Multiple sequence alignment - TraesCS4B01G272200

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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 TraesCS4B01G272200 chr4B 100.000 1866 0 0 744 2609 548863916 548862051 0.000000e+00 3446.0
1 TraesCS4B01G272200 chr4B 100.000 447 0 0 1 447 548864659 548864213 0.000000e+00 826.0
2 TraesCS4B01G272200 chr4B 97.810 137 3 0 1 137 489794683 489794547 1.210000e-58 237.0
3 TraesCS4B01G272200 chr4B 90.323 62 6 0 1439 1500 164308807 164308868 5.980000e-12 82.4
4 TraesCS4B01G272200 chr7B 95.766 1866 71 4 744 2609 616911548 616913405 0.000000e+00 3001.0
5 TraesCS4B01G272200 chr7B 98.519 135 2 0 1 135 13365052 13364918 3.360000e-59 239.0
6 TraesCS4B01G272200 chr7B 94.444 108 6 0 135 242 616911066 616911173 1.610000e-37 167.0
7 TraesCS4B01G272200 chr7B 90.476 63 6 0 382 444 114038852 114038914 1.660000e-12 84.2
8 TraesCS4B01G272200 chr3B 95.552 1866 82 1 744 2609 280583897 280585761 0.000000e+00 2985.0
9 TraesCS4B01G272200 chr3B 91.605 679 56 1 1932 2609 210822519 210823197 0.000000e+00 937.0
10 TraesCS4B01G272200 chr3B 93.016 315 20 2 134 447 280583544 280583857 2.370000e-125 459.0
11 TraesCS4B01G272200 chr3B 99.248 133 1 0 1 133 592908760 592908892 9.330000e-60 241.0
12 TraesCS4B01G272200 chr3B 89.062 64 6 1 382 444 12563624 12563687 7.740000e-11 78.7
13 TraesCS4B01G272200 chr3B 86.885 61 6 2 147 205 734348364 734348424 1.680000e-07 67.6
14 TraesCS4B01G272200 chr6A 94.255 1114 61 3 1499 2609 4929296 4928183 0.000000e+00 1700.0
15 TraesCS4B01G272200 chr6A 91.667 96 8 0 134 229 4937272 4937177 1.630000e-27 134.0
16 TraesCS4B01G272200 chr6A 95.455 66 3 0 382 447 4936587 4936522 3.550000e-19 106.0
17 TraesCS4B01G272200 chr6A 90.625 64 5 1 382 444 22499509 22499572 1.660000e-12 84.2
18 TraesCS4B01G272200 chr6A 81.707 82 11 4 1027 1108 495465163 495465086 6.030000e-07 65.8
19 TraesCS4B01G272200 chr6B 94.837 1046 48 6 1566 2609 464408889 464409930 0.000000e+00 1628.0
20 TraesCS4B01G272200 chr6B 89.403 821 61 12 744 1541 464408079 464408896 0.000000e+00 1011.0
21 TraesCS4B01G272200 chr6B 92.353 170 9 2 134 303 464407513 464407678 3.360000e-59 239.0
22 TraesCS4B01G272200 chr6B 95.862 145 4 2 1 144 405136536 405136393 1.560000e-57 233.0
23 TraesCS4B01G272200 chr6B 81.928 83 11 4 1027 1109 532151725 532151647 1.680000e-07 67.6
24 TraesCS4B01G272200 chr4D 88.879 1115 78 16 1499 2609 251093432 251092360 0.000000e+00 1330.0
25 TraesCS4B01G272200 chr4D 90.419 835 56 5 1499 2330 493213039 493213852 0.000000e+00 1077.0
26 TraesCS4B01G272200 chr4D 92.857 56 4 0 1445 1500 251093524 251093469 5.980000e-12 82.4
27 TraesCS4B01G272200 chr4D 90.323 62 6 0 1439 1500 493212941 493213002 5.980000e-12 82.4
28 TraesCS4B01G272200 chr3D 90.024 832 58 7 1499 2328 77840388 77841196 0.000000e+00 1053.0
29 TraesCS4B01G272200 chr3D 90.323 62 6 0 1439 1500 77840290 77840351 5.980000e-12 82.4
30 TraesCS4B01G272200 chr2B 93.604 641 37 3 1972 2609 733356279 733355640 0.000000e+00 953.0
31 TraesCS4B01G272200 chr2B 87.132 645 59 8 783 1405 653745943 653746585 0.000000e+00 710.0
