Multiple sequence alignment - TraesCS2A01G401300

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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 TraesCS2A01G401300 chr2A 100.000 5723 0 0 1 5723 654918821 654913099 0.000000e+00 10569.0
1 TraesCS2A01G401300 chr2B 92.607 4477 238 51 1040 5461 600750354 600745916 0.000000e+00 6348.0
2 TraesCS2A01G401300 chr2B 87.351 419 48 3 338 751 600775704 600775286 5.190000e-130 475.0
3 TraesCS2A01G401300 chr2B 89.231 195 19 2 733 927 600750675 600750483 5.730000e-60 243.0
4 TraesCS2A01G401300 chr2B 83.158 285 23 13 5457 5723 600745854 600745577 2.670000e-58 237.0
5 TraesCS2A01G401300 chr2B 95.349 86 2 2 2329 2414 794694552 794694469 1.000000e-27 135.0
6 TraesCS2A01G401300 chr2B 95.349 86 2 2 2329 2414 794803453 794803370 1.000000e-27 135.0
7 TraesCS2A01G401300 chr2B 95.349 43 2 0 5570 5612 23545407 23545365 1.030000e-07 69.4
8 TraesCS2A01G401300 chr2B 91.304 46 2 2 5563 5608 600745729 600745772 1.720000e-05 62.1
9 TraesCS2A01G401300 chr2D 93.243 1406 78 7 2412 3810 511696857 511695462 0.000000e+00 2054.0
10 TraesCS2A01G401300 chr2D 90.089 1352 78 29 4118 5461 511695280 511693977 0.000000e+00 1703.0
11 TraesCS2A01G401300 chr2D 91.484 1233 76 8 1111 2335 511698067 511696856 0.000000e+00 1668.0
12 TraesCS2A01G401300 chr2D 90.976 953 40 15 2 928 511699570 511698638 0.000000e+00 1242.0
13 TraesCS2A01G401300 chr2D 88.658 961 36 24 2 928 511755801 511754880 0.000000e+00 1103.0
14 TraesCS2A01G401300 chr2D 85.130 269 22 14 5459 5723 511693896 511693642 5.690000e-65 259.0
15 TraesCS2A01G401300 chr6B 96.429 84 2 1 2334 2417 135505597 135505679 2.780000e-28 137.0
16 TraesCS2A01G401300 chr7D 97.500 80 1 1 2334 2413 234073674 234073752 1.000000e-27 135.0
17 TraesCS2A01G401300 chr1D 93.478 92 4 2 2333 2422 3368763 3368854 1.000000e-27 135.0
18 TraesCS2A01G401300 chr1D 92.857 42 3 0 3809 3850 261881544 261881585 1.720000e-05 62.1
19 TraesCS2A01G401300 chr7A 95.294 85 2 1 2331 2413 527538090 527538174 3.600000e-27 134.0
20 TraesCS2A01G401300 chr3A 89.216 102 6 2 2321 2418 45603256 45603356 7.790000e-24 122.0
21 TraesCS2A01G401300 chr4A 87.500 112 5 5 2334 2437 743443037 743442927 2.800000e-23 121.0
22 TraesCS2A01G401300 chr3D 97.436 39 1 0 5570 5608 560327812 560327850 3.700000e-07 67.6
23 TraesCS2A01G401300 chr3D 94.872 39 2 0 5570 5608 515963362 515963400 1.720000e-05 62.1
24 TraesCS2A01G401300 chr3B 97.436 39 1 0 5570 5608 744584339 744584377 3.700000e-07 67.6
25 TraesCS2A01G401300 chr3B 97.436 39 1 0 5570 5608 746860914 746860876 3.700000e-07 67.6
26 TraesCS2A01G401300 chr1A 97.436 39 1 0 5570 5608 532788179 532788217 3.700000e-07 67.6
27 TraesCS2A01G401300 chr5D 97.368 38 1 0 3809 3846 433514002 433514039 1.330000e-06 65.8
28 TraesCS2A01G401300 chr5B 95.238 42 1 1 3805 3846 524361863 524361903 1.330000e-06 65.8
29 TraesCS2A01G401300 chr1B 94.872 39 2 0 5570 5608 497472910 497472872 1.720000e-05 62.1


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 TraesCS2A01G401300 chr2A 654913099 654918821 5722 True 10569.0 10569 100.0000 1 5723 1 chr2A.!!$R1 5722
1 TraesCS2A01G401300 chr2B 600745577 600750675 5098 True 2276.0 6348 88.3320 733 5723 3 chr2B.!!$R5 4990
2 TraesCS2A01G401300 chr2D 511693642 511699570 5928 True 1385.2 2054 90.1844 2 5723 5 chr2D.!!$R2 5721
3 TraesCS2A01G401300 chr2D 511754880 511755801 921 True 1103.0 1103 88.6580 2 928 1 chr2D.!!$R1 926

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
61 62 1.075536 GTTGGTGGGGTGGAAGAAGAT 59.924 52.381 0.00 0.00 0.0 2.40 F
