Multiple sequence alignment - TraesCS3D01G331300

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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 TraesCS3D01G331300 chr3D 100.000 6325 0 0 1 6325 443592065 443598389 0.000000e+00 11681.0
1 TraesCS3D01G331300 chr3D 85.714 161 19 3 2503 2660 443594516 443594675 3.920000e-37 167.0
2 TraesCS3D01G331300 chr3D 85.714 161 19 3 2452 2611 443594567 443594724 3.920000e-37 167.0
3 TraesCS3D01G331300 chr3A 94.588 5285 181 26 1086 6306 584751920 584757163 0.000000e+00 8078.0
4 TraesCS3D01G331300 chr3A 85.948 612 52 19 1 585 584750255 584750859 1.940000e-174 623.0
5 TraesCS3D01G331300 chr3A 85.714 161 19 3 2503 2660 584753274 584753433 3.920000e-37 167.0
6 TraesCS3D01G331300 chr3A 85.714 161 19 3 2452 2611 584753325 584753482 3.920000e-37 167.0
7 TraesCS3D01G331300 chr3A 97.297 37 1 0 797 833 584751360 584751396 5.290000e-06 63.9
8 TraesCS3D01G331300 chr3B 94.309 4762 164 27 792 5494 581655141 581659854 0.000000e+00 7193.0
9 TraesCS3D01G331300 chr3B 84.894 801 51 20 5554 6306 581659851 581660629 0.000000e+00 745.0
10 TraesCS3D01G331300 chr3B 83.973 599 59 24 1 578 581654008 581654590 2.010000e-149 540.0
11 TraesCS3D01G331300 chr3B 86.559 186 20 4 586 770 581654670 581654851 3.870000e-47 200.0
12 TraesCS3D01G331300 chr3B 85.714 161 19 3 2503 2660 581656801 581656960 3.920000e-37 167.0
13 TraesCS3D01G331300 chr3B 85.714 161 19 3 2452 2611 581656852 581657009 3.920000e-37 167.0
14 TraesCS3D01G331300 chr2B 77.660 188 18 12 5679 5846 456324363 456324180 6.750000e-15 93.5
15 TraesCS3D01G331300 chr2B 97.826 46 1 0 5511 5556 464611125 464611080 5.260000e-11 80.5
16 TraesCS3D01G331300 chr5D 95.918 49 2 0 5508 5556 517678760 517678808 5.260000e-11 80.5
17 TraesCS3D01G331300 chr1B 97.826 46 1 0 5511 5556 24936360 24936405 5.260000e-11 80.5
18 TraesCS3D01G331300 chr6B 92.453 53 2 2 5511 5563 657091754 657091704 2.450000e-09 75.0
19 TraesCS3D01G331300 chr6B 91.379 58 0 1 5497 5549 677072625 677072568 2.450000e-09 75.0
20 TraesCS3D01G331300 chr6B 91.379 58 0 2 5497 5549 677768235 677768178 2.450000e-09 75.0
21 TraesCS3D01G331300 chr5B 86.111 72 5 3 5490 5556 589583890 589583961 8.800000e-09 73.1
22 TraesCS3D01G331300 chr5B 88.333 60 5 2 5498 5556 67032593 67032535 3.160000e-08 71.3


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 TraesCS3D01G331300 chr3D 443592065 443598389 6324 False 4005.00 11681 90.4760 1 6325 3 chr3D.!!$F1 6324
1 TraesCS3D01G331300 chr3A 584750255 584757163 6908 False 1819.78 8078 89.8522 1 6306 5 chr3A.!!$F1 6305
2 TraesCS3D01G331300 chr3B 581654008 581660629 6621 False 1502.00 7193 86.8605 1 6306 6 chr3B.!!$F1 6305

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
621 749 0.179240 GCAGATCGTTGACGCAACAG 60.179 55.000 18.32 12.61 43.70 3.16 F
867 1283 0.315869 CTGACCGTTCGTGCACAAAC 60.316 55.000 18.64 14.57 0.00 2.93 F
1266 1946 0.397816 AGCTCCAGAACCTCGGCTAT 60.398 55.000 0.00 0.00 0.00 2.97 F
1865 2549 0.456221 GATCAGGACACCGTGACGAT 59.544 55.000 6.54 0.00 39.63 3.73 F
2261 2945 0.608640 AGCAGACCTCGGGTTACAAG 59.391 55.000 0.00 0.00 35.25 3.16 F
