Multiple sequence alignment - TraesCS5A01G459900

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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 TraesCS5A01G459900 chr5A 100.000 4424 0 0 896 5319 640600183 640604606 0.000000e+00 8170
1 TraesCS5A01G459900 chr5A 100.000 469 0 0 1 469 640599288 640599756 0.000000e+00 867
2 TraesCS5A01G459900 chr5B 92.478 3124 128 42 896 3956 643167681 643170760 0.000000e+00 4368
3 TraesCS5A01G459900 chr5B 95.712 793 26 4 3986 4775 643170823 643171610 0.000000e+00 1269
4 TraesCS5A01G459900 chr5B 82.857 595 58 22 4726 5284 643171610 643172196 1.330000e-135 494
5 TraesCS5A01G459900 chr5B 83.579 475 46 15 8 469 643167095 643167550 2.960000e-112 416
6 TraesCS5A01G459900 chr5B 95.192 104 4 1 4833 4935 59160670 59160773 4.260000e-36 163
7 TraesCS5A01G459900 chr5D 90.382 1258 57 28 3696 4927 512203158 512204377 0.000000e+00 1594
8 TraesCS5A01G459900 chr5D 88.170 1344 103 18 1724 3033 512201088 512202409 0.000000e+00 1550
9 TraesCS5A01G459900 chr5D 90.180 835 42 11 896 1727 512200165 512200962 0.000000e+00 1051
10 TraesCS5A01G459900 chr5D 88.500 400 25 6 66 460 512199637 512200020 1.040000e-126 464
11 TraesCS5A01G459900 chr5D 87.580 314 25 11 3102 3407 512202569 512202876 8.480000e-93 351
12 TraesCS5A01G459900 chr5D 92.308 117 7 2 5205 5319 512204574 512204690 1.190000e-36 165
13 TraesCS5A01G459900 chr5D 87.179 117 10 3 5038 5151 512204455 512204569 1.550000e-25 128
14 TraesCS5A01G459900 chr2A 96.117 103 2 2 4833 4934 697045320 697045421 3.300000e-37 167
15 TraesCS5A01G459900 chr1D 97.938 97 0 2 4832 4926 462465470 462465566 3.300000e-37 167
16 TraesCS5A01G459900 chr1D 96.040 101 3 1 4827 4926 462471276 462471376 4.260000e-36 163
17 TraesCS5A01G459900 chr2D 96.000 100 4 0 4827 4926 557068840 557068939 4.260000e-36 163
18 TraesCS5A01G459900 chr3A 93.636 110 3 4 4832 4940 744061698 744061804 1.530000e-35 161
19 TraesCS5A01G459900 chr3A 93.519 108 5 2 4830 4937 743965543 743965648 5.510000e-35 159


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 TraesCS5A01G459900 chr5A 640599288 640604606 5318 False 4518.500000 8170 100.000000 1 5319 2 chr5A.!!$F1 5318
1 TraesCS5A01G459900 chr5B 643167095 643172196 5101 False 1636.750000 4368 88.656500 8 5284 4 chr5B.!!$F2 5276
2 TraesCS5A01G459900 chr5D 512199637 512204690 5053 False 757.571429 1594 89.185571 66 5319 7 chr5D.!!$F1 5253

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
396 410 0.661020 CAAAACCAAAGCCGAGACGT 59.339 50.000 0.0 0.0 0.00 4.34 F
449 463 0.882927 GACCAGCACGGCACAGTAAA 60.883 55.000 0.0 0.0 39.03 2.01 F
984 1003 2.042843 GGCGGAGGAGGAGGAAGA 60.043 66.667 0.0 0.0 0.00 2.87 F
1607 1629 0.693049 GGGTGGACCTCTGATGTTGT 59.307 55.000 0.0 0.0 35.85 3.32 F
2655 2861 1.068125 GGGCACAAACGAAATACACCC 60.068 52.381 0.0 0.0 0.00 4.61 F
3673 4039 0.104855 AGATGTCTGTGTGTGCGTGT 59.895 50.000 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 1358 0.175302 CACAAGCAGCAAACCAACCA 59.825 50.000 0.00 0.0 0.00 3.67 R
1339 1359 0.175531 ACACAAGCAGCAAACCAACC 59.824 50.000 0.00 0.0 0.00 3.77 R
2624 2830 0.471591 TTTGTGCCCCAATCAGCCTT 60.472 50.000 0.00 0.0 31.81 4.35 R
3127 3428 1.597742 ACACTGGCAGTTTAGTGCAG 58.402 50.000 19.43 6.6 46.27 4.41 R
3683 4049 1.229400 GAGTCCCTACCCCCACACA 60.229 63.158 0.00 0.0 0.00 3.72 R
