Multiple sequence alignment - TraesCS3D01G207400

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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 TraesCS3D01G207400 chr3D 100.000 4906 0 0 1 4906 272932337 272937242 0.000000e+00 9060.0
1 TraesCS3D01G207400 chr3D 81.497 481 70 10 4426 4906 413654516 413654977 1.290000e-100 377.0
2 TraesCS3D01G207400 chr3D 85.385 130 18 1 330 459 113671045 113671173 3.080000e-27 134.0
3 TraesCS3D01G207400 chr3D 84.722 72 10 1 4193 4264 545697989 545697919 2.450000e-08 71.3
4 TraesCS3D01G207400 chr3A 95.933 2041 57 6 931 2949 356083171 356085207 0.000000e+00 3286.0
5 TraesCS3D01G207400 chr3A 95.868 1089 22 7 2948 4025 356085366 356086442 0.000000e+00 1740.0
6 TraesCS3D01G207400 chr3A 86.600 903 72 14 4009 4906 356086458 356087316 0.000000e+00 952.0
7 TraesCS3D01G207400 chr3A 85.862 290 35 2 4617 4906 553539093 553538810 2.220000e-78 303.0
8 TraesCS3D01G207400 chr3A 88.889 45 4 1 2753 2797 560107731 560107774 2.000000e-03 54.7
9 TraesCS3D01G207400 chr3B 93.896 1835 78 19 326 2140 361021504 361019684 0.000000e+00 2737.0
10 TraesCS3D01G207400 chr3B 92.681 1421 55 18 3137 4556 361012799 361011427 0.000000e+00 2002.0
11 TraesCS3D01G207400 chr3B 94.558 1029 34 5 2136 3145 361014308 361013283 0.000000e+00 1570.0
12 TraesCS3D01G207400 chr3B 86.919 344 41 3 1 340 361025912 361025569 2.770000e-102 383.0
13 TraesCS3D01G207400 chr3B 90.458 262 25 0 2860 3121 383184134 383183873 3.640000e-91 346.0
14 TraesCS3D01G207400 chr3B 89.723 253 24 2 2869 3120 546540270 546540019 6.130000e-84 322.0
15 TraesCS3D01G207400 chr3B 89.362 47 4 1 2753 2799 556668572 556668527 1.910000e-04 58.4
16 TraesCS3D01G207400 chr2B 80.000 715 100 24 4194 4904 195541555 195540880 5.710000e-134 488.0
17 TraesCS3D01G207400 chr2B 87.500 264 31 1 2860 3121 255579396 255579659 2.220000e-78 303.0
18 TraesCS3D01G207400 chr2B 73.448 467 93 25 282 739 653982910 653982466 3.960000e-31 147.0
19 TraesCS3D01G207400 chr2B 92.308 65 5 0 4187 4251 87120417 87120481 5.230000e-15 93.5
20 TraesCS3D01G207400 chr5D 77.807 757 127 22 1 747 327994609 327995334 3.510000e-116 429.0
21 TraesCS3D01G207400 chr5D 80.042 481 80 7 4426 4906 444472186 444472650 4.700000e-90 342.0
22 TraesCS3D01G207400 chr5B 81.988 483 67 11 4426 4906 322288879 322288415 4.600000e-105 392.0
23 TraesCS3D01G207400 chr5B 88.803 259 28 1 2862 3120 523746518 523746261 2.850000e-82 316.0
24 TraesCS3D01G207400 chr5B 78.295 516 82 20 248 756 224328210 224327718 6.170000e-79 305.0
25 TraesCS3D01G207400 chr5B 88.235 68 8 0 2463 2530 189160326 189160259 1.130000e-11 82.4
26 TraesCS3D01G207400 chr7B 77.335 728 105 32 4207 4906 426523569 426522874 4.640000e-100 375.0
27 TraesCS3D01G207400 chr7B 85.714 77 11 0 2454 2530 71351640 71351716 1.130000e-11 82.4
28 TraesCS3D01G207400 chr7D 77.267 739 99 38 4192 4906 412099848 412099155 2.160000e-98 370.0
29 TraesCS3D01G207400 chr7D 90.076 262 26 0 2860 3121 10179628 10179889 1.690000e-89 340.0
30 TraesCS3D01G207400 chr7D 82.521 349 54 3 4557 4905 614182416 614182075 2.870000e-77 300.0
31 TraesCS3D01G207400 chr7D 85.714 210 19 11 3121 3322 25349634 25349840 1.380000e-50 211.0
32 TraesCS3D01G207400 chr7D 81.592 201 28 3 3121 3313 273364296 273364495 1.830000e-34 158.0
33 TraesCS3D01G207400 chr7D 83.626 171 16 7 3122 3287 145831944 145831781 3.060000e-32 150.0
34 TraesCS3D01G207400 chr7D 91.250 80 7 0 4193 4272 135773223 135773144 5.190000e-20 110.0
35 TraesCS3D01G207400 chr7D 88.235 68 8 0 2463 2530 546060936 546060869 1.130000e-11 82.4
