Multiple sequence alignment - TraesCS4B01G268700

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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 TraesCS4B01G268700 chr4B 100.000 3601 0 0 1 3601 543401740 543398140 0.000000e+00 6650.0
1 TraesCS4B01G268700 chr4B 95.238 105 5 0 1 105 12242344 12242240 2.220000e-37 167.0
2 TraesCS4B01G268700 chr4D 90.634 3566 179 63 128 3601 439294269 439290767 0.000000e+00 4591.0
3 TraesCS4B01G268700 chr4A 87.418 2750 157 84 623 3276 28602644 28599988 0.000000e+00 2987.0
4 TraesCS4B01G268700 chr4A 85.050 301 23 12 3301 3588 28599061 28598770 1.640000e-73 287.0
5 TraesCS4B01G268700 chr4A 81.152 191 13 14 385 564 28602827 28602649 8.110000e-27 132.0
6 TraesCS4B01G268700 chr1B 96.117 103 4 0 1 103 21522304 21522202 6.180000e-38 169.0
7 TraesCS4B01G268700 chr1B 95.146 103 5 0 1 103 499193469 499193571 2.880000e-36 163.0
8 TraesCS4B01G268700 chr7B 95.192 104 4 1 1 104 687331422 687331320 2.880000e-36 163.0
9 TraesCS4B01G268700 chr7B 94.286 105 6 0 1 105 636461590 636461486 1.030000e-35 161.0
10 TraesCS4B01G268700 chr7B 92.500 40 3 0 2544 2583 642437 642476 1.400000e-04 58.4
11 TraesCS4B01G268700 chr5B 95.146 103 5 0 1 103 530709367 530709265 2.880000e-36 163.0
12 TraesCS4B01G268700 chr5B 93.519 108 5 2 1 108 539030796 539030901 3.720000e-35 159.0
13 TraesCS4B01G268700 chr5B 92.500 40 3 0 2550 2589 712436670 712436631 1.400000e-04 58.4
14 TraesCS4B01G268700 chr3B 93.578 109 6 1 1 109 685611894 685612001 1.030000e-35 161.0
15 TraesCS4B01G268700 chr6A 90.756 119 7 4 1 118 115273984 115273869 4.810000e-34 156.0
16 TraesCS4B01G268700 chr5D 92.500 40 3 0 2550 2589 562062911 562062872 1.400000e-04 58.4


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 TraesCS4B01G268700 chr4B 543398140 543401740 3600 True 6650.000000 6650 100.000 1 3601 1 chr4B.!!$R2 3600
1 TraesCS4B01G268700 chr4D 439290767 439294269 3502 True 4591.000000 4591 90.634 128 3601 1 chr4D.!!$R1 3473
2 TraesCS4B01G268700 chr4A 28598770 28602827 4057 True 1135.333333 2987 84.540 385 3588 3 chr4A.!!$R1 3203

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
832 897 0.524604 GCACTGCCGTTTTGTTTCGT 60.525 50.0 0.0 0.0 0.0 3.85 F
1225 1297 0.110056 GTGGCTGATTCGTGTGCTTG 60.110 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2077 0.603569 GGTTGAGCTTCTCCGTGAGA 59.396 55.0 0.0 0.11 36.86 3.27 R
3052 3197 0.442699 GCCGGTTCAATTGTCTCGAC 59.557 55.0 1.9 0.00 0.00 4.20 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
20 21 2.231529 CTAGGTGGTCTACGGATCTGG 58.768 57.143 6.47 0.00 0.00 3.86
21 22 0.629596 AGGTGGTCTACGGATCTGGA 59.370 55.000 6.47 0.00 0.00 3.86
22 23 1.218196 AGGTGGTCTACGGATCTGGAT 59.782 52.381 6.47 0.00 0.00 3.41
23 24 1.341531 GGTGGTCTACGGATCTGGATG 59.658 57.143 6.47 0.00 0.00 3.51
24 25 2.032620 GTGGTCTACGGATCTGGATGT 58.967 52.381 6.47 0.00 0.00 3.06
25 26 3.220110 GTGGTCTACGGATCTGGATGTA 58.780 50.000 6.47 0.00 0.00 2.29
26 27 3.635373 GTGGTCTACGGATCTGGATGTAA 59.365 47.826 6.47 0.00 0.00 2.41
27 28 4.281182 GTGGTCTACGGATCTGGATGTAAT 59.719 45.833 6.47 0.00 0.00 1.89
28 29 4.899457 TGGTCTACGGATCTGGATGTAATT 59.101 41.667 6.47 0.00 0.00 1.40
29 30 5.365605 TGGTCTACGGATCTGGATGTAATTT 59.634 40.000 6.47 0.00 0.00 1.82
30 31 5.927115 GGTCTACGGATCTGGATGTAATTTC 59.073 44.000 6.47 0.00 0.00 2.17
31 32 6.239345 GGTCTACGGATCTGGATGTAATTTCT 60.239 42.308 6.47 0.00 0.00 2.52
32 33 7.039923 GGTCTACGGATCTGGATGTAATTTCTA 60.040 40.741 6.47 0.00 0.00 2.10
33 34 8.524487 GTCTACGGATCTGGATGTAATTTCTAT 58.476 37.037 6.47 0.00 0.00 1.98
