Multiple sequence alignment - TraesCS1B01G193200

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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 TraesCS1B01G193200 chr1B 100.000 6090 0 0 1 6090 346174707 346168618 0.000000e+00 11247.0
1 TraesCS1B01G193200 chr1B 90.977 399 35 1 1069 1466 619096736 619097134 2.500000e-148 536.0
2 TraesCS1B01G193200 chr1B 95.092 163 8 0 1304 1466 541402235 541402397 2.180000e-64 257.0
3 TraesCS1B01G193200 chr1B 92.593 54 2 1 1242 1293 541402189 541402242 6.550000e-10 76.8
4 TraesCS1B01G193200 chr1A 94.233 2913 139 22 3189 6090 335833718 335830824 0.000000e+00 4421.0
5 TraesCS1B01G193200 chr1A 94.273 2200 88 23 684 2868 335836399 335834223 0.000000e+00 3330.0
6 TraesCS1B01G193200 chr1A 88.392 715 52 15 1 694 335837251 335836547 0.000000e+00 832.0
7 TraesCS1B01G193200 chr1A 90.083 363 29 4 2797 3155 335834262 335833903 1.200000e-126 464.0
8 TraesCS1B01G193200 chr1A 96.552 58 2 0 5903 5960 47817157 47817214 5.020000e-16 97.1
9 TraesCS1B01G193200 chr1D 94.751 2686 102 23 1937 4596 267376682 267379354 0.000000e+00 4143.0
10 TraesCS1B01G193200 chr1D 92.959 1832 90 20 68 1870 267374864 267376685 0.000000e+00 2632.0
11 TraesCS1B01G193200 chr1D 94.170 1458 62 14 4640 6090 267379349 267380790 0.000000e+00 2200.0
12 TraesCS1B01G193200 chr1D 96.190 105 4 0 5474 5578 474916926 474916822 8.120000e-39 172.0
13 TraesCS1B01G193200 chr1D 90.265 113 8 3 5631 5741 474916814 474916703 1.770000e-30 145.0
14 TraesCS1B01G193200 chr1D 96.610 59 2 0 5901 5959 474916707 474916649 1.400000e-16 99.0
15 TraesCS1B01G193200 chr4D 85.315 572 69 12 1039 1599 481141367 481140800 1.470000e-160 577.0
16 TraesCS1B01G193200 chr4D 76.606 436 78 18 2296 2723 481140412 481139993 1.030000e-52 219.0
17 TraesCS1B01G193200 chr4D 97.143 105 3 0 5474 5578 348307126 348307230 1.740000e-40 178.0
18 TraesCS1B01G193200 chr4D 90.351 114 8 1 5631 5741 348307238 348307351 4.920000e-31 147.0
19 TraesCS1B01G193200 chr5A 85.217 575 67 14 1036 1599 662348008 662348575 5.290000e-160 575.0
20 TraesCS1B01G193200 chr5A 77.011 435 79 17 2296 2723 662348961 662349381 4.750000e-56 230.0
21 TraesCS1B01G193200 chr5A 87.356 174 12 7 5569 5741 37967869 37968033 2.240000e-44 191.0
22 TraesCS1B01G193200 chr5B 92.231 399 30 1 1069 1466 493287066 493287464 1.150000e-156 564.0
23 TraesCS1B01G193200 chr5B 92.793 111 8 0 5631 5741 45021765 45021655 1.760000e-35 161.0
24 TraesCS1B01G193200 chr4B 78.589 794 152 11 3233 4017 609489051 609488267 5.450000e-140 508.0
25 TraesCS1B01G193200 chr4B 86.301 438 50 7 1170 1599 609490663 609490228 9.240000e-128 468.0
26 TraesCS1B01G193200 chr4B 77.295 414 76 14 2296 2706 609489822 609489424 1.710000e-55 228.0
27 TraesCS1B01G193200 chr2D 89.474 399 30 2 1069 1466 69243472 69243085 1.520000e-135 494.0
28 TraesCS1B01G193200 chr2D 97.143 105 3 0 5474 5578 33946107 33946003 1.740000e-40 178.0
29 TraesCS1B01G193200 chr2D 96.190 105 4 0 5474 5578 56188904 56188800 8.120000e-39 172.0
30 TraesCS1B01G193200 chr2D 96.610 59 2 0 5901 5959 33945894 33945836 1.400000e-16 99.0