2763 3447 1.456331 AACATGCATAGGGGGCTGC 60.456 57.895 0.00 0.00 38.87 5.25 F
2772 3456 1.558167 TAGGGGGCTGCGTTCATCAA 61.558 55.000 0.00 0.00 0.00 2.57 F
4422 5136 1.263356 TGGAACTCCCTGAACTACCG 58.737 55.000 0.00 0.00 35.38 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 3065 0.251354 TCAGAGGCAACATGAGAGGC 59.749 55.000 0.00 0.59 41.41 4.70 R
2763 3447 5.005012 CAGCCATGCTTAATTTTGATGAACG 59.995 40.000 0.00 0.00 36.40 3.95 R
2970 3654 6.707440 TGCCTTCTGTTCAAAGATTTGTTA 57.293 33.333 5.29 0.00 39.18 2.41 R
3596 4310 3.472652 TGTTACCACAAGCTAGTTGGTG 58.527 45.455 19.38 7.12 40.90 4.17 R
4040 4754 3.561143 TGTTGACATAAAGTTGCCCAGT 58.439 40.909 0.00 0.00 0.00 4.00 R
4422 5136 0.826715 TGTCAGACAGATAGCCAGGC 59.173 55.000 1.84 1.84 0.00 4.85 R
4471 5185 8.797438 AGTCTTCCAATTACTTTCCTTTTCATC 58.203 33.333 0.00 0.00 0.00 2.92 R
5370 6097 0.616891 AAGTACTTAACTGGGCCCGG 59.383 55.000 30.26 30.26 38.88 5.73 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
29 30 7.295322 TGAGAGAGAAACTTGAAGAGAATCA 57.705 36.000 0.00 0.00 37.82 2.57
36 37 5.438761 AACTTGAAGAGAATCAAAACCCG 57.561 39.130 0.00 0.00 38.75 5.28
71 78 1.296715 GGTCGCCATCTGTCCAAGT 59.703 57.895 0.00 0.00 0.00 3.16
76 83 1.877680 CGCCATCTGTCCAAGTGTCAA 60.878 52.381 0.00 0.00 0.00 3.18
115 122 7.592885 AAACAATAACCTATCTACTAGCCGA 57.407 36.000 0.00 0.00 0.00 5.54
128 135 2.223758 ACTAGCCGAAGCCGAGTTATTC 60.224 50.000 0.00 0.00 41.25 1.75
142 149 2.236395 AGTTATTCCTTCCCGACACTGG 59.764 50.000 0.00 0.00 0.00 4.00
143 150 0.539986 TATTCCTTCCCGACACTGGC 59.460 55.000 0.00 0.00 0.00 4.85
145 152 3.322466 CCTTCCCGACACTGGCCT 61.322 66.667 3.32 0.00 0.00 5.19
173 180 3.426695 GCAACCAAAGAGAATGGATCACG 60.427 47.826 0.00 0.00 40.56 4.35
186 193 7.308782 GAATGGATCACGTCTATTCTTTTGT 57.691 36.000 6.82 0.00 45.95 2.83
192 199 8.138712 GGATCACGTCTATTCTTTTGTAGATCT 58.861 37.037 0.00 0.00 31.54 2.75
227 234 9.187455 CTTCTCTAAACGCTCTTATATTTCCTC 57.813 37.037 0.00 0.00 0.00 3.71
244 251 1.409427 CCTCACGAAGGGAGTACCATC 59.591 57.143 0.00 0.00 42.03 3.51
350 357 7.630242 TTGCTTCCCTATTTAACATCAAGAG 57.370 36.000 0.00 0.00 0.00 2.85
384 391 9.022884 ACTTCCTTACCTAACACTAAGACTAAG 57.977 37.037 0.00 0.00 0.00 2.18
404 424 9.323985 GACTAAGATTTATGCTTCATCACTTCT 57.676 33.333 0.00 0.00 0.00 2.85
412 432 4.582869 TGCTTCATCACTTCTGTTAGCAT 58.417 39.130 0.00 0.00 32.01 3.79
418 438 6.447162 TCATCACTTCTGTTAGCATATACCG 58.553 40.000 0.00 0.00 0.00 4.02
464 492 2.574018 GGACAAAACTGCCCCTGCC 61.574 63.158 0.00 0.00 36.33 4.85
515 543 1.674651 CTCTCCCGACCACGACTCA 60.675 63.158 0.00 0.00 42.66 3.41
524 552 0.251832 ACCACGACTCATCCCTGTCT 60.252 55.000 0.00 0.00 0.00 3.41
610 738 1.377725 CAAAGGGGCTGCAGATCGT 60.378 57.895 20.43 7.01 0.00 3.73
613 741 1.841302 AAGGGGCTGCAGATCGTTGA 61.841 55.000 20.43 0.00 0.00 3.18
621 749 0.179240 GCAGATCGTTGACGCAACAG 60.179 55.000 18.32 12.61 43.70 3.16
674 802 1.596934 CTTGTCTTCGCCCTAGCCA 59.403 57.895 0.00 0.00 34.57 4.75
704 832 1.584495 CCCGACCATCATCGCGATA 59.416 57.895 23.22 10.84 40.87 2.92
733 861 1.219124 GGAGCAGGCTGATCGACAA 59.781 57.895 24.79 0.00 32.73 3.18
