Multiple sequence alignment - TraesCS1B01G319500

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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 TraesCS1B01G319500 chr1B 100.000 3747 0 0 1 3747 543582251 543578505 0.000000e+00 6920.0
1 TraesCS1B01G319500 chr1B 84.192 1689 130 48 677 2292 543741404 543739780 0.000000e+00 1513.0
2 TraesCS1B01G319500 chr1B 92.000 125 8 2 376 498 543741897 543741773 1.380000e-39 174.0
3 TraesCS1B01G319500 chr1A 88.982 1788 102 33 44 1785 499810160 499808422 0.000000e+00 2122.0
4 TraesCS1B01G319500 chr1A 78.825 2229 202 125 567 2644 499928139 499926030 0.000000e+00 1253.0
5 TraesCS1B01G319500 chr1A 90.117 597 26 6 1832 2403 499808284 499807696 0.000000e+00 745.0
6 TraesCS1B01G319500 chr1A 91.935 310 24 1 44 352 499929083 499928774 2.070000e-117 433.0
7 TraesCS1B01G319500 chr1A 79.518 166 28 5 309 469 499805922 499805758 3.060000e-21 113.0
8 TraesCS1B01G319500 chr1A 93.023 43 3 0 10 52 28774224 28774182 3.120000e-06 63.9
9 TraesCS1B01G319500 chr1D 85.729 1878 123 63 561 2366 404240472 404238668 0.000000e+00 1849.0
10 TraesCS1B01G319500 chr1D 83.784 1591 126 62 659 2204 404261398 404259895 0.000000e+00 1387.0
11 TraesCS1B01G319500 chr1D 85.190 709 66 15 2917 3593 404236243 404235542 0.000000e+00 691.0
12 TraesCS1B01G319500 chr1D 91.116 439 34 4 44 478 404262135 404261698 1.160000e-164 590.0
13 TraesCS1B01G319500 chr1D 89.354 263 25 3 60 320 404241173 404240912 1.000000e-85 327.0
14 TraesCS1B01G319500 chr1D 92.254 142 11 0 3606 3747 404235559 404235418 6.350000e-48 202.0
15 TraesCS1B01G319500 chr1D 82.456 171 20 6 308 469 404234367 404234198 1.400000e-29 141.0
16 TraesCS1B01G319500 chr1D 100.000 34 0 0 44 77 404241884 404241851 3.120000e-06 63.9
17 TraesCS1B01G319500 chr3D 95.833 48 1 1 8 54 553657135 553657182 4.010000e-10 76.8
18 TraesCS1B01G319500 chr3D 100.000 37 0 0 10 46 572917590 572917554 6.720000e-08 69.4
19 TraesCS1B01G319500 chr7D 100.000 39 0 0 8 46 564909092 564909054 5.190000e-09 73.1
20 TraesCS1B01G319500 chr5D 100.000 38 0 0 10 47 411142713 411142676 1.870000e-08 71.3
21 TraesCS1B01G319500 chr7A 97.436 39 1 0 10 48 672850995 672851033 2.420000e-07 67.6
22 TraesCS1B01G319500 chr4D 100.000 36 0 0 8 43 489332834 489332869 2.420000e-07 67.6
23 TraesCS1B01G319500 chr4B 100.000 36 0 0 11 46 369605695 369605660 2.420000e-07 67.6
24 TraesCS1B01G319500 chr2D 100.000 36 0 0 10 45 532290870 532290835 2.420000e-07 67.6


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 TraesCS1B01G319500 chr1B 543578505 543582251 3746 True 6920.000000 6920 100.000000 1 3747 1 chr1B.!!$R1 3746
1 TraesCS1B01G319500 chr1B 543739780 543741897 2117 True 843.500000 1513 88.096000 376 2292 2 chr1B.!!$R2 1916
2 TraesCS1B01G319500 chr1A 499805758 499810160 4402 True 993.333333 2122 86.205667 44 2403 3 chr1A.!!$R2 2359
3 TraesCS1B01G319500 chr1A 499926030 499929083 3053 True 843.000000 1253 85.380000 44 2644 2 chr1A.!!$R3 2600
4 TraesCS1B01G319500 chr1D 404259895 404262135 2240 True 988.500000 1387 87.450000 44 2204 2 chr1D.!!$R2 2160
5 TraesCS1B01G319500 chr1D 404234198 404241884 7686 True 545.650000 1849 89.163833 44 3747 6 chr1D.!!$R1 3703

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
106 802 0.595588 TAAATGCACCAGCGGTTGTG 59.404 50.0 13.98 13.98 46.23 3.33 F
