Multiple sequence alignment - TraesCS7A01G271700

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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 TraesCS7A01G271700 chr7A 100.000 3959 0 0 1 3959 285055746 285059704 0.000000e+00 7312.0
1 TraesCS7A01G271700 chr7A 93.333 105 7 0 3855 3959 254228548 254228652 5.300000e-34 156.0
2 TraesCS7A01G271700 chr7A 76.238 202 32 8 289 478 121217793 121217990 4.210000e-15 93.5
3 TraesCS7A01G271700 chr7A 75.000 184 26 16 309 478 215130825 215131002 2.550000e-07 67.6
4 TraesCS7A01G271700 chr7B 95.028 3439 113 19 1 3416 242357670 242354267 0.000000e+00 5350.0
5 TraesCS7A01G271700 chr7B 90.455 440 37 4 3423 3857 242354201 242353762 3.430000e-160 575.0
6 TraesCS7A01G271700 chr7B 88.272 162 19 0 244 405 154366507 154366346 1.120000e-45 195.0
7 TraesCS7A01G271700 chr7B 94.340 106 6 0 3854 3959 137984384 137984489 3.170000e-36 163.0
8 TraesCS7A01G271700 chr7D 96.346 2928 58 10 510 3416 262023522 262026421 0.000000e+00 4769.0
9 TraesCS7A01G271700 chr7D 93.333 105 7 0 3855 3959 534428101 534427997 5.300000e-34 156.0
10 TraesCS7A01G271700 chr7D 95.522 67 3 0 3556 3622 262034312 262034378 1.500000e-19 108.0
11 TraesCS7A01G271700 chr7D 96.226 53 2 0 3423 3475 262026492 262026544 1.960000e-13 87.9
12 TraesCS7A01G271700 chr3B 90.135 223 22 0 1 223 214451431 214451209 1.390000e-74 291.0
13 TraesCS7A01G271700 chr3B 88.889 162 18 0 244 405 803669491 803669330 2.410000e-47 200.0
14 TraesCS7A01G271700 chr2D 89.302 215 22 1 6 220 484584823 484584610 6.520000e-68 268.0
15 TraesCS7A01G271700 chr3D 89.423 208 22 0 13 220 269194099 269193892 3.030000e-66 263.0
16 TraesCS7A01G271700 chr3D 86.239 218 30 0 3 220 290006458 290006675 1.840000e-58 237.0
17 TraesCS7A01G271700 chr3D 82.072 251 25 10 244 478 183958889 183959135 3.120000e-46 196.0
18 TraesCS7A01G271700 chr3D 93.333 105 7 0 3855 3959 65323036 65323140 5.300000e-34 156.0
19 TraesCS7A01G271700 chr3D 88.000 75 8 1 3699 3772 570535523 570535449 1.960000e-13 87.9
20 TraesCS7A01G271700 chr3D 95.556 45 2 0 3728 3772 596879288 596879244 5.490000e-09 73.1
21 TraesCS7A01G271700 chrUn 88.128 219 25 1 3 220 313787056 313787274 3.920000e-65 259.0
22 TraesCS7A01G271700 chrUn 97.059 34 1 0 445 478 47483879 47483846 1.540000e-04 58.4
23 TraesCS7A01G271700 chr5D 88.128 219 25 1 3 220 102758166 102757948 3.920000e-65 259.0
24 TraesCS7A01G271700 chr5D 87.097 217 27 1 7 223 506652739 506652954 1.100000e-60 244.0
25 TraesCS7A01G271700 chr5D 86.854 213 28 0 8 220 226355121 226355333 5.110000e-59 239.0
26 TraesCS7A01G271700 chr3A 88.889 162 18 0 244 405 727352036 727351875 2.410000e-47 200.0
27 TraesCS7A01G271700 chr3A 96.875 32 1 0 445 476 78187341 78187372 2.000000e-03 54.7
28 TraesCS7A01G271700 chr6D 81.818 253 28 10 244 481 347931053 347931302 3.120000e-46 196.0
29 TraesCS7A01G271700 chr5B 81.781 247 33 6 244 478 555149772 555149526 3.120000e-46 196.0
30 TraesCS7A01G271700 chr5B 80.488 246 34 10 244 476 226767661 226767905 4.070000e-40 176.0
31 TraesCS7A01G271700 chr5B 93.333 105 7 0 3855 3959 388180357 388180461 5.300000e-34 156.0
32 TraesCS7A01G271700 chr1A 82.000 250 27 12 244 478 30543311 30543065 3.120000e-46 196.0
33 TraesCS7A01G271700 chr6B 88.272 162 19 0 244 405 544080934 544081095 1.120000e-45 195.0
34 TraesCS7A01G271700 chr6B 88.272 162 19 0 244 405 716111557 716111396 1.120000e-45 195.0
35 TraesCS7A01G271700 chr5A 88.272 162 19 0 244 405 606951757 606951918 1.120000e-45 195.0