32 TraesCS4B01G272200 chr2B 99.248 133 1 0 1 133 382755111 382755243 9.330000e-60 241.0
33 TraesCS4B01G272200 chr2B 99.248 133 1 0 1 133 790928919 790929051 9.330000e-60 241.0
34 TraesCS4B01G272200 chr2B 99.248 133 1 0 1 133 790940531 790940663 9.330000e-60 241.0
35 TraesCS4B01G272200 chr2B 88.525 61 5 2 147 205 26689989 26690049 3.600000e-09 73.1
36 TraesCS4B01G272200 chr7D 89.528 678 48 6 1499 2174 139228932 139228276 0.000000e+00 837.0
37 TraesCS4B01G272200 chr7D 93.284 536 32 3 2077 2609 158645175 158644641 0.000000e+00 787.0
38 TraesCS4B01G272200 chr7D 88.060 67 7 1 382 447 139229147 139229081 7.740000e-11 78.7
39 TraesCS4B01G272200 chr5B 88.757 676 54 5 1499 2173 7211244 7210590 0.000000e+00 808.0
40 TraesCS4B01G272200 chr5B 92.857 56 4 0 1445 1500 7211336 7211281 5.980000e-12 82.4
41 TraesCS4B01G272200 chr5B 92.857 56 4 0 1445 1500 484772366 484772311 5.980000e-12 82.4
42 TraesCS4B01G272200 chr1B 93.284 536 32 3 2077 2609 671832764 671833298 0.000000e+00 787.0
43 TraesCS4B01G272200 chr1B 99.248 133 1 0 1 133 36936684 36936816 9.330000e-60 241.0
44 TraesCS4B01G272200 chr1B 99.248 133 1 0 1 133 84235464 84235596 9.330000e-60 241.0
45 TraesCS4B01G272200 chr2A 93.071 534 35 2 2077 2609 731836847 731837379 0.000000e+00 780.0
46 TraesCS4B01G272200 chr2A 87.246 690 55 10 744 1405 690738086 690738770 0.000000e+00 756.0
47 TraesCS4B01G272200 chr2A 90.625 128 9 3 134 259 350240759 350240633 1.610000e-37 167.0
48 TraesCS4B01G272200 chr2A 92.188 64 4 1 382 444 55948380 55948317 3.580000e-14 89.8
49 TraesCS4B01G272200 chr3A 94.655 449 22 1 1950 2396 612613265 612612817 0.000000e+00 695.0
50 TraesCS4B01G272200 chr3A 88.060 67 7 1 382 447 669145200 669145134 7.740000e-11 78.7
51 TraesCS4B01G272200 chr3A 95.455 44 2 0 134 177 631787353 631787396 1.300000e-08 71.3
52 TraesCS4B01G272200 chr3A 97.368 38 1 0 349 386 133544557 133544520 6.030000e-07 65.8
53 TraesCS4B01G272200 chr5A 87.652 494 39 5 1499 1991 431482640 431482168 2.930000e-154 555.0
54 TraesCS4B01G272200 chr5A 100.000 31 0 0 183 213 665119280 665119310 1.010000e-04 58.4
55 TraesCS4B01G272200 chr2D 86.184 456 37 14 971 1402 547250415 547250868 1.090000e-128 470.0
56 TraesCS4B01G272200 chr2D 86.614 254 28 3 744 997 547250146 547250393 2.560000e-70 276.0
57 TraesCS4B01G272200 chr2D 91.045 67 5 1 382 447 55158764 55158698 3.580000e-14 89.8
58 TraesCS4B01G272200 chr1D 95.455 44 2 0 134 177 369483830 369483787 1.300000e-08 71.3
59 TraesCS4B01G272200 chr7A 95.238 42 2 0 345 386 242470315 242470274 1.680000e-07 67.6
60 TraesCS4B01G272200 chr6D 81.707 82 11 4 1027 1108 348029477 348029554 6.030000e-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 TraesCS4B01G272200 chr4B 548862051 548864659 2608 True 2136.000000 3446 100.000000 1 2609 2 chr4B.!!$R2 2608
1 TraesCS4B01G272200 chr7B 616911066 616913405 2339 False 1584.000000 3001 95.105000 135 2609 2 chr7B.!!$F2 2474
2 TraesCS4B01G272200 chr3B 280583544 280585761 2217 False 1722.000000 2985 94.284000 134 2609 2 chr3B.!!$F5 2475