5152 5654 1.464219 TGACGTGTTCGCTATGACGTA 59.536 47.619 0.00 0.0 44.62 3.57 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 0.928505 TCATGTGCCCCCTCATTGAT 59.071 50.000 0.00 0.00 0.00 2.57
23 24 1.307647 GTGCCCCCTCATTGATGGT 59.692 57.895 7.15 0.00 0.00 3.55
32 33 6.372931 CCCCCTCATTGATGGTAAATAGAAA 58.627 40.000 7.15 0.00 0.00 2.52
34 35 7.014615 CCCCCTCATTGATGGTAAATAGAAAAG 59.985 40.741 7.15 0.00 0.00 2.27
35 36 7.779798 CCCCTCATTGATGGTAAATAGAAAAGA 59.220 37.037 7.15 0.00 0.00 2.52
36 37 9.189156 CCCTCATTGATGGTAAATAGAAAAGAA 57.811 33.333 0.11 0.00 0.00 2.52
56 57 6.767524 AGAAAAACAAGTGTACACCATTCA 57.232 33.333 22.28 0.00 0.00 2.57
57 58 7.346751 AGAAAAACAAGTGTACACCATTCAT 57.653 32.000 22.28 4.02 0.00 2.57
58 59 7.202526 AGAAAAACAAGTGTACACCATTCATG 58.797 34.615 22.28 13.47 0.00 3.07
60 61 2.819608 ACAAGTGTACACCATTCATGCC 59.180 45.455 22.28 0.00 0.00 4.40
61 62 1.737838 AGTGTACACCATTCATGCCG 58.262 50.000 22.28 0.00 0.00 5.69
62 63 1.277842 AGTGTACACCATTCATGCCGA 59.722 47.619 22.28 0.00 0.00 5.54
78 83 1.260297 GCCGACCAAAACAAAACATGC 59.740 47.619 0.00 0.00 0.00 4.06
79 84 2.544685 CCGACCAAAACAAAACATGCA 58.455 42.857 0.00 0.00 0.00 3.96
82 87 3.862267 CGACCAAAACAAAACATGCAAGA 59.138 39.130 0.00 0.00 0.00 3.02
91 96 7.467557 AACAAAACATGCAAGACAAGTTATG 57.532 32.000 0.00 0.00 39.19 1.90
93 98 5.458041 AAACATGCAAGACAAGTTATGCT 57.542 34.783 0.00 0.00 39.19 3.79
101 106 3.448686 AGACAAGTTATGCTTCGATCGG 58.551 45.455 16.41 0.48 34.69 4.18
113 118 4.285149 GATCGGCACATGCGACGC 62.285 66.667 14.19 14.19 43.26 5.19
131 136 4.494690 CGACGCCGACTGTATAAGTAAGAA 60.495 45.833 0.00 0.00 40.07 2.52
153 158 4.281657 ACTTTCCAACTTCTTTCCTTGCT 58.718 39.130 0.00 0.00 0.00 3.91
163 168 3.907260 TTCCTTGCTGCCGCCAGAG 62.907 63.158 0.00 0.00 41.77 3.35
179 184 1.554160 CAGAGGATGAGCACCAAGACT 59.446 52.381 0.00 0.00 0.00 3.24
183 188 3.445008 AGGATGAGCACCAAGACTAAGA 58.555 45.455 0.00 0.00 0.00 2.10
257 267 3.795688 AATGCATCCAACTCCGGATAT 57.204 42.857 3.57 0.00 44.28 1.63
258 268 4.908601 AATGCATCCAACTCCGGATATA 57.091 40.909 3.57 0.00 44.28 0.86
259 269 4.908601 ATGCATCCAACTCCGGATATAA 57.091 40.909 3.57 0.00 44.28 0.98
260 270 4.908601 TGCATCCAACTCCGGATATAAT 57.091 40.909 3.57 0.00 44.28 1.28
261 271 6.560003 ATGCATCCAACTCCGGATATAATA 57.440 37.500 3.57 0.00 44.28 0.98
268 278 8.671384 TCCAACTCCGGATATAATAAAACAAG 57.329 34.615 3.57 0.00 0.00 3.16
270 280 7.228706 CCAACTCCGGATATAATAAAACAAGCT 59.771 37.037 3.57 0.00 0.00 3.74
341 352 2.769652 AATCTCAGCAGCCGGCCAAA 62.770 55.000 26.15 3.34 46.50 3.28
396 410 0.661020 CAAAACCAAAGCCGAGACGT 59.339 50.000 0.00 0.00 0.00 4.34
400 414 1.446272 CCAAAGCCGAGACGTCTCC 60.446 63.158 33.85 23.09 39.79 3.71
405 419 4.790962 CCGAGACGTCTCCCCCGA 62.791 72.222 33.85 0.00 39.79 5.14
406 420 3.203412 CGAGACGTCTCCCCCGAG 61.203 72.222 33.85 18.44 39.79 4.63
435 449 1.537202 CCCAGAAAAAGAAGCGACCAG 59.463 52.381 0.00 0.00 0.00 4.00
449 463 0.882927 GACCAGCACGGCACAGTAAA 60.883 55.000 0.00 0.00 39.03 2.01
983 1002 3.532155 CGGCGGAGGAGGAGGAAG 61.532 72.222 0.00 0.00 0.00 3.46
984 1003 2.042843 GGCGGAGGAGGAGGAAGA 60.043 66.667 0.00 0.00 0.00 2.87
985 1004 2.131067 GGCGGAGGAGGAGGAAGAG 61.131 68.421 0.00 0.00 0.00 2.85
986 1005 2.791868 GCGGAGGAGGAGGAAGAGC 61.792 68.421 0.00 0.00 0.00 4.09
