Multiple sequence alignment - TraesCS3A01G497500

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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 TraesCS3A01G497500 chr3A 100.000 2783 0 0 1 2783 723567310 723564528 0.000000e+00 5140
1 TraesCS3A01G497500 chr3D 93.277 2231 99 12 124 2324 592760086 592762295 0.000000e+00 3241
2 TraesCS3A01G497500 chr3D 89.331 478 15 9 2307 2783 592762395 592762837 4.020000e-158 568
3 TraesCS3A01G497500 chr3B 89.818 2416 141 36 399 2783 794397266 794394925 0.000000e+00 3001
4 TraesCS3A01G497500 chr5D 78.211 872 114 45 1067 1904 437056585 437057414 3.220000e-134 488
5 TraesCS3A01G497500 chr5D 80.296 609 72 18 1000 1593 436971617 436972192 1.540000e-112 416
6 TraesCS3A01G497500 chr5D 78.662 553 83 20 1247 1792 436955910 436956434 4.440000e-88 335
7 TraesCS3A01G497500 chr5B 77.918 874 124 42 1066 1906 531274693 531275530 5.390000e-132 481
8 TraesCS3A01G497500 chr5B 81.281 609 72 16 1000 1593 531187285 531187866 3.270000e-124 455
9 TraesCS3A01G497500 chr5B 79.008 605 88 24 1247 1843 531157799 531158372 7.280000e-101 377
10 TraesCS3A01G497500 chr5A 80.629 604 74 17 993 1582 552232705 552233279 7.120000e-116 427
11 TraesCS3A01G497500 chr5A 78.437 691 97 28 1239 1904 552322121 552322784 1.200000e-108 403
12 TraesCS3A01G497500 chr5A 78.437 691 97 28 1239 1904 552362544 552363207 1.200000e-108 403
13 TraesCS3A01G497500 chr5A 76.239 787 115 38 1067 1843 552165510 552166234 4.410000e-93 351
14 TraesCS3A01G497500 chr5A 83.333 234 28 7 1231 1463 552341820 552342043 3.630000e-49 206
15 TraesCS3A01G497500 chr4B 88.938 226 23 2 2459 2683 447455446 447455222 7.590000e-71 278
16 TraesCS3A01G497500 chr2B 88.106 227 27 0 2459 2685 636775598 636775372 1.270000e-68 270
17 TraesCS3A01G497500 chr4D 87.946 224 23 4 2459 2679 51076323 51076101 7.650000e-66 261
18 TraesCS3A01G497500 chr4D 86.283 226 28 3 2459 2682 341525729 341525505 2.770000e-60 243
19 TraesCS3A01G497500 chr1D 86.547 223 27 3 2459 2680 464601187 464601407 2.770000e-60 243
20 TraesCS3A01G497500 chr1B 86.026 229 28 2 2463 2687 433423033 433422805 2.770000e-60 243
21 TraesCS3A01G497500 chr1B 85.217 230 32 2 2457 2685 664018069 664018297 4.630000e-58 235
22 TraesCS3A01G497500 chr2D 86.161 224 28 3 2459 2681 649755370 649755149 3.580000e-59 239


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 TraesCS3A01G497500 chr3A 723564528 723567310 2782 True 5140.0 5140 100.000 1 2783 1 chr3A.!!$R1 2782
1 TraesCS3A01G497500 chr3D 592760086 592762837 2751 False 1904.5 3241 91.304 124 2783 2 chr3D.!!$F1 2659
2 TraesCS3A01G497500 chr3B 794394925 794397266 2341 True 3001.0 3001 89.818 399 2783 1 chr3B.!!$R1 2384
3 TraesCS3A01G497500 chr5D 437056585 437057414 829 False 488.0 488 78.211 1067 1904 1 chr5D.!!$F3 837
4 TraesCS3A01G497500 chr5D 436971617 436972192 575 False 416.0 416 80.296 1000 1593 1 chr5D.!!$F2 593
5 TraesCS3A01G497500 chr5D 436955910 436956434 524 False 335.0 335 78.662 1247 1792 1 chr5D.!!$F1 545
6 TraesCS3A01G497500 chr5B 531274693 531275530 837 False 481.0 481 77.918 1066 1906 1 chr5B.!!$F3 840
7 TraesCS3A01G497500 chr5B 531187285 531187866 581 False 455.0 455 81.281 1000 1593 1 chr5B.!!$F2 593
