Multiple sequence alignment - TraesCS1D01G350700

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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 TraesCS1D01G350700 chr1D 100.000 2742 0 0 1 2742 436211965 436209224 0.000000e+00 5064.0
1 TraesCS1D01G350700 chr1B 91.345 1294 74 18 752 2030 591228851 591227581 0.000000e+00 1735.0
2 TraesCS1D01G350700 chr1B 86.070 603 63 11 6 599 591229735 591229145 1.790000e-176 628.0
3 TraesCS1D01G350700 chr1B 87.681 276 13 11 2134 2405 591227544 591227286 4.440000e-78 302.0
4 TraesCS1D01G350700 chr1B 88.235 119 11 3 2556 2674 591227203 591227088 3.680000e-29 139.0
5 TraesCS1D01G350700 chr1B 84.884 86 8 1 2443 2528 591227276 591227196 6.290000e-12 82.4
6 TraesCS1D01G350700 chr1A 86.849 1574 99 39 602 2117 533462784 533461261 0.000000e+00 1661.0
7 TraesCS1D01G350700 chr1A 86.401 603 58 8 1 601 533463529 533462949 2.980000e-179 638.0
8 TraesCS1D01G350700 chr1A 93.000 100 5 1 2505 2602 533460891 533460792 7.910000e-31 145.0
9 TraesCS1D01G350700 chr3B 84.477 612 59 19 26 601 565434912 565435523 3.060000e-159 571.0
10 TraesCS1D01G350700 chr3B 83.914 373 40 15 231 601 565564968 565565322 3.380000e-89 339.0
11 TraesCS1D01G350700 chr3B 95.333 150 7 0 116 265 565564826 565564975 3.530000e-59 239.0
12 TraesCS1D01G350700 chr3B 84.416 77 11 1 2042 2118 465215504 465215429 1.050000e-09 75.0
13 TraesCS1D01G350700 chr3D 88.163 490 42 13 116 601 433193281 433193758 1.100000e-158 569.0
14 TraesCS1D01G350700 chr3A 86.437 494 53 10 116 601 571399303 571399790 1.870000e-146 529.0
15 TraesCS1D01G350700 chr3A 90.476 126 12 0 1 126 571399154 571399279 1.690000e-37 167.0
16 TraesCS1D01G350700 chr3A 78.824 255 29 14 621 856 571399996 571400244 6.120000e-32 148.0
17 TraesCS1D01G350700 chr3A 89.062 64 7 0 2055 2118 478674192 478674129 2.260000e-11 80.5


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 TraesCS1D01G350700 chr1D 436209224 436211965 2741 True 5064.000000 5064 100.000000 1 2742 1 chr1D.!!$R1 2741
1 TraesCS1D01G350700 chr1B 591227088 591229735 2647 True 577.280000 1735 87.643000 6 2674 5 chr1B.!!$R1 2668
2 TraesCS1D01G350700 chr1A 533460792 533463529 2737 True 814.666667 1661 88.750000 1 2602 3 chr1A.!!$R1 2601
3 TraesCS1D01G350700 chr3B 565434912 565435523 611 False 571.000000 571 84.477000 26 601 1 chr3B.!!$F1 575
4 TraesCS1D01G350700 chr3A 571399154 571400244 1090 False 281.333333 529 85.245667 1 856 3 chr3A.!!$F1 855

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
490 543 0.896923 TGAGGGCCATGCAATTGAAC 59.103 50.0 10.34 0.0 0.0 3.18 F
864 1186 0.933791 AGATGAGAGGAGGAGGGGGT 60.934 60.0 0.00 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1734 0.099791 CCTTCTTCCTCGTCGCTCTC 59.900 60.0 0.0 0.0 0.0 3.20 R
1903 2253 0.167033 CCGAGCAGATATCGTCGAGG 59.833 60.0 20.2 0.0 38.5 4.63 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
77 78 1.838112 TGCCCATCAGCAGGTTTAAG 58.162 50.000 0.00 0.00 38.00 1.85
90 91 7.334421 TCAGCAGGTTTAAGATAGCAGTTAAAG 59.666 37.037 0.00 0.00 30.62 1.85
298 334 2.363359 CTCCATGAGGATGTCATCGACA 59.637 50.000 6.74 9.34 44.73 4.35
353 390 4.034163 CAGATCACTGTTGCTTATGCTCAG 59.966 45.833 17.55 17.55 42.47 3.35
367 405 1.654954 GCTCAGCCCTGCATGAACAG 61.655 60.000 0.00 0.00 37.42 3.16
375 413 1.067364 CCTGCATGAACAGTTTGCACA 59.933 47.619 8.34 0.00 41.18 4.57
406 444 4.590647 TGAGAGAAAGTCCAACTCACTCAT 59.409 41.667 12.52 3.03 34.84 2.90