1012 1091 0.530744 GGCCGAAATGAAAACCCTCC 59.469 55.000 0.00 0.00 0.0 4.30 F
1588 2034 0.034059 AGAAGAAGGTCACACTGCCG 59.966 55.000 0.00 0.00 0.0 5.69 F
2630 3097 0.108585 GATCCTTGGCCGCCTTATGA 59.891 55.000 11.61 2.56 0.0 2.15 F
2638 3105 0.814010 GCCGCCTTATGATCGTGGTT 60.814 55.000 0.00 0.00 0.0 3.67 F
3059 3531 1.351076 TCACCCTGCTTGTCATCTGA 58.649 50.000 0.00 0.00 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1734 0.395312 GAGACGGGGTGAGTTTTCCA 59.605 55.0 0.00 0.0 0.00 3.53 R
2630 3097 0.035317 TTCTCAGCAGCAACCACGAT 59.965 50.0 0.00 0.0 0.00 3.73 R
3420 3897 0.394216 ACCATATCGGCAGCAAAGCA 60.394 50.0 0.00 0.0 39.03 3.91 R
4342 4863 0.327924 AGGGATGTGGTTGATCGCAA 59.672 50.0 0.00 0.0 35.71 4.85 R
4605 5129 0.953960 ATCCGGTTTCCTGTGCGAAC 60.954 55.0 0.00 0.0 0.00 3.95 R
4936 5460 0.165944 AAATACAGCAGCGCGTGAAC 59.834 50.0 8.43 0.0 0.00 3.18 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
61 62 1.075536 GTTGGTGGGGTGGAAGAAGAT 59.924 52.381 0.00 0.00 0.00 2.40
97 98 8.786826 AGAGACCACGATGTATTTCATTTTTA 57.213 30.769 0.00 0.00 36.83 1.52
122 123 1.682854 AGTGTTGGTGCAGATGGTTTG 59.317 47.619 0.00 0.00 0.00 2.93
185 186 9.777297 AAAAATATGCAAAATGACTTAACCTGT 57.223 25.926 0.00 0.00 0.00 4.00
210 211 5.392811 GCGTTTAACTTAGAGAGTGGCTAGA 60.393 44.000 0.00 0.00 39.00 2.43
223 224 2.093235 GTGGCTAGAGGTGCTTCTTGAT 60.093 50.000 0.00 0.00 0.00 2.57
257 258 9.141400 GGACAATCTTTAGTAGTTTAGACACAG 57.859 37.037 0.00 0.00 0.00 3.66
341 366 4.147826 GGAAAGTAAACTCGAAGTCACGTC 59.852 45.833 0.00 0.00 34.70 4.34
383 408 6.021468 GTGAAACATCAAAAGAACAGACAACG 60.021 38.462 0.00 0.00 36.32 4.10
387 412 1.329292 CAAAAGAACAGACAACGGCGA 59.671 47.619 16.62 0.00 0.00 5.54
418 443 5.044919 TGTGACTCATCCAGACCCAATTATT 60.045 40.000 0.00 0.00 0.00 1.40
464 489 4.038763 CCAAAGGTTGTTAACTTCTTCCCC 59.961 45.833 7.22 0.00 0.00 4.81
482 507 1.533731 CCCGCACGACAATGTAAGTTT 59.466 47.619 0.00 0.00 0.00 2.66
517 543 9.496710 TCATAGAAGTTTAATACCTCTACCCAA 57.503 33.333 0.00 0.00 33.66 4.12
548 582 8.696410 TTTCCAACACAAAATAGTTTCTTGAC 57.304 30.769 1.78 0.00 0.00 3.18
553 587 9.139174 CAACACAAAATAGTTTCTTGACAGTTT 57.861 29.630 1.78 0.00 0.00 2.66
562 596 6.206498 AGTTTCTTGACAGTTTAAATTCCGC 58.794 36.000 0.00 0.00 0.00 5.54
595 629 7.781548 ATAATCCAATGAGCTTTCAATTTGC 57.218 32.000 0.00 0.00 0.00 3.68
604 638 8.836268 ATGAGCTTTCAATTTGCAAGATTAAA 57.164 26.923 12.16 0.00 0.00 1.52
652 686 7.275560 GCCTTAAATGACCATGTTTATTCACAC 59.724 37.037 0.00 0.00 0.00 3.82
673 708 5.236047 ACACATAGGTATAGAGTTCGTCGTC 59.764 44.000 0.00 0.00 0.00 4.20
674 709 5.466058 CACATAGGTATAGAGTTCGTCGTCT 59.534 44.000 0.00 0.00 0.00 4.18
675 710 6.018098 CACATAGGTATAGAGTTCGTCGTCTT 60.018 42.308 0.00 0.00 0.00 3.01
676 711 6.202570 ACATAGGTATAGAGTTCGTCGTCTTC 59.797 42.308 0.00 0.00 0.00 2.87
677 712 4.511527 AGGTATAGAGTTCGTCGTCTTCA 58.488 43.478 0.00 0.00 0.00 3.02
678 713 5.124645 AGGTATAGAGTTCGTCGTCTTCAT 58.875 41.667 0.00 0.00 0.00 2.57
679 714 5.236911 AGGTATAGAGTTCGTCGTCTTCATC 59.763 44.000 0.00 0.00 0.00 2.92
680 715 2.529136 AGAGTTCGTCGTCTTCATCG 57.471 50.000 0.00 0.00 0.00 3.84
681 716 1.805345 AGAGTTCGTCGTCTTCATCGT 59.195 47.619 0.00 0.00 0.00 3.73
682 717 2.998670 AGAGTTCGTCGTCTTCATCGTA 59.001 45.455 0.00 0.00 0.00 3.43
683 718 3.089982 GAGTTCGTCGTCTTCATCGTAC 58.910 50.000 0.00 0.00 0.00 3.67
684 719 2.159599 AGTTCGTCGTCTTCATCGTACC 60.160 50.000 0.00 0.00 0.00 3.34
705 740 2.878406 CCACGTGGATCTTCAACAAACT 59.122 45.455 31.31 0.00 37.39 2.66
766 801 5.294306 ACCATCATTAGCAGTGTGTTATTCG 59.706 40.000 0.00 0.00 0.00 3.34