8 TraesCS3A01G497500 chr5B 531157799 531158372 573 False 377.0 377 79.008 1247 1843 1 chr5B.!!$F1 596
9 TraesCS3A01G497500 chr5A 552232705 552233279 574 False 427.0 427 80.629 993 1582 1 chr5A.!!$F2 589
10 TraesCS3A01G497500 chr5A 552322121 552322784 663 False 403.0 403 78.437 1239 1904 1 chr5A.!!$F3 665
11 TraesCS3A01G497500 chr5A 552362544 552363207 663 False 403.0 403 78.437 1239 1904 1 chr5A.!!$F5 665
12 TraesCS3A01G497500 chr5A 552165510 552166234 724 False 351.0 351 76.239 1067 1843 1 chr5A.!!$F1 776

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
101 102 0.177141 CGGCTTTCCCACGAGGATTA 59.823 55.0 0.00 0.0 46.94 1.75 F
899 935 0.247814 CACATCATCTCCGCGTTTGC 60.248 55.0 4.92 0.0 37.91 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1034 1073 0.036875 CTCACCCTCACCTTTCACCC 59.963 60.0 0.00 0.0 0.00 4.61 R
2616 2918 0.461548 TGGAACGTTTTTGCATGGCA 59.538 45.0 0.46 0.0 36.47 4.92 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
21 22 3.849951 CCGCACCACCCGCTAGAT 61.850 66.667 0.00 0.00 0.00 1.98
22 23 2.279517 CGCACCACCCGCTAGATC 60.280 66.667 0.00 0.00 0.00 2.75
23 24 2.786495 CGCACCACCCGCTAGATCT 61.786 63.158 0.00 0.00 0.00 2.75
24 25 1.068250 GCACCACCCGCTAGATCTC 59.932 63.158 0.00 0.00 0.00 2.75
25 26 1.742768 CACCACCCGCTAGATCTCC 59.257 63.158 0.00 0.00 0.00 3.71
26 27 1.828660 ACCACCCGCTAGATCTCCG 60.829 63.158 0.00 3.39 0.00 4.63
27 28 1.828660 CCACCCGCTAGATCTCCGT 60.829 63.158 0.00 0.00 0.00 4.69
28 29 1.655329 CACCCGCTAGATCTCCGTC 59.345 63.158 0.00 0.00 0.00 4.79
29 30 0.820074 CACCCGCTAGATCTCCGTCT 60.820 60.000 0.00 0.00 0.00 4.18
30 31 0.820074 ACCCGCTAGATCTCCGTCTG 60.820 60.000 0.00 0.00 0.00 3.51
31 32 1.284408 CCGCTAGATCTCCGTCTGC 59.716 63.158 0.00 0.00 0.00 4.26
32 33 1.082431 CGCTAGATCTCCGTCTGCG 60.082 63.158 0.00 3.76 38.42 5.18
33 34 1.371145 GCTAGATCTCCGTCTGCGC 60.371 63.158 0.00 0.00 36.67 6.09
34 35 1.284408 CTAGATCTCCGTCTGCGCC 59.716 63.158 4.18 0.00 36.67 6.53
35 36 1.152943 TAGATCTCCGTCTGCGCCT 60.153 57.895 4.18 0.00 36.67 5.52
36 37 1.167155 TAGATCTCCGTCTGCGCCTC 61.167 60.000 4.18 0.00 36.67 4.70
37 38 3.492311 GATCTCCGTCTGCGCCTCC 62.492 68.421 4.18 0.00 36.67 4.30
48 49 4.253257 CGCCTCCGGAGTCGCTAC 62.253 72.222 29.25 10.62 34.56 3.58
49 50 3.138798 GCCTCCGGAGTCGCTACA 61.139 66.667 29.25 0.00 34.56 2.74
50 51 2.491022 GCCTCCGGAGTCGCTACAT 61.491 63.158 29.25 0.00 34.56 2.29
51 52 1.655329 CCTCCGGAGTCGCTACATC 59.345 63.158 29.25 0.00 34.56 3.06
52 53 1.101635 CCTCCGGAGTCGCTACATCA 61.102 60.000 29.25 0.00 34.56 3.07
53 54 0.738975 CTCCGGAGTCGCTACATCAA 59.261 55.000 24.04 0.00 34.56 2.57
54 55 1.338337 CTCCGGAGTCGCTACATCAAT 59.662 52.381 24.04 0.00 34.56 2.57
55 56 1.337071 TCCGGAGTCGCTACATCAATC 59.663 52.381 0.00 0.00 34.56 2.67
56 57 1.338337 CCGGAGTCGCTACATCAATCT 59.662 52.381 0.00 0.00 34.56 2.40
57 58 2.605823 CCGGAGTCGCTACATCAATCTC 60.606 54.545 0.00 0.00 34.56 2.75
58 59 2.292016 CGGAGTCGCTACATCAATCTCT 59.708 50.000 0.00 0.00 0.00 3.10
59 60 3.637432 GGAGTCGCTACATCAATCTCTG 58.363 50.000 0.00 0.00 0.00 3.35
60 61 3.551863 GGAGTCGCTACATCAATCTCTGG 60.552 52.174 0.00 0.00 0.00 3.86