1054 1073 4.493747 AGCGCTACGAAGACGGCC 62.494 66.667 8.99 0.00 44.46 6.13
1137 1156 7.618019 ATCCTGATGCTTTTAGTGTCCTATA 57.382 36.000 0.00 0.00 0.00 1.31
1138 1157 6.817184 TCCTGATGCTTTTAGTGTCCTATAC 58.183 40.000 0.00 0.00 0.00 1.47
1205 1225 4.349365 CCTCCTGACCTAGATTCCTATCC 58.651 52.174 0.00 0.00 0.00 2.59
1240 1260 3.320256 TGCTTGCATTGGTTTGATGTGTA 59.680 39.130 0.00 0.00 0.00 2.90
1244 1264 4.085009 TGCATTGGTTTGATGTGTATGGA 58.915 39.130 0.00 0.00 0.00 3.41
1310 1330 2.647297 GGTGCTGGTTTGCTGCTC 59.353 61.111 0.00 0.00 0.00 4.26
1376 1396 5.173774 TGTGTGAGCTCTGAATTTGTTTC 57.826 39.130 16.19 0.00 34.72 2.78
1438 1460 5.442260 GCGACAAATATTACCGTTTGTTTGC 60.442 40.000 5.14 8.48 45.59 3.68
1450 1472 0.814457 TTGTTTGCTTCGCTTGTGGT 59.186 45.000 0.00 0.00 0.00 4.16
1476 1498 1.723608 TTGTTTGTGCCGCTGGTCAG 61.724 55.000 0.00 0.00 0.00 3.51
1477 1499 2.186826 GTTTGTGCCGCTGGTCAGT 61.187 57.895 0.00 0.00 0.00 3.41
1478 1500 2.186160 TTTGTGCCGCTGGTCAGTG 61.186 57.895 4.67 4.67 38.60 3.66
1487 1509 1.302033 CTGGTCAGTGGTCACAGGC 60.302 63.158 3.82 0.00 0.00 4.85
1521 1543 6.151648 CACACAAACCACTCTTCATAATCCAT 59.848 38.462 0.00 0.00 0.00 3.41
1523 1545 5.126061 ACAAACCACTCTTCATAATCCATGC 59.874 40.000 0.00 0.00 34.35 4.06
1546 1568 3.178611 CCCCTGATAGGTGCCCCC 61.179 72.222 0.00 0.00 31.93 5.40
1569 1591 4.453819 CCTTTGAGTTTGCTCCTAGTTCAG 59.546 45.833 0.00 0.00 40.95 3.02
1573 1595 3.991121 GAGTTTGCTCCTAGTTCAGTGTC 59.009 47.826 0.00 0.00 35.76 3.67
1585 1607 4.957296 AGTTCAGTGTCGATTTGGTAAGT 58.043 39.130 0.00 0.00 0.00 2.24
1607 1629 0.693049 GGGTGGACCTCTGATGTTGT 59.307 55.000 0.00 0.00 35.85 3.32
1691 1714 8.609176 TCATTATGCGAAGTTTGTAAGGAATAC 58.391 33.333 0.00 0.00 34.92 1.89
1768 1928 2.691526 TGGATGTAGACCGCGTTTAGAT 59.308 45.455 4.92 0.00 0.00 1.98
1785 1945 6.144080 CGTTTAGATATTCCGACCATTGACTC 59.856 42.308 0.00 0.00 0.00 3.36
1789 1949 3.721087 ATTCCGACCATTGACTCCTTT 57.279 42.857 0.00 0.00 0.00 3.11
1898 2059 4.027674 TGGTAGTTTGATAAAGCTGGCA 57.972 40.909 0.00 0.00 0.00 4.92
1923 2084 5.221126 GGAAAGCACCTTCCATGAATATGAC 60.221 44.000 0.00 0.00 43.84 3.06
1969 2130 7.147689 TGCCCATGTAGCTCAAATATCATTTTT 60.148 33.333 0.00 0.00 0.00 1.94
1970 2131 7.383300 GCCCATGTAGCTCAAATATCATTTTTC 59.617 37.037 0.00 0.00 0.00 2.29
1999 2160 1.135575 GTAAATGTGCAGCTGTGAGGC 60.136 52.381 16.64 0.00 0.00 4.70
2029 2196 9.769093 GTCACATAATTTACACCTTAACACATC 57.231 33.333 0.00 0.00 0.00 3.06
2069 2236 8.648698 TGAATATTTCTTTTGGTGATTCCTGA 57.351 30.769 0.00 0.00 37.07 3.86
2109 2284 9.334947 TCCTCTTTAAGCATGATTTGATAAGAG 57.665 33.333 19.61 19.61 0.00 2.85
2128 2303 5.382664 AGAGTCTTTGTAAACTTTGGGGA 57.617 39.130 0.00 0.00 0.00 4.81
2146 2321 6.924913 TGGGGATTAACATTCACATTTTGA 57.075 33.333 0.00 0.00 0.00 2.69
2386 2561 1.670811 CGGCAACACAGATTGGTATCC 59.329 52.381 0.00 0.00 0.00 2.59
2475 2676 1.273886 TGCACGCAGGAATAGTGTGTA 59.726 47.619 8.42 1.62 46.31 2.90
2553 2754 4.409901 AGGATTAAAGGGAATGGCCAAATG 59.590 41.667 10.96 0.00 38.95 2.32
2554 2755 4.408596 GGATTAAAGGGAATGGCCAAATGA 59.591 41.667 10.96 0.00 38.95 2.57
2624 2830 6.368779 AGTTTGGTGCTACCTAATTAGTCA 57.631 37.500 11.50 1.64 39.58 3.41
2655 2861 1.068125 GGGCACAAACGAAATACACCC 60.068 52.381 0.00 0.00 0.00 4.61
2888 3095 7.841282 ATGTTACCATACTAGCATGTAGAGT 57.159 36.000 2.28 5.69 0.00 3.24
