Multiple sequence alignment - TraesCS1B01G310300

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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 TraesCS1B01G310300 chr1B 100.000 3191 0 0 1 3191 533325895 533322705 0.000000e+00 5893.0
1 TraesCS1B01G310300 chr1B 91.855 442 30 3 2751 3187 1452096 1452536 2.100000e-171 612.0
2 TraesCS1B01G310300 chr1B 90.950 442 34 3 2751 3187 355094620 355094180 9.860000e-165 590.0
3 TraesCS1B01G310300 chr1B 100.000 78 0 0 9 86 488650392 488650469 9.230000e-31 145.0
4 TraesCS1B01G310300 chr1A 87.241 3190 177 97 81 3185 495194082 495191038 0.000000e+00 3424.0
5 TraesCS1B01G310300 chr1D 91.353 2255 68 40 304 2502 397974855 397972672 0.000000e+00 2966.0
6 TraesCS1B01G310300 chr1D 90.642 716 42 9 2479 3187 397972645 397971948 0.000000e+00 928.0
7 TraesCS1B01G310300 chr1D 91.964 224 16 2 81 303 397981056 397980834 2.390000e-81 313.0
8 TraesCS1B01G310300 chr7B 91.629 442 31 3 2751 3187 687544111 687543671 9.790000e-170 606.0
9 TraesCS1B01G310300 chr4A 91.629 442 31 3 2751 3187 740379637 740380077 9.790000e-170 606.0
10 TraesCS1B01G310300 chr4A 91.176 442 33 3 2751 3187 717603440 717603000 2.120000e-166 595.0
11 TraesCS1B01G310300 chr4A 96.104 77 3 0 10 86 593202282 593202358 3.340000e-25 126.0
12 TraesCS1B01G310300 chr2B 91.176 442 33 2 2751 3187 355042499 355042059 2.120000e-166 595.0
13 TraesCS1B01G310300 chr2B 90.724 442 35 3 2751 3187 763145513 763145073 4.590000e-163 584.0
14 TraesCS1B01G310300 chr2B 100.000 29 0 0 2690 2718 492985114 492985142 2.000000e-03 54.7
15 TraesCS1B01G310300 chr3B 90.724 442 30 4 2751 3187 377073327 377073762 2.130000e-161 579.0
16 TraesCS1B01G310300 chr3B 90.260 308 30 0 1884 2191 593164400 593164707 1.380000e-108 403.0
17 TraesCS1B01G310300 chr3B 89.610 308 32 0 1884 2191 593541864 593542171 2.980000e-105 392.0
18 TraesCS1B01G310300 chr3B 85.802 324 44 2 1244 1566 593163819 593164141 3.050000e-90 342.0
19 TraesCS1B01G310300 chr3B 85.802 324 44 2 1244 1566 593541303 593541625 3.050000e-90 342.0
20 TraesCS1B01G310300 chr3B 79.511 327 53 9 1246 1562 228690784 228690462 1.490000e-53 220.0
21 TraesCS1B01G310300 chr4B 90.271 442 37 3 2751 3187 672981618 672982058 9.930000e-160 573.0
22 TraesCS1B01G310300 chr4B 100.000 77 0 0 10 86 652951733 652951809 3.320000e-30 143.0
23 TraesCS1B01G310300 chr3D 89.286 308 33 0 1884 2191 451886117 451886424 1.390000e-103 387.0
24 TraesCS1B01G310300 chr3D 88.636 308 35 0 1884 2191 451710642 451710949 3.010000e-100 375.0
25 TraesCS1B01G310300 chr3D 85.410 329 45 3 1240 1566 451885572 451885899 3.940000e-89 339.0
26 TraesCS1B01G310300 chr3D 85.185 324 46 2 1244 1566 451710100 451710422 6.600000e-87 331.0
27 TraesCS1B01G310300 chr3D 82.353 272 34 10 1246 1507 157443377 157443110 1.150000e-54 224.0
28 TraesCS1B01G310300 chr3A 88.961 308 34 0 1884 2191 594493031 594493338 6.460000e-102 381.0
29 TraesCS1B01G310300 chr3A 86.111 324 43 2 1244 1566 594492469 594492791 6.550000e-92 348.0
30 TraesCS1B01G310300 chr6A 82.637 311 48 6 1880 2187 542430365 542430058 1.460000e-68 270.0
31 TraesCS1B01G310300 chr6D 82.650 317 42 10 1880 2188 396010788 396010477 5.250000e-68 268.0
32 TraesCS1B01G310300 chr6B 94.340 53 3 0 1093 1145 592464857 592464805 7.340000e-12 82.4


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 TraesCS1B01G310300 chr1B 533322705 533325895 3190 True 5893.0 5893 100.0000 1 3191 1 chr1B.!!$R2 3190
1 TraesCS1B01G310300 chr1A 495191038 495194082 3044 True 3424.0 3424 87.2410 81 3185 1 chr1A.!!$R1 3104