1048 2560 0.392461 ACAAGTCACAACACCGTGCT 60.392 50.0 0.00 0.00 36.80 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 3333 0.036294 GACTTGAGTTTCCCGAGGGG 60.036 60.000 8.53 0.0 46.11 4.79 R
2773 6370 1.069636 GCGTGAGGCTTTTGAGAGTTG 60.070 52.381 0.00 0.0 39.11 3.16 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
28 29 9.541884 TCCTATACTCTGGTGTATTATAATGCA 57.458 33.333 11.69 11.69 35.14 3.96
29 30 9.587772 CCTATACTCTGGTGTATTATAATGCAC 57.412 37.037 28.58 28.58 46.88 4.57
41 42 9.953697 TGTATTATAATGCACCGTAAAATTTCC 57.046 29.630 11.69 0.00 0.00 3.13
42 43 9.401873 GTATTATAATGCACCGTAAAATTTCCC 57.598 33.333 8.28 0.00 0.00 3.97
83 779 6.108687 CAGACAAACATCTCACTTAGCCATA 58.891 40.000 0.00 0.00 0.00 2.74
106 802 0.595588 TAAATGCACCAGCGGTTGTG 59.404 50.000 13.98 13.98 46.23 3.33
237 935 6.315144 AGAAAAACATGCACAAAGTTTTACCC 59.685 34.615 16.48 11.25 42.65 3.69
241 939 3.810310 TGCACAAAGTTTTACCCCAAG 57.190 42.857 0.00 0.00 0.00 3.61
286 985 3.281727 TTAAGAGGATGATGTGTGGGC 57.718 47.619 0.00 0.00 0.00 5.36
311 1010 8.300286 GCTGAAAAAGTTAGCTAGGAAAGAATT 58.700 33.333 0.00 0.00 34.70 2.17
347 1046 4.686091 TCTCATCACACATGAAGAAACGAC 59.314 41.667 0.00 0.00 38.69 4.34
429 1549 9.423061 AGAAATTACTATGCATTTGACCAAAAC 57.577 29.630 3.54 0.00 33.56 2.43
518 1866 2.923605 GCACACATGACATTGCTTCACC 60.924 50.000 0.00 0.00 32.00 4.02
558 1909 7.994911 TGTAAGATAAGATGCCATCTTCACATT 59.005 33.333 22.62 15.08 46.17 2.71
559 1910 6.879276 AGATAAGATGCCATCTTCACATTG 57.121 37.500 22.62 0.00 46.17 2.82
560 1911 6.363065 AGATAAGATGCCATCTTCACATTGT 58.637 36.000 22.62 0.00 46.17 2.71
561 1912 4.978083 AAGATGCCATCTTCACATTGTC 57.022 40.909 14.17 0.00 46.17 3.18
563 1914 2.583024 TGCCATCTTCACATTGTCCA 57.417 45.000 0.00 0.00 0.00 4.02
564 1915 2.874014 TGCCATCTTCACATTGTCCAA 58.126 42.857 0.00 0.00 0.00 3.53
633 2027 3.493028 TGGTGCATGACAACACAGT 57.507 47.368 12.47 0.00 42.53 3.55
645 2039 9.261180 GCATGACAACACAGTGTATATATAGTT 57.739 33.333 6.63 0.00 0.00 2.24
832 2325 5.708230 ACCATTTCGTAGCATTTCAAAGGTA 59.292 36.000 0.00 0.00 0.00 3.08
833 2326 6.207810 ACCATTTCGTAGCATTTCAAAGGTAA 59.792 34.615 0.00 0.00 0.00 2.85
895 2390 4.334203 CACATTGCATTTGATTTCCCATGG 59.666 41.667 4.14 4.14 0.00 3.66
986 2498 1.423921 CCCCTATAAAACCCCGCATCT 59.576 52.381 0.00 0.00 0.00 2.90
1045 2557 1.735571 GTTCACAAGTCACAACACCGT 59.264 47.619 0.00 0.00 0.00 4.83
1046 2558 1.364721 TCACAAGTCACAACACCGTG 58.635 50.000 0.00 0.00 38.29 4.94
1048 2560 0.392461 ACAAGTCACAACACCGTGCT 60.392 50.000 0.00 0.00 36.80 4.40
1053 2581 1.525995 CACAACACCGTGCTCCCTT 60.526 57.895 0.00 0.00 0.00 3.95
1058 2586 1.276622 ACACCGTGCTCCCTTAGATT 58.723 50.000 0.00 0.00 0.00 2.40
1070 2598 0.878961 CTTAGATTACCGCGCCACCC 60.879 60.000 0.00 0.00 0.00 4.61
1071 2599 2.314415 TTAGATTACCGCGCCACCCC 62.314 60.000 0.00 0.00 0.00 4.95
1072 2600 4.476752 GATTACCGCGCCACCCCA 62.477 66.667 0.00 0.00 0.00 4.96
1073 2601 4.483243 ATTACCGCGCCACCCCAG 62.483 66.667 0.00 0.00 0.00 4.45
1157 2694 3.709633 TCGACCATGCTGCTGGCT 61.710 61.111 15.16 5.80 40.15 4.75
1305 2842 2.203139 CCCACGTCACCTGCAACA 60.203 61.111 0.00 0.00 0.00 3.33
1360 2900 0.818296 CGACACCGATCCTTCTTCCT 59.182 55.000 0.00 0.00 38.22 3.36
1365 2905 1.207329 ACCGATCCTTCTTCCTTTCCG 59.793 52.381 0.00 0.00 0.00 4.30
1395 2938 6.701841 GCTTCTGTTCCATCGTATATTTCTGA 59.298 38.462 0.00 0.00 0.00 3.27