409 447 4.892433 AGAAAGTCCAACTCACTCATCAG 58.108 43.478 0.00 0.00 0.00 2.90
428 466 6.273026 TCATCAGATTTGGCCTCCTATATTCA 59.727 38.462 3.32 0.00 0.00 2.57
429 467 6.708885 TCAGATTTGGCCTCCTATATTCAT 57.291 37.500 3.32 0.00 0.00 2.57
432 470 9.506042 TCAGATTTGGCCTCCTATATTCATATA 57.494 33.333 3.32 0.00 0.00 0.86
433 471 9.553064 CAGATTTGGCCTCCTATATTCATATAC 57.447 37.037 3.32 0.00 0.00 1.47
439 480 6.239064 GGCCTCCTATATTCATATACGGAGTG 60.239 46.154 18.91 14.81 45.73 3.51
440 481 6.736243 GCCTCCTATATTCATATACGGAGTGC 60.736 46.154 18.91 17.76 45.73 4.40
460 501 2.165845 GCTACTCTAAGGCTCCGTTTGA 59.834 50.000 0.00 0.00 0.00 2.69
482 535 2.309613 TGTTGATATTGAGGGCCATGC 58.690 47.619 6.18 0.00 0.00 4.06
490 543 0.896923 TGAGGGCCATGCAATTGAAC 59.103 50.000 10.34 0.00 0.00 3.18
495 548 1.673626 GGCCATGCAATTGAACTGGTG 60.674 52.381 10.34 0.00 0.00 4.17
523 576 8.512956 CAATATCAAATCTCCCAGACATTGATC 58.487 37.037 14.88 0.00 40.40 2.92
535 590 7.398047 TCCCAGACATTGATCTTGAAATTGAAT 59.602 33.333 0.00 0.00 0.00 2.57
555 618 6.506147 TGAATCTGAATTGTGTTGTTTGGAG 58.494 36.000 0.00 0.00 0.00 3.86
565 628 4.524714 TGTGTTGTTTGGAGGTTCAAGAAA 59.475 37.500 0.00 0.00 0.00 2.52
569 632 6.098124 TGTTGTTTGGAGGTTCAAGAAATGAT 59.902 34.615 0.00 0.00 38.03 2.45
592 655 3.007398 ACTTGGAACTCACATGAGAGACC 59.993 47.826 24.57 23.30 44.74 3.85
612 892 9.014297 AGAGACCCAATTCTGTACAAAAATAAG 57.986 33.333 0.00 0.00 0.00 1.73
614 894 9.362151 AGACCCAATTCTGTACAAAAATAAGAA 57.638 29.630 0.00 0.00 0.00 2.52
830 1152 1.219393 CGCAGAGAGGGGGAAAGAC 59.781 63.158 0.00 0.00 0.00 3.01
833 1155 1.990614 AGAGAGGGGGAAAGACGGC 60.991 63.158 0.00 0.00 0.00 5.68
834 1156 3.009714 AGAGGGGGAAAGACGGCC 61.010 66.667 0.00 0.00 0.00 6.13
864 1186 0.933791 AGATGAGAGGAGGAGGGGGT 60.934 60.000 0.00 0.00 0.00 4.95
866 1188 1.531981 ATGAGAGGAGGAGGGGGTGT 61.532 60.000 0.00 0.00 0.00 4.16
910 1232 4.814294 CTTTCCGCCGCCGCTACT 62.814 66.667 0.00 0.00 0.00 2.57
991 1313 6.043706 ACCAAATATGTGGAGGATCTTCTAGG 59.956 42.308 19.42 0.00 41.65 3.02
1049 1377 1.459348 CCCAAACAGGCCCAAAGGT 60.459 57.895 0.00 0.00 35.39 3.50
1061 1389 3.383505 GGCCCAAAGGTATCACCAAATAC 59.616 47.826 0.00 0.00 41.95 1.89
1388 1731 1.514443 GCCTCCGACGACGAAGAAG 60.514 63.158 9.28 0.85 42.66 2.85
1389 1732 1.919956 GCCTCCGACGACGAAGAAGA 61.920 60.000 9.28 0.00 42.66 2.87
1390 1733 0.520404 CCTCCGACGACGAAGAAGAA 59.480 55.000 9.28 0.00 42.66 2.52
1391 1734 1.466024 CCTCCGACGACGAAGAAGAAG 60.466 57.143 9.28 0.00 42.66 2.85
1392 1735 1.463831 CTCCGACGACGAAGAAGAAGA 59.536 52.381 9.28 0.00 42.66 2.87
1393 1736 1.463831 TCCGACGACGAAGAAGAAGAG 59.536 52.381 9.28 0.00 42.66 2.85
1624 1967 2.290367 CGACTAGACAGAGCAGATGAGG 59.710 54.545 0.00 0.00 0.00 3.86
1625 1968 3.287222 GACTAGACAGAGCAGATGAGGT 58.713 50.000 0.00 0.00 0.00 3.85
1626 1969 3.023119 ACTAGACAGAGCAGATGAGGTG 58.977 50.000 0.00 0.00 0.00 4.00
1627 1970 2.228545 AGACAGAGCAGATGAGGTGA 57.771 50.000 0.00 0.00 0.00 4.02
1628 1971 2.533916 AGACAGAGCAGATGAGGTGAA 58.466 47.619 0.00 0.00 0.00 3.18
1683 2026 2.162408 GCTTGTGATCTGCCTTTGTACC 59.838 50.000 0.00 0.00 0.00 3.34
1714 2057 0.242286 CCTCTGTCGCCATAGATCCG 59.758 60.000 0.00 0.00 0.00 4.18
1733 2076 0.466124 GGTAGGATTGCCTCTCGCTT 59.534 55.000 0.00 0.00 45.54 4.68
1784 2129 1.668337 CGCCGATGAGATCAGTGATCC 60.668 57.143 26.14 18.52 39.66 3.36
1828 2173 5.896678 TGTATGGATTTTATGGAGGTTTGGG 59.103 40.000 0.00 0.00 0.00 4.12