61 62 2.131183 GTCGCTACATCAATCTCTGGC 58.869 52.381 0.00 0.00 0.00 4.85
62 63 1.756538 TCGCTACATCAATCTCTGGCA 59.243 47.619 0.00 0.00 0.00 4.92
63 64 2.168313 TCGCTACATCAATCTCTGGCAA 59.832 45.455 0.00 0.00 0.00 4.52
64 65 2.286294 CGCTACATCAATCTCTGGCAAC 59.714 50.000 0.00 0.00 0.00 4.17
65 66 3.539604 GCTACATCAATCTCTGGCAACT 58.460 45.455 0.00 0.00 37.61 3.16
66 67 3.311871 GCTACATCAATCTCTGGCAACTG 59.688 47.826 0.00 0.00 37.61 3.16
67 68 2.089980 ACATCAATCTCTGGCAACTGC 58.910 47.619 0.00 0.00 41.14 4.40
68 69 1.063616 CATCAATCTCTGGCAACTGCG 59.936 52.381 0.00 0.00 43.26 5.18
69 70 1.136147 CAATCTCTGGCAACTGCGC 59.864 57.895 0.00 0.00 43.26 6.09
77 78 3.286751 GCAACTGCGCCACTGGAA 61.287 61.111 4.18 0.00 0.00 3.53
78 79 2.629656 GCAACTGCGCCACTGGAAT 61.630 57.895 4.18 0.00 0.00 3.01
79 80 1.503542 CAACTGCGCCACTGGAATC 59.496 57.895 4.18 0.00 0.00 2.52
80 81 1.073025 AACTGCGCCACTGGAATCA 59.927 52.632 4.18 0.00 0.00 2.57
81 82 0.957395 AACTGCGCCACTGGAATCAG 60.957 55.000 4.18 4.85 46.10 2.90
82 83 2.747460 TGCGCCACTGGAATCAGC 60.747 61.111 4.18 0.00 44.59 4.26
84 85 3.197790 CGCCACTGGAATCAGCGG 61.198 66.667 0.00 0.00 44.04 5.52
86 87 2.270205 CCACTGGAATCAGCGGCT 59.730 61.111 0.00 0.00 44.59 5.52
87 88 1.377725 CCACTGGAATCAGCGGCTT 60.378 57.895 0.00 0.00 44.59 4.35
88 89 0.962356 CCACTGGAATCAGCGGCTTT 60.962 55.000 0.00 0.00 44.59 3.51
89 90 0.449388 CACTGGAATCAGCGGCTTTC 59.551 55.000 0.00 2.42 44.59 2.62
90 91 0.678048 ACTGGAATCAGCGGCTTTCC 60.678 55.000 21.32 21.32 44.59 3.13
91 92 1.378514 TGGAATCAGCGGCTTTCCC 60.379 57.895 23.84 13.44 38.51 3.97
92 93 1.378514 GGAATCAGCGGCTTTCCCA 60.379 57.895 18.61 0.00 34.15 4.37
93 94 1.657751 GGAATCAGCGGCTTTCCCAC 61.658 60.000 18.61 2.16 34.15 4.61
94 95 1.982073 GAATCAGCGGCTTTCCCACG 61.982 60.000 0.00 0.00 0.00 4.94
95 96 2.463589 AATCAGCGGCTTTCCCACGA 62.464 55.000 0.00 0.00 0.00 4.35
96 97 2.859273 ATCAGCGGCTTTCCCACGAG 62.859 60.000 0.00 0.00 0.00 4.18
97 98 4.394712 AGCGGCTTTCCCACGAGG 62.395 66.667 0.00 0.00 0.00 4.63
98 99 4.388499 GCGGCTTTCCCACGAGGA 62.388 66.667 0.00 0.00 45.68 3.71
99 100 2.584608 CGGCTTTCCCACGAGGAT 59.415 61.111 0.00 0.00 46.94 3.24
100 101 1.078426 CGGCTTTCCCACGAGGATT 60.078 57.895 0.00 0.00 46.94 3.01
101 102 0.177141 CGGCTTTCCCACGAGGATTA 59.823 55.000 0.00 0.00 46.94 1.75
102 103 1.806623 CGGCTTTCCCACGAGGATTAG 60.807 57.143 0.00 2.99 46.94 1.73
103 104 1.300481 GCTTTCCCACGAGGATTAGC 58.700 55.000 0.00 8.88 46.94 3.09
104 105 1.571919 CTTTCCCACGAGGATTAGCG 58.428 55.000 0.00 0.00 46.94 4.26
105 106 0.177141 TTTCCCACGAGGATTAGCGG 59.823 55.000 0.00 0.00 46.94 5.52
106 107 0.974010 TTCCCACGAGGATTAGCGGT 60.974 55.000 0.00 0.00 46.94 5.68
107 108 1.227263 CCCACGAGGATTAGCGGTG 60.227 63.158 0.00 0.00 38.24 4.94
108 109 1.883084 CCACGAGGATTAGCGGTGC 60.883 63.158 0.00 0.00 36.89 5.01
109 110 1.883084 CACGAGGATTAGCGGTGCC 60.883 63.158 0.00 0.00 0.00 5.01
110 111 2.355986 ACGAGGATTAGCGGTGCCA 61.356 57.895 0.00 0.00 0.00 4.92
111 112 1.883084 CGAGGATTAGCGGTGCCAC 60.883 63.158 0.00 0.00 0.00 5.01
112 113 1.523938 GAGGATTAGCGGTGCCACC 60.524 63.158 2.98 2.98 34.05 4.61
113 114 2.252072 GAGGATTAGCGGTGCCACCA 62.252 60.000 15.45 0.00 38.47 4.17