3012 3219 5.163602 CGAGGAGATATAGTGGTAAGATGCC 60.164 48.000 0.00 0.00 0.00 4.40
3079 3323 6.049149 GCTACAAGCTGAGACATATTTACCA 58.951 40.000 0.00 0.00 38.45 3.25
3150 3454 2.737252 GCACTAAACTGCCAGTGTAGAC 59.263 50.000 25.45 14.40 38.10 2.59
3158 3462 4.090090 ACTGCCAGTGTAGACTAATCAGT 58.910 43.478 0.00 12.27 37.87 3.41
3244 3549 6.228995 AGATAGTGCATCCAGTTGTGATATG 58.771 40.000 0.00 0.00 33.75 1.78
3297 3602 1.209747 GGACCTGAAAGCTATCCCGTT 59.790 52.381 0.00 0.00 0.00 4.44
3400 3705 7.303182 TGCACTATACTAAACCAGAGCATAT 57.697 36.000 0.00 0.00 31.13 1.78
3411 3716 1.993956 AGAGCATATCTGAGCCGTCT 58.006 50.000 0.00 0.00 36.69 4.18
3437 3763 5.232463 ACTTTTTCCTGCTGCATTATTGTG 58.768 37.500 1.31 0.00 0.00 3.33
3454 3780 2.574450 TGTGTACCGTACTCACAGACA 58.426 47.619 10.03 2.27 37.20 3.41
3541 3906 7.611855 AGCTCTTTGTAAATTAACATACTGGCT 59.388 33.333 0.00 0.00 0.00 4.75
3572 3937 6.017605 GCAGTGTGCAGCTCTATTTATGTAAT 60.018 38.462 0.00 0.00 44.26 1.89
3612 3977 0.737219 GCAAGCAGGGCATACTTCAG 59.263 55.000 0.00 0.00 0.00 3.02
3669 4035 3.251729 ACATTTCAGATGTCTGTGTGTGC 59.748 43.478 9.65 0.00 44.12 4.57
3671 4037 0.389025 TCAGATGTCTGTGTGTGCGT 59.611 50.000 9.65 0.00 44.12 5.24
3673 4039 0.104855 AGATGTCTGTGTGTGCGTGT 59.895 50.000 0.00 0.00 0.00 4.49
3675 4041 1.775039 ATGTCTGTGTGTGCGTGTGC 61.775 55.000 0.00 0.00 43.20 4.57
3699 4071 2.951101 CGTGTGTGGGGGTAGGGAC 61.951 68.421 0.00 0.00 0.00 4.46
3857 4248 4.114015 AAGGGTTAGAACCTTTTCTGGG 57.886 45.455 11.16 0.00 44.92 4.45
3859 4250 4.202577 AAGGGTTAGAACCTTTTCTGGGAG 60.203 45.833 11.16 0.00 44.92 4.30
3870 4261 4.020218 CCTTTTCTGGGAGAGTATGTGTCA 60.020 45.833 0.00 0.00 0.00 3.58
3875 4266 2.766263 TGGGAGAGTATGTGTCATCACC 59.234 50.000 0.00 0.00 43.26 4.02
3901 4292 7.282224 CGGAGATGATATTAAACCTGTTTCCAA 59.718 37.037 0.00 0.00 34.23 3.53
3910 4302 2.567985 ACCTGTTTCCAACTTACCGTG 58.432 47.619 0.00 0.00 0.00 4.94
3922 4314 3.135994 ACTTACCGTGTGTGTTCCATTC 58.864 45.455 0.00 0.00 0.00 2.67
3936 4328 6.265196 TGTGTTCCATTCTAACTTGCAAGATT 59.735 34.615 32.50 22.48 0.00 2.40
4063 4491 7.269477 GCATCAGCAATTTCTAGGTTTCTAT 57.731 36.000 0.00 0.00 41.58 1.98
4081 4509 7.094634 GGTTTCTATGATTTCAAGAGCAAGACA 60.095 37.037 0.00 0.00 0.00 3.41
4090 4518 3.262660 TCAAGAGCAAGACACATCAGGAT 59.737 43.478 0.00 0.00 0.00 3.24
4147 4575 3.345808 GCGCTGCACGTGAAGGAA 61.346 61.111 24.99 0.65 46.11 3.36
4276 4704 0.179062 GCTTCTCCGAGTGGCATGAT 60.179 55.000 0.00 0.00 34.14 2.45
4291 4719 2.360165 GCATGATAACTGGAGCAAAGGG 59.640 50.000 0.00 0.00 0.00 3.95
4402 4830 2.424842 CTAGGCCCCAACCTTGCACA 62.425 60.000 0.00 0.00 41.50 4.57
4431 4859 4.155826 TGCAATAATACAGTGTGGTGCTTC 59.844 41.667 5.88 0.00 0.00 3.86
4547 4975 9.119418 TCACAAATTTTAAGTGTCTGATTCTCA 57.881 29.630 6.94 0.00 34.94 3.27
4645 5074 5.424757 TGTATTTACCAGACCTGAAATCGG 58.575 41.667 0.00 0.00 0.00 4.18
4762 5193 3.769739 AACACACTGGCTCATGAAGTA 57.230 42.857 0.00 0.00 0.00 2.24
4935 5434 1.488705 CCACCACCCCTCTGCTGTTA 61.489 60.000 0.00 0.00 0.00 2.41
4937 5436 0.620556 ACCACCCCTCTGCTGTTATG 59.379 55.000 0.00 0.00 0.00 1.90
4939 5438 1.492176 CCACCCCTCTGCTGTTATGAT 59.508 52.381 0.00 0.00 0.00 2.45
4947 5446 7.901322 ACCCCTCTGCTGTTATGATAGATATTA 59.099 37.037 0.00 0.00 0.00 0.98
5013 5512 5.759506 TTTTCAACCTAAAACTCGCATCA 57.240 34.783 0.00 0.00 0.00 3.07
