Multiple sequence alignment - TraesCS5A01G281700

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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 TraesCS5A01G281700 chr5A 100.000 2364 0 0 1 2364 491092756 491095119 0.000000e+00 4366.0
1 TraesCS5A01G281700 chr5A 88.068 352 37 2 20 371 649647559 649647905 1.690000e-111 412.0
2 TraesCS5A01G281700 chr5A 82.243 107 19 0 1091 1197 491162911 491163017 2.500000e-15 93.5
3 TraesCS5A01G281700 chr5D 96.036 782 18 4 716 1492 387960484 387961257 0.000000e+00 1260.0
4 TraesCS5A01G281700 chr5D 94.017 468 19 5 1593 2052 387961362 387961828 0.000000e+00 701.0
5 TraesCS5A01G281700 chr5D 94.505 273 9 3 2092 2364 387964481 387964747 1.310000e-112 416.0
6 TraesCS5A01G281700 chr5D 90.741 108 5 4 1506 1610 387961239 387961344 3.170000e-29 139.0
7 TraesCS5A01G281700 chr5D 84.762 105 16 0 1093 1197 387989477 387989581 3.210000e-19 106.0
8 TraesCS5A01G281700 chr5B 92.239 786 30 5 716 1492 466525259 466526022 0.000000e+00 1085.0
9 TraesCS5A01G281700 chr5B 92.101 595 22 10 1506 2079 466526004 466526594 0.000000e+00 815.0
10 TraesCS5A01G281700 chr5B 85.956 413 44 5 13 424 609121243 609121642 1.680000e-116 429.0
11 TraesCS5A01G281700 chr5B 89.206 315 29 2 1 314 466523367 466523677 2.850000e-104 388.0
12 TraesCS5A01G281700 chr5B 90.052 191 12 6 2174 2364 466541616 466541799 8.440000e-60 241.0
13 TraesCS5A01G281700 chr5B 95.918 147 4 2 408 552 466525105 466525251 1.090000e-58 237.0
14 TraesCS5A01G281700 chr5B 78.462 195 34 5 1091 1284 466616341 466616528 1.150000e-23 121.0
15 TraesCS5A01G281700 chr5B 96.667 60 2 0 299 358 466524922 466524981 1.500000e-17 100.0
16 TraesCS5A01G281700 chr5B 92.683 41 3 0 2142 2182 466541382 466541422 2.540000e-05 60.2
17 TraesCS5A01G281700 chr4A 86.650 412 50 2 21 432 573205161 573204755 3.580000e-123 451.0
18 TraesCS5A01G281700 chr1D 85.612 417 36 5 13 429 416093901 416094293 1.310000e-112 416.0
19 TraesCS5A01G281700 chr3B 84.211 418 38 9 15 431 707575042 707574652 4.770000e-102 381.0
20 TraesCS5A01G281700 chr2A 88.312 231 22 2 18 247 196351363 196351589 2.990000e-69 272.0
21 TraesCS5A01G281700 chr7A 75.806 186 43 2 21 205 597977222 597977038 2.500000e-15 93.5
22 TraesCS5A01G281700 chr6D 96.875 32 0 1 1092 1123 37449700 37449730 4.000000e-03 52.8
23 TraesCS5A01G281700 chr6B 96.875 32 0 1 1092 1123 87560144 87560174 4.000000e-03 52.8


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 TraesCS5A01G281700 chr5A 491092756 491095119 2363 False 4366 4366 100.00000 1 2364 1 chr5A.!!$F1 2363
