Multiple sequence alignment - TraesCS3D01G531200

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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 TraesCS3D01G531200 chr3D 100.000 3041 0 0 1 3041 607311441 607308401 0.000000e+00 5616.0
1 TraesCS3D01G531200 chr3D 91.146 1954 125 16 733 2668 606929786 606931709 0.000000e+00 2606.0
2 TraesCS3D01G531200 chr3D 92.045 176 12 1 2866 3041 606931814 606931987 2.340000e-61 246.0
3 TraesCS3D01G531200 chr3D 90.426 94 3 2 2739 2832 606931734 606931821 5.330000e-23 119.0
4 TraesCS3D01G531200 chr3A 93.912 1429 79 6 733 2157 739735303 739733879 0.000000e+00 2150.0
5 TraesCS3D01G531200 chr3A 88.032 1011 67 13 1997 2979 739325239 739326223 0.000000e+00 1147.0
6 TraesCS3D01G531200 chr3A 90.052 774 63 7 839 1601 739322417 739323187 0.000000e+00 990.0
7 TraesCS3D01G531200 chr3A 88.792 687 49 8 71 731 739736017 739735333 0.000000e+00 817.0
8 TraesCS3D01G531200 chr3A 93.052 403 19 4 2514 2913 739733558 739733162 5.650000e-162 580.0
9 TraesCS3D01G531200 chr3A 88.312 231 21 6 2260 2487 739733781 739733554 3.860000e-69 272.0
10 TraesCS3D01G531200 chr3A 83.673 98 12 3 2945 3041 739733111 739733017 4.180000e-14 89.8
11 TraesCS3D01G531200 chr3A 86.842 76 6 4 2969 3041 739324395 739324469 6.990000e-12 82.4
12 TraesCS3D01G531200 chr3B 93.537 1439 72 9 733 2155 816692346 816690913 0.000000e+00 2122.0
13 TraesCS3D01G531200 chr3B 94.665 1106 54 1 944 2044 816264528 816265633 0.000000e+00 1711.0
14 TraesCS3D01G531200 chr3B 89.595 519 43 6 2528 3041 816690651 816690139 0.000000e+00 649.0
15 TraesCS3D01G531200 chr3B 85.618 445 37 8 2157 2600 816265652 816266070 2.780000e-120 442.0
16 TraesCS3D01G531200 chr3B 90.429 303 22 5 2160 2455 816690965 816690663 2.840000e-105 392.0
17 TraesCS3D01G531200 chr3B 89.644 309 24 5 2735 3041 816271819 816272121 1.320000e-103 387.0
18 TraesCS3D01G531200 chr3B 90.942 276 14 6 470 734 816692653 816692378 8.020000e-96 361.0
19 TraesCS3D01G531200 chr3B 93.836 146 7 2 2592 2737 816271565 816271708 5.100000e-53 219.0
20 TraesCS3D01G531200 chr1A 83.784 1369 158 34 733 2063 406189509 406190851 0.000000e+00 1240.0
21 TraesCS3D01G531200 chr1B 83.873 1358 152 30 733 2063 327024579 327023262 0.000000e+00 1232.0
22 TraesCS3D01G531200 chr1B 85.998 857 90 17 733 1572 435194144 435194987 0.000000e+00 891.0
23 TraesCS3D01G531200 chr1B 82.382 403 42 12 1672 2063 435195411 435195795 1.050000e-84 324.0
24 TraesCS3D01G531200 chr1B 93.671 79 5 0 71 149 93866970 93867048 5.330000e-23 119.0
25 TraesCS3D01G531200 chr1D 86.565 856 93 13 733 1572 322285168 322286017 0.000000e+00 924.0
26 TraesCS3D01G531200 chr1D 82.619 420 48 8 1653 2063 227129634 227129231 6.240000e-92 348.0
27 TraesCS3D01G531200 chr1D 81.777 439 50 14 1637 2063 322286062 322286482 1.040000e-89 340.0
28 TraesCS3D01G531200 chr6B 93.671 79 5 0 71 149 621341732 621341810 5.330000e-23 119.0
29 TraesCS3D01G531200 chr5B 93.671 79 5 0 71 149 713104604 713104526 5.330000e-23 119.0
30 TraesCS3D01G531200 chr5B 92.405 79 6 0 71 149 713103432 713103510 2.480000e-21 113.0
31 TraesCS3D01G531200 chrUn 92.405 79 6 0 71 149 466452090 466452012 2.480000e-21 113.0
32 TraesCS3D01G531200 chrUn 90.541 74 6 1 71 144 217898449 217898377 2.500000e-16 97.1
33 TraesCS3D01G531200 chrUn 100.000 35 0 0 150 184 466451993 466451959 7.040000e-07 65.8
34 TraesCS3D01G531200 chr6A 92.405 79 6 0 71 149 84427286 84427364 2.480000e-21 113.0
35 TraesCS3D01G531200 chr5D 92.405 79 6 0 71 149 80064458 80064536 2.480000e-21 113.0
36 TraesCS3D01G531200 chr5D 90.541 74 7 0 71 144 79828030 79828103 6.940000e-17 99.0
