Multiple sequence alignment - TraesCS5D01G080600

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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 TraesCS5D01G080600 chr5D 100.000 3465 0 0 1 3465 80435765 80439229 0.000000e+00 6399
1 TraesCS5D01G080600 chr5D 95.266 169 8 0 3297 3465 560286125 560286293 5.700000e-68 268
2 TraesCS5D01G080600 chr5D 95.758 165 7 0 3301 3465 319751590 319751426 2.050000e-67 267
3 TraesCS5D01G080600 chr5B 94.958 3114 94 24 233 3303 89304134 89307227 0.000000e+00 4822
4 TraesCS5D01G080600 chr5B 89.328 253 20 5 1 253 89303288 89303533 9.340000e-81 311
5 TraesCS5D01G080600 chr5A 94.807 2311 58 18 439 2711 76955263 76957549 0.000000e+00 3546
6 TraesCS5D01G080600 chr5A 95.745 564 8 8 2748 3303 76957556 76958111 0.000000e+00 894
7 TraesCS5D01G080600 chr5A 92.308 130 10 0 313 442 76953483 76953612 5.910000e-43 185
8 TraesCS5D01G080600 chr1A 94.780 1226 42 6 1229 2448 508205178 508203969 0.000000e+00 1890
9 TraesCS5D01G080600 chr1A 94.061 623 24 4 1554 2171 588667253 588667867 0.000000e+00 933
10 TraesCS5D01G080600 chr2A 94.223 1229 46 8 1229 2448 651807095 651805883 0.000000e+00 1853
11 TraesCS5D01G080600 chr6A 93.922 1234 45 11 1229 2448 558037092 558038309 0.000000e+00 1836
12 TraesCS5D01G080600 chr4B 88.838 654 61 7 1445 2097 580890499 580889857 0.000000e+00 793
13 TraesCS5D01G080600 chr7D 89.752 605 47 6 1494 2097 599758650 599758060 0.000000e+00 760
14 TraesCS5D01G080600 chr6D 89.535 602 48 6 1494 2094 47298814 47299401 0.000000e+00 749
15 TraesCS5D01G080600 chr4D 96.364 165 6 0 3301 3465 487284282 487284446 4.410000e-69 272
16 TraesCS5D01G080600 chr4D 93.714 175 10 1 3291 3465 426600290 426600463 9.540000e-66 261
17 TraesCS5D01G080600 chr3D 96.364 165 6 0 3301 3465 14804171 14804335 4.410000e-69 272
18 TraesCS5D01G080600 chr2D 95.833 168 7 0 3298 3465 538954845 538955012 4.410000e-69 272
19 TraesCS5D01G080600 chr2D 95.808 167 7 0 3299 3465 314360785 314360619 1.580000e-68 270
20 TraesCS5D01G080600 chr2D 95.266 169 8 0 3297 3465 555391570 555391402 5.700000e-68 268
21 TraesCS5D01G080600 chr3B 95.238 168 8 0 3298 3465 9107371 9107204 2.050000e-67 267


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 TraesCS5D01G080600 chr5D 80435765 80439229 3464 False 6399.000000 6399 100.000000 1 3465 1 chr5D.!!$F1 3464
1 TraesCS5D01G080600 chr5B 89303288 89307227 3939 False 2566.500000 4822 92.143000 1 3303 2 chr5B.!!$F1 3302
2 TraesCS5D01G080600 chr5A 76953483 76958111 4628 False 1541.666667 3546 94.286667 313 3303 3 chr5A.!!$F1 2990
3 TraesCS5D01G080600 chr1A 508203969 508205178 1209 True 1890.000000 1890 94.780000 1229 2448 1 chr1A.!!$R1 1219
4 TraesCS5D01G080600 chr1A 588667253 588667867 614 False 933.000000 933 94.061000 1554 2171 1 chr1A.!!$F1 617
5 TraesCS5D01G080600 chr2A 651805883 651807095 1212 True 1853.000000 1853 94.223000 1229 2448 1 chr2A.!!$R1 1219
6 TraesCS5D01G080600 chr6A 558037092 558038309 1217 False 1836.000000 1836 93.922000 1229 2448 1 chr6A.!!$F1 1219