36 TraesCS3D01G207400 chr6D 81.345 461 69 10 4447 4906 48891735 48891291 4.670000e-95 359.0
37 TraesCS3D01G207400 chr6D 87.166 187 15 5 3121 3302 140095320 140095138 2.320000e-48 204.0
38 TraesCS3D01G207400 chr7A 88.235 272 32 0 2859 3130 42734043 42733772 4.740000e-85 326.0
39 TraesCS3D01G207400 chr7A 89.706 68 7 0 2463 2530 46221230 46221163 2.430000e-13 87.9
40 TraesCS3D01G207400 chr7A 85.897 78 8 3 4181 4256 148511632 148511556 4.070000e-11 80.5
41 TraesCS3D01G207400 chr5A 88.168 262 31 0 2860 3121 204277724 204277985 3.690000e-81 313.0
42 TraesCS3D01G207400 chr5A 84.416 77 12 0 2454 2530 674370360 674370436 5.270000e-10 76.8
43 TraesCS3D01G207400 chr5A 88.889 54 5 1 2745 2797 444878433 444878486 1.140000e-06 65.8
44 TraesCS3D01G207400 chr2A 88.360 189 12 4 3122 3302 148597386 148597572 8.270000e-53 219.0
45 TraesCS3D01G207400 chr2A 89.706 68 7 0 4189 4256 755810971 755811038 2.430000e-13 87.9
46 TraesCS3D01G207400 chr2A 80.247 81 13 3 4213 4292 537471875 537471953 1.910000e-04 58.4
47 TraesCS3D01G207400 chr4D 82.955 176 25 2 3142 3313 363507918 363508092 2.360000e-33 154.0
48 TraesCS3D01G207400 chr1D 91.892 111 8 1 3193 3303 468025486 468025377 2.360000e-33 154.0
49 TraesCS3D01G207400 chr6A 82.292 96 17 0 2435 2530 196825169 196825074 3.150000e-12 84.2
50 TraesCS3D01G207400 chr4A 87.143 70 9 0 4187 4256 149082439 149082508 4.070000e-11 80.5
51 TraesCS3D01G207400 chr4A 86.364 66 7 2 4192 4256 637868737 637868673 2.450000e-08 71.3
52 TraesCS3D01G207400 chr4A 79.412 102 17 4 2453 2552 454779574 454779475 8.810000e-08 69.4
53 TraesCS3D01G207400 chr6B 83.529 85 12 2 2469 2552 33523118 33523035 1.460000e-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 TraesCS3D01G207400 chr3D 272932337 272937242 4905 False 9060.000000 9060 100.000000 1 4906 1 chr3D.!!$F2 4905
1 TraesCS3D01G207400 chr3A 356083171 356087316 4145 False 1992.666667 3286 92.800333 931 4906 3 chr3A.!!$F2 3975
2 TraesCS3D01G207400 chr3B 361019684 361021504 1820 True 2737.000000 2737 93.896000 326 2140 1 chr3B.!!$R1 1814
3 TraesCS3D01G207400 chr3B 361011427 361014308 2881 True 1786.000000 2002 93.619500 2136 4556 2 chr3B.!!$R6 2420
4 TraesCS3D01G207400 chr2B 195540880 195541555 675 True 488.000000 488 80.000000 4194 4904 1 chr2B.!!$R1 710
5 TraesCS3D01G207400 chr5D 327994609 327995334 725 False 429.000000 429 77.807000 1 747 1 chr5D.!!$F1 746
6 TraesCS3D01G207400 chr7B 426522874 426523569 695 True 375.000000 375 77.335000 4207 4906 1 chr7B.!!$R1 699
7 TraesCS3D01G207400 chr7D 412099155 412099848 693 True 370.000000 370 77.267000 4192 4906 1 chr7D.!!$R3 714

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
673 678 0.039165 GCGTGAGGGCTTTTGGAAAG 60.039 55.000 0.00 0.00 0.00 2.62 F
924 944 0.105401 CTCCCCTCCTAGGAAGGGTC 60.105 65.000 35.40 0.00 44.35 4.46 F
926 946 0.269173 CCCCTCCTAGGAAGGGTCAT 59.731 60.000 31.09 0.00 43.84 3.06 F
989 1011 1.070758 GCATAGATTTCAGGCCGGAGA 59.929 52.381 5.05 1.29 0.00 3.71 F
2534 2559 1.133823 TGTGCCAGCACCCCATAATAG 60.134 52.381 19.47 0.00 45.63 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 2398 4.030913 AGGAAGGTTTCAGTCATCGGATA 58.969 43.478 0.00 0.00 0.00 2.59 R
2857 2902 1.153168 CCCATTACGACCAGCCTGG 60.153 63.158 9.83 9.83 45.02 4.45 R
2910 2955 2.637872 TGGTACTATGCATTAGGGAGGC 59.362 50.000 3.54 0.00 31.68 4.70 R
2961 3166 4.753610 GCTAGTATGTGTCATGCATGTCAT 59.246 41.667 25.62 25.20 35.31 3.06 R
4031 4775 1.053424 TTGCGGGGAAACTAGACTGT 58.947 50.000 0.00 0.00 0.00 3.55 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