114 115 2.112815 GGATTAGCGGTGCCACCAC 61.113 63.158 15.45 3.78 38.47 4.16
122 123 2.282391 GTGCCACCACCTCATGCA 60.282 61.111 0.00 0.00 35.92 3.96
129 130 2.359107 CACCTCATGCACAGCGGT 60.359 61.111 0.00 0.00 0.00 5.68
147 148 3.434319 GCCACCACCTCATGCACG 61.434 66.667 0.00 0.00 0.00 5.34
172 173 2.685380 CCCTCCTTGCCCTCGACT 60.685 66.667 0.00 0.00 0.00 4.18
175 176 1.674057 CTCCTTGCCCTCGACTTGT 59.326 57.895 0.00 0.00 0.00 3.16
197 198 0.461961 CTCGAACTCCCCACCATCTC 59.538 60.000 0.00 0.00 0.00 2.75
202 203 3.144120 CTCCCCACCATCTCGCTCG 62.144 68.421 0.00 0.00 0.00 5.03
241 242 2.821366 GCTCGTGGGCTGTGGATG 60.821 66.667 0.00 0.00 0.00 3.51
245 247 2.361610 GTGGGCTGTGGATGTGGG 60.362 66.667 0.00 0.00 0.00 4.61
249 251 2.439156 GCTGTGGATGTGGGGAGC 60.439 66.667 0.00 0.00 0.00 4.70
266 268 1.152525 GCGATGAGGAGGAGGGGTA 60.153 63.158 0.00 0.00 0.00 3.69
271 273 2.204803 AGGAGGAGGGGTAGGGGT 60.205 66.667 0.00 0.00 0.00 4.95
397 399 7.517734 GCTGCCATGCTATCATAATTTTGTTTG 60.518 37.037 0.00 0.00 0.00 2.93
404 406 8.469200 TGCTATCATAATTTTGTTTGGGAGAAG 58.531 33.333 0.00 0.00 0.00 2.85
409 411 8.156165 TCATAATTTTGTTTGGGAGAAGCAATT 58.844 29.630 0.00 0.00 0.00 2.32
431 433 3.089284 GAGGTGGGTAATTTTCTGGTGG 58.911 50.000 0.00 0.00 0.00 4.61
433 435 3.658705 AGGTGGGTAATTTTCTGGTGGTA 59.341 43.478 0.00 0.00 0.00 3.25
456 458 2.758979 CTGCTGATCAGGAGCCAAAAAT 59.241 45.455 28.36 0.00 39.96 1.82
566 578 4.657408 TGGATGCCGTGCTGCCAA 62.657 61.111 0.00 0.00 31.88 4.52
608 620 2.905415 ACCATTGTCCACATCCATGT 57.095 45.000 0.00 0.00 42.84 3.21
640 652 7.884816 ACATTCAATAAATCCGTACCTATCG 57.115 36.000 0.00 0.00 0.00 2.92
694 730 2.158959 GCCCGACGTGAAGACATCG 61.159 63.158 0.00 0.00 0.00 3.84
730 766 2.976509 GACATCGTATCTGATCTGTGCG 59.023 50.000 0.00 0.86 0.00 5.34
788 824 2.729882 GGACGCCGCAATTACTACATAG 59.270 50.000 0.00 0.00 0.00 2.23
789 825 3.378339 GACGCCGCAATTACTACATAGT 58.622 45.455 0.00 0.00 40.24 2.12
790 826 4.539870 GACGCCGCAATTACTACATAGTA 58.460 43.478 0.00 0.00 37.73 1.82
808 844 4.133013 AGTACGAATTAAGGCCGTGATT 57.867 40.909 8.41 8.41 37.69 2.57
850 886 1.001624 TGTGATCTCGCGCAATCTTG 58.998 50.000 8.75 0.00 0.00 3.02
852 888 1.257415 GTGATCTCGCGCAATCTTGAG 59.743 52.381 8.75 4.63 0.00 3.02
854 890 2.196749 GATCTCGCGCAATCTTGAGAA 58.803 47.619 8.75 0.00 40.55 2.87
899 935 0.247814 CACATCATCTCCGCGTTTGC 60.248 55.000 4.92 0.00 37.91 3.68
966 1003 2.028112 TCCCATCCAAGAACTCAACTCG 60.028 50.000 0.00 0.00 0.00 4.18
967 1004 1.734465 CCATCCAAGAACTCAACTCGC 59.266 52.381 0.00 0.00 0.00 5.03
1034 1073 4.096003 AACCGCGTCCATGGAGGG 62.096 66.667 30.36 24.93 38.24 4.30
1043 1082 1.214305 TCCATGGAGGGGGTGAAAGG 61.214 60.000 11.44 0.00 38.24 3.11
1044 1083 1.509548 CCATGGAGGGGGTGAAAGGT 61.510 60.000 5.56 0.00 0.00 3.50
1463 1577 2.892425 CGGCAGGTCATTCCTCGC 60.892 66.667 0.00 0.00 46.24 5.03
1645 1768 1.342074 CATATCGGCCTTCCCTGAGA 58.658 55.000 0.00 0.00 0.00 3.27
1713 1836 1.749609 GAAGTGATAACGGCGGCGAC 61.750 60.000 38.93 24.28 0.00 5.19
1819 1945 0.880718 GGTCCGATCATTTCTCCGCC 60.881 60.000 0.00 0.00 0.00 6.13
1922 2063 6.202188 TCCGTTCTTTCTTAATTGTGTCAGTC 59.798 38.462 0.00 0.00 0.00 3.51