31 TraesCS1B01G193200 chr2D 96.610 59 2 0 5901 5959 56188683 56188625 1.400000e-16 99.0
32 TraesCS1B01G193200 chr2D 100.000 40 0 0 940 979 427554350 427554389 2.350000e-09 75.0
33 TraesCS1B01G193200 chr7D 88.312 231 15 1 1153 1383 266895097 266894879 3.620000e-67 267.0
34 TraesCS1B01G193200 chr7D 96.154 104 4 0 5475 5578 293591676 293591779 2.920000e-38 171.0
35 TraesCS1B01G193200 chr7D 96.610 59 2 0 5901 5959 293591894 293591952 1.400000e-16 99.0
36 TraesCS1B01G193200 chr5D 97.143 105 3 0 5474 5578 563593129 563593025 1.740000e-40 178.0
37 TraesCS1B01G193200 chr5D 96.190 105 4 0 5474 5578 213075030 213075134 8.120000e-39 172.0
38 TraesCS1B01G193200 chr5D 96.610 59 2 0 5901 5959 563592910 563592852 1.400000e-16 99.0
39 TraesCS1B01G193200 chr2A 94.286 105 6 0 5631 5735 36029119 36029223 1.760000e-35 161.0
40 TraesCS1B01G193200 chr2A 77.959 245 36 8 362 590 34306127 34306369 2.960000e-28 137.0
41 TraesCS1B01G193200 chr6A 90.090 111 11 0 5631 5741 41340332 41340222 1.770000e-30 145.0
42 TraesCS1B01G193200 chr3B 91.429 105 9 0 5631 5735 262837402 262837506 1.770000e-30 145.0
43 TraesCS1B01G193200 chr6D 96.610 59 2 0 5901 5959 263961546 263961488 1.400000e-16 99.0
44 TraesCS1B01G193200 chr7A 95.000 60 3 0 3 62 726616929 726616870 1.810000e-15 95.3
45 TraesCS1B01G193200 chr2B 94.000 50 3 0 523 572 212295479 212295430 6.550000e-10 76.8


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 TraesCS1B01G193200 chr1B 346168618 346174707 6089 True 11247.000000 11247 100.000000 1 6090 1 chr1B.!!$R1 6089
1 TraesCS1B01G193200 chr1A 335830824 335837251 6427 True 2261.750000 4421 91.745250 1 6090 4 chr1A.!!$R1 6089
2 TraesCS1B01G193200 chr1D 267374864 267380790 5926 False 2991.666667 4143 93.960000 68 6090 3 chr1D.!!$F1 6022
3 TraesCS1B01G193200 chr4D 481139993 481141367 1374 True 398.000000 577 80.960500 1039 2723 2 chr4D.!!$R1 1684
4 TraesCS1B01G193200 chr5A 662348008 662349381 1373 False 402.500000 575 81.114000 1036 2723 2 chr5A.!!$F2 1687
5 TraesCS1B01G193200 chr4B 609488267 609490663 2396 True 401.333333 508 80.728333 1170 4017 3 chr4B.!!$R1 2847

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
492 499 0.398696 TGGAGCCCAAACGAGCTTTA 59.601 50.000 0.00 0.00 40.11 1.85 F
514 521 0.529773 TGAAAATCGGCGGAGATCGG 60.530 55.000 7.21 0.00 39.69 4.18 F
841 1024 1.142748 CCACCCATCTCTGCTCGTC 59.857 63.158 0.00 0.00 0.00 4.20 F
925 1108 1.360551 CGCCTCGCTGCTGTATAGT 59.639 57.895 0.00 0.00 0.00 2.12 F
1861 2072 1.781786 TTCTACCCTCCTGCTAGCTG 58.218 55.000 17.23 15.65 0.00 4.24 F
3459 4008 0.605319 GGGTCTGCGATGGTGAACAA 60.605 55.000 0.00 0.00 0.00 2.83 F
4538 5109 1.094073 CCATTGCAGGAGCTTCGAGG 61.094 60.000 0.00 0.00 42.74 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2471 1.197721 CAGTTGGAAATCAGCGTGGTC 59.802 52.381 0.00 0.0 0.00 4.02 R
2483 2778 4.386312 CCTGTCAAGGCCAAATATAAGGGA 60.386 45.833 5.01 0.0 36.56 4.20 R
2788 3149 4.084485 GGCGTACTGAAAAGAAGAACAGAC 60.084 45.833 0.00 0.0 34.88 3.51 R
2872 3265 3.131223 TCCTAGCAGAACTGAATCTTCCG 59.869 47.826 5.97 0.0 0.00 4.30 R