878 913 2.064573 CAAACCGAATTTGGCTCCAC 57.935 50.000 12.02 0.00 43.52 4.02
883 918 3.426615 ACCGAATTTGGCTCCACAATAA 58.573 40.909 12.02 0.00 0.00 1.40
928 963 2.849294 AAGAGACAGCAGAAAGACCC 57.151 50.000 0.00 0.00 0.00 4.46
1012 1091 0.530744 GGCCGAAATGAAAACCCTCC 59.469 55.000 0.00 0.00 0.00 4.30
1269 1714 0.887933 CCATTTCCCCGAACACCTTG 59.112 55.000 0.00 0.00 0.00 3.61
1313 1758 0.612453 AACTCACCCCGTCTCCTCTC 60.612 60.000 0.00 0.00 0.00 3.20
1377 1823 4.827087 ACGAGCATCCTGGCGCTG 62.827 66.667 14.16 0.00 38.99 5.18
1477 1923 3.472652 TGACTTGATTTTGTACTGGCGT 58.527 40.909 0.00 0.00 0.00 5.68
1498 1944 0.908910 TCGTGGCTGTATGGATTGGT 59.091 50.000 0.00 0.00 0.00 3.67
1499 1945 1.280710 TCGTGGCTGTATGGATTGGTT 59.719 47.619 0.00 0.00 0.00 3.67
1544 1990 1.852157 AGGGGGCTTGATGTGGTGA 60.852 57.895 0.00 0.00 0.00 4.02
1588 2034 0.034059 AGAAGAAGGTCACACTGCCG 59.966 55.000 0.00 0.00 0.00 5.69
1672 2118 2.438868 TTCAGACCTGTGTGATGTCG 57.561 50.000 0.00 0.00 32.70 4.35
1673 2119 0.603065 TCAGACCTGTGTGATGTCGG 59.397 55.000 0.00 0.00 34.24 4.79
1674 2120 0.318441 CAGACCTGTGTGATGTCGGT 59.682 55.000 0.00 0.00 34.24 4.69
1675 2121 0.318441 AGACCTGTGTGATGTCGGTG 59.682 55.000 0.00 0.00 34.24 4.94
1676 2122 0.317160 GACCTGTGTGATGTCGGTGA 59.683 55.000 0.00 0.00 0.00 4.02
1677 2123 0.976641 ACCTGTGTGATGTCGGTGAT 59.023 50.000 0.00 0.00 0.00 3.06
1678 2124 2.165641 GACCTGTGTGATGTCGGTGATA 59.834 50.000 0.00 0.00 0.00 2.15
1679 2125 2.565391 ACCTGTGTGATGTCGGTGATAA 59.435 45.455 0.00 0.00 0.00 1.75
1681 2127 2.604914 CTGTGTGATGTCGGTGATAAGC 59.395 50.000 0.00 0.00 0.00 3.09
1723 2170 9.581099 CAAAAAGACATGTTAGTTACCTTGTTT 57.419 29.630 0.00 0.00 0.00 2.83
1732 2179 7.676947 TGTTAGTTACCTTGTTTCTAGCTCAT 58.323 34.615 0.00 0.00 0.00 2.90
1738 2185 4.081420 ACCTTGTTTCTAGCTCATCATCGT 60.081 41.667 0.00 0.00 0.00 3.73
1759 2207 4.201910 CGTTTGGTTTCACACTCAGAATGT 60.202 41.667 0.00 0.00 37.40 2.71
1760 2208 5.273944 GTTTGGTTTCACACTCAGAATGTC 58.726 41.667 0.00 0.00 37.40 3.06
1768 2216 6.490566 TCACACTCAGAATGTCATGATTTG 57.509 37.500 0.00 0.00 37.40 2.32
1770 2218 6.487668 TCACACTCAGAATGTCATGATTTGTT 59.512 34.615 0.00 0.00 37.40 2.83
1773 2221 7.879677 ACACTCAGAATGTCATGATTTGTTCTA 59.120 33.333 0.00 0.00 37.40 2.10
1785 2233 7.774625 TCATGATTTGTTCTAGATTATGCACCA 59.225 33.333 0.00 0.00 0.00 4.17
1794 2242 4.240881 AGATTATGCACCAATGACAGGT 57.759 40.909 0.00 0.00 40.85 4.00
1796 2244 3.431673 TTATGCACCAATGACAGGTCA 57.568 42.857 4.37 4.37 44.59 4.02
1975 2432 2.224378 TGGAACCAGAACTTCAGCAGAG 60.224 50.000 0.00 0.00 0.00 3.35
1989 2446 7.597386 ACTTCAGCAGAGATTTTAACAATTCC 58.403 34.615 0.00 0.00 0.00 3.01
2004 2461 3.319122 ACAATTCCTCACACCTTTTGAGC 59.681 43.478 0.00 0.00 39.43 4.26
2005 2462 2.727123 TTCCTCACACCTTTTGAGCA 57.273 45.000 0.00 0.00 39.43 4.26
2061 2524 0.751277 CACACAGCACCCAAACCTCA 60.751 55.000 0.00 0.00 0.00 3.86
2076 2539 6.222389 CCAAACCTCACATTTGATAGCAAAA 58.778 36.000 10.62 0.00 46.19 2.44
2087 2550 4.906065 TGATAGCAAAATCTGACATGGC 57.094 40.909 0.00 0.00 0.00 4.40
2123 2586 5.047590 TCAGAGCTTACTGAATAAACACGGA 60.048 40.000 2.73 0.00 42.79 4.69
2227 2690 4.512484 TCGCACCAGAATGTTTATCATCA 58.488 39.130 0.00 0.00 35.48 3.07
2337 2800 7.747155 TGTTCAGTGATATAGGTAGCTACTC 57.253 40.000 22.74 12.68 0.00 2.59
2630 3097 0.108585 GATCCTTGGCCGCCTTATGA 59.891 55.000 11.61 2.56 0.00 2.15
2638 3105 0.814010 GCCGCCTTATGATCGTGGTT 60.814 55.000 0.00 0.00 0.00 3.67
2641 3108 1.668419 GCCTTATGATCGTGGTTGCT 58.332 50.000 0.00 0.00 0.00 3.91
2679 3146 2.239681 AGTAGCTCTGGTAGTTGCCT 57.760 50.000 0.00 0.00 0.00 4.75