1 TraesCS5A01G281700 chr5D 387960484 387964747 4263 False 629 1260 93.82475 716 2364 4 chr5D.!!$F2 1648
2 TraesCS5A01G281700 chr5B 466523367 466526594 3227 False 525 1085 93.22620 1 2079 5 chr5B.!!$F3 2078

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
693 2031 0.034756 TTCTGCGCCTTGCTAACTGA 59.965 50.0 4.18 0.0 46.63 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 3040 0.824109 TCACGAATAGGGTCAGGCAG 59.176 55.0 0.0 0.0 0.0 4.85 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
23 24 2.612212 TGTGGAGCAGTTTCGTTCTTTC 59.388 45.455 0.00 0.00 0.00 2.62
27 28 4.201910 TGGAGCAGTTTCGTTCTTTCTTTG 60.202 41.667 0.00 0.00 0.00 2.77
28 29 3.695816 AGCAGTTTCGTTCTTTCTTTGC 58.304 40.909 0.00 0.00 0.00 3.68
29 30 3.128589 AGCAGTTTCGTTCTTTCTTTGCA 59.871 39.130 0.00 0.00 0.00 4.08
50 52 5.945784 TGCAGGAAATAACTTGCATTACTCT 59.054 36.000 0.00 0.00 45.21 3.24
61 63 6.615088 ACTTGCATTACTCTTGTAGCATTTG 58.385 36.000 0.00 0.00 32.42 2.32
81 83 7.065085 GCATTTGCTACTTCAGAATTACAGAGA 59.935 37.037 0.00 0.00 38.21 3.10
90 92 8.944029 ACTTCAGAATTACAGAGATCAACAATG 58.056 33.333 0.00 0.00 0.00 2.82
91 93 7.312657 TCAGAATTACAGAGATCAACAATGC 57.687 36.000 0.00 0.00 0.00 3.56
92 94 6.317140 TCAGAATTACAGAGATCAACAATGCC 59.683 38.462 0.00 0.00 0.00 4.40
113 115 0.545309 ACAGGACTAGAGGCAAGCCA 60.545 55.000 14.40 0.00 38.92 4.75
117 119 1.003696 GGACTAGAGGCAAGCCAAACT 59.996 52.381 14.40 11.47 38.92 2.66
136 138 0.685097 TGCAGTTCTACCACTGGTCC 59.315 55.000 3.21 0.00 43.94 4.46
157 159 4.093011 CCTCCCATAGCTAGCTAAGACAT 58.907 47.826 27.47 9.83 31.73 3.06
169 171 5.171339 AGCTAAGACATGACTCACCAAAT 57.829 39.130 0.00 0.00 0.00 2.32
171 173 5.645497 AGCTAAGACATGACTCACCAAATTC 59.355 40.000 0.00 0.00 0.00 2.17
191 193 3.444916 TCTGGTTTCGTCGAATATGAGC 58.555 45.455 8.78 4.14 0.00 4.26
194 196 4.188462 TGGTTTCGTCGAATATGAGCAAT 58.812 39.130 8.78 0.00 0.00 3.56
254 256 4.771577 TCACATACACCATGAAGCCAAAAT 59.228 37.500 0.00 0.00 38.10 1.82
265 267 6.489022 CCATGAAGCCAAAATGAGATCTATCA 59.511 38.462 0.00 0.00 0.00 2.15
266 268 7.176865 CCATGAAGCCAAAATGAGATCTATCAT 59.823 37.037 0.00 0.00 41.72 2.45
365 1627 2.038659 CCAAAGCCAAACCTTCCTTGA 58.961 47.619 0.00 0.00 0.00 3.02
368 1630 1.826385 AGCCAAACCTTCCTTGATCG 58.174 50.000 0.00 0.00 0.00 3.69
369 1631 0.171231 GCCAAACCTTCCTTGATCGC 59.829 55.000 0.00 0.00 0.00 4.58
370 1632 0.811281 CCAAACCTTCCTTGATCGCC 59.189 55.000 0.00 0.00 0.00 5.54
380 1678 1.153568 TTGATCGCCAAGAGCTCCG 60.154 57.895 10.93 6.95 40.39 4.63
386 1684 2.510238 CCAAGAGCTCCGCTTCCG 60.510 66.667 10.93 0.00 39.88 4.30
409 1707 6.129393 CGATGCTTCGGAACAATTGTATAAG 58.871 40.000 12.39 13.17 41.74 1.73