7 TraesCS5D01G080600 chr4B 580889857 580890499 642 True 793.000000 793 88.838000 1445 2097 1 chr4B.!!$R1 652
8 TraesCS5D01G080600 chr7D 599758060 599758650 590 True 760.000000 760 89.752000 1494 2097 1 chr7D.!!$R1 603
9 TraesCS5D01G080600 chr6D 47298814 47299401 587 False 749.000000 749 89.535000 1494 2094 1 chr6D.!!$F1 600

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
28 29 0.178975 CAGAGGCCGGGATACTCTCT 60.179 60.0 2.18 6.09 39.44 3.1 F
994 3321 0.315886 TTGCAGTAACGAGAGGCGAA 59.684 50.0 0.00 0.00 44.57 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 3705 1.244019 GCAAATCAGGTGCCGGTTCT 61.244 55.000 1.9 0.0 35.91 3.01 R
2771 5137 1.893808 GGCATCCACCACTATGGCG 60.894 63.158 0.0 0.0 42.67 5.69 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
18 19 2.184830 CATGTGATGCAGAGGCCGG 61.185 63.158 0.00 0.00 40.13 6.13
24 25 1.460305 ATGCAGAGGCCGGGATACT 60.460 57.895 2.18 0.00 40.13 2.12
28 29 0.178975 CAGAGGCCGGGATACTCTCT 60.179 60.000 2.18 6.09 39.44 3.10
77 78 8.709308 ACCTTATGATTCTTGCTCTATTAGTGT 58.291 33.333 0.00 0.00 0.00 3.55
81 82 8.885494 ATGATTCTTGCTCTATTAGTGTCTTC 57.115 34.615 0.00 0.00 0.00 2.87
119 120 2.938451 TCTCATAATGCACGCAAAGAGG 59.062 45.455 0.00 0.00 0.00 3.69
120 121 2.679837 CTCATAATGCACGCAAAGAGGT 59.320 45.455 0.00 0.00 0.00 3.85
127 128 3.932822 TGCACGCAAAGAGGTAATCTAA 58.067 40.909 0.00 0.00 37.23 2.10
128 129 3.932710 TGCACGCAAAGAGGTAATCTAAG 59.067 43.478 0.00 0.00 37.23 2.18
131 132 4.268884 CACGCAAAGAGGTAATCTAAGAGC 59.731 45.833 0.00 0.00 37.23 4.09
135 136 2.667470 AGAGGTAATCTAAGAGCGGCA 58.333 47.619 1.45 0.00 36.10 5.69
151 152 2.217112 GCAGTCGCGCCTAATACAG 58.783 57.895 0.00 0.00 0.00 2.74
154 155 1.067582 GTCGCGCCTAATACAGCCT 59.932 57.895 0.00 0.00 0.00 4.58
164 165 4.489810 CCTAATACAGCCTGATCACGATC 58.510 47.826 0.00 0.00 38.29 3.69
205 206 9.158364 CGATGACTATTTTCATTTGAATTACGG 57.842 33.333 0.00 0.00 36.30 4.02
218 219 9.816354 CATTTGAATTACGGGATTTTTAGGATT 57.184 29.630 0.00 0.00 0.00 3.01
387 1022 6.164176 TCATCCTTTTCTTCTACCGAGAAAC 58.836 40.000 0.00 0.00 41.42 2.78
391 1026 5.758784 CCTTTTCTTCTACCGAGAAACAACT 59.241 40.000 0.00 0.00 41.42 3.16
404 1039 5.086888 AGAAACAACTAAAGTTAACCGCG 57.913 39.130 0.00 0.00 36.32 6.46
532 2822 1.948145 CCTAGGCGACCACAGTACTAG 59.052 57.143 0.00 0.00 0.00 2.57
701 3025 3.722908 TCCCGTTGGATTTAACCATCA 57.277 42.857 0.00 0.00 39.82 3.07
719 3043 4.809426 CCATCACCGTAACTATCCAAGAAC 59.191 45.833 0.00 0.00 0.00 3.01
752 3076 2.105323 GGCACGTGAAAAGAACAGTG 57.895 50.000 22.23 0.00 0.00 3.66
796 3120 6.312918 TGATGAAACGAGAGGCACTTAAATAC 59.687 38.462 0.00 0.00 41.55 1.89
994 3321 0.315886 TTGCAGTAACGAGAGGCGAA 59.684 50.000 0.00 0.00 44.57 4.70
1113 3440 1.514443 CGACGGCGACCTCTTCTTC 60.514 63.158 16.62 0.00 40.82 2.87
1119 3446 2.478200 CGGCGACCTCTTCTTCTTCTAC 60.478 54.545 0.00 0.00 0.00 2.59
1120 3447 2.756207 GGCGACCTCTTCTTCTTCTACT 59.244 50.000 0.00 0.00 0.00 2.57