17 18 4.778143 GGTTGCGGGCGTCAGGAT 62.778 66.667 0.00 0.00 0.00 3.24
36 37 1.523938 GGTTGGCCATAGGTCTCGC 60.524 63.158 6.09 0.00 34.09 5.03
39 40 3.161450 GGCCATAGGTCTCGCCCA 61.161 66.667 0.00 0.00 38.26 5.36
40 41 2.520536 GGCCATAGGTCTCGCCCAT 61.521 63.158 0.00 0.00 38.26 4.00
41 42 1.302033 GCCATAGGTCTCGCCCATG 60.302 63.158 0.00 0.00 38.26 3.66
43 44 1.121407 CCATAGGTCTCGCCCATGGA 61.121 60.000 15.22 0.00 36.26 3.41
60 61 1.114627 GGATGGTTCCTTTGCATCCC 58.885 55.000 0.00 0.00 39.14 3.85
61 62 1.114627 GATGGTTCCTTTGCATCCCC 58.885 55.000 0.00 0.00 0.00 4.81
63 64 2.710902 GGTTCCTTTGCATCCCCGC 61.711 63.158 0.00 0.00 0.00 6.13
109 110 0.104120 CAGGTGTGACGTTGAGGTCA 59.896 55.000 2.65 2.65 44.25 4.02
116 117 0.669318 GACGTTGAGGTCAATGCCGA 60.669 55.000 11.14 0.00 44.48 5.54
137 138 3.006728 CGGGGGAAGTGGTGGCTA 61.007 66.667 0.00 0.00 0.00 3.93
148 149 3.323136 GTGGCTAGCGCGATCACG 61.323 66.667 12.10 0.00 42.93 4.35
159 160 2.104331 GATCACGCCGATGTCCGT 59.896 61.111 0.00 0.00 38.35 4.69
163 164 4.471726 ACGCCGATGTCCGTCGAC 62.472 66.667 5.18 5.18 42.78 4.20
179 180 3.621892 GACGTGGAGAACCGGGTCG 62.622 68.421 15.29 4.65 39.42 4.79
192 193 2.280119 GGTCGCGCCATGCTCATA 60.280 61.111 13.61 0.00 43.27 2.15
194 195 2.280119 TCGCGCCATGCTCATACC 60.280 61.111 0.00 0.00 43.27 2.73
197 198 2.666190 CGCCATGCTCATACCCCG 60.666 66.667 0.00 0.00 0.00 5.73
198 199 2.828868 GCCATGCTCATACCCCGA 59.171 61.111 0.00 0.00 0.00 5.14
204 205 2.325583 TGCTCATACCCCGAATGAAC 57.674 50.000 0.00 0.00 33.13 3.18
207 208 2.561569 CTCATACCCCGAATGAACACC 58.438 52.381 0.00 0.00 33.13 4.16
209 210 1.134640 CATACCCCGAATGAACACCGA 60.135 52.381 0.00 0.00 0.00 4.69
211 212 1.743995 CCCCGAATGAACACCGACC 60.744 63.158 0.00 0.00 0.00 4.79
212 213 2.098233 CCCGAATGAACACCGACCG 61.098 63.158 0.00 0.00 0.00 4.79
213 214 1.373748 CCGAATGAACACCGACCGT 60.374 57.895 0.00 0.00 0.00 4.83
214 215 1.349259 CCGAATGAACACCGACCGTC 61.349 60.000 0.00 0.00 0.00 4.79
215 216 0.388134 CGAATGAACACCGACCGTCT 60.388 55.000 0.00 0.00 0.00 4.18
216 217 1.135603 CGAATGAACACCGACCGTCTA 60.136 52.381 0.00 0.00 0.00 2.59
217 218 2.479049 CGAATGAACACCGACCGTCTAT 60.479 50.000 0.00 0.00 0.00 1.98
224 225 0.245539 ACCGACCGTCTATGGTGTTG 59.754 55.000 0.00 0.00 44.01 3.33
227 228 1.068125 CGACCGTCTATGGTGTTGTGA 60.068 52.381 0.00 0.00 44.01 3.58
232 233 3.254060 CGTCTATGGTGTTGTGAAGGAG 58.746 50.000 0.00 0.00 0.00 3.69
235 236 2.664402 ATGGTGTTGTGAAGGAGCTT 57.336 45.000 0.00 0.00 0.00 3.74
236 237 2.435372 TGGTGTTGTGAAGGAGCTTT 57.565 45.000 0.00 0.00 0.00 3.51
237 238 2.733956 TGGTGTTGTGAAGGAGCTTTT 58.266 42.857 0.00 0.00 0.00 2.27
243 244 2.483876 TGTGAAGGAGCTTTTCGACTG 58.516 47.619 0.00 0.00 0.00 3.51
249 250 0.519077 GAGCTTTTCGACTGGCCTTG 59.481 55.000 3.32 0.00 0.00 3.61
261 262 3.056328 GCCTTGTGGAGGGCGAAC 61.056 66.667 0.00 0.00 46.40 3.95
265 266 3.524648 TTGTGGAGGGCGAACGACC 62.525 63.158 11.46 11.46 45.79 4.79
312 313 2.254350 GGCAACGGAAAGAACGCC 59.746 61.111 0.00 0.00 34.00 5.68
313 314 2.258726 GGCAACGGAAAGAACGCCT 61.259 57.895 0.00 0.00 36.58 5.52
314 315 1.082104 GCAACGGAAAGAACGCCTG 60.082 57.895 0.00 0.00 34.00 4.85
315 316 1.574428 CAACGGAAAGAACGCCTGG 59.426 57.895 0.00 0.00 34.00 4.45
316 317 2.258726 AACGGAAAGAACGCCTGGC 61.259 57.895 9.11 9.11 34.00 4.85
363 364 2.738521 GGCATGTGTCGTCGCTGT 60.739 61.111 0.00 0.00 0.00 4.40
376 377 2.047274 GCTGTCTGCGTGGCCTTA 60.047 61.111 3.32 0.00 0.00 2.69
460 461 3.551496 CTCGGCAGTGGCTTTCCCA 62.551 63.158 15.48 0.00 42.79 4.37