1396 2939 7.306866 GCTTCTGTTCCATCGTATATTTCTGAC 60.307 40.741 0.00 0.00 0.00 3.51
1554 3111 1.171308 CCCATCTGTTTCTGCCTGTG 58.829 55.000 0.00 0.00 0.00 3.66
1572 3129 2.417239 TGTGGCGATTAATTGTTCCGTC 59.583 45.455 4.60 0.00 0.00 4.79
1732 3329 3.636231 CCTCTCGGGGCACACCAA 61.636 66.667 0.00 0.00 42.91 3.67
1734 3331 3.164977 TCTCGGGGCACACCAACA 61.165 61.111 0.00 0.00 42.91 3.33
1735 3332 2.669569 CTCGGGGCACACCAACAG 60.670 66.667 0.00 0.00 42.91 3.16
1736 3333 4.947147 TCGGGGCACACCAACAGC 62.947 66.667 0.00 0.00 42.91 4.40
1830 3457 1.391485 GTTCTGCTCGTACAGTGCATG 59.609 52.381 12.42 0.00 46.57 4.06
1967 3670 1.063951 CGACCAGACGAGCGTGTAAC 61.064 60.000 0.00 0.00 35.09 2.50
1988 3703 4.246458 ACTAGGACGATTTTCTCAGTTGC 58.754 43.478 0.00 0.00 0.00 4.17
2039 3767 4.815308 CCAGTGATCTTCATCTCCATTGTC 59.185 45.833 0.00 0.00 0.00 3.18
2043 3771 5.296283 GTGATCTTCATCTCCATTGTCTTGG 59.704 44.000 0.00 0.00 38.18 3.61
2159 3887 2.266055 GCGGCAACTGCTAGACCT 59.734 61.111 1.06 0.00 41.70 3.85
2161 3889 0.528684 GCGGCAACTGCTAGACCTAG 60.529 60.000 1.06 0.00 41.70 3.02
2219 3980 2.772691 GCATGCAGCCAGAGAAGCC 61.773 63.158 14.21 0.00 37.23 4.35
2244 4006 1.351707 GCCGGTTCATGCATGTACG 59.648 57.895 25.43 24.20 0.00 3.67
2245 4007 1.366111 GCCGGTTCATGCATGTACGT 61.366 55.000 25.43 0.00 0.00 3.57
2249 4011 2.281498 CGGTTCATGCATGTACGTACTG 59.719 50.000 25.43 20.02 0.00 2.74
2323 4087 2.615912 CAGAGCAGGCAGGCTAATTTAC 59.384 50.000 3.56 0.00 45.99 2.01
2329 4095 4.377021 CAGGCAGGCTAATTTACGTATGA 58.623 43.478 0.00 0.00 0.00 2.15
2410 4257 5.511545 GGATGAGTTACCTAATGGAATCGCT 60.512 44.000 0.00 0.00 37.04 4.93
2413 4260 6.455647 TGAGTTACCTAATGGAATCGCTATG 58.544 40.000 0.00 0.00 37.04 2.23
2423 4270 2.939103 GGAATCGCTATGAAGTTGCTGT 59.061 45.455 0.00 0.00 0.00 4.40
2440 4287 2.123342 CTGTTCTGCTCGATCGAATCC 58.877 52.381 19.92 10.78 0.00 3.01
2466 4338 3.002656 CACAGAGTTGACTGCATTCGTTT 59.997 43.478 0.00 0.00 41.06 3.60
2487 4370 0.386476 TTCTGTGCGTTCAGTACCGT 59.614 50.000 8.35 0.00 36.85 4.83
2491 4374 0.160182 GTGCGTTCAGTACCGTTTCG 59.840 55.000 0.00 0.00 0.00 3.46
2493 4376 0.432361 GCGTTCAGTACCGTTTCGAC 59.568 55.000 0.00 0.00 0.00 4.20
2500 4383 0.661187 GTACCGTTTCGACGCTGACA 60.661 55.000 0.00 0.00 0.00 3.58
2514 4397 4.240888 ACGCTGACATATATGATCACAGC 58.759 43.478 27.29 27.29 43.48 4.40
2558 4444 9.444600 TTTTAGTACTTCAGAACAGAAAGTTGT 57.555 29.630 0.00 0.00 41.51 3.32
2575 4461 8.120465 AGAAAGTTGTGTTATGTTTTGAGTACG 58.880 33.333 0.00 0.00 0.00 3.67
2592 4478 5.936372 TGAGTACGTTGCTCTAGAGTTAGAA 59.064 40.000 20.75 6.59 35.55 2.10
2644 4539 0.468226 ACATGACTCAACGGTGTGGT 59.532 50.000 7.52 4.53 0.00 4.16
2645 4540 0.867746 CATGACTCAACGGTGTGGTG 59.132 55.000 7.52 0.00 0.00 4.17
2646 4541 0.468226 ATGACTCAACGGTGTGGTGT 59.532 50.000 7.52 0.00 0.00 4.16
2647 4542 1.112950 TGACTCAACGGTGTGGTGTA 58.887 50.000 7.52 0.00 0.00 2.90
2660 4555 2.280628 GTGGTGTAGATGCTACTTGGC 58.719 52.381 6.21 0.00 0.00 4.52
2664 4559 2.932614 GTGTAGATGCTACTTGGCAGTG 59.067 50.000 6.21 0.00 45.75 3.66
2686 6283 2.609459 CCCACTACATTTTGAGCTAGCG 59.391 50.000 9.55 0.00 0.00 4.26
2695 6292 0.539518 TTGAGCTAGCGGCCATTGTA 59.460 50.000 9.55 0.00 43.05 2.41
2696 6293 0.179084 TGAGCTAGCGGCCATTGTAC 60.179 55.000 9.55 0.00 43.05 2.90
2697 6294 1.215655 GAGCTAGCGGCCATTGTACG 61.216 60.000 9.55 0.00 43.05 3.67