5017 5516 6.325919 TCAACCTAAAACTCGCATCAATTT 57.674 33.333 0.00 0.00 0.00 1.82
5018 5517 6.744112 TCAACCTAAAACTCGCATCAATTTT 58.256 32.000 0.00 0.00 0.00 1.82
5090 5592 5.048643 CGGGTCAAGAGATACAGTATACAGG 60.049 48.000 5.50 0.00 0.00 4.00
5145 5647 9.434275 TGAACCTAAACATAGAGGAGATTATCA 57.566 33.333 0.00 0.00 36.61 2.15
5147 5649 8.196378 ACCTAAACATAGAGGAGATTATCACC 57.804 38.462 0.24 0.24 36.61 4.02
5148 5650 7.039644 ACCTAAACATAGAGGAGATTATCACCG 60.040 40.741 3.16 0.00 36.61 4.94
5150 5652 6.582677 AACATAGAGGAGATTATCACCGAG 57.417 41.667 3.16 0.00 32.07 4.63
5152 5654 3.237268 AGAGGAGATTATCACCGAGCT 57.763 47.619 3.16 0.00 32.07 4.09
5153 5655 4.374689 AGAGGAGATTATCACCGAGCTA 57.625 45.455 3.16 0.00 32.07 3.32
5154 5656 4.076394 AGAGGAGATTATCACCGAGCTAC 58.924 47.826 3.16 0.00 32.07 3.58
5155 5657 2.814919 AGGAGATTATCACCGAGCTACG 59.185 50.000 3.16 0.00 42.18 3.51
5190 5701 3.596214 GTCATCGTTTCACCACCATAGT 58.404 45.455 0.00 0.00 0.00 2.12
5200 5711 3.392947 TCACCACCATAGTTCTCACCAAA 59.607 43.478 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.256752 TCAATGAGGGGGCACATGAG 59.743 55.000 0.00 0.00 0.00 2.90
1 2 0.928505 ATCAATGAGGGGGCACATGA 59.071 50.000 0.00 0.00 0.00 3.07
3 4 0.105862 CCATCAATGAGGGGGCACAT 60.106 55.000 5.96 0.00 28.91 3.21
4 5 1.307309 CCATCAATGAGGGGGCACA 59.693 57.895 5.96 0.00 28.91 4.57
7 8 2.452600 TTTACCATCAATGAGGGGGC 57.547 50.000 18.70 0.00 37.87 5.80
8 9 5.582950 TCTATTTACCATCAATGAGGGGG 57.417 43.478 18.70 7.78 37.87 5.40
9 10 7.779798 TCTTTTCTATTTACCATCAATGAGGGG 59.220 37.037 18.70 10.31 37.87 4.79
10 11 8.752005 TCTTTTCTATTTACCATCAATGAGGG 57.248 34.615 12.89 12.89 39.63 4.30
32 33 7.164230 TGAATGGTGTACACTTGTTTTTCTT 57.836 32.000 24.55 6.19 0.00 2.52
34 35 6.074356 GCATGAATGGTGTACACTTGTTTTTC 60.074 38.462 24.55 16.84 0.00 2.29
35 36 5.752955 GCATGAATGGTGTACACTTGTTTTT 59.247 36.000 24.55 9.88 0.00 1.94
36 37 5.288804 GCATGAATGGTGTACACTTGTTTT 58.711 37.500 24.55 11.45 0.00 2.43
38 39 3.255642 GGCATGAATGGTGTACACTTGTT 59.744 43.478 24.55 16.21 0.00 2.83
43 44 1.396996 GTCGGCATGAATGGTGTACAC 59.603 52.381 18.01 18.01 0.00 2.90
56 57 2.969628 TGTTTTGTTTTGGTCGGCAT 57.030 40.000 0.00 0.00 0.00 4.40
57 58 2.544685 CATGTTTTGTTTTGGTCGGCA 58.455 42.857 0.00 0.00 0.00 5.69
58 59 1.260297 GCATGTTTTGTTTTGGTCGGC 59.740 47.619 0.00 0.00 0.00 5.54
60 61 3.862267 TCTTGCATGTTTTGTTTTGGTCG 59.138 39.130 0.00 0.00 0.00 4.79
61 62 4.629200 TGTCTTGCATGTTTTGTTTTGGTC 59.371 37.500 0.00 0.00 0.00 4.02
62 63 4.573900 TGTCTTGCATGTTTTGTTTTGGT 58.426 34.783 0.00 0.00 0.00 3.67
78 83 4.259970 CCGATCGAAGCATAACTTGTCTTG 60.260 45.833 18.66 0.00 39.29 3.02
79 84 3.865745 CCGATCGAAGCATAACTTGTCTT 59.134 43.478 18.66 0.00 39.29 3.01
82 87 1.933853 GCCGATCGAAGCATAACTTGT 59.066 47.619 18.66 0.00 39.29 3.16
91 96 2.325857 GCATGTGCCGATCGAAGC 59.674 61.111 18.66 13.22 34.31 3.86
93 98 2.164663 GTCGCATGTGCCGATCGAA 61.165 57.895 18.66 0.77 37.91 3.71
113 118 7.318141 TGGAAAGTTCTTACTTATACAGTCGG 58.682 38.462 0.00 0.00 43.74 4.79
131 136 4.098501 CAGCAAGGAAAGAAGTTGGAAAGT 59.901 41.667 0.00 0.00 0.00 2.66
153 158 4.166888 GCTCATCCTCTGGCGGCA 62.167 66.667 12.58 12.58 0.00 5.69
163 168 3.196685 AGTCTTAGTCTTGGTGCTCATCC 59.803 47.826 0.00 0.00 0.00 3.51
220 229 9.995003 TGGATGCATTATTTGGGTTTTATATTC 57.005 29.630 0.00 0.00 0.00 1.75