3 TraesCS4B01G272200 chr3B 210822519 210823197 678 False 937.000000 937 91.605000 1932 2609 1 chr3B.!!$F2 677
4 TraesCS4B01G272200 chr6A 4928183 4929296 1113 True 1700.000000 1700 94.255000 1499 2609 1 chr6A.!!$R1 1110
5 TraesCS4B01G272200 chr6B 464407513 464409930 2417 False 959.333333 1628 92.197667 134 2609 3 chr6B.!!$F1 2475
6 TraesCS4B01G272200 chr4D 251092360 251093524 1164 True 706.200000 1330 90.868000 1445 2609 2 chr4D.!!$R1 1164
7 TraesCS4B01G272200 chr4D 493212941 493213852 911 False 579.700000 1077 90.371000 1439 2330 2 chr4D.!!$F1 891
8 TraesCS4B01G272200 chr3D 77840290 77841196 906 False 567.700000 1053 90.173500 1439 2328 2 chr3D.!!$F1 889
9 TraesCS4B01G272200 chr2B 733355640 733356279 639 True 953.000000 953 93.604000 1972 2609 1 chr2B.!!$R1 637
10 TraesCS4B01G272200 chr2B 653745943 653746585 642 False 710.000000 710 87.132000 783 1405 1 chr2B.!!$F3 622
11 TraesCS4B01G272200 chr7D 158644641 158645175 534 True 787.000000 787 93.284000 2077 2609 1 chr7D.!!$R1 532
12 TraesCS4B01G272200 chr7D 139228276 139229147 871 True 457.850000 837 88.794000 382 2174 2 chr7D.!!$R2 1792
13 TraesCS4B01G272200 chr5B 7210590 7211336 746 True 445.200000 808 90.807000 1445 2173 2 chr5B.!!$R2 728
14 TraesCS4B01G272200 chr1B 671832764 671833298 534 False 787.000000 787 93.284000 2077 2609 1 chr1B.!!$F3 532
15 TraesCS4B01G272200 chr2A 731836847 731837379 532 False 780.000000 780 93.071000 2077 2609 1 chr2A.!!$F2 532
16 TraesCS4B01G272200 chr2A 690738086 690738770 684 False 756.000000 756 87.246000 744 1405 1 chr2A.!!$F1 661
17 TraesCS4B01G272200 chr2D 547250146 547250868 722 False 373.000000 470 86.399000 744 1402 2 chr2D.!!$F1 658

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
257 258 0.323816 TCCTCCATCTCGCTCACACT 60.324 55.0 0.0 0.0 0.0 3.55 F
330 331 0.613777 CTGTCACCCCCACCTTCTAC 59.386 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1359 0.936764 ATCGATCGACATGTCTGCGC 60.937 55.0 22.06 0.0 0.0 6.09 R
1733 1846 1.753930 CATCCATGCACTGTAGGCAA 58.246 50.0 0.00 0.0 45.6 4.52 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
30 31 9.499479 AATATATTTGATGCTACTGGTTCTCTG 57.501 33.333 0.00 0.00 0.00 3.35
31 32 4.623932 TTTGATGCTACTGGTTCTCTGT 57.376 40.909 0.00 0.00 0.00 3.41
32 33 4.623932 TTGATGCTACTGGTTCTCTGTT 57.376 40.909 0.00 0.00 0.00 3.16
33 34 4.623932 TGATGCTACTGGTTCTCTGTTT 57.376 40.909 0.00 0.00 0.00 2.83
34 35 5.738619 TGATGCTACTGGTTCTCTGTTTA 57.261 39.130 0.00 0.00 0.00 2.01
35 36 6.299805 TGATGCTACTGGTTCTCTGTTTAT 57.700 37.500 0.00 0.00 0.00 1.40
36 37 6.341316 TGATGCTACTGGTTCTCTGTTTATC 58.659 40.000 0.00 0.00 0.00 1.75
37 38 5.738619 TGCTACTGGTTCTCTGTTTATCA 57.261 39.130 0.00 0.00 0.00 2.15
38 39 6.109156 TGCTACTGGTTCTCTGTTTATCAA 57.891 37.500 0.00 0.00 0.00 2.57
39 40 6.166279 TGCTACTGGTTCTCTGTTTATCAAG 58.834 40.000 0.00 0.00 0.00 3.02
40 41 5.064071 GCTACTGGTTCTCTGTTTATCAAGC 59.936 44.000 0.00 0.00 0.00 4.01
41 42 5.234466 ACTGGTTCTCTGTTTATCAAGCT 57.766 39.130 0.00 0.00 0.00 3.74
42 43 5.625150 ACTGGTTCTCTGTTTATCAAGCTT 58.375 37.500 0.00 0.00 0.00 3.74