2 TraesCS1B01G310300 chr1D 397971948 397974855 2907 True 1947.0 2966 90.9975 304 3187 2 chr1D.!!$R2 2883
3 TraesCS1B01G310300 chr3B 593163819 593164707 888 False 372.5 403 88.0310 1244 2191 2 chr3B.!!$F2 947
4 TraesCS1B01G310300 chr3B 593541303 593542171 868 False 367.0 392 87.7060 1244 2191 2 chr3B.!!$F3 947
5 TraesCS1B01G310300 chr3D 451885572 451886424 852 False 363.0 387 87.3480 1240 2191 2 chr3D.!!$F2 951
6 TraesCS1B01G310300 chr3D 451710100 451710949 849 False 353.0 375 86.9105 1244 2191 2 chr3D.!!$F1 947
7 TraesCS1B01G310300 chr3A 594492469 594493338 869 False 364.5 381 87.5360 1244 2191 2 chr3A.!!$F1 947

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
44 45 0.109597 CGCGACGTACCCAAGTTACT 60.110 55.0 0.00 0.00 0.0 2.24 F
61 62 0.180406 ACTTTGAACTCCTGCCGTGT 59.820 50.0 0.00 0.00 0.0 4.49 F
129 130 0.385974 GATCCAACACACGCAGCAAC 60.386 55.0 0.00 0.00 0.0 4.17 F
1282 1323 0.401738 ATGGCAACCTGTACAGCACT 59.598 50.0 17.86 0.53 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1042 0.519077 GAAAAAGAGAGCACCGGCAG 59.481 55.000 0.00 0.00 44.61 4.85 R
1264 1305 0.534877 CAGTGCTGTACAGGTTGCCA 60.535 55.000 23.95 10.26 0.00 4.92 R
1862 2042 1.874019 GATCATGCGACGCGTCAGT 60.874 57.895 35.71 19.50 0.00 3.41 R
3081 3373 0.039437 CGGGCGATCACGTTAGCTAT 60.039 55.000 0.00 0.00 41.98 2.97 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
18 19 3.780624 AATTTGGACGCCGCTCTAT 57.219 47.368 0.00 0.00 0.00 1.98
19 20 2.038387 AATTTGGACGCCGCTCTATT 57.962 45.000 0.00 0.00 0.00 1.73
20 21 1.583054 ATTTGGACGCCGCTCTATTC 58.417 50.000 0.00 0.00 0.00 1.75
21 22 0.804544 TTTGGACGCCGCTCTATTCG 60.805 55.000 0.00 0.00 0.00 3.34
22 23 3.030882 GGACGCCGCTCTATTCGC 61.031 66.667 0.00 0.00 0.00 4.70
23 24 3.030882 GACGCCGCTCTATTCGCC 61.031 66.667 0.00 0.00 0.00 5.54
24 25 3.486252 GACGCCGCTCTATTCGCCT 62.486 63.158 0.00 0.00 0.00 5.52
25 26 2.731348 CGCCGCTCTATTCGCCTC 60.731 66.667 0.00 0.00 0.00 4.70
26 27 2.731348 GCCGCTCTATTCGCCTCG 60.731 66.667 0.00 0.00 0.00 4.63
27 28 2.731348 CCGCTCTATTCGCCTCGC 60.731 66.667 0.00 0.00 0.00 5.03
38 39 4.424566 GCCTCGCGACGTACCCAA 62.425 66.667 3.71 0.00 0.00 4.12
39 40 2.202570 CCTCGCGACGTACCCAAG 60.203 66.667 3.71 0.00 0.00 3.61
40 41 2.564975 CTCGCGACGTACCCAAGT 59.435 61.111 3.71 0.00 0.00 3.16
41 42 1.080974 CTCGCGACGTACCCAAGTT 60.081 57.895 3.71 0.00 0.00 2.66
42 43 0.168788 CTCGCGACGTACCCAAGTTA 59.831 55.000 3.71 0.00 0.00 2.24
43 44 0.109781 TCGCGACGTACCCAAGTTAC 60.110 55.000 3.71 0.00 0.00 2.50
44 45 0.109597 CGCGACGTACCCAAGTTACT 60.110 55.000 0.00 0.00 0.00 2.24
45 46 1.666888 CGCGACGTACCCAAGTTACTT 60.667 52.381 0.00 0.00 0.00 2.24
46 47 2.407090 GCGACGTACCCAAGTTACTTT 58.593 47.619 0.00 0.00 0.00 2.66
47 48 2.156310 GCGACGTACCCAAGTTACTTTG 59.844 50.000 0.00 0.00 0.00 2.77
48 49 3.641648 CGACGTACCCAAGTTACTTTGA 58.358 45.455 0.00 0.00 0.00 2.69
49 50 4.050553 CGACGTACCCAAGTTACTTTGAA 58.949 43.478 0.00 0.00 0.00 2.69
50 51 4.084900 CGACGTACCCAAGTTACTTTGAAC 60.085 45.833 0.00 0.00 0.00 3.18
51 52 5.027293 ACGTACCCAAGTTACTTTGAACT 57.973 39.130 0.00 0.00 41.50 3.01
52 53 5.052481 ACGTACCCAAGTTACTTTGAACTC 58.948 41.667 0.00 0.00 38.75 3.01
53 54 4.450080 CGTACCCAAGTTACTTTGAACTCC 59.550 45.833 0.00 0.00 38.75 3.85
54 55 4.790718 ACCCAAGTTACTTTGAACTCCT 57.209 40.909 0.00 0.00 38.75 3.69
55 56 4.461198 ACCCAAGTTACTTTGAACTCCTG 58.539 43.478 0.00 0.00 38.75 3.86
56 57 3.253432 CCCAAGTTACTTTGAACTCCTGC 59.747 47.826 0.00 0.00 38.75 4.85