1121 3448 3.181494 GGCGACCTCTTCTTCTTCTACTC 60.181 52.174 0.00 0.00 0.00 2.59
1378 3705 0.821517 ATCGGTCACTGACGCCATTA 59.178 50.000 3.04 0.00 32.65 1.90
1514 3841 3.620419 ATCAATCACCGCACCGCCA 62.620 57.895 0.00 0.00 0.00 5.69
1579 3914 2.731587 GATGTGGTTGTGTGCGTGCC 62.732 60.000 0.00 0.00 0.00 5.01
1580 3915 3.209097 GTGGTTGTGTGCGTGCCT 61.209 61.111 0.00 0.00 0.00 4.75
1581 3916 2.439338 TGGTTGTGTGCGTGCCTT 60.439 55.556 0.00 0.00 0.00 4.35
1582 3917 2.026014 GGTTGTGTGCGTGCCTTG 59.974 61.111 0.00 0.00 0.00 3.61
1583 3918 2.026014 GTTGTGTGCGTGCCTTGG 59.974 61.111 0.00 0.00 0.00 3.61
1584 3919 2.439338 TTGTGTGCGTGCCTTGGT 60.439 55.556 0.00 0.00 0.00 3.67
1585 3920 2.769539 TTGTGTGCGTGCCTTGGTG 61.770 57.895 0.00 0.00 0.00 4.17
1586 3921 4.629115 GTGTGCGTGCCTTGGTGC 62.629 66.667 0.00 0.00 0.00 5.01
1927 4271 3.366396 AGGTCATCTTCGTCCTACACAT 58.634 45.455 0.00 0.00 0.00 3.21
2148 4493 4.142403 TGAGAAGGTTTCTTGCACAAACTG 60.142 41.667 16.39 0.00 40.87 3.16
2179 4540 6.127535 CCCTTTTGCATCACTTTGATCATAGT 60.128 38.462 12.47 12.47 34.28 2.12
2180 4541 7.067372 CCCTTTTGCATCACTTTGATCATAGTA 59.933 37.037 17.05 7.85 34.28 1.82
2181 4542 7.912250 CCTTTTGCATCACTTTGATCATAGTAC 59.088 37.037 17.05 8.92 34.28 2.73
2293 4654 0.321564 TGATGGTTGGCGACTTGAGG 60.322 55.000 4.59 0.00 0.00 3.86
2572 4936 8.401046 TGTTCAAATTTGTTTAGGTTCTTTCG 57.599 30.769 17.47 0.00 0.00 3.46
2577 4943 2.223745 TGTTTAGGTTCTTTCGGCCAC 58.776 47.619 2.24 0.00 0.00 5.01
2636 5002 1.177401 GATTGGTTTGTGAGAGGGGC 58.823 55.000 0.00 0.00 0.00 5.80
2771 5137 4.744631 CCAAATCTGCACTGTTTTTGGTAC 59.255 41.667 10.65 0.00 40.77 3.34
2796 5163 4.321718 CATAGTGGTGGATGCCATCTTAG 58.678 47.826 4.41 0.00 41.08 2.18
2915 5285 3.606595 AGTGGATGTGTGATCAGTGAG 57.393 47.619 0.00 0.00 0.00 3.51
2916 5286 2.235650 AGTGGATGTGTGATCAGTGAGG 59.764 50.000 0.00 0.00 0.00 3.86
2917 5287 2.234661 GTGGATGTGTGATCAGTGAGGA 59.765 50.000 0.00 0.00 0.00 3.71
2986 5356 4.098654 TGGGTTACATTGGTTTGTGACAAG 59.901 41.667 0.00 0.00 37.72 3.16
3071 5441 5.346551 CAGATTGGTGCATTTTGTGTATGTG 59.653 40.000 0.00 0.00 0.00 3.21
3075 5445 4.580580 TGGTGCATTTTGTGTATGTGTGTA 59.419 37.500 0.00 0.00 0.00 2.90
3082 5452 4.354071 TTGTGTATGTGTGTATGCATGC 57.646 40.909 11.82 11.82 0.00 4.06
3083 5453 3.341823 TGTGTATGTGTGTATGCATGCA 58.658 40.909 25.04 25.04 35.84 3.96
3084 5454 3.946558 TGTGTATGTGTGTATGCATGCAT 59.053 39.130 33.92 33.92 39.23 3.96
3085 5455 4.201930 TGTGTATGTGTGTATGCATGCATG 60.202 41.667 37.43 22.70 39.23 4.06
3134 5513 0.035725 TGATCAGTTCTGCTGCAGGG 60.036 55.000 27.79 15.50 44.66 4.45
3153 5532 3.007182 AGGGTTTTCAGTGCCATTCATTG 59.993 43.478 0.00 0.00 34.12 2.82
3178 5557 2.352127 GCTGTGCCAATGTTTTCTCCTC 60.352 50.000 0.00 0.00 0.00 3.71
3310 5690 9.726438 ATTAGTGAACTAACAATAAGAGCAACT 57.274 29.630 5.08 0.00 40.81 3.16
3311 5691 7.659652 AGTGAACTAACAATAAGAGCAACTC 57.340 36.000 0.00 0.00 0.00 3.01
3312 5692 6.651225 AGTGAACTAACAATAAGAGCAACTCC 59.349 38.462 0.00 0.00 0.00 3.85