1923 2064 6.018262 CCGTTCTTTCTTAATTGTGTCAGTCA 60.018 38.462 0.00 0.00 0.00 3.41
1924 2065 7.065894 CGTTCTTTCTTAATTGTGTCAGTCAG 58.934 38.462 0.00 0.00 0.00 3.51
1925 2066 7.254455 CGTTCTTTCTTAATTGTGTCAGTCAGT 60.254 37.037 0.00 0.00 0.00 3.41
2007 2153 4.225942 AGTGCAAGACTTCATCCTTCCATA 59.774 41.667 0.00 0.00 0.00 2.74
2128 2283 0.934496 TCCAAGCAACGTCGAGTTTG 59.066 50.000 0.00 5.71 42.02 2.93
2207 2368 2.290641 CCTACCGCATGTAAAATCAGGC 59.709 50.000 0.00 0.00 40.92 4.85
2232 2393 5.790618 TGTAGGGGATAAATTAGGAGGGATG 59.209 44.000 0.00 0.00 0.00 3.51
2339 2618 5.997746 TCTTTGATTGAAGGACCACAGTTAG 59.002 40.000 0.00 0.00 0.00 2.34
2394 2673 6.348621 TGCAATTTTCAAGAAAAGCAGTTC 57.651 33.333 14.42 0.00 42.72 3.01
2453 2732 9.677567 ATTTACGAAAATGATAAATCCCGAATG 57.322 29.630 0.00 0.00 33.97 2.67
2454 2733 6.693315 ACGAAAATGATAAATCCCGAATGT 57.307 33.333 0.00 0.00 0.00 2.71
2455 2734 7.095695 ACGAAAATGATAAATCCCGAATGTT 57.904 32.000 0.00 0.00 0.00 2.71
2456 2735 7.193595 ACGAAAATGATAAATCCCGAATGTTC 58.806 34.615 0.00 0.00 0.00 3.18
2513 2792 6.103330 ACGTTTTTCATGGCAACTTTAGTTT 58.897 32.000 0.00 0.00 35.83 2.66
2515 2794 7.923878 ACGTTTTTCATGGCAACTTTAGTTTAT 59.076 29.630 0.00 0.00 35.83 1.40
2529 2808 3.492421 AGTTTATGCGATGTTGGCAAG 57.508 42.857 0.00 0.00 44.66 4.01
2604 2906 2.729028 ACTAAAGTTGCCACCACACT 57.271 45.000 0.00 0.00 0.00 3.55
2605 2907 2.572290 ACTAAAGTTGCCACCACACTC 58.428 47.619 0.00 0.00 0.00 3.51
2606 2908 1.880027 CTAAAGTTGCCACCACACTCC 59.120 52.381 0.00 0.00 0.00 3.85
2607 2909 0.033601 AAAGTTGCCACCACACTCCA 60.034 50.000 0.00 0.00 0.00 3.86
2608 2910 0.033601 AAGTTGCCACCACACTCCAA 60.034 50.000 0.00 0.00 0.00 3.53
2609 2911 0.751643 AGTTGCCACCACACTCCAAC 60.752 55.000 0.00 0.00 36.83 3.77
2610 2912 0.751643 GTTGCCACCACACTCCAACT 60.752 55.000 0.00 0.00 34.51 3.16
2611 2913 0.840617 TTGCCACCACACTCCAACTA 59.159 50.000 0.00 0.00 0.00 2.24
2612 2914 0.840617 TGCCACCACACTCCAACTAA 59.159 50.000 0.00 0.00 0.00 2.24
2613 2915 1.213182 TGCCACCACACTCCAACTAAA 59.787 47.619 0.00 0.00 0.00 1.85
2614 2916 1.880027 GCCACCACACTCCAACTAAAG 59.120 52.381 0.00 0.00 0.00 1.85
2615 2917 2.748465 GCCACCACACTCCAACTAAAGT 60.748 50.000 0.00 0.00 0.00 2.66
2616 2918 3.551846 CCACCACACTCCAACTAAAGTT 58.448 45.455 0.00 0.00 39.12 2.66
2634 2936 1.576356 TTGCCATGCAAAAACGTTCC 58.424 45.000 0.00 0.00 45.96 3.62
2643 2945 3.243035 TGCAAAAACGTTCCAGATGACAG 60.243 43.478 0.00 0.00 0.00 3.51
2698 3000 5.163332 GGGTCCTATTTAATCTGAACCGTCT 60.163 44.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.792053 GATCTAGCGGGTGGTGCGG 62.792 68.421 0.00 0.00 37.44 5.69
5 6 2.279517 GATCTAGCGGGTGGTGCG 60.280 66.667 0.00 0.00 37.44 5.34
6 7 1.068250 GAGATCTAGCGGGTGGTGC 59.932 63.158 0.00 0.00 0.00 5.01
7 8 1.742768 GGAGATCTAGCGGGTGGTG 59.257 63.158 0.00 0.00 0.00 4.17
8 9 1.828660 CGGAGATCTAGCGGGTGGT 60.829 63.158 0.00 0.00 0.00 4.16
9 10 1.797211 GACGGAGATCTAGCGGGTGG 61.797 65.000 0.00 0.00 0.00 4.61
10 11 0.820074 AGACGGAGATCTAGCGGGTG 60.820 60.000 0.00 0.00 0.00 4.61
11 12 0.820074 CAGACGGAGATCTAGCGGGT 60.820 60.000 0.00 0.00 0.00 5.28
12 13 1.953017 CAGACGGAGATCTAGCGGG 59.047 63.158 0.00 0.00 0.00 6.13
13 14 1.284408 GCAGACGGAGATCTAGCGG 59.716 63.158 0.00 0.00 0.00 5.52