36 TraesCS7A01G271700 chr1B 94.286 105 6 0 3855 3959 274563706 274563810 1.140000e-35 161.0
37 TraesCS7A01G271700 chr2B 94.175 103 6 0 3855 3957 311609814 311609916 1.470000e-34 158.0
38 TraesCS7A01G271700 chr2B 93.333 105 7 0 3855 3959 14729475 14729579 5.300000e-34 156.0
39 TraesCS7A01G271700 chr2B 93.333 105 7 0 3855 3959 385693465 385693569 5.300000e-34 156.0
40 TraesCS7A01G271700 chr2A 78.571 252 35 13 244 478 764765653 764765902 8.860000e-32 148.0
41 TraesCS7A01G271700 chr4D 75.904 166 38 2 1408 1572 386369890 386370054 2.540000e-12 84.2
42 TraesCS7A01G271700 chr4A 75.904 166 38 2 1408 1572 67415310 67415474 2.540000e-12 84.2
43 TraesCS7A01G271700 chr4B 87.879 66 6 2 1408 1472 473105445 473105509 4.240000e-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 TraesCS7A01G271700 chr7A 285055746 285059704 3958 False 7312.00 7312 100.0000 1 3959 1 chr7A.!!$F4 3958
1 TraesCS7A01G271700 chr7B 242353762 242357670 3908 True 2962.50 5350 92.7415 1 3857 2 chr7B.!!$R2 3856
2 TraesCS7A01G271700 chr7D 262023522 262026544 3022 False 2428.45 4769 96.2860 510 3475 2 chr7D.!!$F2 2965

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
166 167 0.106619 AAACACACTTGGCCGGGTTA 60.107 50.0 2.18 0.0 0.0 2.85 F
249 250 0.390735 GTCGAAGGTGCCGGTAACAT 60.391 55.0 11.20 0.0 0.0 2.71 F
521 522 0.768622 TCTTGTGGGTCCATTTCCGT 59.231 50.0 0.00 0.0 0.0 4.69 F
710 712 0.811281 GGGAAATGACAAGGCCGAAG 59.189 55.0 0.00 0.0 0.0 3.79 F
2519 2524 1.065647 CTCCTCATCCCCTGCATCAT 58.934 55.0 0.00 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1430 1.273495 TGCTCCCAGATGAGGAAGAGT 60.273 52.381 0.00 0.00 31.49 3.24 R
1542 1544 1.678627 CCGTCCTCTTCGATGATGAGT 59.321 52.381 6.55 0.00 33.68 3.41 R
2505 2510 1.512996 GCGACATGATGCAGGGGATG 61.513 60.000 0.00 0.00 0.00 3.51 R
2658 2663 0.037605 GGTCCACGTGGAGGTAGTTG 60.038 60.000 37.04 6.94 46.49 3.16 R
3902 3996 0.032130 GCATTCTGGATAGCGGTCGA 59.968 55.000 0.00 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
44 45 1.126113 GCTGGACGTCATTAACACACG 59.874 52.381 18.91 2.07 39.48 4.49
47 48 0.441145 GACGTCATTAACACACGCCC 59.559 55.000 11.55 0.00 37.02 6.13
48 49 1.286354 ACGTCATTAACACACGCCCG 61.286 55.000 3.28 0.00 37.02 6.13
98 99 1.906574 TCTCCGGGTTAGCTTCAATGT 59.093 47.619 0.00 0.00 0.00 2.71
114 115 0.898320 ATGTCCCGTTCTGAGACCAG 59.102 55.000 0.00 0.00 41.74 4.00
126 127 5.745312 TCTGAGACCAGAAAATCTAGCAA 57.255 39.130 0.00 0.00 45.74 3.91
144 145 2.288395 GCAATTTACCTGCAAGCACACT 60.288 45.455 0.00 0.00 39.69 3.55
155 156 3.192422 TGCAAGCACACTAAAAACACACT 59.808 39.130 0.00 0.00 0.00 3.55
156 157 4.173256 GCAAGCACACTAAAAACACACTT 58.827 39.130 0.00 0.00 0.00 3.16
158 159 4.370364 AGCACACTAAAAACACACTTGG 57.630 40.909 0.00 0.00 0.00 3.61
162 163 1.679153 ACTAAAAACACACTTGGCCGG 59.321 47.619 0.00 0.00 0.00 6.13
166 167 0.106619 AAACACACTTGGCCGGGTTA 60.107 50.000 2.18 0.00 0.00 2.85
170 171 2.359478 ACTTGGCCGGGTTAAGCG 60.359 61.111 2.18 0.00 0.00 4.68
171 172 3.810896 CTTGGCCGGGTTAAGCGC 61.811 66.667 2.18 0.00 0.00 5.92
211 212 7.750903 CGGAGATTATCAAAAGTTTCCTTCAAC 59.249 37.037 0.00 0.00 0.00 3.18
223 224 5.703130 AGTTTCCTTCAACTCATCAAGTAGC 59.297 40.000 0.00 0.00 37.17 3.58
226 227 3.862267 CCTTCAACTCATCAAGTAGCGAG 59.138 47.826 0.00 0.00 37.17 5.03
249 250 0.390735 GTCGAAGGTGCCGGTAACAT 60.391 55.000 11.20 0.00 0.00 2.71
263 264 3.673338 CGGTAACATAGATGCCACATACG 59.327 47.826 0.00 0.00 0.00 3.06
264 265 3.432252 GGTAACATAGATGCCACATACGC 59.568 47.826 0.00 0.00 0.00 4.42