3313 5693 6.426937 GTGAACTAACAATAAGAGCAACTCCA 59.573 38.462 0.00 0.00 0.00 3.86
3314 5694 6.995686 TGAACTAACAATAAGAGCAACTCCAA 59.004 34.615 0.00 0.00 0.00 3.53
3315 5695 6.803154 ACTAACAATAAGAGCAACTCCAAC 57.197 37.500 0.00 0.00 0.00 3.77
3316 5696 4.749245 AACAATAAGAGCAACTCCAACG 57.251 40.909 0.00 0.00 0.00 4.10
3317 5697 3.074412 ACAATAAGAGCAACTCCAACGG 58.926 45.455 0.00 0.00 0.00 4.44
3318 5698 2.403252 ATAAGAGCAACTCCAACGGG 57.597 50.000 0.00 0.00 0.00 5.28
3319 5699 0.321298 TAAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
3320 5700 3.056328 GAGCAACTCCAACGGGCC 61.056 66.667 0.00 0.00 0.00 5.80
3323 5703 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
3324 5704 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
3338 5718 2.031465 GACCCAAAAGGACGGCGA 59.969 61.111 16.62 0.00 39.89 5.54
3339 5719 1.376812 GACCCAAAAGGACGGCGAT 60.377 57.895 16.62 0.00 39.89 4.58
3340 5720 0.958876 GACCCAAAAGGACGGCGATT 60.959 55.000 16.62 1.89 39.89 3.34
3341 5721 0.538746 ACCCAAAAGGACGGCGATTT 60.539 50.000 16.62 8.82 39.89 2.17
3342 5722 0.170339 CCCAAAAGGACGGCGATTTC 59.830 55.000 16.62 0.00 38.24 2.17
3343 5723 0.179200 CCAAAAGGACGGCGATTTCG 60.179 55.000 16.62 0.74 43.27 3.46
3344 5724 0.515564 CAAAAGGACGGCGATTTCGT 59.484 50.000 16.62 0.00 44.03 3.85
3353 5733 3.378013 GCGATTTCGTCCGCTTTTT 57.622 47.368 0.00 0.00 46.96 1.94
3354 5734 0.974836 GCGATTTCGTCCGCTTTTTG 59.025 50.000 0.00 0.00 46.96 2.44
3355 5735 1.662026 GCGATTTCGTCCGCTTTTTGT 60.662 47.619 0.00 0.00 46.96 2.83
3356 5736 2.230864 CGATTTCGTCCGCTTTTTGTC 58.769 47.619 0.00 0.00 34.11 3.18
3357 5737 2.581637 GATTTCGTCCGCTTTTTGTCC 58.418 47.619 0.00 0.00 0.00 4.02
3358 5738 1.380524 TTTCGTCCGCTTTTTGTCCA 58.619 45.000 0.00 0.00 0.00 4.02
3359 5739 1.600023 TTCGTCCGCTTTTTGTCCAT 58.400 45.000 0.00 0.00 0.00 3.41
3360 5740 1.600023 TCGTCCGCTTTTTGTCCATT 58.400 45.000 0.00 0.00 0.00 3.16
3361 5741 1.950909 TCGTCCGCTTTTTGTCCATTT 59.049 42.857 0.00 0.00 0.00 2.32
3362 5742 2.050691 CGTCCGCTTTTTGTCCATTTG 58.949 47.619 0.00 0.00 0.00 2.32
3363 5743 2.403259 GTCCGCTTTTTGTCCATTTGG 58.597 47.619 0.00 0.00 0.00 3.28
3364 5744 1.342819 TCCGCTTTTTGTCCATTTGGG 59.657 47.619 0.00 0.00 35.41 4.12
3365 5745 1.069978 CCGCTTTTTGTCCATTTGGGT 59.930 47.619 0.00 0.00 38.11 4.51
3366 5746 2.403259 CGCTTTTTGTCCATTTGGGTC 58.597 47.619 0.00 0.00 38.11 4.46
3367 5747 2.403259 GCTTTTTGTCCATTTGGGTCG 58.597 47.619 0.00 0.00 38.11 4.79
3368 5748 2.866065 GCTTTTTGTCCATTTGGGTCGG 60.866 50.000 0.00 0.00 38.11 4.79
3369 5749 0.676736 TTTTGTCCATTTGGGTCGGC 59.323 50.000 0.00 0.00 38.11 5.54
3370 5750 1.182385 TTTGTCCATTTGGGTCGGCC 61.182 55.000 0.00 0.00 38.11 6.13
3371 5751 3.131478 GTCCATTTGGGTCGGCCG 61.131 66.667 22.12 22.12 38.11 6.13
3393 5773 4.636435 CCCGGTGTTCGCCCTGTT 62.636 66.667 0.00 0.00 37.59 3.16
3394 5774 2.593436 CCGGTGTTCGCCCTGTTT 60.593 61.111 0.00 0.00 37.59 2.83
3395 5775 2.190841 CCGGTGTTCGCCCTGTTTT 61.191 57.895 0.00 0.00 37.59 2.43
3396 5776 1.730451 CCGGTGTTCGCCCTGTTTTT 61.730 55.000 0.00 0.00 37.59 1.94
