Multiple sequence alignment - TraesCS4B01G079600

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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 TraesCS4B01G079600 chr4B 100.000 4259 0 0 983 5241 77510871 77515129 0.000000e+00 7866.0
1 TraesCS4B01G079600 chr4B 100.000 676 0 0 1 676 77509889 77510564 0.000000e+00 1249.0
2 TraesCS4B01G079600 chr4B 84.264 788 93 20 2214 2987 438098389 438099159 0.000000e+00 739.0
3 TraesCS4B01G079600 chr4B 79.469 565 97 16 3704 4257 77002703 77003259 2.960000e-102 383.0
4 TraesCS4B01G079600 chr4B 83.082 331 36 6 3353 3683 438099611 438099921 3.090000e-72 283.0
5 TraesCS4B01G079600 chr4B 78.810 269 33 19 983 1237 438098094 438098352 5.430000e-35 159.0
6 TraesCS4B01G079600 chr4D 93.990 1564 87 4 3681 5241 52753352 52754911 0.000000e+00 2361.0
7 TraesCS4B01G079600 chr4D 95.125 1477 60 9 2213 3683 52751806 52753276 0.000000e+00 2318.0
8 TraesCS4B01G079600 chr4D 90.300 433 26 4 260 676 52751000 52751432 2.130000e-153 553.0
9 TraesCS4B01G079600 chr4D 78.445 566 103 16 3704 4257 52495888 52496446 8.350000e-93 351.0
10 TraesCS4B01G079600 chr4D 90.000 150 13 2 3489 3637 52495408 52495556 5.360000e-45 193.0
11 TraesCS4B01G079600 chr4A 94.122 1259 70 2 3985 5241 544058703 544057447 0.000000e+00 1912.0
12 TraesCS4B01G079600 chr4A 90.644 1165 76 20 2215 3355 544060569 544059414 0.000000e+00 1517.0
13 TraesCS4B01G079600 chr4A 91.698 530 37 3 3406 3935 544059318 544058796 0.000000e+00 728.0
14 TraesCS4B01G079600 chr4A 88.427 337 19 8 162 479 544061505 544061170 6.360000e-104 388.0
15 TraesCS4B01G079600 chr4A 91.220 205 13 2 476 676 544061144 544060941 1.860000e-69 274.0
16 TraesCS4B01G079600 chr4A 90.164 183 18 0 1058 1240 544060790 544060608 6.780000e-59 239.0
17 TraesCS4B01G079600 chr4A 91.935 62 5 0 21 82 544061582 544061521 2.600000e-13 87.9
18 TraesCS4B01G079600 chr7A 93.432 944 38 7 1274 2207 109082620 109081691 0.000000e+00 1378.0
19 TraesCS4B01G079600 chr7A 83.397 1054 116 36 2214 3253 611770761 611771769 0.000000e+00 922.0
20 TraesCS4B01G079600 chr7A 85.498 331 36 4 3353 3683 611772026 611772344 8.410000e-88 335.0
21 TraesCS4B01G079600 chr7A 78.491 265 41 13 983 1237 611770466 611770724 5.430000e-35 159.0
22 TraesCS4B01G079600 chr7A 91.525 59 4 1 99 157 214311123 214311180 4.350000e-11 80.5
23 TraesCS4B01G079600 chr3A 90.522 939 58 12 1273 2207 548008011 548008922 0.000000e+00 1212.0
24 TraesCS4B01G079600 chr3A 88.699 938 54 12 1274 2207 744263864 744264753 0.000000e+00 1098.0
25 TraesCS4B01G079600 chr5A 90.192 938 61 10 1274 2207 659525317 659526227 0.000000e+00 1194.0
26 TraesCS4B01G079600 chr5A 95.652 138 5 1 2071 2207 663103126 663103263 2.460000e-53 220.0
27 TraesCS4B01G079600 chr2A 83.523 1056 112 38 2214 3253 115433402 115434411 0.000000e+00 929.0
28 TraesCS4B01G079600 chr2A 82.770 296 36 14 2913 3197 687066990 687067281 3.130000e-62 250.0
29 TraesCS4B01G079600 chr2A 78.947 266 39 13 983 1237 115433106 115433365 1.170000e-36 165.0
30 TraesCS4B01G079600 chr2A 98.077 52 1 0 2156 2207 16375439 16375388 2.010000e-14 91.6
31 TraesCS4B01G079600 chr1B 83.412 1055 115 37 2214 3253 93953282 93954291 0.000000e+00 924.0
32 TraesCS4B01G079600 chr1B 85.498 331 36 4 3353 3683 93954549 93954867 8.410000e-88 335.0
33 TraesCS4B01G079600 chr1B 87.248 149 18 1 1274 1421 284396576 284396724 9.030000e-38 169.0
34 TraesCS4B01G079600 chr2D 81.818 1078 123 44 2303 3351 640354951 640355984 0.000000e+00 837.0
35 TraesCS4B01G079600 chr2D 86.710 459 42 9 1552 2006 124475636 124475193 4.720000e-135 492.0