293 294 5.565509 TGGTGATGTGGCAAAGAGTTAATA 58.434 37.500 0.00 0.00 0.00 0.98
298 299 8.296713 GTGATGTGGCAAAGAGTTAATAAGAAA 58.703 33.333 0.00 0.00 0.00 2.52
350 351 4.702831 TCATCACATAGCGCTTTCCAATA 58.297 39.130 18.68 0.00 0.00 1.90
355 356 5.356751 TCACATAGCGCTTTCCAATACAAAT 59.643 36.000 18.68 0.00 0.00 2.32
357 358 7.066404 TCACATAGCGCTTTCCAATACAAATTA 59.934 33.333 18.68 0.00 0.00 1.40
364 365 7.428472 GCGCTTTCCAATACAAATTAAGTCTAC 59.572 37.037 0.00 0.00 0.00 2.59
405 406 7.396339 AGACATCTATATTACCACGCCTATGAA 59.604 37.037 0.00 0.00 0.00 2.57
410 411 9.081204 TCTATATTACCACGCCTATGAAGTTAA 57.919 33.333 0.00 0.00 0.00 2.01
421 422 7.982919 ACGCCTATGAAGTTAATAACATACACA 59.017 33.333 5.89 0.00 0.00 3.72
506 507 6.819146 GGAATGGAGGAAGTACTTAGTTCTTG 59.181 42.308 8.42 0.00 36.22 3.02
507 508 6.936968 ATGGAGGAAGTACTTAGTTCTTGT 57.063 37.500 8.42 0.00 36.22 3.16
508 509 6.097915 TGGAGGAAGTACTTAGTTCTTGTG 57.902 41.667 8.42 0.00 36.22 3.33
521 522 0.768622 TCTTGTGGGTCCATTTCCGT 59.231 50.000 0.00 0.00 0.00 4.69
543 544 5.631026 GTGAGATTGTGTGCGTTTGAATAT 58.369 37.500 0.00 0.00 0.00 1.28
562 563 7.512130 TGAATATCTGCATAGTGGACTGAAAT 58.488 34.615 0.00 0.00 0.00 2.17
607 608 5.186021 TCAGGTCTCTCTCAAACTTATCCAC 59.814 44.000 0.00 0.00 0.00 4.02
688 689 2.360585 GCCCAAAAGGGAGGGGAG 59.639 66.667 4.37 0.00 45.08 4.30
710 712 0.811281 GGGAAATGACAAGGCCGAAG 59.189 55.000 0.00 0.00 0.00 3.79
856 858 3.137446 TCCGTCCCCAAATAAACGAAA 57.863 42.857 0.00 0.00 37.31 3.46
1371 1373 1.666872 GTCCAACTACGCCAACGCT 60.667 57.895 0.00 0.00 45.53 5.07
1428 1430 1.558167 TTGCCCAGAACGAGCCCATA 61.558 55.000 0.00 0.00 0.00 2.74
1737 1739 2.765969 CCCATGAAGGTGCAGGGT 59.234 61.111 0.00 0.00 38.01 4.34
1824 1826 2.434884 AACGTGATCCGCCTGCTG 60.435 61.111 0.00 0.00 41.42 4.41
1842 1844 2.430367 GTGTCCCACCTCGCCTTT 59.570 61.111 0.00 0.00 0.00 3.11
2039 2044 2.180017 CGGTAGTAACGCCGCTGT 59.820 61.111 0.00 0.00 41.53 4.40
2519 2524 1.065647 CTCCTCATCCCCTGCATCAT 58.934 55.000 0.00 0.00 0.00 2.45
2592 2597 2.266055 CCGCTGGTGAACCTCCTC 59.734 66.667 0.37 0.00 36.82 3.71
2658 2663 2.665185 AAGTTCGCCTGCACGGAC 60.665 61.111 0.00 0.00 42.06 4.79
2730 2735 2.348998 CACCTGGTCCAGCTGGTC 59.651 66.667 31.58 25.87 36.34 4.02
2864 2869 4.752879 GGCGTCCAAGCAGGCGTA 62.753 66.667 11.39 0.00 38.58 4.42
3323 3348 7.962964 TGGTATAGCCATTTCTTCTTATTCG 57.037 36.000 0.00 0.00 43.61 3.34
3328 3353 4.878397 AGCCATTTCTTCTTATTCGGAGTG 59.122 41.667 0.00 0.00 0.00 3.51
3400 3425 9.362539 GTATTCACTTAATTACGAGAAGGAACA 57.637 33.333 7.64 0.00 0.00 3.18
3416 3441 8.697507 AGAAGGAACATGTCAAGTTTAAATCT 57.302 30.769 0.00 0.00 0.00 2.40
3418 3443 9.399403 GAAGGAACATGTCAAGTTTAAATCTTC 57.601 33.333 0.00 2.12 0.00 2.87
3419 3444 8.463930 AGGAACATGTCAAGTTTAAATCTTCA 57.536 30.769 0.00 0.00 0.00 3.02
3420 3445 8.571336 AGGAACATGTCAAGTTTAAATCTTCAG 58.429 33.333 0.00 0.00 0.00 3.02
3495 3584 5.121454 TGACAAAACAGTTCAATTTTGCACC 59.879 36.000 8.87 1.52 45.55 5.01
3501 3590 4.190772 CAGTTCAATTTTGCACCTGGTTT 58.809 39.130 0.00 0.00 0.00 3.27
3529 3618 2.058829 AAAGCCACGAACAACGCCAG 62.059 55.000 0.00 0.00 46.94 4.85
3543 3632 5.886992 ACAACGCCAGGCTTTATAAATTAC 58.113 37.500 10.54 0.00 0.00 1.89
3546 3635 7.337436 ACAACGCCAGGCTTTATAAATTACTAA 59.663 33.333 10.54 0.00 0.00 2.24
3570 3659 2.034558 CCGCACCAATAAGGCCAATTAG 59.965 50.000 5.01 0.00 43.14 1.73
3575 3664 5.126384 GCACCAATAAGGCCAATTAGTTACA 59.874 40.000 5.01 0.00 43.14 2.41