3397 5777 0.593773 CGGTGTTCGCCCTGTTTTTG 60.594 55.000 0.00 0.00 0.00 2.44
3398 5778 0.741915 GGTGTTCGCCCTGTTTTTGA 59.258 50.000 0.00 0.00 0.00 2.69
3399 5779 1.339929 GGTGTTCGCCCTGTTTTTGAT 59.660 47.619 0.00 0.00 0.00 2.57
3400 5780 2.554893 GGTGTTCGCCCTGTTTTTGATA 59.445 45.455 0.00 0.00 0.00 2.15
3401 5781 3.192633 GGTGTTCGCCCTGTTTTTGATAT 59.807 43.478 0.00 0.00 0.00 1.63
3402 5782 4.165779 GTGTTCGCCCTGTTTTTGATATG 58.834 43.478 0.00 0.00 0.00 1.78
3403 5783 3.192422 TGTTCGCCCTGTTTTTGATATGG 59.808 43.478 0.00 0.00 0.00 2.74
3404 5784 2.374184 TCGCCCTGTTTTTGATATGGG 58.626 47.619 0.00 0.00 37.76 4.00
3405 5785 2.099405 CGCCCTGTTTTTGATATGGGT 58.901 47.619 0.00 0.00 37.09 4.51
3406 5786 2.099098 CGCCCTGTTTTTGATATGGGTC 59.901 50.000 0.00 0.00 37.09 4.46
3407 5787 2.099098 GCCCTGTTTTTGATATGGGTCG 59.901 50.000 0.00 0.00 37.09 4.79
3408 5788 2.687935 CCCTGTTTTTGATATGGGTCGG 59.312 50.000 0.00 0.00 0.00 4.79
3409 5789 2.099098 CCTGTTTTTGATATGGGTCGGC 59.901 50.000 0.00 0.00 0.00 5.54
3410 5790 2.752354 CTGTTTTTGATATGGGTCGGCA 59.248 45.455 0.00 0.00 0.00 5.69
3411 5791 2.752354 TGTTTTTGATATGGGTCGGCAG 59.248 45.455 0.00 0.00 0.00 4.85
3412 5792 1.388547 TTTTGATATGGGTCGGCAGC 58.611 50.000 0.00 0.00 0.00 5.25
3413 5793 0.813610 TTTGATATGGGTCGGCAGCG 60.814 55.000 0.00 0.00 0.00 5.18
3414 5794 3.044305 GATATGGGTCGGCAGCGC 61.044 66.667 0.00 0.00 0.00 5.92
3415 5795 4.969196 ATATGGGTCGGCAGCGCG 62.969 66.667 0.00 0.00 0.00 6.86
3434 5814 4.823419 CCAACGCGCCGACCCATA 62.823 66.667 5.73 0.00 0.00 2.74
3435 5815 2.587753 CAACGCGCCGACCCATAT 60.588 61.111 5.73 0.00 0.00 1.78
3436 5816 2.587753 AACGCGCCGACCCATATG 60.588 61.111 5.73 0.00 0.00 1.78
3437 5817 3.379865 AACGCGCCGACCCATATGT 62.380 57.895 5.73 0.00 0.00 2.29
3438 5818 3.337889 CGCGCCGACCCATATGTG 61.338 66.667 0.00 0.00 0.00 3.21
3439 5819 3.649986 GCGCCGACCCATATGTGC 61.650 66.667 0.00 0.00 0.00 4.57
3440 5820 2.203001 CGCCGACCCATATGTGCA 60.203 61.111 1.24 0.00 0.00 4.57
3441 5821 1.817520 CGCCGACCCATATGTGCAA 60.818 57.895 1.24 0.00 0.00 4.08
3442 5822 1.775039 CGCCGACCCATATGTGCAAG 61.775 60.000 1.24 0.00 0.00 4.01
3443 5823 2.024918 CCGACCCATATGTGCAAGC 58.975 57.895 1.24 0.00 0.00 4.01
3444 5824 1.643292 CGACCCATATGTGCAAGCG 59.357 57.895 1.24 0.00 0.00 4.68
3445 5825 1.089481 CGACCCATATGTGCAAGCGT 61.089 55.000 1.24 0.00 0.00 5.07
3446 5826 0.378257 GACCCATATGTGCAAGCGTG 59.622 55.000 1.24 0.00 0.00 5.34
3447 5827 1.031571 ACCCATATGTGCAAGCGTGG 61.032 55.000 0.79 0.00 0.00 4.94
3448 5828 1.064621 CCATATGTGCAAGCGTGGC 59.935 57.895 0.79 0.00 0.00 5.01
3449 5829 1.064621 CATATGTGCAAGCGTGGCC 59.935 57.895 0.00 0.00 0.00 5.36
3450 5830 2.472059 ATATGTGCAAGCGTGGCCG 61.472 57.895 0.79 0.00 37.07 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.031277 GCAAGAATCATAAGGTTGATCAACTTT 58.969 33.333 30.99 30.99 42.20 2.66
41 42 7.395489 AGCAAGAATCATAAGGTTGATCAACTT 59.605 33.333 31.81 25.00 40.94 2.66