2698 6295 1.227147 GCTAGCGGCCATTGTACGA 60.227 57.895 2.24 0.00 34.27 3.43
2699 6296 0.600255 GCTAGCGGCCATTGTACGAT 60.600 55.000 2.24 0.00 34.27 3.73
2700 6297 1.419374 CTAGCGGCCATTGTACGATC 58.581 55.000 2.24 0.00 0.00 3.69
2701 6298 0.747852 TAGCGGCCATTGTACGATCA 59.252 50.000 2.24 0.00 0.00 2.92
2711 6308 4.505556 CCATTGTACGATCAGACTGTGATG 59.494 45.833 1.59 0.00 46.64 3.07
2720 6317 4.341366 TCAGACTGTGATGAACATGTGT 57.659 40.909 0.00 0.00 38.39 3.72
2755 6352 3.529734 TGGATGCCATTTTCCCCTAGTAA 59.470 43.478 0.00 0.00 0.00 2.24
2791 6388 5.444663 AAATCAACTCTCAAAAGCCTCAC 57.555 39.130 0.00 0.00 0.00 3.51
2831 6457 5.277974 GCATGTCTGCTGTGAAAAGAGTAAA 60.278 40.000 0.00 0.00 45.32 2.01
2833 6459 4.816385 TGTCTGCTGTGAAAAGAGTAAAGG 59.184 41.667 0.00 0.00 0.00 3.11
2861 6487 6.715280 AGACATGTATTCTCAGTCCAACATT 58.285 36.000 0.00 0.00 0.00 2.71
2886 6512 8.633075 TTTTTGAGAAGAGTAAATGTTTGCTG 57.367 30.769 0.76 0.00 33.17 4.41
2893 6519 6.648879 AGAGTAAATGTTTGCTGCCTTAAA 57.351 33.333 0.76 0.00 33.17 1.52
2910 6536 7.543756 TGCCTTAAATTTACAAAGCCTACATC 58.456 34.615 0.00 0.00 0.00 3.06
2912 6538 8.899771 GCCTTAAATTTACAAAGCCTACATCTA 58.100 33.333 0.00 0.00 0.00 1.98
2914 6540 9.937175 CTTAAATTTACAAAGCCTACATCTAGC 57.063 33.333 0.00 0.00 0.00 3.42
2915 6541 6.944234 AATTTACAAAGCCTACATCTAGCC 57.056 37.500 0.00 0.00 0.00 3.93
2919 6608 2.074729 AAGCCTACATCTAGCCTCGT 57.925 50.000 0.00 0.00 0.00 4.18
2929 6618 6.260870 ACATCTAGCCTCGTATGTGAATAG 57.739 41.667 0.00 0.00 31.56 1.73
2933 6622 7.612668 TCTAGCCTCGTATGTGAATAGATAC 57.387 40.000 0.00 0.00 31.55 2.24
2974 6663 1.048601 GAGGCATGGACCTTCGGATA 58.951 55.000 0.00 0.00 41.32 2.59
2984 6673 2.354821 GACCTTCGGATATGCAACAACC 59.645 50.000 0.00 0.00 0.00 3.77
2987 6676 0.621082 TCGGATATGCAACAACCCCA 59.379 50.000 0.00 0.00 0.00 4.96
2991 6680 3.233507 GGATATGCAACAACCCCATCAT 58.766 45.455 0.00 0.00 0.00 2.45
2995 6684 6.835488 GGATATGCAACAACCCCATCATATAT 59.165 38.462 0.00 0.00 30.12 0.86
2998 6687 5.453158 TGCAACAACCCCATCATATATGAA 58.547 37.500 19.03 3.67 40.69 2.57
3005 6696 7.619302 ACAACCCCATCATATATGAAGTGTTTT 59.381 33.333 19.03 10.27 40.69 2.43
3070 6761 3.011818 TGATGCACACAGCCATTCTTAG 58.988 45.455 0.00 0.00 44.83 2.18
3079 6770 5.048504 ACACAGCCATTCTTAGTGATTGTTG 60.049 40.000 0.00 0.00 34.47 3.33
3086 6777 6.149973 CCATTCTTAGTGATTGTTGAGCAGAA 59.850 38.462 0.00 0.00 0.00 3.02
3108 6799 8.506437 CAGAATACAAAGCAAAGTCAACTATGA 58.494 33.333 0.00 0.00 0.00 2.15
3135 6826 7.864379 CCCAAGCATTACAAGATATGAAATCAC 59.136 37.037 0.00 0.00 0.00 3.06
3136 6827 8.627403 CCAAGCATTACAAGATATGAAATCACT 58.373 33.333 0.00 0.00 0.00 3.41
3172 6863 9.662545 TGTCATTATAATATTTCGTTGCACATG 57.337 29.630 0.00 0.00 0.00 3.21
3188 6879 7.538575 GTTGCACATGTCTTTGTAATTAGGAT 58.461 34.615 0.00 0.00 0.00 3.24
3238 6932 2.833794 AGCAAGACAGAACACGCTTAA 58.166 42.857 0.00 0.00 0.00 1.85
3253 6947 6.847400 ACACGCTTAAATATACATGCAAACA 58.153 32.000 0.00 0.00 0.00 2.83
3278 6972 2.808543 GAGTCCTTTTACCTGCACACAG 59.191 50.000 0.00 0.00 44.05 3.66
3348 7042 0.179067 TATGATCCGACGGCCCAAAC 60.179 55.000 9.66 0.00 0.00 2.93
3359 7053 2.224572 ACGGCCCAAACTACACAATACA 60.225 45.455 0.00 0.00 0.00 2.29
3360 7054 2.418628 CGGCCCAAACTACACAATACAG 59.581 50.000 0.00 0.00 0.00 2.74
3362 7056 2.163613 GCCCAAACTACACAATACAGCC 59.836 50.000 0.00 0.00 0.00 4.85