3649 3738 3.636153 GAGCATCTCTAACAAACCCCT 57.364 47.619 0.00 0.00 0.00 4.79
3657 3748 1.329599 CTAACAAACCCCTTATCGCGC 59.670 52.381 0.00 0.00 0.00 6.86
3662 3753 4.963428 CCCCTTATCGCGCGGACC 62.963 72.222 31.69 0.00 0.00 4.46
3678 3769 3.624410 GCGGACCCTTAAAATCGTTATGT 59.376 43.478 0.00 0.00 0.00 2.29
3684 3775 3.697045 CCTTAAAATCGTTATGTGGGCCA 59.303 43.478 0.00 0.00 0.00 5.36
3690 3781 2.432444 TCGTTATGTGGGCCAAGAAAG 58.568 47.619 8.40 5.34 0.00 2.62
3691 3782 2.159382 CGTTATGTGGGCCAAGAAAGT 58.841 47.619 8.40 0.00 0.00 2.66
3704 3796 4.098807 GCCAAGAAAGTGTGTTTTAAGGGA 59.901 41.667 0.00 0.00 0.00 4.20
3716 3809 5.633601 GTGTTTTAAGGGACAATTTAGCTGC 59.366 40.000 0.00 0.00 0.00 5.25
3720 3813 1.312371 GGGACAATTTAGCTGCGGCA 61.312 55.000 21.93 1.29 41.70 5.69
3721 3814 0.525761 GGACAATTTAGCTGCGGCAA 59.474 50.000 21.93 6.51 41.70 4.52
3726 3819 2.799412 CAATTTAGCTGCGGCAAAACAA 59.201 40.909 21.93 4.82 41.70 2.83
3728 3821 1.846541 TTAGCTGCGGCAAAACAAAC 58.153 45.000 21.93 0.00 41.70 2.93
3729 3822 0.031449 TAGCTGCGGCAAAACAAACC 59.969 50.000 21.93 0.00 41.70 3.27
3732 3825 2.026945 CTGCGGCAAAACAAACCCCT 62.027 55.000 3.44 0.00 0.00 4.79
3743 3836 6.370442 GCAAAACAAACCCCTTATAATCAACC 59.630 38.462 0.00 0.00 0.00 3.77
3782 3876 0.250166 AAATATACCCGCCACCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
3792 3886 2.835431 CACCTCGCCTCCCTCGAT 60.835 66.667 0.00 0.00 35.25 3.59
3823 3917 1.915078 CTCGCCACCAATCCTCCCTT 61.915 60.000 0.00 0.00 0.00 3.95
3831 3925 3.682292 AATCCTCCCTTGACGCGCC 62.682 63.158 5.73 0.00 0.00 6.53
3857 3951 1.527433 CCACTGTGCCTCTCTCGACA 61.527 60.000 1.29 0.00 0.00 4.35
3858 3952 0.315251 CACTGTGCCTCTCTCGACAA 59.685 55.000 0.00 0.00 0.00 3.18
3859 3953 0.600557 ACTGTGCCTCTCTCGACAAG 59.399 55.000 0.00 0.00 0.00 3.16
3860 3954 0.600557 CTGTGCCTCTCTCGACAAGT 59.399 55.000 0.00 0.00 0.00 3.16
3861 3955 1.813178 CTGTGCCTCTCTCGACAAGTA 59.187 52.381 0.00 0.00 0.00 2.24
3862 3956 1.813178 TGTGCCTCTCTCGACAAGTAG 59.187 52.381 0.00 0.00 0.00 2.57
3863 3957 2.085320 GTGCCTCTCTCGACAAGTAGA 58.915 52.381 0.00 0.00 0.00 2.59
3864 3958 2.085320 TGCCTCTCTCGACAAGTAGAC 58.915 52.381 0.00 0.00 0.00 2.59
3865 3959 2.290387 TGCCTCTCTCGACAAGTAGACT 60.290 50.000 0.00 0.00 0.00 3.24
3866 3960 2.096819 GCCTCTCTCGACAAGTAGACTG 59.903 54.545 0.00 0.00 0.00 3.51
3867 3961 3.601435 CCTCTCTCGACAAGTAGACTGA 58.399 50.000 0.00 0.00 0.00 3.41
3868 3962 3.372822 CCTCTCTCGACAAGTAGACTGAC 59.627 52.174 0.00 0.00 0.00 3.51
3869 3963 4.250464 CTCTCTCGACAAGTAGACTGACT 58.750 47.826 0.00 0.00 0.00 3.41
3870 3964 4.247258 TCTCTCGACAAGTAGACTGACTC 58.753 47.826 0.00 0.00 0.00 3.36
3871 3965 3.336468 TCTCGACAAGTAGACTGACTCC 58.664 50.000 0.00 0.00 0.00 3.85
3872 3966 3.008157 TCTCGACAAGTAGACTGACTCCT 59.992 47.826 0.00 0.00 0.00 3.69
3873 3967 3.075148 TCGACAAGTAGACTGACTCCTG 58.925 50.000 0.00 0.00 0.00 3.86
3874 3968 2.814919 CGACAAGTAGACTGACTCCTGT 59.185 50.000 0.00 0.00 0.00 4.00
3875 3969 3.120130 CGACAAGTAGACTGACTCCTGTC 60.120 52.174 0.00 0.00 43.20 3.51
3877 3971 3.823873 ACAAGTAGACTGACTCCTGTCTG 59.176 47.826 12.99 2.44 46.59 3.51
3878 3972 2.442413 AGTAGACTGACTCCTGTCTGC 58.558 52.381 12.99 11.83 46.59 4.26
3879 3973 2.163509 GTAGACTGACTCCTGTCTGCA 58.836 52.381 12.99 0.00 46.59 4.41
3880 3974 1.935799 AGACTGACTCCTGTCTGCAT 58.064 50.000 0.00 0.00 45.82 3.96
3881 3975 1.824230 AGACTGACTCCTGTCTGCATC 59.176 52.381 0.00 0.00 45.82 3.91
3882 3976 1.824230 GACTGACTCCTGTCTGCATCT 59.176 52.381 0.00 0.00 43.21 2.90