34 35 9.090103 TCTACGGATCTGGATGTAATTTCTATT 57.910 33.333 6.47 0.00 0.00 1.73
52 53 9.886132 ATTTCTATTATTTCTGGTACTCGTTGT 57.114 29.630 0.00 0.00 0.00 3.32
62 63 3.226346 GTACTCGTTGTACTGCCATGA 57.774 47.619 11.96 0.00 45.91 3.07
63 64 3.782046 GTACTCGTTGTACTGCCATGAT 58.218 45.455 11.96 0.00 45.91 2.45
64 65 3.334583 ACTCGTTGTACTGCCATGATT 57.665 42.857 0.00 0.00 0.00 2.57
65 66 3.002791 ACTCGTTGTACTGCCATGATTG 58.997 45.455 0.00 0.00 0.00 2.67
66 67 3.261580 CTCGTTGTACTGCCATGATTGA 58.738 45.455 0.00 0.00 0.00 2.57
67 68 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
68 69 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
69 70 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
70 71 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
71 72 5.523552 CGTTGTACTGCCATGATTGAAGATA 59.476 40.000 0.00 0.00 0.00 1.98
72 73 6.037062 CGTTGTACTGCCATGATTGAAGATAA 59.963 38.462 0.00 0.00 0.00 1.75
73 74 7.413988 CGTTGTACTGCCATGATTGAAGATAAA 60.414 37.037 0.00 0.00 0.00 1.40
74 75 8.408601 GTTGTACTGCCATGATTGAAGATAAAT 58.591 33.333 0.00 0.00 0.00 1.40
75 76 9.625747 TTGTACTGCCATGATTGAAGATAAATA 57.374 29.630 0.00 0.00 0.00 1.40
76 77 9.276590 TGTACTGCCATGATTGAAGATAAATAG 57.723 33.333 0.00 0.00 0.00 1.73
77 78 9.494271 GTACTGCCATGATTGAAGATAAATAGA 57.506 33.333 0.00 0.00 0.00 1.98
79 80 9.228949 ACTGCCATGATTGAAGATAAATAGATC 57.771 33.333 0.00 0.00 0.00 2.75
80 81 8.260270 TGCCATGATTGAAGATAAATAGATCG 57.740 34.615 0.00 0.00 0.00 3.69
81 82 8.096414 TGCCATGATTGAAGATAAATAGATCGA 58.904 33.333 0.00 0.00 0.00 3.59
82 83 8.939929 GCCATGATTGAAGATAAATAGATCGAA 58.060 33.333 0.00 0.00 0.00 3.71
94 95 8.919695 ATAAATAGATCGAAATTTTTCTCGCG 57.080 30.769 0.00 0.00 35.07 5.87
95 96 6.583912 AATAGATCGAAATTTTTCTCGCGA 57.416 33.333 9.26 9.26 35.07 5.87
96 97 4.921470 AGATCGAAATTTTTCTCGCGAA 57.079 36.364 11.33 0.00 35.07 4.70
97 98 5.277601 AGATCGAAATTTTTCTCGCGAAA 57.722 34.783 11.33 0.88 37.36 3.46
98 99 5.685841 AGATCGAAATTTTTCTCGCGAAAA 58.314 33.333 11.33 9.15 44.89 2.29
120 121 5.613358 AAAAAGATAGAGGCGTCAACAAG 57.387 39.130 9.41 0.00 0.00 3.16
121 122 4.537135 AAAGATAGAGGCGTCAACAAGA 57.463 40.909 9.41 0.00 0.00 3.02
122 123 4.744795 AAGATAGAGGCGTCAACAAGAT 57.255 40.909 9.41 0.00 0.00 2.40
123 124 5.854010 AAGATAGAGGCGTCAACAAGATA 57.146 39.130 9.41 0.00 0.00 1.98
124 125 5.854010 AGATAGAGGCGTCAACAAGATAA 57.146 39.130 9.41 0.00 0.00 1.75
125 126 5.837437 AGATAGAGGCGTCAACAAGATAAG 58.163 41.667 9.41 0.00 0.00 1.73
126 127 3.963428 AGAGGCGTCAACAAGATAAGT 57.037 42.857 9.41 0.00 0.00 2.24
133 134 5.220605 GGCGTCAACAAGATAAGTGATAACC 60.221 44.000 0.00 0.00 0.00 2.85
137 138 7.331791 GTCAACAAGATAAGTGATAACCCTCT 58.668 38.462 0.00 0.00 0.00 3.69
138 139 7.278868 GTCAACAAGATAAGTGATAACCCTCTG 59.721 40.741 0.00 0.00 0.00 3.35
160 161 5.639757 TGATGTTAATCATTGCTGGTTTCG 58.360 37.500 0.00 0.00 37.91 3.46
167 168 3.738982 TCATTGCTGGTTTCGAGAAAGA 58.261 40.909 0.00 0.00 0.00 2.52
188 189 4.462834 AGAGGTGACTTAACGACATCATCA 59.537 41.667 0.00 0.00 44.43 3.07
190 191 5.734720 AGGTGACTTAACGACATCATCAAT 58.265 37.500 0.00 0.00 37.44 2.57
206 207 6.556974 TCATCAATCAGAGATGAGGTCTTT 57.443 37.500 2.00 0.00 44.98 2.52
237 238 3.857521 TAGCCTTGTGGGGTCCGGT 62.858 63.158 0.00 0.00 45.70 5.28
249 250 2.606213 TCCGGTCAGGCATGTCCA 60.606 61.111 14.73 0.00 40.77 4.02
256 257 1.197721 GTCAGGCATGTCCAAAACTCG 59.802 52.381 0.00 0.00 37.29 4.18
266 267 4.373527 TGTCCAAAACTCGATCGAGAAAA 58.626 39.130 42.97 22.35 44.53 2.29