2710 3177 2.168728 GGACTTAGCTGTTGGAGGGTAG 59.831 54.545 0.00 0.00 0.00 3.18
2766 3233 7.333423 GCTGGTACTTAACTGTTCATTCATACA 59.667 37.037 0.00 0.00 0.00 2.29
3059 3531 1.351076 TCACCCTGCTTGTCATCTGA 58.649 50.000 0.00 0.00 0.00 3.27
3132 3609 1.905215 CCCAGATGACAGTCCTGTTCT 59.095 52.381 0.79 0.00 45.05 3.01
3307 3784 6.422400 GGAGTGCTGATAAGTAGCTGTAATTC 59.578 42.308 0.00 0.00 41.66 2.17
3351 3828 2.546789 TGAGCAGCAATTGAGATATGCG 59.453 45.455 10.34 0.00 44.60 4.73
3393 3870 4.037923 ACAATTTGGTTGCTTGACTACTGG 59.962 41.667 0.78 0.00 41.69 4.00
3484 3962 6.818644 CGATCCTAATATCACAAGTAATGGGG 59.181 42.308 0.00 0.00 31.35 4.96
3866 4348 6.127619 GCAAGTTAAGAGGGAGTATTTTGCAT 60.128 38.462 0.00 0.00 37.65 3.96
3910 4392 1.628846 TGAAACCTCCAGGAGCTTACC 59.371 52.381 11.57 0.96 38.94 2.85
3915 4397 1.415200 CTCCAGGAGCTTACCTACCC 58.585 60.000 2.60 0.00 38.32 3.69
3989 4508 8.352137 AGTGTTGAAATCCATTTGATCATGTA 57.648 30.769 0.00 0.00 31.61 2.29
4046 4566 6.147437 TGGTTAATCCTTGAATTAGGGTGT 57.853 37.500 0.00 0.00 35.90 4.16
4047 4567 5.949354 TGGTTAATCCTTGAATTAGGGTGTG 59.051 40.000 0.00 0.00 35.90 3.82
4048 4568 6.184789 GGTTAATCCTTGAATTAGGGTGTGA 58.815 40.000 0.00 0.00 35.90 3.58
4082 4603 7.827729 ACCCCTATATGTTCTGTTTGTTAGTTC 59.172 37.037 0.00 0.00 0.00 3.01
4084 4605 8.883731 CCCTATATGTTCTGTTTGTTAGTTCTG 58.116 37.037 0.00 0.00 0.00 3.02
4277 4798 1.899814 AGGTTGGCACGAGTTATCTCA 59.100 47.619 0.00 0.00 40.44 3.27
4298 4819 7.704271 TCTCATTTTGCATCATCTGAATTCTC 58.296 34.615 7.05 0.00 0.00 2.87
4307 4828 7.558807 TGCATCATCTGAATTCTCCAATACTTT 59.441 33.333 7.05 0.00 0.00 2.66
4342 4863 6.645415 CAGTAACGATGAACTTGTTCTAGGTT 59.355 38.462 13.65 14.50 33.35 3.50
4393 4914 9.431887 GTCAAGAGTATGGTGAAAAATGTACTA 57.568 33.333 0.00 0.00 0.00 1.82
4525 5046 2.422832 GGCTGAATTTCTGAAGCTGGAG 59.577 50.000 7.40 0.00 35.93 3.86
4552 5073 4.862371 TGAAGGTAAACCCTGTCTTGTTT 58.138 39.130 0.00 0.00 45.47 2.83
4553 5074 6.003859 TGAAGGTAAACCCTGTCTTGTTTA 57.996 37.500 0.00 0.00 45.47 2.01
4555 5076 6.488683 TGAAGGTAAACCCTGTCTTGTTTATG 59.511 38.462 0.00 0.00 45.47 1.90
4556 5077 4.765339 AGGTAAACCCTGTCTTGTTTATGC 59.235 41.667 0.00 0.00 44.08 3.14
4558 5079 5.106277 GGTAAACCCTGTCTTGTTTATGCTC 60.106 44.000 0.00 0.00 38.69 4.26
4559 5080 4.373156 AACCCTGTCTTGTTTATGCTCT 57.627 40.909 0.00 0.00 0.00 4.09
4563 5087 3.369147 CCTGTCTTGTTTATGCTCTCGTG 59.631 47.826 0.00 0.00 0.00 4.35
4568 5092 4.686091 TCTTGTTTATGCTCTCGTGTCTTG 59.314 41.667 0.00 0.00 0.00 3.02
4590 5114 7.662258 TCTTGTGATTTATCCCGTCAACTAAAA 59.338 33.333 0.00 0.00 0.00 1.52
4603 5127 7.863375 CCCGTCAACTAAAATTTCATGTTTGTA 59.137 33.333 0.00 0.00 0.00 2.41
4604 5128 9.405587 CCGTCAACTAAAATTTCATGTTTGTAT 57.594 29.630 0.00 0.00 0.00 2.29
4620 5144 2.147958 TGTATGTTCGCACAGGAAACC 58.852 47.619 0.00 0.00 35.94 3.27
4647 5171 1.284657 CGCACATGAGGATCTGTGAC 58.715 55.000 15.00 6.96 42.72 3.67
4653 5177 1.226717 GAGGATCTGTGACGGCGTC 60.227 63.158 31.68 31.68 0.00 5.19
4920 5444 5.243283 AGTCCTCTTAGTTCGAGTGCTTTTA 59.757 40.000 0.00 0.00 0.00 1.52
4984 5508 4.310022 AATCTGGGTATTTTTCGGGTCA 57.690 40.909 0.00 0.00 0.00 4.02
5009 5533 4.357018 TGTAGTCTATTGAGCTGTCGTG 57.643 45.455 0.00 0.00 0.00 4.35
5117 5641 9.815936 CTTGCATTTTTATTTTTGGTCTGAATC 57.184 29.630 0.00 0.00 0.00 2.52
5146 5670 4.932200 GTCCCAACTGTCTGAACTTATGAG 59.068 45.833 0.00 0.00 0.00 2.90
5205 5736 7.361031 GCTCAAATGCTCTTGATATGGATAGTG 60.361 40.741 2.15 0.00 34.86 2.74
5273 5805 1.881591 ACAACAAACATTGCATGGGC 58.118 45.000 0.00 0.00 41.68 5.36