433 1769 5.765176 CATCTGCATGAAGAGAAAACAACA 58.235 37.500 9.83 0.00 30.57 3.33
552 1890 9.603921 AAACTAACTAGCTTGCCGTTATTATTA 57.396 29.630 0.00 0.00 0.00 0.98
554 1892 9.204570 ACTAACTAGCTTGCCGTTATTATTATG 57.795 33.333 0.00 0.00 0.00 1.90
555 1893 9.204570 CTAACTAGCTTGCCGTTATTATTATGT 57.795 33.333 0.00 0.00 0.00 2.29
556 1894 8.446599 AACTAGCTTGCCGTTATTATTATGTT 57.553 30.769 0.00 0.00 0.00 2.71
633 1971 6.422776 AAATAACTCTATGAGCACCAAACG 57.577 37.500 0.00 0.00 32.04 3.60
634 1972 3.402628 AACTCTATGAGCACCAAACGT 57.597 42.857 0.00 0.00 32.04 3.99
635 1973 3.402628 ACTCTATGAGCACCAAACGTT 57.597 42.857 0.00 0.00 32.04 3.99
636 1974 3.326747 ACTCTATGAGCACCAAACGTTC 58.673 45.455 0.00 0.00 32.04 3.95
637 1975 3.244078 ACTCTATGAGCACCAAACGTTCA 60.244 43.478 0.00 0.00 32.04 3.18
638 1976 3.734463 TCTATGAGCACCAAACGTTCAA 58.266 40.909 0.00 0.00 0.00 2.69
639 1977 3.745975 TCTATGAGCACCAAACGTTCAAG 59.254 43.478 0.00 0.00 0.00 3.02
640 1978 0.380378 TGAGCACCAAACGTTCAAGC 59.620 50.000 0.00 4.00 0.00 4.01
641 1979 0.317854 GAGCACCAAACGTTCAAGCC 60.318 55.000 0.00 0.00 0.00 4.35
642 1980 1.657181 GCACCAAACGTTCAAGCCG 60.657 57.895 0.00 0.00 0.00 5.52
643 1981 2.018544 CACCAAACGTTCAAGCCGA 58.981 52.632 0.00 0.00 0.00 5.54
644 1982 0.041312 CACCAAACGTTCAAGCCGAG 60.041 55.000 0.00 0.00 0.00 4.63
645 1983 0.179067 ACCAAACGTTCAAGCCGAGA 60.179 50.000 0.00 0.00 0.00 4.04
646 1984 1.156736 CCAAACGTTCAAGCCGAGAT 58.843 50.000 0.00 0.00 0.00 2.75
647 1985 1.535462 CCAAACGTTCAAGCCGAGATT 59.465 47.619 0.00 0.00 0.00 2.40
648 1986 2.031157 CCAAACGTTCAAGCCGAGATTT 60.031 45.455 0.00 0.00 0.00 2.17
649 1987 3.187637 CCAAACGTTCAAGCCGAGATTTA 59.812 43.478 0.00 0.00 0.00 1.40
650 1988 4.319911 CCAAACGTTCAAGCCGAGATTTAA 60.320 41.667 0.00 0.00 0.00 1.52
651 1989 5.209240 CAAACGTTCAAGCCGAGATTTAAA 58.791 37.500 0.00 0.00 0.00 1.52
652 1990 4.400036 ACGTTCAAGCCGAGATTTAAAC 57.600 40.909 0.00 0.00 0.00 2.01
653 1991 3.187842 ACGTTCAAGCCGAGATTTAAACC 59.812 43.478 0.00 0.00 0.00 3.27
654 1992 3.435671 CGTTCAAGCCGAGATTTAAACCT 59.564 43.478 0.00 0.00 0.00 3.50
655 1993 4.083484 CGTTCAAGCCGAGATTTAAACCTT 60.083 41.667 0.00 0.00 0.00 3.50
656 1994 5.154222 GTTCAAGCCGAGATTTAAACCTTG 58.846 41.667 0.00 0.00 0.00 3.61
657 1995 3.756434 TCAAGCCGAGATTTAAACCTTGG 59.244 43.478 11.27 11.27 37.08 3.61
658 1996 3.434940 AGCCGAGATTTAAACCTTGGT 57.565 42.857 16.21 2.15 36.53 3.67
659 1997 3.081804 AGCCGAGATTTAAACCTTGGTG 58.918 45.455 16.21 0.00 36.53 4.17
660 1998 2.163613 GCCGAGATTTAAACCTTGGTGG 59.836 50.000 16.21 2.88 42.93 4.61