308 313 1.270412 ACCGCAAACACCTATCGTTCA 60.270 47.619 0.00 0.00 0.00 3.18
309 314 1.393539 CCGCAAACACCTATCGTTCAG 59.606 52.381 0.00 0.00 0.00 3.02
324 329 2.375110 GTTCAGTGACACGCAAACATG 58.625 47.619 12.81 0.00 0.00 3.21
325 330 1.662517 TCAGTGACACGCAAACATGT 58.337 45.000 0.00 0.00 0.00 3.21
440 451 7.103641 AGACTTTGGAAAAAGGAAAGAAAACC 58.896 34.615 0.00 0.00 34.18 3.27
491 502 0.577269 GTGCGCTACGATTTGGCTAG 59.423 55.000 9.73 0.00 0.00 3.42
492 503 1.151777 TGCGCTACGATTTGGCTAGC 61.152 55.000 9.73 6.04 0.00 3.42
493 504 0.876342 GCGCTACGATTTGGCTAGCT 60.876 55.000 15.72 0.00 32.27 3.32
494 505 1.602165 GCGCTACGATTTGGCTAGCTA 60.602 52.381 15.72 5.44 32.27 3.32
530 549 1.377333 CGGTGGAGGAAAAGGGAGC 60.377 63.158 0.00 0.00 0.00 4.70
556 582 2.081462 GACGGGTTCACCTTTACATGG 58.919 52.381 0.00 0.00 36.97 3.66
565 591 4.343231 TCACCTTTACATGGCATGACATT 58.657 39.130 32.74 13.66 0.00 2.71
621 652 2.646175 CGGTGATGACGTCCCAGGT 61.646 63.158 14.12 0.00 0.00 4.00
646 690 3.697747 CGTAACCCGCACTCCCCA 61.698 66.667 0.00 0.00 0.00 4.96
774 825 0.976073 CCTTGCCTTCTACCTCCGGA 60.976 60.000 2.93 2.93 0.00 5.14
786 837 1.602771 CTCCGGACCTTTCCTTCCC 59.397 63.158 0.00 0.00 40.23 3.97
832 897 0.524604 GCACTGCCGTTTTGTTTCGT 60.525 50.000 0.00 0.00 0.00 3.85
891 956 2.763645 AAAACACCCACGCTCCCCT 61.764 57.895 0.00 0.00 0.00 4.79
933 1001 2.428085 GGAGACCCGGAGAAGGAGC 61.428 68.421 0.73 0.00 0.00 4.70
940 1008 1.410365 CCCGGAGAAGGAGCTAGAGAA 60.410 57.143 0.73 0.00 0.00 2.87
949 1017 3.898482 AGGAGCTAGAGAAGAAGAGTCC 58.102 50.000 0.00 0.00 0.00 3.85
954 1022 4.949856 AGCTAGAGAAGAAGAGTCCAGAAG 59.050 45.833 0.00 0.00 0.00 2.85
955 1023 4.440112 GCTAGAGAAGAAGAGTCCAGAAGC 60.440 50.000 0.00 0.00 0.00 3.86
1165 1237 2.833121 ATCCCGCCGCCAATTTCC 60.833 61.111 0.00 0.00 0.00 3.13
1168 1240 3.825611 CCGCCGCCAATTTCCCTG 61.826 66.667 0.00 0.00 0.00 4.45
1169 1241 4.496927 CGCCGCCAATTTCCCTGC 62.497 66.667 0.00 0.00 0.00 4.85
1170 1242 3.070576 GCCGCCAATTTCCCTGCT 61.071 61.111 0.00 0.00 0.00 4.24
1171 1243 3.068729 GCCGCCAATTTCCCTGCTC 62.069 63.158 0.00 0.00 0.00 4.26
1172 1244 2.418083 CCGCCAATTTCCCTGCTCC 61.418 63.158 0.00 0.00 0.00 4.70
1173 1245 2.418083 CGCCAATTTCCCTGCTCCC 61.418 63.158 0.00 0.00 0.00 4.30
1174 1246 2.418083 GCCAATTTCCCTGCTCCCG 61.418 63.158 0.00 0.00 0.00 5.14
1175 1247 1.000896 CCAATTTCCCTGCTCCCGT 60.001 57.895 0.00 0.00 0.00 5.28
1176 1248 1.315257 CCAATTTCCCTGCTCCCGTG 61.315 60.000 0.00 0.00 0.00 4.94
1177 1249 1.678970 AATTTCCCTGCTCCCGTGC 60.679 57.895 0.00 0.00 0.00 5.34
1178 1250 2.142292 AATTTCCCTGCTCCCGTGCT 62.142 55.000 0.00 0.00 0.00 4.40
1197 1269 2.094854 GCTCCCTTCTCTGCATTTTGTG 60.095 50.000 0.00 0.00 0.00 3.33
1200 1272 4.724399 TCCCTTCTCTGCATTTTGTGTTA 58.276 39.130 0.00 0.00 0.00 2.41
1225 1297 0.110056 GTGGCTGATTCGTGTGCTTG 60.110 55.000 0.00 0.00 0.00 4.01
1226 1298 0.534877 TGGCTGATTCGTGTGCTTGT 60.535 50.000 0.00 0.00 0.00 3.16
1227 1299 0.166814 GGCTGATTCGTGTGCTTGTC 59.833 55.000 0.00 0.00 0.00 3.18
1228 1300 1.151668 GCTGATTCGTGTGCTTGTCT 58.848 50.000 0.00 0.00 0.00 3.41
1231 1303 1.069978 TGATTCGTGTGCTTGTCTGGA 59.930 47.619 0.00 0.00 0.00 3.86
1441 1513 1.229209 AAGAGCCCCGACAAGGAGA 60.229 57.895 0.00 0.00 45.00 3.71
1442 1514 0.836400 AAGAGCCCCGACAAGGAGAA 60.836 55.000 0.00 0.00 45.00 2.87
1443 1515 0.618968 AGAGCCCCGACAAGGAGAAT 60.619 55.000 0.00 0.00 45.00 2.40
1444 1516 0.179070 GAGCCCCGACAAGGAGAATC 60.179 60.000 0.00 0.00 45.00 2.52
1483 1576 1.526225 GCCGACAAGGGGGATAAGC 60.526 63.158 0.00 0.00 41.48 3.09
