACTATAGTTACACAT 58.167 41.667 17.62 2.92 36.32 3.21
2268 3578 7.611770 AGCAACTATAGTTACACATGAAGTCA 58.388 34.615 17.62 0.00 36.32 3.41
2296 3729 2.040544 GCTGGGCACACGCAACTAT 61.041 57.895 5.64 0.00 41.24 2.12
2311 3745 4.142708 CGCAACTATAGTTTGCACATTCCA 60.143 41.667 25.79 0.00 35.83 3.53
2330 3764 3.156293 CCATGTTTTCCCATCAGTCACA 58.844 45.455 0.00 0.00 0.00 3.58
2331 3765 3.573538 CCATGTTTTCCCATCAGTCACAA 59.426 43.478 0.00 0.00 0.00 3.33
2332 3766 4.549458 CATGTTTTCCCATCAGTCACAAC 58.451 43.478 0.00 0.00 0.00 3.32
2335 3769 2.270352 TTCCCATCAGTCACAACACC 57.730 50.000 0.00 0.00 0.00 4.16
2361 3799 2.281139 TGGTCCACGAATTGCGCA 60.281 55.556 5.66 5.66 46.04 6.09
2439 3878 8.789825 ATTAGAACATTAGAGATCATGCCATC 57.210 34.615 0.00 0.00 0.00 3.51
2554 4444 0.316204 GCTCTGGTGCAGCACAAAAT 59.684 50.000 26.78 0.00 36.82 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.606631 TGTGTGTAACTTGCATGTCATATATTA 57.393 29.630 5.61 0.00 38.04 0.98
11 12 8.504812 TGTGTGTAACTTGCATGTCATATATT 57.495 30.769 5.61 0.00 38.04 1.28
12 13 8.681486 ATGTGTGTAACTTGCATGTCATATAT 57.319 30.769 5.61 1.09 38.04 0.86
13 14 9.040939 GTATGTGTGTAACTTGCATGTCATATA 57.959 33.333 5.61 5.38 38.04 0.86
14 15 7.770433 AGTATGTGTGTAACTTGCATGTCATAT 59.230 33.333 5.61 6.24 38.04 1.78
15 16 7.064490 CAGTATGTGTGTAACTTGCATGTCATA 59.936 37.037 5.61 5.74 38.04 2.15
16 17 5.939883 AGTATGTGTGTAACTTGCATGTCAT 59.060 36.000 5.61 6.63 38.04 3.06
17 18 5.179182 CAGTATGTGTGTAACTTGCATGTCA 59.821 40.000 5.61 0.00 38.04 3.58
18 19 5.621422 CAGTATGTGTGTAACTTGCATGTC 58.379 41.667 5.61 0.00 38.04 3.06
19 20 5.611796 CAGTATGTGTGTAACTTGCATGT 57.388 39.130 0.00 0.00 38.04 3.21
35 36 4.336932 TCACGTACGAATTCGACAGTATG 58.663 43.478 33.05 20.82 43.02 2.39
36 37 4.604843 TCACGTACGAATTCGACAGTAT 57.395 40.909 33.05 12.89 43.02 2.12
37 38 4.403015 TTCACGTACGAATTCGACAGTA 57.597 40.909 33.05 12.95 43.02 2.74
38 39 2.975410 TCACGTACGAATTCGACAGT 57.025 45.000 33.05 23.39 43.02 3.55
39 40 3.059044 CCTTTCACGTACGAATTCGACAG 59.941 47.826 33.05 22.80 43.02 3.51
40 41 2.981805 CCTTTCACGTACGAATTCGACA 59.018 45.455 33.05 17.52 43.02 4.35
41 42 3.236816 TCCTTTCACGTACGAATTCGAC 58.763 45.455 33.05 23.03 43.02 4.20
42 43 3.495193 CTCCTTTCACGTACGAATTCGA 58.505 45.455 33.05 14.57 43.02 3.71
43 44 2.027688 GCTCCTTTCACGTACGAATTCG 59.972 50.000 25.64 25.64 46.33 3.34
44 45 2.027688 CGCTCCTTTCACGTACGAATTC 59.972 50.000 24.41 0.00 0.00 2.17
45 46 1.990563 CGCTCCTTTCACGTACGAATT 59.009 47.619 24.41 0.00 0.00 2.17
46 47 1.068055 ACGCTCCTTTCACGTACGAAT 60.068 47.619 24.41 0.00 38.45 3.34
47 48 0.311790 ACGCTCCTTTCACGTACGAA 59.688 50.000 24.41 3.37 38.45 3.85
48 49 0.110056 GACGCTCCTTTCACGTACGA 60.110 55.000 24.41 0.00 40.69 3.43