5278 5810 2.028748 ACAAACATTGCATGGGCTTCTC 60.029 45.455 0.00 0.00 41.91 2.87
5279 5811 2.226962 AACATTGCATGGGCTTCTCT 57.773 45.000 0.00 0.00 41.91 3.10
5280 5812 1.471119 ACATTGCATGGGCTTCTCTG 58.529 50.000 0.00 0.00 41.91 3.35
5281 5813 0.102481 CATTGCATGGGCTTCTCTGC 59.898 55.000 0.00 0.00 41.91 4.26
5291 5823 4.986645 TTCTCTGCCTGCGCGCAA 62.987 61.111 35.50 19.87 38.56 4.85
5292 5824 4.986645 TCTCTGCCTGCGCGCAAA 62.987 61.111 35.50 21.61 38.56 3.68
5293 5825 3.807538 CTCTGCCTGCGCGCAAAT 61.808 61.111 35.50 0.00 38.56 2.32
5294 5826 3.332493 CTCTGCCTGCGCGCAAATT 62.332 57.895 35.50 0.00 38.56 1.82
5295 5827 2.431260 CTGCCTGCGCGCAAATTT 60.431 55.556 35.50 0.00 38.56 1.82
5296 5828 2.430582 TGCCTGCGCGCAAATTTC 60.431 55.556 35.50 20.61 35.32 2.17
5297 5829 2.126346 GCCTGCGCGCAAATTTCT 60.126 55.556 35.50 0.00 0.00 2.52
5298 5830 2.438954 GCCTGCGCGCAAATTTCTG 61.439 57.895 35.50 20.72 0.00 3.02
5412 5947 5.376854 TGTTTCTTTTAGCCAGAGCATTC 57.623 39.130 0.00 0.00 43.56 2.67
5486 6108 2.867109 ACTCCATGTCCCAGAGTTTG 57.133 50.000 0.00 0.00 37.60 2.93
5560 6182 4.360951 ACTCCCTACGTTCCAAAATGAA 57.639 40.909 0.00 0.00 0.00 2.57
5564 6186 5.074115 TCCCTACGTTCCAAAATGAATGTT 58.926 37.500 0.00 0.00 40.65 2.71
5568 6190 3.801594 ACGTTCCAAAATGAATGTTGTGC 59.198 39.130 0.00 0.00 40.65 4.57
5610 6247 7.996644 ACTTATTTTGAAACAGAGGGAGTACAA 59.003 33.333 0.00 0.00 0.00 2.41
5611 6248 8.754991 TTATTTTGAAACAGAGGGAGTACAAA 57.245 30.769 0.00 0.00 0.00 2.83
5612 6249 7.839680 ATTTTGAAACAGAGGGAGTACAAAT 57.160 32.000 0.00 0.00 31.16 2.32
5613 6250 8.934023 ATTTTGAAACAGAGGGAGTACAAATA 57.066 30.769 0.00 0.00 31.16 1.40
5614 6251 7.739498 TTTGAAACAGAGGGAGTACAAATAC 57.261 36.000 0.00 0.00 0.00 1.89
5615 6252 6.681729 TGAAACAGAGGGAGTACAAATACT 57.318 37.500 0.00 0.00 44.74 2.12
5688 6329 3.555966 CTGGATACCATTCTTGGAACCC 58.444 50.000 0.00 0.00 46.92 4.11
5715 6357 2.552315 TGCCTCAAAAGAACCGAACATC 59.448 45.455 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.393539 CTTTGTCGATGTAGCCAACCG 59.606 52.381 0.00 0.00 0.00 4.44
12 13 1.442184 GTCGCGCTCTCTTTGTCGA 60.442 57.895 5.56 0.00 0.00 4.20
61 62 2.174854 TCGTGGTCTCTAGGGATGATCA 59.825 50.000 0.00 0.00 0.00 2.92
97 98 5.116084 ACCATCTGCACCAACACTAATAT 57.884 39.130 0.00 0.00 0.00 1.28
102 103 1.682854 CAAACCATCTGCACCAACACT 59.317 47.619 0.00 0.00 0.00 3.55
163 164 6.332630 GCACAGGTTAAGTCATTTTGCATAT 58.667 36.000 0.00 0.00 0.00 1.78
164 165 5.618863 CGCACAGGTTAAGTCATTTTGCATA 60.619 40.000 0.00 0.00 0.00 3.14
165 166 4.559153 GCACAGGTTAAGTCATTTTGCAT 58.441 39.130 0.00 0.00 0.00 3.96
185 186 3.006537 AGCCACTCTCTAAGTTAAACGCA 59.993 43.478 0.00 0.00 35.45 5.24
249 250 6.693466 TGACGATTTTTATGGACTGTGTCTA 58.307 36.000 0.00 0.00 32.47 2.59
257 258 4.900635 AGCCATGACGATTTTTATGGAC 57.099 40.909 6.30 0.00 42.05 4.02
341 366 4.720649 TTCACTCCATCTTAGAAGACCG 57.279 45.455 0.00 0.00 37.98 4.79
383 408 3.492313 GATGAGTCACATGTTTTTCGCC 58.508 45.455 0.00 0.00 39.56 5.54
387 412 4.520492 GGTCTGGATGAGTCACATGTTTTT 59.480 41.667 0.00 0.00 39.56 1.94
441 466 4.038763 GGGGAAGAAGTTAACAACCTTTGG 59.961 45.833 8.61 0.00 34.12 3.28
464 489 4.149221 TGTCTAAACTTACATTGTCGTGCG 59.851 41.667 0.00 0.00 0.00 5.34
517 543 9.696917 GAAACTATTTTGTGTTGGAAATCTCAT 57.303 29.630 0.00 0.00 0.00 2.90
548 582 3.506067 AGGTCCTTGCGGAATTTAAACTG 59.494 43.478 0.00 0.00 42.08 3.16
553 587 6.183361 TGGATTATAGGTCCTTGCGGAATTTA 60.183 38.462 0.00 0.00 42.08 1.40
554 588 5.070685 GGATTATAGGTCCTTGCGGAATTT 58.929 41.667 0.00 0.00 42.08 1.82
555 589 4.104102 TGGATTATAGGTCCTTGCGGAATT 59.896 41.667 0.00 0.00 42.08 2.17