57 58 3.253432 CCAAGTTACTTTGAACTCCTGCC 59.747 47.826 0.00 0.00 38.75 4.85
58 59 2.767505 AGTTACTTTGAACTCCTGCCG 58.232 47.619 0.00 0.00 34.48 5.69
59 60 2.104281 AGTTACTTTGAACTCCTGCCGT 59.896 45.455 0.00 0.00 34.48 5.68
60 61 2.163818 TACTTTGAACTCCTGCCGTG 57.836 50.000 0.00 0.00 0.00 4.94
61 62 0.180406 ACTTTGAACTCCTGCCGTGT 59.820 50.000 0.00 0.00 0.00 4.49
62 63 0.868406 CTTTGAACTCCTGCCGTGTC 59.132 55.000 0.00 0.00 0.00 3.67
63 64 0.534203 TTTGAACTCCTGCCGTGTCC 60.534 55.000 0.00 0.00 0.00 4.02
64 65 2.432628 GAACTCCTGCCGTGTCCG 60.433 66.667 0.00 0.00 0.00 4.79
74 75 4.803426 CGTGTCCGGAGCAGCTCC 62.803 72.222 29.53 29.53 46.44 4.70
81 82 3.293702 GGAGCAGCTCCTTCGTCT 58.706 61.111 31.54 0.00 46.41 4.18
82 83 1.140804 GGAGCAGCTCCTTCGTCTC 59.859 63.158 31.54 4.76 46.41 3.36
83 84 1.140804 GAGCAGCTCCTTCGTCTCC 59.859 63.158 11.84 0.00 0.00 3.71
84 85 1.304879 AGCAGCTCCTTCGTCTCCT 60.305 57.895 0.00 0.00 0.00 3.69
85 86 1.140804 GCAGCTCCTTCGTCTCCTC 59.859 63.158 0.00 0.00 0.00 3.71
105 106 2.219903 TCACTGCAACAATACGTTCGTG 59.780 45.455 8.14 0.00 34.86 4.35
127 128 2.316867 CGATCCAACACACGCAGCA 61.317 57.895 0.00 0.00 0.00 4.41
129 130 0.385974 GATCCAACACACGCAGCAAC 60.386 55.000 0.00 0.00 0.00 4.17
148 149 1.721664 CTTCCTGGACCATGCATGCG 61.722 60.000 21.69 16.19 0.00 4.73
150 151 2.438975 CTGGACCATGCATGCGGT 60.439 61.111 21.69 16.15 38.56 5.68
153 154 2.342650 GGACCATGCATGCGGTTGT 61.343 57.895 21.69 12.98 34.99 3.32
156 157 1.201181 GACCATGCATGCGGTTGTTAA 59.799 47.619 21.69 0.00 34.99 2.01
165 166 4.917415 GCATGCGGTTGTTAATTATCCATC 59.083 41.667 0.00 0.00 0.00 3.51
204 205 1.228245 AAGGTCGGCATGCACTTGT 60.228 52.632 21.36 0.00 0.00 3.16
205 206 0.823356 AAGGTCGGCATGCACTTGTT 60.823 50.000 21.36 3.97 0.00 2.83
213 214 1.265635 GCATGCACTTGTTCCGTTACA 59.734 47.619 14.21 0.00 0.00 2.41
255 259 5.888691 ATCATCACGTATCTAGTAGCAGG 57.111 43.478 0.00 0.00 0.00 4.85
300 304 2.094659 GGTCGAGCACCATGACACG 61.095 63.158 10.30 0.00 45.98 4.49
301 305 1.080772 GTCGAGCACCATGACACGA 60.081 57.895 0.00 0.00 32.91 4.35
326 332 2.040779 ACCGGATTCCCCTCCCTC 60.041 66.667 9.46 0.00 31.04 4.30
327 333 2.849646 CCGGATTCCCCTCCCTCC 60.850 72.222 0.00 0.00 31.04 4.30
335 341 3.368501 CCCTCCCTCCCTCCCTCA 61.369 72.222 0.00 0.00 0.00 3.86
376 382 1.168407 ACGGCTATGCATGCATGGTC 61.168 55.000 37.43 34.59 37.27 4.02
380 386 0.509929 CTATGCATGCATGGTCGACG 59.490 55.000 37.43 15.77 37.82 5.12
382 388 4.580044 GCATGCATGGTCGACGCG 62.580 66.667 27.34 3.53 0.00 6.01
491 510 1.599047 GTCCTGGCTCAGCTAAGCA 59.401 57.895 11.93 0.00 44.35 3.91
521 540 1.443407 CCATGTGGAGAGTAGGGCG 59.557 63.158 0.00 0.00 37.39 6.13
524 543 3.851128 GTGGAGAGTAGGGCGCCC 61.851 72.222 39.29 39.29 0.00 6.13
566 585 4.660938 GCCACCAGTCCACCCCAC 62.661 72.222 0.00 0.00 0.00 4.61
678 697 0.726827 CGCATGTACGCCTGATTTGT 59.273 50.000 0.00 0.00 0.00 2.83
679 698 1.930503 CGCATGTACGCCTGATTTGTA 59.069 47.619 0.00 0.00 0.00 2.41
680 699 2.033747 CGCATGTACGCCTGATTTGTAG 60.034 50.000 0.00 0.00 0.00 2.74
703 722 3.726595 TATTAACTGCCGCGCGCCT 62.727 57.895 27.36 8.43 36.24 5.52
762 785 6.598850 GCCTTCAATCTCTCATTTTCTTCTCT 59.401 38.462 0.00 0.00 0.00 3.10
948 973 5.565834 GCCTAGCTAGCTTTAGTCACCATAG 60.566 48.000 24.88 9.13 0.00 2.23
999 1034 1.612395 AAGGAAGCTCTCTCCCAGCG 61.612 60.000 0.00 0.00 42.14 5.18
1023 1058 2.359230 GCTGCCGGTGCTCTCTTT 60.359 61.111 1.90 0.00 38.71 2.52
1029 1064 1.338769 GCCGGTGCTCTCTTTTTCCTA 60.339 52.381 1.90 0.00 33.53 2.94
1142 1177 2.452064 CCTCCGGCACCATGGGTAT 61.452 63.158 18.09 0.00 32.11 2.73