37 TraesCS3D01G531200 chr5A 92.405 79 6 0 71 149 157794834 157794912 2.480000e-21 113.0
38 TraesCS3D01G531200 chr4B 92.405 79 6 0 71 149 495528888 495528810 2.480000e-21 113.0
39 TraesCS3D01G531200 chr4B 90.541 74 7 0 71 144 209097425 209097352 6.940000e-17 99.0
40 TraesCS3D01G531200 chr4B 100.000 35 0 0 150 184 495528791 495528757 7.040000e-07 65.8
41 TraesCS3D01G531200 chr6D 91.892 74 6 0 71 144 458950586 458950659 1.490000e-18 104.0
42 TraesCS3D01G531200 chr4D 90.667 75 7 0 70 144 87364522 87364448 1.930000e-17 100.0
43 TraesCS3D01G531200 chr4A 89.189 74 8 0 71 144 509788509 509788582 3.230000e-15 93.5
44 TraesCS3D01G531200 chr4A 95.455 44 2 0 2998 3041 59319702 59319659 1.510000e-08 71.3
45 TraesCS3D01G531200 chr4A 92.000 50 1 3 2993 3041 656488779 656488732 1.960000e-07 67.6
46 TraesCS3D01G531200 chr7A 95.349 43 2 0 2999 3041 47155536 47155578 5.440000e-08 69.4
47 TraesCS3D01G531200 chr2D 92.000 50 1 3 2993 3041 63709572 63709525 1.960000e-07 67.6


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 TraesCS3D01G531200 chr3D 607308401 607311441 3040 True 5616.000000 5616 100.000000 1 3041 1 chr3D.!!$R1 3040
1 TraesCS3D01G531200 chr3D 606929786 606931987 2201 False 990.333333 2606 91.205667 733 3041 3 chr3D.!!$F1 2308
2 TraesCS3D01G531200 chr3A 739733017 739736017 3000 True 781.760000 2150 89.548200 71 3041 5 chr3A.!!$R1 2970
3 TraesCS3D01G531200 chr3A 739322417 739326223 3806 False 739.800000 1147 88.308667 839 3041 3 chr3A.!!$F1 2202
4 TraesCS3D01G531200 chr3B 816264528 816266070 1542 False 1076.500000 1711 90.141500 944 2600 2 chr3B.!!$F1 1656
5 TraesCS3D01G531200 chr3B 816690139 816692653 2514 True 881.000000 2122 91.125750 470 3041 4 chr3B.!!$R1 2571
6 TraesCS3D01G531200 chr3B 816271565 816272121 556 False 303.000000 387 91.740000 2592 3041 2 chr3B.!!$F2 449
7 TraesCS3D01G531200 chr1A 406189509 406190851 1342 False 1240.000000 1240 83.784000 733 2063 1 chr1A.!!$F1 1330
8 TraesCS3D01G531200 chr1B 327023262 327024579 1317 True 1232.000000 1232 83.873000 733 2063 1 chr1B.!!$R1 1330
9 TraesCS3D01G531200 chr1B 435194144 435195795 1651 False 607.500000 891 84.190000 733 2063 2 chr1B.!!$F2 1330
10 TraesCS3D01G531200 chr1D 322285168 322286482 1314 False 632.000000 924 84.171000 733 2063 2 chr1D.!!$F1 1330

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
62 63 0.108662 GGGACCTGTAAACCCGTACG 60.109 60.0 8.69 8.69 34.03 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 4185 0.940126 GATGAGCGCCGATTGACAAT 59.06 50.0 2.29 0.0 0.0 2.71 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 3.637297 GCAGCAGCCTTCTAAATGC 57.363 52.632 0.00 0.00 38.97 3.56
22 23 0.248377 GCAGCAGCCTTCTAAATGCG 60.248 55.000 0.00 0.00 43.41 4.73
23 24 0.248377 CAGCAGCCTTCTAAATGCGC 60.248 55.000 0.00 0.00 43.41 6.09
24 25 0.677731 AGCAGCCTTCTAAATGCGCA 60.678 50.000 14.96 14.96 43.41 6.09
25 26 0.524180 GCAGCCTTCTAAATGCGCAC 60.524 55.000 14.90 0.00 0.00 5.34
26 27 0.804364 CAGCCTTCTAAATGCGCACA 59.196 50.000 14.90 0.00 0.00 4.57
27 28 0.804989 AGCCTTCTAAATGCGCACAC 59.195 50.000 14.90 0.00 0.00 3.82
28 29 0.521242 GCCTTCTAAATGCGCACACG 60.521 55.000 14.90 1.15 44.07 4.49
46 47 4.100084 CATGCGGTGCTCAGGGGA 62.100 66.667 0.00 0.00 0.00 4.81
47 48 4.101448 ATGCGGTGCTCAGGGGAC 62.101 66.667 0.00 0.00 35.44 4.46
61 62 3.840831 GGGACCTGTAAACCCGTAC 57.159 57.895 0.00 0.00 34.03 3.67
62 63 0.108662 GGGACCTGTAAACCCGTACG 60.109 60.000 8.69 8.69 34.03 3.67
63 64 0.108662 GGACCTGTAAACCCGTACGG 60.109 60.000 27.68 27.68 37.81 4.02
64 65 0.887933 GACCTGTAAACCCGTACGGA 59.112 55.000 35.41 13.02 37.50 4.69
65 66 0.890683 ACCTGTAAACCCGTACGGAG 59.109 55.000 35.41 25.52 37.50 4.63