43 44 6.064717 ACTGGTTCTCTGTTTATCAAGCTTT 58.935 36.000 0.00 0.00 0.00 3.51
44 45 6.547510 ACTGGTTCTCTGTTTATCAAGCTTTT 59.452 34.615 0.00 0.00 0.00 2.27
45 46 6.738114 TGGTTCTCTGTTTATCAAGCTTTTG 58.262 36.000 0.00 0.00 0.00 2.44
46 47 6.321181 TGGTTCTCTGTTTATCAAGCTTTTGT 59.679 34.615 0.00 0.00 0.00 2.83
47 48 6.858478 GGTTCTCTGTTTATCAAGCTTTTGTC 59.142 38.462 0.00 0.00 0.00 3.18
48 49 7.255277 GGTTCTCTGTTTATCAAGCTTTTGTCT 60.255 37.037 0.00 0.00 0.00 3.41
49 50 8.774586 GTTCTCTGTTTATCAAGCTTTTGTCTA 58.225 33.333 0.00 0.00 0.00 2.59
50 51 8.311650 TCTCTGTTTATCAAGCTTTTGTCTAC 57.688 34.615 0.00 0.00 0.00 2.59
51 52 7.387948 TCTCTGTTTATCAAGCTTTTGTCTACC 59.612 37.037 0.00 0.00 0.00 3.18
52 53 6.995686 TCTGTTTATCAAGCTTTTGTCTACCA 59.004 34.615 0.00 0.00 0.00 3.25
53 54 7.173218 TCTGTTTATCAAGCTTTTGTCTACCAG 59.827 37.037 0.00 0.00 0.00 4.00
54 55 6.995686 TGTTTATCAAGCTTTTGTCTACCAGA 59.004 34.615 0.00 0.00 0.00 3.86
55 56 7.500892 TGTTTATCAAGCTTTTGTCTACCAGAA 59.499 33.333 0.00 0.00 0.00 3.02
56 57 8.349983 GTTTATCAAGCTTTTGTCTACCAGAAA 58.650 33.333 0.00 0.00 0.00 2.52
57 58 6.566197 ATCAAGCTTTTGTCTACCAGAAAG 57.434 37.500 0.00 0.00 33.41 2.62
58 59 4.821805 TCAAGCTTTTGTCTACCAGAAAGG 59.178 41.667 0.00 0.00 45.67 3.11
59 60 4.706842 AGCTTTTGTCTACCAGAAAGGA 57.293 40.909 0.00 0.00 41.22 3.36
60 61 5.248380 AGCTTTTGTCTACCAGAAAGGAT 57.752 39.130 0.00 0.00 41.22 3.24
61 62 5.006386 AGCTTTTGTCTACCAGAAAGGATG 58.994 41.667 0.00 0.00 41.22 3.51
62 63 5.003804 GCTTTTGTCTACCAGAAAGGATGA 58.996 41.667 0.00 0.00 41.22 2.92
63 64 5.106515 GCTTTTGTCTACCAGAAAGGATGAC 60.107 44.000 0.00 0.00 41.22 3.06
64 65 5.825593 TTTGTCTACCAGAAAGGATGACT 57.174 39.130 0.00 0.00 40.78 3.41
65 66 5.825593 TTGTCTACCAGAAAGGATGACTT 57.174 39.130 0.00 0.00 42.52 3.01
78 79 5.896073 AGGATGACTTTTCCTATACTGGG 57.104 43.478 0.00 0.00 41.89 4.45
79 80 5.538877 AGGATGACTTTTCCTATACTGGGA 58.461 41.667 0.00 0.00 41.89 4.37
80 81 6.153924 AGGATGACTTTTCCTATACTGGGAT 58.846 40.000 0.00 0.00 41.89 3.85
81 82 6.621514 AGGATGACTTTTCCTATACTGGGATT 59.378 38.462 0.00 0.00 41.89 3.01
82 83 7.129504 AGGATGACTTTTCCTATACTGGGATTT 59.870 37.037 0.00 0.00 41.89 2.17
83 84 8.437575 GGATGACTTTTCCTATACTGGGATTTA 58.562 37.037 0.00 0.00 32.41 1.40
84 85 9.847224 GATGACTTTTCCTATACTGGGATTTAA 57.153 33.333 0.00 0.00 32.41 1.52
86 87 9.681062 TGACTTTTCCTATACTGGGATTTAAAG 57.319 33.333 0.00 0.00 35.76 1.85
87 88 9.901172 GACTTTTCCTATACTGGGATTTAAAGA 57.099 33.333 10.47 0.00 34.45 2.52
91 92 9.640952 TTTCCTATACTGGGATTTAAAGATTGG 57.359 33.333 0.00 0.00 32.41 3.16
92 93 8.344939 TCCTATACTGGGATTTAAAGATTGGT 57.655 34.615 0.00 0.00 0.00 3.67
93 94 8.787818 TCCTATACTGGGATTTAAAGATTGGTT 58.212 33.333 0.00 0.00 0.00 3.67
94 95 9.421399 CCTATACTGGGATTTAAAGATTGGTTT 57.579 33.333 0.00 0.00 0.00 3.27
97 98 7.855784 ACTGGGATTTAAAGATTGGTTTTCT 57.144 32.000 0.00 0.00 0.00 2.52
98 99 7.896811 ACTGGGATTTAAAGATTGGTTTTCTC 58.103 34.615 0.00 0.00 0.00 2.87
99 100 7.508977 ACTGGGATTTAAAGATTGGTTTTCTCA 59.491 33.333 0.00 0.00 0.00 3.27
100 101 8.256356 TGGGATTTAAAGATTGGTTTTCTCAA 57.744 30.769 0.00 0.00 0.00 3.02