3567 4119 0.466124 ATCTGCTACGCCTTCCTTCC 59.534 55.000 0.00 0.0 0.00 3.46 R
4854 5425 0.616371 TTACCATTGACGGGGACAGG 59.384 55.000 0.00 0.0 0.00 4.00 R
5959 6535 1.075151 TCACCCCACCCCAAAAACC 60.075 57.895 0.00 0.0 0.00 3.27 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
63 64 1.580845 GCTTCACGGTGATGCTGCTT 61.581 55.000 30.56 0.00 42.26 3.91
75 76 0.950555 TGCTGCTTCACGGTGATGAC 60.951 55.000 23.49 15.92 0.00 3.06
120 122 2.832129 AGTCATCGGTAGGCTTTGAGAA 59.168 45.455 0.00 0.00 0.00 2.87
142 144 2.250031 TGTGCCATTGCCTCAAATTCT 58.750 42.857 0.00 0.00 36.33 2.40
152 154 5.901413 TGCCTCAAATTCTATCTCTCCAT 57.099 39.130 0.00 0.00 0.00 3.41
194 197 2.723322 AGCTCAATGCCTCAATGCTA 57.277 45.000 0.00 0.00 44.23 3.49
236 239 1.001181 ACATGGTGTTTGGCTCAATGC 59.999 47.619 0.00 0.00 41.94 3.56
270 273 1.303561 GGCAGTCACCATGCTCCAA 60.304 57.895 0.00 0.00 43.35 3.53
285 288 0.541392 TCCAATAGCATGCCGACTGT 59.459 50.000 15.66 0.00 0.00 3.55
286 289 1.065491 TCCAATAGCATGCCGACTGTT 60.065 47.619 15.66 0.00 0.00 3.16
304 307 0.835971 TTGAGGGCTGTAGGTGCTCA 60.836 55.000 0.00 0.00 32.41 4.26
309 312 1.544825 GGCTGTAGGTGCTCAGACCA 61.545 60.000 0.00 0.00 38.63 4.02
332 335 1.001376 GTCTCTACCCGTCCCCCTT 59.999 63.158 0.00 0.00 0.00 3.95
347 350 1.966451 CCTTTCCCGCACGCTTCTT 60.966 57.895 0.00 0.00 0.00 2.52
355 358 2.892334 GCACGCTTCTTGCCAACGA 61.892 57.895 0.00 0.00 38.78 3.85
426 429 2.302733 TCACCATCAAGCTCTAGTGCAA 59.697 45.455 18.36 4.54 34.99 4.08
428 431 2.568956 ACCATCAAGCTCTAGTGCAAGA 59.431 45.455 18.36 14.72 34.99 3.02
444 451 5.024555 GTGCAAGAATAACGCTGAATTCTC 58.975 41.667 7.05 0.00 40.66 2.87
492 499 0.398696 TGGAGCCCAAACGAGCTTTA 59.601 50.000 0.00 0.00 40.11 1.85
505 512 3.181510 ACGAGCTTTATGTGAAAATCGGC 60.182 43.478 0.00 0.00 33.46 5.54
506 513 3.354397 GAGCTTTATGTGAAAATCGGCG 58.646 45.455 0.00 0.00 0.00 6.46
508 515 2.096819 GCTTTATGTGAAAATCGGCGGA 59.903 45.455 7.21 0.00 0.00 5.54
513 520 0.577269 GTGAAAATCGGCGGAGATCG 59.423 55.000 7.21 0.00 42.76 3.69
514 521 0.529773 TGAAAATCGGCGGAGATCGG 60.530 55.000 7.21 0.00 39.69 4.18
575 589 2.151202 GGGTTTGATTCAGACTTCGCA 58.849 47.619 7.22 0.00 0.00 5.10
827 1008 3.451894 CAAGCGCATTCCCCCACC 61.452 66.667 11.47 0.00 0.00 4.61
841 1024 1.142748 CCACCCATCTCTGCTCGTC 59.857 63.158 0.00 0.00 0.00 4.20
868 1051 4.485554 GTGCAGATCGCGAGTTCT 57.514 55.556 16.66 11.06 46.97 3.01
895 1078 2.035832 CGGAGCACCAAAATCCAAAACT 59.964 45.455 0.00 0.00 35.59 2.66
896 1079 3.492482 CGGAGCACCAAAATCCAAAACTT 60.492 43.478 0.00 0.00 35.59 2.66
924 1107 4.235065 CGCCTCGCTGCTGTATAG 57.765 61.111 0.00 0.00 0.00 1.31
925 1108 1.360551 CGCCTCGCTGCTGTATAGT 59.639 57.895 0.00 0.00 0.00 2.12
933 1116 4.449131 TCGCTGCTGTATAGTACTGTAGT 58.551 43.478 5.39 0.22 40.57 2.73
1206 1392 3.386237 GCCGTGCTCCTCACCTCT 61.386 66.667 0.00 0.00 42.69 3.69
1783 1982 9.924650 AAGACTTCATAGTAACTAATTGTTCGT 57.075 29.630 0.00 0.00 39.89 3.85
1859 2070 3.006003 GTGTATTCTACCCTCCTGCTAGC 59.994 52.174 8.10 8.10 0.00 3.42