1178 1213 1.066002 GCTGGCGAATGCAATGTGTAT 59.934 47.619 0.00 0.00 45.35 2.29
1181 1216 4.282068 CTGGCGAATGCAATGTGTATAAC 58.718 43.478 0.00 0.00 45.35 1.89
1282 1323 0.401738 ATGGCAACCTGTACAGCACT 59.598 50.000 17.86 0.53 0.00 4.40
1578 1629 5.125578 ACAGAAGGTGAGAACAAAGTTTTCC 59.874 40.000 0.00 0.00 0.00 3.13
1588 1642 7.062839 TGAGAACAAAGTTTTCCGTCAAAAATG 59.937 33.333 0.00 0.00 35.68 2.32
1815 1995 4.126164 CGTCACCGTGTCACGTAG 57.874 61.111 23.01 14.91 40.58 3.51
1817 1997 0.512518 CGTCACCGTGTCACGTAGTA 59.487 55.000 23.01 3.97 41.61 1.82
1818 1998 1.463034 CGTCACCGTGTCACGTAGTAG 60.463 57.143 23.01 10.41 41.61 2.57
1819 1999 1.532868 GTCACCGTGTCACGTAGTAGT 59.467 52.381 23.01 11.04 41.61 2.73
1820 2000 2.736721 GTCACCGTGTCACGTAGTAGTA 59.263 50.000 23.01 2.88 41.61 1.82
1821 2001 2.736721 TCACCGTGTCACGTAGTAGTAC 59.263 50.000 23.01 0.00 41.61 2.73
1822 2002 2.738846 CACCGTGTCACGTAGTAGTACT 59.261 50.000 23.01 8.14 41.61 2.73
1823 2003 3.926527 CACCGTGTCACGTAGTAGTACTA 59.073 47.826 23.01 5.90 41.61 1.82
1824 2004 4.388773 CACCGTGTCACGTAGTAGTACTAA 59.611 45.833 23.01 0.00 41.61 2.24
1825 2005 4.627467 ACCGTGTCACGTAGTAGTACTAAG 59.373 45.833 23.01 18.29 41.61 2.18
1851 2031 2.736670 AATCCTGCATGTTACCCCTC 57.263 50.000 0.00 0.00 0.00 4.30
1853 2033 1.819632 CCTGCATGTTACCCCTCGC 60.820 63.158 0.00 0.00 0.00 5.03
1854 2034 2.125310 TGCATGTTACCCCTCGCG 60.125 61.111 0.00 0.00 0.00 5.87
1855 2035 2.185867 GCATGTTACCCCTCGCGA 59.814 61.111 9.26 9.26 0.00 5.87
1856 2036 1.227556 GCATGTTACCCCTCGCGAT 60.228 57.895 10.36 0.00 0.00 4.58
1857 2037 0.814010 GCATGTTACCCCTCGCGATT 60.814 55.000 10.36 0.00 0.00 3.34
2193 2384 2.359967 GGGCGCCCAGTTCTAGTCT 61.360 63.158 40.73 0.00 35.81 3.24
2197 2388 0.179124 CGCCCAGTTCTAGTCTGCTC 60.179 60.000 10.57 5.42 0.00 4.26
2210 2401 0.032615 TCTGCTCCCTCCTCTTCTCC 60.033 60.000 0.00 0.00 0.00 3.71
2233 2424 2.239402 TCTCCACAGGCATAAGCATTGA 59.761 45.455 0.00 0.00 44.61 2.57
2264 2455 2.287427 ACGGACGGAGCGTATTCTATTG 60.287 50.000 0.00 0.00 41.37 1.90
2418 2619 9.212641 TCTCATCAAAGTCTCAAGTTTATTGAG 57.787 33.333 10.64 10.64 45.38 3.02
2423 2624 7.993183 TCAAAGTCTCAAGTTTATTGAGGACTT 59.007 33.333 15.52 17.51 44.43 3.01
2431 2632 6.635030 AGTTTATTGAGGACTTGAACAACC 57.365 37.500 0.00 0.00 0.00 3.77
2432 2633 6.126409 AGTTTATTGAGGACTTGAACAACCA 58.874 36.000 0.00 0.00 0.00 3.67
2433 2634 6.777580 AGTTTATTGAGGACTTGAACAACCAT 59.222 34.615 0.00 0.00 0.00 3.55
2600 2861 2.042297 TGGTGGCCCTTGTGATGAAATA 59.958 45.455 0.00 0.00 0.00 1.40
2674 2943 0.179468 GCCACCCGTAGCTTCCATAA 59.821 55.000 0.00 0.00 0.00 1.90
2678 2947 3.340034 CACCCGTAGCTTCCATAAAACA 58.660 45.455 0.00 0.00 0.00 2.83
2726 3002 1.678101 GGGCTGTATCTTGTTGATGGC 59.322 52.381 0.00 0.00 36.65 4.40
2840 3120 5.118990 GTGTAGATGATAGGCTTCTGCAAA 58.881 41.667 6.33 0.00 42.19 3.68
2841 3121 5.762218 GTGTAGATGATAGGCTTCTGCAAAT 59.238 40.000 6.33 0.00 42.19 2.32
2844 3124 2.658285 TGATAGGCTTCTGCAAATGGG 58.342 47.619 0.00 0.00 41.91 4.00
2845 3125 2.241941 TGATAGGCTTCTGCAAATGGGA 59.758 45.455 0.00 0.00 41.91 4.37
2846 3126 2.897271 TAGGCTTCTGCAAATGGGAA 57.103 45.000 0.00 0.00 41.91 3.97
2847 3127 2.242882 AGGCTTCTGCAAATGGGAAT 57.757 45.000 0.00 0.00 41.91 3.01
2848 3128 1.829222 AGGCTTCTGCAAATGGGAATG 59.171 47.619 0.00 0.00 41.91 2.67
2849 3129 1.826720 GGCTTCTGCAAATGGGAATGA 59.173 47.619 0.00 0.00 41.91 2.57
2851 3131 3.118519 GGCTTCTGCAAATGGGAATGATT 60.119 43.478 0.00 0.00 41.91 2.57
2852 3132 3.869246 GCTTCTGCAAATGGGAATGATTG 59.131 43.478 0.00 0.00 39.41 2.67