36 TraesCS4B01G079600 chr2D 87.446 231 27 2 3454 3683 640356122 640356351 1.120000e-66 265.0
37 TraesCS4B01G079600 chr2D 80.216 278 21 17 983 1237 640344682 640344948 1.500000e-40 178.0
38 TraesCS4B01G079600 chr2D 79.524 210 39 4 1275 1481 46356663 46356871 4.230000e-31 147.0
39 TraesCS4B01G079600 chr7D 84.891 781 89 14 2214 2980 511059859 511060624 0.000000e+00 761.0
40 TraesCS4B01G079600 chr7D 83.867 781 95 17 2214 2980 580125292 580124529 0.000000e+00 715.0
41 TraesCS4B01G079600 chr7D 85.498 331 36 4 3353 3683 511060736 511061054 8.410000e-88 335.0
42 TraesCS4B01G079600 chr7D 84.592 331 39 4 3353 3683 580124417 580124099 8.470000e-83 318.0
43 TraesCS4B01G079600 chr7D 78.868 265 40 13 983 1237 511059564 511059822 1.170000e-36 165.0
44 TraesCS4B01G079600 chr7D 90.909 77 4 2 983 1059 580125570 580125497 3.340000e-17 100.0
45 TraesCS4B01G079600 chr7D 96.429 56 2 0 99 154 563208079 563208134 5.590000e-15 93.5
46 TraesCS4B01G079600 chr6B 84.884 774 93 14 2214 2980 182639488 182638732 0.000000e+00 760.0
47 TraesCS4B01G079600 chr6B 92.982 57 3 1 99 155 36778468 36778523 1.210000e-11 82.4
48 TraesCS4B01G079600 chr6B 92.857 56 2 2 99 153 665497401 665497347 4.350000e-11 80.5
49 TraesCS4B01G079600 chr3B 84.238 774 96 15 2214 2980 71452909 71452155 0.000000e+00 730.0
50 TraesCS4B01G079600 chr2B 84.491 619 64 11 1590 2207 177117564 177116977 2.720000e-162 582.0
51 TraesCS4B01G079600 chr3D 93.525 278 8 4 1273 1550 164637573 164637840 6.320000e-109 405.0
52 TraesCS4B01G079600 chr3D 98.214 56 0 1 2156 2211 383184183 383184129 4.320000e-16 97.1
53 TraesCS4B01G079600 chr1A 89.320 103 11 0 1269 1371 516726024 516725922 4.260000e-26 130.0
54 TraesCS4B01G079600 chrUn 96.154 52 2 0 2156 2207 62143898 62143949 9.350000e-13 86.1
55 TraesCS4B01G079600 chrUn 93.103 58 3 1 99 155 331923113 331923056 3.360000e-12 84.2
56 TraesCS4B01G079600 chrUn 93.103 58 3 1 99 155 331951361 331951304 3.360000e-12 84.2
57 TraesCS4B01G079600 chrUn 93.103 58 3 1 99 155 464230358 464230301 3.360000e-12 84.2
58 TraesCS4B01G079600 chr1D 92.982 57 3 1 99 155 357440293 357440238 1.210000e-11 82.4
59 TraesCS4B01G079600 chr1D 91.379 58 3 2 99 155 322070685 322070629 1.560000e-10 78.7


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 TraesCS4B01G079600 chr4B 77509889 77515129 5240 False 4557.500000 7866 100.000000 1 5241 2 chr4B.!!$F2 5240
1 TraesCS4B01G079600 chr4B 438098094 438099921 1827 False 393.666667 739 82.052000 983 3683 3 chr4B.!!$F3 2700
2 TraesCS4B01G079600 chr4B 77002703 77003259 556 False 383.000000 383 79.469000 3704 4257 1 chr4B.!!$F1 553
3 TraesCS4B01G079600 chr4D 52751000 52754911 3911 False 1744.000000 2361 93.138333 260 5241 3 chr4D.!!$F2 4981
4 TraesCS4B01G079600 chr4D 52495408 52496446 1038 False 272.000000 351 84.222500 3489 4257 2 chr4D.!!$F1 768
5 TraesCS4B01G079600 chr4A 544057447 544061582 4135 True 735.128571 1912 91.172857 21 5241 7 chr4A.!!$R1 5220
6 TraesCS4B01G079600 chr7A 109081691 109082620 929 True 1378.000000 1378 93.432000 1274 2207 1 chr7A.!!$R1 933
7 TraesCS4B01G079600 chr7A 611770466 611772344 1878 False 472.000000 922 82.462000 983 3683 3 chr7A.!!$F2 2700
8 TraesCS4B01G079600 chr3A 548008011 548008922 911 False 1212.000000 1212 90.522000 1273 2207 1 chr3A.!!$F1 934
9 TraesCS4B01G079600 chr3A 744263864 744264753 889 False 1098.000000 1098 88.699000 1274 2207 1 chr3A.!!$F2 933
10 TraesCS4B01G079600 chr5A 659525317 659526227 910 False 1194.000000 1194 90.192000 1274 2207 1 chr5A.!!$F1 933