49 50 1.069378 GGACGCTCCTTTCACGTACG 61.069 60.000 15.01 15.01 40.69 3.67
50 51 0.038892 TGGACGCTCCTTTCACGTAC 60.039 55.000 0.00 0.00 40.69 3.67
51 52 0.675083 TTGGACGCTCCTTTCACGTA 59.325 50.000 0.00 0.00 40.69 3.57
52 53 0.034896 ATTGGACGCTCCTTTCACGT 59.965 50.000 5.77 0.00 43.83 4.49
53 54 0.443869 CATTGGACGCTCCTTTCACG 59.556 55.000 5.77 0.00 37.46 4.35
54 55 1.808411 TCATTGGACGCTCCTTTCAC 58.192 50.000 5.77 0.00 37.46 3.18
55 56 2.787473 ATCATTGGACGCTCCTTTCA 57.213 45.000 5.77 0.00 37.46 2.69
56 57 7.440523 AATTATATCATTGGACGCTCCTTTC 57.559 36.000 5.77 0.00 37.46 2.62
57 58 7.823745 AAATTATATCATTGGACGCTCCTTT 57.176 32.000 5.77 0.00 37.46 3.11
58 59 7.502226 TGAAAATTATATCATTGGACGCTCCTT 59.498 33.333 5.77 0.00 37.46 3.36
59 60 6.998074 TGAAAATTATATCATTGGACGCTCCT 59.002 34.615 5.77 0.00 37.46 3.69
60 61 7.202016 TGAAAATTATATCATTGGACGCTCC 57.798 36.000 0.00 0.00 36.96 4.70
103 104 9.346725 GCCTTTGACTATTGACAAGATTAAAAG 57.653 33.333 3.95 3.95 0.00 2.27
104 105 8.855110 TGCCTTTGACTATTGACAAGATTAAAA 58.145 29.630 0.00 0.00 0.00 1.52
105 106 8.402798 TGCCTTTGACTATTGACAAGATTAAA 57.597 30.769 0.00 0.00 0.00 1.52
106 107 7.994425 TGCCTTTGACTATTGACAAGATTAA 57.006 32.000 0.00 0.00 0.00 1.40
107 108 7.994425 TTGCCTTTGACTATTGACAAGATTA 57.006 32.000 0.00 0.00 0.00 1.75
108 109 6.899393 TTGCCTTTGACTATTGACAAGATT 57.101 33.333 0.00 0.00 0.00 2.40
109 110 6.888632 AGATTGCCTTTGACTATTGACAAGAT 59.111 34.615 0.00 0.00 0.00 2.40
110 111 6.240894 AGATTGCCTTTGACTATTGACAAGA 58.759 36.000 0.00 0.00 0.00 3.02
111 112 6.404074 GGAGATTGCCTTTGACTATTGACAAG 60.404 42.308 0.00 0.00 0.00 3.16
112 113 5.415701 GGAGATTGCCTTTGACTATTGACAA 59.584 40.000 0.00 0.00 0.00 3.18
113 114 4.943705 GGAGATTGCCTTTGACTATTGACA 59.056 41.667 0.00 0.00 0.00 3.58
114 115 4.943705 TGGAGATTGCCTTTGACTATTGAC 59.056 41.667 0.00 0.00 0.00 3.18
115 116 5.178096 TGGAGATTGCCTTTGACTATTGA 57.822 39.130 0.00 0.00 0.00 2.57
116 117 5.902613 TTGGAGATTGCCTTTGACTATTG 57.097 39.130 0.00 0.00 0.00 1.90
117 118 6.916360 TTTTGGAGATTGCCTTTGACTATT 57.084 33.333 0.00 0.00 0.00 1.73
118 119 6.916360 TTTTTGGAGATTGCCTTTGACTAT 57.084 33.333 0.00 0.00 0.00 2.12
119 120 6.916360 ATTTTTGGAGATTGCCTTTGACTA 57.084 33.333 0.00 0.00 0.00 2.59
120 121 5.813513 ATTTTTGGAGATTGCCTTTGACT 57.186 34.783 0.00 0.00 0.00 3.41
121 122 6.366061 GTGTATTTTTGGAGATTGCCTTTGAC 59.634 38.462 0.00 0.00 0.00 3.18
122 123 6.454795 GTGTATTTTTGGAGATTGCCTTTGA 58.545 36.000 0.00 0.00 0.00 2.69
123 124 5.639082 GGTGTATTTTTGGAGATTGCCTTTG 59.361 40.000 0.00 0.00 0.00 2.77
124 125 5.279960 GGGTGTATTTTTGGAGATTGCCTTT 60.280 40.000 0.00 0.00 0.00 3.11
125 126 4.222810 GGGTGTATTTTTGGAGATTGCCTT 59.777 41.667 0.00 0.00 0.00 4.35