1547 1640 4.966787 GAAGCAACCGCCCACCCA 62.967 66.667 0.00 0.00 39.83 4.51
1551 1644 4.885270 CAACCGCCCACCCACACA 62.885 66.667 0.00 0.00 0.00 3.72
1563 1662 2.104792 CACCCACACAGAGGAGAAGAAA 59.895 50.000 0.00 0.00 0.00 2.52
1591 1690 0.389948 GCTCCAGGTCGGTACACAAG 60.390 60.000 0.00 0.00 35.57 3.16
1592 1691 0.389948 CTCCAGGTCGGTACACAAGC 60.390 60.000 0.00 0.00 35.57 4.01
1593 1692 1.116536 TCCAGGTCGGTACACAAGCA 61.117 55.000 0.00 0.00 35.57 3.91
1666 1767 4.680237 CCGACCTTGCGGCTCACA 62.680 66.667 0.00 0.00 45.38 3.58
1794 1895 3.223589 GGTGCGGTTTTGCTGGGT 61.224 61.111 0.00 0.00 35.36 4.51
1802 1903 2.882137 CGGTTTTGCTGGGTTTCTTCTA 59.118 45.455 0.00 0.00 0.00 2.10
1803 1904 3.316868 CGGTTTTGCTGGGTTTCTTCTAA 59.683 43.478 0.00 0.00 0.00 2.10
1817 1918 7.692705 GGGTTTCTTCTAAATTCTTCGAATTCG 59.307 37.037 21.78 21.78 41.45 3.34
1843 1944 6.693545 CGGTTTGTTCTGCTGTTAATTTTGTA 59.306 34.615 0.00 0.00 0.00 2.41
2038 2139 2.335712 GCAAGAAGGACAAGGGCGG 61.336 63.158 0.00 0.00 0.00 6.13
2040 2141 2.829384 AAGAAGGACAAGGGCGGCA 61.829 57.895 12.47 0.00 0.00 5.69
2148 2255 1.602237 GGGAAAGGCATCGAGGTGA 59.398 57.895 0.00 0.00 0.00 4.02
2384 2503 1.218047 CGGCTACTACCAGCAGCAA 59.782 57.895 0.00 0.00 43.67 3.91
2453 2572 1.218047 CGGCTACTACCAGCAGCAA 59.782 57.895 0.00 0.00 43.67 3.91
2456 2575 1.079503 GCTACTACCAGCAGCAACAC 58.920 55.000 0.00 0.00 41.40 3.32
2487 2606 0.752009 CGGCTACTACCAGCAGGAGA 60.752 60.000 0.35 0.00 43.67 3.71
2742 2872 1.676746 AGCTCTAGTTACGCGGATCA 58.323 50.000 12.47 0.00 0.00 2.92
2803 2937 0.471022 TTTGGTTCCCCCTGCCTTTC 60.471 55.000 0.00 0.00 0.00 2.62
2819 2953 1.471829 TTTCCTCCGCTGTCTCTGCA 61.472 55.000 0.00 0.00 0.00 4.41
2820 2954 1.881903 TTCCTCCGCTGTCTCTGCAG 61.882 60.000 7.63 7.63 39.37 4.41
2891 3028 9.549078 TTAATTTGATTTTAACCCAGTTGTTCC 57.451 29.630 0.00 0.00 0.00 3.62
2905 3042 5.163754 CCAGTTGTTCCGCTAAATTAAGAGG 60.164 44.000 0.00 0.00 37.76 3.69
3001 3146 3.065371 CCGGTTTTGCTTAATCTAGCCTG 59.935 47.826 0.00 0.00 40.49 4.85
3052 3197 0.457853 ACGTGGTGATCAATCGTCGG 60.458 55.000 12.92 0.00 0.00 4.79
3153 3299 0.658897 GTCGTGACGGGCAAGAAAAA 59.341 50.000 4.70 0.00 36.76 1.94
3170 3316 8.442605 CAAGAAAAATTGCAGGCATTTAATTG 57.557 30.769 0.00 0.19 0.00 2.32
3172 3318 8.168790 AGAAAAATTGCAGGCATTTAATTGTT 57.831 26.923 0.00 0.00 0.00 2.83
3174 3320 5.883503 AATTGCAGGCATTTAATTGTTGG 57.116 34.783 0.00 0.00 0.00 3.77
3175 3321 2.697654 TGCAGGCATTTAATTGTTGGC 58.302 42.857 0.00 0.00 36.28 4.52
3232 3402 2.483538 GCAAAATTGGTGTTGTGCTCCT 60.484 45.455 0.00 0.00 0.00 3.69
3245 3415 4.831307 CTCCTTCCCGCGTCGTCG 62.831 72.222 4.92 0.00 40.37 5.12
3301 4379 2.067605 CCGGCATGGGGTACACCTA 61.068 63.158 16.93 1.83 40.03 3.08
3342 4420 5.309543 TGGAATATTCTCCCGGTGTTGATAT 59.690 40.000 14.95 0.00 34.22 1.63
3382 4468 2.854185 GGAATTATTCTGCGTGCTTTGC 59.146 45.455 4.87 0.00 0.00 3.68
3393 4479 2.992543 GCGTGCTTTGCATATTTTTGGA 59.007 40.909 0.00 0.00 41.91 3.53
3421 4515 4.616953 TCTGTGTATGTGTGTGTGTACTG 58.383 43.478 0.00 0.00 0.00 2.74
3442 4536 0.949105 GTGTGTTGGACGGCAGTAGG 60.949 60.000 0.00 0.00 0.00 3.18
3513 4608 0.107993 GCTGCAGCCTGATGTACTGA 60.108 55.000 28.76 0.00 33.10 3.41
3515 4610 2.210961 CTGCAGCCTGATGTACTGATG 58.789 52.381 0.00 0.00 33.10 3.07
3519 4614 4.101430 TGCAGCCTGATGTACTGATGATAA 59.899 41.667 0.00 0.00 33.10 1.75
3520 4615 4.450419 GCAGCCTGATGTACTGATGATAAC 59.550 45.833 0.00 0.00 33.10 1.89
3521 4616 5.604565 CAGCCTGATGTACTGATGATAACA 58.395 41.667 0.00 0.00 33.10 2.41
3522 4617 6.051074 CAGCCTGATGTACTGATGATAACAA 58.949 40.000 0.00 0.00 33.10 2.83