101 102 8.879227 TGGGATTTAAAGATTGGTTTTCTCAAT 58.121 29.630 0.00 0.00 37.52 2.57
130 131 5.496133 TTTTATTGAAAAACCGGTCGTGA 57.504 34.783 8.04 0.00 31.51 4.35
131 132 4.471157 TTATTGAAAAACCGGTCGTGAC 57.529 40.909 8.04 0.00 0.00 3.67
132 133 1.735386 TTGAAAAACCGGTCGTGACA 58.265 45.000 8.04 2.16 0.00 3.58
144 145 4.735132 GTGACACGCCGCTGCCTA 62.735 66.667 0.00 0.00 0.00 3.93
257 258 0.323816 TCCTCCATCTCGCTCACACT 60.324 55.000 0.00 0.00 0.00 3.55
265 266 2.029518 CGCTCACACTCACAGCCA 59.970 61.111 0.00 0.00 0.00 4.75
317 318 1.448540 CACCCTGATCCGCTGTCAC 60.449 63.158 0.00 0.00 0.00 3.67
330 331 0.613777 CTGTCACCCCCACCTTCTAC 59.386 60.000 0.00 0.00 0.00 2.59
335 336 1.305887 CCCCCACCTTCTACGACCT 60.306 63.158 0.00 0.00 0.00 3.85
367 368 3.959991 GAGGCGGTGCTTCCAGACC 62.960 68.421 0.00 0.00 35.57 3.85
373 374 4.373116 TGCTTCCAGACCCGCGAC 62.373 66.667 8.23 0.00 0.00 5.19
917 922 2.941583 GGGGCCAAGACCTCCCTT 60.942 66.667 4.39 0.00 39.95 3.95
919 924 2.539081 GGGCCAAGACCTCCCTTGT 61.539 63.158 4.39 0.00 41.34 3.16
1134 1200 1.198713 CCCTTGCTTCCTCTGCTCTA 58.801 55.000 0.00 0.00 0.00 2.43
1142 1208 3.055458 GCTTCCTCTGCTCTACTTTTCCT 60.055 47.826 0.00 0.00 0.00 3.36
1238 1307 2.935122 CTTGTTGCGCCGCTGTTGTT 62.935 55.000 11.67 0.00 0.00 2.83
1260 1329 7.776107 TGTTTGTGATTCATTAGTTGGTTTCA 58.224 30.769 0.00 0.00 0.00 2.69
1265 1338 4.481930 TTCATTAGTTGGTTTCACTGCG 57.518 40.909 0.00 0.00 0.00 5.18
1286 1359 2.203070 GCCATGGGAGGCGTACAG 60.203 66.667 15.13 0.00 46.12 2.74
1320 1393 0.904649 TCGATCTGACCAAGCACCAT 59.095 50.000 0.00 0.00 0.00 3.55
1370 1443 1.475682 CTACTACACCGTCAAGTCCCC 59.524 57.143 0.00 0.00 0.00 4.81
1405 1478 1.899814 ACATCTTCTTCCAGGTACGCA 59.100 47.619 0.00 0.00 0.00 5.24
1406 1479 2.501723 ACATCTTCTTCCAGGTACGCAT 59.498 45.455 0.00 0.00 0.00 4.73
1417 1490 1.369091 GGTACGCATGCTTCCTGGTG 61.369 60.000 17.13 0.00 0.00 4.17
1435 1508 3.727258 TGGCGCCCCTGCTACATT 61.727 61.111 26.77 0.00 34.43 2.71
1514 1626 1.003118 CTGGGCACTGCAACTACCTAA 59.997 52.381 2.82 0.00 0.00 2.69
1521 1633 3.428870 CACTGCAACTACCTAAGTGAACG 59.571 47.826 0.00 0.00 40.54 3.95
1523 1635 2.224090 TGCAACTACCTAAGTGAACGCA 60.224 45.455 0.00 0.00 38.88 5.24
1570 1682 7.773489 TTGGTGTTGATTTGATTGATTCCTA 57.227 32.000 0.00 0.00 0.00 2.94
1607 1719 7.232188 TCTTCTTCTCAGGTACTCTTCTGTTA 58.768 38.462 0.00 0.00 34.60 2.41
1628 1740 1.507140 TGAACTTCCTCCACACCTGT 58.493 50.000 0.00 0.00 0.00 4.00
1733 1846 2.428890 CGTACCTGCCTGAGAAAGATCT 59.571 50.000 0.00 0.00 39.10 2.75
1815 1929 4.673441 AGCAGTAGTCTAGTTACAATGCG 58.327 43.478 8.96 0.00 36.31 4.73
1875 1990 3.258123 TGCATGCCTATGAAGCGTATCTA 59.742 43.478 16.68 0.00 36.36 1.98
2122 2237 3.610040 TTGGTCAATCACGATAGCAGT 57.390 42.857 0.00 0.00 42.67 4.40
2212 2329 8.422566 TCCTCATAAAATATTTGCATGCATGAA 58.577 29.630 30.64 18.49 0.00 2.57
2233 2351 3.837213 AAAGCTCTAACGCGTACACTA 57.163 42.857 14.46 0.00 34.40 2.74
2324 2444 2.749621 GTGTGGGGCACTCTCATTTAAG 59.250 50.000 0.00 0.00 44.41 1.85
2533 2654 3.138884 TCTGCTTGCAGGTCATTGTTA 57.861 42.857 20.62 0.00 0.00 2.41