3394 7092 8.763984 TTCTTGTAGTGTATTTGGGGTTTAAA 57.236 30.769 0.00 0.00 0.00 1.52
3422 7120 6.337356 ACTTTGGGTAGTTCACATGTTTTTG 58.663 36.000 0.00 0.00 0.00 2.44
3423 7121 5.923733 TTGGGTAGTTCACATGTTTTTGT 57.076 34.783 0.00 0.00 0.00 2.83
3425 7123 4.339814 TGGGTAGTTCACATGTTTTTGTCC 59.660 41.667 0.00 0.00 0.00 4.02
3433 7131 6.083098 TCACATGTTTTTGTCCGATCAATT 57.917 33.333 0.00 0.00 0.00 2.32
3440 7138 0.322098 TGTCCGATCAATTTGCCGGT 60.322 50.000 21.11 0.00 42.34 5.28
3441 7139 0.808755 GTCCGATCAATTTGCCGGTT 59.191 50.000 21.11 0.00 42.34 4.44
3452 7150 3.428282 GCCGGTTTGTGGCGTAGG 61.428 66.667 1.90 0.00 43.70 3.18
3468 7170 0.756294 TAGGGTGGGTGCATATGTCG 59.244 55.000 4.29 0.00 0.00 4.35
3471 7173 2.203001 TGGGTGCATATGTCGGCG 60.203 61.111 0.00 0.00 0.00 6.46
3488 7214 2.224079 CGGCGGTGATCAGGATTAATTG 59.776 50.000 0.00 0.00 0.00 2.32
3541 7268 6.699642 CCAAAATACCAAGTTGTCGTCAAATT 59.300 34.615 2.33 2.33 41.51 1.82
3549 7276 5.684550 AGTTGTCGTCAAATTAAACTCCC 57.315 39.130 0.00 0.00 35.20 4.30
3570 7297 4.214310 CCAGCCAAACCATATTGACCATA 58.786 43.478 0.00 0.00 31.84 2.74
3573 7300 5.771666 CAGCCAAACCATATTGACCATAGAT 59.228 40.000 0.00 0.00 31.84 1.98
3574 7301 6.006449 AGCCAAACCATATTGACCATAGATC 58.994 40.000 0.00 0.00 31.84 2.75
3575 7302 5.769662 GCCAAACCATATTGACCATAGATCA 59.230 40.000 0.00 0.00 31.84 2.92
3576 7303 6.265196 GCCAAACCATATTGACCATAGATCAA 59.735 38.462 0.00 0.00 40.25 2.57
3577 7304 7.651808 CCAAACCATATTGACCATAGATCAAC 58.348 38.462 0.00 0.00 38.84 3.18
3578 7305 7.503566 CCAAACCATATTGACCATAGATCAACT 59.496 37.037 0.00 0.00 38.84 3.16
3579 7306 8.906867 CAAACCATATTGACCATAGATCAACTT 58.093 33.333 0.00 0.00 38.84 2.66
3656 7386 9.982651 GTAGTATGATGCATCCTAAAACTCTAA 57.017 33.333 23.67 0.71 0.00 2.10
3703 7433 5.347364 GCTACATGAAGCTAGCTATAGTTGC 59.653 44.000 19.70 20.26 39.50 4.17
3714 7444 7.029563 GCTAGCTATAGTTGCACATTTTTGTT 58.970 34.615 7.70 0.00 0.00 2.83
3719 7449 7.061094 GCTATAGTTGCACATTTTTGTTCAGTC 59.939 37.037 0.84 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.541884 TGCATTATAATACACCAGAGTATAGGA 57.458 33.333 0.00 0.00 33.73 2.94
3 4 9.587772 GTGCATTATAATACACCAGAGTATAGG 57.412 37.037 15.35 0.00 33.73 2.57
13 14 9.738832 AAATTTTACGGTGCATTATAATACACC 57.261 29.630 27.91 27.91 45.41 4.16
15 16 9.953697 GGAAATTTTACGGTGCATTATAATACA 57.046 29.630 0.00 0.00 0.00 2.29
16 17 9.401873 GGGAAATTTTACGGTGCATTATAATAC 57.598 33.333 0.00 0.00 0.00 1.89
17 18 9.357161 AGGGAAATTTTACGGTGCATTATAATA 57.643 29.630 0.00 0.00 0.00 0.98
18 19 8.245195 AGGGAAATTTTACGGTGCATTATAAT 57.755 30.769 0.00 0.00 0.00 1.28
19 20 7.648039 AGGGAAATTTTACGGTGCATTATAA 57.352 32.000 0.00 0.00 0.00 0.98
20 21 8.749026 TTAGGGAAATTTTACGGTGCATTATA 57.251 30.769 0.00 0.00 0.00 0.98
21 22 7.648039 TTAGGGAAATTTTACGGTGCATTAT 57.352 32.000 0.00 0.00 0.00 1.28
22 23 7.463961 TTTAGGGAAATTTTACGGTGCATTA 57.536 32.000 0.00 0.00 0.00 1.90
23 24 5.986501 TTAGGGAAATTTTACGGTGCATT 57.013 34.783 0.00 0.00 0.00 3.56
24 25 5.986501 TTTAGGGAAATTTTACGGTGCAT 57.013 34.783 0.00 0.00 0.00 3.96
25 26 5.244178 ACATTTAGGGAAATTTTACGGTGCA 59.756 36.000 0.00 0.00 32.73 4.57
26 27 5.716094 ACATTTAGGGAAATTTTACGGTGC 58.284 37.500 0.00 0.00 32.73 5.01
37 38 9.998106 GTCTGCTTAGATATACATTTAGGGAAA 57.002 33.333 0.00 0.00 0.00 3.13