11 TraesCS4B01G079600 chr2A 115433106 115434411 1305 False 547.000000 929 81.235000 983 3253 2 chr2A.!!$F2 2270
12 TraesCS4B01G079600 chr1B 93953282 93954867 1585 False 629.500000 924 84.455000 2214 3683 2 chr1B.!!$F2 1469
13 TraesCS4B01G079600 chr2D 640354951 640356351 1400 False 551.000000 837 84.632000 2303 3683 2 chr2D.!!$F3 1380
14 TraesCS4B01G079600 chr7D 511059564 511061054 1490 False 420.333333 761 83.085667 983 3683 3 chr7D.!!$F2 2700
15 TraesCS4B01G079600 chr7D 580124099 580125570 1471 True 377.666667 715 86.456000 983 3683 3 chr7D.!!$R1 2700
16 TraesCS4B01G079600 chr6B 182638732 182639488 756 True 760.000000 760 84.884000 2214 2980 1 chr6B.!!$R1 766
17 TraesCS4B01G079600 chr3B 71452155 71452909 754 True 730.000000 730 84.238000 2214 2980 1 chr3B.!!$R1 766
18 TraesCS4B01G079600 chr2B 177116977 177117564 587 True 582.000000 582 84.491000 1590 2207 1 chr2B.!!$R1 617

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
97 98 0.105593 ACTCTCATACATGCGCTGGG 59.894 55.0 9.73 0.0 0.00 4.45 F
107 108 0.179045 ATGCGCTGGGTGTATTCCTC 60.179 55.0 9.73 0.0 0.00 3.71 F
110 111 0.389391 CGCTGGGTGTATTCCTCGAT 59.611 55.0 0.00 0.0 0.00 3.59 F
1896 2029 0.466739 TACGGCTCGCCTTCCTGATA 60.467 55.0 6.35 0.0 0.00 2.15 F
2709 2866 0.388907 AATGCAGAAATGGTGCGTGC 60.389 50.0 0.00 0.0 44.35 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1117 0.107831 TTGGGACTGTTGGGAACTCG 59.892 55.0 0.00 0.00 0.0 4.18 R
1896 2029 0.619832 TCCAGGCCATGAAGAGCTCT 60.620 55.0 11.45 11.45 0.0 4.09 R
2022 2155 0.749454 GGTATGTTGAGCCCTGCCTG 60.749 60.0 0.00 0.00 0.0 4.85 R
3185 3358 0.962356 CTCAAATGGGACGCTTGGCT 60.962 55.0 0.00 0.00 0.0 4.75 R
4634 5333 0.179127 ACGATGATGAGCAGGACACG 60.179 55.0 0.00 0.00 0.0 4.49 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
25 26 3.327757 TGTTGATGGCTGTAGAAGACCTT 59.672 43.478 0.00 0.00 29.74 3.50
28 29 3.776969 TGATGGCTGTAGAAGACCTTGAT 59.223 43.478 0.00 0.00 29.74 2.57
33 34 4.160626 GGCTGTAGAAGACCTTGATGTAGT 59.839 45.833 0.00 0.00 0.00 2.73
94 95 6.516718 ACTTTTATACTCTCATACATGCGCT 58.483 36.000 9.73 0.00 0.00 5.92
95 96 6.422100 ACTTTTATACTCTCATACATGCGCTG 59.578 38.462 9.73 7.16 0.00 5.18
96 97 2.800881 TACTCTCATACATGCGCTGG 57.199 50.000 9.73 2.61 0.00 4.85
97 98 0.105593 ACTCTCATACATGCGCTGGG 59.894 55.000 9.73 0.00 0.00 4.45
98 99 0.105593 CTCTCATACATGCGCTGGGT 59.894 55.000 9.73 6.68 0.00 4.51
99 100 0.179076 TCTCATACATGCGCTGGGTG 60.179 55.000 9.73 5.01 0.00 4.61
100 101 0.462581 CTCATACATGCGCTGGGTGT 60.463 55.000 9.73 10.97 0.00 4.16
101 102 0.827368 TCATACATGCGCTGGGTGTA 59.173 50.000 9.73 12.82 33.35 2.90
102 103 1.416030 TCATACATGCGCTGGGTGTAT 59.584 47.619 9.73 14.46 39.05 2.29
103 104 2.158827 TCATACATGCGCTGGGTGTATT 60.159 45.455 18.62 7.93 37.04 1.89
104 105 1.948104 TACATGCGCTGGGTGTATTC 58.052 50.000 9.73 0.00 0.00 1.75
105 106 0.748005 ACATGCGCTGGGTGTATTCC 60.748 55.000 9.73 0.00 0.00 3.01
106 107 0.464373 CATGCGCTGGGTGTATTCCT 60.464 55.000 9.73 0.00 0.00 3.36
107 108 0.179045 ATGCGCTGGGTGTATTCCTC 60.179 55.000 9.73 0.00 0.00 3.71
108 109 1.883084 GCGCTGGGTGTATTCCTCG 60.883 63.158 0.00 0.00 0.00 4.63
109 110 1.813859 CGCTGGGTGTATTCCTCGA 59.186 57.895 0.00 0.00 0.00 4.04
110 111 0.389391 CGCTGGGTGTATTCCTCGAT 59.611 55.000 0.00 0.00 0.00 3.59
111 112 1.869754 CGCTGGGTGTATTCCTCGATG 60.870 57.143 0.00 0.00 0.00 3.84
112 113 1.871080 CTGGGTGTATTCCTCGATGC 58.129 55.000 0.00 0.00 0.00 3.91
113 114 1.414181 CTGGGTGTATTCCTCGATGCT 59.586 52.381 0.00 0.00 0.00 3.79
114 115 2.628178 CTGGGTGTATTCCTCGATGCTA 59.372 50.000 0.00 0.00 0.00 3.49
115 116 3.239449 TGGGTGTATTCCTCGATGCTAT 58.761 45.455 0.00 0.00 0.00 2.97