1857 2207 2.995939 CAGAGCGTGCTTGTCTTGATTA 59.004 45.455 0.00 0.00 0.00 1.75
1874 2224 7.227512 GTCTTGATTATGGAGAAATCCGAATGT 59.772 37.037 0.00 0.00 33.28 2.71
1902 2252 0.531532 CTGCTCTCCGTGGGCATAAG 60.532 60.000 0.65 0.00 35.37 1.73
1903 2253 1.889573 GCTCTCCGTGGGCATAAGC 60.890 63.158 0.00 0.00 41.10 3.09
1918 2268 2.991434 TAAGCCTCGACGATATCTGC 57.009 50.000 0.00 0.00 0.00 4.26
1919 2269 1.323412 AAGCCTCGACGATATCTGCT 58.677 50.000 0.00 0.00 0.00 4.24
1932 2282 4.626042 GATATCTGCTCGGTCAGAAATGT 58.374 43.478 10.66 0.00 45.17 2.71
2034 2384 6.522625 TGGAACAAACTCTGAACATTTCAA 57.477 33.333 0.00 0.00 35.15 2.69
2036 2386 7.555087 TGGAACAAACTCTGAACATTTCAATT 58.445 30.769 0.00 0.00 35.15 2.32
2045 2395 7.094205 ACTCTGAACATTTCAATTCCATGTACC 60.094 37.037 0.00 0.00 39.58 3.34
2052 2415 7.656948 ACATTTCAATTCCATGTACCACAAAAG 59.343 33.333 0.00 0.00 29.07 2.27
2112 2475 7.823745 ACAGAAAGTGATCAAATAGTTGGTT 57.176 32.000 2.65 0.00 35.29 3.67
2113 2476 8.237811 ACAGAAAGTGATCAAATAGTTGGTTT 57.762 30.769 2.65 0.00 35.29 3.27
2114 2477 8.695456 ACAGAAAGTGATCAAATAGTTGGTTTT 58.305 29.630 2.65 0.00 35.29 2.43
2115 2478 9.185192 CAGAAAGTGATCAAATAGTTGGTTTTC 57.815 33.333 2.65 3.72 35.29 2.29
2116 2479 8.912988 AGAAAGTGATCAAATAGTTGGTTTTCA 58.087 29.630 12.02 5.22 35.29 2.69
2117 2480 8.871686 AAAGTGATCAAATAGTTGGTTTTCAC 57.128 30.769 15.09 15.09 35.29 3.18
2118 2481 7.823745 AGTGATCAAATAGTTGGTTTTCACT 57.176 32.000 17.64 17.64 36.90 3.41
2119 2482 7.651808 AGTGATCAAATAGTTGGTTTTCACTG 58.348 34.615 20.28 0.00 38.37 3.66
2120 2483 6.363357 GTGATCAAATAGTTGGTTTTCACTGC 59.637 38.462 2.65 0.00 35.29 4.40
2121 2484 5.843673 TCAAATAGTTGGTTTTCACTGCA 57.156 34.783 2.65 0.00 35.29 4.41
2122 2485 5.830912 TCAAATAGTTGGTTTTCACTGCAG 58.169 37.500 13.48 13.48 35.29 4.41
2123 2486 3.923017 ATAGTTGGTTTTCACTGCAGC 57.077 42.857 15.27 0.00 0.00 5.25
2124 2487 1.473258 AGTTGGTTTTCACTGCAGCA 58.527 45.000 15.27 0.00 0.00 4.41
2125 2488 1.824230 AGTTGGTTTTCACTGCAGCAA 59.176 42.857 15.27 3.81 0.00 3.91
2126 2489 2.233431 AGTTGGTTTTCACTGCAGCAAA 59.767 40.909 15.27 10.53 30.14 3.68
2127 2490 3.118665 AGTTGGTTTTCACTGCAGCAAAT 60.119 39.130 15.27 4.32 30.14 2.32
2128 2491 2.823984 TGGTTTTCACTGCAGCAAATG 58.176 42.857 15.27 4.46 0.00 2.32
2189 2552 7.334090 ACAAGTATAGATTCAAGCACACATCT 58.666 34.615 0.00 0.00 0.00 2.90
2232 2595 4.508124 ACTCTTTCGAACACACTCAATGAC 59.492 41.667 0.00 0.00 0.00 3.06
2297 2661 7.798596 AAACACCATGAACATTGCAAATAAA 57.201 28.000 1.71 0.00 0.00 1.40
2298 2662 7.798596 AACACCATGAACATTGCAAATAAAA 57.201 28.000 1.71 0.00 0.00 1.52
2300 2664 8.393671 ACACCATGAACATTGCAAATAAAAAT 57.606 26.923 1.71 0.00 0.00 1.82
2301 2665 8.505625 ACACCATGAACATTGCAAATAAAAATC 58.494 29.630 1.71 0.00 0.00 2.17
2335 2702 2.102420 TGTACTATCCCAGAACCATGCG 59.898 50.000 0.00 0.00 0.00 4.73
2346 2713 2.099062 CCATGCGCGTGCTTCTTC 59.901 61.111 24.29 0.00 43.34 2.87
2347 2714 2.099062 CATGCGCGTGCTTCTTCC 59.901 61.111 23.16 0.00 43.34 3.46
2389 2756 6.485830 TGGAATAGCTCTACTGCTAATTGT 57.514 37.500 0.00 0.00 46.81 2.71
2416 2783 4.080299 AGACAGGCAAGTAAATAGAAGGGG 60.080 45.833 0.00 0.00 0.00 4.79
2436 2803 3.344515 GGAACCAACCTAGGACATGAAC 58.655 50.000 17.98 1.06 0.00 3.18
2439 2810 3.955471 ACCAACCTAGGACATGAACATG 58.045 45.455 17.98 12.43 44.15 3.21
2459 2830 1.917303 GTTGTTTGCTGGAACACAACG 59.083 47.619 17.02 0.00 39.60 4.10