38 39 9.154632 TGTCTGCTTAGATATACATTTAGGGAA 57.845 33.333 0.00 0.00 0.00 3.97
39 40 8.721133 TGTCTGCTTAGATATACATTTAGGGA 57.279 34.615 0.00 0.00 0.00 4.20
40 41 9.778741 TTTGTCTGCTTAGATATACATTTAGGG 57.221 33.333 0.00 0.00 0.00 3.53
83 779 2.682856 CAACCGCTGGTGCATTTATAGT 59.317 45.455 0.94 0.00 39.64 2.12
106 802 3.181461 CCTGTGGATACTCTTGATGTCCC 60.181 52.174 0.00 0.00 37.61 4.46
237 935 1.244019 GCTTGGCCACCTGTACTTGG 61.244 60.000 3.88 0.00 35.81 3.61
241 939 3.668386 GTGCTTGGCCACCTGTAC 58.332 61.111 3.88 4.88 0.00 2.90
311 1010 8.780249 CATGTGTGATGAGATAAGATTTGCATA 58.220 33.333 0.00 0.00 0.00 3.14
558 1909 6.729690 AAAAATCTTGGACAATCTTGGACA 57.270 33.333 0.00 0.00 0.00 4.02
559 1910 8.110860 TCTAAAAATCTTGGACAATCTTGGAC 57.889 34.615 0.00 0.00 0.00 4.02
560 1911 8.884124 ATCTAAAAATCTTGGACAATCTTGGA 57.116 30.769 0.00 0.00 0.00 3.53
645 2039 9.595823 GCATAGTAGTTTTTGGACAGATACTAA 57.404 33.333 0.00 0.00 30.52 2.24
648 2042 7.843490 TGCATAGTAGTTTTTGGACAGATAC 57.157 36.000 0.00 0.00 0.00 2.24
761 2251 0.602905 CCTTTTCCTCGAACTGCCGT 60.603 55.000 0.00 0.00 0.00 5.68
832 2325 0.469705 TTGGACAATGGCAGCTGGTT 60.470 50.000 17.12 0.00 0.00 3.67
833 2326 0.469705 TTTGGACAATGGCAGCTGGT 60.470 50.000 17.12 3.76 0.00 4.00
895 2390 0.947244 CCTCCTTGTCAACACTGTGC 59.053 55.000 7.90 0.00 0.00 4.57
986 2498 0.533032 TGATCGTCATGCCGTGGTTA 59.467 50.000 0.00 0.00 0.00 2.85
1045 2557 0.387929 CGCGGTAATCTAAGGGAGCA 59.612 55.000 0.00 0.00 0.00 4.26
1046 2558 0.944788 GCGCGGTAATCTAAGGGAGC 60.945 60.000 8.83 0.00 0.00 4.70
1048 2560 1.044231 TGGCGCGGTAATCTAAGGGA 61.044 55.000 8.83 0.00 0.00 4.20
1053 2581 2.799452 GGGGTGGCGCGGTAATCTA 61.799 63.158 8.83 0.00 0.00 1.98
1071 2599 4.133373 CATGGGGACTGGGGGCTG 62.133 72.222 0.00 0.00 0.00 4.85
1205 2742 2.128507 GTCCTGTAGGCCTCTCCGG 61.129 68.421 9.68 10.33 40.77 5.14
1360 2900 2.103432 TGGAACAGAAGCAGTACGGAAA 59.897 45.455 0.00 0.00 0.00 3.13
1395 2938 0.173708 GATGAAGAAGACGAGGCGGT 59.826 55.000 0.00 0.00 0.00 5.68
1396 2939 0.528684 GGATGAAGAAGACGAGGCGG 60.529 60.000 0.00 0.00 0.00 6.13
1517 3068 1.478916 GGGTTAGAGAGGCTCACAGTC 59.521 57.143 18.26 5.28 32.06 3.51
1554 3111 1.928503 TCGACGGAACAATTAATCGCC 59.071 47.619 0.00 0.00 0.00 5.54
1558 3115 1.662122 GGCGTCGACGGAACAATTAAT 59.338 47.619 36.13 0.00 40.23 1.40
1559 3116 1.070038 GGCGTCGACGGAACAATTAA 58.930 50.000 36.13 0.00 40.23 1.40
1560 3117 1.072116 CGGCGTCGACGGAACAATTA 61.072 55.000 36.13 0.00 40.23 1.40
1561 3118 2.377310 CGGCGTCGACGGAACAATT 61.377 57.895 36.13 0.00 40.23 2.32
1572 3129 1.081556 TTGATCCATCAACGGCGTCG 61.082 55.000 15.17 8.42 41.51 5.12
1667 3264 0.178990 GGTTCTCCAAGTTGCCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
1727 3324 4.722700 CCCGAGGGGCTGTTGGTG 62.723 72.222 0.00 0.00 35.35 4.17
1729 3326 3.204467 TTTCCCGAGGGGCTGTTGG 62.204 63.158 8.53 0.00 43.94 3.77
1730 3327 1.971695 GTTTCCCGAGGGGCTGTTG 60.972 63.158 8.53 0.00 43.94 3.33
1731 3328 2.125766 GAGTTTCCCGAGGGGCTGTT 62.126 60.000 8.53 0.00 43.94 3.16
1732 3329 2.529389 AGTTTCCCGAGGGGCTGT 60.529 61.111 8.53 0.00 43.94 4.40
1734 3331 1.842381 CTTGAGTTTCCCGAGGGGCT 61.842 60.000 8.53 4.57 43.94 5.19
1735 3332 1.377333 CTTGAGTTTCCCGAGGGGC 60.377 63.158 8.53 0.00 43.94 5.80
1736 3333 0.036294 GACTTGAGTTTCCCGAGGGG 60.036 60.000 8.53 0.00 46.11 4.79
1737 3334 0.977395 AGACTTGAGTTTCCCGAGGG 59.023 55.000 0.65 0.65 0.00 4.30