66 67 0.174162 CCTGTAAACCCGTACGGAGG 59.826 60.000 35.41 26.56 37.50 4.30
67 68 0.890683 CTGTAAACCCGTACGGAGGT 59.109 55.000 35.41 22.24 38.27 3.85
68 69 2.091541 CTGTAAACCCGTACGGAGGTA 58.908 52.381 35.41 19.37 34.45 3.08
69 70 2.091541 TGTAAACCCGTACGGAGGTAG 58.908 52.381 35.41 20.02 34.45 3.18
70 71 2.092323 GTAAACCCGTACGGAGGTAGT 58.908 52.381 35.41 20.72 34.45 2.73
71 72 2.507407 AAACCCGTACGGAGGTAGTA 57.493 50.000 35.41 0.00 34.45 1.82
72 73 2.044123 AACCCGTACGGAGGTAGTAG 57.956 55.000 35.41 17.79 34.45 2.57
73 74 0.912486 ACCCGTACGGAGGTAGTAGT 59.088 55.000 35.41 18.47 37.50 2.73
108 109 4.562143 GGATTTGAAAAGCCACAGCAGATT 60.562 41.667 5.22 0.00 43.73 2.40
117 119 4.529897 AGCCACAGCAGATTGATAAATCA 58.470 39.130 5.56 0.00 43.56 2.57
141 143 7.817962 TCACTAATTTAGCTAAGTCAACTCCAC 59.182 37.037 6.24 0.00 0.00 4.02
223 243 8.193953 ACATGGTTCTAAAAATCATTTCTGGT 57.806 30.769 0.00 0.00 0.00 4.00
233 253 6.899393 AAATCATTTCTGGTGCTTGAGTTA 57.101 33.333 0.00 0.00 0.00 2.24
234 254 7.472334 AAATCATTTCTGGTGCTTGAGTTAT 57.528 32.000 0.00 0.00 0.00 1.89
244 271 5.178623 TGGTGCTTGAGTTATTTGTCTAACG 59.821 40.000 0.00 0.00 36.83 3.18
269 296 6.947903 TCCGGTTTGTTTAACAAGAAAAAC 57.052 33.333 10.51 5.93 39.53 2.43
270 297 5.572126 TCCGGTTTGTTTAACAAGAAAAACG 59.428 36.000 10.51 10.10 39.53 3.60
273 300 6.010675 GGTTTGTTTAACAAGAAAAACGCAC 58.989 36.000 10.51 3.28 39.53 5.34
314 341 5.500234 AGCTATGTACTCCATCTGCAAAAA 58.500 37.500 0.00 0.00 36.31 1.94
321 348 4.501071 ACTCCATCTGCAAAAATGAATGC 58.499 39.130 5.25 0.00 42.86 3.56
326 353 5.180492 CCATCTGCAAAAATGAATGCACTTT 59.820 36.000 0.00 0.00 46.87 2.66
330 357 5.609423 TGCAAAAATGAATGCACTTTAGGT 58.391 33.333 0.00 0.00 46.87 3.08
365 392 6.172136 TGTGTGGACCAAATCAAAAATCAT 57.828 33.333 0.00 0.00 0.00 2.45
432 459 7.061688 GGAGAACTAAGGTATGGAAGAGTCTA 58.938 42.308 0.00 0.00 0.00 2.59
597 625 8.744568 TGAGGTTTGTGCATATTATGTATTGA 57.255 30.769 5.60 0.00 0.00 2.57
681 717 3.864789 AGAGAATATCCAACGGCCAAT 57.135 42.857 2.24 0.00 0.00 3.16
786 887 4.638865 GGGACTCTGTGTGTTAGTTGTTTT 59.361 41.667 0.00 0.00 0.00 2.43
817 918 2.455674 TTCTCTTGTGTGTCGGATGG 57.544 50.000 0.00 0.00 0.00 3.51
910 1027 2.093764 CCAACAAACCAAGCAGGAAACA 60.094 45.455 1.83 0.00 41.22 2.83
913 1033 3.860641 ACAAACCAAGCAGGAAACAAAG 58.139 40.909 1.83 0.00 41.22 2.77
985 1107 8.041323 TCTCTTGTCTAACATTCTGGTTATTCC 58.959 37.037 0.00 0.00 33.13 3.01
1034 1156 0.102481 CGCATAGGTCGCCAGTACTT 59.898 55.000 0.00 0.00 0.00 2.24
1073 1198 1.690633 GTGATGGCCCTCCTCCTCA 60.691 63.158 0.00 0.00 0.00 3.86
1102 1227 4.082190 CACGAGAAAGGTCTATCTCACCAA 60.082 45.833 0.00 0.00 41.73 3.67
1605 1811 4.469657 GTGGCCCACATGAGGAATTTATA 58.530 43.478 9.55 0.00 34.08 0.98
1713 2234 0.798776 ACGAGAAGAATGCAAAGCCG 59.201 50.000 0.00 0.00 0.00 5.52
1846 2367 3.726557 TTCATTCCCTCACTTGCATCT 57.273 42.857 0.00 0.00 0.00 2.90
1861 2382 6.800408 CACTTGCATCTAAGTCACTGAAAATG 59.200 38.462 0.00 0.00 38.78 2.32
1915 2440 2.520536 GGGGTCAGCGGCTATGGAT 61.521 63.158 0.26 0.00 0.00 3.41
2056 4185 5.336372 CGTCCTTGATTTGGGCTTTTGATTA 60.336 40.000 0.00 0.00 0.00 1.75
2063 4192 7.448420 TGATTTGGGCTTTTGATTATTGTCAA 58.552 30.769 0.00 0.00 36.38 3.18
2070 4199 3.332761 TTGATTATTGTCAATCGGCGC 57.667 42.857 0.00 0.00 37.68 6.53
2118 4247 2.234661 TCTCTGGTACTGATGCTTGTGG 59.765 50.000 0.00 0.00 35.31 4.17
2119 4248 1.977854 TCTGGTACTGATGCTTGTGGT 59.022 47.619 0.00 0.00 0.00 4.16
2120 4249 2.079158 CTGGTACTGATGCTTGTGGTG 58.921 52.381 0.00 0.00 0.00 4.17
2121 4250 1.696884 TGGTACTGATGCTTGTGGTGA 59.303 47.619 0.00 0.00 0.00 4.02