843 1252 5.529060 CCAGATCAAAATACTCCTAGTTGGC 59.471 44.000 0.00 0.00 35.26 4.52
845 1254 6.037610 CAGATCAAAATACTCCTAGTTGGCAC 59.962 42.308 0.00 0.00 35.26 5.01
847 1256 5.488341 TCAAAATACTCCTAGTTGGCACTC 58.512 41.667 0.00 0.00 34.06 3.51
849 1258 2.921834 TACTCCTAGTTGGCACTCCT 57.078 50.000 0.00 0.00 34.06 3.69
850 1259 1.270907 ACTCCTAGTTGGCACTCCTG 58.729 55.000 0.00 0.00 34.06 3.86
858 1267 2.432628 GGCACTCCTGACCGTTCG 60.433 66.667 0.00 0.00 0.00 3.95
859 1268 2.338984 GCACTCCTGACCGTTCGT 59.661 61.111 0.00 0.00 0.00 3.85
862 1271 2.338620 CTCCTGACCGTTCGTGCA 59.661 61.111 0.00 0.00 0.00 4.57
863 1272 2.022129 CTCCTGACCGTTCGTGCAC 61.022 63.158 6.82 6.82 0.00 4.57
867 1283 0.315869 CTGACCGTTCGTGCACAAAC 60.316 55.000 18.64 14.57 0.00 2.93
898 1314 3.364068 GGCGTTTGTAAGCAGAAGAGAAC 60.364 47.826 0.00 0.00 34.54 3.01
1031 1451 4.124943 CTCCCCTCCCTCCGTCGA 62.125 72.222 0.00 0.00 0.00 4.20
1266 1946 0.397816 AGCTCCAGAACCTCGGCTAT 60.398 55.000 0.00 0.00 0.00 2.97
1320 2000 0.682855 AACAACACCACCACCACCAG 60.683 55.000 0.00 0.00 0.00 4.00
1580 2260 2.205074 CGTTGATGGGAAAGATCGGAG 58.795 52.381 0.00 0.00 0.00 4.63
1623 2303 0.896923 TGGGTGAATCATTTGCTGCC 59.103 50.000 0.00 0.00 0.00 4.85
1636 2316 6.414732 TCATTTGCTGCCTAATAACACTACT 58.585 36.000 0.00 0.00 0.00 2.57
1669 2349 0.795085 GGATCATATCAGCGCACTGC 59.205 55.000 11.47 0.00 44.10 4.40
1683 2363 1.068610 GCACTGCAGCGGTTATTGAAA 60.069 47.619 15.27 0.00 0.00 2.69
1684 2364 2.606795 GCACTGCAGCGGTTATTGAAAA 60.607 45.455 15.27 0.00 0.00 2.29
1816 2500 5.614308 TGTCATGTCTTTCAGAGTGATGTT 58.386 37.500 0.00 0.00 0.00 2.71
1838 2522 3.300388 TCTCTATGGGTGTTAGCAGGAG 58.700 50.000 0.00 0.00 0.00 3.69
1865 2549 0.456221 GATCAGGACACCGTGACGAT 59.544 55.000 6.54 0.00 39.63 3.73
1990 2674 0.774276 TGCCACACACCAGGGAATTA 59.226 50.000 0.00 0.00 0.00 1.40
2065 2749 4.967036 ACTAAGCTCTATTCTGAATGCCC 58.033 43.478 13.01 0.00 0.00 5.36
2077 2761 3.006110 TCTGAATGCCCTTCTGCTTTTTG 59.994 43.478 0.00 0.00 34.75 2.44
2156 2840 7.571080 AATGCTTTTGTGATTGTTTTGGAAT 57.429 28.000 0.00 0.00 0.00 3.01
2241 2925 6.072452 CGCTATATCATCACTAACCTCTCACA 60.072 42.308 0.00 0.00 0.00 3.58
2254 2938 1.079543 CTCACAAGCAGACCTCGGG 60.080 63.158 0.00 0.00 0.00 5.14
2261 2945 0.608640 AGCAGACCTCGGGTTACAAG 59.391 55.000 0.00 0.00 35.25 3.16
2295 2979 6.734532 TGTTACTTAGATGTACTGGTCCCTA 58.265 40.000 0.00 0.00 0.00 3.53
2296 2980 6.604795 TGTTACTTAGATGTACTGGTCCCTAC 59.395 42.308 0.00 0.00 0.00 3.18
2318 3002 2.847327 ATGTACAGCACAGCTCTGTT 57.153 45.000 11.39 0.00 41.61 3.16
2355 3039 8.836413 TGTTTCTCTTAATTTGTCACAGGTAAG 58.164 33.333 0.00 0.02 0.00 2.34
2381 3065 6.692681 CCAAACTAATAACAAATCAGATGGCG 59.307 38.462 0.00 0.00 0.00 5.69
2763 3447 1.456331 AACATGCATAGGGGGCTGC 60.456 57.895 0.00 0.00 38.87 5.25
2772 3456 1.558167 TAGGGGGCTGCGTTCATCAA 61.558 55.000 0.00 0.00 0.00 2.57
2782 3466 4.563976 GCTGCGTTCATCAAAATTAAGCAT 59.436 37.500 0.00 0.00 0.00 3.79
2908 3592 3.186409 TGAACTCTTAACTTGTGATGCGC 59.814 43.478 0.00 0.00 0.00 6.09
2930 3614 5.563842 GCTTGACATAATGTGTAGCTTCAC 58.436 41.667 15.91 15.91 42.36 3.18