126 127 3.769300 GGGTGTATTTTTGGAGATTGCCT 59.231 43.478 0.00 0.00 0.00 4.75
127 128 3.513515 TGGGTGTATTTTTGGAGATTGCC 59.486 43.478 0.00 0.00 0.00 4.52
128 129 4.799564 TGGGTGTATTTTTGGAGATTGC 57.200 40.909 0.00 0.00 0.00 3.56
129 130 5.111293 GCATGGGTGTATTTTTGGAGATTG 58.889 41.667 0.00 0.00 0.00 2.67
130 131 4.776837 TGCATGGGTGTATTTTTGGAGATT 59.223 37.500 0.00 0.00 0.00 2.40
131 132 4.352009 TGCATGGGTGTATTTTTGGAGAT 58.648 39.130 0.00 0.00 0.00 2.75
132 133 3.772387 TGCATGGGTGTATTTTTGGAGA 58.228 40.909 0.00 0.00 0.00 3.71
133 134 4.244862 GTTGCATGGGTGTATTTTTGGAG 58.755 43.478 0.00 0.00 0.00 3.86
134 135 3.643320 TGTTGCATGGGTGTATTTTTGGA 59.357 39.130 0.00 0.00 0.00 3.53
135 136 4.000331 TGTTGCATGGGTGTATTTTTGG 58.000 40.909 0.00 0.00 0.00 3.28
136 137 5.998454 TTTGTTGCATGGGTGTATTTTTG 57.002 34.783 0.00 0.00 0.00 2.44
307 310 1.925185 GTCCGAGAGCAATTACCGTTC 59.075 52.381 0.00 0.00 0.00 3.95
368 373 3.270027 CCACTCACCATTGATTTAGCGA 58.730 45.455 0.00 0.00 0.00 4.93
469 477 4.573607 ACTTTTGTCAGTTCTCGTAAACCC 59.426 41.667 0.18 0.00 0.00 4.11
602 1519 5.551977 TCTTAGAAAACCTCTCCCCTCAAAT 59.448 40.000 0.00 0.00 35.41 2.32
638 1561 1.002134 CGTGGGGGCTGAGAACAAT 60.002 57.895 0.00 0.00 0.00 2.71
642 1565 2.429930 CAACGTGGGGGCTGAGAA 59.570 61.111 0.00 0.00 0.00 2.87
646 1569 2.912025 AAAGCAACGTGGGGGCTG 60.912 61.111 5.25 0.00 38.04 4.85
670 1593 2.158534 TGGGGGATTTGATACGGGATTG 60.159 50.000 0.00 0.00 0.00 2.67
697 1833 2.205074 CTCCACCACGATCAATGCTAC 58.795 52.381 0.00 0.00 0.00 3.58
864 2001 8.525290 AGGAAATCTCGAATGGTATGATTTTT 57.475 30.769 7.66 0.00 37.44 1.94
911 2048 4.342951 CCTCCAAATGGTATGCATGTCATT 59.657 41.667 10.16 15.19 36.63 2.57
914 2051 3.290710 ACCTCCAAATGGTATGCATGTC 58.709 45.455 10.16 2.14 35.80 3.06
919 2056 2.614057 CTCGAACCTCCAAATGGTATGC 59.386 50.000 0.00 0.00 36.69 3.14
920 2057 4.137116 TCTCGAACCTCCAAATGGTATG 57.863 45.455 0.00 0.00 36.69 2.39
921 2058 5.373812 AATCTCGAACCTCCAAATGGTAT 57.626 39.130 0.00 0.00 36.69 2.73
922 2059 4.837093 AATCTCGAACCTCCAAATGGTA 57.163 40.909 0.00 0.00 36.69 3.25
923 2060 3.721087 AATCTCGAACCTCCAAATGGT 57.279 42.857 0.00 0.00 39.91 3.55
924 2061 3.378427 GGAAATCTCGAACCTCCAAATGG 59.622 47.826 0.00 0.00 0.00 3.16
925 2062 4.265073 AGGAAATCTCGAACCTCCAAATG 58.735 43.478 5.57 0.00 0.00 2.32
926 2063 4.518249 GAGGAAATCTCGAACCTCCAAAT 58.482 43.478 0.00 0.00 41.89 2.32
927 2064 3.939066 GAGGAAATCTCGAACCTCCAAA 58.061 45.455 0.00 0.00 41.89 3.28
928 2065 3.611766 GAGGAAATCTCGAACCTCCAA 57.388 47.619 0.00 0.00 41.89 3.53
931 2068 2.211353 CGGAGGAAATCTCGAACCTC 57.789 55.000 0.00 0.00 45.50 3.85
1032 2170 1.539124 GAGGGTTGAGGAGGGGTGT 60.539 63.158 0.00 0.00 0.00 4.16