2122 4251 2.305635 TGGTACTGATGCTTGTGGTGAT 59.694 45.455 0.00 0.00 0.00 3.06
2123 4252 2.679837 GGTACTGATGCTTGTGGTGATG 59.320 50.000 0.00 0.00 0.00 3.07
2124 4253 1.830279 ACTGATGCTTGTGGTGATGG 58.170 50.000 0.00 0.00 0.00 3.51
2125 4254 1.074405 ACTGATGCTTGTGGTGATGGT 59.926 47.619 0.00 0.00 0.00 3.55
2126 4255 1.471287 CTGATGCTTGTGGTGATGGTG 59.529 52.381 0.00 0.00 0.00 4.17
2127 4256 0.171903 GATGCTTGTGGTGATGGTGC 59.828 55.000 0.00 0.00 0.00 5.01
2128 4257 1.252904 ATGCTTGTGGTGATGGTGCC 61.253 55.000 0.00 0.00 0.00 5.01
2129 4258 1.604593 GCTTGTGGTGATGGTGCCT 60.605 57.895 0.00 0.00 0.00 4.75
2130 4259 1.181098 GCTTGTGGTGATGGTGCCTT 61.181 55.000 0.00 0.00 0.00 4.35
2131 4260 0.599558 CTTGTGGTGATGGTGCCTTG 59.400 55.000 0.00 0.00 0.00 3.61
2132 4261 0.106268 TTGTGGTGATGGTGCCTTGT 60.106 50.000 0.00 0.00 0.00 3.16
2133 4262 0.106268 TGTGGTGATGGTGCCTTGTT 60.106 50.000 0.00 0.00 0.00 2.83
2134 4263 0.598065 GTGGTGATGGTGCCTTGTTC 59.402 55.000 0.00 0.00 0.00 3.18
2135 4264 0.184692 TGGTGATGGTGCCTTGTTCA 59.815 50.000 0.00 0.00 0.00 3.18
2136 4265 0.883833 GGTGATGGTGCCTTGTTCAG 59.116 55.000 0.00 0.00 0.00 3.02
2137 4266 1.545428 GGTGATGGTGCCTTGTTCAGA 60.545 52.381 0.00 0.00 0.00 3.27
2138 4267 2.229792 GTGATGGTGCCTTGTTCAGAA 58.770 47.619 0.00 0.00 0.00 3.02
2139 4268 2.227388 GTGATGGTGCCTTGTTCAGAAG 59.773 50.000 0.00 0.00 0.00 2.85
2140 4269 2.106338 TGATGGTGCCTTGTTCAGAAGA 59.894 45.455 0.00 0.00 0.00 2.87
2141 4270 1.967319 TGGTGCCTTGTTCAGAAGAC 58.033 50.000 0.00 0.00 0.00 3.01
2142 4271 1.490490 TGGTGCCTTGTTCAGAAGACT 59.510 47.619 0.00 0.00 0.00 3.24
2143 4272 1.876156 GGTGCCTTGTTCAGAAGACTG 59.124 52.381 0.00 0.00 44.66 3.51
2144 4273 2.565841 GTGCCTTGTTCAGAAGACTGT 58.434 47.619 0.00 0.00 43.81 3.55
2145 4274 3.494398 GGTGCCTTGTTCAGAAGACTGTA 60.494 47.826 0.00 0.00 43.81 2.74
2146 4275 4.127171 GTGCCTTGTTCAGAAGACTGTAA 58.873 43.478 0.00 0.00 43.81 2.41
2147 4276 4.024809 GTGCCTTGTTCAGAAGACTGTAAC 60.025 45.833 0.00 0.00 43.81 2.50
2148 4277 3.498777 GCCTTGTTCAGAAGACTGTAACC 59.501 47.826 0.00 0.00 43.81 2.85
2149 4278 4.703897 CCTTGTTCAGAAGACTGTAACCA 58.296 43.478 0.00 0.00 43.81 3.67
2150 4279 5.308825 CCTTGTTCAGAAGACTGTAACCAT 58.691 41.667 0.00 0.00 43.81 3.55
2151 4280 5.180117 CCTTGTTCAGAAGACTGTAACCATG 59.820 44.000 0.00 0.00 43.81 3.66
2152 4281 5.545063 TGTTCAGAAGACTGTAACCATGA 57.455 39.130 0.00 0.00 43.81 3.07
2153 4282 5.924356 TGTTCAGAAGACTGTAACCATGAA 58.076 37.500 0.00 0.00 43.81 2.57
2154 4283 6.533730 TGTTCAGAAGACTGTAACCATGAAT 58.466 36.000 0.00 0.00 43.81 2.57
2155 4284 6.427853 TGTTCAGAAGACTGTAACCATGAATG 59.572 38.462 0.00 0.00 43.81 2.67
2156 4285 4.937620 TCAGAAGACTGTAACCATGAATGC 59.062 41.667 0.00 0.00 43.81 3.56
2157 4286 4.940046 CAGAAGACTGTAACCATGAATGCT 59.060 41.667 0.00 0.00 39.11 3.79
2158 4287 5.413833 CAGAAGACTGTAACCATGAATGCTT 59.586 40.000 0.00 0.00 39.11 3.91
2159 4288 5.413833 AGAAGACTGTAACCATGAATGCTTG 59.586 40.000 0.00 0.00 0.00 4.01
2160 4289 4.655963 AGACTGTAACCATGAATGCTTGT 58.344 39.130 0.00 0.00 0.00 3.16
2161 4290 5.804639 AGACTGTAACCATGAATGCTTGTA 58.195 37.500 0.00 0.00 0.00 2.41
2162 4291 5.643777 AGACTGTAACCATGAATGCTTGTAC 59.356 40.000 0.00 0.00 0.00 2.90
2163 4292 5.560724 ACTGTAACCATGAATGCTTGTACT 58.439 37.500 0.00 0.00 0.00 2.73
2164 4293 5.412594 ACTGTAACCATGAATGCTTGTACTG 59.587 40.000 0.00 0.00 0.00 2.74
2165 4294 5.555966 TGTAACCATGAATGCTTGTACTGA 58.444 37.500 0.00 0.00 0.00 3.41
2166 4295 6.179756 TGTAACCATGAATGCTTGTACTGAT 58.820 36.000 0.00 0.00 0.00 2.90
2167 4296 5.824904 AACCATGAATGCTTGTACTGATC 57.175 39.130 0.00 0.00 0.00 2.92
2168 4297 4.202441 ACCATGAATGCTTGTACTGATCC 58.798 43.478 0.00 0.00 0.00 3.36