2474 2845 1.816224 ACAACGTCACCAAGCAAAACT 59.184 42.857 0.00 0.00 0.00 2.66
2485 2856 5.462068 CACCAAGCAAAACTAAACCTTAAGC 59.538 40.000 0.00 0.00 0.00 3.09
2534 2941 5.147162 CCGTGTAAACAGAGAAAAGAATGC 58.853 41.667 0.00 0.00 0.00 3.56
2544 2951 0.671251 AAAAGAATGCGCAAACGGGA 59.329 45.000 17.11 0.00 40.57 5.14
2595 3002 5.791336 AAAGATTGGGTTCTTCTTTCCAC 57.209 39.130 0.00 0.00 35.36 4.02
2613 3020 0.796312 ACGCTTAGATGTGGTTTGCG 59.204 50.000 0.00 0.00 46.02 4.85
2681 3088 7.962964 AAAAGAAACTGTAGTCGATGAATCA 57.037 32.000 0.00 0.00 0.00 2.57
2682 3089 7.588143 AAAGAAACTGTAGTCGATGAATCAG 57.412 36.000 0.00 0.00 0.00 2.90
2683 3090 5.105752 AGAAACTGTAGTCGATGAATCAGC 58.894 41.667 0.00 0.00 0.00 4.26
2684 3091 4.727507 AACTGTAGTCGATGAATCAGCT 57.272 40.909 0.00 0.00 0.00 4.24
2685 3092 5.836821 AACTGTAGTCGATGAATCAGCTA 57.163 39.130 0.00 0.00 0.00 3.32
2686 3093 5.836821 ACTGTAGTCGATGAATCAGCTAA 57.163 39.130 0.00 0.00 0.00 3.09
2687 3094 6.398234 ACTGTAGTCGATGAATCAGCTAAT 57.602 37.500 0.00 0.00 0.00 1.73
2688 3095 7.511959 ACTGTAGTCGATGAATCAGCTAATA 57.488 36.000 0.00 0.00 0.00 0.98
2689 3096 7.364200 ACTGTAGTCGATGAATCAGCTAATAC 58.636 38.462 4.14 4.14 0.00 1.89
2690 3097 7.013369 ACTGTAGTCGATGAATCAGCTAATACA 59.987 37.037 11.57 11.57 0.00 2.29
2691 3098 7.139392 TGTAGTCGATGAATCAGCTAATACAC 58.861 38.462 8.78 0.00 0.00 2.90
2692 3099 6.149129 AGTCGATGAATCAGCTAATACACA 57.851 37.500 0.00 0.00 0.00 3.72
2693 3100 6.573434 AGTCGATGAATCAGCTAATACACAA 58.427 36.000 0.00 0.00 0.00 3.33
2694 3101 7.212976 AGTCGATGAATCAGCTAATACACAAT 58.787 34.615 0.00 0.00 0.00 2.71
2695 3102 7.170489 AGTCGATGAATCAGCTAATACACAATG 59.830 37.037 0.00 0.00 0.00 2.82
2696 3103 7.169813 GTCGATGAATCAGCTAATACACAATGA 59.830 37.037 0.00 0.00 0.00 2.57
2697 3104 7.383300 TCGATGAATCAGCTAATACACAATGAG 59.617 37.037 0.00 0.00 0.00 2.90
2698 3105 7.359849 CGATGAATCAGCTAATACACAATGAGG 60.360 40.741 0.00 0.00 0.00 3.86
2699 3106 6.653020 TGAATCAGCTAATACACAATGAGGT 58.347 36.000 0.00 0.00 0.00 3.85
2700 3107 6.763135 TGAATCAGCTAATACACAATGAGGTC 59.237 38.462 0.00 0.00 0.00 3.85
2701 3108 5.939764 TCAGCTAATACACAATGAGGTCT 57.060 39.130 0.00 0.00 0.00 3.85
2702 3109 6.299805 TCAGCTAATACACAATGAGGTCTT 57.700 37.500 0.00 0.00 0.00 3.01
2703 3110 6.108687 TCAGCTAATACACAATGAGGTCTTG 58.891 40.000 0.00 0.00 0.00 3.02
2704 3111 5.877012 CAGCTAATACACAATGAGGTCTTGT 59.123 40.000 0.00 0.00 37.31 3.16
2705 3112 6.372659 CAGCTAATACACAATGAGGTCTTGTT 59.627 38.462 0.00 0.00 34.69 2.83
2706 3113 6.595716 AGCTAATACACAATGAGGTCTTGTTC 59.404 38.462 0.00 0.00 34.69 3.18
2707 3114 6.183360 GCTAATACACAATGAGGTCTTGTTCC 60.183 42.308 0.00 0.00 34.69 3.62
2708 3115 3.576078 ACACAATGAGGTCTTGTTCCA 57.424 42.857 0.00 0.00 34.69 3.53
2709 3116 3.480470 ACACAATGAGGTCTTGTTCCAG 58.520 45.455 0.00 0.00 34.69 3.86
2710 3117 3.117888 ACACAATGAGGTCTTGTTCCAGT 60.118 43.478 0.00 0.00 34.69 4.00
2711 3118 3.885297 CACAATGAGGTCTTGTTCCAGTT 59.115 43.478 0.00 0.00 34.69 3.16
2712 3119 4.339247 CACAATGAGGTCTTGTTCCAGTTT 59.661 41.667 0.00 0.00 34.69 2.66
2713 3120 4.339247 ACAATGAGGTCTTGTTCCAGTTTG 59.661 41.667 0.00 0.00 33.10 2.93
2714 3121 3.924114 TGAGGTCTTGTTCCAGTTTGA 57.076 42.857 0.00 0.00 0.00 2.69
2715 3122 4.437682 TGAGGTCTTGTTCCAGTTTGAT 57.562 40.909 0.00 0.00 0.00 2.57
2716 3123 4.136796 TGAGGTCTTGTTCCAGTTTGATG 58.863 43.478 0.00 0.00 0.00 3.07
2717 3124 4.137543 GAGGTCTTGTTCCAGTTTGATGT 58.862 43.478 0.00 0.00 0.00 3.06