2547 2669 2.685106 TTGTTATGAAGGCCCCACAA 57.315 45.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.499479 CAGAGAACCAGTAGCATCAAATATATT 57.501 33.333 0.00 0.00 0.00 1.28
5 6 8.654997 ACAGAGAACCAGTAGCATCAAATATAT 58.345 33.333 0.00 0.00 0.00 0.86
6 7 8.023021 ACAGAGAACCAGTAGCATCAAATATA 57.977 34.615 0.00 0.00 0.00 0.86
7 8 6.893583 ACAGAGAACCAGTAGCATCAAATAT 58.106 36.000 0.00 0.00 0.00 1.28
8 9 6.299805 ACAGAGAACCAGTAGCATCAAATA 57.700 37.500 0.00 0.00 0.00 1.40
9 10 5.171339 ACAGAGAACCAGTAGCATCAAAT 57.829 39.130 0.00 0.00 0.00 2.32
10 11 4.623932 ACAGAGAACCAGTAGCATCAAA 57.376 40.909 0.00 0.00 0.00 2.69
11 12 4.623932 AACAGAGAACCAGTAGCATCAA 57.376 40.909 0.00 0.00 0.00 2.57
12 13 4.623932 AAACAGAGAACCAGTAGCATCA 57.376 40.909 0.00 0.00 0.00 3.07
13 14 6.341316 TGATAAACAGAGAACCAGTAGCATC 58.659 40.000 0.00 0.00 0.00 3.91
14 15 6.299805 TGATAAACAGAGAACCAGTAGCAT 57.700 37.500 0.00 0.00 0.00 3.79
15 16 5.738619 TGATAAACAGAGAACCAGTAGCA 57.261 39.130 0.00 0.00 0.00 3.49
16 17 5.064071 GCTTGATAAACAGAGAACCAGTAGC 59.936 44.000 0.00 0.00 0.00 3.58
17 18 6.402222 AGCTTGATAAACAGAGAACCAGTAG 58.598 40.000 0.00 0.00 0.00 2.57
18 19 6.360370 AGCTTGATAAACAGAGAACCAGTA 57.640 37.500 0.00 0.00 0.00 2.74
19 20 5.234466 AGCTTGATAAACAGAGAACCAGT 57.766 39.130 0.00 0.00 0.00 4.00
20 21 6.566197 AAAGCTTGATAAACAGAGAACCAG 57.434 37.500 0.00 0.00 0.00 4.00
21 22 6.321181 ACAAAAGCTTGATAAACAGAGAACCA 59.679 34.615 0.00 0.00 36.33 3.67
22 23 6.739112 ACAAAAGCTTGATAAACAGAGAACC 58.261 36.000 0.00 0.00 36.33 3.62
23 24 7.643579 AGACAAAAGCTTGATAAACAGAGAAC 58.356 34.615 0.00 0.00 36.33 3.01
24 25 7.807977 AGACAAAAGCTTGATAAACAGAGAA 57.192 32.000 0.00 0.00 36.33 2.87
25 26 7.387948 GGTAGACAAAAGCTTGATAAACAGAGA 59.612 37.037 0.00 0.00 36.33 3.10
26 27 7.173218 TGGTAGACAAAAGCTTGATAAACAGAG 59.827 37.037 0.00 0.00 36.33 3.35
27 28 6.995686 TGGTAGACAAAAGCTTGATAAACAGA 59.004 34.615 0.00 0.00 36.33 3.41
28 29 7.173218 TCTGGTAGACAAAAGCTTGATAAACAG 59.827 37.037 0.00 2.69 36.33 3.16
29 30 6.995686 TCTGGTAGACAAAAGCTTGATAAACA 59.004 34.615 0.00 0.00 36.33 2.83
30 31 7.435068 TCTGGTAGACAAAAGCTTGATAAAC 57.565 36.000 0.00 0.00 36.33 2.01
31 32 8.458573 TTTCTGGTAGACAAAAGCTTGATAAA 57.541 30.769 0.00 0.00 36.33 1.40
32 33 7.174946 CCTTTCTGGTAGACAAAAGCTTGATAA 59.825 37.037 0.00 0.00 36.33 1.75
33 34 6.655003 CCTTTCTGGTAGACAAAAGCTTGATA 59.345 38.462 0.00 0.00 36.33 2.15
34 35 5.474876 CCTTTCTGGTAGACAAAAGCTTGAT 59.525 40.000 0.00 0.00 36.33 2.57
35 36 4.821805 CCTTTCTGGTAGACAAAAGCTTGA 59.178 41.667 0.00 0.00 36.33 3.02
36 37 4.821805 TCCTTTCTGGTAGACAAAAGCTTG 59.178 41.667 0.00 0.00 36.48 4.01
37 38 5.048846 TCCTTTCTGGTAGACAAAAGCTT 57.951 39.130 0.00 0.00 37.07 3.74
38 39 4.706842 TCCTTTCTGGTAGACAAAAGCT 57.293 40.909 0.00 0.00 37.07 3.74
39 40 5.003804 TCATCCTTTCTGGTAGACAAAAGC 58.996 41.667 0.00 0.00 37.07 3.51
40 41 6.234177 AGTCATCCTTTCTGGTAGACAAAAG 58.766 40.000 0.00 0.00 40.48 2.27
41 42 6.187727 AGTCATCCTTTCTGGTAGACAAAA 57.812 37.500 0.00 0.00 40.48 2.44
42 43 5.825593 AGTCATCCTTTCTGGTAGACAAA 57.174 39.130 0.00 0.00 40.48 2.83