243 253 7.227910 GCTTGTTTTATTATATCCGGAGTTGGA 59.772 37.037 11.34 0.00 43.58 3.53
268 278 4.600692 TCCAAAAGGGAAAGCTTTTAGC 57.399 40.909 14.05 0.02 44.80 3.09
288 299 9.509855 GTTTCTTCTCCTTTTTCTTCTCTTTTC 57.490 33.333 0.00 0.00 0.00 2.29
292 303 6.065374 GGGTTTCTTCTCCTTTTTCTTCTCT 58.935 40.000 0.00 0.00 0.00 3.10
293 304 5.828328 TGGGTTTCTTCTCCTTTTTCTTCTC 59.172 40.000 0.00 0.00 0.00 2.87
294 305 5.766590 TGGGTTTCTTCTCCTTTTTCTTCT 58.233 37.500 0.00 0.00 0.00 2.85
295 306 6.465439 TTGGGTTTCTTCTCCTTTTTCTTC 57.535 37.500 0.00 0.00 0.00 2.87
296 307 6.867519 TTTGGGTTTCTTCTCCTTTTTCTT 57.132 33.333 0.00 0.00 0.00 2.52
297 308 6.212589 TGTTTTGGGTTTCTTCTCCTTTTTCT 59.787 34.615 0.00 0.00 0.00 2.52
298 309 6.403049 TGTTTTGGGTTTCTTCTCCTTTTTC 58.597 36.000 0.00 0.00 0.00 2.29
299 310 6.367374 TGTTTTGGGTTTCTTCTCCTTTTT 57.633 33.333 0.00 0.00 0.00 1.94
341 352 4.660938 GGGGGTCGTGCTGGCTTT 62.661 66.667 0.00 0.00 0.00 3.51
969 988 2.131067 GGCTCTTCCTCCTCCTCCG 61.131 68.421 0.00 0.00 0.00 4.63
972 991 2.042435 CCGGCTCTTCCTCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
973 992 3.157949 CCCGGCTCTTCCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
974 993 3.855853 GCCCGGCTCTTCCTCCTC 61.856 72.222 0.71 0.00 0.00 3.71
975 994 4.722535 TGCCCGGCTCTTCCTCCT 62.723 66.667 11.61 0.00 0.00 3.69
976 995 4.168291 CTGCCCGGCTCTTCCTCC 62.168 72.222 11.61 0.00 0.00 4.30
977 996 4.168291 CCTGCCCGGCTCTTCCTC 62.168 72.222 11.61 0.00 0.00 3.71
980 999 3.081409 TACCCTGCCCGGCTCTTC 61.081 66.667 11.61 0.00 0.00 2.87
981 1000 3.083997 CTACCCTGCCCGGCTCTT 61.084 66.667 11.61 0.00 0.00 2.85
986 1005 3.797353 ACATGCTACCCTGCCCGG 61.797 66.667 0.00 0.00 0.00 5.73
1041 1060 2.277120 CGTCGGCCGTCTTCGTAG 60.277 66.667 27.15 1.25 35.01 3.51
1137 1156 1.270839 CGCCCCAATCTAATCGGATGT 60.271 52.381 0.00 0.00 0.00 3.06
1138 1157 1.001974 TCGCCCCAATCTAATCGGATG 59.998 52.381 0.00 0.00 0.00 3.51
1205 1225 0.886490 GCAAGCATCTCATACGGGGG 60.886 60.000 0.00 0.00 0.00 5.40
1215 1235 3.259876 ACATCAAACCAATGCAAGCATCT 59.740 39.130 8.14 0.00 35.31 2.90
1222 1242 4.082300 GTCCATACACATCAAACCAATGCA 60.082 41.667 0.00 0.00 0.00 3.96
1258 1278 3.036084 CACGACGGCGCAAACTCT 61.036 61.111 12.58 0.00 42.48 3.24
1301 1321 1.855213 GCATGACCACGAGCAGCAAA 61.855 55.000 0.00 0.00 0.00 3.68
1338 1358 0.175302 CACAAGCAGCAAACCAACCA 59.825 50.000 0.00 0.00 0.00 3.67
1339 1359 0.175531 ACACAAGCAGCAAACCAACC 59.824 50.000 0.00 0.00 0.00 3.77
1340 1360 1.135141 TCACACAAGCAGCAAACCAAC 60.135 47.619 0.00 0.00 0.00 3.77
1341 1361 1.134753 CTCACACAAGCAGCAAACCAA 59.865 47.619 0.00 0.00 0.00 3.67
1376 1396 9.982651 ACTACAACTAATATACCATGCTTACAG 57.017 33.333 0.00 0.00 0.00 2.74
1405 1425 6.586463 ACGGTAATATTTGTCGCTATCATCAG 59.414 38.462 0.00 0.00 0.00 2.90
1438 1460 4.606961 ACAAAATGTAACCACAAGCGAAG 58.393 39.130 0.00 0.00 38.42 3.79
1450 1472 3.119291 CAGCGGCACAAACAAAATGTAA 58.881 40.909 1.45 0.00 0.00 2.41
1476 1498 0.533308 TTGTAACCGCCTGTGACCAC 60.533 55.000 0.00 0.00 0.00 4.16
1477 1499 0.533308 GTTGTAACCGCCTGTGACCA 60.533 55.000 0.00 0.00 0.00 4.02
1478 1500 0.533308 TGTTGTAACCGCCTGTGACC 60.533 55.000 0.00 0.00 0.00 4.02
1479 1501 0.584876 GTGTTGTAACCGCCTGTGAC 59.415 55.000 0.00 0.00 0.00 3.67
1480 1502 0.178301 TGTGTTGTAACCGCCTGTGA 59.822 50.000 0.00 0.00 0.00 3.58