661 1999 2.752903 CCGAGATTTAAACCTTGGTGGG 59.247 50.000 7.65 0.00 41.11 4.61
662 2000 2.163613 CGAGATTTAAACCTTGGTGGGC 59.836 50.000 0.00 0.00 41.11 5.36
663 2001 3.431415 GAGATTTAAACCTTGGTGGGCT 58.569 45.455 0.00 0.00 41.11 5.19
664 2002 3.165071 AGATTTAAACCTTGGTGGGCTG 58.835 45.455 0.00 0.00 41.11 4.85
665 2003 1.710816 TTTAAACCTTGGTGGGCTGG 58.289 50.000 0.00 0.00 41.11 4.85
666 2004 0.830023 TTAAACCTTGGTGGGCTGGC 60.830 55.000 0.00 0.00 41.11 4.85
667 2005 1.725169 TAAACCTTGGTGGGCTGGCT 61.725 55.000 0.00 0.00 41.11 4.75
668 2006 1.725169 AAACCTTGGTGGGCTGGCTA 61.725 55.000 0.00 0.00 41.11 3.93
669 2007 2.142292 AACCTTGGTGGGCTGGCTAG 62.142 60.000 0.00 0.00 41.11 3.42
670 2008 2.273449 CTTGGTGGGCTGGCTAGG 59.727 66.667 0.00 0.00 0.00 3.02
671 2009 2.204074 TTGGTGGGCTGGCTAGGA 60.204 61.111 0.00 0.00 0.00 2.94
672 2010 1.850289 TTGGTGGGCTGGCTAGGAA 60.850 57.895 0.00 0.00 0.00 3.36
673 2011 2.137177 TTGGTGGGCTGGCTAGGAAC 62.137 60.000 0.00 0.00 0.00 3.62
674 2012 2.301738 GGTGGGCTGGCTAGGAACT 61.302 63.158 0.00 0.00 46.37 3.01
675 2013 1.685820 GTGGGCTGGCTAGGAACTT 59.314 57.895 0.00 0.00 41.75 2.66
676 2014 0.393132 GTGGGCTGGCTAGGAACTTC 60.393 60.000 0.00 0.00 41.75 3.01
677 2015 0.547712 TGGGCTGGCTAGGAACTTCT 60.548 55.000 0.00 0.00 41.75 2.85
678 2016 0.107459 GGGCTGGCTAGGAACTTCTG 60.107 60.000 0.00 0.00 41.75 3.02
679 2017 0.746204 GGCTGGCTAGGAACTTCTGC 60.746 60.000 0.00 0.00 41.75 4.26
680 2018 1.086634 GCTGGCTAGGAACTTCTGCG 61.087 60.000 0.00 0.00 41.75 5.18
681 2019 1.079127 TGGCTAGGAACTTCTGCGC 60.079 57.895 0.00 0.00 41.75 6.09
682 2020 1.815840 GGCTAGGAACTTCTGCGCC 60.816 63.158 4.18 0.00 41.75 6.53
683 2021 1.219393 GCTAGGAACTTCTGCGCCT 59.781 57.895 4.18 0.00 41.75 5.52
684 2022 0.391793 GCTAGGAACTTCTGCGCCTT 60.392 55.000 4.18 0.00 41.75 4.35
685 2023 1.363744 CTAGGAACTTCTGCGCCTTG 58.636 55.000 4.18 0.00 41.75 3.61
686 2024 0.673644 TAGGAACTTCTGCGCCTTGC 60.674 55.000 4.18 0.00 42.48 4.01
687 2025 1.968540 GGAACTTCTGCGCCTTGCT 60.969 57.895 4.18 0.00 46.63 3.91
688 2026 0.673644 GGAACTTCTGCGCCTTGCTA 60.674 55.000 4.18 0.00 46.63 3.49
689 2027 1.156736 GAACTTCTGCGCCTTGCTAA 58.843 50.000 4.18 0.00 46.63 3.09
690 2028 0.875059 AACTTCTGCGCCTTGCTAAC 59.125 50.000 4.18 0.00 46.63 2.34
691 2029 0.035458 ACTTCTGCGCCTTGCTAACT 59.965 50.000 4.18 0.00 46.63 2.24
692 2030 0.445436 CTTCTGCGCCTTGCTAACTG 59.555 55.000 4.18 0.00 46.63 3.16
693 2031 0.034756 TTCTGCGCCTTGCTAACTGA 59.965 50.000 4.18 0.00 46.63 3.41
694 2032 0.390340 TCTGCGCCTTGCTAACTGAG 60.390 55.000 4.18 0.00 46.63 3.35
704 2042 3.920144 CTAACTGAGCTACGTCCGG 57.080 57.895 0.00 0.00 0.00 5.14