46 47 8.845413 ATAGAGCAAGAATCATAAGGTTGATC 57.155 34.615 0.00 0.00 35.29 2.92
57 58 8.072321 AGAAGACACTAATAGAGCAAGAATCA 57.928 34.615 0.00 0.00 0.00 2.57
63 64 9.190317 TCATTAGAGAAGACACTAATAGAGCAA 57.810 33.333 0.00 0.00 37.64 3.91
95 96 3.940852 TCTTTGCGTGCATTATGAGACAT 59.059 39.130 0.00 0.00 0.00 3.06
106 107 2.472695 AGATTACCTCTTTGCGTGCA 57.527 45.000 0.00 0.00 0.00 4.57
119 120 2.386249 CGACTGCCGCTCTTAGATTAC 58.614 52.381 0.00 0.00 0.00 1.89
120 121 2.776312 CGACTGCCGCTCTTAGATTA 57.224 50.000 0.00 0.00 0.00 1.75
135 136 1.067582 GGCTGTATTAGGCGCGACT 59.932 57.895 22.96 22.96 42.55 4.18
141 142 7.519808 TGATCGTGATCAGGCTGTATTAGGC 62.520 48.000 15.27 0.00 42.42 3.93
154 155 7.366513 GAGATGTCTCTTTATGATCGTGATCA 58.633 38.462 14.42 14.42 43.93 2.92
164 165 9.689976 AAATAGTCATCGAGATGTCTCTTTATG 57.310 33.333 14.23 8.73 40.75 1.90
231 232 9.817365 TTCATGTTGTTGTGTTTGTTTATTTTG 57.183 25.926 0.00 0.00 0.00 2.44
236 237 7.327275 GTCACTTCATGTTGTTGTGTTTGTTTA 59.673 33.333 0.00 0.00 0.00 2.01
252 871 6.564709 TTCTTGAATTCCAGTCACTTCATG 57.435 37.500 2.27 0.00 0.00 3.07
387 1022 8.223100 AGTTTATTACGCGGTTAACTTTAGTTG 58.777 33.333 12.47 0.00 38.90 3.16
391 1026 7.014702 GCAAGTTTATTACGCGGTTAACTTTA 58.985 34.615 12.47 0.00 34.59 1.85
432 1067 6.527423 AGGACGAAAAGAACTATGTGGTTTA 58.473 36.000 0.00 0.00 0.00 2.01
532 2822 4.579454 AACACATAATGGATGCTCATGC 57.421 40.909 0.00 0.00 39.39 4.06
653 2951 5.011840 GGGATGAGATGAGATTCATGAGTGA 59.988 44.000 0.00 0.00 37.20 3.41
654 2952 5.221661 TGGGATGAGATGAGATTCATGAGTG 60.222 44.000 0.00 0.00 37.20 3.51
655 2953 4.906060 TGGGATGAGATGAGATTCATGAGT 59.094 41.667 0.00 0.00 37.20 3.41
656 2954 5.485209 TGGGATGAGATGAGATTCATGAG 57.515 43.478 0.00 0.00 37.20 2.90
657 2955 6.449830 AATGGGATGAGATGAGATTCATGA 57.550 37.500 0.00 0.00 37.20 3.07
701 3025 2.417787 GGCGTTCTTGGATAGTTACGGT 60.418 50.000 0.00 0.00 35.26 4.83
768 3092 3.679389 AGTGCCTCTCGTTTCATCAAAT 58.321 40.909 0.00 0.00 0.00 2.32
914 3241 1.821136 GCTTAAGCAAGAAGCATGGGT 59.179 47.619 22.59 0.00 46.97 4.51
994 3321 3.933722 CATCCCCGGCATCTCGCT 61.934 66.667 0.00 0.00 41.91 4.93
1356 3683 2.579787 GCGTCAGTGACCGATCGG 60.580 66.667 32.20 32.20 42.03 4.18
1378 3705 1.244019 GCAAATCAGGTGCCGGTTCT 61.244 55.000 1.90 0.00 35.91 3.01
1514 3841 6.002082 AGAGAGGCTAAATTTGTTTTACGGT 58.998 36.000 0.00 0.00 0.00 4.83
2002 4347 2.036475 AGATGGCCTGTAATCTAGCACG 59.964 50.000 3.32 0.00 31.31 5.34
2148 4493 6.454795 TCAAAGTGATGCAAAAGGGTTATTC 58.545 36.000 0.00 0.00 0.00 1.75
2293 4654 3.254166 TCTTGCCATTGCTCTTTCTGTTC 59.746 43.478 0.00 0.00 38.71 3.18
2636 5002 3.003068 CCCTTATCTTTGCTCATCGCTTG 59.997 47.826 0.00 0.00 40.11 4.01
2771 5137 1.893808 GGCATCCACCACTATGGCG 60.894 63.158 0.00 0.00 42.67 5.69
2954 5324 2.967201 CCAATGTAACCCATGCATCCAT 59.033 45.455 0.00 0.00 32.69 3.41
3002 5372 6.787085 AGCAGATGTTACAGAAGTTACAAC 57.213 37.500 0.00 0.00 40.25 3.32
3071 5441 2.532235 CCAACACATGCATGCATACAC 58.468 47.619 31.73 0.00 34.91 2.90
3075 5445 1.219664 GGCCAACACATGCATGCAT 59.780 52.632 27.46 27.46 37.08 3.96