116 117 4.412843 TGGGTGTATTCCTCGATGCTATA 58.587 43.478 0.00 0.00 0.00 1.31
117 118 5.023452 TGGGTGTATTCCTCGATGCTATAT 58.977 41.667 0.00 0.00 0.00 0.86
118 119 5.483937 TGGGTGTATTCCTCGATGCTATATT 59.516 40.000 0.00 0.00 0.00 1.28
119 120 6.013725 TGGGTGTATTCCTCGATGCTATATTT 60.014 38.462 0.00 0.00 0.00 1.40
120 121 6.879458 GGGTGTATTCCTCGATGCTATATTTT 59.121 38.462 0.00 0.00 0.00 1.82
121 122 7.148407 GGGTGTATTCCTCGATGCTATATTTTG 60.148 40.741 0.00 0.00 0.00 2.44
122 123 7.602644 GGTGTATTCCTCGATGCTATATTTTGA 59.397 37.037 0.00 0.00 0.00 2.69
123 124 8.651588 GTGTATTCCTCGATGCTATATTTTGAG 58.348 37.037 0.00 0.00 0.00 3.02
124 125 8.367911 TGTATTCCTCGATGCTATATTTTGAGT 58.632 33.333 0.00 0.00 0.00 3.41
125 126 7.897575 ATTCCTCGATGCTATATTTTGAGTC 57.102 36.000 0.00 0.00 0.00 3.36
126 127 6.405278 TCCTCGATGCTATATTTTGAGTCA 57.595 37.500 0.00 0.00 0.00 3.41
127 128 6.816136 TCCTCGATGCTATATTTTGAGTCAA 58.184 36.000 0.08 0.08 0.00 3.18
128 129 7.445121 TCCTCGATGCTATATTTTGAGTCAAT 58.555 34.615 6.36 0.00 0.00 2.57
129 130 8.585018 TCCTCGATGCTATATTTTGAGTCAATA 58.415 33.333 6.36 1.98 0.00 1.90
130 131 9.208022 CCTCGATGCTATATTTTGAGTCAATAA 57.792 33.333 6.36 4.84 0.00 1.40
191 192 0.785979 CAAAGAAAAGGTGCGCATGC 59.214 50.000 15.91 7.91 43.20 4.06
236 238 3.029570 GTTACCATCCTTAGGACCGAGT 58.970 50.000 1.74 1.31 32.98 4.18
238 240 0.753262 CCATCCTTAGGACCGAGTGG 59.247 60.000 1.74 2.94 42.84 4.00
253 255 2.483013 CGAGTGGTCACTTGGACTGAAA 60.483 50.000 9.86 0.00 46.16 2.69
256 258 2.872858 GTGGTCACTTGGACTGAAAGAC 59.127 50.000 0.00 0.00 46.16 3.01
303 307 2.486918 GTTTAGTACGTGTGGGTGCTT 58.513 47.619 0.00 0.00 34.58 3.91
317 321 1.334689 GGTGCTTGTGCGGTTCTAAAC 60.335 52.381 0.00 0.00 43.34 2.01
392 396 3.691744 CTCGTCCTGCTCAGACGGC 62.692 68.421 18.84 0.00 41.94 5.68
451 472 1.374125 CTGTCGTCCGCATCAACCA 60.374 57.895 0.00 0.00 0.00 3.67
452 473 0.948623 CTGTCGTCCGCATCAACCAA 60.949 55.000 0.00 0.00 0.00 3.67
453 474 0.533085 TGTCGTCCGCATCAACCAAA 60.533 50.000 0.00 0.00 0.00 3.28
525 574 1.383248 CCCCTCTCCCTCCATTCGT 60.383 63.158 0.00 0.00 0.00 3.85
620 673 1.287730 GAGGCAGCACAACAGAGACG 61.288 60.000 0.00 0.00 0.00 4.18
645 698 7.050970 AGGGTATTTCTTTCAAACTTCCAAC 57.949 36.000 0.00 0.00 0.00 3.77
654 707 1.068333 CAAACTTCCAACCATCTGGCG 60.068 52.381 0.00 0.00 39.32 5.69
1051 1104 4.937696 TTACGTGACAAATGGTGCTATG 57.062 40.909 0.00 0.00 0.00 2.23
1059 1112 1.024046 AATGGTGCTATGCGCGTTCA 61.024 50.000 7.78 3.52 43.27 3.18
1064 1117 2.995482 CTATGCGCGTTCACGGTC 59.005 61.111 7.78 0.00 40.23 4.79
1065 1118 2.845739 CTATGCGCGTTCACGGTCG 61.846 63.158 7.78 0.00 40.23 4.79
1066 1119 3.325493 TATGCGCGTTCACGGTCGA 62.325 57.895 7.78 0.00 40.23 4.20
1069 1122 2.728383 CGCGTTCACGGTCGAGTT 60.728 61.111 0.00 0.00 40.23 3.01
1082 1171 0.761323 TCGAGTTCCCAACAGTCCCA 60.761 55.000 0.00 0.00 0.00 4.37
1156 1245 2.755650 CGAAGTTGCAGTACAGGAAGT 58.244 47.619 0.00 0.00 0.00 3.01
1237 1326 6.219417 TGAACCATCATGTTTCTGTTGTTT 57.781 33.333 0.00 0.00 0.00 2.83
1240 1329 6.219417 ACCATCATGTTTCTGTTGTTTTCA 57.781 33.333 0.00 0.00 0.00 2.69
1241 1330 6.042143 ACCATCATGTTTCTGTTGTTTTCAC 58.958 36.000 0.00 0.00 0.00 3.18
1298 1404 7.346175 TGAGCTCTTTTATGGTACCCTGTATTA 59.654 37.037 16.19 0.00 0.00 0.98
1596 1708 3.771160 CCCTTCCACGCTACGGCT 61.771 66.667 0.00 0.00 36.09 5.52
1687 1799 1.059838 CATGACGACAGTGCATGCG 59.940 57.895 14.09 0.76 33.04 4.73
1739 1872 3.822192 CCGACGATGAGGCCACGA 61.822 66.667 5.01 0.00 0.00 4.35
1740 1873 2.413351 CGACGATGAGGCCACGAT 59.587 61.111 5.01 0.00 0.00 3.73