2970 3654 3.570125 GCAAGGAAAGTAGGAAGCAAAGT 59.430 43.478 0.00 0.00 0.00 2.66
3108 3796 2.820787 GCTGTGTAGTCTAGTCCACTGT 59.179 50.000 0.00 0.00 0.00 3.55
3268 3982 3.442625 TCGAGTCACGTATTTGATCACCT 59.557 43.478 0.00 0.00 43.13 4.00
3548 4262 7.052248 ACATGTTTTGATATCTGCATCTCTCA 58.948 34.615 3.98 0.00 0.00 3.27
3596 4310 5.050490 TCTTCATCATTTCTAGCGCTAACC 58.950 41.667 19.37 0.00 0.00 2.85
3869 4583 4.894784 TCCAGTTCACATGTTCTTAGACC 58.105 43.478 0.00 0.00 0.00 3.85
4422 5136 1.263356 TGGAACTCCCTGAACTACCG 58.737 55.000 0.00 0.00 35.38 4.02
4471 5185 4.760047 CCAGGGGACGTCAAGGCG 62.760 72.222 18.91 1.03 37.94 5.52
4914 5628 2.558359 CAGCCTCGGTTTGAAGGAAAAT 59.442 45.455 0.00 0.00 0.00 1.82
4955 5669 4.598894 CAGCGGCGAGGAGGATGG 62.599 72.222 12.98 0.00 0.00 3.51
5009 5723 3.560068 GGTGCTGATACTGAAATAACCGG 59.440 47.826 0.00 0.00 0.00 5.28
5043 5757 1.880340 GGATTCCGACGCAGAGCAG 60.880 63.158 0.00 0.00 0.00 4.24
5047 5761 4.731612 CCGACGCAGAGCAGTGCT 62.732 66.667 19.86 19.86 43.88 4.40
5048 5762 3.476646 CGACGCAGAGCAGTGCTG 61.477 66.667 25.35 11.54 39.88 4.41
5049 5763 2.356793 GACGCAGAGCAGTGCTGT 60.357 61.111 25.35 17.30 39.88 4.40
5064 5778 1.294659 GCTGTGCGAGTGAAGAAGGG 61.295 60.000 0.00 0.00 0.00 3.95
5079 5793 4.464069 AGAAGGGTTCTCAGATTTCTCG 57.536 45.455 0.00 0.00 34.07 4.04
5158 5883 4.917906 AAGCCTCCTCACAACTTTATCT 57.082 40.909 0.00 0.00 0.00 1.98
5193 5918 7.088589 AGCTATGATTTCGTTGTAATGCTTT 57.911 32.000 0.00 0.00 0.00 3.51
5221 5946 5.564768 TGGTAAAATGATATCGTTGTTGCG 58.435 37.500 10.93 0.00 0.00 4.85
5246 5971 1.003464 ACAGCAGGCACATGTGATGTA 59.997 47.619 29.80 0.00 41.36 2.29
5247 5972 2.294979 CAGCAGGCACATGTGATGTAT 58.705 47.619 29.80 15.40 42.70 2.29
5248 5973 2.686405 CAGCAGGCACATGTGATGTATT 59.314 45.455 29.80 12.91 42.70 1.89
5249 5974 2.947652 AGCAGGCACATGTGATGTATTC 59.052 45.455 29.80 12.85 42.70 1.75
5250 5975 2.033801 GCAGGCACATGTGATGTATTCC 59.966 50.000 29.80 17.85 42.70 3.01
5251 5976 3.548770 CAGGCACATGTGATGTATTCCT 58.451 45.455 29.80 19.76 42.70 3.36
5252 5977 4.707105 CAGGCACATGTGATGTATTCCTA 58.293 43.478 29.80 0.00 42.70 2.94
5258 5983 6.489675 CACATGTGATGTATTCCTAACTTGC 58.510 40.000 21.64 0.00 42.70 4.01
5322 6047 4.155826 CGATGCCCTAATGTTGTTTTCTCA 59.844 41.667 0.00 0.00 0.00 3.27
5356 6083 4.347453 GCCAAACAGTGCGCAGGG 62.347 66.667 12.22 8.82 0.00 4.45
5370 6097 0.457443 GCAGGGAAAACAGCATAGGC 59.543 55.000 0.00 0.00 41.61 3.93
5371 6098 1.106285 CAGGGAAAACAGCATAGGCC 58.894 55.000 0.00 0.00 42.56 5.19
5372 6099 0.394352 AGGGAAAACAGCATAGGCCG 60.394 55.000 0.00 0.00 42.56 6.13
5373 6100 1.384222 GGGAAAACAGCATAGGCCGG 61.384 60.000 0.00 0.00 42.56 6.13
5374 6101 1.384222 GGAAAACAGCATAGGCCGGG 61.384 60.000 2.18 0.00 42.56 5.73
5507 6238 6.321435 TGTCATGCTATATTATACTCCCTCCG 59.679 42.308 0.00 0.00 0.00 4.63
5526 6257 6.449698 CCTCCGTCAAGTTAGTACAAAGTTA 58.550 40.000 0.00 0.00 0.00 2.24
5546 6277 7.653767 AGTTAAGACACTTATTTTGAGACGG 57.346 36.000 0.00 0.00 0.00 4.79
5550 6281 4.527038 AGACACTTATTTTGAGACGGAGGA 59.473 41.667 0.00 0.00 0.00 3.71
5554 6285 6.014840 ACACTTATTTTGAGACGGAGGAAGTA 60.015 38.462 0.00 0.00 0.00 2.24