526 528 2.124487 AGTCGCTAGAGCTCCGCT 60.124 61.111 19.59 11.22 43.88 5.52
527 529 2.025441 GTCGCTAGAGCTCCGCTG 59.975 66.667 19.59 14.18 39.88 5.18
530 532 3.842923 GCTAGAGCTCCGCTGGCA 61.843 66.667 10.93 0.00 39.88 4.92
595 600 4.767255 GAGGTGGCAGCTGGGACG 62.767 72.222 25.83 0.00 0.00 4.79
642 647 3.797353 GGCCATGGAGCGGGAAGA 61.797 66.667 18.40 0.00 0.00 2.87
648 653 4.214327 GGAGCGGGAAGAGGCGAG 62.214 72.222 0.00 0.00 0.00 5.03
649 654 4.214327 GAGCGGGAAGAGGCGAGG 62.214 72.222 0.00 0.00 0.00 4.63
652 657 3.532155 CGGGAAGAGGCGAGGGAG 61.532 72.222 0.00 0.00 0.00 4.30
653 658 3.157949 GGGAAGAGGCGAGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
654 659 3.157949 GGAAGAGGCGAGGGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
655 660 3.855853 GAAGAGGCGAGGGAGGGC 61.856 72.222 0.00 0.00 0.00 5.19
670 675 2.282180 GGCGTGAGGGCTTTTGGA 60.282 61.111 0.00 0.00 38.40 3.53
673 678 0.039165 GCGTGAGGGCTTTTGGAAAG 60.039 55.000 0.00 0.00 0.00 2.62
757 765 2.567049 CTCGTCCGTGTCCTGTCC 59.433 66.667 0.00 0.00 0.00 4.02
758 766 2.203379 TCGTCCGTGTCCTGTCCA 60.203 61.111 0.00 0.00 0.00 4.02
774 782 4.378356 CCTGTCCATGTCAATACAAACACG 60.378 45.833 0.00 0.00 39.58 4.49
776 784 2.486203 TCCATGTCAATACAAACACGGC 59.514 45.455 0.00 0.00 39.58 5.68
787 795 8.358148 TCAATACAAACACGGCCTAAATTTAAA 58.642 29.630 0.00 0.00 0.00 1.52
790 798 5.859648 ACAAACACGGCCTAAATTTAAATCG 59.140 36.000 0.00 2.37 0.00 3.34
797 805 8.079809 CACGGCCTAAATTTAAATCGGAAATAT 58.920 33.333 0.00 0.00 0.00 1.28
843 862 0.580578 CTCTCGCGAGCCATGATTTG 59.419 55.000 30.97 4.68 0.00 2.32
845 864 1.136110 TCTCGCGAGCCATGATTTGTA 59.864 47.619 30.97 6.43 0.00 2.41
848 867 1.195448 CGCGAGCCATGATTTGTATCC 59.805 52.381 0.00 0.00 0.00 2.59
849 868 2.221169 GCGAGCCATGATTTGTATCCA 58.779 47.619 0.00 0.00 0.00 3.41
851 870 3.470709 CGAGCCATGATTTGTATCCAGT 58.529 45.455 0.00 0.00 0.00 4.00
859 878 5.408880 TGATTTGTATCCAGTACGTCCAA 57.591 39.130 0.00 0.00 36.01 3.53
860 879 5.984725 TGATTTGTATCCAGTACGTCCAAT 58.015 37.500 0.00 0.00 36.01 3.16
861 880 5.815222 TGATTTGTATCCAGTACGTCCAATG 59.185 40.000 0.00 0.00 36.01 2.82
864 883 0.179084 ATCCAGTACGTCCAATGCGG 60.179 55.000 0.00 0.00 0.00 5.69
865 884 2.461110 CCAGTACGTCCAATGCGGC 61.461 63.158 0.00 0.00 33.14 6.53
888 908 1.272212 GGACAAAATGGGTCGTGCATT 59.728 47.619 0.00 0.00 36.12 3.56
923 943 1.604592 CCTCCCCTCCTAGGAAGGGT 61.605 65.000 35.40 0.00 44.35 4.34
924 944 0.105401 CTCCCCTCCTAGGAAGGGTC 60.105 65.000 35.40 0.00 44.35 4.46
925 945 0.858598 TCCCCTCCTAGGAAGGGTCA 60.859 60.000 35.40 20.81 44.35 4.02
926 946 0.269173 CCCCTCCTAGGAAGGGTCAT 59.731 60.000 31.09 0.00 43.84 3.06
989 1011 1.070758 GCATAGATTTCAGGCCGGAGA 59.929 52.381 5.05 1.29 0.00 3.71
1022 1044 1.677052 GACTACGAGGAGATGGTGGAC 59.323 57.143 0.00 0.00 0.00 4.02
1106 1128 1.598130 GTGTGCGCACCTCCTTTCT 60.598 57.895 35.72 0.00 39.61 2.52
1138 1160 1.750399 CTTGGATTCCAGCCACCCG 60.750 63.158 5.36 0.00 34.56 5.28
1589 1613 2.355209 TGGCATTTGGCAGTATACGTCA 60.355 45.455 2.26 0.00 46.12 4.35
1660 1684 6.530181 GGATTTTGTCCATTGAAATAACGGAC 59.470 38.462 0.00 0.00 46.96 4.79
1730 1754 7.438459 ACACTCTGAAAACATTCACTAGTACAC 59.562 37.037 0.00 0.00 0.00 2.90
1754 1778 5.380043 CAGTGCTTAACCATCATAATCCCT 58.620 41.667 0.00 0.00 0.00 4.20
1816 1840 5.484173 TTGGAACGATCATGTCTTTATGC 57.516 39.130 0.00 0.00 0.00 3.14
2185 2209 5.068591 ACAGTTAACACCCCTCAAATGTTTC 59.931 40.000 8.61 0.00 37.68 2.78
2373 2397 8.299570 ACAATTGGTCTAAATCAAATGTGACTC 58.700 33.333 10.83 0.00 36.16 3.36