705 2043 1.093159 CTAACTGAGCTACGTCCGGT 58.907 55.000 0.00 0.00 0.00 5.28
706 2044 1.471684 CTAACTGAGCTACGTCCGGTT 59.528 52.381 0.00 0.31 0.00 4.44
707 2045 0.243095 AACTGAGCTACGTCCGGTTC 59.757 55.000 0.00 0.00 0.00 3.62
708 2046 0.608582 ACTGAGCTACGTCCGGTTCT 60.609 55.000 0.00 0.00 0.00 3.01
709 2047 0.099082 CTGAGCTACGTCCGGTTCTC 59.901 60.000 0.00 1.16 0.00 2.87
710 2048 0.322277 TGAGCTACGTCCGGTTCTCT 60.322 55.000 0.00 0.00 31.93 3.10
711 2049 0.810016 GAGCTACGTCCGGTTCTCTT 59.190 55.000 0.00 0.00 0.00 2.85
712 2050 2.012673 GAGCTACGTCCGGTTCTCTTA 58.987 52.381 0.00 0.00 0.00 2.10
713 2051 2.617774 GAGCTACGTCCGGTTCTCTTAT 59.382 50.000 0.00 0.00 0.00 1.73
714 2052 3.022406 AGCTACGTCCGGTTCTCTTATT 58.978 45.455 0.00 0.00 0.00 1.40
715 2053 4.202441 AGCTACGTCCGGTTCTCTTATTA 58.798 43.478 0.00 0.00 0.00 0.98
716 2054 4.826183 AGCTACGTCCGGTTCTCTTATTAT 59.174 41.667 0.00 0.00 0.00 1.28
717 2055 6.000219 AGCTACGTCCGGTTCTCTTATTATA 59.000 40.000 0.00 0.00 0.00 0.98
809 2156 8.850454 TTGTAGCAAAACTAAGACAATTCAAC 57.150 30.769 0.00 0.00 30.90 3.18
943 2291 2.666619 GCACGCATGAAAGTTCTGAAGG 60.667 50.000 0.00 0.00 0.00 3.46
983 2331 6.375736 TCTCTCTCTATAAATACATCGGCCAG 59.624 42.308 2.24 0.00 0.00 4.85
984 2332 5.073311 TCTCTATAAATACATCGGCCAGC 57.927 43.478 2.24 0.00 0.00 4.85
1002 2350 3.924238 CACGCTATGCAAATCCACC 57.076 52.632 0.00 0.00 0.00 4.61
1003 2351 1.093972 CACGCTATGCAAATCCACCA 58.906 50.000 0.00 0.00 0.00 4.17
1004 2352 1.472082 CACGCTATGCAAATCCACCAA 59.528 47.619 0.00 0.00 0.00 3.67
1005 2353 1.745087 ACGCTATGCAAATCCACCAAG 59.255 47.619 0.00 0.00 0.00 3.61
1006 2354 1.534595 CGCTATGCAAATCCACCAAGC 60.535 52.381 0.00 0.00 0.00 4.01
1007 2355 1.477700 GCTATGCAAATCCACCAAGCA 59.522 47.619 0.00 0.00 39.79 3.91
1008 2356 2.094078 GCTATGCAAATCCACCAAGCAA 60.094 45.455 0.00 0.00 38.85 3.91
1009 2357 2.460757 ATGCAAATCCACCAAGCAAC 57.539 45.000 0.00 0.00 38.85 4.17
1010 2358 1.117994 TGCAAATCCACCAAGCAACA 58.882 45.000 0.00 0.00 31.42 3.33
1288 2653 2.171448 CCCATTGTTGGCTAGCTCTAGT 59.829 50.000 15.72 0.00 42.15 2.57
1314 2679 1.070134 ACTAGCCTTGCTTGTCGTTGA 59.930 47.619 0.00 0.00 40.15 3.18
1421 2786 7.997107 TGTATGTGTCTACAATTTCGGTATC 57.003 36.000 0.00 0.00 40.84 2.24
1543 2908 6.763303 ATTTGGCGTCAAGTTATTGTTTTC 57.237 33.333 1.31 0.00 37.68 2.29
1551 2919 8.365210 GCGTCAAGTTATTGTTTTCACATTATG 58.635 33.333 0.00 0.00 37.68 1.90
1926 3349 6.547880 CAGCTTCTAGAAGGGTAGATGAGTTA 59.452 42.308 29.22 0.00 38.80 2.24
1932 3355 9.268282 TCTAGAAGGGTAGATGAGTTATTTTGT 57.732 33.333 0.00 0.00 0.00 2.83