5838 6587 9.696917 AACATTTCTCATGGTAAAGAAAACATC 57.303 29.630 10.35 0.00 42.86 3.06
5886 6635 8.375506 TGGTTGTAATAAAATTGCCATGGTAAA 58.624 29.630 19.72 11.66 0.00 2.01
5944 6716 7.446319 TGATTGAAATGAAGTTGACATGAGAGT 59.554 33.333 0.00 0.00 0.00 3.24
6054 6826 5.237048 TGCTGAACTAAAATTTTCATGGCC 58.763 37.500 6.72 0.00 31.41 5.36
6082 6855 2.503356 AGAAGTTGCCATAGTCCAGGAG 59.497 50.000 0.00 0.00 0.00 3.69
6099 6872 4.280819 CAGGAGAAATAAATTGCCCTGGA 58.719 43.478 0.00 0.00 36.85 3.86
6102 6875 4.281941 GGAGAAATAAATTGCCCTGGATCC 59.718 45.833 4.20 4.20 0.00 3.36
6135 6911 8.674263 AAATTGCCATGTCTGTAAAAATCAAA 57.326 26.923 0.00 0.00 0.00 2.69
6157 6933 5.578005 ATTTTCATGGTCTCTCAATGCAG 57.422 39.130 0.00 0.00 0.00 4.41
6189 6966 4.517453 GGCCCCCAAAAGTTTGAATTTTAC 59.483 41.667 5.34 0.00 40.55 2.01
6292 7069 6.767902 ACTCTAATTTGGCATGGTATGTACAG 59.232 38.462 0.33 0.00 0.00 2.74
6297 7074 6.751514 TTTGGCATGGTATGTACAGTAAAG 57.248 37.500 0.33 0.00 0.00 1.85
6306 7083 5.878116 GGTATGTACAGTAAAGTTGCCATGA 59.122 40.000 0.33 0.00 0.00 3.07
6307 7084 6.373216 GGTATGTACAGTAAAGTTGCCATGAA 59.627 38.462 0.33 0.00 0.00 2.57
6308 7085 5.682943 TGTACAGTAAAGTTGCCATGAAC 57.317 39.130 0.00 0.00 0.00 3.18
6309 7086 5.126779 TGTACAGTAAAGTTGCCATGAACA 58.873 37.500 0.00 0.00 0.00 3.18
6310 7087 5.590663 TGTACAGTAAAGTTGCCATGAACAA 59.409 36.000 0.00 0.00 0.00 2.83
6311 7088 4.932146 ACAGTAAAGTTGCCATGAACAAC 58.068 39.130 18.52 18.52 46.18 3.32
6319 7096 5.941948 GTTGCCATGAACAACTAGTAAGT 57.058 39.130 18.76 0.00 43.23 2.24
6320 7097 5.689819 GTTGCCATGAACAACTAGTAAGTG 58.310 41.667 18.76 0.00 43.23 3.16
6321 7098 4.323417 TGCCATGAACAACTAGTAAGTGG 58.677 43.478 0.00 0.78 35.62 4.00
6322 7099 3.127030 GCCATGAACAACTAGTAAGTGGC 59.873 47.826 14.62 14.62 40.91 5.01
6323 7100 4.323417 CCATGAACAACTAGTAAGTGGCA 58.677 43.478 0.00 1.69 35.62 4.92
6324 7101 4.154195 CCATGAACAACTAGTAAGTGGCAC 59.846 45.833 10.29 10.29 35.62 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.295322 TGATTCTCTTCAAGTTTCTCTCTCA 57.705 36.000 0.00 0.00 0.00 3.27
29 30 5.298527 CCTTCTTGTTAGTCTTTCGGGTTTT 59.701 40.000 0.00 0.00 0.00 2.43
36 37 3.432592 GCGACCCTTCTTGTTAGTCTTTC 59.567 47.826 0.00 0.00 0.00 2.62
115 122 1.134491 CGGGAAGGAATAACTCGGCTT 60.134 52.381 0.00 0.00 0.00 4.35
128 135 2.804828 GAAGGCCAGTGTCGGGAAGG 62.805 65.000 5.01 0.00 0.00 3.46
142 149 3.412386 TCTCTTTGGTTGCTTAGAAGGC 58.588 45.455 0.00 0.00 0.00 4.35
143 150 5.105997 CCATTCTCTTTGGTTGCTTAGAAGG 60.106 44.000 0.00 0.00 0.00 3.46
145 152 5.630121 TCCATTCTCTTTGGTTGCTTAGAA 58.370 37.500 0.00 0.00 35.64 2.10
227 234 4.081862 TGTTTAGATGGTACTCCCTTCGTG 60.082 45.833 0.00 0.00 41.27 4.35
244 251 4.213270 TGTCGTCTTTGGCATCTTGTTTAG 59.787 41.667 0.00 0.00 0.00 1.85
310 317 6.761242 AGGGAAGCAAAGTTTAAAACAATGTC 59.239 34.615 0.00 0.00 0.00 3.06
357 364 7.852550 AGTCTTAGTGTTAGGTAAGGAAGTT 57.147 36.000 0.00 0.00 0.00 2.66
358 365 8.946797 TTAGTCTTAGTGTTAGGTAAGGAAGT 57.053 34.615 0.00 0.00 0.00 3.01
379 386 9.107177 CAGAAGTGATGAAGCATAAATCTTAGT 57.893 33.333 0.00 0.00 0.00 2.24