1741 1874 1.946156 CGACGATGAGGCCACGATG 60.946 63.158 5.01 0.00 0.00 3.84
1742 1875 1.141881 GACGATGAGGCCACGATGT 59.858 57.895 5.01 0.00 0.00 3.06
1743 1876 0.872021 GACGATGAGGCCACGATGTC 60.872 60.000 5.01 3.34 0.00 3.06
1827 1960 1.066002 CGTCGGAACCTCGCCTATTTA 59.934 52.381 0.00 0.00 0.00 1.40
1896 2029 0.466739 TACGGCTCGCCTTCCTGATA 60.467 55.000 6.35 0.00 0.00 2.15
2018 2151 2.261215 GCTCAAAAGCTCACCCAGG 58.739 57.895 0.00 0.00 45.55 4.45
2019 2152 1.871126 GCTCAAAAGCTCACCCAGGC 61.871 60.000 0.00 0.00 45.55 4.85
2020 2153 0.538057 CTCAAAAGCTCACCCAGGCA 60.538 55.000 0.00 0.00 0.00 4.75
2021 2154 0.538057 TCAAAAGCTCACCCAGGCAG 60.538 55.000 0.00 0.00 0.00 4.85
2022 2155 1.905354 AAAAGCTCACCCAGGCAGC 60.905 57.895 0.00 0.75 0.00 5.25
2023 2156 2.645394 AAAAGCTCACCCAGGCAGCA 62.645 55.000 10.13 0.00 35.46 4.41
2280 2421 7.385267 AGGAATCACATGATATGCTCTCTTAC 58.615 38.462 0.00 0.00 33.73 2.34
2328 2469 0.593128 ACACCGCAGAAATTGTCAGC 59.407 50.000 0.00 0.00 35.48 4.26
2346 2488 1.425066 AGCACACATTCCTTCCTTCCA 59.575 47.619 0.00 0.00 0.00 3.53
2377 2519 4.511826 ACCGTCTCATTTTCTGAAGTTGAC 59.488 41.667 0.00 0.00 32.14 3.18
2389 2531 4.885325 TCTGAAGTTGACCCCAGTTTTAAC 59.115 41.667 0.00 0.00 0.00 2.01
2407 2554 9.659830 AGTTTTAACTGAACTACTTTTATTGCG 57.340 29.630 0.00 0.00 37.98 4.85
2549 2706 4.023536 TGCAGTTTCCGAATCCTTTTGTAC 60.024 41.667 0.00 0.00 0.00 2.90
2680 2837 4.870426 TCTGGTTATTCAGATCGCACTTTC 59.130 41.667 0.00 0.00 38.70 2.62
2709 2866 0.388907 AATGCAGAAATGGTGCGTGC 60.389 50.000 0.00 0.00 44.35 5.34
3185 3358 8.610248 TTCAGTTACGATTCAACTAAATGGAA 57.390 30.769 0.00 0.00 34.50 3.53
3339 3609 2.026641 CCATAGGATTTGGTGCCTGTG 58.973 52.381 0.00 0.00 41.46 3.66
3388 3722 0.938008 TGTGCGCACAATACGTTTGA 59.062 45.000 39.13 13.41 38.56 2.69
3432 3766 7.175347 TGCAGAAGACAGACAAAGATAGTAT 57.825 36.000 0.00 0.00 0.00 2.12
3685 4163 5.139435 TCAGTCACTTGAACTCTATGGTG 57.861 43.478 0.00 0.00 0.00 4.17
3719 4325 1.112459 CGCTTTGTTTTGTCGCAGTC 58.888 50.000 0.00 0.00 0.00 3.51
3913 4519 4.938832 GGCCAAAGTATATACACACACACA 59.061 41.667 15.18 0.00 0.00 3.72
3998 4695 3.890756 TGCTTCTGTTGTGATGTTTGGAT 59.109 39.130 0.00 0.00 0.00 3.41
4134 4831 0.545171 ACCACCATGGATCAGCTGAG 59.455 55.000 22.96 9.67 40.96 3.35
4145 4842 1.942776 TCAGCTGAGGGAGAACATCA 58.057 50.000 13.74 0.00 0.00 3.07
4285 4982 2.672195 GCAAATAACAGCAACCCTCAGC 60.672 50.000 0.00 0.00 0.00 4.26
4369 5066 9.416794 GTCAGTGTATATCATTGTTCTGGATAG 57.583 37.037 0.00 0.00 35.65 2.08
4380 5077 0.459899 TCTGGATAGACATTGCGCGT 59.540 50.000 8.43 0.00 0.00 6.01
4399 5096 4.947933 CGCGTTAAGAGTTAATAAAGTGCG 59.052 41.667 0.00 0.00 0.00 5.34
4416 5113 0.179111 GCGTCGGATGTCCAGATTCA 60.179 55.000 0.00 0.00 35.14 2.57
4457 5154 2.922740 ACACGAGTTACAACCCACAT 57.077 45.000 0.00 0.00 0.00 3.21
4465 5162 5.642063 CGAGTTACAACCCACATTATTCAGT 59.358 40.000 0.00 0.00 0.00 3.41
4488 5185 4.462508 TTTGCACACAAAGACCAAATCA 57.537 36.364 0.00 0.00 40.84 2.57
4505 5202 3.644884 ATCACATAATCCGACGAGTCC 57.355 47.619 0.00 0.00 0.00 3.85
4508 5205 2.099263 CACATAATCCGACGAGTCCTGT 59.901 50.000 0.00 0.00 0.00 4.00
4523 5220 5.220873 CGAGTCCTGTGATCGATTTCTCTAA 60.221 44.000 0.00 0.00 38.72 2.10
4568 5267 7.119699 TCCATTCAGTTTTACAGTCAAGCATAG 59.880 37.037 0.00 0.00 0.00 2.23
4634 5333 1.669999 ATCCATTCGCCTGCCTTTGC 61.670 55.000 0.00 0.00 38.26 3.68
4739 5438 2.125753 CTGCGACCACTCTCTGCC 60.126 66.667 0.00 0.00 0.00 4.85
4781 5480 1.425448 AGCTGCTTTCTTACCCAAGGT 59.575 47.619 0.00 0.00 40.16 3.50
4856 5555 0.601057 GGCAACTGGCGTATGGTTTT 59.399 50.000 0.00 0.00 46.16 2.43