14 15 1.082431 CGCAGACGGAGATCTAGCG 60.082 63.158 0.00 1.54 38.72 4.26
15 16 1.371145 GCGCAGACGGAGATCTAGC 60.371 63.158 0.30 0.00 40.57 3.42
16 17 1.284408 GGCGCAGACGGAGATCTAG 59.716 63.158 10.83 0.00 40.57 2.43
17 18 3.433319 GGCGCAGACGGAGATCTA 58.567 61.111 10.83 0.00 40.57 1.98
34 35 0.738975 TTGATGTAGCGACTCCGGAG 59.261 55.000 30.11 30.11 36.06 4.63
35 36 1.337071 GATTGATGTAGCGACTCCGGA 59.663 52.381 2.93 2.93 36.06 5.14
36 37 1.338337 AGATTGATGTAGCGACTCCGG 59.662 52.381 0.00 0.00 36.06 5.14
37 38 2.292016 AGAGATTGATGTAGCGACTCCG 59.708 50.000 0.00 0.00 39.16 4.63
38 39 3.551863 CCAGAGATTGATGTAGCGACTCC 60.552 52.174 0.00 0.00 0.00 3.85
39 40 3.637432 CCAGAGATTGATGTAGCGACTC 58.363 50.000 0.00 0.00 0.00 3.36
40 41 2.223923 GCCAGAGATTGATGTAGCGACT 60.224 50.000 0.00 0.00 0.00 4.18
41 42 2.131183 GCCAGAGATTGATGTAGCGAC 58.869 52.381 0.00 0.00 0.00 5.19
42 43 1.756538 TGCCAGAGATTGATGTAGCGA 59.243 47.619 0.00 0.00 0.00 4.93
43 44 2.229675 TGCCAGAGATTGATGTAGCG 57.770 50.000 0.00 0.00 0.00 4.26
44 45 3.311871 CAGTTGCCAGAGATTGATGTAGC 59.688 47.826 0.00 0.00 0.00 3.58
45 46 3.311871 GCAGTTGCCAGAGATTGATGTAG 59.688 47.826 0.00 0.00 34.31 2.74
46 47 3.273434 GCAGTTGCCAGAGATTGATGTA 58.727 45.455 0.00 0.00 34.31 2.29
47 48 2.089980 GCAGTTGCCAGAGATTGATGT 58.910 47.619 0.00 0.00 34.31 3.06
48 49 1.063616 CGCAGTTGCCAGAGATTGATG 59.936 52.381 0.00 0.00 37.91 3.07
49 50 1.376543 CGCAGTTGCCAGAGATTGAT 58.623 50.000 0.00 0.00 37.91 2.57
50 51 1.300971 GCGCAGTTGCCAGAGATTGA 61.301 55.000 0.30 0.00 37.91 2.57
51 52 1.136147 GCGCAGTTGCCAGAGATTG 59.864 57.895 0.30 0.00 37.91 2.67
52 53 3.583383 GCGCAGTTGCCAGAGATT 58.417 55.556 0.30 0.00 37.91 2.40
60 61 2.533391 GATTCCAGTGGCGCAGTTGC 62.533 60.000 10.83 0.00 37.78 4.17
61 62 1.236616 TGATTCCAGTGGCGCAGTTG 61.237 55.000 10.83 3.23 0.00 3.16
62 63 0.957395 CTGATTCCAGTGGCGCAGTT 60.957 55.000 10.83 0.00 35.70 3.16
63 64 1.376424 CTGATTCCAGTGGCGCAGT 60.376 57.895 10.83 0.00 35.70 4.40
64 65 2.758089 GCTGATTCCAGTGGCGCAG 61.758 63.158 10.83 16.70 42.35 5.18
65 66 2.747460 GCTGATTCCAGTGGCGCA 60.747 61.111 10.83 1.17 42.35 6.09
66 67 3.869272 CGCTGATTCCAGTGGCGC 61.869 66.667 3.51 0.00 44.84 6.53
71 72 0.678048 GGAAAGCCGCTGATTCCAGT 60.678 55.000 16.07 0.00 41.80 4.00
72 73 1.379642 GGGAAAGCCGCTGATTCCAG 61.380 60.000 20.60 0.00 43.56 3.86
73 74 1.378514 GGGAAAGCCGCTGATTCCA 60.379 57.895 20.60 0.00 43.56 3.53
74 75 1.378514 TGGGAAAGCCGCTGATTCC 60.379 57.895 13.51 13.51 41.53 3.01
75 76 1.803289 GTGGGAAAGCCGCTGATTC 59.197 57.895 0.00 0.00 33.83 2.52
76 77 2.040544 CGTGGGAAAGCCGCTGATT 61.041 57.895 0.00 0.00 33.83 2.57
77 78 2.436646 CGTGGGAAAGCCGCTGAT 60.437 61.111 0.00 0.00 33.83 2.90
78 79 3.589654 CTCGTGGGAAAGCCGCTGA 62.590 63.158 0.00 0.00 33.83 4.26
79 80 3.121030 CTCGTGGGAAAGCCGCTG 61.121 66.667 0.00 0.00 33.83 5.18
80 81 4.394712 CCTCGTGGGAAAGCCGCT 62.395 66.667 0.00 0.00 37.23 5.52
81 82 4.388499 TCCTCGTGGGAAAGCCGC 62.388 66.667 3.23 0.00 41.91 6.53
89 90 1.227263 CACCGCTAATCCTCGTGGG 60.227 63.158 3.23 0.00 35.14 4.61
90 91 1.883084 GCACCGCTAATCCTCGTGG 60.883 63.158 0.00 0.00 36.86 4.94
91 92 1.883084 GGCACCGCTAATCCTCGTG 60.883 63.158 0.00 0.00 0.00 4.35