2895 3175 1.598130 GCCTCCACACGCTCAAGTT 60.598 57.895 0.00 0.00 0.00 2.66
2896 3176 1.166531 GCCTCCACACGCTCAAGTTT 61.167 55.000 0.00 0.00 0.00 2.66
2897 3177 0.588252 CCTCCACACGCTCAAGTTTG 59.412 55.000 0.00 0.00 0.00 2.93
2898 3178 0.040958 CTCCACACGCTCAAGTTTGC 60.041 55.000 0.00 0.00 0.00 3.68
2899 3179 1.008538 CCACACGCTCAAGTTTGCC 60.009 57.895 0.00 0.00 0.00 4.52
2900 3180 1.723608 CCACACGCTCAAGTTTGCCA 61.724 55.000 0.00 0.00 0.00 4.92
2901 3181 0.100325 CACACGCTCAAGTTTGCCAA 59.900 50.000 0.00 0.00 0.00 4.52
2902 3182 1.032014 ACACGCTCAAGTTTGCCAAT 58.968 45.000 0.00 0.00 0.00 3.16
2903 3183 1.269206 ACACGCTCAAGTTTGCCAATG 60.269 47.619 0.00 0.00 0.00 2.82
2904 3184 0.314935 ACGCTCAAGTTTGCCAATGG 59.685 50.000 0.00 0.00 0.00 3.16
2923 3203 1.826921 TGGTCGTAGGATCGGCTCC 60.827 63.158 0.00 0.00 45.33 4.70
2928 3208 1.400530 CGTAGGATCGGCTCCCCTTT 61.401 60.000 0.00 0.00 46.27 3.11
2960 3240 2.103094 CCATGGGAGCTTTCGAGATACA 59.897 50.000 2.85 0.00 0.00 2.29
2970 3250 4.577283 GCTTTCGAGATACACTCCTAGAGT 59.423 45.833 0.00 0.00 44.44 3.24
2979 3259 2.158295 ACACTCCTAGAGTCCTGGTGTT 60.158 50.000 0.00 0.00 41.37 3.32
3012 3292 0.886938 TTTCGCAGTCCGCAATTGGA 60.887 50.000 7.72 0.00 42.60 3.53
3057 3337 2.089349 GCGTGCTCGTCCTGAAGAC 61.089 63.158 10.18 0.00 42.54 3.01
3097 3389 1.716581 GCAGATAGCTAACGTGATCGC 59.283 52.381 0.00 0.00 41.15 4.58
3134 3426 4.615223 CGTCCCATCGTATCACGTTATCAT 60.615 45.833 0.00 0.00 43.14 2.45
3136 3428 4.521256 TCCCATCGTATCACGTTATCATGA 59.479 41.667 0.00 0.00 43.14 3.07
3137 3429 5.185056 TCCCATCGTATCACGTTATCATGAT 59.815 40.000 13.81 13.81 43.14 2.45
3155 3448 5.746721 TCATGATACGTGACTATTGTTTCCG 59.253 40.000 0.00 0.00 0.00 4.30
3156 3449 4.426416 TGATACGTGACTATTGTTTCCGG 58.574 43.478 0.00 0.00 0.00 5.14
3176 3469 5.003160 CCGGCATTTAGGATCATTGATGTA 58.997 41.667 3.32 0.00 0.00 2.29
3188 3481 8.982723 AGGATCATTGATGTAGTACTTGTAAGT 58.017 33.333 3.32 2.51 42.91 2.24
3189 3482 9.601217 GGATCATTGATGTAGTACTTGTAAGTT 57.399 33.333 3.32 0.00 40.37 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.940613 GAATAGAGCGGCGTCCAAATT 59.059 47.619 9.37 2.54 0.00 1.82
1 2 1.583054 GAATAGAGCGGCGTCCAAAT 58.417 50.000 9.37 0.00 0.00 2.32
2 3 0.804544 CGAATAGAGCGGCGTCCAAA 60.805 55.000 9.37 0.00 0.00 3.28
3 4 1.226859 CGAATAGAGCGGCGTCCAA 60.227 57.895 9.37 0.00 0.00 3.53
4 5 2.411701 CGAATAGAGCGGCGTCCA 59.588 61.111 9.37 0.00 0.00 4.02
5 6 3.030882 GCGAATAGAGCGGCGTCC 61.031 66.667 9.37 0.00 0.00 4.79
6 7 3.030882 GGCGAATAGAGCGGCGTC 61.031 66.667 9.37 5.00 44.17 5.19
10 11 2.731348 GCGAGGCGAATAGAGCGG 60.731 66.667 0.00 0.00 35.00 5.52
21 22 4.424566 TTGGGTACGTCGCGAGGC 62.425 66.667 27.18 12.74 0.00 4.70
22 23 2.202570 CTTGGGTACGTCGCGAGG 60.203 66.667 25.84 25.84 37.00 4.63
23 24 0.168788 TAACTTGGGTACGTCGCGAG 59.831 55.000 10.24 6.53 43.51 5.03
24 25 0.109781 GTAACTTGGGTACGTCGCGA 60.110 55.000 3.71 3.71 0.00 5.87
25 26 0.109597 AGTAACTTGGGTACGTCGCG 60.110 55.000 0.00 0.00 0.00 5.87
26 27 2.070262 AAGTAACTTGGGTACGTCGC 57.930 50.000 0.00 0.00 0.00 5.19
27 28 3.641648 TCAAAGTAACTTGGGTACGTCG 58.358 45.455 0.00 0.00 0.00 5.12
28 29 5.052481 AGTTCAAAGTAACTTGGGTACGTC 58.948 41.667 0.00 0.00 36.26 4.34
29 30 5.027293 AGTTCAAAGTAACTTGGGTACGT 57.973 39.130 0.00 0.00 36.26 3.57
30 31 4.450080 GGAGTTCAAAGTAACTTGGGTACG 59.550 45.833 0.00 0.00 39.78 3.67
31 32 5.469084 CAGGAGTTCAAAGTAACTTGGGTAC 59.531 44.000 0.00 0.00 39.78 3.34
32 33 5.617252 CAGGAGTTCAAAGTAACTTGGGTA 58.383 41.667 0.00 0.00 39.78 3.69