2718 3125 5.163248 TGAGGTCTTGTTCCAGTTTGATGTA 60.163 40.000 0.00 0.00 0.00 2.29
2719 3126 5.063880 AGGTCTTGTTCCAGTTTGATGTAC 58.936 41.667 0.00 0.00 0.00 2.90
2720 3127 4.215613 GGTCTTGTTCCAGTTTGATGTACC 59.784 45.833 0.00 0.00 0.00 3.34
2721 3128 5.063880 GTCTTGTTCCAGTTTGATGTACCT 58.936 41.667 0.00 0.00 0.00 3.08
2722 3129 6.228258 GTCTTGTTCCAGTTTGATGTACCTA 58.772 40.000 0.00 0.00 0.00 3.08
2723 3130 6.708949 GTCTTGTTCCAGTTTGATGTACCTAA 59.291 38.462 0.00 0.00 0.00 2.69
2724 3131 7.390718 GTCTTGTTCCAGTTTGATGTACCTAAT 59.609 37.037 0.00 0.00 0.00 1.73
2725 3132 7.942341 TCTTGTTCCAGTTTGATGTACCTAATT 59.058 33.333 0.00 0.00 0.00 1.40
2726 3133 7.447374 TGTTCCAGTTTGATGTACCTAATTG 57.553 36.000 0.00 0.00 0.00 2.32
2727 3134 6.432783 TGTTCCAGTTTGATGTACCTAATTGG 59.567 38.462 0.00 0.00 42.93 3.16
2728 3135 6.381498 TCCAGTTTGATGTACCTAATTGGA 57.619 37.500 6.50 6.50 39.71 3.53
2729 3136 6.785076 TCCAGTTTGATGTACCTAATTGGAA 58.215 36.000 7.60 0.00 34.65 3.53
2730 3137 7.410174 TCCAGTTTGATGTACCTAATTGGAAT 58.590 34.615 7.60 0.00 34.65 3.01
2731 3138 8.553153 TCCAGTTTGATGTACCTAATTGGAATA 58.447 33.333 7.60 0.00 34.65 1.75
2732 3139 8.621286 CCAGTTTGATGTACCTAATTGGAATAC 58.379 37.037 0.00 0.00 39.71 1.89
2733 3140 9.173021 CAGTTTGATGTACCTAATTGGAATACA 57.827 33.333 7.87 7.87 39.71 2.29
2734 3141 9.920946 AGTTTGATGTACCTAATTGGAATACAT 57.079 29.630 14.40 14.40 39.35 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 7.259882 TGTCCAATGACATTTCTGCATTTATC 58.740 34.615 0.00 0.00 46.40 1.75
295 331 5.350365 TGAAATGCCTTGTTACTACGATGTC 59.650 40.000 0.00 0.00 0.00 3.06
298 334 4.634443 GGTGAAATGCCTTGTTACTACGAT 59.366 41.667 0.00 0.00 0.00 3.73
348 385 1.654954 CTGTTCATGCAGGGCTGAGC 61.655 60.000 0.00 0.00 33.11 4.26
353 390 0.668401 GCAAACTGTTCATGCAGGGC 60.668 55.000 11.29 0.00 40.59 5.19
375 413 2.237143 TGGACTTTCTCTCATCGGCATT 59.763 45.455 0.00 0.00 0.00 3.56
406 444 6.708885 ATGAATATAGGAGGCCAAATCTGA 57.291 37.500 5.01 0.00 0.00 3.27
409 447 7.657761 CCGTATATGAATATAGGAGGCCAAATC 59.342 40.741 5.01 0.00 34.63 2.17
428 466 4.701171 GCCTTAGAGTAGCACTCCGTATAT 59.299 45.833 11.24 0.00 46.18 0.86
429 467 4.070716 GCCTTAGAGTAGCACTCCGTATA 58.929 47.826 11.24 0.00 46.18 1.47
432 470 1.104630 GCCTTAGAGTAGCACTCCGT 58.895 55.000 11.24 0.01 46.18 4.69
433 471 1.335496 GAGCCTTAGAGTAGCACTCCG 59.665 57.143 11.24 3.21 46.18 4.63
439 480 2.165845 TCAAACGGAGCCTTAGAGTAGC 59.834 50.000 0.00 0.00 0.00 3.58
440 481 4.451629 TTCAAACGGAGCCTTAGAGTAG 57.548 45.455 0.00 0.00 0.00 2.57
460 501 3.322828 GCATGGCCCTCAATATCAACATT 59.677 43.478 0.00 0.00 0.00 2.71
482 535 5.327616 TGATATTGGCACCAGTTCAATTG 57.672 39.130 0.00 0.00 33.72 2.32
490 543 3.571401 GGGAGATTTGATATTGGCACCAG 59.429 47.826 0.00 0.00 0.00 4.00
495 548 4.464008 TGTCTGGGAGATTTGATATTGGC 58.536 43.478 0.00 0.00 0.00 4.52
523 576 9.037737 ACAACACAATTCAGATTCAATTTCAAG 57.962 29.630 0.00 0.00 0.00 3.02
535 590 4.277476 ACCTCCAAACAACACAATTCAGA 58.723 39.130 0.00 0.00 0.00 3.27
543 604 4.712122 TTCTTGAACCTCCAAACAACAC 57.288 40.909 0.00 0.00 0.00 3.32
555 618 7.174946 TGAGTTCCAAGTATCATTTCTTGAACC 59.825 37.037 6.50 5.08 42.22 3.62
565 628 6.382282 TCTCTCATGTGAGTTCCAAGTATCAT 59.618 38.462 20.99 0.00 42.60 2.45
569 632 4.220821 GGTCTCTCATGTGAGTTCCAAGTA 59.779 45.833 20.99 0.49 42.60 2.24
612 892 3.788797 GCGGCTGCTGTTGTATAATGTTC 60.789 47.826 11.21 0.00 38.39 3.18