92 93 2.355986 TGGCACCGCTAATCCTCGT 61.356 57.895 0.00 0.00 0.00 4.18
93 94 1.883084 GTGGCACCGCTAATCCTCG 60.883 63.158 6.29 0.00 0.00 4.63
94 95 1.523938 GGTGGCACCGCTAATCCTC 60.524 63.158 22.83 0.00 0.00 3.71
95 96 2.297895 TGGTGGCACCGCTAATCCT 61.298 57.895 30.14 0.00 42.58 3.24
96 97 2.112815 GTGGTGGCACCGCTAATCC 61.113 63.158 36.47 11.10 45.06 3.01
97 98 3.497879 GTGGTGGCACCGCTAATC 58.502 61.111 36.47 16.81 45.06 1.75
104 105 3.064324 GCATGAGGTGGTGGCACC 61.064 66.667 29.75 29.75 45.31 5.01
105 106 2.282391 TGCATGAGGTGGTGGCAC 60.282 61.111 9.70 9.70 0.00 5.01
106 107 2.282391 GTGCATGAGGTGGTGGCA 60.282 61.111 0.00 0.00 0.00 4.92
107 108 2.282391 TGTGCATGAGGTGGTGGC 60.282 61.111 0.00 0.00 0.00 5.01
108 109 2.338015 GCTGTGCATGAGGTGGTGG 61.338 63.158 0.00 0.00 0.00 4.61
109 110 2.683859 CGCTGTGCATGAGGTGGTG 61.684 63.158 0.00 0.00 0.00 4.17
110 111 2.359107 CGCTGTGCATGAGGTGGT 60.359 61.111 0.00 0.00 0.00 4.16
111 112 3.129502 CCGCTGTGCATGAGGTGG 61.130 66.667 0.00 0.00 0.00 4.61
112 113 2.359107 ACCGCTGTGCATGAGGTG 60.359 61.111 15.00 2.05 36.30 4.00
113 114 2.359107 CACCGCTGTGCATGAGGT 60.359 61.111 11.16 11.16 38.10 3.85
129 130 2.282391 GTGCATGAGGTGGTGGCA 60.282 61.111 0.00 0.00 0.00 4.92
152 153 3.801997 CGAGGGCAAGGAGGGCAT 61.802 66.667 0.00 0.00 34.52 4.40
161 162 0.033504 GAGTCACAAGTCGAGGGCAA 59.966 55.000 0.00 0.00 0.00 4.52
172 173 0.391597 GTGGGGAGTTCGAGTCACAA 59.608 55.000 1.94 0.00 0.00 3.33
175 176 0.544357 ATGGTGGGGAGTTCGAGTCA 60.544 55.000 0.00 0.00 0.00 3.41
229 230 3.660571 CCCCACATCCACAGCCCA 61.661 66.667 0.00 0.00 0.00 5.36
241 242 2.801631 CCTCCTCATCGCTCCCCAC 61.802 68.421 0.00 0.00 0.00 4.61
245 247 2.206536 CCCTCCTCCTCATCGCTCC 61.207 68.421 0.00 0.00 0.00 4.70
249 251 0.540830 CCTACCCCTCCTCCTCATCG 60.541 65.000 0.00 0.00 0.00 3.84
266 268 1.061579 GGTTATCTACTCCCCACCCCT 60.062 57.143 0.00 0.00 0.00 4.79
271 273 3.538980 ACCTTAGGGTTATCTACTCCCCA 59.461 47.826 2.32 0.00 44.73 4.96
373 375 6.762187 CCAAACAAAATTATGATAGCATGGCA 59.238 34.615 3.11 0.00 35.94 4.92
397 399 1.467920 CCACCTCAATTGCTTCTCCC 58.532 55.000 0.00 0.00 0.00 4.30
404 406 5.170748 CAGAAAATTACCCACCTCAATTGC 58.829 41.667 0.00 0.00 0.00 3.56
409 411 3.499563 CCACCAGAAAATTACCCACCTCA 60.500 47.826 0.00 0.00 0.00 3.86
488 493 4.095946 TGCTAGAAAATTTTCAGGGCCAT 58.904 39.130 28.00 11.59 39.61 4.40
566 578 4.955811 TCAGGATTTGGTACGCTATCAT 57.044 40.909 0.00 0.00 0.00 2.45
629 641 3.853475 AGTTTTCCAACGATAGGTACGG 58.147 45.455 0.00 0.00 43.77 4.02
694 730 4.058817 ACGATGTCTCCAGTTTTGAACTC 58.941 43.478 0.00 0.00 40.46 3.01
730 766 8.035394 TGTCACTCTTTCATACTTTCCATACTC 58.965 37.037 0.00 0.00 0.00 2.59
788 824 4.549489 CGAAATCACGGCCTTAATTCGTAC 60.549 45.833 15.15 0.00 35.23 3.67
789 825 3.552699 CGAAATCACGGCCTTAATTCGTA 59.447 43.478 15.15 0.00 35.23 3.43
790 826 2.350498 CGAAATCACGGCCTTAATTCGT 59.650 45.455 15.15 0.00 34.97 3.85
808 844 3.071479 GCTGGAGTTTAATGTGGTCGAA 58.929 45.455 0.00 0.00 0.00 3.71
909 945 0.601558 TATACAAGGGATCGGAGCGC 59.398 55.000 0.00 0.00 0.00 5.92
966 1003 0.179124 TTTGGTGTTTCTTGGCACGC 60.179 50.000 0.00 0.00 36.54 5.34