556 590 3.650942 TGGATTATAGGTCCTTGCGGAAT 59.349 43.478 0.00 0.00 42.08 3.01
562 596 5.874093 AGCTCATTGGATTATAGGTCCTTG 58.126 41.667 0.00 5.94 36.68 3.61
571 605 7.332557 TGCAAATTGAAAGCTCATTGGATTAT 58.667 30.769 0.00 0.00 0.00 1.28
652 686 6.202379 TGAAGACGACGAACTCTATACCTATG 59.798 42.308 0.00 0.00 0.00 2.23
680 715 2.289195 TGTTGAAGATCCACGTGGGTAC 60.289 50.000 33.40 21.33 38.11 3.34
681 716 1.972075 TGTTGAAGATCCACGTGGGTA 59.028 47.619 33.40 16.87 38.11 3.69
682 717 0.762418 TGTTGAAGATCCACGTGGGT 59.238 50.000 33.40 29.01 38.11 4.51
683 718 1.890876 TTGTTGAAGATCCACGTGGG 58.109 50.000 33.40 15.70 35.41 4.61
684 719 2.878406 AGTTTGTTGAAGATCCACGTGG 59.122 45.455 29.26 29.26 0.00 4.94
705 740 6.017934 GCTTGAAGTTGACAAGACAATCAGTA 60.018 38.462 11.08 0.00 44.92 2.74
878 913 4.860022 ACATCTCTTTCCCACCCTTATTG 58.140 43.478 0.00 0.00 0.00 1.90
883 918 5.333566 TTTTTACATCTCTTTCCCACCCT 57.666 39.130 0.00 0.00 0.00 4.34
928 963 0.321671 ACCACACGAATCTGGAGGTG 59.678 55.000 0.00 0.00 36.50 4.00
976 1053 2.492090 CCTCGGTCGCTCTCAAGG 59.508 66.667 0.00 0.00 0.00 3.61
1279 1724 2.548057 GTGAGTTTTCCATGTTGCGAGA 59.452 45.455 0.00 0.00 0.00 4.04
1289 1734 0.395312 GAGACGGGGTGAGTTTTCCA 59.605 55.000 0.00 0.00 0.00 3.53
1455 1901 3.880490 ACGCCAGTACAAAATCAAGTCAA 59.120 39.130 0.00 0.00 0.00 3.18
1477 1923 1.138859 CCAATCCATACAGCCACGAGA 59.861 52.381 0.00 0.00 0.00 4.04
1498 1944 1.135112 CACGGATCGACCATCAGACAA 60.135 52.381 0.00 0.00 38.90 3.18
1499 1945 0.455815 CACGGATCGACCATCAGACA 59.544 55.000 0.00 0.00 38.90 3.41
1544 1990 3.686726 GCGAACATCTTGATCTTGTTCCT 59.313 43.478 17.64 0.00 43.94 3.36
1658 2104 0.976641 ATCACCGACATCACACAGGT 59.023 50.000 0.00 0.00 35.24 4.00
1672 2118 1.618837 TCGGGCTATCAGCTTATCACC 59.381 52.381 0.00 0.00 41.99 4.02
1673 2119 2.558795 TCTCGGGCTATCAGCTTATCAC 59.441 50.000 0.00 0.00 41.99 3.06
1674 2120 2.876581 TCTCGGGCTATCAGCTTATCA 58.123 47.619 0.00 0.00 41.99 2.15
1675 2121 3.944055 TTCTCGGGCTATCAGCTTATC 57.056 47.619 0.00 0.00 41.99 1.75
1676 2122 3.388024 TGTTTCTCGGGCTATCAGCTTAT 59.612 43.478 0.00 0.00 41.99 1.73
1677 2123 2.764010 TGTTTCTCGGGCTATCAGCTTA 59.236 45.455 0.00 0.00 41.99 3.09
1678 2124 1.555075 TGTTTCTCGGGCTATCAGCTT 59.445 47.619 0.00 0.00 41.99 3.74
1679 2125 1.195115 TGTTTCTCGGGCTATCAGCT 58.805 50.000 0.00 0.00 41.99 4.24
1681 2127 4.695455 TCTTTTTGTTTCTCGGGCTATCAG 59.305 41.667 0.00 0.00 0.00 2.90
1723 2170 4.471904 AACCAAACGATGATGAGCTAGA 57.528 40.909 0.00 0.00 0.00 2.43
1732 2179 3.536570 TGAGTGTGAAACCAAACGATGA 58.463 40.909 0.00 0.00 34.36 2.92
1738 2185 4.946772 TGACATTCTGAGTGTGAAACCAAA 59.053 37.500 10.72 0.00 34.36 3.28
1759 2207 7.774625 TGGTGCATAATCTAGAACAAATCATGA 59.225 33.333 0.00 0.00 0.00 3.07
1760 2208 7.933396 TGGTGCATAATCTAGAACAAATCATG 58.067 34.615 0.00 0.00 0.00 3.07
1768 2216 6.017605 CCTGTCATTGGTGCATAATCTAGAAC 60.018 42.308 0.00 0.00 0.00 3.01
1770 2218 5.130975 ACCTGTCATTGGTGCATAATCTAGA 59.869 40.000 0.00 0.00 36.30 2.43
1773 2221 4.202441 GACCTGTCATTGGTGCATAATCT 58.798 43.478 0.00 0.00 38.03 2.40
1882 2330 8.726988 GCAGTTGTGGTTCTAAGTAATTCATTA 58.273 33.333 0.00 0.00 0.00 1.90
1894 2345 1.416030 TCTGCTGCAGTTGTGGTTCTA 59.584 47.619 27.24 2.95 32.61 2.10
1907 2358 9.745323 GTGATAAATTGTTAAAATTTCTGCTGC 57.255 29.630 0.00 0.00 32.64 5.25
1962 2413 9.122613 GAATTGTTAAAATCTCTGCTGAAGTTC 57.877 33.333 0.00 0.00 0.00 3.01
1963 2414 8.084684 GGAATTGTTAAAATCTCTGCTGAAGTT 58.915 33.333 0.00 0.00 0.00 2.66
1964 2415 7.449704 AGGAATTGTTAAAATCTCTGCTGAAGT 59.550 33.333 0.00 0.00 0.00 3.01