2374 2398 8.517878 CAATTGGTCTAAATCAAATGTGACTCT 58.482 33.333 0.00 0.00 36.31 3.24
2431 2455 6.868864 TCTTGACTCTTATCTGTACAAGTTGC 59.131 38.462 1.81 0.00 35.99 4.17
2480 2505 2.497273 GACTGAATTGATGGGTTTGGGG 59.503 50.000 0.00 0.00 0.00 4.96
2481 2506 2.111613 ACTGAATTGATGGGTTTGGGGA 59.888 45.455 0.00 0.00 0.00 4.81
2534 2559 1.133823 TGTGCCAGCACCCCATAATAG 60.134 52.381 19.47 0.00 45.63 1.73
2599 2624 6.486320 TGAGCATCAGTTCATCTAAAACACAA 59.514 34.615 0.00 0.00 42.56 3.33
2631 2656 5.479306 TCTTCTGTCATTGGTAGTGTAAGC 58.521 41.667 0.00 0.00 0.00 3.09
2665 2690 9.620259 AAGTAAAAGGATGATATCAGGAAAGAC 57.380 33.333 11.78 4.27 0.00 3.01
2800 2845 6.187682 ACAATTAATTTGAATCGGAGGGACT 58.812 36.000 0.00 0.00 39.47 3.85
2939 2984 9.279233 TCCCTAATGCATAGTACCATACATTAT 57.721 33.333 0.00 0.00 31.63 1.28
3180 3877 5.335661 CCCAAGGTAAGTTTGCTTATGTGTC 60.336 44.000 0.00 0.00 39.17 3.67
3183 3880 6.560253 AGGTAAGTTTGCTTATGTGTCAAG 57.440 37.500 0.00 0.00 39.17 3.02
3205 3902 5.937111 AGTAGTTAATGAGGTGTTTGTGGT 58.063 37.500 0.00 0.00 0.00 4.16
4031 4775 9.069078 CAGAACGTCGAGTCAAAATTAGTATAA 57.931 33.333 0.00 0.00 0.00 0.98
4032 4776 9.070149 AGAACGTCGAGTCAAAATTAGTATAAC 57.930 33.333 0.00 0.00 0.00 1.89
4107 4851 4.752101 GTCAGCCTTGCGTATGAATTATCT 59.248 41.667 0.00 0.00 0.00 1.98
4111 4855 4.991056 GCCTTGCGTATGAATTATCTCTGA 59.009 41.667 0.00 0.00 0.00 3.27
4285 5038 1.082104 CGTCCGGCTGTTTTCTTGC 60.082 57.895 0.00 0.00 0.00 4.01
4286 5039 1.781025 CGTCCGGCTGTTTTCTTGCA 61.781 55.000 0.00 0.00 0.00 4.08
4287 5040 0.040067 GTCCGGCTGTTTTCTTGCAG 60.040 55.000 0.00 0.00 35.93 4.41
4288 5041 0.465460 TCCGGCTGTTTTCTTGCAGT 60.465 50.000 0.00 0.00 35.33 4.40
4289 5042 0.318107 CCGGCTGTTTTCTTGCAGTG 60.318 55.000 0.00 0.00 35.33 3.66
4290 5043 0.936297 CGGCTGTTTTCTTGCAGTGC 60.936 55.000 8.58 8.58 35.33 4.40
4291 5044 0.936297 GGCTGTTTTCTTGCAGTGCG 60.936 55.000 11.20 0.00 35.33 5.34
4292 5045 0.248621 GCTGTTTTCTTGCAGTGCGT 60.249 50.000 11.20 0.00 35.33 5.24
4293 5046 1.746760 CTGTTTTCTTGCAGTGCGTC 58.253 50.000 11.20 0.00 0.00 5.19
4294 5047 0.380378 TGTTTTCTTGCAGTGCGTCC 59.620 50.000 11.20 0.00 0.00 4.79
4295 5048 0.380378 GTTTTCTTGCAGTGCGTCCA 59.620 50.000 11.20 0.00 0.00 4.02
4296 5049 1.098869 TTTTCTTGCAGTGCGTCCAA 58.901 45.000 11.20 0.00 0.00 3.53
4297 5050 0.380378 TTTCTTGCAGTGCGTCCAAC 59.620 50.000 11.20 0.00 0.00 3.77
4298 5051 1.771073 TTCTTGCAGTGCGTCCAACG 61.771 55.000 11.20 0.00 45.88 4.10
4467 5241 9.847706 TGAATAAAAGCGCAATCAAATAGTTTA 57.152 25.926 11.47 0.00 0.00 2.01
4505 5279 4.771590 TGTCTTGAATGCATGGAAAGAC 57.228 40.909 26.93 26.93 44.45 3.01
4508 5282 4.919754 GTCTTGAATGCATGGAAAGACAAC 59.080 41.667 27.83 13.38 43.91 3.32
4571 5345 3.077359 GCTTAGTGTGCTCAACCAAGAT 58.923 45.455 8.59 0.00 0.00 2.40
4605 5379 3.003689 GGAAATGAGTATGCCAATCACGG 59.996 47.826 0.00 0.00 0.00 4.94
4613 5387 5.620206 AGTATGCCAATCACGGATTTCATA 58.380 37.500 10.68 10.68 30.70 2.15
4674 5449 3.763097 TGCTCAGGCATAACATTTTCG 57.237 42.857 0.00 0.00 44.28 3.46
4696 5471 2.695147 CCCTGATATTCAAACCCTTGGC 59.305 50.000 0.00 0.00 33.01 4.52
4752 5527 7.776500 TCCTCAATGATCATGTTGTGTATGATT 59.224 33.333 9.46 0.00 43.37 2.57
4774 5549 4.908601 ACACAAATAGTCATCACCTCCA 57.091 40.909 0.00 0.00 0.00 3.86
4781 5556 5.957771 ATAGTCATCACCTCCAAAAGCTA 57.042 39.130 0.00 0.00 0.00 3.32
4786 5561 1.079503 CACCTCCAAAAGCTACTCGC 58.920 55.000 0.00 0.00 39.57 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.134127 GCCAACCATCCTGACGCC 61.134 66.667 0.00 0.00 0.00 5.68