1830 3457 8.031277 AGCCAAACTTGTTTTATCATGAGAATC 58.969 33.333 3.15 1.69 0.00 2.52
1967 3670 4.499183 AGCAACTGAGAAAATCGTCCTAG 58.501 43.478 0.00 0.00 0.00 3.02
1988 3703 3.453424 TGATCGTCGAGAGAGAAGAGAG 58.547 50.000 0.00 0.00 43.49 3.20
2043 3771 4.598062 GTTGTTTGAGAGGTTACTGCAAC 58.402 43.478 0.00 0.00 36.32 4.17
2138 3866 2.359850 CTAGCAGTTGCCGCCCAA 60.360 61.111 0.00 0.00 43.38 4.12
2244 4006 3.119245 TCACGAATCCACCTAAGCAGTAC 60.119 47.826 0.00 0.00 0.00 2.73
2245 4007 3.093814 TCACGAATCCACCTAAGCAGTA 58.906 45.455 0.00 0.00 0.00 2.74
2249 4011 1.291132 GCTCACGAATCCACCTAAGC 58.709 55.000 0.00 0.00 0.00 3.09
2323 4087 2.789339 CTCGGCTTGTACACATCATACG 59.211 50.000 0.00 0.00 0.00 3.06
2329 4095 1.749063 TCGATCTCGGCTTGTACACAT 59.251 47.619 0.00 0.00 40.29 3.21
2372 4138 1.944035 CATCCCATCGATGGCAACG 59.056 57.895 34.77 22.53 46.70 4.10
2410 4257 2.995939 CGAGCAGAACAGCAACTTCATA 59.004 45.455 0.00 0.00 36.85 2.15
2413 4260 1.502231 TCGAGCAGAACAGCAACTTC 58.498 50.000 0.00 0.00 36.85 3.01
2423 4270 3.181476 TGAATGGATTCGATCGAGCAGAA 60.181 43.478 18.54 3.09 39.62 3.02
2440 4287 4.668431 CGAATGCAGTCAACTCTGTGAATG 60.668 45.833 15.31 0.00 44.42 2.67
2466 4338 1.860676 GGTACTGAACGCACAGAACA 58.139 50.000 14.74 0.00 40.63 3.18
2487 4370 5.629435 GTGATCATATATGTCAGCGTCGAAA 59.371 40.000 12.42 0.00 0.00 3.46
2491 4374 4.325741 GCTGTGATCATATATGTCAGCGTC 59.674 45.833 23.57 12.91 37.62 5.19
2493 4376 4.836931 GCTGTGATCATATATGTCAGCG 57.163 45.455 23.57 15.97 37.62 5.18
2500 4383 8.501580 CGTCAAATTTGAGCTGTGATCATATAT 58.498 33.333 21.05 0.00 37.98 0.86
2554 4440 6.075780 GCAACGTACTCAAAACATAACACAAC 60.076 38.462 0.00 0.00 0.00 3.32
2558 4444 5.756347 AGAGCAACGTACTCAAAACATAACA 59.244 36.000 17.83 0.00 36.58 2.41
2622 4517 2.066262 CACACCGTTGAGTCATGTACC 58.934 52.381 0.00 0.00 0.00 3.34
2623 4518 2.066262 CCACACCGTTGAGTCATGTAC 58.934 52.381 0.00 0.00 0.00 2.90
2644 4539 2.677902 GCACTGCCAAGTAGCATCTACA 60.678 50.000 6.74 0.00 43.09 2.74
2645 4540 1.936547 GCACTGCCAAGTAGCATCTAC 59.063 52.381 0.00 0.00 43.09 2.59
2646 4541 2.315925 GCACTGCCAAGTAGCATCTA 57.684 50.000 0.00 0.00 43.09 1.98
2647 4542 3.165606 GCACTGCCAAGTAGCATCT 57.834 52.632 0.00 0.00 43.09 2.90
2660 4555 2.095059 GCTCAAAATGTAGTGGGCACTG 60.095 50.000 0.00 0.00 41.13 3.66
2664 4559 2.356069 GCTAGCTCAAAATGTAGTGGGC 59.644 50.000 7.70 0.00 41.83 5.36
2686 6283 2.205074 CAGTCTGATCGTACAATGGCC 58.795 52.381 0.00 0.00 0.00 5.36
2695 6292 3.942130 TGTTCATCACAGTCTGATCGT 57.058 42.857 6.91 0.00 37.53 3.73
2696 6293 4.032558 CACATGTTCATCACAGTCTGATCG 59.967 45.833 6.91 0.00 37.53 3.69
2697 6294 4.934001 ACACATGTTCATCACAGTCTGATC 59.066 41.667 6.91 0.00 37.53 2.92
2698 6295 4.903054 ACACATGTTCATCACAGTCTGAT 58.097 39.130 6.91 0.00 40.59 2.90
2699 6296 4.341366 ACACATGTTCATCACAGTCTGA 57.659 40.909 6.91 0.00 39.40 3.27
2700 6297 5.428496 AAACACATGTTCATCACAGTCTG 57.572 39.130 0.00 0.00 39.40 3.51
2701 6298 6.455360 AAAAACACATGTTCATCACAGTCT 57.545 33.333 0.00 0.00 39.40 3.24
2740 6337 7.396055 TGGATTTTGTCTTACTAGGGGAAAATG 59.604 37.037 0.00 0.00 0.00 2.32
2773 6370 1.069636 GCGTGAGGCTTTTGAGAGTTG 60.070 52.381 0.00 0.00 39.11 3.16
2831 6457 5.362430 GGACTGAGAATACATGTCTTCTCCT 59.638 44.000 33.72 24.78 44.36 3.69
2833 6459 6.214191 TGGACTGAGAATACATGTCTTCTC 57.786 41.667 31.97 31.97 44.92 2.87