1945 3371 7.279615 TGAGTTATTTTGTTCTCAAGGAGACA 58.720 34.615 0.00 0.00 38.51 3.41
2006 3433 6.042093 TGTTTATTTTGCCCCATCAACTTACA 59.958 34.615 0.00 0.00 0.00 2.41
2086 3547 9.744468 AACTAAATGAGTTTAAATGTTGTGTCC 57.256 29.630 0.00 0.00 46.79 4.02
2087 3548 8.908903 ACTAAATGAGTTTAAATGTTGTGTCCA 58.091 29.630 0.00 0.00 33.13 4.02
2088 3549 9.398170 CTAAATGAGTTTAAATGTTGTGTCCAG 57.602 33.333 0.00 0.00 29.86 3.86
2089 3550 5.181690 TGAGTTTAAATGTTGTGTCCAGC 57.818 39.130 0.00 0.00 0.00 4.85
2090 3551 4.642437 TGAGTTTAAATGTTGTGTCCAGCA 59.358 37.500 0.00 0.00 36.18 4.41
2106 6146 6.237901 TGTCCAGCAACACATACTAAAGATT 58.762 36.000 0.00 0.00 0.00 2.40
2153 6193 8.357402 GCTTTTTATTAGTGGAAAACCAAGAGA 58.643 33.333 0.00 0.00 0.00 3.10
2183 6223 9.793252 CTCTCTTTCATTCAAGAAAAAGAACAA 57.207 29.630 9.62 1.66 35.01 2.83
2191 6231 9.833894 CATTCAAGAAAAAGAACAAATGTTACG 57.166 29.630 0.00 0.00 38.56 3.18
2196 6236 7.936584 AGAAAAAGAACAAATGTTACGATGGA 58.063 30.769 0.00 0.00 38.56 3.41
2226 6266 4.112634 GCCAAGACTTTTGTTGACCTTTC 58.887 43.478 0.00 0.00 0.00 2.62
2233 6273 8.117813 AGACTTTTGTTGACCTTTCAGTAAAA 57.882 30.769 0.00 0.00 32.24 1.52
2234 6274 8.244113 AGACTTTTGTTGACCTTTCAGTAAAAG 58.756 33.333 16.06 16.06 43.51 2.27
2271 6311 5.396436 GGCTTATCGTATATATGCCAACCCT 60.396 44.000 13.95 0.00 41.65 4.34
2272 6312 5.523916 GCTTATCGTATATATGCCAACCCTG 59.476 44.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.092716 AGTAATGCAAGTTATTTCCTGCAAAG 58.907 34.615 0.00 0.00 35.86 2.77
27 28 6.442513 AGAGTAATGCAAGTTATTTCCTGC 57.557 37.500 0.00 0.00 0.00 4.85
28 29 7.820648 ACAAGAGTAATGCAAGTTATTTCCTG 58.179 34.615 0.00 0.00 0.00 3.86
29 30 9.167311 CTACAAGAGTAATGCAAGTTATTTCCT 57.833 33.333 0.00 0.00 0.00 3.36
61 63 7.761704 TGTTGATCTCTGTAATTCTGAAGTAGC 59.238 37.037 0.00 0.00 0.00 3.58
68 70 6.094464 TGGCATTGTTGATCTCTGTAATTCTG 59.906 38.462 0.00 0.00 0.00 3.02
81 83 2.880443 AGTCCTGTTGGCATTGTTGAT 58.120 42.857 0.00 0.00 0.00 2.57
90 92 0.324943 TTGCCTCTAGTCCTGTTGGC 59.675 55.000 0.00 0.00 40.62 4.52
91 93 1.677217 GCTTGCCTCTAGTCCTGTTGG 60.677 57.143 0.00 0.00 0.00 3.77
92 94 1.677217 GGCTTGCCTCTAGTCCTGTTG 60.677 57.143 4.11 0.00 0.00 3.33
113 115 2.172717 ACCAGTGGTAGAACTGCAGTTT 59.827 45.455 31.58 22.25 45.17 2.66
117 119 0.685097 GGACCAGTGGTAGAACTGCA 59.315 55.000 16.72 0.00 45.17 4.41
136 138 4.769488 TCATGTCTTAGCTAGCTATGGGAG 59.231 45.833 28.06 20.99 0.00 4.30
169 171 3.863424 GCTCATATTCGACGAAACCAGAA 59.137 43.478 15.22 0.00 0.00 3.02
171 173 3.186909 TGCTCATATTCGACGAAACCAG 58.813 45.455 15.22 9.21 0.00 4.00