43 44 0.684153 CGGGGATGCAAAGGAACCAT 60.684 55.000 0.00 0.00 0.00 3.55
46 47 2.885113 GCGGGGATGCAAAGGAAC 59.115 61.111 0.00 0.00 34.15 3.62
79 80 3.001406 ACACCTGGGTCCGGTAGC 61.001 66.667 0.00 0.00 32.37 3.58
81 82 1.909781 GTCACACCTGGGTCCGGTA 60.910 63.158 0.00 0.00 32.37 4.02
90 91 0.104120 TGACCTCAACGTCACACCTG 59.896 55.000 0.00 0.00 37.85 4.00
94 95 1.225855 GCATTGACCTCAACGTCACA 58.774 50.000 0.00 0.00 42.37 3.58
121 122 2.998949 CTAGCCACCACTTCCCCC 59.001 66.667 0.00 0.00 0.00 5.40
126 127 2.907897 GATCGCGCTAGCCACCACTT 62.908 60.000 9.66 0.00 41.18 3.16
127 128 3.432051 GATCGCGCTAGCCACCACT 62.432 63.158 9.66 0.00 41.18 4.00
128 129 2.962253 GATCGCGCTAGCCACCAC 60.962 66.667 9.66 0.00 41.18 4.16
129 130 3.457263 TGATCGCGCTAGCCACCA 61.457 61.111 9.66 0.00 41.18 4.17
130 131 2.962253 GTGATCGCGCTAGCCACC 60.962 66.667 9.66 0.00 41.18 4.61
148 149 4.471726 ACGTCGACGGACATCGGC 62.472 66.667 37.89 0.00 43.61 5.54
150 151 2.576053 CCACGTCGACGGACATCG 60.576 66.667 37.89 19.56 43.61 3.84
151 152 1.226323 CTCCACGTCGACGGACATC 60.226 63.158 37.89 0.00 43.61 3.06
152 153 1.239296 TTCTCCACGTCGACGGACAT 61.239 55.000 37.89 17.63 43.61 3.06
153 154 1.893335 TTCTCCACGTCGACGGACA 60.893 57.895 37.89 21.19 43.61 4.02
154 155 1.441682 GTTCTCCACGTCGACGGAC 60.442 63.158 37.89 22.12 44.95 4.79
155 156 2.620112 GGTTCTCCACGTCGACGGA 61.620 63.158 37.89 25.86 44.95 4.69
159 160 3.367743 CCCGGTTCTCCACGTCGA 61.368 66.667 0.00 0.00 0.00 4.20
179 180 2.980233 GGGGTATGAGCATGGCGC 60.980 66.667 0.00 0.00 42.91 6.53
181 182 0.250901 ATTCGGGGTATGAGCATGGC 60.251 55.000 0.00 0.00 0.00 4.40
182 183 1.072173 TCATTCGGGGTATGAGCATGG 59.928 52.381 0.00 0.00 0.00 3.66
188 189 1.134640 CGGTGTTCATTCGGGGTATGA 60.135 52.381 0.00 0.00 0.00 2.15
189 190 1.134640 TCGGTGTTCATTCGGGGTATG 60.135 52.381 0.00 0.00 0.00 2.39
190 191 1.134610 GTCGGTGTTCATTCGGGGTAT 60.135 52.381 0.00 0.00 0.00 2.73
192 193 1.004200 GTCGGTGTTCATTCGGGGT 60.004 57.895 0.00 0.00 0.00 4.95
194 195 2.098233 CGGTCGGTGTTCATTCGGG 61.098 63.158 0.00 0.00 0.00 5.14
197 198 2.642139 TAGACGGTCGGTGTTCATTC 57.358 50.000 1.89 0.00 0.00 2.67
198 199 2.418197 CCATAGACGGTCGGTGTTCATT 60.418 50.000 1.89 0.00 0.00 2.57
204 205 4.806571 CACCATAGACGGTCGGTG 57.193 61.111 15.96 15.96 42.72 4.94
207 208 1.068125 TCACAACACCATAGACGGTCG 60.068 52.381 1.89 0.00 37.07 4.79
209 210 2.289444 CCTTCACAACACCATAGACGGT 60.289 50.000 0.00 0.00 41.07 4.83
211 212 3.254060 CTCCTTCACAACACCATAGACG 58.746 50.000 0.00 0.00 0.00 4.18
212 213 3.003480 GCTCCTTCACAACACCATAGAC 58.997 50.000 0.00 0.00 0.00 2.59
213 214 2.906389 AGCTCCTTCACAACACCATAGA 59.094 45.455 0.00 0.00 0.00 1.98
214 215 3.340814 AGCTCCTTCACAACACCATAG 57.659 47.619 0.00 0.00 0.00 2.23
215 216 3.788227 AAGCTCCTTCACAACACCATA 57.212 42.857 0.00 0.00 0.00 2.74
216 217 2.664402 AAGCTCCTTCACAACACCAT 57.336 45.000 0.00 0.00 0.00 3.55
217 218 2.435372 AAAGCTCCTTCACAACACCA 57.565 45.000 0.00 0.00 0.00 4.17
224 225 1.801178 CCAGTCGAAAAGCTCCTTCAC 59.199 52.381 8.71 6.29 0.00 3.18
227 228 0.606673 GGCCAGTCGAAAAGCTCCTT 60.607 55.000 0.00 0.00 0.00 3.36
232 233 0.040067 CACAAGGCCAGTCGAAAAGC 60.040 55.000 5.01 0.00 0.00 3.51
235 236 0.250295 CTCCACAAGGCCAGTCGAAA 60.250 55.000 5.01 0.00 33.74 3.46
236 237 1.371183 CTCCACAAGGCCAGTCGAA 59.629 57.895 5.01 0.00 33.74 3.71
237 238 2.583441 CCTCCACAAGGCCAGTCGA 61.583 63.158 5.01 0.00 38.67 4.20
260 261 2.126463 CACATGCTCGTCGGTCGT 60.126 61.111 0.00 0.00 40.80 4.34
261 262 3.545481 GCACATGCTCGTCGGTCG 61.545 66.667 0.00 0.00 41.41 4.79