1120 2258 4.767255 GGCCGCCTGACAGGACAG 62.767 72.222 26.25 14.43 37.67 3.51
1182 2320 4.166011 GCGCAACACAGATCGCCC 62.166 66.667 0.30 0.00 41.53 6.13
1208 2347 3.560068 ACACTCCGTTAGCTTTCAAGTTG 59.440 43.478 0.00 0.00 0.00 3.16
1314 2453 2.825836 GATGTCAGGCTTGCCCGG 60.826 66.667 8.17 0.00 39.21 5.73
1437 2576 1.860950 CAATCATCCCGTGTCATCGTC 59.139 52.381 0.00 0.00 0.00 4.20
1533 2674 2.906354 AGATCCAACGTTACATGGCTC 58.094 47.619 0.00 0.00 36.62 4.70
1534 2675 3.350219 AAGATCCAACGTTACATGGCT 57.650 42.857 0.00 0.00 36.62 4.75
1621 2778 6.660521 TGGTGAGCAATCTTCAAACTATTCAT 59.339 34.615 0.00 0.00 0.00 2.57
1627 2784 3.316308 GTGTGGTGAGCAATCTTCAAACT 59.684 43.478 0.00 0.00 0.00 2.66
1628 2785 3.316308 AGTGTGGTGAGCAATCTTCAAAC 59.684 43.478 0.00 0.00 0.00 2.93
1812 3063 8.593945 ATCAATGGTATTCTAGGCAAAAAGAA 57.406 30.769 0.00 0.00 36.24 2.52
1834 3085 6.861055 GCAAAGTTTCACGAAAAAGGATATCA 59.139 34.615 4.83 0.00 31.33 2.15
1959 3216 3.389925 TCGGTCAACGGTGTAGATTTT 57.610 42.857 0.00 0.00 44.45 1.82
1960 3217 3.389925 TTCGGTCAACGGTGTAGATTT 57.610 42.857 0.00 0.00 44.45 2.17
1961 3218 3.389925 TTTCGGTCAACGGTGTAGATT 57.610 42.857 0.00 0.00 44.45 2.40
1962 3219 3.604875 ATTTCGGTCAACGGTGTAGAT 57.395 42.857 0.00 0.00 44.45 1.98
1969 3226 4.389382 TGTGTACATAATTTCGGTCAACGG 59.611 41.667 0.00 0.00 44.45 4.44
1970 3227 5.310489 GTGTGTACATAATTTCGGTCAACG 58.690 41.667 0.00 0.00 46.11 4.10
2212 3475 2.101582 TGGGCGTGCAACTGTAATTTTT 59.898 40.909 0.00 0.00 31.75 1.94
2213 3476 1.683917 TGGGCGTGCAACTGTAATTTT 59.316 42.857 0.00 0.00 31.75 1.82
2214 3477 1.000717 GTGGGCGTGCAACTGTAATTT 60.001 47.619 0.00 0.00 31.75 1.82
2215 3478 0.596082 GTGGGCGTGCAACTGTAATT 59.404 50.000 0.00 0.00 31.75 1.40
2216 3479 0.536233 TGTGGGCGTGCAACTGTAAT 60.536 50.000 0.00 0.00 31.75 1.89
2217 3480 0.536233 ATGTGGGCGTGCAACTGTAA 60.536 50.000 0.00 0.00 31.75 2.41
2218 3481 1.072332 ATGTGGGCGTGCAACTGTA 59.928 52.632 0.00 0.00 31.75 2.74
2219 3482 2.203337 ATGTGGGCGTGCAACTGT 60.203 55.556 0.00 0.00 31.75 3.55
2220 3483 2.256158 CATGTGGGCGTGCAACTG 59.744 61.111 0.00 0.00 31.75 3.16
2239 3502 6.806751 TCATGTGTAACTATAGTTGCTCTCC 58.193 40.000 27.17 16.03 40.55 3.71
2261 3571 2.049156 CGTGCTCGCCTGACTTCA 60.049 61.111 0.00 0.00 0.00 3.02
2311 3745 4.037923 GTGTTGTGACTGATGGGAAAACAT 59.962 41.667 0.00 0.00 0.00 2.71
2335 3769 4.181578 CAATTCGTGGACCACCTTACTAG 58.818 47.826 19.11 3.11 37.04 2.57
2412 3851 9.664332 ATGGCATGATCTCTAATGTTCTAATAC 57.336 33.333 0.00 0.00 0.00 1.89
2554 4444 8.472007 AGAAAAGACCAAATATTGTGTGGTTA 57.528 30.769 10.87 0.00 45.72 2.85


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

AutoCloner maintained by Alex Coulton.