205 207 5.798132 AGAGCACTCATGTCACATAGAAAA 58.202 37.500 0.00 0.00 0.00 2.29
206 208 5.047092 TGAGAGCACTCATGTCACATAGAAA 60.047 40.000 10.01 0.00 46.55 2.52
207 209 4.463891 TGAGAGCACTCATGTCACATAGAA 59.536 41.667 10.01 0.00 46.55 2.10
208 210 4.019174 TGAGAGCACTCATGTCACATAGA 58.981 43.478 10.01 0.00 46.55 1.98
209 211 4.382345 TGAGAGCACTCATGTCACATAG 57.618 45.455 10.01 0.00 46.55 2.23
223 225 3.451902 TCATGGTGTATGTGATGAGAGCA 59.548 43.478 0.00 0.00 38.01 4.26
225 227 4.510711 GCTTCATGGTGTATGTGATGAGAG 59.489 45.833 0.00 0.00 38.01 3.20
292 294 4.780275 TGAGACAGACTCTGTTGATGAG 57.220 45.455 13.06 0.00 45.44 2.90
293 295 5.735285 ATTGAGACAGACTCTGTTGATGA 57.265 39.130 13.06 0.40 45.44 2.92
295 297 7.415592 TCATATTGAGACAGACTCTGTTGAT 57.584 36.000 13.06 7.65 45.44 2.57
376 1638 2.233654 CGAAGCATCGGAAGCGGAG 61.234 63.158 2.82 0.00 45.32 4.63
386 1684 5.909610 GCTTATACAATTGTTCCGAAGCATC 59.090 40.000 25.60 9.58 38.31 3.91
402 1700 6.165700 TCTCTTCATGCAGATGCTTATACA 57.834 37.500 6.35 0.00 42.66 2.29
403 1701 7.488187 TTTCTCTTCATGCAGATGCTTATAC 57.512 36.000 6.35 0.00 42.66 1.47
409 1707 4.430137 TGTTTTCTCTTCATGCAGATGC 57.570 40.909 0.00 0.00 42.50 3.91
480 1816 3.236003 GATGTCGGGCCCGGGATAC 62.236 68.421 42.36 32.12 40.25 2.24
490 1826 7.052142 AGAAAAACTACCTATAGATGTCGGG 57.948 40.000 0.00 0.00 32.23 5.14
561 1899 2.600470 GCCCGGGCTGGTCTTTTT 60.600 61.111 38.76 0.00 38.26 1.94
608 1946 7.040686 ACGTTTGGTGCTCATAGAGTTATTTTT 60.041 33.333 0.00 0.00 31.39 1.94
609 1947 6.430000 ACGTTTGGTGCTCATAGAGTTATTTT 59.570 34.615 0.00 0.00 31.39 1.82
610 1948 5.938125 ACGTTTGGTGCTCATAGAGTTATTT 59.062 36.000 0.00 0.00 31.39 1.40
611 1949 5.488341 ACGTTTGGTGCTCATAGAGTTATT 58.512 37.500 0.00 0.00 31.39 1.40
612 1950 5.086104 ACGTTTGGTGCTCATAGAGTTAT 57.914 39.130 0.00 0.00 31.39 1.89
613 1951 4.530710 ACGTTTGGTGCTCATAGAGTTA 57.469 40.909 0.00 0.00 31.39 2.24
614 1952 3.402628 ACGTTTGGTGCTCATAGAGTT 57.597 42.857 0.00 0.00 31.39 3.01
615 1953 3.244078 TGAACGTTTGGTGCTCATAGAGT 60.244 43.478 0.46 0.00 31.39 3.24
616 1954 3.325870 TGAACGTTTGGTGCTCATAGAG 58.674 45.455 0.46 0.00 0.00 2.43
617 1955 3.394674 TGAACGTTTGGTGCTCATAGA 57.605 42.857 0.46 0.00 0.00 1.98
618 1956 3.667960 GCTTGAACGTTTGGTGCTCATAG 60.668 47.826 0.46 0.00 0.00 2.23
619 1957 2.225491 GCTTGAACGTTTGGTGCTCATA 59.775 45.455 0.46 0.00 0.00 2.15
620 1958 1.001378 GCTTGAACGTTTGGTGCTCAT 60.001 47.619 0.46 0.00 0.00 2.90
621 1959 0.380378 GCTTGAACGTTTGGTGCTCA 59.620 50.000 0.46 0.00 0.00 4.26
622 1960 0.317854 GGCTTGAACGTTTGGTGCTC 60.318 55.000 0.46 0.00 0.00 4.26