1861 2072 1.781786 TTCTACCCTCCTGCTAGCTG 58.218 55.000 17.23 15.65 0.00 4.24
1933 2157 9.154847 GCTAAAGTTAAATCATTGCATTCCTTT 57.845 29.630 0.00 0.00 0.00 3.11
2048 2278 6.707440 TTAGGAGTGATCTGATCTTGTCTC 57.293 41.667 17.82 16.88 0.00 3.36
2049 2279 4.870636 AGGAGTGATCTGATCTTGTCTCT 58.129 43.478 17.82 7.27 0.00 3.10
2126 2357 9.162764 AGTTTATGTTAGTATGACCACATGAAC 57.837 33.333 0.00 13.73 42.30 3.18
2180 2411 5.869579 TCTACACAAGGAATTTCTCAGCTT 58.130 37.500 0.00 0.00 0.00 3.74
2246 2477 5.068234 TGTATCAGAGTTAAAGGACCACG 57.932 43.478 0.00 0.00 0.00 4.94
2388 2683 2.684881 CCTTGTTTCACTTCACTGTGCT 59.315 45.455 2.12 0.00 37.81 4.40
2872 3265 4.037923 TGAGTTTCAGTTTCTTTCCCATGC 59.962 41.667 0.00 0.00 0.00 4.06
2968 3361 7.067008 GTGCTCCTTGTTAACATAACCACATAT 59.933 37.037 9.56 0.00 0.00 1.78
2989 3382 3.366396 TGTCAGTGAGGATAGGGAAGAC 58.634 50.000 0.00 0.00 0.00 3.01
3030 3427 6.038997 TGTAGGAAACTTTCTTCTAGAGGC 57.961 41.667 0.00 0.00 43.67 4.70
3048 3445 9.102453 TCTAGAGGCATAGACTATACAGTTAGA 57.898 37.037 0.00 0.00 34.21 2.10
3085 3482 5.505181 ACTGGTTCCAAGAGATACACAAT 57.495 39.130 0.00 0.00 0.00 2.71
3132 3529 3.255149 CCTACGTATGGACTATGGTCACC 59.745 52.174 11.67 0.00 43.77 4.02
3133 3530 2.037144 ACGTATGGACTATGGTCACCC 58.963 52.381 11.67 0.00 43.77 4.61
3165 3574 2.826428 TCGGCAAGATAAGAGCATGTC 58.174 47.619 0.00 0.00 0.00 3.06
3166 3575 1.869767 CGGCAAGATAAGAGCATGTCC 59.130 52.381 0.00 0.00 0.00 4.02
3168 3577 2.877168 GGCAAGATAAGAGCATGTCCTG 59.123 50.000 0.00 0.00 0.00 3.86
3459 4008 0.605319 GGGTCTGCGATGGTGAACAA 60.605 55.000 0.00 0.00 0.00 2.83
3899 4451 6.327386 TGCCCTAAGGACAAGAGATAATTT 57.673 37.500 0.00 0.00 33.47 1.82
3985 4540 2.092699 GCTACAAAGAGGGATCCTGCTT 60.093 50.000 12.58 12.30 31.76 3.91
4056 4613 2.764010 GTCTCTCCCTCTCCCTCTTTTC 59.236 54.545 0.00 0.00 0.00 2.29
4081 4638 1.985159 TGCTGTTCCCTAACCTGTCAT 59.015 47.619 0.00 0.00 34.49 3.06
4087 4644 6.134535 TGTTCCCTAACCTGTCATGTATTT 57.865 37.500 0.00 0.00 34.49 1.40
4088 4645 7.260387 TGTTCCCTAACCTGTCATGTATTTA 57.740 36.000 0.00 0.00 34.49 1.40
4223 4780 4.220163 CCCTTTCCAGTTAGTACTCGTTCT 59.780 45.833 0.00 0.00 30.26 3.01
4252 4809 9.646427 GAAGATATGGTGAGAGGTGAATATAAC 57.354 37.037 0.00 0.00 0.00 1.89
4259 4816 7.399191 TGGTGAGAGGTGAATATAACACTAGTT 59.601 37.037 0.00 0.00 41.74 2.24
4328 4886 7.707893 CCTCTTGGTAATTTTTAGATGCAATGG 59.292 37.037 0.00 0.00 0.00 3.16
4342 4900 1.265095 GCAATGGCATCTATGGTCACG 59.735 52.381 0.00 0.00 40.72 4.35
4343 4901 2.564771 CAATGGCATCTATGGTCACGT 58.435 47.619 0.00 0.00 0.00 4.49
4414 4973 9.573133 GAAAACTACCAACTTAATTCCATGATG 57.427 33.333 0.00 0.00 0.00 3.07
4429 4992 9.807649 AATTCCATGATGTGCTTAAAATAAGTC 57.192 29.630 0.00 0.00 0.00 3.01
4441 5004 9.817809 TGCTTAAAATAAGTCCTAGTGTATCTG 57.182 33.333 0.00 0.00 0.00 2.90
4447 5010 8.694581 AATAAGTCCTAGTGTATCTGGTACTC 57.305 38.462 0.00 0.00 34.27 2.59
4453 5016 6.068971 TCCTAGTGTATCTGGTACTCCTCTTT 60.069 42.308 0.00 0.00 34.27 2.52
4458 5021 4.722361 ATCTGGTACTCCTCTTTCGTTC 57.278 45.455 0.00 0.00 34.23 3.95
4464 5027 4.574013 GGTACTCCTCTTTCGTTCGATCTA 59.426 45.833 0.00 0.00 0.00 1.98