33 34 4.461198 CAGGAGTTCAAAGTAACTTGGGT 58.539 43.478 0.00 0.00 39.78 4.51
34 35 3.253432 GCAGGAGTTCAAAGTAACTTGGG 59.747 47.826 0.00 0.00 39.78 4.12
35 36 3.253432 GGCAGGAGTTCAAAGTAACTTGG 59.747 47.826 0.00 0.00 39.78 3.61
36 37 3.058914 CGGCAGGAGTTCAAAGTAACTTG 60.059 47.826 0.00 0.00 39.78 3.16
37 38 3.139077 CGGCAGGAGTTCAAAGTAACTT 58.861 45.455 0.00 0.00 39.78 2.66
38 39 2.104281 ACGGCAGGAGTTCAAAGTAACT 59.896 45.455 0.00 0.00 42.36 2.24
39 40 2.223377 CACGGCAGGAGTTCAAAGTAAC 59.777 50.000 0.00 0.00 0.00 2.50
40 41 2.158871 ACACGGCAGGAGTTCAAAGTAA 60.159 45.455 0.00 0.00 0.00 2.24
41 42 1.414919 ACACGGCAGGAGTTCAAAGTA 59.585 47.619 0.00 0.00 0.00 2.24
42 43 0.180406 ACACGGCAGGAGTTCAAAGT 59.820 50.000 0.00 0.00 0.00 2.66
43 44 0.868406 GACACGGCAGGAGTTCAAAG 59.132 55.000 0.00 0.00 0.00 2.77
44 45 0.534203 GGACACGGCAGGAGTTCAAA 60.534 55.000 0.00 0.00 0.00 2.69
45 46 1.070786 GGACACGGCAGGAGTTCAA 59.929 57.895 0.00 0.00 0.00 2.69
46 47 2.741092 GGACACGGCAGGAGTTCA 59.259 61.111 0.00 0.00 0.00 3.18
47 48 2.432628 CGGACACGGCAGGAGTTC 60.433 66.667 0.00 0.00 36.18 3.01
57 58 4.803426 GGAGCTGCTCCGGACACG 62.803 72.222 31.03 0.00 41.08 4.49
65 66 1.140804 GGAGACGAAGGAGCTGCTC 59.859 63.158 21.17 21.17 0.00 4.26
66 67 1.304879 AGGAGACGAAGGAGCTGCT 60.305 57.895 0.00 0.00 0.00 4.24
67 68 1.140804 GAGGAGACGAAGGAGCTGC 59.859 63.158 0.00 0.00 0.00 5.25
68 69 0.172352 GTGAGGAGACGAAGGAGCTG 59.828 60.000 0.00 0.00 0.00 4.24
69 70 0.039035 AGTGAGGAGACGAAGGAGCT 59.961 55.000 0.00 0.00 0.00 4.09
70 71 0.172352 CAGTGAGGAGACGAAGGAGC 59.828 60.000 0.00 0.00 0.00 4.70
71 72 0.172352 GCAGTGAGGAGACGAAGGAG 59.828 60.000 0.00 0.00 0.00 3.69
72 73 0.539669 TGCAGTGAGGAGACGAAGGA 60.540 55.000 0.00 0.00 0.00 3.36
73 74 0.318441 TTGCAGTGAGGAGACGAAGG 59.682 55.000 0.00 0.00 0.00 3.46
74 75 1.269778 TGTTGCAGTGAGGAGACGAAG 60.270 52.381 0.00 0.00 0.00 3.79
75 76 0.750249 TGTTGCAGTGAGGAGACGAA 59.250 50.000 0.00 0.00 0.00 3.85
76 77 0.750249 TTGTTGCAGTGAGGAGACGA 59.250 50.000 0.00 0.00 0.00 4.20
77 78 1.800805 ATTGTTGCAGTGAGGAGACG 58.199 50.000 0.00 0.00 0.00 4.18
78 79 2.668457 CGTATTGTTGCAGTGAGGAGAC 59.332 50.000 0.00 0.00 0.00 3.36
79 80 2.299013 ACGTATTGTTGCAGTGAGGAGA 59.701 45.455 0.00 0.00 0.00 3.71
80 81 2.688507 ACGTATTGTTGCAGTGAGGAG 58.311 47.619 0.00 0.00 0.00 3.69
81 82 2.831685 ACGTATTGTTGCAGTGAGGA 57.168 45.000 0.00 0.00 0.00 3.71
82 83 2.159841 CGAACGTATTGTTGCAGTGAGG 60.160 50.000 0.00 0.00 42.09 3.86
83 84 2.475111 ACGAACGTATTGTTGCAGTGAG 59.525 45.455 0.00 0.00 42.09 3.51
84 85 2.219903 CACGAACGTATTGTTGCAGTGA 59.780 45.455 0.00 0.00 42.09 3.41
85 86 2.559872 CACGAACGTATTGTTGCAGTG 58.440 47.619 0.00 0.00 42.09 3.66
105 106 1.225376 TGCGTGTGTTGGATCGTTCC 61.225 55.000 5.52 5.52 42.94 3.62
110 111 0.385974 GTTGCTGCGTGTGTTGGATC 60.386 55.000 0.00 0.00 0.00 3.36
121 122 2.328099 GGTCCAGGAAGTTGCTGCG 61.328 63.158 18.25 11.74 34.22 5.18
127 128 1.843368 CATGCATGGTCCAGGAAGTT 58.157 50.000 19.40 0.00 0.00 2.66
129 130 1.721664 CGCATGCATGGTCCAGGAAG 61.722 60.000 27.34 0.00 0.00 3.46
148 149 5.897250 ACTTGGGGATGGATAATTAACAACC 59.103 40.000 9.83 9.83 0.00 3.77
150 151 7.878495 ACTACTTGGGGATGGATAATTAACAA 58.122 34.615 0.00 0.00 0.00 2.83
153 154 7.699709 TGACTACTTGGGGATGGATAATTAA 57.300 36.000 0.00 0.00 0.00 1.40
156 157 5.672194 ACTTGACTACTTGGGGATGGATAAT 59.328 40.000 0.00 0.00 0.00 1.28
186 187 0.823356 AACAAGTGCATGCCGACCTT 60.823 50.000 16.68 9.06 0.00 3.50
213 214 0.465705 AATCCACTCATGATCGGCGT 59.534 50.000 6.85 0.00 0.00 5.68