1965 2416 7.824672 AGGAATTGTTAAAATCTCTGCTGAAG 58.175 34.615 0.00 0.00 0.00 3.02
1966 2417 7.448161 TGAGGAATTGTTAAAATCTCTGCTGAA 59.552 33.333 0.00 0.00 0.00 3.02
1967 2418 6.942005 TGAGGAATTGTTAAAATCTCTGCTGA 59.058 34.615 0.00 0.00 0.00 4.26
1975 2432 8.764287 CAAAAGGTGTGAGGAATTGTTAAAATC 58.236 33.333 0.00 0.00 0.00 2.17
2020 2483 6.094061 GTGAATAGTTAGAGCGAGACTTGTT 58.906 40.000 0.00 0.00 0.00 2.83
2025 2488 4.982999 TGTGTGAATAGTTAGAGCGAGAC 58.017 43.478 0.00 0.00 0.00 3.36
2061 2524 7.262772 CCATGTCAGATTTTGCTATCAAATGT 58.737 34.615 0.00 0.00 41.37 2.71
2076 2539 4.195334 GGGCCCGCCATGTCAGAT 62.195 66.667 5.69 0.00 37.98 2.90
2087 2550 2.503061 CTCTGATGAGTGGGCCCG 59.497 66.667 19.37 0.00 35.67 6.13
2123 2586 2.158385 TGTTTAGGGGCAATTGACAGGT 60.158 45.455 14.60 0.00 0.00 4.00
2227 2690 4.505566 GCCATCCATACCATGTGTCACTAT 60.506 45.833 4.27 0.00 0.00 2.12
2337 2800 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2385 2852 8.929487 ACTCCCTCTGTAAAGAAATATAAGAGG 58.071 37.037 8.54 8.54 39.86 3.69
2630 3097 0.035317 TTCTCAGCAGCAACCACGAT 59.965 50.000 0.00 0.00 0.00 3.73
2638 3105 3.423539 AACATTACCTTCTCAGCAGCA 57.576 42.857 0.00 0.00 0.00 4.41
2641 3108 6.070767 AGCTACTAAACATTACCTTCTCAGCA 60.071 38.462 0.00 0.00 0.00 4.41
2679 3146 4.351874 ACAGCTAAGTCCTTGCAAAGTA 57.648 40.909 0.00 0.00 44.25 2.24
2710 3177 6.924060 TCTTCTAGCTAAGACAACAAAGACAC 59.076 38.462 0.00 0.00 32.51 3.67
2766 3233 7.069455 GGGTAAATATTTTGGACAGTTATGGCT 59.931 37.037 5.91 0.00 33.55 4.75
2784 3251 4.080015 CCAGGAGTCCACATTGGGTAAATA 60.080 45.833 12.86 0.00 38.32 1.40
3113 3590 2.934364 GCAGAACAGGACTGTCATCTGG 60.934 54.545 24.49 13.30 43.46 3.86
3132 3609 7.039082 AGGCTAATTTCATTTTCCTTAACTGCA 60.039 33.333 0.00 0.00 0.00 4.41
3307 3784 2.618045 GGTGGTTGGAATCAGTACCCTG 60.618 54.545 0.00 0.00 40.25 4.45
3420 3897 0.394216 ACCATATCGGCAGCAAAGCA 60.394 50.000 0.00 0.00 39.03 3.91
3510 3988 4.141711 ACAACCTCTTCAGCAAGAACACTA 60.142 41.667 0.00 0.00 38.23 2.74
3573 4051 1.830279 AACATCCACTCCACATGCAG 58.170 50.000 0.00 0.00 0.00 4.41
3641 4119 1.952296 CTCATGGGATAGGCAAAGTGC 59.048 52.381 0.00 0.00 44.08 4.40
3840 4322 5.673818 GCAAAATACTCCCTCTTAACTTGCG 60.674 44.000 0.00 0.00 0.00 4.85
3846 4328 7.234577 ACCAAAATGCAAAATACTCCCTCTTAA 59.765 33.333 0.00 0.00 0.00 1.85
3866 4348 7.836685 TCATATTAGCCATCCTTGTTACCAAAA 59.163 33.333 0.00 0.00 0.00 2.44
3989 4508 9.726438 GGCAATAAGAACAATATAGTGGTATCT 57.274 33.333 5.03 2.80 0.00 1.98
4046 4566 6.270000 CAGAACATATAGGGGTGTTAGGATCA 59.730 42.308 0.00 0.00 38.57 2.92
4047 4567 6.270231 ACAGAACATATAGGGGTGTTAGGATC 59.730 42.308 0.00 0.00 38.57 3.36
4048 4568 6.151049 ACAGAACATATAGGGGTGTTAGGAT 58.849 40.000 0.00 0.00 38.57 3.24
4277 4798 6.785337 TGGAGAATTCAGATGATGCAAAAT 57.215 33.333 8.44 0.00 0.00 1.82
4307 4828 9.658475 CAAGTTCATCGTTACTGTTAATTGAAA 57.342 29.630 0.00 0.00 0.00 2.69
4320 4841 6.073440 GCAAACCTAGAACAAGTTCATCGTTA 60.073 38.462 14.69 0.00 41.84 3.18
4332 4853 3.071479 GGTTGATCGCAAACCTAGAACA 58.929 45.455 6.26 0.00 35.65 3.18
4342 4863 0.327924 AGGGATGTGGTTGATCGCAA 59.672 50.000 0.00 0.00 35.71 4.85
4393 4914 2.357569 GGCCTCATCAAACTTCCCATCT 60.358 50.000 0.00 0.00 0.00 2.90
4543 5064 3.987868 GACACGAGAGCATAAACAAGACA 59.012 43.478 0.00 0.00 0.00 3.41
4552 5073 4.456280 AATCACAAGACACGAGAGCATA 57.544 40.909 0.00 0.00 0.00 3.14
4553 5074 3.325293 AATCACAAGACACGAGAGCAT 57.675 42.857 0.00 0.00 0.00 3.79
4555 5076 4.268884 GGATAAATCACAAGACACGAGAGC 59.731 45.833 0.00 0.00 0.00 4.09
4556 5077 4.806247 GGGATAAATCACAAGACACGAGAG 59.194 45.833 0.00 0.00 0.00 3.20