614 894 1.670811 GCGGCTGCTGTTGTATAATGT 59.329 47.619 11.21 0.00 38.39 2.71
657 942 2.044946 CCGAGCCTTTCCCCCTTG 60.045 66.667 0.00 0.00 0.00 3.61
658 943 2.531942 ACCGAGCCTTTCCCCCTT 60.532 61.111 0.00 0.00 0.00 3.95
749 1046 4.933064 CTCGGATGCGGCTCGGTC 62.933 72.222 6.82 0.00 0.00 4.79
836 1158 3.237741 CTCTCATCTCCCCGCCCC 61.238 72.222 0.00 0.00 0.00 5.80
911 1233 3.607370 AAAAGCGCGGGAGGAGACC 62.607 63.158 8.83 0.00 0.00 3.85
933 1255 1.497722 GCGCTCCCGAAAAACAGAG 59.502 57.895 0.00 0.00 36.29 3.35
963 1285 5.041191 AGATCCTCCACATATTTGGTGAC 57.959 43.478 10.82 3.65 38.54 3.67
966 1288 5.983333 AGAAGATCCTCCACATATTTGGT 57.017 39.130 7.77 0.00 37.93 3.67
1049 1377 1.513858 AGCCCGGGTATTTGGTGATA 58.486 50.000 24.63 0.00 0.00 2.15
1112 1443 5.535753 AAACAGAAAACAATTCCAGAGGG 57.464 39.130 0.00 0.00 0.00 4.30
1222 1556 2.438614 TCGGCCTCGGAGTCTGAG 60.439 66.667 20.46 20.46 36.95 3.35
1388 1731 1.088306 TCTTCCTCGTCGCTCTCTTC 58.912 55.000 0.00 0.00 0.00 2.87
1389 1732 1.470890 CTTCTTCCTCGTCGCTCTCTT 59.529 52.381 0.00 0.00 0.00 2.85
1390 1733 1.091537 CTTCTTCCTCGTCGCTCTCT 58.908 55.000 0.00 0.00 0.00 3.10
1391 1734 0.099791 CCTTCTTCCTCGTCGCTCTC 59.900 60.000 0.00 0.00 0.00 3.20
1392 1735 1.939769 GCCTTCTTCCTCGTCGCTCT 61.940 60.000 0.00 0.00 0.00 4.09
1393 1736 1.517475 GCCTTCTTCCTCGTCGCTC 60.517 63.158 0.00 0.00 0.00 5.03
1624 1967 3.751175 TGATTTGTGGGTCGAGAATTCAC 59.249 43.478 8.44 0.00 0.00 3.18
1625 1968 3.751175 GTGATTTGTGGGTCGAGAATTCA 59.249 43.478 8.44 0.00 0.00 2.57
1626 1969 4.003648 AGTGATTTGTGGGTCGAGAATTC 58.996 43.478 0.00 0.00 0.00 2.17
1627 1970 3.753272 CAGTGATTTGTGGGTCGAGAATT 59.247 43.478 0.00 0.00 0.00 2.17
1628 1971 3.244561 ACAGTGATTTGTGGGTCGAGAAT 60.245 43.478 0.00 0.00 0.00 2.40
1714 2057 0.466124 AAGCGAGAGGCAATCCTACC 59.534 55.000 0.00 0.00 44.46 3.18
1733 2076 3.424302 CGCACGAATTTCATTTCCGAAGA 60.424 43.478 0.00 0.00 0.00 2.87
1784 2129 2.031420 CACAAGAACAGCATCCAGTGTG 60.031 50.000 0.00 0.00 0.00 3.82
1857 2207 4.380867 GCAACAACATTCGGATTTCTCCAT 60.381 41.667 0.00 0.00 42.19 3.41
1874 2224 1.962822 CGGAGAGCAGCAGCAACAA 60.963 57.895 3.17 0.00 45.49 2.83
1902 2252 0.453615 CGAGCAGATATCGTCGAGGC 60.454 60.000 15.86 6.81 35.48 4.70
1903 2253 0.167033 CCGAGCAGATATCGTCGAGG 59.833 60.000 20.20 0.00 38.50 4.63
1918 2268 5.391310 CCTTTTGATCACATTTCTGACCGAG 60.391 44.000 0.00 0.00 0.00 4.63
1919 2269 4.455533 CCTTTTGATCACATTTCTGACCGA 59.544 41.667 0.00 0.00 0.00 4.69
1932 2282 7.046652 TGAAAATTTCACAAGCCTTTTGATCA 58.953 30.769 4.03 0.00 34.08 2.92
2030 2380 5.600484 ACCTTTTGTGGTACATGGAATTGAA 59.400 36.000 0.00 0.00 44.52 2.69
2034 2384 4.735369 TCACCTTTTGTGGTACATGGAAT 58.265 39.130 0.00 0.00 45.48 3.01
2036 2386 3.866703 TCACCTTTTGTGGTACATGGA 57.133 42.857 0.00 0.00 45.48 3.41
2045 2395 6.690530 ACCAATTACATGATCACCTTTTGTG 58.309 36.000 8.78 0.00 46.88 3.33
2052 2415 6.293407 CCGTGAATACCAATTACATGATCACC 60.293 42.308 0.00 0.00 33.01 4.02
2089 2452 9.185192 GAAAACCAACTATTTGATCACTTTCTG 57.815 33.333 0.00 0.00 34.24 3.02
2092 2455 8.695456 AGTGAAAACCAACTATTTGATCACTTT 58.305 29.630 0.00 0.00 38.09 2.66
2093 2456 8.137437 CAGTGAAAACCAACTATTTGATCACTT 58.863 33.333 14.65 0.00 38.59 3.16
2094 2457 7.651808 CAGTGAAAACCAACTATTTGATCACT 58.348 34.615 0.00 12.94 39.76 3.41
2095 2458 6.363357 GCAGTGAAAACCAACTATTTGATCAC 59.637 38.462 0.00 4.30 34.98 3.06