3523 4618 6.709397 CAGCCTGATGTACTGATGATAACAAT 59.291 38.462 0.00 0.00 33.10 2.71
3524 4619 6.709397 AGCCTGATGTACTGATGATAACAATG 59.291 38.462 0.00 0.00 0.00 2.82
3525 4620 6.567321 GCCTGATGTACTGATGATAACAATGC 60.567 42.308 0.00 0.00 0.00 3.56
3570 4666 1.135660 CATACTCGATCGTGATCCGGG 60.136 57.143 22.80 0.00 37.11 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.158652 TCCAGATCCGTAGACCACCTAG 60.159 54.545 0.00 0.00 0.00 3.02
1 2 1.848388 TCCAGATCCGTAGACCACCTA 59.152 52.381 0.00 0.00 0.00 3.08
2 3 0.629596 TCCAGATCCGTAGACCACCT 59.370 55.000 0.00 0.00 0.00 4.00
3 4 1.341531 CATCCAGATCCGTAGACCACC 59.658 57.143 0.00 0.00 0.00 4.61
4 5 2.032620 ACATCCAGATCCGTAGACCAC 58.967 52.381 0.00 0.00 0.00 4.16
5 6 2.454336 ACATCCAGATCCGTAGACCA 57.546 50.000 0.00 0.00 0.00 4.02
6 7 5.470047 AATTACATCCAGATCCGTAGACC 57.530 43.478 0.00 0.00 0.00 3.85
7 8 6.750148 AGAAATTACATCCAGATCCGTAGAC 58.250 40.000 0.00 0.00 0.00 2.59
8 9 6.978674 AGAAATTACATCCAGATCCGTAGA 57.021 37.500 0.00 0.00 0.00 2.59
26 27 9.886132 ACAACGAGTACCAGAAATAATAGAAAT 57.114 29.630 0.00 0.00 0.00 2.17
28 29 9.793252 GTACAACGAGTACCAGAAATAATAGAA 57.207 33.333 10.44 0.00 45.94 2.10
43 44 4.081917 TCAATCATGGCAGTACAACGAGTA 60.082 41.667 0.00 0.00 0.00 2.59
44 45 3.002791 CAATCATGGCAGTACAACGAGT 58.997 45.455 0.00 0.00 0.00 4.18
45 46 3.261580 TCAATCATGGCAGTACAACGAG 58.738 45.455 0.00 0.00 0.00 4.18
46 47 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
47 48 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
48 49 5.824904 ATCTTCAATCATGGCAGTACAAC 57.175 39.130 0.00 0.00 0.00 3.32
49 50 7.936496 TTTATCTTCAATCATGGCAGTACAA 57.064 32.000 0.00 0.00 0.00 2.41
50 51 9.276590 CTATTTATCTTCAATCATGGCAGTACA 57.723 33.333 0.00 0.00 0.00 2.90
51 52 9.494271 TCTATTTATCTTCAATCATGGCAGTAC 57.506 33.333 0.00 0.00 0.00 2.73
53 54 9.228949 GATCTATTTATCTTCAATCATGGCAGT 57.771 33.333 0.00 0.00 0.00 4.40
54 55 8.388853 CGATCTATTTATCTTCAATCATGGCAG 58.611 37.037 0.00 0.00 0.00 4.85
55 56 8.096414 TCGATCTATTTATCTTCAATCATGGCA 58.904 33.333 0.00 0.00 0.00 4.92
56 57 8.484641 TCGATCTATTTATCTTCAATCATGGC 57.515 34.615 0.00 0.00 0.00 4.40
68 69 9.031191 CGCGAGAAAAATTTCGATCTATTTATC 57.969 33.333 0.00 0.00 41.92 1.75
69 70 8.761497 TCGCGAGAAAAATTTCGATCTATTTAT 58.239 29.630 3.71 0.00 41.92 1.40
70 71 8.122306 TCGCGAGAAAAATTTCGATCTATTTA 57.878 30.769 3.71 0.00 41.92 1.40
71 72 7.000575 TCGCGAGAAAAATTTCGATCTATTT 57.999 32.000 3.71 0.00 41.92 1.40
72 73 6.583912 TCGCGAGAAAAATTTCGATCTATT 57.416 33.333 3.71 0.00 41.92 1.73
98 99 5.305585 TCTTGTTGACGCCTCTATCTTTTT 58.694 37.500 0.00 0.00 0.00 1.94
99 100 4.894784 TCTTGTTGACGCCTCTATCTTTT 58.105 39.130 0.00 0.00 0.00 2.27
100 101 4.537135 TCTTGTTGACGCCTCTATCTTT 57.463 40.909 0.00 0.00 0.00 2.52
101 102 4.744795 ATCTTGTTGACGCCTCTATCTT 57.255 40.909 0.00 0.00 0.00 2.40
102 103 5.361285 ACTTATCTTGTTGACGCCTCTATCT 59.639 40.000 0.00 0.00 0.00 1.98
103 104 5.460419 CACTTATCTTGTTGACGCCTCTATC 59.540 44.000 0.00 0.00 0.00 2.08
104 105 5.127194 TCACTTATCTTGTTGACGCCTCTAT 59.873 40.000 0.00 0.00 0.00 1.98
105 106 4.461431 TCACTTATCTTGTTGACGCCTCTA 59.539 41.667 0.00 0.00 0.00 2.43
106 107 3.258372 TCACTTATCTTGTTGACGCCTCT 59.742 43.478 0.00 0.00 0.00 3.69
107 108 3.585862 TCACTTATCTTGTTGACGCCTC 58.414 45.455 0.00 0.00 0.00 4.70
108 109 3.678056 TCACTTATCTTGTTGACGCCT 57.322 42.857 0.00 0.00 0.00 5.52
109 110 5.220605 GGTTATCACTTATCTTGTTGACGCC 60.221 44.000 0.00 0.00 0.00 5.68
110 111 5.220605 GGGTTATCACTTATCTTGTTGACGC 60.221 44.000 0.00 0.00 0.00 5.19