3883 3977 3.020274 GACTGACTCCTGTCTGCATCTA 58.980 50.000 0.00 0.00 43.21 1.98
3884 3978 2.757868 ACTGACTCCTGTCTGCATCTAC 59.242 50.000 0.00 0.00 43.21 2.59
3885 3979 3.023119 CTGACTCCTGTCTGCATCTACT 58.977 50.000 0.00 0.00 43.29 2.57
3886 3980 4.203226 CTGACTCCTGTCTGCATCTACTA 58.797 47.826 0.00 0.00 43.29 1.82
3887 3981 3.948473 TGACTCCTGTCTGCATCTACTAC 59.052 47.826 0.00 0.00 43.29 2.73
3888 3982 4.204012 GACTCCTGTCTGCATCTACTACT 58.796 47.826 0.00 0.00 39.94 2.57
3889 3983 5.104485 TGACTCCTGTCTGCATCTACTACTA 60.104 44.000 0.00 0.00 43.29 1.82
3890 3984 5.947663 ACTCCTGTCTGCATCTACTACTAT 58.052 41.667 0.00 0.00 0.00 2.12
3891 3985 6.001460 ACTCCTGTCTGCATCTACTACTATC 58.999 44.000 0.00 0.00 0.00 2.08
3892 3986 5.941788 TCCTGTCTGCATCTACTACTATCA 58.058 41.667 0.00 0.00 0.00 2.15
3893 3987 6.000840 TCCTGTCTGCATCTACTACTATCAG 58.999 44.000 0.00 0.00 0.00 2.90
3894 3988 5.767665 CCTGTCTGCATCTACTACTATCAGT 59.232 44.000 0.00 0.00 0.00 3.41
3895 3989 6.072728 CCTGTCTGCATCTACTACTATCAGTC 60.073 46.154 0.00 0.00 0.00 3.51
3896 3990 5.765677 TGTCTGCATCTACTACTATCAGTCC 59.234 44.000 0.00 0.00 0.00 3.85
3897 3991 5.765677 GTCTGCATCTACTACTATCAGTCCA 59.234 44.000 0.00 0.00 0.00 4.02
3898 3992 5.765677 TCTGCATCTACTACTATCAGTCCAC 59.234 44.000 0.00 0.00 0.00 4.02
3899 3993 5.445964 TGCATCTACTACTATCAGTCCACA 58.554 41.667 0.00 0.00 0.00 4.17
3900 3994 5.299531 TGCATCTACTACTATCAGTCCACAC 59.700 44.000 0.00 0.00 0.00 3.82
3901 3995 5.299531 GCATCTACTACTATCAGTCCACACA 59.700 44.000 0.00 0.00 0.00 3.72
3902 3996 6.015856 GCATCTACTACTATCAGTCCACACAT 60.016 42.308 0.00 0.00 0.00 3.21
3903 3997 7.589395 CATCTACTACTATCAGTCCACACATC 58.411 42.308 0.00 0.00 0.00 3.06
3904 3998 4.902443 ACTACTATCAGTCCACACATCG 57.098 45.455 0.00 0.00 0.00 3.84
3905 3999 4.524053 ACTACTATCAGTCCACACATCGA 58.476 43.478 0.00 0.00 0.00 3.59
3906 4000 3.784701 ACTATCAGTCCACACATCGAC 57.215 47.619 0.00 0.00 0.00 4.20
3907 4001 2.427453 ACTATCAGTCCACACATCGACC 59.573 50.000 0.00 0.00 0.00 4.79
3908 4002 0.173481 ATCAGTCCACACATCGACCG 59.827 55.000 0.00 0.00 0.00 4.79
3909 4003 2.094659 CAGTCCACACATCGACCGC 61.095 63.158 0.00 0.00 0.00 5.68
3910 4004 2.261671 GTCCACACATCGACCGCT 59.738 61.111 0.00 0.00 0.00 5.52
3911 4005 0.963856 AGTCCACACATCGACCGCTA 60.964 55.000 0.00 0.00 0.00 4.26
3912 4006 0.102481 GTCCACACATCGACCGCTAT 59.898 55.000 0.00 0.00 0.00 2.97
3913 4007 0.384309 TCCACACATCGACCGCTATC 59.616 55.000 0.00 0.00 0.00 2.08
3914 4008 0.597637 CCACACATCGACCGCTATCC 60.598 60.000 0.00 0.00 0.00 2.59
3915 4009 0.102300 CACACATCGACCGCTATCCA 59.898 55.000 0.00 0.00 0.00 3.41
3916 4010 0.385751 ACACATCGACCGCTATCCAG 59.614 55.000 0.00 0.00 0.00 3.86
3917 4011 0.668535 CACATCGACCGCTATCCAGA 59.331 55.000 0.00 0.00 0.00 3.86
3918 4012 1.067060 CACATCGACCGCTATCCAGAA 59.933 52.381 0.00 0.00 0.00 3.02
3919 4013 1.964223 ACATCGACCGCTATCCAGAAT 59.036 47.619 0.00 0.00 0.00 2.40
3920 4014 2.288457 ACATCGACCGCTATCCAGAATG 60.288 50.000 0.00 0.00 0.00 2.67
3921 4015 0.032130 TCGACCGCTATCCAGAATGC 59.968 55.000 0.00 0.00 31.97 3.56
3922 4016 0.249447 CGACCGCTATCCAGAATGCA 60.249 55.000 0.00 0.00 31.97 3.96
3923 4017 1.606480 CGACCGCTATCCAGAATGCAT 60.606 52.381 0.00 0.00 31.97 3.96
3924 4018 2.072298 GACCGCTATCCAGAATGCATC 58.928 52.381 0.00 0.00 31.97 3.91
3925 4019 1.696336 ACCGCTATCCAGAATGCATCT 59.304 47.619 0.00 0.00 39.68 2.90
3926 4020 2.899900 ACCGCTATCCAGAATGCATCTA 59.100 45.455 0.00 0.00 36.32 1.98