384 391 7.854916 GCTAACAGAAGTGATGAAGCATAAATC 59.145 37.037 0.00 0.00 33.43 2.17
404 424 6.704289 AGTGTCTAACGGTATATGCTAACA 57.296 37.500 0.00 0.00 0.00 2.41
412 432 3.765511 ACTGGCAAGTGTCTAACGGTATA 59.234 43.478 0.00 0.00 34.48 1.47
418 438 3.467803 ACAGAACTGGCAAGTGTCTAAC 58.532 45.455 0.00 0.00 36.51 2.34
590 718 2.363406 ATCTGCAGCCCCTTTGCC 60.363 61.111 9.47 0.00 40.81 4.52
596 724 2.109126 GTCAACGATCTGCAGCCCC 61.109 63.158 9.47 0.00 0.00 5.80
600 728 0.179240 GTTGCGTCAACGATCTGCAG 60.179 55.000 7.63 7.63 43.02 4.41
603 731 0.179240 GCTGTTGCGTCAACGATCTG 60.179 55.000 6.75 1.60 46.13 2.90
613 741 3.628646 GAGGGGGATGCTGTTGCGT 62.629 63.158 0.00 0.00 43.34 5.24
621 749 2.190578 CGTGGAAGAGGGGGATGC 59.809 66.667 0.00 0.00 0.00 3.91
674 802 4.817909 GTCGGGGATGGGAGGGGT 62.818 72.222 0.00 0.00 0.00 4.95
716 844 1.416813 CGTTGTCGATCAGCCTGCTC 61.417 60.000 0.00 0.00 39.71 4.26
733 861 1.947212 GCAATTTTACCCCGAGGTCGT 60.947 52.381 0.00 0.00 46.45 4.34
788 1167 7.929245 TGCGTATGTAACCATGTATCACTAATT 59.071 33.333 0.00 0.00 32.29 1.40
789 1168 7.438564 TGCGTATGTAACCATGTATCACTAAT 58.561 34.615 0.00 0.00 32.29 1.73
790 1169 6.807789 TGCGTATGTAACCATGTATCACTAA 58.192 36.000 0.00 0.00 32.29 2.24
791 1170 6.394025 TGCGTATGTAACCATGTATCACTA 57.606 37.500 0.00 0.00 32.29 2.74
792 1171 5.270893 TGCGTATGTAACCATGTATCACT 57.729 39.130 0.00 0.00 32.29 3.41
793 1172 5.751509 TCTTGCGTATGTAACCATGTATCAC 59.248 40.000 0.00 0.00 32.29 3.06
794 1173 5.908341 TCTTGCGTATGTAACCATGTATCA 58.092 37.500 0.00 0.00 32.29 2.15
795 1174 5.107453 GCTCTTGCGTATGTAACCATGTATC 60.107 44.000 0.00 0.00 32.29 2.24
802 1181 1.933853 CTGGCTCTTGCGTATGTAACC 59.066 52.381 0.00 0.00 40.82 2.85
843 1252 2.022129 GCACGAACGGTCAGGAGTG 61.022 63.158 0.00 1.06 0.00 3.51
845 1254 2.022129 GTGCACGAACGGTCAGGAG 61.022 63.158 0.00 0.00 0.00 3.69
847 1256 1.433053 TTTGTGCACGAACGGTCAGG 61.433 55.000 15.77 0.00 0.00 3.86
849 1258 1.716760 GTTTGTGCACGAACGGTCA 59.283 52.632 29.31 1.93 31.32 4.02
850 1259 4.582452 GTTTGTGCACGAACGGTC 57.418 55.556 29.31 11.18 31.32 4.79
858 1267 0.384230 CCGTGTGATCGTTTGTGCAC 60.384 55.000 10.75 10.75 0.00 4.57
859 1268 1.938125 CCGTGTGATCGTTTGTGCA 59.062 52.632 0.00 0.00 0.00 4.57
862 1271 1.155424 AACGCCGTGTGATCGTTTGT 61.155 50.000 0.00 0.00 42.84 2.83
863 1272 1.567537 AACGCCGTGTGATCGTTTG 59.432 52.632 0.00 0.00 42.84 2.93
867 1283 0.785378 TTACAAACGCCGTGTGATCG 59.215 50.000 15.54 0.00 0.00 3.69
898 1314 3.175240 CGTTCGTGCGCTCCTGAG 61.175 66.667 9.73 0.00 0.00 3.35
969 1389 1.273986 GGGTAGGGTTTTAGGGGCGA 61.274 60.000 0.00 0.00 0.00 5.54
970 1390 1.225426 GGGTAGGGTTTTAGGGGCG 59.775 63.158 0.00 0.00 0.00 6.13
971 1391 0.705842 TTGGGTAGGGTTTTAGGGGC 59.294 55.000 0.00 0.00 0.00 5.80
972 1392 3.546429 TTTTGGGTAGGGTTTTAGGGG 57.454 47.619 0.00 0.00 0.00 4.79
973 1393 4.942944 AGATTTTGGGTAGGGTTTTAGGG 58.057 43.478 0.00 0.00 0.00 3.53
1020 1440 3.822192 CGCATGTCGACGGAGGGA 61.822 66.667 11.62 0.00 41.67 4.20
1031 1451 4.740822 GGTGGAAGGGGCGCATGT 62.741 66.667 10.83 0.00 0.00 3.21
1320 2000 1.142474 GATTTTGCTGCTGTTGTGGC 58.858 50.000 0.00 0.00 0.00 5.01