111 112 6.106673 AGGGTTATCACTTATCTTGTTGACG 58.893 40.000 0.00 0.00 0.00 4.35
112 113 7.278868 CAGAGGGTTATCACTTATCTTGTTGAC 59.721 40.741 0.00 0.00 0.00 3.18
113 114 7.180229 TCAGAGGGTTATCACTTATCTTGTTGA 59.820 37.037 0.00 0.00 0.00 3.18
114 115 7.331026 TCAGAGGGTTATCACTTATCTTGTTG 58.669 38.462 0.00 0.00 0.00 3.33
115 116 7.496346 TCAGAGGGTTATCACTTATCTTGTT 57.504 36.000 0.00 0.00 0.00 2.83
116 117 7.126421 ACATCAGAGGGTTATCACTTATCTTGT 59.874 37.037 0.00 0.00 0.00 3.16
117 118 7.504403 ACATCAGAGGGTTATCACTTATCTTG 58.496 38.462 0.00 0.00 0.00 3.02
118 119 7.682787 ACATCAGAGGGTTATCACTTATCTT 57.317 36.000 0.00 0.00 0.00 2.40
119 120 7.682787 AACATCAGAGGGTTATCACTTATCT 57.317 36.000 0.00 0.00 0.00 1.98
122 123 8.988060 TGATTAACATCAGAGGGTTATCACTTA 58.012 33.333 0.00 0.00 34.22 2.24
123 124 7.861629 TGATTAACATCAGAGGGTTATCACTT 58.138 34.615 0.00 0.00 34.22 3.16
124 125 7.437713 TGATTAACATCAGAGGGTTATCACT 57.562 36.000 0.00 0.00 34.22 3.41
125 126 8.562892 CAATGATTAACATCAGAGGGTTATCAC 58.437 37.037 4.02 0.00 42.93 3.06
126 127 7.229306 GCAATGATTAACATCAGAGGGTTATCA 59.771 37.037 4.40 4.40 42.93 2.15
133 134 4.885907 ACCAGCAATGATTAACATCAGAGG 59.114 41.667 0.00 0.00 42.93 3.69
137 138 5.414144 TCGAAACCAGCAATGATTAACATCA 59.586 36.000 0.00 0.00 43.85 3.07
138 139 5.879237 TCGAAACCAGCAATGATTAACATC 58.121 37.500 0.00 0.00 38.38 3.06
160 161 4.868067 TGTCGTTAAGTCACCTCTTTCTC 58.132 43.478 0.00 0.00 0.00 2.87
167 168 4.801330 TGATGATGTCGTTAAGTCACCT 57.199 40.909 0.00 0.00 0.00 4.00
188 189 6.294397 GCAAACAAAAGACCTCATCTCTGATT 60.294 38.462 0.00 0.00 36.27 2.57
190 191 4.516698 GCAAACAAAAGACCTCATCTCTGA 59.483 41.667 0.00 0.00 36.27 3.27
237 238 1.071542 TCGAGTTTTGGACATGCCTGA 59.928 47.619 0.00 0.00 37.63 3.86
266 267 7.760340 GCGGTATAGTAGCAGCTCTATATTTTT 59.240 37.037 17.55 2.45 33.56 1.94
271 272 4.840271 TGCGGTATAGTAGCAGCTCTATA 58.160 43.478 0.00 7.74 35.81 1.31
282 287 4.580167 ACGATAGGTGTTTGCGGTATAGTA 59.420 41.667 0.00 0.00 43.77 1.82
308 313 4.816392 TCTATACATGTTTGCGTGTCACT 58.184 39.130 2.30 0.00 43.22 3.41
309 314 5.120208 ACTTCTATACATGTTTGCGTGTCAC 59.880 40.000 2.30 0.00 43.22 3.67
368 375 7.450124 TTGGCCTTTACATTGTTTTCGTATA 57.550 32.000 3.32 0.00 0.00 1.47
369 376 5.968528 TGGCCTTTACATTGTTTTCGTAT 57.031 34.783 3.32 0.00 0.00 3.06
381 388 1.960689 GCTGTCCTTTTGGCCTTTACA 59.039 47.619 3.32 0.00 40.12 2.41
440 451 5.335976 GGAGTGGCTTTCTGATTACAAAAGG 60.336 44.000 0.00 0.00 32.01 3.11
491 502 0.321671 TCGGATTGCCTGGCTATAGC 59.678 55.000 21.03 16.78 41.14 2.97
492 503 1.338200 GGTCGGATTGCCTGGCTATAG 60.338 57.143 21.03 14.62 0.00 1.31
493 504 0.685097 GGTCGGATTGCCTGGCTATA 59.315 55.000 21.03 5.70 0.00 1.31
494 505 1.451936 GGTCGGATTGCCTGGCTAT 59.548 57.895 21.03 18.18 0.00 2.97
530 549 1.234615 AAGGTGAACCCGTCATTGCG 61.235 55.000 0.00 0.00 38.90 4.85
556 582 2.103538 CGGCTGGCAATGTCATGC 59.896 61.111 1.08 0.00 45.67 4.06
581 612 1.869132 GTTGAGTTGACCGGTGTTACC 59.131 52.381 14.63 0.00 34.05 2.85
590 621 0.949105 ATCACCGCGTTGAGTTGACC 60.949 55.000 13.02 0.00 0.00 4.02
591 622 0.163788 CATCACCGCGTTGAGTTGAC 59.836 55.000 13.02 0.00 0.00 3.18
665 709 4.648626 TTTCTGCCCGCTGCTGCT 62.649 61.111 14.03 0.00 42.00 4.24
666 710 4.410743 GTTTCTGCCCGCTGCTGC 62.411 66.667 5.34 5.34 42.00 5.25
667 711 0.955428 TAAGTTTCTGCCCGCTGCTG 60.955 55.000 0.00 0.00 42.00 4.41
668 712 0.955919 GTAAGTTTCTGCCCGCTGCT 60.956 55.000 0.00 0.00 42.00 4.24
669 713 1.502190 GTAAGTTTCTGCCCGCTGC 59.498 57.895 0.00 0.00 41.77 5.25