4538 5109 1.094073 CCATTGCAGGAGCTTCGAGG 61.094 60.000 0.00 0.00 42.74 4.63
4546 5117 3.712187 CAGGAGCTTCGAGGAGTTTATC 58.288 50.000 0.00 0.00 0.00 1.75
4715 5286 2.689553 TGCCAGTCATGCTTTCGATA 57.310 45.000 0.00 0.00 0.00 2.92
4802 5373 5.136068 TCCTTTGGTATGCCCATTTATGA 57.864 39.130 0.00 0.00 44.74 2.15
4813 5384 5.916318 TGCCCATTTATGAATCACCATTTC 58.084 37.500 0.00 0.00 0.00 2.17
4822 5393 4.749976 TGAATCACCATTTCATGCACATG 58.250 39.130 4.18 4.18 40.09 3.21
4864 5437 3.249189 ATGCACACCTGTCCCCGT 61.249 61.111 0.00 0.00 0.00 5.28
4909 5482 6.739331 ATTTTTATCACAAAACAGGACCCA 57.261 33.333 0.00 0.00 0.00 4.51
4930 5503 5.016173 CCATTAATGTTCTGGACCAGGAAA 58.984 41.667 21.56 8.63 31.38 3.13
4933 5506 7.310609 CCATTAATGTTCTGGACCAGGAAATTT 60.311 37.037 21.44 10.15 31.38 1.82
4959 5532 5.003804 ACTGCCATTGACTAACTCGAAAAT 58.996 37.500 0.00 0.00 0.00 1.82
4960 5533 6.092122 CACTGCCATTGACTAACTCGAAAATA 59.908 38.462 0.00 0.00 0.00 1.40
5123 5696 4.384537 CCATCCATCTGCTTTAGGAGAACA 60.385 45.833 5.04 0.00 45.49 3.18
5124 5697 4.478206 TCCATCTGCTTTAGGAGAACAG 57.522 45.455 5.04 0.00 45.49 3.16
5158 5731 3.609853 TCATCAGTGTTGTATTCTGGCC 58.390 45.455 0.00 0.00 0.00 5.36
5185 5758 3.117322 TGGGGGTTCATTCAGTTTTCTCA 60.117 43.478 0.00 0.00 0.00 3.27
5191 5764 7.041848 GGGGTTCATTCAGTTTTCTCATTTTTG 60.042 37.037 0.00 0.00 0.00 2.44
5823 6399 1.029408 TTGTTGCTTGTGCTGTCCGT 61.029 50.000 0.00 0.00 40.48 4.69
5934 6510 2.125106 GAGGATGGACGTGGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
5935 6511 3.682292 GAGGATGGACGTGGTGGCC 62.682 68.421 0.00 0.00 0.00 5.36
5936 6512 4.796495 GGATGGACGTGGTGGCCC 62.796 72.222 0.00 0.00 0.00 5.80
5953 6529 4.758251 CGGCTGTGCGTCCATGGA 62.758 66.667 11.44 11.44 0.00 3.41
5970 6546 1.150986 TGGATGATGGGTTTTTGGGGT 59.849 47.619 0.00 0.00 0.00 4.95
5971 6547 1.554617 GGATGATGGGTTTTTGGGGTG 59.445 52.381 0.00 0.00 0.00 4.61
5972 6548 1.554617 GATGATGGGTTTTTGGGGTGG 59.445 52.381 0.00 0.00 0.00 4.61
5973 6549 0.472734 TGATGGGTTTTTGGGGTGGG 60.473 55.000 0.00 0.00 0.00 4.61
5974 6550 1.151921 ATGGGTTTTTGGGGTGGGG 60.152 57.895 0.00 0.00 0.00 4.96
5975 6551 1.979389 ATGGGTTTTTGGGGTGGGGT 61.979 55.000 0.00 0.00 0.00 4.95
5976 6552 2.144078 GGGTTTTTGGGGTGGGGTG 61.144 63.158 0.00 0.00 0.00 4.61
5977 6553 1.075151 GGTTTTTGGGGTGGGGTGA 60.075 57.895 0.00 0.00 0.00 4.02
5978 6554 1.118965 GGTTTTTGGGGTGGGGTGAG 61.119 60.000 0.00 0.00 0.00 3.51
5979 6555 1.118965 GTTTTTGGGGTGGGGTGAGG 61.119 60.000 0.00 0.00 0.00 3.86
6059 6636 4.200283 CGACGAGCTGCTCTCCCC 62.200 72.222 25.59 11.54 38.62 4.81
6060 6637 2.757917 GACGAGCTGCTCTCCCCT 60.758 66.667 25.59 4.48 38.62 4.79
6068 6648 3.844090 GCTCTCCCCTCTCGTGGC 61.844 72.222 0.00 0.00 0.00 5.01
6073 6653 0.830648 CTCCCCTCTCGTGGCAATAA 59.169 55.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.177401 CCACACTCTCGATGACTCCA 58.823 55.000 0.00 0.00 0.00 3.86
9 10 0.457851 CCCACACTCTCGATGACTCC 59.542 60.000 0.00 0.00 0.00 3.85
17 18 0.244994 CACCTTCTCCCACACTCTCG 59.755 60.000 0.00 0.00 0.00 4.04