1487 1509 2.420722 AGTGGTTTGTGTGTTGTAACCG 59.579 45.455 0.00 0.00 42.29 4.44
1521 1543 1.077787 CCTATCAGGGGCAAACGCA 60.078 57.895 0.00 0.00 33.80 5.24
1523 1545 2.780595 CACCTATCAGGGGCAAACG 58.219 57.895 0.00 0.00 40.58 3.60
1546 1568 4.389374 TGAACTAGGAGCAAACTCAAAGG 58.611 43.478 0.00 0.00 45.42 3.11
1569 1591 4.390909 CACCCTAACTTACCAAATCGACAC 59.609 45.833 0.00 0.00 0.00 3.67
1573 1595 3.937079 GTCCACCCTAACTTACCAAATCG 59.063 47.826 0.00 0.00 0.00 3.34
1585 1607 2.571653 CAACATCAGAGGTCCACCCTAA 59.428 50.000 0.00 0.00 46.51 2.69
1607 1629 5.534207 AAGTCATCAAAACTTGCCATCAA 57.466 34.783 0.00 0.00 35.68 2.57
1768 1928 4.837093 AAAGGAGTCAATGGTCGGAATA 57.163 40.909 0.00 0.00 0.00 1.75
1785 1945 7.482169 AAAAGGGAGAATTTAAGCCTAAAGG 57.518 36.000 0.00 0.00 38.53 3.11
1789 1949 9.574516 GATGATAAAAGGGAGAATTTAAGCCTA 57.425 33.333 0.00 0.00 0.00 3.93
1898 2059 2.978156 TTCATGGAAGGTGCTTTCCT 57.022 45.000 13.10 3.92 45.59 3.36
1969 2130 6.039270 ACAGCTGCACATTTACAAGTAAAAGA 59.961 34.615 15.27 0.00 38.38 2.52
1970 2131 6.142798 CACAGCTGCACATTTACAAGTAAAAG 59.857 38.462 15.27 7.73 38.38 2.27
1999 2160 8.779303 TGTTAAGGTGTAAATTATGTGACAGTG 58.221 33.333 0.00 0.00 0.00 3.66
2029 2196 6.474427 AGAAATATTCATTGAAATGTGCAGCG 59.526 34.615 2.68 0.00 37.65 5.18
2069 2236 6.597280 GCTTAAAGAGGAACAATGTCTCATCT 59.403 38.462 5.14 6.06 34.32 2.90
2109 2284 7.718525 TGTTAATCCCCAAAGTTTACAAAGAC 58.281 34.615 0.00 0.00 0.00 3.01
2122 2297 7.308450 TCAAAATGTGAATGTTAATCCCCAA 57.692 32.000 0.00 0.00 31.51 4.12
2146 2321 6.780457 AAAGTATCCACTATGCAAAAGCAT 57.220 33.333 8.14 8.14 33.48 3.79
2333 2508 5.897050 TGTTCCAAAACAACTTGGTATGAC 58.103 37.500 2.48 0.13 45.29 3.06
2386 2561 1.798813 GAACACGTTGGAGCTAACTGG 59.201 52.381 0.00 0.00 0.00 4.00
2533 2734 4.164030 GGTCATTTGGCCATTCCCTTTAAT 59.836 41.667 6.09 0.00 40.23 1.40
2553 2754 2.297033 ACTTTGTTGCATGACCATGGTC 59.703 45.455 33.97 33.97 44.77 4.02
2554 2755 2.318908 ACTTTGTTGCATGACCATGGT 58.681 42.857 19.89 19.89 39.16 3.55
2624 2830 0.471591 TTTGTGCCCCAATCAGCCTT 60.472 50.000 0.00 0.00 31.81 4.35
2655 2861 7.684670 AGTAAGCACATGTATGTTAATGTTCG 58.315 34.615 0.00 0.00 39.39 3.95
2692 2898 7.362662 TGCAGAGAAATTCATTACAAGACAAC 58.637 34.615 0.00 0.00 0.00 3.32
2752 2958 5.357314 TCTGATCGGACTTCCTACTGTAAAG 59.643 44.000 0.00 0.00 0.00 1.85
2760 2966 8.651589 AATATGTATTCTGATCGGACTTCCTA 57.348 34.615 2.94 0.00 0.00 2.94
3012 3219 9.778993 CTGACATGAAAATACCATCTTTTACAG 57.221 33.333 0.00 0.00 0.00 2.74
3079 3323 7.676947 TGTCTAGCAAGTTAAGGAAACATACT 58.323 34.615 0.00 0.00 40.83 2.12
3127 3428 1.597742 ACACTGGCAGTTTAGTGCAG 58.402 50.000 19.43 6.60 46.27 4.41
3411 3716 5.726980 ATAATGCAGCAGGAAAAAGTTGA 57.273 34.783 0.00 0.00 0.00 3.18
3437 3763 3.251729 TGAGTTGTCTGTGAGTACGGTAC 59.748 47.826 10.29 10.29 34.68 3.34
3474 3800 9.093970 TGTACTGTAGTTGCAAATGTATCATAC 57.906 33.333 10.14 5.48 0.00 2.39
3477 3803 7.158697 ACTGTACTGTAGTTGCAAATGTATCA 58.841 34.615 10.14 3.11 0.00 2.15
3479 3805 7.806690 CAACTGTACTGTAGTTGCAAATGTAT 58.193 34.615 10.14 0.00 45.70 2.29
3480 3806 7.184800 CAACTGTACTGTAGTTGCAAATGTA 57.815 36.000 10.14 0.36 45.70 2.29
3481 3807 6.060028 CAACTGTACTGTAGTTGCAAATGT 57.940 37.500 10.14 1.41 45.70 2.71
3612 3977 4.506654 TCTTTCGAGCAAAGTGTGAACTAC 59.493 41.667 0.00 0.00 42.16 2.73