284 288 0.032815 TTTCGTGTCATGGTGCTCGA 59.967 50.000 0.00 0.00 0.00 4.04
293 297 1.804151 CCGGTCATGTTTTCGTGTCAT 59.196 47.619 0.00 0.00 37.97 3.06
300 304 1.749063 GGGGAATCCGGTCATGTTTTC 59.251 52.381 0.00 0.00 0.00 2.29
301 305 1.357761 AGGGGAATCCGGTCATGTTTT 59.642 47.619 0.00 0.00 41.52 2.43
364 370 3.498834 GCGTCGACCATGCATGCA 61.499 61.111 25.04 25.04 36.94 3.96
453 472 2.369633 ATGCAGGACTCGGCCATGA 61.370 57.895 2.24 0.00 33.09 3.07
491 510 3.005539 ACATGGCTCTCACCGGCT 61.006 61.111 0.00 0.00 0.00 5.52
497 516 2.382882 CTACTCTCCACATGGCTCTCA 58.617 52.381 0.00 0.00 34.44 3.27
666 685 8.202137 AGTTAATACATACTACAAATCAGGCGT 58.798 33.333 0.00 0.00 0.00 5.68
678 697 3.311106 GCGCGGCAGTTAATACATACTA 58.689 45.455 8.83 0.00 0.00 1.82
679 698 2.132762 GCGCGGCAGTTAATACATACT 58.867 47.619 8.83 0.00 0.00 2.12
680 699 1.136721 CGCGCGGCAGTTAATACATAC 60.137 52.381 24.84 0.00 0.00 2.39
762 785 5.328565 TGAAGATTTGGTGAGAGAGAGAGA 58.671 41.667 0.00 0.00 0.00 3.10
852 877 9.067986 GGTATTTATAGCCAAAGTAAAGCTCAT 57.932 33.333 0.00 0.00 38.06 2.90
948 973 0.464452 TAGCTTAGCTTTCGAGGGGC 59.536 55.000 13.44 0.00 40.44 5.80
1007 1042 0.519077 GAAAAAGAGAGCACCGGCAG 59.481 55.000 0.00 0.00 44.61 4.85
1008 1043 0.889186 GGAAAAAGAGAGCACCGGCA 60.889 55.000 0.00 0.00 44.61 5.69
1023 1058 3.456277 GGCAGAAGGAGGAGAATAGGAAA 59.544 47.826 0.00 0.00 0.00 3.13
1029 1064 1.009429 AGGAGGCAGAAGGAGGAGAAT 59.991 52.381 0.00 0.00 0.00 2.40
1178 1213 3.176708 GCGTTCAAGTAGCGATGAGTTA 58.823 45.455 0.00 0.00 32.92 2.24
1181 1216 0.924090 GGCGTTCAAGTAGCGATGAG 59.076 55.000 0.00 0.00 32.92 2.90
1264 1305 0.534877 CAGTGCTGTACAGGTTGCCA 60.535 55.000 23.95 10.26 0.00 4.92
1282 1323 2.029369 GTGTTCGTGCCGTACCCA 59.971 61.111 2.89 0.00 0.00 4.51
1315 1356 3.036084 CCGTCGTTGAACAGCGCT 61.036 61.111 2.64 2.64 34.98 5.92
1480 1521 2.351276 GCCATGTCGAAGTGGGGT 59.649 61.111 16.53 0.00 36.00 4.95
1751 1926 2.930040 GCACATGCGATGTAACTGTAGT 59.070 45.455 0.00 0.00 42.70 2.73
1819 1999 8.534954 AACATGCAGGATTAGTACTCTTAGTA 57.465 34.615 4.84 0.00 0.00 1.82
1820 2000 7.425224 AACATGCAGGATTAGTACTCTTAGT 57.575 36.000 4.84 0.00 0.00 2.24
1821 2001 7.868415 GGTAACATGCAGGATTAGTACTCTTAG 59.132 40.741 4.84 0.00 0.00 2.18
1822 2002 7.201974 GGGTAACATGCAGGATTAGTACTCTTA 60.202 40.741 4.84 0.00 39.74 2.10
1823 2003 6.408206 GGGTAACATGCAGGATTAGTACTCTT 60.408 42.308 4.84 0.00 39.74 2.85
1824 2004 5.070580 GGGTAACATGCAGGATTAGTACTCT 59.929 44.000 4.84 0.00 39.74 3.24
1825 2005 5.298347 GGGTAACATGCAGGATTAGTACTC 58.702 45.833 4.84 0.00 39.74 2.59
1862 2042 1.874019 GATCATGCGACGCGTCAGT 60.874 57.895 35.71 19.50 0.00 3.41
2193 2384 0.415429 AAGGAGAAGAGGAGGGAGCA 59.585 55.000 0.00 0.00 0.00 4.26
2197 2388 1.007721 TGGAGAAGGAGAAGAGGAGGG 59.992 57.143 0.00 0.00 0.00 4.30
2210 2401 2.408271 TGCTTATGCCTGTGGAGAAG 57.592 50.000 0.00 0.00 38.71 2.85
2233 2424 1.455248 CTCCGTCCGTCTCTTCTCTT 58.545 55.000 0.00 0.00 0.00 2.85
2264 2455 5.707357 CACGCGAATGCAAAATAATTCTTC 58.293 37.500 15.93 0.00 42.97 2.87
2278 2469 4.799473 CCTGCACGCACGCGAATG 62.799 66.667 19.66 8.07 42.83 2.67
2418 2619 2.755103 GGATGGATGGTTGTTCAAGTCC 59.245 50.000 0.00 0.00 0.00 3.85
2423 2624 3.735720 TGATGGATGGATGGTTGTTCA 57.264 42.857 0.00 0.00 0.00 3.18
2430 2631 2.104792 ACGGTACTTGATGGATGGATGG 59.895 50.000 0.00 0.00 0.00 3.51
2431 2632 3.475566 ACGGTACTTGATGGATGGATG 57.524 47.619 0.00 0.00 0.00 3.51
2432 2633 3.005472 CGTACGGTACTTGATGGATGGAT 59.995 47.826 15.69 0.00 0.00 3.41