2861 6487 7.222611 GCAGCAAACATTTACTCTTCTCAAAAA 59.777 33.333 0.00 0.00 0.00 1.94
2886 6512 7.772166 AGATGTAGGCTTTGTAAATTTAAGGC 58.228 34.615 14.70 14.70 42.74 4.35
2910 6536 6.374613 TGGTATCTATTCACATACGAGGCTAG 59.625 42.308 0.00 0.00 0.00 3.42
2912 6538 5.077564 TGGTATCTATTCACATACGAGGCT 58.922 41.667 0.00 0.00 0.00 4.58
2913 6539 5.386958 TGGTATCTATTCACATACGAGGC 57.613 43.478 0.00 0.00 0.00 4.70
2914 6540 7.397892 AGATGGTATCTATTCACATACGAGG 57.602 40.000 0.00 0.00 38.00 4.63
2929 6618 8.916654 CACACGATCTATTGTTAAGATGGTATC 58.083 37.037 0.00 0.00 39.50 2.24
2933 6622 6.422100 CCTCACACGATCTATTGTTAAGATGG 59.578 42.308 0.00 0.00 33.82 3.51
2945 6634 1.409064 GTCCATGCCTCACACGATCTA 59.591 52.381 0.00 0.00 0.00 1.98
2974 6663 5.643176 TCATATATGATGGGGTTGTTGCAT 58.357 37.500 11.49 0.00 0.00 3.96
3045 6736 1.171308 ATGGCTGTGTGCATCAGAAC 58.829 50.000 20.74 14.21 45.15 3.01
3060 6751 4.156556 TGCTCAACAATCACTAAGAATGGC 59.843 41.667 0.00 0.00 31.16 4.40
3070 6761 5.570589 GCTTTGTATTCTGCTCAACAATCAC 59.429 40.000 0.00 0.00 32.31 3.06
3079 6770 5.362556 TGACTTTGCTTTGTATTCTGCTC 57.637 39.130 0.00 0.00 0.00 4.26
3108 6799 7.560991 TGATTTCATATCTTGTAATGCTTGGGT 59.439 33.333 0.00 0.00 0.00 4.51
3167 6858 8.498054 ACTCATCCTAATTACAAAGACATGTG 57.502 34.615 1.15 0.00 34.75 3.21
3188 6879 5.509716 TCAACTCGAGACTTACAAACTCA 57.490 39.130 21.68 0.00 0.00 3.41
3238 6932 6.886459 AGGACTCTTGTGTTTGCATGTATATT 59.114 34.615 0.00 0.00 0.00 1.28
3253 6947 3.118038 TGTGCAGGTAAAAGGACTCTTGT 60.118 43.478 0.00 0.00 32.75 3.16
3278 6972 3.391049 ACTGTAAAAGGACTCTTGCGTC 58.609 45.455 0.00 0.00 32.75 5.19
3316 7010 5.810074 CGTCGGATCATATAAATACATGGCA 59.190 40.000 0.00 0.00 0.00 4.92
3322 7016 4.117685 GGGCCGTCGGATCATATAAATAC 58.882 47.826 17.49 0.00 0.00 1.89
3348 7042 6.913170 AGAATTTTGTGGCTGTATTGTGTAG 58.087 36.000 0.00 0.00 0.00 2.74
3359 7053 7.524717 AATACACTACAAGAATTTTGTGGCT 57.475 32.000 13.08 5.34 34.76 4.75
3360 7054 7.116233 CCAAATACACTACAAGAATTTTGTGGC 59.884 37.037 13.08 0.00 34.76 5.01
3362 7056 7.598493 CCCCAAATACACTACAAGAATTTTGTG 59.402 37.037 13.08 0.00 34.11 3.33
3394 7092 4.349930 ACATGTGAACTACCCAAAGTACCT 59.650 41.667 0.00 0.00 0.00 3.08
3415 7113 4.054671 GGCAAATTGATCGGACAAAAACA 58.945 39.130 0.00 0.00 33.44 2.83
3422 7120 0.808755 AACCGGCAAATTGATCGGAC 59.191 50.000 25.98 0.00 44.69 4.79
3423 7121 1.201181 CAAACCGGCAAATTGATCGGA 59.799 47.619 25.98 0.00 44.69 4.55
3425 7123 1.984990 CACAAACCGGCAAATTGATCG 59.015 47.619 0.00 0.00 0.00 3.69
3440 7138 2.432563 CCCACCCTACGCCACAAA 59.567 61.111 0.00 0.00 0.00 2.83
3441 7139 2.850130 ACCCACCCTACGCCACAA 60.850 61.111 0.00 0.00 0.00 3.33
3452 7150 2.186826 GCCGACATATGCACCCACC 61.187 63.158 1.58 0.00 0.00 4.61
3468 7170 2.030805 GCAATTAATCCTGATCACCGCC 60.031 50.000 0.00 0.00 0.00 6.13
3471 7173 4.464008 TCCTGCAATTAATCCTGATCACC 58.536 43.478 0.00 0.00 0.00 4.02
3517 7243 7.692908 AATTTGACGACAACTTGGTATTTTG 57.307 32.000 0.00 0.00 35.63 2.44
3541 7268 2.990740 ATGGTTTGGCTGGGAGTTTA 57.009 45.000 0.00 0.00 0.00 2.01
3549 7276 5.132502 TCTATGGTCAATATGGTTTGGCTG 58.867 41.667 0.00 0.00 31.84 4.85
3641 7368 6.634436 GCATCGCATTTTAGAGTTTTAGGATG 59.366 38.462 0.00 0.00 0.00 3.51
3703 7433 4.339247 AGGACTGGACTGAACAAAAATGTG 59.661 41.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.