43 44 5.825593 AAGTCATCCTTTCTGGTAGACAA 57.174 39.130 0.00 0.00 40.48 3.18
44 45 5.825593 AAAGTCATCCTTTCTGGTAGACA 57.174 39.130 0.00 0.00 39.17 3.41
45 46 5.644206 GGAAAAGTCATCCTTTCTGGTAGAC 59.356 44.000 0.00 0.00 42.62 2.59
46 47 5.548056 AGGAAAAGTCATCCTTTCTGGTAGA 59.452 40.000 0.00 0.00 45.06 2.59
47 48 5.810095 AGGAAAAGTCATCCTTTCTGGTAG 58.190 41.667 0.00 0.00 45.06 3.18
48 49 5.843019 AGGAAAAGTCATCCTTTCTGGTA 57.157 39.130 0.00 0.00 45.06 3.25
49 50 4.731313 AGGAAAAGTCATCCTTTCTGGT 57.269 40.909 0.00 0.00 45.06 4.00
50 51 7.497249 CAGTATAGGAAAAGTCATCCTTTCTGG 59.503 40.741 0.00 0.00 45.06 3.86
51 52 7.497249 CCAGTATAGGAAAAGTCATCCTTTCTG 59.503 40.741 0.00 7.20 45.06 3.02
52 53 7.366011 CCCAGTATAGGAAAAGTCATCCTTTCT 60.366 40.741 0.00 0.00 45.06 2.52
53 54 6.768381 CCCAGTATAGGAAAAGTCATCCTTTC 59.232 42.308 0.00 0.00 45.06 2.62
54 55 6.447084 TCCCAGTATAGGAAAAGTCATCCTTT 59.553 38.462 0.00 0.00 45.06 3.11
55 56 5.970640 TCCCAGTATAGGAAAAGTCATCCTT 59.029 40.000 0.00 0.00 45.06 3.36
57 58 5.888982 TCCCAGTATAGGAAAAGTCATCC 57.111 43.478 0.00 0.00 37.22 3.51
58 59 9.847224 TTAAATCCCAGTATAGGAAAAGTCATC 57.153 33.333 0.00 0.00 36.85 2.92
60 61 9.681062 CTTTAAATCCCAGTATAGGAAAAGTCA 57.319 33.333 0.00 0.00 36.85 3.41
61 62 9.901172 TCTTTAAATCCCAGTATAGGAAAAGTC 57.099 33.333 0.00 0.00 36.85 3.01
65 66 9.640952 CCAATCTTTAAATCCCAGTATAGGAAA 57.359 33.333 0.00 0.00 36.85 3.13
66 67 8.787818 ACCAATCTTTAAATCCCAGTATAGGAA 58.212 33.333 0.00 0.00 36.85 3.36
67 68 8.344939 ACCAATCTTTAAATCCCAGTATAGGA 57.655 34.615 0.00 0.00 37.93 2.94
68 69 8.996651 AACCAATCTTTAAATCCCAGTATAGG 57.003 34.615 0.00 0.00 0.00 2.57
71 72 9.547279 AGAAAACCAATCTTTAAATCCCAGTAT 57.453 29.630 0.00 0.00 0.00 2.12
72 73 8.950007 AGAAAACCAATCTTTAAATCCCAGTA 57.050 30.769 0.00 0.00 0.00 2.74
73 74 7.508977 TGAGAAAACCAATCTTTAAATCCCAGT 59.491 33.333 0.00 0.00 0.00 4.00
74 75 7.895759 TGAGAAAACCAATCTTTAAATCCCAG 58.104 34.615 0.00 0.00 0.00 4.45
75 76 7.847711 TGAGAAAACCAATCTTTAAATCCCA 57.152 32.000 0.00 0.00 0.00 4.37
107 108 5.742926 GTCACGACCGGTTTTTCAATAAAAA 59.257 36.000 9.42 0.00 41.21 1.94
108 109 5.163683 TGTCACGACCGGTTTTTCAATAAAA 60.164 36.000 9.42 0.00 32.75 1.52
109 110 4.334759 TGTCACGACCGGTTTTTCAATAAA 59.665 37.500 9.42 0.00 0.00 1.40
110 111 3.875727 TGTCACGACCGGTTTTTCAATAA 59.124 39.130 9.42 0.00 0.00 1.40
111 112 3.248125 GTGTCACGACCGGTTTTTCAATA 59.752 43.478 9.42 0.00 0.00 1.90
112 113 2.032426 GTGTCACGACCGGTTTTTCAAT 59.968 45.455 9.42 0.00 0.00 2.57
113 114 1.397692 GTGTCACGACCGGTTTTTCAA 59.602 47.619 9.42 0.00 0.00 2.69
114 115 1.008329 GTGTCACGACCGGTTTTTCA 58.992 50.000 9.42 2.23 0.00 2.69
115 116 0.042794 CGTGTCACGACCGGTTTTTC 60.043 55.000 20.75 0.00 46.05 2.29
116 117 2.008328 CGTGTCACGACCGGTTTTT 58.992 52.632 20.75 0.00 46.05 1.94
117 118 2.527867 GCGTGTCACGACCGGTTTT 61.528 57.895 28.83 0.00 46.05 2.43
118 119 2.963320 GCGTGTCACGACCGGTTT 60.963 61.111 28.83 0.00 46.05 3.27
119 120 4.955774 GGCGTGTCACGACCGGTT 62.956 66.667 28.83 0.00 45.60 4.44