4858 5557 2.058057 GCAACTGGCGTATGGTTTTTG 58.942 47.619 0.00 0.00 0.00 2.44
4911 5610 2.555757 GCAAAGAAGACTTGCCACAGAT 59.444 45.455 0.00 0.00 36.39 2.90
5014 5713 6.006449 AGACAAAAGGACTACAATGCAGAAT 58.994 36.000 0.00 0.00 0.00 2.40
5025 5724 5.490139 ACAATGCAGAATAGGAATGAACG 57.510 39.130 0.00 0.00 0.00 3.95
5083 5782 0.676184 TGATGCTGGATCTACCGAGC 59.324 55.000 10.56 0.00 42.61 5.03
5119 5818 1.064654 GCTTCTTGGGATCATGAACGC 59.935 52.381 12.40 12.40 34.62 4.84
5144 5843 2.029020 TCAGTTCCTTGACGTGGATCTG 60.029 50.000 18.70 18.70 45.64 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.256920 GTCTTCTACAGCCATCAACATGT 58.743 43.478 0.00 0.00 0.00 3.21
1 2 3.624861 GGTCTTCTACAGCCATCAACATG 59.375 47.826 0.00 0.00 0.00 3.21
3 4 2.906389 AGGTCTTCTACAGCCATCAACA 59.094 45.455 0.00 0.00 0.00 3.33
4 5 3.618690 AGGTCTTCTACAGCCATCAAC 57.381 47.619 0.00 0.00 0.00 3.18
5 6 3.582647 TCAAGGTCTTCTACAGCCATCAA 59.417 43.478 0.00 0.00 0.00 2.57
6 7 3.173151 TCAAGGTCTTCTACAGCCATCA 58.827 45.455 0.00 0.00 0.00 3.07
7 8 3.895232 TCAAGGTCTTCTACAGCCATC 57.105 47.619 0.00 0.00 0.00 3.51
8 9 3.521126 ACATCAAGGTCTTCTACAGCCAT 59.479 43.478 0.00 0.00 0.00 4.40
9 10 2.906389 ACATCAAGGTCTTCTACAGCCA 59.094 45.455 0.00 0.00 0.00 4.75
10 11 3.618690 ACATCAAGGTCTTCTACAGCC 57.381 47.619 0.00 0.00 0.00 4.85
11 12 5.331876 ACTACATCAAGGTCTTCTACAGC 57.668 43.478 0.00 0.00 0.00 4.40
12 13 8.608844 AAAAACTACATCAAGGTCTTCTACAG 57.391 34.615 0.00 0.00 0.00 2.74
19 20 9.975218 ACCATAATAAAAACTACATCAAGGTCT 57.025 29.630 0.00 0.00 0.00 3.85
82 83 0.827368 TACACCCAGCGCATGTATGA 59.173 50.000 11.47 0.00 0.00 2.15
84 85 2.494059 GAATACACCCAGCGCATGTAT 58.506 47.619 11.47 14.68 40.44 2.29
85 86 1.474320 GGAATACACCCAGCGCATGTA 60.474 52.381 11.47 12.95 33.54 2.29
86 87 0.748005 GGAATACACCCAGCGCATGT 60.748 55.000 11.47 11.00 0.00 3.21
89 90 1.220749 GAGGAATACACCCAGCGCA 59.779 57.895 11.47 0.00 0.00 6.09
90 91 1.883084 CGAGGAATACACCCAGCGC 60.883 63.158 0.00 0.00 0.00 5.92
91 92 0.389391 ATCGAGGAATACACCCAGCG 59.611 55.000 0.00 0.00 0.00 5.18
94 95 1.496060 AGCATCGAGGAATACACCCA 58.504 50.000 0.00 0.00 0.00 4.51
95 96 3.963428 ATAGCATCGAGGAATACACCC 57.037 47.619 0.00 0.00 0.00 4.61
96 97 7.602644 TCAAAATATAGCATCGAGGAATACACC 59.397 37.037 0.00 0.00 0.00 4.16
97 98 8.534333 TCAAAATATAGCATCGAGGAATACAC 57.466 34.615 0.00 0.00 0.00 2.90
98 99 8.367911 ACTCAAAATATAGCATCGAGGAATACA 58.632 33.333 0.00 0.00 0.00 2.29
99 100 8.764524 ACTCAAAATATAGCATCGAGGAATAC 57.235 34.615 0.00 0.00 0.00 1.89
100 101 8.585018 TGACTCAAAATATAGCATCGAGGAATA 58.415 33.333 0.00 0.00 0.00 1.75
101 102 7.445121 TGACTCAAAATATAGCATCGAGGAAT 58.555 34.615 0.00 0.00 0.00 3.01
102 103 6.816136 TGACTCAAAATATAGCATCGAGGAA 58.184 36.000 0.00 0.00 0.00 3.36
103 104 6.405278 TGACTCAAAATATAGCATCGAGGA 57.595 37.500 0.00 0.00 0.00 3.71
104 105 7.664082 ATTGACTCAAAATATAGCATCGAGG 57.336 36.000 0.00 0.00 0.00 4.63
160 161 6.934083 GCACCTTTTCTTTGGAAAAATATCCA 59.066 34.615 5.61 0.00 46.57 3.41
191 192 3.074412 AGCACATCGTTTTCTTACAGGG 58.926 45.455 0.00 0.00 0.00 4.45
236 238 2.158813 GGTCTTTCAGTCCAAGTGACCA 60.159 50.000 0.00 0.00 45.68 4.02
238 240 2.158813 TGGGTCTTTCAGTCCAAGTGAC 60.159 50.000 0.00 0.00 44.82 3.67
241 243 2.711009 TCATGGGTCTTTCAGTCCAAGT 59.289 45.455 0.00 0.00 32.56 3.16
242 244 3.423539 TCATGGGTCTTTCAGTCCAAG 57.576 47.619 0.00 0.00 32.56 3.61
243 245 3.486383 GTTCATGGGTCTTTCAGTCCAA 58.514 45.455 0.00 0.00 32.56 3.53
245 247 2.076863 CGTTCATGGGTCTTTCAGTCC 58.923 52.381 0.00 0.00 0.00 3.85