2169 4298 4.080129 ACCATGAATGCTTGTACTGATCCT 60.080 41.667 0.00 0.00 0.00 3.24
2170 4299 4.885907 CCATGAATGCTTGTACTGATCCTT 59.114 41.667 0.00 0.00 0.00 3.36
2171 4300 5.220989 CCATGAATGCTTGTACTGATCCTTG 60.221 44.000 0.00 0.00 0.00 3.61
2172 4301 4.910195 TGAATGCTTGTACTGATCCTTGT 58.090 39.130 0.00 0.00 0.00 3.16
2192 4321 1.391157 GGTGCTGGTGCCTTGTTCAA 61.391 55.000 0.00 0.00 38.71 2.69
2200 4329 2.802247 GGTGCCTTGTTCAAAAGATTGC 59.198 45.455 0.00 0.00 36.45 3.56
2257 4496 6.974622 GCAATTCATTGTACTTAACAGGATGG 59.025 38.462 1.59 0.00 39.87 3.51
2261 4500 5.431731 TCATTGTACTTAACAGGATGGGGAT 59.568 40.000 0.00 0.00 43.62 3.85
2307 4567 8.459521 TCTTTTGATTGGTAAACATTATTGCG 57.540 30.769 0.00 0.00 0.00 4.85
2396 4660 7.539034 AGGATAACAGCAACCTAATGTTTTT 57.461 32.000 0.00 0.00 38.14 1.94
2405 4669 6.041979 AGCAACCTAATGTTTTTCATTCACCT 59.958 34.615 0.00 0.00 44.50 4.00
2415 4679 3.735237 TTCATTCACCTATCTCGCCTC 57.265 47.619 0.00 0.00 0.00 4.70
2550 4820 5.331975 TCAGGTGTTGAAGCACAGGATGT 62.332 47.826 0.00 0.00 41.65 3.06
2583 4853 1.867233 AGAATTGCGTGCGATATGGAC 59.133 47.619 0.00 0.00 35.21 4.02
2593 4863 4.613167 CGTGCGATATGGACTAGTTAGGTC 60.613 50.000 0.00 0.00 36.65 3.85
2604 4874 5.294060 GGACTAGTTAGGTCTGTTACTCTCG 59.706 48.000 0.00 0.00 34.47 4.04
2787 5171 9.961265 AAGAAAAGGCAAAGTTAAGTTATGTAC 57.039 29.630 0.00 0.00 0.00 2.90
2788 5172 9.127277 AGAAAAGGCAAAGTTAAGTTATGTACA 57.873 29.630 0.00 0.00 0.00 2.90
2794 5178 7.021790 GCAAAGTTAAGTTATGTACAGCTTCC 58.978 38.462 11.70 6.36 0.00 3.46
2802 5186 7.719871 AGTTATGTACAGCTTCCTAAGAGAA 57.280 36.000 0.33 0.00 0.00 2.87
2803 5187 8.135382 AGTTATGTACAGCTTCCTAAGAGAAA 57.865 34.615 0.33 0.00 0.00 2.52
2804 5188 8.763601 AGTTATGTACAGCTTCCTAAGAGAAAT 58.236 33.333 0.33 0.00 0.00 2.17
2805 5189 9.384764 GTTATGTACAGCTTCCTAAGAGAAATT 57.615 33.333 0.33 0.00 0.00 1.82
2863 5332 5.870978 CACTGGGATTTTTAATTTGCAGAGG 59.129 40.000 0.00 0.00 0.00 3.69
2936 5405 1.905637 CTGCCCCGTTCTTACCTTTT 58.094 50.000 0.00 0.00 0.00 2.27
2943 5414 5.705902 CCCCGTTCTTACCTTTTTATGTTG 58.294 41.667 0.00 0.00 0.00 3.33
2998 5501 7.745620 ATAGAGTTAACTTGTCCAAAACAGG 57.254 36.000 10.02 0.00 39.58 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.248377 CGCATTTAGAAGGCTGCTGC 60.248 55.000 4.87 7.10 35.74 5.25
5 6 0.677731 TGCGCATTTAGAAGGCTGCT 60.678 50.000 5.66 0.00 38.09 4.24
6 7 0.524180 GTGCGCATTTAGAAGGCTGC 60.524 55.000 15.91 0.00 37.88 5.25
7 8 0.804364 TGTGCGCATTTAGAAGGCTG 59.196 50.000 15.91 0.00 35.74 4.85
8 9 0.804989 GTGTGCGCATTTAGAAGGCT 59.195 50.000 15.91 0.00 35.74 4.58
9 10 0.521242 CGTGTGCGCATTTAGAAGGC 60.521 55.000 15.91 0.00 34.28 4.35
10 11 3.586039 CGTGTGCGCATTTAGAAGG 57.414 52.632 15.91 0.00 0.00 3.46
29 30 4.100084 TCCCCTGAGCACCGCATG 62.100 66.667 0.00 0.00 0.00 4.06
30 31 4.101448 GTCCCCTGAGCACCGCAT 62.101 66.667 0.00 0.00 0.00 4.73
41 42 0.116940 TACGGGTTTACAGGTCCCCT 59.883 55.000 0.00 0.00 38.09 4.79
42 43 0.250234 GTACGGGTTTACAGGTCCCC 59.750 60.000 0.00 0.00 38.09 4.81
43 44 0.108662 CGTACGGGTTTACAGGTCCC 60.109 60.000 7.57 0.00 37.98 4.46
44 45 0.108662 CCGTACGGGTTTACAGGTCC 60.109 60.000 27.00 0.00 0.00 4.46
45 46 0.887933 TCCGTACGGGTTTACAGGTC 59.112 55.000 32.80 0.00 37.00 3.85
46 47 0.890683 CTCCGTACGGGTTTACAGGT 59.109 55.000 32.80 0.00 37.00 4.00
47 48 0.174162 CCTCCGTACGGGTTTACAGG 59.826 60.000 32.80 25.55 37.00 4.00
48 49 0.890683 ACCTCCGTACGGGTTTACAG 59.109 55.000 32.80 21.00 37.00 2.74
49 50 2.091541 CTACCTCCGTACGGGTTTACA 58.908 52.381 32.80 12.60 37.07 2.41
50 51 2.092323 ACTACCTCCGTACGGGTTTAC 58.908 52.381 32.80 0.00 37.07 2.01