3927 4021 3.056250 ACCGCTATCCAGAATGCATCTAG 60.056 47.826 0.00 0.00 36.32 2.43
3928 4022 3.194329 CCGCTATCCAGAATGCATCTAGA 59.806 47.826 0.00 0.00 36.32 2.43
3929 4023 4.422840 CGCTATCCAGAATGCATCTAGAG 58.577 47.826 0.00 0.00 36.32 2.43
3930 4024 4.082300 CGCTATCCAGAATGCATCTAGAGT 60.082 45.833 0.00 0.00 36.32 3.24
3931 4025 5.124617 CGCTATCCAGAATGCATCTAGAGTA 59.875 44.000 0.00 0.00 36.32 2.59
3932 4026 6.183360 CGCTATCCAGAATGCATCTAGAGTAT 60.183 42.308 0.00 0.00 36.32 2.12
3933 4027 7.555087 GCTATCCAGAATGCATCTAGAGTATT 58.445 38.462 0.00 2.25 36.32 1.89
3934 4028 8.690884 GCTATCCAGAATGCATCTAGAGTATTA 58.309 37.037 0.00 0.00 36.32 0.98
3937 4031 8.484214 TCCAGAATGCATCTAGAGTATTAAGT 57.516 34.615 0.00 0.00 36.32 2.24
3938 4032 8.928448 TCCAGAATGCATCTAGAGTATTAAGTT 58.072 33.333 0.00 0.00 36.32 2.66
3939 4033 9.202273 CCAGAATGCATCTAGAGTATTAAGTTC 57.798 37.037 0.00 0.00 36.32 3.01
3940 4034 9.755804 CAGAATGCATCTAGAGTATTAAGTTCA 57.244 33.333 0.00 0.00 36.32 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.036294 ACTTCACTTCCTAAGCGGGC 60.036 55.000 0.00 0.00 0.00 6.13
47 48 2.932614 CCATCACTTCACTTCCTAAGCG 59.067 50.000 0.00 0.00 0.00 4.68
48 49 2.680339 GCCATCACTTCACTTCCTAAGC 59.320 50.000 0.00 0.00 0.00 3.09
114 115 6.254373 GCTTGCAGGTAAATTGCTAGATTTTC 59.746 38.462 11.71 0.00 43.83 2.29
119 120 3.440173 GTGCTTGCAGGTAAATTGCTAGA 59.560 43.478 11.71 0.00 43.83 2.43
126 127 5.782893 TTTTAGTGTGCTTGCAGGTAAAT 57.217 34.783 0.00 0.00 0.00 1.40
144 145 1.033574 CCCGGCCAAGTGTGTTTTTA 58.966 50.000 2.24 0.00 0.00 1.52
162 163 2.608090 GTCTACAAGATGGCGCTTAACC 59.392 50.000 7.64 0.00 0.00 2.85
166 167 0.107654 GGGTCTACAAGATGGCGCTT 60.108 55.000 7.64 0.00 0.00 4.68
170 171 0.105039 CTCCGGGTCTACAAGATGGC 59.895 60.000 0.00 0.00 0.00 4.40
171 172 1.776662 TCTCCGGGTCTACAAGATGG 58.223 55.000 0.00 0.00 0.00 3.51
211 212 0.596083 CGCCCTCGCTACTTGATGAG 60.596 60.000 0.00 0.00 0.00 2.90
249 250 4.202000 CCATTTTTGCGTATGTGGCATCTA 60.202 41.667 0.00 0.00 40.62 1.98
263 264 2.166821 TGCCACATCACCATTTTTGC 57.833 45.000 0.00 0.00 0.00 3.68
264 265 4.378774 TCTTTGCCACATCACCATTTTTG 58.621 39.130 0.00 0.00 0.00 2.44
324 325 4.511454 TGGAAAGCGCTATGTGATGATAAC 59.489 41.667 12.05 0.00 0.00 1.89
334 335 7.915397 ACTTAATTTGTATTGGAAAGCGCTATG 59.085 33.333 12.05 0.00 0.00 2.23
375 376 6.041637 AGGCGTGGTAATATAGATGTCTTCAA 59.958 38.462 0.00 0.00 0.00 2.69
396 397 8.360325 TGTGTATGTTATTAACTTCATAGGCG 57.640 34.615 7.99 0.00 0.00 5.52
462 463 7.901322 TCCATTCCATATTAGGCTAGTCATAGT 59.099 37.037 0.00 0.00 0.00 2.12
506 507 0.323629 TCTCACGGAAATGGACCCAC 59.676 55.000 0.00 0.00 0.00 4.61
507 508 1.285280 ATCTCACGGAAATGGACCCA 58.715 50.000 0.00 0.00 0.00 4.51
508 509 2.017049 CAATCTCACGGAAATGGACCC 58.983 52.381 0.00 0.00 0.00 4.46
521 522 5.643348 AGATATTCAAACGCACACAATCTCA 59.357 36.000 0.00 0.00 0.00 3.27
543 544 5.809001 AGAAATTTCAGTCCACTATGCAGA 58.191 37.500 19.99 0.00 0.00 4.26
562 563 6.294342 CCTGATTGCTCATTTGAGTCAAGAAA 60.294 38.462 5.56 0.00 43.85 2.52
607 608 8.368668 ACCTCTCTTTTAACCATCCGATAATAG 58.631 37.037 0.00 0.00 0.00 1.73
710 712 1.654023 CGGCGGTTTCCATTCTTCCC 61.654 60.000 0.00 0.00 0.00 3.97
856 858 2.175202 TGGGGAATGCGCTAATTTTGT 58.825 42.857 9.73 0.00 0.00 2.83
1185 1187 3.263503 CTTGCCGGTGTCGTCGAGA 62.264 63.158 1.90 0.00 27.94 4.04
1365 1367 2.434884 AGGTCATCGCCAGCGTTG 60.435 61.111 15.16 15.16 40.74 4.10
1371 1373 1.522092 GTCATCCAGGTCATCGCCA 59.478 57.895 0.00 0.00 0.00 5.69