75 76 1.374758 GTGGAACCGAGCTGTGAGG 60.375 63.158 0.00 0.00 0.00 3.86
108 110 3.153369 TGGCACAATTCTCAAAGCCTA 57.847 42.857 0.00 0.00 42.46 3.93
142 144 4.202161 GGCGAAAGACAAGATGGAGAGATA 60.202 45.833 0.00 0.00 40.66 1.98
194 197 3.009695 TGTCCCAAATAAACCACCGATCT 59.990 43.478 0.00 0.00 0.00 2.75
236 239 3.771160 CCCTTCCGTCGGAGTGGG 61.771 72.222 28.57 28.57 39.54 4.61
270 273 1.473965 CCTCAACAGTCGGCATGCTAT 60.474 52.381 18.92 0.00 0.00 2.97
285 288 0.835971 TGAGCACCTACAGCCCTCAA 60.836 55.000 0.00 0.00 30.30 3.02
286 289 1.229177 TGAGCACCTACAGCCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
332 335 3.353836 GCAAGAAGCGTGCGGGAA 61.354 61.111 0.00 0.00 31.20 3.97
347 350 5.933790 GACACTTTTATATTGTCGTTGGCA 58.066 37.500 0.00 0.00 30.95 4.92
389 392 3.337358 TGGTGACATAGTGCTCAACATG 58.663 45.455 0.00 0.00 28.84 3.21
426 429 4.698575 GAGGGAGAATTCAGCGTTATTCT 58.301 43.478 8.44 9.13 42.27 2.40
428 431 3.118738 ACGAGGGAGAATTCAGCGTTATT 60.119 43.478 8.44 0.00 0.00 1.40
444 451 4.508128 ATGGCGCACGTACGAGGG 62.508 66.667 24.41 23.06 34.06 4.30
492 499 2.213499 GATCTCCGCCGATTTTCACAT 58.787 47.619 0.00 0.00 0.00 3.21
505 512 0.038159 GTAATCCTGGCCGATCTCCG 60.038 60.000 0.00 0.00 38.18 4.63
506 513 1.001406 CTGTAATCCTGGCCGATCTCC 59.999 57.143 0.00 0.00 0.00 3.71
508 515 1.051812 CCTGTAATCCTGGCCGATCT 58.948 55.000 0.00 0.00 0.00 2.75
513 520 1.453928 GCACCCTGTAATCCTGGCC 60.454 63.158 0.00 0.00 0.00 5.36
514 521 1.453928 GGCACCCTGTAATCCTGGC 60.454 63.158 0.00 0.00 0.00 4.85
517 524 1.372501 AACTGGCACCCTGTAATCCT 58.627 50.000 0.00 0.00 34.63 3.24
575 589 7.444183 TGAGAAAAGTTCAACCTGAATTCGTAT 59.556 33.333 0.04 0.00 38.79 3.06
586 600 7.414814 TTTGTTGTTTGAGAAAAGTTCAACC 57.585 32.000 0.00 0.00 34.50 3.77
649 672 7.421530 TCAAGAGTCAAAAGATTTTCGTAGG 57.578 36.000 0.00 0.00 0.00 3.18
827 1008 0.108615 AAACGGACGAGCAGAGATGG 60.109 55.000 0.00 0.00 0.00 3.51
841 1024 1.752501 CGATCTGCACGGCTAAACGG 61.753 60.000 0.00 0.00 38.39 4.44
868 1051 0.320374 ATTTTGGTGCTCCGAGTCGA 59.680 50.000 15.64 0.00 36.30 4.20
895 1078 3.760035 GAGGCGCGGTCTCTGGAA 61.760 66.667 8.83 0.00 30.76 3.53
922 1105 4.535294 AGAGGACACTCCACTACAGTACTA 59.465 45.833 0.00 0.00 45.11 1.82
923 1106 3.331294 AGAGGACACTCCACTACAGTACT 59.669 47.826 0.00 0.00 45.11 2.73
924 1107 3.440872 CAGAGGACACTCCACTACAGTAC 59.559 52.174 0.00 0.00 45.11 2.73
925 1108 3.687125 CAGAGGACACTCCACTACAGTA 58.313 50.000 0.00 0.00 45.11 2.74
1065 1251 1.069090 GTTGAGCGTCACCACCAGA 59.931 57.895 0.00 0.00 0.00 3.86
1606 1798 3.588277 GCAGAAATAGCGGATCCGA 57.412 52.632 37.64 18.62 42.83 4.55
1693 1885 8.511604 ACAATGCTAGAGCTAAACATTAACAT 57.488 30.769 2.72 0.00 42.66 2.71
1701 1893 6.763610 ACCATAGAACAATGCTAGAGCTAAAC 59.236 38.462 2.72 0.00 42.66 2.01
1890 2101 8.556213 AACTTTAGCATACAAAAATAGGACGA 57.444 30.769 0.00 0.00 0.00 4.20
1940 2164 8.995220 TCGTGAGTTACTTTAGCATACAAAATT 58.005 29.630 0.00 0.00 0.00 1.82
1963 2187 9.689976 CTGATCATCTTTACTGATTCTTATCGT 57.310 33.333 0.00 0.00 33.56 3.73
1964 2188 9.905171 TCTGATCATCTTTACTGATTCTTATCG 57.095 33.333 0.00 0.00 33.56 2.92