248 250 5.237344 GGATTATCGTTCATGGGTCTTTCAG 59.763 44.000 0.00 0.00 0.00 3.02
253 255 4.982241 ATGGATTATCGTTCATGGGTCT 57.018 40.909 0.00 0.00 0.00 3.85
256 258 3.822735 AGCAATGGATTATCGTTCATGGG 59.177 43.478 0.00 0.00 0.00 4.00
303 307 0.947180 GGCTCGTTTAGAACCGCACA 60.947 55.000 0.00 0.00 0.00 4.57
317 321 3.242413 CCTGAAAAACATATGTCGGCTCG 60.242 47.826 9.23 0.00 0.00 5.03
352 356 2.122768 AGGCACCAACAAAAATGGGAA 58.877 42.857 0.00 0.00 42.48 3.97
392 396 1.359848 CATGAAGGGAAAGACGGTCG 58.640 55.000 1.89 0.00 0.00 4.79
403 414 0.181114 TGGCGAAGATCCATGAAGGG 59.819 55.000 0.00 0.00 38.24 3.95
525 574 2.693017 GGAGGGGAGGAGAGCTCA 59.307 66.667 17.77 0.00 0.00 4.26
563 616 1.805945 CAGTTCACCGGCGAGCTAC 60.806 63.158 9.30 0.00 0.00 3.58
567 620 0.734253 CTCTTCAGTTCACCGGCGAG 60.734 60.000 9.30 0.06 0.00 5.03
620 673 6.894339 TGGAAGTTTGAAAGAAATACCCTC 57.106 37.500 0.00 0.00 0.00 4.30
645 698 1.656652 CACTTTAGTCCGCCAGATGG 58.343 55.000 0.00 0.00 38.53 3.51
654 707 2.939103 CAGTATGCAGCCACTTTAGTCC 59.061 50.000 0.00 0.00 0.00 3.85
1030 1083 3.126171 GCATAGCACCATTTGTCACGTAA 59.874 43.478 0.00 0.00 0.00 3.18
1059 1112 1.366366 CTGTTGGGAACTCGACCGT 59.634 57.895 0.00 0.00 0.00 4.83
1064 1117 0.107831 TTGGGACTGTTGGGAACTCG 59.892 55.000 0.00 0.00 0.00 4.18
1065 1118 2.158667 TCTTTGGGACTGTTGGGAACTC 60.159 50.000 0.00 0.00 0.00 3.01
1066 1119 1.850345 TCTTTGGGACTGTTGGGAACT 59.150 47.619 0.00 0.00 0.00 3.01
1067 1120 2.358322 TCTTTGGGACTGTTGGGAAC 57.642 50.000 0.00 0.00 0.00 3.62
1069 1122 1.075374 CCATCTTTGGGACTGTTGGGA 59.925 52.381 0.00 0.00 39.56 4.37
1082 1171 1.079127 CGTCTCCGGTGCCATCTTT 60.079 57.895 0.00 0.00 0.00 2.52
1114 1203 4.077184 TTCCTGCGCCGACCGAAT 62.077 61.111 4.18 0.00 40.02 3.34
1174 1263 4.402474 TCCAAGAGTTATCTCGCTGATGAA 59.598 41.667 7.25 0.00 44.65 2.57
1176 1265 4.313277 TCCAAGAGTTATCTCGCTGATG 57.687 45.455 7.25 0.02 44.65 3.07
1596 1708 1.573829 GGACGGCAAAGAACATCGCA 61.574 55.000 0.00 0.00 0.00 5.10
1687 1799 4.043200 GCTGCGCAGGGTGGTTTC 62.043 66.667 36.47 15.14 0.00 2.78
1722 1834 3.138930 ATCGTGGCCTCATCGTCGG 62.139 63.158 3.32 0.00 0.00 4.79
1738 1871 2.275510 CGACGTTGTACACATCGACATC 59.724 50.000 17.14 6.03 40.40 3.06
1739 1872 2.247637 CGACGTTGTACACATCGACAT 58.752 47.619 17.14 0.00 40.40 3.06
1740 1873 1.002576 ACGACGTTGTACACATCGACA 60.003 47.619 22.56 0.00 40.40 4.35
1741 1874 1.381100 CACGACGTTGTACACATCGAC 59.619 52.381 22.56 14.49 40.40 4.20
1742 1875 1.663730 CCACGACGTTGTACACATCGA 60.664 52.381 22.56 0.00 40.40 3.59
1743 1876 0.706184 CCACGACGTTGTACACATCG 59.294 55.000 8.44 16.86 42.75 3.84
1809 1942 2.100252 CACTAAATAGGCGAGGTTCCGA 59.900 50.000 0.00 0.00 0.00 4.55
1896 2029 0.619832 TCCAGGCCATGAAGAGCTCT 60.620 55.000 11.45 11.45 0.00 4.09
1943 2076 2.184579 GTAGCTGCTCCACGTCCC 59.815 66.667 4.91 0.00 0.00 4.46
2019 2152 3.060615 GTTGAGCCCTGCCTGCTG 61.061 66.667 0.00 0.00 39.69 4.41
2020 2153 1.565390 TATGTTGAGCCCTGCCTGCT 61.565 55.000 0.00 0.00 43.03 4.24
2021 2154 1.077501 TATGTTGAGCCCTGCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
2022 2155 0.749454 GGTATGTTGAGCCCTGCCTG 60.749 60.000 0.00 0.00 0.00 4.85
2023 2156 0.916358 AGGTATGTTGAGCCCTGCCT 60.916 55.000 0.00 0.00 0.00 4.75
2247 2388 7.015974 AGCATATCATGTGATTCCTTCTCTGTA 59.984 37.037 0.19 0.00 36.05 2.74
2280 2421 3.760151 TGTTGATGCCCTGATCAAAAGAG 59.240 43.478 0.00 0.00 42.58 2.85
2328 2469 4.081406 TGAATGGAAGGAAGGAATGTGTG 58.919 43.478 0.00 0.00 0.00 3.82
2346 2488 4.216257 CAGAAAATGAGACGGTGGTTGAAT 59.784 41.667 0.00 0.00 0.00 2.57