1410 1412 1.992834 TATGGGCTCGTTCTGGGCA 60.993 57.895 0.00 0.00 0.00 5.36
1428 1430 1.273495 TGCTCCCAGATGAGGAAGAGT 60.273 52.381 0.00 0.00 31.49 3.24
1542 1544 1.678627 CCGTCCTCTTCGATGATGAGT 59.321 52.381 6.55 0.00 33.68 3.41
1842 1844 2.917227 TGCTCCTGCACCGTCTCA 60.917 61.111 0.00 0.00 45.31 3.27
2024 2029 3.671723 CGACAGCGGCGTTACTAC 58.328 61.111 9.37 0.00 0.00 2.73
2505 2510 1.512996 GCGACATGATGCAGGGGATG 61.513 60.000 0.00 0.00 0.00 3.51
2658 2663 0.037605 GGTCCACGTGGAGGTAGTTG 60.038 60.000 37.04 6.94 46.49 3.16
2730 2735 1.517832 CACCTGCTCCCCGAAGTAG 59.482 63.158 0.00 0.00 0.00 2.57
2864 2869 1.148273 AACGTGTCCTGCACCATGT 59.852 52.632 0.00 0.00 44.97 3.21
3323 3348 4.399618 TGAGAGTACAAGATGCTACACTCC 59.600 45.833 0.00 0.00 34.33 3.85
3328 3353 6.256757 GGTGAAATGAGAGTACAAGATGCTAC 59.743 42.308 0.00 0.00 0.00 3.58
3416 3441 9.252635 ACATAGATATGCAGAGATGATACTGAA 57.747 33.333 7.44 0.00 37.19 3.02
3501 3590 3.196463 TGTTCGTGGCTTTCGTCTAAAA 58.804 40.909 0.00 0.00 0.00 1.52
3543 3632 1.065551 GCCTTATTGGTGCGGCTTTAG 59.934 52.381 0.00 0.00 39.42 1.85
3546 3635 2.052104 GGCCTTATTGGTGCGGCTT 61.052 57.895 0.00 0.00 42.13 4.35
3551 3640 4.736126 AACTAATTGGCCTTATTGGTGC 57.264 40.909 16.67 0.00 38.35 5.01
3554 3643 6.756542 GCTTTGTAACTAATTGGCCTTATTGG 59.243 38.462 3.32 8.56 39.35 3.16
3570 3659 7.913297 TGTTTTGTAATCAGTGAGCTTTGTAAC 59.087 33.333 0.00 0.00 0.00 2.50
3575 3664 6.476706 GCTTTGTTTTGTAATCAGTGAGCTTT 59.523 34.615 0.00 0.00 0.00 3.51
3641 3730 2.707039 CGCGCGATAAGGGGTTTG 59.293 61.111 28.94 0.00 0.00 2.93
3643 3732 3.463585 TCCGCGCGATAAGGGGTT 61.464 61.111 34.63 0.00 41.75 4.11
3646 3735 4.963428 GGGTCCGCGCGATAAGGG 62.963 72.222 34.63 13.91 0.00 3.95
3647 3736 2.079020 TAAGGGTCCGCGCGATAAGG 62.079 60.000 34.63 14.77 0.00 2.69
3648 3737 0.249155 TTAAGGGTCCGCGCGATAAG 60.249 55.000 34.63 15.21 0.00 1.73
3649 3738 0.175302 TTTAAGGGTCCGCGCGATAA 59.825 50.000 34.63 13.87 0.00 1.75
3657 3748 4.034742 CCACATAACGATTTTAAGGGTCCG 59.965 45.833 0.00 0.00 0.00 4.79
3662 3753 3.697045 TGGCCCACATAACGATTTTAAGG 59.303 43.478 0.00 0.00 0.00 2.69
3678 3769 1.859302 AAACACACTTTCTTGGCCCA 58.141 45.000 0.00 0.00 0.00 5.36
3684 3775 6.844097 TTGTCCCTTAAAACACACTTTCTT 57.156 33.333 0.00 0.00 0.00 2.52
3690 3781 6.640907 CAGCTAAATTGTCCCTTAAAACACAC 59.359 38.462 0.00 0.00 0.00 3.82
3691 3782 6.737346 GCAGCTAAATTGTCCCTTAAAACACA 60.737 38.462 0.00 0.00 0.00 3.72
3704 3796 2.223923 TGTTTTGCCGCAGCTAAATTGT 60.224 40.909 4.87 0.00 43.78 2.71
3716 3809 4.522722 TTATAAGGGGTTTGTTTTGCCG 57.477 40.909 0.00 0.00 0.00 5.69
3720 3813 6.790461 AGGGTTGATTATAAGGGGTTTGTTTT 59.210 34.615 0.00 0.00 0.00 2.43
3721 3814 6.327781 AGGGTTGATTATAAGGGGTTTGTTT 58.672 36.000 0.00 0.00 0.00 2.83
3754 3848 7.696017 AGGTGGCGGGTATATTTAAAGAATAT 58.304 34.615 0.00 0.00 0.00 1.28
3761 3855 2.548493 GCGAGGTGGCGGGTATATTTAA 60.548 50.000 0.00 0.00 0.00 1.52
3782 3876 4.899239 GCGGTGCATCGAGGGAGG 62.899 72.222 26.37 0.00 0.00 4.30
3805 3899 1.923395 AAGGGAGGATTGGTGGCGA 60.923 57.895 0.00 0.00 0.00 5.54
3842 3936 1.813178 CTACTTGTCGAGAGAGGCACA 59.187 52.381 2.93 0.00 43.49 4.57
3866 3960 4.204012 AGTAGTAGATGCAGACAGGAGTC 58.796 47.826 0.00 0.00 45.31 3.36
3867 3961 4.243793 AGTAGTAGATGCAGACAGGAGT 57.756 45.455 0.00 0.00 0.00 3.85
3868 3962 6.000840 TGATAGTAGTAGATGCAGACAGGAG 58.999 44.000 0.00 0.00 0.00 3.69
3869 3963 5.941788 TGATAGTAGTAGATGCAGACAGGA 58.058 41.667 0.00 0.00 0.00 3.86