287 288 1.228003 TTTCCGTTGCCGACATGGT 60.228 52.632 0.00 0.00 41.21 3.55
293 294 2.600475 GCGTTCTTTCCGTTGCCGA 61.600 57.895 0.00 0.00 35.63 5.54
297 298 1.574428 CCAGGCGTTCTTTCCGTTG 59.426 57.895 0.00 0.00 0.00 4.10
298 299 2.258726 GCCAGGCGTTCTTTCCGTT 61.259 57.895 0.00 0.00 0.00 4.44
299 300 2.668550 GCCAGGCGTTCTTTCCGT 60.669 61.111 0.00 0.00 0.00 4.69
320 321 0.611896 ATGCTAGGGTTGTGCCAACC 60.612 55.000 22.05 22.05 39.65 3.77
321 322 0.527565 CATGCTAGGGTTGTGCCAAC 59.472 55.000 8.94 8.94 39.65 3.77
322 323 0.403655 TCATGCTAGGGTTGTGCCAA 59.596 50.000 0.00 0.00 39.65 4.52
323 324 0.035152 CTCATGCTAGGGTTGTGCCA 60.035 55.000 0.00 0.00 39.65 4.92
363 364 3.378602 TCGCTAAGGCCACGCAGA 61.379 61.111 5.01 3.65 34.44 4.26
477 478 1.183549 GACTAAGTGGAGAGCCCGAA 58.816 55.000 0.00 0.00 37.93 4.30
526 528 1.117749 CGAGGGAGGAGATCATGCCA 61.118 60.000 7.78 0.00 40.75 4.92
527 529 1.670590 CGAGGGAGGAGATCATGCC 59.329 63.158 0.00 0.00 38.47 4.40
530 532 0.105246 AAGCCGAGGGAGGAGATCAT 60.105 55.000 0.00 0.00 0.00 2.45
576 581 4.980592 TCCCAGCTGCCACCTCCA 62.981 66.667 8.66 0.00 0.00 3.86
635 640 3.532155 CTCCCTCGCCTCTTCCCG 61.532 72.222 0.00 0.00 0.00 5.14
649 654 3.569200 AAAAGCCCTCACGCCCTCC 62.569 63.158 0.00 0.00 0.00 4.30
650 655 2.034221 AAAAGCCCTCACGCCCTC 59.966 61.111 0.00 0.00 0.00 4.30
651 656 2.282462 CAAAAGCCCTCACGCCCT 60.282 61.111 0.00 0.00 0.00 5.19
652 657 3.373565 CCAAAAGCCCTCACGCCC 61.374 66.667 0.00 0.00 0.00 6.13
653 658 1.460273 TTTCCAAAAGCCCTCACGCC 61.460 55.000 0.00 0.00 0.00 5.68
654 659 0.039165 CTTTCCAAAAGCCCTCACGC 60.039 55.000 0.00 0.00 0.00 5.34
655 660 1.604604 TCTTTCCAAAAGCCCTCACG 58.395 50.000 0.00 0.00 0.00 4.35
656 661 2.297315 CCTTCTTTCCAAAAGCCCTCAC 59.703 50.000 0.00 0.00 0.00 3.51
657 662 2.176798 TCCTTCTTTCCAAAAGCCCTCA 59.823 45.455 0.00 0.00 0.00 3.86
670 675 3.084786 CGCTTCCATTTCCTCCTTCTTT 58.915 45.455 0.00 0.00 0.00 2.52
673 678 2.115343 ACGCTTCCATTTCCTCCTTC 57.885 50.000 0.00 0.00 0.00 3.46
752 760 4.711721 CGTGTTTGTATTGACATGGACAG 58.288 43.478 0.00 0.00 34.86 3.51
757 765 2.487762 AGGCCGTGTTTGTATTGACATG 59.512 45.455 0.00 0.00 34.86 3.21
758 766 2.790433 AGGCCGTGTTTGTATTGACAT 58.210 42.857 0.00 0.00 34.86 3.06
787 795 3.056393 TCCGCCGTCAATATATTTCCGAT 60.056 43.478 12.75 0.00 0.00 4.18
790 798 3.432252 CAGTCCGCCGTCAATATATTTCC 59.568 47.826 0.00 0.00 0.00 3.13
797 805 1.138036 CGTCAGTCCGCCGTCAATA 59.862 57.895 0.00 0.00 0.00 1.90
826 845 1.570813 TACAAATCATGGCTCGCGAG 58.429 50.000 31.37 31.37 0.00 5.03
843 862 2.124903 CGCATTGGACGTACTGGATAC 58.875 52.381 0.00 0.00 0.00 2.24
845 864 0.179084 CCGCATTGGACGTACTGGAT 60.179 55.000 0.00 0.00 42.00 3.41
848 867 2.461110 GGCCGCATTGGACGTACTG 61.461 63.158 0.00 0.00 42.00 2.74
849 868 2.125269 GGCCGCATTGGACGTACT 60.125 61.111 0.00 0.00 42.00 2.73
859 878 2.362375 ATTTTGTCCGGGCCGCAT 60.362 55.556 23.20 1.65 0.00 4.73
860 879 3.369400 CATTTTGTCCGGGCCGCA 61.369 61.111 23.20 11.86 0.00 5.69
861 880 4.128388 CCATTTTGTCCGGGCCGC 62.128 66.667 23.20 8.77 0.00 6.53
864 883 2.696759 CGACCCATTTTGTCCGGGC 61.697 63.158 0.00 0.00 44.49 6.13
865 884 1.302993 ACGACCCATTTTGTCCGGG 60.303 57.895 0.00 0.00 46.22 5.73
912 932 3.515562 AGCATCTATGACCCTTCCTAGG 58.484 50.000 0.82 0.82 41.60 3.02
956 978 1.035385 TCTATGCAGAGTTCCGGCGA 61.035 55.000 9.30 0.00 38.88 5.54
989 1011 1.138247 GTAGTCATCGCCGTCCGTT 59.862 57.895 0.00 0.00 38.35 4.44
1106 1128 1.152567 CCAAGCACAAGGGTGGGAA 60.153 57.895 0.00 0.00 45.38 3.97
1138 1160 1.472878 GAAAGGGGTTCAGGAAATCGC 59.527 52.381 0.00 0.00 36.15 4.58