1580 2260 4.208686 CGACCCCTCCGCTACTGC 62.209 72.222 0.00 0.00 0.00 4.40
1636 2316 7.880195 GCTGATATGATCCTAAAGGCTAAAAGA 59.120 37.037 0.00 0.00 34.44 2.52
1816 2500 3.706594 CTCCTGCTAACACCCATAGAGAA 59.293 47.826 0.00 0.00 0.00 2.87
1838 2522 2.213499 CGGTGTCCTGATCCTAAATGC 58.787 52.381 0.00 0.00 0.00 3.56
1865 2549 8.248253 GCATTGCCATTCATCATTATCAGAATA 58.752 33.333 0.00 0.00 0.00 1.75
1990 2674 9.386122 ACAAGAGATACCAATACTCCAATAGAT 57.614 33.333 0.00 0.00 0.00 1.98
2031 2715 3.107601 AGAGCTTAGTTGTGCCCATAGA 58.892 45.455 0.00 0.00 0.00 1.98
2087 2771 8.624776 AGTAAGAAAGTTTGAGAAGGACAAATG 58.375 33.333 0.00 0.00 39.01 2.32
2130 2814 7.014092 TCCAAAACAATCACAAAAGCATTTC 57.986 32.000 0.00 0.00 37.28 2.17
2241 2925 1.002087 CTTGTAACCCGAGGTCTGCTT 59.998 52.381 0.00 0.00 33.12 3.91
2295 2979 3.259374 ACAGAGCTGTGCTGTACATTAGT 59.741 43.478 11.42 0.00 44.27 2.24
2296 2980 3.854666 ACAGAGCTGTGCTGTACATTAG 58.145 45.455 11.42 0.00 44.27 1.73
2355 3039 6.476706 GCCATCTGATTTGTTATTAGTTTGGC 59.523 38.462 0.00 0.00 34.38 4.52
2381 3065 0.251354 TCAGAGGCAACATGAGAGGC 59.749 55.000 0.00 0.59 41.41 4.70
2763 3447 5.005012 CAGCCATGCTTAATTTTGATGAACG 59.995 40.000 0.00 0.00 36.40 3.95
2908 3592 6.974932 AGTGAAGCTACACATTATGTCAAG 57.025 37.500 0.00 0.00 42.09 3.02
2930 3614 7.377766 TCCTTGCAGTTATAAGCACTTAAAG 57.622 36.000 0.00 0.00 41.05 1.85
2970 3654 6.707440 TGCCTTCTGTTCAAAGATTTGTTA 57.293 33.333 5.29 0.00 39.18 2.41
3108 3796 7.934665 ACTTACACACAATATGTACAAGGAACA 59.065 33.333 0.00 0.00 40.64 3.18
3268 3982 7.295322 ACATGCTCTTCTATCATGTAGCTAA 57.705 36.000 0.00 0.00 46.10 3.09
3548 4262 8.135382 ACAGTTTTCTACTATACACAGACCAT 57.865 34.615 0.00 0.00 34.56 3.55
3596 4310 3.472652 TGTTACCACAAGCTAGTTGGTG 58.527 45.455 19.38 7.12 40.90 4.17
3712 4426 5.424252 ACAAGGATTCAATCATTTGCCAGAT 59.576 36.000 11.73 0.00 29.75 2.90
4040 4754 3.561143 TGTTGACATAAAGTTGCCCAGT 58.439 40.909 0.00 0.00 0.00 4.00
4291 5005 1.935933 ATATTGGAACAGCGTCGTCC 58.064 50.000 0.00 0.00 42.39 4.79
4422 5136 0.826715 TGTCAGACAGATAGCCAGGC 59.173 55.000 1.84 1.84 0.00 4.85
4471 5185 8.797438 AGTCTTCCAATTACTTTCCTTTTCATC 58.203 33.333 0.00 0.00 0.00 2.92
4914 5628 1.143838 CGATTCCGGCTGATCACCA 59.856 57.895 0.00 0.00 0.00 4.17
4943 5657 0.103937 CTCACTTCCATCCTCCTCGC 59.896 60.000 0.00 0.00 0.00 5.03
4944 5658 0.749649 CCTCACTTCCATCCTCCTCG 59.250 60.000 0.00 0.00 0.00 4.63
4955 5669 0.236711 TTCGTCGTCGTCCTCACTTC 59.763 55.000 1.33 0.00 38.33 3.01
5009 5723 3.759086 GGAATCCTCACCTGAAACCTTTC 59.241 47.826 0.00 0.00 37.69 2.62
5021 5735 0.526524 CTCTGCGTCGGAATCCTCAC 60.527 60.000 0.00 0.00 0.00 3.51
5043 5757 0.510359 CTTCTTCACTCGCACAGCAC 59.490 55.000 0.00 0.00 0.00 4.40
5047 5761 0.468226 AACCCTTCTTCACTCGCACA 59.532 50.000 0.00 0.00 0.00 4.57
5048 5762 1.149148 GAACCCTTCTTCACTCGCAC 58.851 55.000 0.00 0.00 0.00 5.34
5049 5763 1.000955 GAGAACCCTTCTTCACTCGCA 59.999 52.381 0.00 0.00 40.87 5.10
5050 5764 1.000955 TGAGAACCCTTCTTCACTCGC 59.999 52.381 0.00 0.00 40.87 5.03
5051 5765 2.558795 TCTGAGAACCCTTCTTCACTCG 59.441 50.000 0.00 0.00 40.87 4.18
5052 5766 4.817318 ATCTGAGAACCCTTCTTCACTC 57.183 45.455 0.00 0.00 40.87 3.51