3082 5452 1.203052 GGTCATCAAGGCCAACACATG 59.797 52.381 5.01 0.00 43.39 3.21
3083 5453 1.549203 GGTCATCAAGGCCAACACAT 58.451 50.000 5.01 0.00 43.39 3.21
3084 5454 0.539438 GGGTCATCAAGGCCAACACA 60.539 55.000 5.01 0.00 46.80 3.72
3085 5455 0.251341 AGGGTCATCAAGGCCAACAC 60.251 55.000 5.01 0.00 46.80 3.32
3134 5513 4.682860 CACTCAATGAATGGCACTGAAAAC 59.317 41.667 0.00 0.00 31.56 2.43
3153 5532 2.035066 AGAAAACATTGGCACAGCACTC 59.965 45.455 0.00 0.00 42.39 3.51
3178 5557 2.224867 TGCAAAAAGGGAGAGGAAGAGG 60.225 50.000 0.00 0.00 0.00 3.69
3303 5683 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
3306 5686 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
3307 5687 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
3317 5697 3.053896 CGTCCTTTTGGGTCGGCC 61.054 66.667 0.00 0.00 41.59 6.13
3320 5700 3.419759 CGCCGTCCTTTTGGGTCG 61.420 66.667 0.00 0.00 44.10 4.79
3321 5701 0.958876 AATCGCCGTCCTTTTGGGTC 60.959 55.000 0.00 0.00 40.87 4.46
3322 5702 0.538746 AAATCGCCGTCCTTTTGGGT 60.539 50.000 0.00 0.00 40.87 4.51
3323 5703 0.170339 GAAATCGCCGTCCTTTTGGG 59.830 55.000 0.00 0.00 40.87 4.12
3324 5704 0.179200 CGAAATCGCCGTCCTTTTGG 60.179 55.000 0.00 0.00 42.21 3.28
3325 5705 0.515564 ACGAAATCGCCGTCCTTTTG 59.484 50.000 2.15 0.00 44.43 2.44
3326 5706 2.922779 ACGAAATCGCCGTCCTTTT 58.077 47.368 2.15 0.00 44.43 2.27
3327 5707 4.687464 ACGAAATCGCCGTCCTTT 57.313 50.000 2.15 0.00 44.43 3.11
3336 5716 2.230864 GACAAAAAGCGGACGAAATCG 58.769 47.619 0.48 0.48 46.33 3.34
3337 5717 2.031508 TGGACAAAAAGCGGACGAAATC 60.032 45.455 0.00 0.00 0.00 2.17
3338 5718 1.950909 TGGACAAAAAGCGGACGAAAT 59.049 42.857 0.00 0.00 0.00 2.17
3339 5719 1.380524 TGGACAAAAAGCGGACGAAA 58.619 45.000 0.00 0.00 0.00 3.46
3340 5720 1.600023 ATGGACAAAAAGCGGACGAA 58.400 45.000 0.00 0.00 0.00 3.85
3341 5721 1.600023 AATGGACAAAAAGCGGACGA 58.400 45.000 0.00 0.00 0.00 4.20
3342 5722 2.050691 CAAATGGACAAAAAGCGGACG 58.949 47.619 0.00 0.00 0.00 4.79
3343 5723 2.403259 CCAAATGGACAAAAAGCGGAC 58.597 47.619 0.00 0.00 37.39 4.79
3344 5724 1.342819 CCCAAATGGACAAAAAGCGGA 59.657 47.619 0.00 0.00 37.39 5.54
3345 5725 1.069978 ACCCAAATGGACAAAAAGCGG 59.930 47.619 0.00 0.00 37.39 5.52
3346 5726 2.403259 GACCCAAATGGACAAAAAGCG 58.597 47.619 0.00 0.00 37.39 4.68
3347 5727 2.403259 CGACCCAAATGGACAAAAAGC 58.597 47.619 0.00 0.00 37.39 3.51
3348 5728 2.866065 GCCGACCCAAATGGACAAAAAG 60.866 50.000 0.00 0.00 37.39 2.27
3349 5729 1.069358 GCCGACCCAAATGGACAAAAA 59.931 47.619 0.00 0.00 37.39 1.94
3350 5730 0.676736 GCCGACCCAAATGGACAAAA 59.323 50.000 0.00 0.00 37.39 2.44
3351 5731 1.182385 GGCCGACCCAAATGGACAAA 61.182 55.000 0.00 0.00 37.39 2.83
3352 5732 1.605165 GGCCGACCCAAATGGACAA 60.605 57.895 0.00 0.00 37.39 3.18
3353 5733 2.034999 GGCCGACCCAAATGGACA 59.965 61.111 0.00 0.00 37.39 4.02
3354 5734 3.131478 CGGCCGACCCAAATGGAC 61.131 66.667 24.07 0.00 37.39 4.02
3376 5756 4.636435 AACAGGGCGAACACCGGG 62.636 66.667 6.32 0.00 39.04 5.73