3660 4026 3.563088 ACGCACACGCACACACAG 61.563 61.111 0.00 0.00 45.53 3.66
3669 4035 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
3671 4037 3.858989 CACACACGCACACGCACA 61.859 61.111 0.00 0.00 45.53 4.57
3681 4047 2.605295 TCCCTACCCCCACACACG 60.605 66.667 0.00 0.00 0.00 4.49
3683 4049 1.229400 GAGTCCCTACCCCCACACA 60.229 63.158 0.00 0.00 0.00 3.72
3684 4050 2.356780 CGAGTCCCTACCCCCACAC 61.357 68.421 0.00 0.00 0.00 3.82
3685 4051 2.038329 CGAGTCCCTACCCCCACA 59.962 66.667 0.00 0.00 0.00 4.17
3686 4052 3.468140 GCGAGTCCCTACCCCCAC 61.468 72.222 0.00 0.00 0.00 4.61
3687 4053 3.248248 AAGCGAGTCCCTACCCCCA 62.248 63.158 0.00 0.00 0.00 4.96
3789 4162 5.652014 AGAAATTGTCAGTTTGTCACAGGAA 59.348 36.000 0.00 0.00 0.00 3.36
3859 4250 6.949392 TCATCTCCGGTGATGACACATACTC 61.949 48.000 34.39 0.00 45.29 2.59
3870 4261 6.043243 ACAGGTTTAATATCATCTCCGGTGAT 59.957 38.462 13.23 13.23 39.50 3.06
3875 4266 6.765989 TGGAAACAGGTTTAATATCATCTCCG 59.234 38.462 0.00 0.00 35.01 4.63
3922 4314 9.499585 CAGTTCATGAATAATCTTGCAAGTTAG 57.500 33.333 25.19 10.91 32.29 2.34
3936 4328 7.397476 ACTCCTTCAGTAGACAGTTCATGAATA 59.603 37.037 12.12 0.00 31.37 1.75
4063 4491 5.065235 TGATGTGTCTTGCTCTTGAAATCA 58.935 37.500 0.00 0.00 0.00 2.57
4081 4509 2.110967 GCAGCACGCATCCTGATGT 61.111 57.895 8.79 0.00 40.80 3.06
4213 4641 2.354704 CCACTGGTACCGACATTGTGAT 60.355 50.000 7.57 0.00 0.00 3.06
4276 4704 1.382629 GCCCCCTTTGCTCCAGTTA 59.617 57.895 0.00 0.00 0.00 2.24
4402 4830 6.867816 CACCACACTGTATTATTGCAATTTGT 59.132 34.615 18.75 6.69 0.00 2.83
4431 4859 5.536538 TGACCTACTAGGCATCATCAAGTAG 59.463 44.000 1.55 0.00 39.63 2.57
4547 4975 6.861065 ATTTGAGAAATAATATGACGCCGT 57.139 33.333 0.00 0.00 0.00 5.68
4645 5074 5.050702 GCTCTGAGTCAACAAGTACACTTTC 60.051 44.000 6.53 0.00 33.11 2.62
4709 5139 7.159372 TCCAGCTAAATCGTTTTACTTCTTCT 58.841 34.615 0.00 0.00 0.00 2.85
4710 5140 7.360575 TCCAGCTAAATCGTTTTACTTCTTC 57.639 36.000 0.00 0.00 0.00 2.87
4711 5141 7.444487 ACTTCCAGCTAAATCGTTTTACTTCTT 59.556 33.333 0.00 0.00 0.00 2.52
4825 5315 3.763360 CTCACCCCACATTTTTGCTATCA 59.237 43.478 0.00 0.00 0.00 2.15
4963 5462 7.498239 AGTCTACAGATCACATTACGCTAGTAA 59.502 37.037 0.00 0.00 45.71 2.24
4964 5463 6.990939 AGTCTACAGATCACATTACGCTAGTA 59.009 38.462 0.00 0.00 0.00 1.82
4965 5464 5.823570 AGTCTACAGATCACATTACGCTAGT 59.176 40.000 0.00 0.00 0.00 2.57
4966 5465 6.307031 AGTCTACAGATCACATTACGCTAG 57.693 41.667 0.00 0.00 0.00 3.42
4967 5466 7.981102 ATAGTCTACAGATCACATTACGCTA 57.019 36.000 0.00 0.00 0.00 4.26
5055 5554 5.011090 TCTCTTGACCCGATACAAATCAG 57.989 43.478 0.00 0.00 31.93 2.90
5066 5565 5.048643 CCTGTATACTGTATCTCTTGACCCG 60.049 48.000 3.09 0.00 0.00 5.28
5069 5568 7.768807 ATCCCTGTATACTGTATCTCTTGAC 57.231 40.000 3.09 0.00 0.00 3.18
5152 5654 1.464219 TGACGTGTTCGCTATGACGTA 59.536 47.619 0.00 0.00 44.62 3.57
5154 5656 1.513178 GATGACGTGTTCGCTATGACG 59.487 52.381 0.00 0.00 41.18 4.35
5155 5657 1.513178 CGATGACGTGTTCGCTATGAC 59.487 52.381 0.00 0.00 41.18 3.06
5182 5693 4.641396 TGAGTTTGGTGAGAACTATGGTG 58.359 43.478 0.00 0.00 37.46 4.17
5190 5701 4.580167 CCATTGTCTTGAGTTTGGTGAGAA 59.420 41.667 0.00 0.00 0.00 2.87
5200 5711 3.576078 TGAACACCCATTGTCTTGAGT 57.424 42.857 0.00 0.00 37.51 3.41


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

AutoCloner maintained by Alex Coulton.