4558 5079 3.551890 CGGGATAAATCACAAGACACGAG 59.448 47.826 0.00 0.00 0.00 4.18
4559 5080 3.056393 ACGGGATAAATCACAAGACACGA 60.056 43.478 0.00 0.00 0.00 4.35
4563 5087 4.935808 AGTTGACGGGATAAATCACAAGAC 59.064 41.667 0.00 0.00 0.00 3.01
4568 5092 9.285770 GAAATTTTAGTTGACGGGATAAATCAC 57.714 33.333 0.00 0.00 0.00 3.06
4590 5114 5.767269 TGTGCGAACATACAAACATGAAAT 58.233 33.333 0.00 0.00 0.00 2.17
4603 5127 1.234615 CCGGTTTCCTGTGCGAACAT 61.235 55.000 0.00 0.00 0.00 2.71
4604 5128 1.890041 CCGGTTTCCTGTGCGAACA 60.890 57.895 0.00 0.00 0.00 3.18
4605 5129 0.953960 ATCCGGTTTCCTGTGCGAAC 60.954 55.000 0.00 0.00 0.00 3.95
4620 5144 1.063006 CCTCATGTGCGCAAATCCG 59.937 57.895 14.00 5.03 0.00 4.18
4647 5171 3.659089 AAGGAATGACCCGACGCCG 62.659 63.158 0.00 0.00 40.05 6.46
4653 5177 1.740025 GAAAGCTGAAGGAATGACCCG 59.260 52.381 0.00 0.00 40.05 5.28
4861 5385 6.319152 CACTAGTCACTACAGGCTACAACTAT 59.681 42.308 0.00 0.00 0.00 2.12
4903 5427 3.332034 GGGCTAAAAGCACTCGAACTAA 58.668 45.455 0.78 0.00 42.59 2.24
4936 5460 0.165944 AAATACAGCAGCGCGTGAAC 59.834 50.000 8.43 0.00 0.00 3.18
4984 5508 6.311445 CACGACAGCTCAATAGACTACAAAAT 59.689 38.462 0.00 0.00 0.00 1.82
5009 5533 0.743097 GGTTCCTTCATGATGCTGGC 59.257 55.000 0.00 0.00 0.00 4.85
5107 5631 3.516586 TGGGACTGTAAGATTCAGACCA 58.483 45.455 13.90 11.27 44.82 4.02
5125 5649 3.686726 GCTCATAAGTTCAGACAGTTGGG 59.313 47.826 0.00 0.00 0.00 4.12
5146 5670 3.391049 AGACCACTTTCGTAAACTCTGC 58.609 45.455 0.00 0.00 0.00 4.26
5278 5810 2.431260 AAATTTGCGCGCAGGCAG 60.431 55.556 34.25 0.00 44.94 4.85
5279 5811 2.430582 GAAATTTGCGCGCAGGCA 60.431 55.556 34.25 22.04 42.12 4.75
5280 5812 2.126346 AGAAATTTGCGCGCAGGC 60.126 55.556 34.25 20.93 0.00 4.85
5281 5813 1.081242 ACAGAAATTTGCGCGCAGG 60.081 52.632 34.25 19.20 0.00 4.85
5282 5814 0.385849 TCACAGAAATTTGCGCGCAG 60.386 50.000 34.25 22.42 0.00 5.18
5288 5820 4.622313 TGCGATTTCATCACAGAAATTTGC 59.378 37.500 14.90 14.90 45.51 3.68
5291 5823 6.869913 ACAAATGCGATTTCATCACAGAAATT 59.130 30.769 3.74 0.00 45.51 1.82
5293 5825 5.630264 CACAAATGCGATTTCATCACAGAAA 59.370 36.000 0.00 0.00 41.31 2.52
5294 5826 5.155643 CACAAATGCGATTTCATCACAGAA 58.844 37.500 0.00 0.00 0.00 3.02
5295 5827 4.379708 CCACAAATGCGATTTCATCACAGA 60.380 41.667 0.00 0.00 0.00 3.41
5296 5828 3.855379 CCACAAATGCGATTTCATCACAG 59.145 43.478 0.00 0.00 0.00 3.66
5297 5829 3.505293 TCCACAAATGCGATTTCATCACA 59.495 39.130 0.00 0.00 0.00 3.58
5298 5830 4.095410 TCCACAAATGCGATTTCATCAC 57.905 40.909 0.00 0.00 0.00 3.06
5352 5884 9.611284 AAAAGAACTGTTTTTGAAAGCATTTTC 57.389 25.926 0.00 1.66 39.27 2.29
5369 5901 9.853921 GAAACAAAATCAATGCTAAAAGAACTG 57.146 29.630 0.00 0.00 0.00 3.16
5400 5935 0.917533 ACATCCTGAATGCTCTGGCT 59.082 50.000 0.00 0.00 39.84 4.75
5401 5936 1.760192 AACATCCTGAATGCTCTGGC 58.240 50.000 0.00 0.00 39.84 4.85
5445 5980 6.665465 AGTTTCTACACTTAATTTTCCGCAC 58.335 36.000 0.00 0.00 0.00 5.34
5449 5984 8.793592 ACATGGAGTTTCTACACTTAATTTTCC 58.206 33.333 0.00 0.00 0.00 3.13
5486 6108 3.904136 ATGTGAACACAAAGTAGCTGC 57.096 42.857 11.60 0.00 45.41 5.25
5560 6182 5.163468 TGTCATGGTTTTAGTTGCACAACAT 60.163 36.000 15.40 4.00 43.47 2.71
5564 6186 3.951037 AGTGTCATGGTTTTAGTTGCACA 59.049 39.130 0.00 0.00 0.00 4.57
5568 6190 9.743057 TCAAAATAAGTGTCATGGTTTTAGTTG 57.257 29.630 0.00 0.00 0.00 3.16
5640 6277 7.789273 AGCAATCAGTCATCTAGAAAGAATG 57.211 36.000 15.71 15.71 34.73 2.67
5688 6329 1.000171 GGTTCTTTTGAGGCAGCCTTG 60.000 52.381 17.46 4.29 31.76 3.61


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

AutoCloner maintained by Alex Coulton.