2096 2459 6.040278 TGCAGTGAAAACCAACTATTTGATCA 59.960 34.615 0.00 0.00 34.24 2.92
2097 2460 6.446318 TGCAGTGAAAACCAACTATTTGATC 58.554 36.000 0.00 0.00 34.24 2.92
2098 2461 6.403866 TGCAGTGAAAACCAACTATTTGAT 57.596 33.333 0.00 0.00 34.24 2.57
2099 2462 5.735922 GCTGCAGTGAAAACCAACTATTTGA 60.736 40.000 16.64 0.00 34.24 2.69
2100 2463 4.445385 GCTGCAGTGAAAACCAACTATTTG 59.555 41.667 16.64 0.00 0.00 2.32
2101 2464 4.099266 TGCTGCAGTGAAAACCAACTATTT 59.901 37.500 16.64 0.00 0.00 1.40
2102 2465 3.636300 TGCTGCAGTGAAAACCAACTATT 59.364 39.130 16.64 0.00 0.00 1.73
2103 2466 3.221771 TGCTGCAGTGAAAACCAACTAT 58.778 40.909 16.64 0.00 0.00 2.12
2104 2467 2.649190 TGCTGCAGTGAAAACCAACTA 58.351 42.857 16.64 0.00 0.00 2.24
2105 2468 1.473258 TGCTGCAGTGAAAACCAACT 58.527 45.000 16.64 0.00 0.00 3.16
2106 2469 2.292103 TTGCTGCAGTGAAAACCAAC 57.708 45.000 16.64 0.00 0.00 3.77
2107 2470 3.196463 CATTTGCTGCAGTGAAAACCAA 58.804 40.909 16.64 6.08 0.00 3.67
2108 2471 2.823984 CATTTGCTGCAGTGAAAACCA 58.176 42.857 16.64 0.00 0.00 3.67
2120 2483 4.508492 TGATCACTTTTTGTGCATTTGCTG 59.492 37.500 3.94 0.00 45.81 4.41
2121 2484 4.695396 TGATCACTTTTTGTGCATTTGCT 58.305 34.783 3.94 0.00 45.81 3.91
2122 2485 5.407387 AGATGATCACTTTTTGTGCATTTGC 59.593 36.000 0.00 0.00 45.81 3.68
2123 2486 8.523523 TTAGATGATCACTTTTTGTGCATTTG 57.476 30.769 0.00 0.00 45.81 2.32
2124 2487 9.715121 AATTAGATGATCACTTTTTGTGCATTT 57.285 25.926 0.00 0.00 45.81 2.32
2125 2488 9.146984 CAATTAGATGATCACTTTTTGTGCATT 57.853 29.630 0.00 0.00 45.81 3.56
2126 2489 7.762615 CCAATTAGATGATCACTTTTTGTGCAT 59.237 33.333 0.00 0.00 45.81 3.96
2127 2490 7.092079 CCAATTAGATGATCACTTTTTGTGCA 58.908 34.615 0.00 0.00 45.81 4.57
2128 2491 7.092716 ACCAATTAGATGATCACTTTTTGTGC 58.907 34.615 0.00 0.00 45.81 4.57
2171 2534 3.941573 TGCAGATGTGTGCTTGAATCTA 58.058 40.909 3.75 0.00 44.32 1.98
2189 2552 1.000496 TGCTGTTTTTGCGATGATGCA 60.000 42.857 0.00 0.00 44.61 3.96
2277 2641 8.618702 TGATTTTTATTTGCAATGTTCATGGT 57.381 26.923 0.00 0.00 0.00 3.55
2298 2662 9.628500 GGGATAGTACAGAGGTAAATTTTGATT 57.372 33.333 0.00 0.00 0.00 2.57
2300 2664 8.153221 TGGGATAGTACAGAGGTAAATTTTGA 57.847 34.615 0.00 0.00 0.00 2.69
2301 2665 8.265055 TCTGGGATAGTACAGAGGTAAATTTTG 58.735 37.037 0.00 0.00 38.71 2.44
2310 2677 3.643237 TGGTTCTGGGATAGTACAGAGG 58.357 50.000 0.00 0.00 43.84 3.69
2335 2702 1.131771 GCAAAAAGGAAGAAGCACGC 58.868 50.000 0.00 0.00 0.00 5.34
2346 2713 1.028905 TTCACCCGTCAGCAAAAAGG 58.971 50.000 0.00 0.00 0.00 3.11
2347 2714 2.607771 CCATTCACCCGTCAGCAAAAAG 60.608 50.000 0.00 0.00 0.00 2.27
2389 2756 7.610305 CCCTTCTATTTACTTGCCTGTCTTAAA 59.390 37.037 0.00 0.00 0.00 1.52
2416 2783 4.015872 TGTTCATGTCCTAGGTTGGTTC 57.984 45.455 9.08 0.00 0.00 3.62
2427 2794 3.737266 CAGCAAACAACATGTTCATGTCC 59.263 43.478 17.02 0.00 40.14 4.02
2428 2795 3.737266 CCAGCAAACAACATGTTCATGTC 59.263 43.478 17.02 5.65 40.14 3.06
2429 2796 3.384146 TCCAGCAAACAACATGTTCATGT 59.616 39.130 8.48 11.97 40.14 3.21
2430 2797 3.979948 TCCAGCAAACAACATGTTCATG 58.020 40.909 8.48 9.05 40.14 3.07
2432 2799 3.194329 TGTTCCAGCAAACAACATGTTCA 59.806 39.130 8.48 0.00 40.14 3.18
2433 2800 3.551485 GTGTTCCAGCAAACAACATGTTC 59.449 43.478 8.48 0.00 40.14 3.18
2436 2803 3.162202 TGTGTTCCAGCAAACAACATG 57.838 42.857 0.00 0.00 40.62 3.21
2439 2810 1.917303 CGTTGTGTTCCAGCAAACAAC 59.083 47.619 7.32 7.32 45.62 3.32
2459 2830 4.649088 AGGTTTAGTTTTGCTTGGTGAC 57.351 40.909 0.00 0.00 0.00 3.67