51 52 2.507407 ACTACCTCCGTACGGGTTTA 57.493 50.000 32.80 19.15 37.07 2.01
52 53 2.290960 ACTACTACCTCCGTACGGGTTT 60.291 50.000 32.80 19.05 37.07 3.27
53 54 1.282157 ACTACTACCTCCGTACGGGTT 59.718 52.381 32.80 19.40 37.07 4.11
54 55 0.912486 ACTACTACCTCCGTACGGGT 59.088 55.000 32.80 24.92 39.40 5.28
55 56 1.943340 GAACTACTACCTCCGTACGGG 59.057 57.143 32.80 22.51 35.59 5.28
56 57 1.594862 CGAACTACTACCTCCGTACGG 59.405 57.143 28.66 28.66 0.00 4.02
57 58 1.594862 CCGAACTACTACCTCCGTACG 59.405 57.143 8.69 8.69 0.00 3.67
58 59 2.633488 ACCGAACTACTACCTCCGTAC 58.367 52.381 0.00 0.00 0.00 3.67
59 60 3.350219 AACCGAACTACTACCTCCGTA 57.650 47.619 0.00 0.00 0.00 4.02
60 61 2.206576 AACCGAACTACTACCTCCGT 57.793 50.000 0.00 0.00 0.00 4.69
61 62 3.535561 TCTAACCGAACTACTACCTCCG 58.464 50.000 0.00 0.00 0.00 4.63
62 63 4.335037 CACTCTAACCGAACTACTACCTCC 59.665 50.000 0.00 0.00 0.00 4.30
63 64 4.335037 CCACTCTAACCGAACTACTACCTC 59.665 50.000 0.00 0.00 0.00 3.85
64 65 4.018960 TCCACTCTAACCGAACTACTACCT 60.019 45.833 0.00 0.00 0.00 3.08
65 66 4.265073 TCCACTCTAACCGAACTACTACC 58.735 47.826 0.00 0.00 0.00 3.18
66 67 6.448207 AATCCACTCTAACCGAACTACTAC 57.552 41.667 0.00 0.00 0.00 2.73
67 68 6.660521 TCAAATCCACTCTAACCGAACTACTA 59.339 38.462 0.00 0.00 0.00 1.82
68 69 5.479375 TCAAATCCACTCTAACCGAACTACT 59.521 40.000 0.00 0.00 0.00 2.57
69 70 5.717119 TCAAATCCACTCTAACCGAACTAC 58.283 41.667 0.00 0.00 0.00 2.73
70 71 5.988310 TCAAATCCACTCTAACCGAACTA 57.012 39.130 0.00 0.00 0.00 2.24
71 72 4.884668 TCAAATCCACTCTAACCGAACT 57.115 40.909 0.00 0.00 0.00 3.01
72 73 5.934935 TTTCAAATCCACTCTAACCGAAC 57.065 39.130 0.00 0.00 0.00 3.95
73 74 5.048991 GCTTTTCAAATCCACTCTAACCGAA 60.049 40.000 0.00 0.00 0.00 4.30
117 119 7.908453 AGTGGAGTTGACTTAGCTAAATTAGT 58.092 34.615 7.74 1.23 0.00 2.24
149 151 5.990668 ACTACTTGTCTCATTGGGAATACC 58.009 41.667 0.00 0.00 40.81 2.73
150 152 7.923414 AAACTACTTGTCTCATTGGGAATAC 57.077 36.000 0.00 0.00 0.00 1.89
192 212 8.986477 AATGATTTTTAGAACCATGTAAGTGC 57.014 30.769 0.00 0.00 0.00 4.40
200 220 7.038799 AGCACCAGAAATGATTTTTAGAACCAT 60.039 33.333 0.00 0.00 0.00 3.55
220 240 5.178623 CGTTAGACAAATAACTCAAGCACCA 59.821 40.000 0.00 0.00 34.19 4.17
221 241 5.178809 ACGTTAGACAAATAACTCAAGCACC 59.821 40.000 0.00 0.00 34.19 5.01
223 243 6.073440 GGAACGTTAGACAAATAACTCAAGCA 60.073 38.462 0.00 0.00 34.19 3.91
244 271 6.947903 TTTTCTTGTTAAACAAACCGGAAC 57.052 33.333 9.46 0.00 37.69 3.62
292 319 5.818136 TTTTTGCAGATGGAGTACATAGC 57.182 39.130 5.49 5.49 40.72 2.97
314 341 6.543831 GGTAGAATCACCTAAAGTGCATTCAT 59.456 38.462 14.54 0.00 46.81 2.57
326 353 5.097742 CCACACAATGGTAGAATCACCTA 57.902 43.478 4.12 0.00 44.46 3.08
344 371 8.428063 ACTTTATGATTTTTGATTTGGTCCACA 58.572 29.630 0.00 0.00 0.00 4.17
377 404 9.056005 GTTTTCCTTCCAAAAGAATTAGCATTT 57.944 29.630 0.00 0.00 34.14 2.32
649 685 9.914131 CGTTGGATATTCTCTTCAATACATCTA 57.086 33.333 0.00 0.00 0.00 1.98
650 686 7.875041 CCGTTGGATATTCTCTTCAATACATCT 59.125 37.037 0.00 0.00 0.00 2.90
657 693 3.054728 TGGCCGTTGGATATTCTCTTCAA 60.055 43.478 0.00 0.00 0.00 2.69
681 717 3.362706 AGCCAGACAAATCCGAGTAGTA 58.637 45.455 0.00 0.00 0.00 1.82
769 870 8.911662 GCCATAAATAAAACAACTAACACACAG 58.088 33.333 0.00 0.00 0.00 3.66
771 872 8.804688 TGCCATAAATAAAACAACTAACACAC 57.195 30.769 0.00 0.00 0.00 3.82
786 887 7.413988 CGACACACAAGAGAATTGCCATAAATA 60.414 37.037 0.00 0.00 0.00 1.40
799 900 1.338107 ACCATCCGACACACAAGAGA 58.662 50.000 0.00 0.00 0.00 3.10
801 902 2.631160 AAACCATCCGACACACAAGA 57.369 45.000 0.00 0.00 0.00 3.02
852 961 6.347888 CGTTTCCACTACGTATTTGTCCAATT 60.348 38.462 0.00 0.00 34.47 2.32