2004 2231 7.719633 TCCTAAAAGGGCATACAGAATATCAAC 59.280 37.037 0.00 0.00 35.59 3.18
2228 2459 1.968493 AGCGTGGTCCTTTAACTCTGA 59.032 47.619 0.00 0.00 0.00 3.27
2240 2471 1.197721 CAGTTGGAAATCAGCGTGGTC 59.802 52.381 0.00 0.00 0.00 4.02
2246 2477 7.713764 AAATGTTTAACAGTTGGAAATCAGC 57.286 32.000 10.02 0.00 34.88 4.26
2483 2778 4.386312 CCTGTCAAGGCCAAATATAAGGGA 60.386 45.833 5.01 0.00 36.56 4.20
2537 2832 6.093219 GCTCAAAAGATAGTCAATCAGAGCAA 59.907 38.462 0.00 0.00 41.74 3.91
2788 3149 4.084485 GGCGTACTGAAAAGAAGAACAGAC 60.084 45.833 0.00 0.00 34.88 3.51
2872 3265 3.131223 TCCTAGCAGAACTGAATCTTCCG 59.869 47.826 5.97 0.00 0.00 4.30
2968 3361 3.245622 TGTCTTCCCTATCCTCACTGACA 60.246 47.826 0.00 0.00 0.00 3.58
2989 3382 6.515832 TCCTACATATACATCACTTGCACTG 58.484 40.000 0.00 0.00 0.00 3.66
3048 3445 4.593634 GGAACCAGTAGGCAGGTCTATTAT 59.406 45.833 0.00 0.00 37.07 1.28
3085 3482 6.646240 GGCAAAAGAACTAAAGATTGCATCAA 59.354 34.615 10.05 0.00 43.59 2.57
3132 3529 4.386867 TCTTGCCGAAGTTCATAGTAGG 57.613 45.455 3.32 0.00 0.00 3.18
3133 3530 7.426410 TCTTATCTTGCCGAAGTTCATAGTAG 58.574 38.462 3.32 0.00 0.00 2.57
3165 3574 0.602562 TTCATTTTCCTTGCGGCAGG 59.397 50.000 4.94 4.94 34.86 4.85
3166 3575 2.264813 CATTCATTTTCCTTGCGGCAG 58.735 47.619 1.67 0.00 0.00 4.85
3168 3577 1.066929 ACCATTCATTTTCCTTGCGGC 60.067 47.619 0.00 0.00 0.00 6.53
3210 3759 7.225931 GGCATCTCGTGTACCTATTATTGAAAA 59.774 37.037 0.00 0.00 0.00 2.29
3459 4008 3.498774 AGTTGGCTTTCATCTGTCTGT 57.501 42.857 0.00 0.00 0.00 3.41
3567 4119 0.466124 ATCTGCTACGCCTTCCTTCC 59.534 55.000 0.00 0.00 0.00 3.46
3587 4139 5.362717 GGTCTCTTTTTCCCTTTCTTTCCAA 59.637 40.000 0.00 0.00 0.00 3.53
3899 4451 6.379703 TCTTTCTCTTGAAACATGAAAACCCA 59.620 34.615 0.00 0.00 37.27 4.51
4056 4613 3.452627 ACAGGTTAGGGAACAGCATAGAG 59.547 47.826 0.00 0.00 37.29 2.43
4206 4763 5.411977 TCTTCAGAGAACGAGTACTAACTGG 59.588 44.000 0.00 0.00 35.56 4.00
4223 4780 4.871822 TCACCTCTCACCATATCTTCAGA 58.128 43.478 0.00 0.00 0.00 3.27
4259 4816 6.151985 ACCGGTGCATAATCTTTAATTTCACA 59.848 34.615 6.12 0.00 0.00 3.58
4328 4886 4.882671 AAAATGACGTGACCATAGATGC 57.117 40.909 0.00 0.00 0.00 3.91
4378 4937 5.258051 AGTTGGTAGTTTTCAACCAGAACA 58.742 37.500 0.00 0.00 46.11 3.18
4379 4938 5.830000 AGTTGGTAGTTTTCAACCAGAAC 57.170 39.130 0.00 0.00 46.11 3.01
4381 4940 8.528044 AATTAAGTTGGTAGTTTTCAACCAGA 57.472 30.769 0.00 0.00 46.11 3.86
4383 4942 7.342284 TGGAATTAAGTTGGTAGTTTTCAACCA 59.658 33.333 0.00 0.00 43.99 3.67
4384 4943 7.718525 TGGAATTAAGTTGGTAGTTTTCAACC 58.281 34.615 0.00 0.00 42.87 3.77
4393 4952 6.319658 AGCACATCATGGAATTAAGTTGGTAG 59.680 38.462 0.00 0.00 0.00 3.18
4403 4962 9.807649 GACTTATTTTAAGCACATCATGGAATT 57.192 29.630 0.00 0.00 0.00 2.17
4410 4969 8.100791 ACACTAGGACTTATTTTAAGCACATCA 58.899 33.333 0.00 0.00 0.00 3.07
4414 4973 9.819267 AGATACACTAGGACTTATTTTAAGCAC 57.181 33.333 0.00 0.00 0.00 4.40
4429 4992 5.313280 AGAGGAGTACCAGATACACTAGG 57.687 47.826 0.00 0.00 38.94 3.02
4441 5004 3.377798 AGATCGAACGAAAGAGGAGTACC 59.622 47.826 0.12 0.00 0.00 3.34