2474 2845 7.179338 TGAATTTTATGCAGGGCTTAAGGTTTA 59.821 33.333 4.29 0.00 31.63 2.01
2485 2856 6.211587 TGATTGTCTGAATTTTATGCAGGG 57.788 37.500 0.00 0.00 0.00 4.45
2534 2941 2.911819 AATATGTGTTCCCGTTTGCG 57.088 45.000 0.00 0.00 37.95 4.85
2544 2951 7.509546 CCTCACCTTCCTATGTAATATGTGTT 58.490 38.462 0.00 0.00 0.00 3.32
2595 3002 3.586039 CGCAAACCACATCTAAGCG 57.414 52.632 0.00 0.00 37.68 4.68
2670 3077 6.828502 TTGTGTATTAGCTGATTCATCGAC 57.171 37.500 0.00 0.00 0.00 4.20
2674 3081 7.285566 ACCTCATTGTGTATTAGCTGATTCAT 58.714 34.615 0.00 0.00 0.00 2.57
2675 3082 6.653020 ACCTCATTGTGTATTAGCTGATTCA 58.347 36.000 0.00 0.00 0.00 2.57
2676 3083 6.989169 AGACCTCATTGTGTATTAGCTGATTC 59.011 38.462 0.00 0.00 0.00 2.52
2677 3084 6.893583 AGACCTCATTGTGTATTAGCTGATT 58.106 36.000 0.00 0.00 0.00 2.57
2678 3085 6.491714 AGACCTCATTGTGTATTAGCTGAT 57.508 37.500 0.00 0.00 0.00 2.90
2679 3086 5.939764 AGACCTCATTGTGTATTAGCTGA 57.060 39.130 0.00 0.00 0.00 4.26
2680 3087 5.877012 ACAAGACCTCATTGTGTATTAGCTG 59.123 40.000 0.00 0.00 39.36 4.24
2681 3088 6.054860 ACAAGACCTCATTGTGTATTAGCT 57.945 37.500 0.00 0.00 39.36 3.32
2682 3089 6.183360 GGAACAAGACCTCATTGTGTATTAGC 60.183 42.308 0.00 0.00 39.91 3.09
2683 3090 6.878923 TGGAACAAGACCTCATTGTGTATTAG 59.121 38.462 0.00 0.00 39.91 1.73
2684 3091 6.774673 TGGAACAAGACCTCATTGTGTATTA 58.225 36.000 0.00 0.00 39.91 0.98
2685 3092 5.630121 TGGAACAAGACCTCATTGTGTATT 58.370 37.500 0.00 0.00 39.91 1.89
2686 3093 5.221925 ACTGGAACAAGACCTCATTGTGTAT 60.222 40.000 0.00 0.00 39.91 2.29
2687 3094 4.102524 ACTGGAACAAGACCTCATTGTGTA 59.897 41.667 0.00 0.00 39.91 2.90
2688 3095 3.117888 ACTGGAACAAGACCTCATTGTGT 60.118 43.478 0.00 0.00 39.91 3.72
2689 3096 3.480470 ACTGGAACAAGACCTCATTGTG 58.520 45.455 0.00 0.00 39.91 3.33
2690 3097 3.864789 ACTGGAACAAGACCTCATTGT 57.135 42.857 0.00 0.00 42.55 2.71
2691 3098 4.580167 TCAAACTGGAACAAGACCTCATTG 59.420 41.667 0.00 0.00 38.70 2.82
2692 3099 4.792068 TCAAACTGGAACAAGACCTCATT 58.208 39.130 0.00 0.00 38.70 2.57
2693 3100 4.437682 TCAAACTGGAACAAGACCTCAT 57.562 40.909 0.00 0.00 38.70 2.90
2694 3101 3.924114 TCAAACTGGAACAAGACCTCA 57.076 42.857 0.00 0.00 38.70 3.86
2695 3102 4.137543 ACATCAAACTGGAACAAGACCTC 58.862 43.478 0.00 0.00 38.70 3.85
2696 3103 4.170468 ACATCAAACTGGAACAAGACCT 57.830 40.909 0.00 0.00 38.70 3.85
2697 3104 4.215613 GGTACATCAAACTGGAACAAGACC 59.784 45.833 0.00 0.00 38.70 3.85
2698 3105 5.063880 AGGTACATCAAACTGGAACAAGAC 58.936 41.667 0.00 0.00 38.70 3.01
2699 3106 5.304686 AGGTACATCAAACTGGAACAAGA 57.695 39.130 0.00 0.00 38.70 3.02
2700 3107 7.687941 ATTAGGTACATCAAACTGGAACAAG 57.312 36.000 0.00 0.00 38.70 3.16
2701 3108 7.040062 CCAATTAGGTACATCAAACTGGAACAA 60.040 37.037 0.00 0.00 38.70 2.83
2702 3109 6.432783 CCAATTAGGTACATCAAACTGGAACA 59.567 38.462 0.00 0.00 0.00 3.18
2703 3110 6.657541 TCCAATTAGGTACATCAAACTGGAAC 59.342 38.462 0.00 0.00 39.02 3.62
2704 3111 6.785076 TCCAATTAGGTACATCAAACTGGAA 58.215 36.000 0.00 0.00 39.02 3.53
2705 3112 6.381498 TCCAATTAGGTACATCAAACTGGA 57.619 37.500 0.00 0.00 39.02 3.86
2706 3113 7.645058 ATTCCAATTAGGTACATCAAACTGG 57.355 36.000 0.00 0.00 39.02 4.00
2707 3114 9.173021 TGTATTCCAATTAGGTACATCAAACTG 57.827 33.333 0.00 0.00 39.02 3.16
2708 3115 9.920946 ATGTATTCCAATTAGGTACATCAAACT 57.079 29.630 0.00 0.00 35.68 2.66


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

AutoCloner maintained by Alex Coulton.