3870 3964 5.767665 ACTGATAGTAGTAGATGCAGACAGG 59.232 44.000 0.00 0.00 0.00 4.00
3871 3965 6.072728 GGACTGATAGTAGTAGATGCAGACAG 60.073 46.154 0.00 0.00 0.00 3.51
3872 3966 5.765677 GGACTGATAGTAGTAGATGCAGACA 59.234 44.000 0.00 0.00 0.00 3.41
3873 3967 5.765677 TGGACTGATAGTAGTAGATGCAGAC 59.234 44.000 0.00 0.00 0.00 3.51
3874 3968 5.765677 GTGGACTGATAGTAGTAGATGCAGA 59.234 44.000 0.00 0.00 0.00 4.26
3875 3969 5.532779 TGTGGACTGATAGTAGTAGATGCAG 59.467 44.000 0.00 0.00 0.00 4.41
3876 3970 5.299531 GTGTGGACTGATAGTAGTAGATGCA 59.700 44.000 0.00 0.00 0.00 3.96
3877 3971 5.299531 TGTGTGGACTGATAGTAGTAGATGC 59.700 44.000 0.00 0.00 0.00 3.91
3878 3972 6.944234 TGTGTGGACTGATAGTAGTAGATG 57.056 41.667 0.00 0.00 0.00 2.90
3879 3973 6.428465 CGATGTGTGGACTGATAGTAGTAGAT 59.572 42.308 0.00 0.00 0.00 1.98
3880 3974 5.758784 CGATGTGTGGACTGATAGTAGTAGA 59.241 44.000 0.00 0.00 0.00 2.59
3881 3975 5.758784 TCGATGTGTGGACTGATAGTAGTAG 59.241 44.000 0.00 0.00 0.00 2.57
3882 3976 5.526479 GTCGATGTGTGGACTGATAGTAGTA 59.474 44.000 0.00 0.00 31.18 1.82
3883 3977 4.335874 GTCGATGTGTGGACTGATAGTAGT 59.664 45.833 0.00 0.00 31.18 2.73
3884 3978 4.261238 GGTCGATGTGTGGACTGATAGTAG 60.261 50.000 0.00 0.00 33.98 2.57
3885 3979 3.630769 GGTCGATGTGTGGACTGATAGTA 59.369 47.826 0.00 0.00 33.98 1.82
3886 3980 2.427453 GGTCGATGTGTGGACTGATAGT 59.573 50.000 0.00 0.00 33.98 2.12
3887 3981 2.541794 CGGTCGATGTGTGGACTGATAG 60.542 54.545 0.00 0.00 40.67 2.08
3888 3982 1.404035 CGGTCGATGTGTGGACTGATA 59.596 52.381 0.00 0.00 40.67 2.15
3889 3983 0.173481 CGGTCGATGTGTGGACTGAT 59.827 55.000 0.00 0.00 40.67 2.90
3890 3984 1.584495 CGGTCGATGTGTGGACTGA 59.416 57.895 0.00 0.00 40.67 3.41
3891 3985 2.094659 GCGGTCGATGTGTGGACTG 61.095 63.158 0.00 0.00 41.02 3.51
3892 3986 0.963856 TAGCGGTCGATGTGTGGACT 60.964 55.000 0.00 0.00 33.98 3.85
3893 3987 0.102481 ATAGCGGTCGATGTGTGGAC 59.898 55.000 0.00 0.00 32.86 4.02
3894 3988 0.384309 GATAGCGGTCGATGTGTGGA 59.616 55.000 0.00 0.00 0.00 4.02
3895 3989 0.597637 GGATAGCGGTCGATGTGTGG 60.598 60.000 0.00 0.00 0.00 4.17
3896 3990 0.102300 TGGATAGCGGTCGATGTGTG 59.898 55.000 0.00 0.00 0.00 3.82
3897 3991 0.385751 CTGGATAGCGGTCGATGTGT 59.614 55.000 0.00 0.00 0.00 3.72
3898 3992 0.668535 TCTGGATAGCGGTCGATGTG 59.331 55.000 0.00 0.00 0.00 3.21
3899 3993 1.399714 TTCTGGATAGCGGTCGATGT 58.600 50.000 0.00 0.00 0.00 3.06
3900 3994 2.332104 CATTCTGGATAGCGGTCGATG 58.668 52.381 0.00 0.00 0.00 3.84
3901 3995 1.337260 GCATTCTGGATAGCGGTCGAT 60.337 52.381 0.00 0.00 0.00 3.59
3902 3996 0.032130 GCATTCTGGATAGCGGTCGA 59.968 55.000 0.00 0.00 0.00 4.20
3903 3997 0.249447 TGCATTCTGGATAGCGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
3904 3998 2.072298 GATGCATTCTGGATAGCGGTC 58.928 52.381 0.00 0.00 0.00 4.79
3905 3999 1.696336 AGATGCATTCTGGATAGCGGT 59.304 47.619 0.00 0.00 31.79 5.68
3906 4000 2.469274 AGATGCATTCTGGATAGCGG 57.531 50.000 0.00 0.00 31.79 5.52
3907 4001 4.082300 ACTCTAGATGCATTCTGGATAGCG 60.082 45.833 0.00 0.00 40.73 4.26
3908 4002 5.404466 ACTCTAGATGCATTCTGGATAGC 57.596 43.478 0.00 0.00 40.73 2.97
3911 4005 9.099071 ACTTAATACTCTAGATGCATTCTGGAT 57.901 33.333 0.00 1.48 40.73 3.41
3912 4006 8.484214 ACTTAATACTCTAGATGCATTCTGGA 57.516 34.615 0.00 6.36 39.43 3.86
3913 4007 9.202273 GAACTTAATACTCTAGATGCATTCTGG 57.798 37.037 0.00 1.94 35.79 3.86
3914 4008 9.755804 TGAACTTAATACTCTAGATGCATTCTG 57.244 33.333 0.00 0.00 35.79 3.02


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

AutoCloner maintained by Alex Coulton.