5053 5767 5.309282 AGAAATCTGAGAACCCTTCTTCACT 59.691 40.000 0.00 0.00 40.87 3.41
5054 5768 5.555966 AGAAATCTGAGAACCCTTCTTCAC 58.444 41.667 0.00 0.00 40.87 3.18
5055 5769 5.567623 CGAGAAATCTGAGAACCCTTCTTCA 60.568 44.000 0.00 0.00 40.87 3.02
5064 5778 2.093973 TCAGGCCGAGAAATCTGAGAAC 60.094 50.000 0.00 0.00 33.07 3.01
5079 5793 3.502595 GGTTTAGTCAAGAAACTCAGGCC 59.497 47.826 0.00 0.00 37.05 5.19
5158 5883 2.401583 ATCATAGCTCACGGCAACAA 57.598 45.000 0.00 0.00 44.79 2.83
5193 5918 9.566530 CAACAACGATATCATTTTACCATTCAA 57.433 29.630 3.12 0.00 0.00 2.69
5221 5946 1.068748 CACATGTGCCTGCTGTTTCTC 60.069 52.381 13.94 0.00 0.00 2.87
5246 5971 5.450818 TGATACCCTTGCAAGTTAGGAAT 57.549 39.130 24.35 10.78 33.13 3.01
5247 5972 4.919774 TGATACCCTTGCAAGTTAGGAA 57.080 40.909 24.35 4.03 33.13 3.36
5248 5973 5.450818 AATGATACCCTTGCAAGTTAGGA 57.549 39.130 24.35 10.44 33.13 2.94
5249 5974 5.418840 ACAAATGATACCCTTGCAAGTTAGG 59.581 40.000 24.35 19.90 0.00 2.69
5250 5975 6.324819 CACAAATGATACCCTTGCAAGTTAG 58.675 40.000 24.35 14.94 0.00 2.34
5251 5976 5.336372 GCACAAATGATACCCTTGCAAGTTA 60.336 40.000 24.35 15.26 0.00 2.24
5252 5977 4.561326 GCACAAATGATACCCTTGCAAGTT 60.561 41.667 24.35 13.58 0.00 2.66
5258 5983 4.789012 AAGTGCACAAATGATACCCTTG 57.211 40.909 21.04 0.00 0.00 3.61
5356 6083 2.004808 GCCCGGCCTATGCTGTTTTC 62.005 60.000 0.00 0.00 42.66 2.29
5370 6097 0.616891 AAGTACTTAACTGGGCCCGG 59.383 55.000 30.26 30.26 38.88 5.73
5371 6098 2.027469 AGAAAGTACTTAACTGGGCCCG 60.027 50.000 19.37 14.85 38.88 6.13
5372 6099 3.008704 TCAGAAAGTACTTAACTGGGCCC 59.991 47.826 27.26 17.59 38.88 5.80
5373 6100 4.281898 TCAGAAAGTACTTAACTGGGCC 57.718 45.455 27.26 0.00 38.88 5.80
5374 6101 6.628919 TTTTCAGAAAGTACTTAACTGGGC 57.371 37.500 27.26 8.69 38.88 5.36
5495 6226 5.121380 ACTAACTTGACGGAGGGAGTATA 57.879 43.478 0.00 0.00 0.00 1.47
5507 6238 9.310716 AGTGTCTTAACTTTGTACTAACTTGAC 57.689 33.333 0.00 0.00 0.00 3.18
5526 6257 5.011738 TCCTCCGTCTCAAAATAAGTGTCTT 59.988 40.000 0.00 0.00 0.00 3.01
5546 6277 4.517285 TGATGGCAGTTTCATACTTCCTC 58.483 43.478 0.00 0.00 40.44 3.71
5666 6397 5.603813 AGGGGGTATTTTCTGCGTAAGTATA 59.396 40.000 0.00 0.00 41.68 1.47
6054 6826 4.378459 GGACTATGGCAACTTCTTTTCACG 60.378 45.833 0.00 0.00 37.61 4.35
6082 6855 3.888930 TCGGATCCAGGGCAATTTATTTC 59.111 43.478 13.41 0.00 0.00 2.17
6099 6872 5.360714 AGACATGGCAATTTATTGTTCGGAT 59.639 36.000 0.00 0.00 39.88 4.18
6102 6875 5.401550 ACAGACATGGCAATTTATTGTTCG 58.598 37.500 0.00 0.00 39.88 3.95
6135 6911 5.014858 ACTGCATTGAGAGACCATGAAAAT 58.985 37.500 0.00 0.00 0.00 1.82
6157 6933 2.061790 TTTTGGGGGCCATGGCAAAC 62.062 55.000 36.56 24.93 44.11 2.93
6205 6982 3.890756 TGAAGATTCTGTGGCACATTTGT 59.109 39.130 22.35 7.70 44.52 2.83
6211 6988 7.412237 GCAAATTATTTGAAGATTCTGTGGCAC 60.412 37.037 20.37 11.55 43.26 5.01
6278 7055 5.448632 GGCAACTTTACTGTACATACCATGC 60.449 44.000 0.00 2.08 0.00 4.06
6297 7074 5.334879 CCACTTACTAGTTGTTCATGGCAAC 60.335 44.000 19.43 19.43 44.57 4.17


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

AutoCloner maintained by Alex Coulton.