670 714 1.635663 CGGTAAGTTTCTGCCCGCTG 61.636 60.000 0.00 0.00 0.00 5.18
671 715 1.375523 CGGTAAGTTTCTGCCCGCT 60.376 57.895 0.00 0.00 0.00 5.52
672 716 3.174788 CGGTAAGTTTCTGCCCGC 58.825 61.111 0.00 0.00 0.00 6.13
673 717 3.174788 GCGGTAAGTTTCTGCCCG 58.825 61.111 2.00 0.00 41.50 6.13
752 796 1.153349 GAGGTAGAAGGCAAGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
753 797 1.153349 GGAGGTAGAAGGCAAGGCG 60.153 63.158 0.00 0.00 0.00 5.52
754 798 1.153349 CGGAGGTAGAAGGCAAGGC 60.153 63.158 0.00 0.00 0.00 4.35
786 837 1.298667 CGGGGATAAATAGGCGGGG 59.701 63.158 0.00 0.00 0.00 5.73
873 938 2.203437 GGGGAGCGTGGGTGTTTT 60.203 61.111 0.00 0.00 0.00 2.43
933 1001 4.097892 GGCTTCTGGACTCTTCTTCTCTAG 59.902 50.000 0.00 0.00 0.00 2.43
955 1023 3.074999 GCTCTGTGGCTCTCCGAGG 62.075 68.421 0.00 0.00 34.14 4.63
983 1055 2.317040 CCATAGAAACCGAGGAGGCTA 58.683 52.381 0.00 0.00 46.52 3.93
990 1062 1.227556 CGCCCCCATAGAAACCGAG 60.228 63.158 0.00 0.00 0.00 4.63
1166 1238 3.672295 GAAGGGAGCACGGGAGCAG 62.672 68.421 0.00 0.00 36.85 4.24
1167 1239 3.706373 GAAGGGAGCACGGGAGCA 61.706 66.667 0.00 0.00 36.85 4.26
1168 1240 3.378399 GAGAAGGGAGCACGGGAGC 62.378 68.421 0.00 0.00 0.00 4.70
1169 1241 1.684049 AGAGAAGGGAGCACGGGAG 60.684 63.158 0.00 0.00 0.00 4.30
1170 1242 1.984570 CAGAGAAGGGAGCACGGGA 60.985 63.158 0.00 0.00 0.00 5.14
1171 1243 2.581354 CAGAGAAGGGAGCACGGG 59.419 66.667 0.00 0.00 0.00 5.28
1172 1244 2.125350 GCAGAGAAGGGAGCACGG 60.125 66.667 0.00 0.00 0.00 4.94
1173 1245 0.392193 AATGCAGAGAAGGGAGCACG 60.392 55.000 0.00 0.00 40.14 5.34
1174 1246 1.831580 AAATGCAGAGAAGGGAGCAC 58.168 50.000 0.00 0.00 40.14 4.40
1175 1247 2.165167 CAAAATGCAGAGAAGGGAGCA 58.835 47.619 0.00 0.00 41.73 4.26
1176 1248 2.094854 CACAAAATGCAGAGAAGGGAGC 60.095 50.000 0.00 0.00 0.00 4.70
1177 1249 3.152341 ACACAAAATGCAGAGAAGGGAG 58.848 45.455 0.00 0.00 0.00 4.30
1178 1250 3.228188 ACACAAAATGCAGAGAAGGGA 57.772 42.857 0.00 0.00 0.00 4.20
1197 1269 2.271800 CGAATCAGCCACCAGACTAAC 58.728 52.381 0.00 0.00 0.00 2.34
1200 1272 0.036952 CACGAATCAGCCACCAGACT 60.037 55.000 0.00 0.00 0.00 3.24
1225 1297 2.355837 TGCGCGACAAGTCCAGAC 60.356 61.111 12.10 0.00 0.00 3.51
1226 1298 2.049156 CTGCGCGACAAGTCCAGA 60.049 61.111 12.10 0.00 0.00 3.86
1227 1299 3.114616 CCTGCGCGACAAGTCCAG 61.115 66.667 12.10 5.34 0.00 3.86
1273 1345 2.640989 CACGACGACCCTGTTCGA 59.359 61.111 0.00 0.00 41.78 3.71
1338 1410 1.738099 CTCGACGGGCTTCTTGGTG 60.738 63.158 0.00 0.00 0.00 4.17
1462 1534 1.342672 TTATCCCCCTTGTCGGCTCC 61.343 60.000 0.00 0.00 0.00 4.70
1463 1535 0.106894 CTTATCCCCCTTGTCGGCTC 59.893 60.000 0.00 0.00 0.00 4.70
1464 1536 1.984288 GCTTATCCCCCTTGTCGGCT 61.984 60.000 0.00 0.00 0.00 5.52
1465 1537 1.526225 GCTTATCCCCCTTGTCGGC 60.526 63.158 0.00 0.00 0.00 5.54
1547 1640 2.104963 GTGGGTTTCTTCTCCTCTGTGT 59.895 50.000 0.00 0.00 0.00 3.72
1551 1644 0.977395 CCGTGGGTTTCTTCTCCTCT 59.023 55.000 0.00 0.00 0.00 3.69
1563 1662 4.640690 ACCTGGAGCTCCGTGGGT 62.641 66.667 33.97 31.16 39.43 4.51
1591 1690 1.387295 GGGGTAGGATTTGCTGCTGC 61.387 60.000 8.89 8.89 40.20 5.25
1592 1691 0.753111 GGGGGTAGGATTTGCTGCTG 60.753 60.000 0.00 0.00 0.00 4.41
1593 1692 1.214305 TGGGGGTAGGATTTGCTGCT 61.214 55.000 0.00 0.00 0.00 4.24
1656 1757 1.375908 GGAGACATTGTGAGCCGCA 60.376 57.895 0.00 0.00 0.00 5.69
1666 1767 2.159517 GCAAAATCGAAGCGGAGACATT 60.160 45.455 0.00 0.00 0.00 2.71
1755 1856 3.398954 TTGATTTTGTAGATTCGGCGC 57.601 42.857 0.00 0.00 0.00 6.53
1764 1865 3.915437 ACCGCACCTTTGATTTTGTAG 57.085 42.857 0.00 0.00 0.00 2.74