2433 2634 2.359848 CGTACGGTACTTGATGGATGGA 59.640 50.000 15.69 0.00 0.00 3.41
2471 2673 7.432350 TTCTTCTTCTTCTTCTTCAATGAGC 57.568 36.000 0.00 0.00 0.00 4.26
2514 2772 9.064706 GGTACTGCTACTGATCATAACTAGTAA 57.935 37.037 0.00 0.00 0.00 2.24
2515 2773 8.438373 AGGTACTGCTACTGATCATAACTAGTA 58.562 37.037 0.00 0.81 37.18 1.82
2516 2774 7.291566 AGGTACTGCTACTGATCATAACTAGT 58.708 38.462 0.00 1.78 37.18 2.57
2591 2852 6.406177 GGCCTTGCAAATCTTCTATTTCATCA 60.406 38.462 0.00 0.00 0.00 3.07
2600 2861 5.945144 AAATATGGCCTTGCAAATCTTCT 57.055 34.783 3.32 0.00 0.00 2.85
2674 2943 2.413310 AAGTCCGTCCACACTTGTTT 57.587 45.000 0.00 0.00 31.42 2.83
2678 2947 0.818040 GCCAAAGTCCGTCCACACTT 60.818 55.000 0.00 0.00 34.16 3.16
2726 3002 4.838152 CGTCTCCCGCCCATGTGG 62.838 72.222 0.00 0.00 42.11 4.17
2840 3120 3.480470 GACGATGGACAATCATTCCCAT 58.520 45.455 1.32 1.32 41.70 4.00
2841 3121 2.741553 CGACGATGGACAATCATTCCCA 60.742 50.000 0.00 0.00 34.68 4.37
2844 3124 4.380839 CATCGACGATGGACAATCATTC 57.619 45.455 26.65 0.00 36.51 2.67
2899 3179 1.538204 CCGATCCTACGACCACCATTG 60.538 57.143 0.00 0.00 35.09 2.82
2900 3180 0.750850 CCGATCCTACGACCACCATT 59.249 55.000 0.00 0.00 35.09 3.16
2901 3181 1.745320 GCCGATCCTACGACCACCAT 61.745 60.000 0.00 0.00 35.09 3.55
2902 3182 2.420568 GCCGATCCTACGACCACCA 61.421 63.158 0.00 0.00 35.09 4.17
2903 3183 2.073037 GAGCCGATCCTACGACCACC 62.073 65.000 0.00 0.00 35.09 4.61
2904 3184 1.359475 GAGCCGATCCTACGACCAC 59.641 63.158 0.00 0.00 35.09 4.16
2923 3203 2.616001 CCATGGCACCATTTCAAAAGGG 60.616 50.000 0.00 4.70 44.94 3.95
2928 3208 1.559368 CTCCCATGGCACCATTTCAA 58.441 50.000 6.09 0.00 33.90 2.69
2960 3240 2.158295 ACAACACCAGGACTCTAGGAGT 60.158 50.000 0.00 0.00 46.42 3.85
2970 3250 1.348064 CACCCTAGACAACACCAGGA 58.652 55.000 0.00 0.00 0.00 3.86
2979 3259 1.621317 TGCGAAATCACACCCTAGACA 59.379 47.619 0.00 0.00 0.00 3.41
3074 3366 5.189878 GCGATCACGTTAGCTATCTGCTAG 61.190 50.000 0.00 0.00 45.75 3.42
3075 3367 3.365064 GCGATCACGTTAGCTATCTGCTA 60.365 47.826 0.00 0.00 45.44 3.49
3076 3368 3.275400 CGATCACGTTAGCTATCTGCT 57.725 47.619 0.00 0.00 43.91 4.24
3077 3369 1.716581 GCGATCACGTTAGCTATCTGC 59.283 52.381 0.00 0.00 41.98 4.26
3078 3370 2.320367 GGCGATCACGTTAGCTATCTG 58.680 52.381 0.00 0.00 41.98 2.90
3079 3371 1.269998 GGGCGATCACGTTAGCTATCT 59.730 52.381 0.00 0.00 41.98 1.98
3080 3372 1.699343 GGGCGATCACGTTAGCTATC 58.301 55.000 0.00 0.00 41.98 2.08
3081 3373 0.039437 CGGGCGATCACGTTAGCTAT 60.039 55.000 0.00 0.00 41.98 2.97
3082 3374 1.096967 TCGGGCGATCACGTTAGCTA 61.097 55.000 0.00 0.00 41.98 3.32
3083 3375 2.104331 CGGGCGATCACGTTAGCT 59.896 61.111 0.00 0.00 41.98 3.32
3084 3376 1.944676 CTCGGGCGATCACGTTAGC 60.945 63.158 0.00 0.00 41.98 3.09
3085 3377 1.299165 CCTCGGGCGATCACGTTAG 60.299 63.158 0.00 0.00 41.98 2.34
3086 3378 1.750018 TCCTCGGGCGATCACGTTA 60.750 57.895 0.00 0.00 41.98 3.18
3087 3379 3.066190 TCCTCGGGCGATCACGTT 61.066 61.111 0.00 0.00 41.98 3.99
3088 3380 3.823330 GTCCTCGGGCGATCACGT 61.823 66.667 0.00 0.00 41.98 4.49
3107 3399 0.660595 GTGATACGATGGGACGCTCG 60.661 60.000 0.00 8.90 40.98 5.03
3134 3426 4.426416 CCGGAAACAATAGTCACGTATCA 58.574 43.478 0.00 0.00 0.00 2.15
3136 3428 3.192466 GCCGGAAACAATAGTCACGTAT 58.808 45.455 5.05 0.00 0.00 3.06
3137 3429 2.029200 TGCCGGAAACAATAGTCACGTA 60.029 45.455 5.05 0.00 0.00 3.57
3155 3448 7.880195 AGTACTACATCAATGATCCTAAATGCC 59.120 37.037 0.00 0.00 0.00 4.40
3156 3449 8.839310 AGTACTACATCAATGATCCTAAATGC 57.161 34.615 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.