1589 1613 5.243730 CCCAATCCACACAAAACTGACTTAT 59.756 40.000 0.00 0.00 0.00 1.73
1697 1721 9.209175 AGTGAATGTTTTCAGAGTGTAGATAAC 57.791 33.333 0.00 0.00 42.41 1.89
1730 1754 4.520492 GGGATTATGATGGTTAAGCACTGG 59.480 45.833 9.99 0.00 0.00 4.00
1754 1778 5.185442 ACATGCAACATACACCATGATTTCA 59.815 36.000 6.48 0.00 38.65 2.69
1816 1840 4.668431 CGCAGAATGAGTCAGACAACAATG 60.668 45.833 2.66 5.34 39.69 2.82
2051 2075 7.944729 AAGATGCAATGTTATTACCTTGAGT 57.055 32.000 4.35 0.00 33.32 3.41
2373 2397 4.100189 AGGAAGGTTTCAGTCATCGGATAG 59.900 45.833 0.00 0.00 0.00 2.08
2374 2398 4.030913 AGGAAGGTTTCAGTCATCGGATA 58.969 43.478 0.00 0.00 0.00 2.59
2431 2455 9.177608 TGGAGGTTTTTAATCAGATATGACTTG 57.822 33.333 0.00 0.00 0.00 3.16
2480 2505 7.201600 GCAGAGAAACTCCAAGATATTCAACTC 60.202 40.741 0.00 0.00 0.00 3.01
2481 2506 6.597280 GCAGAGAAACTCCAAGATATTCAACT 59.403 38.462 0.00 0.00 0.00 3.16
2534 2559 4.060205 GCCATGTTTGCAATGGATATTCC 58.940 43.478 19.52 0.00 37.66 3.01
2599 2624 4.290722 ACCAATGACAGAAGAAGAGGGATT 59.709 41.667 0.00 0.00 0.00 3.01
2800 2845 9.457436 GTTTTGGAATAAAATACTACTCCCTCA 57.543 33.333 0.00 0.00 0.00 3.86
2857 2902 1.153168 CCCATTACGACCAGCCTGG 60.153 63.158 9.83 9.83 45.02 4.45
2910 2955 2.637872 TGGTACTATGCATTAGGGAGGC 59.362 50.000 3.54 0.00 31.68 4.70
2961 3166 4.753610 GCTAGTATGTGTCATGCATGTCAT 59.246 41.667 25.62 25.20 35.31 3.06
3180 3877 6.262273 ACCACAAACACCTCATTAACTACTTG 59.738 38.462 0.00 0.00 0.00 3.16
3183 3880 7.227116 TGTTACCACAAACACCTCATTAACTAC 59.773 37.037 0.00 0.00 34.50 2.73
3599 4306 1.616374 TGTGCTGTTGGTCAGTATCGA 59.384 47.619 0.00 0.00 45.23 3.59
3822 4529 5.480422 TCATTAGCGTATGGTCCACATAGAT 59.520 40.000 0.00 0.00 42.50 1.98
4031 4775 1.053424 TTGCGGGGAAACTAGACTGT 58.947 50.000 0.00 0.00 0.00 3.55
4032 4776 2.178912 TTTGCGGGGAAACTAGACTG 57.821 50.000 0.00 0.00 0.00 3.51
4076 4820 1.361668 CGCAAGGCTGACGCAACTAT 61.362 55.000 0.00 0.00 38.10 2.12
4107 4851 3.173151 TCCTTACTGTGAGGCAATCAGA 58.827 45.455 13.43 0.00 39.07 3.27
4111 4855 4.520492 CAGTTTTCCTTACTGTGAGGCAAT 59.480 41.667 13.43 0.00 38.51 3.56
4321 5074 1.227234 TGGCAGACCATATGCGTCG 60.227 57.895 14.70 11.88 42.67 5.12
4351 5104 7.122055 AGTTCAAAAAGTGTCTACATTTGACCA 59.878 33.333 8.96 0.00 40.95 4.02
4354 5107 8.275015 TCAGTTCAAAAAGTGTCTACATTTGA 57.725 30.769 6.36 6.36 40.24 2.69
4450 5223 4.265320 GGCTGTTAAACTATTTGATTGCGC 59.735 41.667 0.00 0.00 0.00 6.09
4467 5241 3.157087 AGACAATTTCGATTGGGCTGTT 58.843 40.909 3.94 0.00 35.93 3.16
4505 5279 9.745880 ACAACCAGTAGATATATTAGTTCGTTG 57.254 33.333 0.00 0.00 0.00 4.10
4508 5282 9.961265 TTGACAACCAGTAGATATATTAGTTCG 57.039 33.333 0.00 0.00 0.00 3.95
4571 5345 6.516527 GCATACTCATTTCCAACTCCAAAACA 60.517 38.462 0.00 0.00 0.00 2.83
4605 5379 7.785033 AGTTCACCCAATTCCATTATGAAATC 58.215 34.615 0.00 0.00 0.00 2.17
4613 5387 4.739793 TGAAGAGTTCACCCAATTCCATT 58.260 39.130 0.00 0.00 34.08 3.16
4674 5449 2.695147 CCAAGGGTTTGAATATCAGGGC 59.305 50.000 0.00 0.00 36.36 5.19
4696 5471 2.216046 TGACTACATCTACGGCTACGG 58.784 52.381 0.00 0.00 46.48 4.02
4752 5527 6.367374 TTGGAGGTGATGACTATTTGTGTA 57.633 37.500 0.00 0.00 0.00 2.90
4759 5534 4.851639 AGCTTTTGGAGGTGATGACTAT 57.148 40.909 0.00 0.00 34.08 2.12
4781 5556 1.217511 CTGACATGGAGCAGCGAGT 59.782 57.895 0.00 0.00 0.00 4.18
4786 5561 2.467962 CTGCACTGACATGGAGCAG 58.532 57.895 10.97 10.97 45.44 4.24
4822 5597 6.458206 GCTTTTGGTGTGCTTCAATATCGATA 60.458 38.462 7.75 7.75 0.00 2.92


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

AutoCloner maintained by Alex Coulton.