4609 5180 6.449635 TCGGCAATCTACATAAAGCATTTT 57.550 33.333 0.00 0.00 40.09 1.82
4667 5238 3.965347 AGCTCCGCCTTCTTATTAACCTA 59.035 43.478 0.00 0.00 0.00 3.08
4715 5286 1.078143 GCGTCCAGCTCTCCCAAAT 60.078 57.895 0.00 0.00 44.04 2.32
4813 5384 7.197703 TCTTAAATATTGCTGTCATGTGCATG 58.802 34.615 5.86 5.86 39.07 4.06
4854 5425 0.616371 TTACCATTGACGGGGACAGG 59.384 55.000 0.00 0.00 0.00 4.00
4891 5464 6.951198 ACATTAATGGGTCCTGTTTTGTGATA 59.049 34.615 19.37 0.00 0.00 2.15
4909 5482 7.093333 GGAAATTTCCTGGTCCAGAACATTAAT 60.093 37.037 26.94 7.23 44.11 1.40
4930 5503 4.666512 AGTTAGTCAATGGCAGTGGAAAT 58.333 39.130 15.62 3.92 0.00 2.17
4933 5506 2.353704 CGAGTTAGTCAATGGCAGTGGA 60.354 50.000 15.62 0.00 0.00 4.02
4935 5508 2.959516 TCGAGTTAGTCAATGGCAGTG 58.040 47.619 8.96 8.96 0.00 3.66
4936 5509 3.678056 TTCGAGTTAGTCAATGGCAGT 57.322 42.857 0.00 0.00 0.00 4.40
4938 5511 7.041030 TGTTTATTTTCGAGTTAGTCAATGGCA 60.041 33.333 0.00 0.00 0.00 4.92
4939 5512 7.302524 TGTTTATTTTCGAGTTAGTCAATGGC 58.697 34.615 0.00 0.00 0.00 4.40
4941 5514 9.878599 AACTGTTTATTTTCGAGTTAGTCAATG 57.121 29.630 0.00 0.00 0.00 2.82
4943 5516 9.321562 AGAACTGTTTATTTTCGAGTTAGTCAA 57.678 29.630 0.00 0.00 0.00 3.18
5158 5731 2.440247 GAATGAACCCCCAGGCCG 60.440 66.667 0.00 0.00 36.11 6.13
5173 5746 4.810491 GGCAGCAAAAATGAGAAAACTGAA 59.190 37.500 0.00 0.00 0.00 3.02
5185 5758 3.118665 ACTGAACACTTGGCAGCAAAAAT 60.119 39.130 0.00 0.00 33.03 1.82
5191 5764 2.195922 CAAAACTGAACACTTGGCAGC 58.804 47.619 0.00 0.00 33.03 5.25
5371 5944 2.481104 GCTGTGGAAGGAAGAGATCGAG 60.481 54.545 0.00 0.00 0.00 4.04
5440 6013 2.203938 AGCTGGGACCCGGAGAAA 60.204 61.111 24.69 0.00 29.82 2.52
5907 6483 2.060383 TCCATCCTCTCGGCACCTG 61.060 63.158 0.00 0.00 0.00 4.00
5913 6489 2.052690 ACCACGTCCATCCTCTCGG 61.053 63.158 0.00 0.00 0.00 4.63
5914 6490 1.139734 CACCACGTCCATCCTCTCG 59.860 63.158 0.00 0.00 0.00 4.04
5917 6493 2.125106 GCCACCACGTCCATCCTC 60.125 66.667 0.00 0.00 0.00 3.71
5936 6512 4.758251 TCCATGGACGCACAGCCG 62.758 66.667 11.44 0.00 0.00 5.52
5949 6525 2.225856 ACCCCAAAAACCCATCATCCAT 60.226 45.455 0.00 0.00 0.00 3.41
5951 6527 1.554617 CACCCCAAAAACCCATCATCC 59.445 52.381 0.00 0.00 0.00 3.51
5953 6529 1.655372 CCACCCCAAAAACCCATCAT 58.345 50.000 0.00 0.00 0.00 2.45
5959 6535 1.075151 TCACCCCACCCCAAAAACC 60.075 57.895 0.00 0.00 0.00 3.27
5961 6537 1.234529 CCTCACCCCACCCCAAAAA 59.765 57.895 0.00 0.00 0.00 1.94
5962 6538 2.784654 CCCTCACCCCACCCCAAAA 61.785 63.158 0.00 0.00 0.00 2.44
5972 6548 4.741239 TCTCCAGCCCCCTCACCC 62.741 72.222 0.00 0.00 0.00 4.61
5973 6549 3.086600 CTCTCCAGCCCCCTCACC 61.087 72.222 0.00 0.00 0.00 4.02
5974 6550 3.791586 GCTCTCCAGCCCCCTCAC 61.792 72.222 0.00 0.00 40.14 3.51
6059 6636 3.736252 CGATAAGGTTATTGCCACGAGAG 59.264 47.826 0.00 0.00 0.00 3.20
6060 6637 3.713288 CGATAAGGTTATTGCCACGAGA 58.287 45.455 0.00 0.00 0.00 4.04
6068 6648 2.228822 GCCCATGGCGATAAGGTTATTG 59.771 50.000 6.09 0.00 39.62 1.90


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

AutoCloner maintained by Alex Coulton.