890 1000 3.244033 TGTTTCCTGCTTGGTTTGTTG 57.756 42.857 0.00 0.00 37.07 3.33
910 1027 9.606631 TGATTTTTAAAACCACATAAGTGCTTT 57.393 25.926 0.00 0.00 44.53 3.51
985 1107 4.074970 CCTGCCATTTATAGCCCTGTAAG 58.925 47.826 0.00 0.00 0.00 2.34
1034 1156 2.611971 CGAAATCCTCGTGGTTCCTCAA 60.612 50.000 2.99 0.00 42.89 3.02
1073 1198 4.404073 AGATAGACCTTTCTCGTGCAAGAT 59.596 41.667 1.88 0.00 32.75 2.40
1102 1227 3.144193 CTCTCCCTCGAAGCGCCT 61.144 66.667 2.29 0.00 0.00 5.52
1323 1448 2.158943 CCTAAGGGGTTCTAAAGAGCGG 60.159 54.545 0.00 0.00 0.00 5.52
1531 1660 2.024414 AGCAGAAACACAAACCAGGAC 58.976 47.619 0.00 0.00 0.00 3.85
1605 1811 6.670695 GGGGGAATGCATTGAAATACTAAT 57.329 37.500 18.59 0.00 0.00 1.73
1713 2234 1.748122 CACCTGTGCCATCAGCTCC 60.748 63.158 0.00 0.00 44.23 4.70
1846 2367 5.008613 GCCACAACTCATTTTCAGTGACTTA 59.991 40.000 0.00 0.00 0.00 2.24
1861 2382 3.939066 ACATACAGGTTAGCCACAACTC 58.061 45.455 0.00 0.00 37.19 3.01
1915 2440 1.987855 CAGGAGGTGGCCCGTAAGA 60.988 63.158 0.00 0.00 43.02 2.10
2056 4185 0.940126 GATGAGCGCCGATTGACAAT 59.060 50.000 2.29 0.00 0.00 2.71
2070 4199 2.408704 GGAACTTTGTCACGACGATGAG 59.591 50.000 0.00 0.00 0.00 2.90
2118 4247 1.896220 TCTGAACAAGGCACCATCAC 58.104 50.000 0.00 0.00 0.00 3.06
2119 4248 2.106338 TCTTCTGAACAAGGCACCATCA 59.894 45.455 0.00 0.00 0.00 3.07
2120 4249 2.485814 GTCTTCTGAACAAGGCACCATC 59.514 50.000 0.00 0.00 0.00 3.51
2121 4250 2.107204 AGTCTTCTGAACAAGGCACCAT 59.893 45.455 0.00 0.00 29.68 3.55
2122 4251 1.490490 AGTCTTCTGAACAAGGCACCA 59.510 47.619 0.00 0.00 29.68 4.17
2123 4252 1.876156 CAGTCTTCTGAACAAGGCACC 59.124 52.381 0.00 0.00 43.76 5.01
2124 4253 2.565841 ACAGTCTTCTGAACAAGGCAC 58.434 47.619 2.17 0.00 43.76 5.01
2125 4254 4.127171 GTTACAGTCTTCTGAACAAGGCA 58.873 43.478 2.17 0.00 43.76 4.75
2126 4255 3.498777 GGTTACAGTCTTCTGAACAAGGC 59.501 47.826 2.17 0.00 43.76 4.35
2127 4256 4.703897 TGGTTACAGTCTTCTGAACAAGG 58.296 43.478 2.17 0.00 43.76 3.61
2128 4257 5.991606 TCATGGTTACAGTCTTCTGAACAAG 59.008 40.000 2.17 0.00 43.76 3.16
2129 4258 5.924356 TCATGGTTACAGTCTTCTGAACAA 58.076 37.500 2.17 0.00 43.76 2.83
2130 4259 5.545063 TCATGGTTACAGTCTTCTGAACA 57.455 39.130 2.17 0.00 43.76 3.18
2131 4260 6.621596 GCATTCATGGTTACAGTCTTCTGAAC 60.622 42.308 2.17 3.12 43.76 3.18
2132 4261 5.412594 GCATTCATGGTTACAGTCTTCTGAA 59.587 40.000 2.17 0.00 43.76 3.02
2133 4262 4.937620 GCATTCATGGTTACAGTCTTCTGA 59.062 41.667 2.17 0.00 43.76 3.27
2134 4263 4.940046 AGCATTCATGGTTACAGTCTTCTG 59.060 41.667 0.00 0.00 40.33 3.02
2135 4264 5.171339 AGCATTCATGGTTACAGTCTTCT 57.829 39.130 0.00 0.00 34.35 2.85
2136 4265 5.182001 ACAAGCATTCATGGTTACAGTCTTC 59.818 40.000 3.97 0.00 45.69 2.87
2137 4266 5.072741 ACAAGCATTCATGGTTACAGTCTT 58.927 37.500 3.97 0.00 45.69 3.01
2138 4267 4.655963 ACAAGCATTCATGGTTACAGTCT 58.344 39.130 3.97 0.00 45.69 3.24
2139 4268 5.643777 AGTACAAGCATTCATGGTTACAGTC 59.356 40.000 3.97 0.00 45.69 3.51
2140 4269 5.412594 CAGTACAAGCATTCATGGTTACAGT 59.587 40.000 3.97 2.05 45.69 3.55
2141 4270 5.643348 TCAGTACAAGCATTCATGGTTACAG 59.357 40.000 3.97 0.00 45.69 2.74
2142 4271 5.555966 TCAGTACAAGCATTCATGGTTACA 58.444 37.500 3.97 0.00 45.69 2.41
2143 4272 6.238484 GGATCAGTACAAGCATTCATGGTTAC 60.238 42.308 3.97 1.05 45.69 2.50
2144 4273 5.822519 GGATCAGTACAAGCATTCATGGTTA 59.177 40.000 3.97 0.00 45.69 2.85
2146 4275 4.080129 AGGATCAGTACAAGCATTCATGGT 60.080 41.667 0.00 0.00 40.78 3.55
2147 4276 4.458397 AGGATCAGTACAAGCATTCATGG 58.542 43.478 0.00 0.00 0.00 3.66
2148 4277 5.356190 ACAAGGATCAGTACAAGCATTCATG 59.644 40.000 0.00 0.00 0.00 3.07
2149 4278 5.356190 CACAAGGATCAGTACAAGCATTCAT 59.644 40.000 0.00 0.00 0.00 2.57