3377 5757 1.730451 AAAAACAGGGCGAACACCGG 61.730 55.000 0.00 0.00 39.04 5.28
3378 5758 0.593773 CAAAAACAGGGCGAACACCG 60.594 55.000 0.00 0.00 42.21 4.94
3379 5759 0.741915 TCAAAAACAGGGCGAACACC 59.258 50.000 0.00 0.00 0.00 4.16
3380 5760 2.793278 ATCAAAAACAGGGCGAACAC 57.207 45.000 0.00 0.00 0.00 3.32
3381 5761 3.192422 CCATATCAAAAACAGGGCGAACA 59.808 43.478 0.00 0.00 0.00 3.18
3382 5762 3.428862 CCCATATCAAAAACAGGGCGAAC 60.429 47.826 0.00 0.00 0.00 3.95
3383 5763 2.757868 CCCATATCAAAAACAGGGCGAA 59.242 45.455 0.00 0.00 0.00 4.70
3384 5764 2.291282 ACCCATATCAAAAACAGGGCGA 60.291 45.455 0.00 0.00 39.97 5.54
3385 5765 2.099098 GACCCATATCAAAAACAGGGCG 59.901 50.000 0.00 0.00 39.97 6.13
3386 5766 2.099098 CGACCCATATCAAAAACAGGGC 59.901 50.000 0.00 0.00 39.97 5.19
3387 5767 2.687935 CCGACCCATATCAAAAACAGGG 59.312 50.000 0.00 0.00 42.07 4.45
3388 5768 2.099098 GCCGACCCATATCAAAAACAGG 59.901 50.000 0.00 0.00 0.00 4.00
3389 5769 2.752354 TGCCGACCCATATCAAAAACAG 59.248 45.455 0.00 0.00 0.00 3.16
3390 5770 2.752354 CTGCCGACCCATATCAAAAACA 59.248 45.455 0.00 0.00 0.00 2.83
3391 5771 2.479560 GCTGCCGACCCATATCAAAAAC 60.480 50.000 0.00 0.00 0.00 2.43
3392 5772 1.748493 GCTGCCGACCCATATCAAAAA 59.252 47.619 0.00 0.00 0.00 1.94
3393 5773 1.388547 GCTGCCGACCCATATCAAAA 58.611 50.000 0.00 0.00 0.00 2.44
3394 5774 0.813610 CGCTGCCGACCCATATCAAA 60.814 55.000 0.00 0.00 36.29 2.69
3395 5775 1.227527 CGCTGCCGACCCATATCAA 60.228 57.895 0.00 0.00 36.29 2.57
3396 5776 2.421314 CGCTGCCGACCCATATCA 59.579 61.111 0.00 0.00 36.29 2.15
3397 5777 3.044305 GCGCTGCCGACCCATATC 61.044 66.667 0.00 0.00 36.29 1.63
3398 5778 4.969196 CGCGCTGCCGACCCATAT 62.969 66.667 5.56 0.00 36.29 1.78
3417 5797 4.823419 TATGGGTCGGCGCGTTGG 62.823 66.667 8.43 0.00 0.00 3.77
3418 5798 2.587753 ATATGGGTCGGCGCGTTG 60.588 61.111 8.43 0.00 0.00 4.10
3419 5799 2.587753 CATATGGGTCGGCGCGTT 60.588 61.111 8.43 0.00 0.00 4.84
3420 5800 3.845259 ACATATGGGTCGGCGCGT 61.845 61.111 8.43 3.65 0.00 6.01
3421 5801 3.337889 CACATATGGGTCGGCGCG 61.338 66.667 7.80 0.00 0.00 6.86
3422 5802 3.649986 GCACATATGGGTCGGCGC 61.650 66.667 6.86 0.00 0.00 6.53
3423 5803 1.775039 CTTGCACATATGGGTCGGCG 61.775 60.000 6.86 0.00 0.00 6.46
3424 5804 2.024918 CTTGCACATATGGGTCGGC 58.975 57.895 6.86 3.06 0.00 5.54
3425 5805 1.775039 CGCTTGCACATATGGGTCGG 61.775 60.000 6.86 0.00 0.00 4.79
3426 5806 1.089481 ACGCTTGCACATATGGGTCG 61.089 55.000 6.86 7.97 0.00 4.79
3427 5807 0.378257 CACGCTTGCACATATGGGTC 59.622 55.000 6.86 0.00 0.00 4.46
3428 5808 1.031571 CCACGCTTGCACATATGGGT 61.032 55.000 6.86 0.00 0.00 4.51
3429 5809 1.729276 CCACGCTTGCACATATGGG 59.271 57.895 7.80 3.61 0.00 4.00
3430 5810 1.064621 GCCACGCTTGCACATATGG 59.935 57.895 7.80 0.00 0.00 2.74
3431 5811 1.064621 GGCCACGCTTGCACATATG 59.935 57.895 0.00 0.00 0.00 1.78
3432 5812 2.472059 CGGCCACGCTTGCACATAT 61.472 57.895 2.24 0.00 0.00 1.78
3433 5813 3.124270 CGGCCACGCTTGCACATA 61.124 61.111 2.24 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.