1794 1895 6.953743 CGCGAATTCGAAGAATTTAGAAGAAA 59.046 34.615 31.01 0.00 45.90 2.52
1802 1903 3.824414 AACCGCGAATTCGAAGAATTT 57.176 38.095 31.01 13.50 45.90 1.82
1803 1904 3.058501 ACAAACCGCGAATTCGAAGAATT 60.059 39.130 31.01 16.53 45.90 2.17
1817 1918 2.766970 TTAACAGCAGAACAAACCGC 57.233 45.000 0.00 0.00 0.00 5.68
1843 1944 3.581755 TCGTCAATTTCGAACGGAAGAT 58.418 40.909 0.00 0.00 35.70 2.40
1976 2077 0.603569 GGTTGAGCTTCTCCGTGAGA 59.396 55.000 0.00 0.11 36.86 3.27
1982 2083 3.491652 GCGCGGTTGAGCTTCTCC 61.492 66.667 8.83 0.00 37.97 3.71
2038 2139 1.073768 GTCCTTCTTCTCGTCGCTGC 61.074 60.000 0.00 0.00 0.00 5.25
2040 2141 0.959553 TTGTCCTTCTTCTCGTCGCT 59.040 50.000 0.00 0.00 0.00 4.93
2357 2476 1.065436 GTAGTAGCCGCCGGAGTTC 59.935 63.158 7.68 0.00 0.00 3.01
2361 2480 2.831742 CTGGTAGTAGCCGCCGGA 60.832 66.667 7.68 0.00 0.00 5.14
2399 2518 2.123597 TGGTAGTAGCCGCCGGAT 60.124 61.111 7.68 1.51 0.00 4.18
2400 2519 2.831742 CTGGTAGTAGCCGCCGGA 60.832 66.667 7.68 0.00 0.00 5.14
2684 2811 1.502190 CTCGTCGCTGTCTGCTACA 59.498 57.895 7.08 0.00 37.22 2.74
2735 2865 0.673022 GATGGATGCCTCTGATCCGC 60.673 60.000 0.00 0.00 42.22 5.54
2742 2872 1.144503 GGTTCATGGATGGATGCCTCT 59.855 52.381 0.00 0.00 0.00 3.69
2803 2937 2.183811 CTGCAGAGACAGCGGAGG 59.816 66.667 8.42 0.00 40.83 4.30
2819 2953 1.066858 ACGAACAATGGTCGATCAGCT 60.067 47.619 28.35 0.00 0.00 4.24
2820 2954 1.359848 ACGAACAATGGTCGATCAGC 58.640 50.000 28.35 0.00 0.00 4.26
2879 3016 2.579410 ATTTAGCGGAACAACTGGGT 57.421 45.000 0.00 0.00 0.00 4.51
2886 3023 5.155278 TCACCTCTTAATTTAGCGGAACA 57.845 39.130 7.46 0.00 0.00 3.18
2891 3028 7.358765 CGATCTCATTCACCTCTTAATTTAGCG 60.359 40.741 0.00 0.00 0.00 4.26
2905 3042 2.797156 CCCATTCGTCGATCTCATTCAC 59.203 50.000 0.00 0.00 0.00 3.18
3012 3157 0.524392 GCTCTCACATCGACGACAGG 60.524 60.000 0.00 0.00 0.00 4.00
3052 3197 0.442699 GCCGGTTCAATTGTCTCGAC 59.557 55.000 1.90 0.00 0.00 4.20
3153 3299 3.690628 GCCAACAATTAAATGCCTGCAAT 59.309 39.130 0.00 0.00 0.00 3.56
3165 3311 4.156922 CGTTACCATCAAGGCCAACAATTA 59.843 41.667 5.01 0.00 43.14 1.40
3170 3316 1.816074 TCGTTACCATCAAGGCCAAC 58.184 50.000 5.01 0.00 43.14 3.77
3172 3318 1.339631 CCTTCGTTACCATCAAGGCCA 60.340 52.381 5.01 0.00 43.14 5.36
3174 3320 2.396590 TCCTTCGTTACCATCAAGGC 57.603 50.000 0.00 0.00 43.14 4.35
3175 3321 4.122776 CAGATCCTTCGTTACCATCAAGG 58.877 47.826 0.00 0.00 45.67 3.61
3292 4370 2.103736 GAGCGGCGTAGGTGTACC 59.896 66.667 9.37 0.00 0.00 3.34
3393 4479 7.744087 ACACACACACATACACAGAATAATT 57.256 32.000 0.00 0.00 0.00 1.40
3421 4515 0.531090 TACTGCCGTCCAACACACAC 60.531 55.000 0.00 0.00 0.00 3.82
3442 4536 4.029087 GCACGCAGACGAAAATATCAAAAC 59.971 41.667 0.00 0.00 43.93 2.43
3513 4608 9.647797 CCTTAATAATGCATGCATTGTTATCAT 57.352 29.630 39.77 28.96 43.90 2.45
3515 4610 7.816031 AGCCTTAATAATGCATGCATTGTTATC 59.184 33.333 39.77 32.74 43.90 1.75
3519 4614 5.540400 AGCCTTAATAATGCATGCATTGT 57.460 34.783 42.30 36.52 45.15 2.71
3520 4615 5.407387 GGAAGCCTTAATAATGCATGCATTG 59.593 40.000 42.30 29.76 45.15 2.82
3521 4616 5.544650 GGAAGCCTTAATAATGCATGCATT 58.455 37.500 39.40 39.40 46.85 3.56
3522 4617 4.321452 CGGAAGCCTTAATAATGCATGCAT 60.321 41.667 27.46 27.46 38.46 3.96
3523 4618 3.004629 CGGAAGCCTTAATAATGCATGCA 59.995 43.478 25.04 25.04 0.00 3.96
3524 4619 3.253188 TCGGAAGCCTTAATAATGCATGC 59.747 43.478 11.82 11.82 0.00 4.06
3525 4620 5.181811 TCATCGGAAGCCTTAATAATGCATG 59.818 40.000 0.00 0.00 0.00 4.06
3570 4666 7.771183 TGTGAATGCAATACCTAATCCTTTTC 58.229 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.