967 1004 1.135257 TGTTTGGTGTTTCTTGGCACG 60.135 47.619 0.00 0.00 36.54 5.34
1034 1073 0.036875 CTCACCCTCACCTTTCACCC 59.963 60.000 0.00 0.00 0.00 4.61
1043 1082 1.229209 TCCTCACCCTCACCCTCAC 60.229 63.158 0.00 0.00 0.00 3.51
1044 1083 1.079256 CTCCTCACCCTCACCCTCA 59.921 63.158 0.00 0.00 0.00 3.86
1474 1588 4.524318 ATAGAACGGCGGCGTGGG 62.524 66.667 38.07 9.18 0.00 4.61
1480 1594 1.961277 GCATCCCATAGAACGGCGG 60.961 63.158 13.24 0.00 0.00 6.13
1654 1777 3.138798 CGAGATCCCGGTCACCGT 61.139 66.667 16.87 0.00 46.80 4.83
1682 1805 2.859273 ATCACTTCCGCTCCCGCTTG 62.859 60.000 0.00 0.00 0.00 4.01
1689 1812 1.480219 CGCCGTTATCACTTCCGCTC 61.480 60.000 0.00 0.00 0.00 5.03
1700 1823 1.006571 CTATGGTCGCCGCCGTTAT 60.007 57.895 0.00 0.00 35.54 1.89
1713 1836 9.859427 TTTTTCTTCAACTCATTAATGCTATGG 57.141 29.630 10.76 0.00 0.00 2.74
1855 1991 4.755266 ACCAACTAAATGACGGATAGCT 57.245 40.909 0.00 0.00 0.00 3.32
1922 2063 1.938577 CAGCTAGCTTACCATGCACTG 59.061 52.381 16.46 0.00 0.00 3.66
1923 2064 1.833630 TCAGCTAGCTTACCATGCACT 59.166 47.619 16.46 0.00 0.00 4.40
1924 2065 2.159043 TCTCAGCTAGCTTACCATGCAC 60.159 50.000 16.46 0.00 0.00 4.57
1925 2066 2.110578 TCTCAGCTAGCTTACCATGCA 58.889 47.619 16.46 0.00 0.00 3.96
2128 2283 2.879026 ACGGGAAAAGCAAAGAGAAGTC 59.121 45.455 0.00 0.00 0.00 3.01
2207 2368 5.412384 TCCCTCCTAATTTATCCCCTACAG 58.588 45.833 0.00 0.00 0.00 2.74
2232 2393 4.329545 TGCGGGACCCAGCAAGAC 62.330 66.667 22.51 0.00 40.78 3.01
2379 2658 4.279169 CCATCTTGGAACTGCTTTTCTTGA 59.721 41.667 0.00 0.00 40.96 3.02
2394 2673 4.301072 TTGGTAAGAGGAACCATCTTGG 57.699 45.455 4.38 0.00 46.16 3.61
2452 2731 5.618195 GCTTAAAATCCGAACATTCCGAACA 60.618 40.000 0.00 0.00 0.00 3.18
2453 2732 4.791676 GCTTAAAATCCGAACATTCCGAAC 59.208 41.667 0.00 0.00 0.00 3.95
2454 2733 4.456222 TGCTTAAAATCCGAACATTCCGAA 59.544 37.500 0.00 0.00 0.00 4.30
2455 2734 4.004314 TGCTTAAAATCCGAACATTCCGA 58.996 39.130 0.00 0.00 0.00 4.55
2456 2735 4.349663 TGCTTAAAATCCGAACATTCCG 57.650 40.909 0.00 0.00 0.00 4.30
2457 2736 5.743872 GTCATGCTTAAAATCCGAACATTCC 59.256 40.000 0.00 0.00 0.00 3.01
2458 2737 5.743872 GGTCATGCTTAAAATCCGAACATTC 59.256 40.000 0.00 0.00 0.00 2.67
2459 2738 5.184864 TGGTCATGCTTAAAATCCGAACATT 59.815 36.000 0.00 0.00 0.00 2.71
2460 2739 4.704540 TGGTCATGCTTAAAATCCGAACAT 59.295 37.500 0.00 0.00 0.00 2.71
2461 2740 4.075682 TGGTCATGCTTAAAATCCGAACA 58.924 39.130 0.00 0.00 0.00 3.18
2513 2792 1.065851 CATGCTTGCCAACATCGCATA 59.934 47.619 2.07 0.00 39.72 3.14
2515 2794 1.213275 CATGCTTGCCAACATCGCA 59.787 52.632 0.00 0.00 37.11 5.10
2529 2808 2.294233 TCTTGACAGAAAGTTGCCATGC 59.706 45.455 0.00 0.00 0.00 4.06
2616 2918 0.461548 TGGAACGTTTTTGCATGGCA 59.538 45.000 0.46 0.00 36.47 4.92
2617 2919 1.139163 CTGGAACGTTTTTGCATGGC 58.861 50.000 0.46 0.00 0.00 4.40
2618 2920 2.791383 TCTGGAACGTTTTTGCATGG 57.209 45.000 0.46 0.00 0.00 3.66
2619 2921 3.670055 GTCATCTGGAACGTTTTTGCATG 59.330 43.478 0.46 2.27 0.00 4.06
2634 2936 4.191544 TCGGATTTTAAGCCTGTCATCTG 58.808 43.478 0.00 0.00 30.63 2.90
2643 2945 2.765918 CGAACGTTCGGATTTTAAGCC 58.234 47.619 36.53 3.84 46.30 4.35


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

AutoCloner maintained by Alex Coulton.