127 128 4.735132 TAGGCAGCGGCGTGTCAC 62.735 66.667 14.37 0.00 42.47 3.67
128 129 3.716539 GATAGGCAGCGGCGTGTCA 62.717 63.158 19.81 0.00 43.05 3.58
129 130 2.962253 GATAGGCAGCGGCGTGTC 60.962 66.667 14.37 13.02 42.47 3.67
130 131 3.432051 GAGATAGGCAGCGGCGTGT 62.432 63.158 14.37 7.44 42.47 4.49
131 132 2.659897 GAGATAGGCAGCGGCGTG 60.660 66.667 14.37 6.94 42.47 5.34
132 133 2.835431 AGAGATAGGCAGCGGCGT 60.835 61.111 9.37 9.38 42.47 5.68
139 140 0.691078 GTGGGTGGGAGAGATAGGCA 60.691 60.000 0.00 0.00 0.00 4.75
144 145 2.042930 GGGGTGGGTGGGAGAGAT 59.957 66.667 0.00 0.00 0.00 2.75
244 245 0.108898 GCTGTGAGTGTGAGCGAGAT 60.109 55.000 0.00 0.00 0.00 2.75
317 318 0.032813 TAGGTCGTAGAAGGTGGGGG 60.033 60.000 0.00 0.00 39.69 5.40
325 326 3.189618 TGCTCGATCTAGGTCGTAGAA 57.810 47.619 23.99 12.42 41.31 2.10
330 331 0.658829 CGCTTGCTCGATCTAGGTCG 60.659 60.000 19.53 19.53 42.74 4.79
335 336 1.360551 GCCTCGCTTGCTCGATCTA 59.639 57.895 0.00 0.00 37.87 1.98
768 770 5.534563 GTGAATCACAATCCGGGACGAGA 62.535 52.174 8.74 0.00 44.86 4.04
812 817 2.281345 GCCATCCCGGAGCTCATG 60.281 66.667 17.19 10.29 36.56 3.07
907 912 3.382832 CGCCGACAAGGGAGGTCT 61.383 66.667 0.00 0.00 41.48 3.85
969 974 1.987855 CCTCCGCCTTGACCACCTA 60.988 63.158 0.00 0.00 0.00 3.08
1134 1200 1.944709 CGGAACCGAAACAGGAAAAGT 59.055 47.619 7.53 0.00 42.83 2.66
1142 1208 2.662527 GGCGACGGAACCGAAACA 60.663 61.111 20.14 0.00 42.83 2.83
1238 1307 7.424803 CAGTGAAACCAACTAATGAATCACAA 58.575 34.615 0.00 0.00 37.76 3.33
1286 1359 0.936764 ATCGATCGACATGTCTGCGC 60.937 55.000 22.06 0.00 0.00 6.09
1290 1363 2.292016 GGTCAGATCGATCGACATGTCT 59.708 50.000 31.84 16.31 34.42 3.41
1405 1478 2.360350 CGCCACACCAGGAAGCAT 60.360 61.111 0.00 0.00 0.00 3.79
1435 1508 1.949133 GTGACGCTTGCACTCGTGA 60.949 57.895 15.93 6.11 39.22 4.35
1514 1626 3.251004 GGAAGAAGAATTGTGCGTTCACT 59.749 43.478 0.00 0.00 43.49 3.41
1521 1633 4.393062 TCGAATCAGGAAGAAGAATTGTGC 59.607 41.667 0.00 0.00 0.00 4.57
1523 1635 7.362401 CCAAATCGAATCAGGAAGAAGAATTGT 60.362 37.037 0.00 0.00 0.00 2.71
1525 1637 6.660949 ACCAAATCGAATCAGGAAGAAGAATT 59.339 34.615 0.00 0.00 0.00 2.17
1570 1682 5.814705 CCTGAGAAGAAGAATTAGATGCGTT 59.185 40.000 0.00 0.00 0.00 4.84
1607 1719 2.443255 ACAGGTGTGGAGGAAGTTCATT 59.557 45.455 5.01 0.00 0.00 2.57
1628 1740 7.103641 ACTTCTTCAGTGTTTTCTTGTCACTA 58.896 34.615 0.00 0.00 39.89 2.74
1733 1846 1.753930 CATCCATGCACTGTAGGCAA 58.246 50.000 0.00 0.00 45.60 4.52
1753 1867 9.533253 AAAACTGAATCATGAAACAAACCTTAG 57.467 29.630 0.00 0.00 0.00 2.18
1815 1929 4.993584 TCTGCATGTCTTTCTTCAGAAGAC 59.006 41.667 12.75 2.72 37.23 3.01
1875 1990 3.879295 CCAAGACGGATAGCATTGACAAT 59.121 43.478 0.00 0.00 36.56 2.71
2062 2177 6.071896 ACAGGGAGCTTTTAAGTAAAATCTGC 60.072 38.462 9.23 9.23 38.31 4.26
2122 2237 2.764128 GGAGCTCCCCCGACATCA 60.764 66.667 23.19 0.00 0.00 3.07
2212 2329 3.022607 AGTGTACGCGTTAGAGCTTTT 57.977 42.857 20.78 0.00 34.40 2.27
2533 2654 0.040204 CCTTCTTGTGGGGCCTTCAT 59.960 55.000 0.84 0.00 0.00 2.57
2547 2669 1.000896 CAAATCCCCCACGCCTTCT 60.001 57.895 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.