2150 4279 4.696877 CACAAGGATCAGTACAAGCATTCA 59.303 41.667 0.00 0.00 0.00 2.57
2151 4280 4.095483 CCACAAGGATCAGTACAAGCATTC 59.905 45.833 0.00 0.00 36.89 2.67
2152 4281 4.012374 CCACAAGGATCAGTACAAGCATT 58.988 43.478 0.00 0.00 36.89 3.56
2153 4282 3.009473 ACCACAAGGATCAGTACAAGCAT 59.991 43.478 0.00 0.00 38.69 3.79
2154 4283 2.371841 ACCACAAGGATCAGTACAAGCA 59.628 45.455 0.00 0.00 38.69 3.91
2155 4284 2.744202 CACCACAAGGATCAGTACAAGC 59.256 50.000 0.00 0.00 38.69 4.01
2156 4285 2.744202 GCACCACAAGGATCAGTACAAG 59.256 50.000 0.00 0.00 38.69 3.16
2157 4286 2.371841 AGCACCACAAGGATCAGTACAA 59.628 45.455 0.00 0.00 38.69 2.41
2158 4287 1.977854 AGCACCACAAGGATCAGTACA 59.022 47.619 0.00 0.00 38.69 2.90
2159 4288 2.350522 CAGCACCACAAGGATCAGTAC 58.649 52.381 0.00 0.00 38.69 2.73
2160 4289 1.278985 CCAGCACCACAAGGATCAGTA 59.721 52.381 0.00 0.00 38.69 2.74
2161 4290 0.037303 CCAGCACCACAAGGATCAGT 59.963 55.000 0.00 0.00 38.69 3.41
2162 4291 0.037303 ACCAGCACCACAAGGATCAG 59.963 55.000 0.00 0.00 38.69 2.90
2163 4292 0.250858 CACCAGCACCACAAGGATCA 60.251 55.000 0.00 0.00 38.69 2.92
2164 4293 1.589716 GCACCAGCACCACAAGGATC 61.590 60.000 0.00 0.00 41.58 3.36
2165 4294 1.604593 GCACCAGCACCACAAGGAT 60.605 57.895 0.00 0.00 41.58 3.24
2166 4295 2.203337 GCACCAGCACCACAAGGA 60.203 61.111 0.00 0.00 41.58 3.36
2167 4296 3.297620 GGCACCAGCACCACAAGG 61.298 66.667 0.00 0.00 44.61 3.61
2168 4297 1.829533 AAGGCACCAGCACCACAAG 60.830 57.895 0.00 0.00 44.61 3.16
2169 4298 2.126596 CAAGGCACCAGCACCACAA 61.127 57.895 0.00 0.00 44.61 3.33
2170 4299 2.519063 CAAGGCACCAGCACCACA 60.519 61.111 0.00 0.00 44.61 4.17
2171 4300 2.075426 GAACAAGGCACCAGCACCAC 62.075 60.000 0.00 0.00 44.61 4.16
2172 4301 1.827789 GAACAAGGCACCAGCACCA 60.828 57.895 0.00 0.00 44.61 4.17
2192 4321 2.093341 GGCATCCATGGTTGCAATCTTT 60.093 45.455 36.62 0.00 41.20 2.52
2200 4329 2.417257 CCACGGGCATCCATGGTTG 61.417 63.158 17.14 17.14 29.77 3.77
2257 4496 4.273318 AGCAACAGTATCAAAAGGATCCC 58.727 43.478 8.55 0.00 37.44 3.85
2261 4500 8.635765 AAAGATTAGCAACAGTATCAAAAGGA 57.364 30.769 0.00 0.00 0.00 3.36
2295 4555 4.210955 CACTTTTGGCACGCAATAATGTTT 59.789 37.500 0.00 0.00 0.00 2.83
2396 4660 1.609072 CGAGGCGAGATAGGTGAATGA 59.391 52.381 0.00 0.00 0.00 2.57
2405 4669 4.753107 AGAAAACAAAAACGAGGCGAGATA 59.247 37.500 0.00 0.00 0.00 1.98
2457 4722 1.602377 GAAAACTTGTGCTGCGTACCT 59.398 47.619 0.00 0.00 0.00 3.08
2463 4728 2.584492 ACCAAGAAAACTTGTGCTGC 57.416 45.000 0.00 0.00 32.80 5.25
2483 4748 1.063070 TGTTTAGGGGCCACCACTCA 61.063 55.000 0.00 0.00 43.89 3.41
2487 4752 0.178975 CACTTGTTTAGGGGCCACCA 60.179 55.000 0.00 0.00 43.89 4.17
2545 4815 1.487976 TCTGAGGCATCCAGAACATCC 59.512 52.381 0.00 0.00 37.68 3.51
2583 4853 6.512091 GCATCGAGAGTAACAGACCTAACTAG 60.512 46.154 0.00 0.00 0.00 2.57
2593 4863 2.791560 CGGATTGCATCGAGAGTAACAG 59.208 50.000 0.00 0.00 0.00 3.16
2604 4874 2.874701 ACTTGCACTATCGGATTGCATC 59.125 45.455 15.83 0.29 45.35 3.91
2836 5303 7.957002 TCTGCAAATTAAAAATCCCAGTGTTA 58.043 30.769 0.00 0.00 0.00 2.41
2843 5310 7.069950 AGGTATCCTCTGCAAATTAAAAATCCC 59.930 37.037 0.00 0.00 0.00 3.85
2852 5320 7.486407 AATGAAAAGGTATCCTCTGCAAATT 57.514 32.000 0.00 0.00 30.89 1.82
2857 5326 9.875691 AAATTTTAATGAAAAGGTATCCTCTGC 57.124 29.630 0.00 0.00 37.94 4.26
2936 5405 8.224389 AGTGAGCAATACAATATGCAACATAA 57.776 30.769 0.00 0.00 44.95 1.90
2943 5414 5.049818 GTCTGGAGTGAGCAATACAATATGC 60.050 44.000 0.00 0.00 42.87 3.14
2998 5501 1.890979 ACCAGATGCGCTGCTATGC 60.891 57.895 9.73 0.00 43.50 3.14


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

AutoCloner maintained by Alex Coulton.