2394 2536 7.063308 TCGGGTACTAAAACGCAATAAAAGTAG 59.937 37.037 0.00 0.00 32.86 2.57
2407 2554 4.325972 TGGGTTGAATCGGGTACTAAAAC 58.674 43.478 0.00 0.00 0.00 2.43
2549 2706 4.292186 TCTGAAGTGGAAATCAGGGAAG 57.708 45.455 3.23 0.00 42.62 3.46
2709 2866 6.774656 ACTTTCCTTTATATTGGGAGCATCAG 59.225 38.462 0.00 0.00 36.25 2.90
3085 3256 6.783708 TTTGGAGCCAAAGTTCTCTTTTTA 57.216 33.333 10.49 0.00 41.31 1.52
3185 3358 0.962356 CTCAAATGGGACGCTTGGCT 60.962 55.000 0.00 0.00 0.00 4.75
3339 3609 8.868916 ACACAACAATCATAAAGTGTGAAAAAC 58.131 29.630 8.47 0.00 38.62 2.43
3388 3722 4.403752 TGCATATGCTCTGAGTGAACTACT 59.596 41.667 27.13 0.00 41.67 2.57
3432 3766 6.124340 TGGTCTACGGTTACAGATCTATGAA 58.876 40.000 0.00 0.00 0.00 2.57
3441 3775 9.837525 GAATTATATACTGGTCTACGGTTACAG 57.162 37.037 0.00 0.00 39.94 2.74
3442 3776 8.796475 GGAATTATATACTGGTCTACGGTTACA 58.204 37.037 0.00 0.00 39.94 2.41
3685 4163 1.726853 AAGCGTGCAGACTCCATTAC 58.273 50.000 0.00 0.00 0.00 1.89
3719 4325 1.005340 GGCAGACTTCAGCAAGATCG 58.995 55.000 0.00 0.00 33.34 3.69
3972 4633 5.005971 CCAAACATCACAACAGAAGCAAAAG 59.994 40.000 0.00 0.00 0.00 2.27
3973 4634 4.869297 CCAAACATCACAACAGAAGCAAAA 59.131 37.500 0.00 0.00 0.00 2.44
3977 4638 3.988379 TCCAAACATCACAACAGAAGC 57.012 42.857 0.00 0.00 0.00 3.86
3998 4695 2.360165 GGTATTCCTTCGTCGCTTCCTA 59.640 50.000 0.00 0.00 0.00 2.94
4022 4719 0.449388 CCATGCTTCTTCGCAACCTC 59.551 55.000 0.00 0.00 44.06 3.85
4134 4831 0.442699 GAACGCGTTGATGTTCTCCC 59.557 55.000 31.89 6.74 40.94 4.30
4176 4873 1.014044 GTCATCGAGAACTTGCGGCA 61.014 55.000 0.00 0.00 0.00 5.69
4285 4982 0.321564 TTCCTTGGTCTGTGCATCCG 60.322 55.000 0.00 0.00 0.00 4.18
4369 5066 2.875080 AACTCTTAACGCGCAATGTC 57.125 45.000 5.73 0.00 0.00 3.06
4375 5072 4.722447 GCACTTTATTAACTCTTAACGCGC 59.278 41.667 5.73 0.00 0.00 6.86
4380 5077 6.389091 TCCGACGCACTTTATTAACTCTTAA 58.611 36.000 0.00 0.00 0.00 1.85
4399 5096 2.482142 GGAGTGAATCTGGACATCCGAC 60.482 54.545 0.00 0.00 39.43 4.79
4416 5113 1.816835 CATTCAGTGCTGCAATGGAGT 59.183 47.619 27.09 12.44 29.97 3.85
4457 5154 7.013750 TGGTCTTTGTGTGCAAATACTGAATAA 59.986 33.333 0.00 0.00 42.88 1.40
4465 5162 5.982516 GTGATTTGGTCTTTGTGTGCAAATA 59.017 36.000 0.00 0.00 42.88 1.40
4478 5175 4.119862 CGTCGGATTATGTGATTTGGTCT 58.880 43.478 0.00 0.00 0.00 3.85
4488 5185 2.099263 CACAGGACTCGTCGGATTATGT 59.901 50.000 0.00 0.00 0.00 2.29
4523 5220 8.704668 TGAATGGAAGTGTGTATGTATAGATGT 58.295 33.333 0.00 0.00 0.00 3.06
4534 5231 7.051623 ACTGTAAAACTGAATGGAAGTGTGTA 58.948 34.615 0.00 0.00 0.00 2.90
4568 5267 2.262915 CGGGTCTCCTGCACTGAC 59.737 66.667 0.00 0.00 0.00 3.51
4634 5333 0.179127 ACGATGATGAGCAGGACACG 60.179 55.000 0.00 0.00 0.00 4.49
4739 5438 2.910482 CGAATTGATTGACCAGCAAACG 59.090 45.455 0.00 0.00 40.48 3.60
4781 5480 0.548031 GGCTTCATCCAGATGACCCA 59.452 55.000 9.84 0.00 46.49 4.51
4856 5555 0.609681 GGTGGGATAACCGGCAACAA 60.610 55.000 0.00 0.00 44.64 2.83
4858 5557 1.001887 TGGTGGGATAACCGGCAAC 60.002 57.895 0.00 0.00 43.73 4.17
4911 5610 4.955811 TCAAGTACAGAGAAAGGCTTCA 57.044 40.909 0.00 0.00 33.64 3.02
5008 5707 4.870426 TGACTTCGTTCATTCCTATTCTGC 59.130 41.667 0.00 0.00 0.00 4.26
5014 5713 5.243060 TCTCAGTTGACTTCGTTCATTCCTA 59.757 40.000 0.00 0.00 0.00 2.94
5025 5724 6.585389 AGTACGTTTTTCTCAGTTGACTTC 57.415 37.500 0.00 0.00 0.00 3.01
5083 5782 5.767168 CCAAGAAGCCTAGGAATGATAAAGG 59.233 44.000 14.75 0.00 0.00 3.11
5119 5818 3.138304 TCCACGTCAAGGAACTGAATTG 58.862 45.455 0.00 0.00 40.86 2.32
5144 5843 8.391075 TCCTAATTCGAAATCCATTATTCCAC 57.609 34.615 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.