623 1961 1.733526 GGCTTGAACGTTTGGTGCT 59.266 52.632 0.46 0.00 0.00 4.40
624 1962 1.657181 CGGCTTGAACGTTTGGTGC 60.657 57.895 0.46 5.15 0.00 5.01
625 1963 0.041312 CTCGGCTTGAACGTTTGGTG 60.041 55.000 0.46 0.00 0.00 4.17
626 1964 0.179067 TCTCGGCTTGAACGTTTGGT 60.179 50.000 0.46 0.00 0.00 3.67
627 1965 1.156736 ATCTCGGCTTGAACGTTTGG 58.843 50.000 0.46 0.00 0.00 3.28
628 1966 2.969443 AATCTCGGCTTGAACGTTTG 57.031 45.000 0.46 0.00 0.00 2.93
629 1967 5.209977 GTTTAAATCTCGGCTTGAACGTTT 58.790 37.500 0.46 0.00 0.00 3.60
630 1968 4.319984 GGTTTAAATCTCGGCTTGAACGTT 60.320 41.667 0.00 0.00 0.00 3.99
631 1969 3.187842 GGTTTAAATCTCGGCTTGAACGT 59.812 43.478 0.00 0.00 0.00 3.99
632 1970 3.435671 AGGTTTAAATCTCGGCTTGAACG 59.564 43.478 0.00 0.00 0.00 3.95
633 1971 5.154222 CAAGGTTTAAATCTCGGCTTGAAC 58.846 41.667 0.38 0.00 0.00 3.18
634 1972 4.217550 CCAAGGTTTAAATCTCGGCTTGAA 59.782 41.667 0.38 0.00 0.00 2.69
635 1973 3.756434 CCAAGGTTTAAATCTCGGCTTGA 59.244 43.478 0.38 0.00 0.00 3.02
636 1974 3.506067 ACCAAGGTTTAAATCTCGGCTTG 59.494 43.478 5.30 0.00 0.00 4.01
637 1975 3.506067 CACCAAGGTTTAAATCTCGGCTT 59.494 43.478 5.30 0.00 0.00 4.35
638 1976 3.081804 CACCAAGGTTTAAATCTCGGCT 58.918 45.455 5.30 0.00 0.00 5.52
639 1977 2.163613 CCACCAAGGTTTAAATCTCGGC 59.836 50.000 5.30 0.00 0.00 5.54
640 1978 2.752903 CCCACCAAGGTTTAAATCTCGG 59.247 50.000 3.77 3.77 34.66 4.63
641 1979 2.163613 GCCCACCAAGGTTTAAATCTCG 59.836 50.000 0.38 0.00 34.66 4.04
642 1980 3.193479 CAGCCCACCAAGGTTTAAATCTC 59.807 47.826 0.38 0.00 34.66 2.75
643 1981 3.165071 CAGCCCACCAAGGTTTAAATCT 58.835 45.455 0.00 0.00 34.66 2.40
644 1982 2.233676 CCAGCCCACCAAGGTTTAAATC 59.766 50.000 0.00 0.00 34.66 2.17
645 1983 2.256306 CCAGCCCACCAAGGTTTAAAT 58.744 47.619 0.00 0.00 34.66 1.40
646 1984 1.710816 CCAGCCCACCAAGGTTTAAA 58.289 50.000 0.00 0.00 34.66 1.52
647 1985 0.830023 GCCAGCCCACCAAGGTTTAA 60.830 55.000 0.00 0.00 34.66 1.52
648 1986 1.228737 GCCAGCCCACCAAGGTTTA 60.229 57.895 0.00 0.00 34.66 2.01
649 1987 1.725169 TAGCCAGCCCACCAAGGTTT 61.725 55.000 0.00 0.00 34.66 3.27
650 1988 2.142292 CTAGCCAGCCCACCAAGGTT 62.142 60.000 0.00 0.00 34.66 3.50
651 1989 2.531685 TAGCCAGCCCACCAAGGT 60.532 61.111 0.00 0.00 34.66 3.50
652 1990 2.273449 CTAGCCAGCCCACCAAGG 59.727 66.667 0.00 0.00 37.03 3.61
653 1991 1.852157 TTCCTAGCCAGCCCACCAAG 61.852 60.000 0.00 0.00 0.00 3.61
654 1992 1.850289 TTCCTAGCCAGCCCACCAA 60.850 57.895 0.00 0.00 0.00 3.67
655 1993 2.204074 TTCCTAGCCAGCCCACCA 60.204 61.111 0.00 0.00 0.00 4.17
656 1994 1.853250 AAGTTCCTAGCCAGCCCACC 61.853 60.000 0.00 0.00 0.00 4.61
657 1995 0.393132 GAAGTTCCTAGCCAGCCCAC 60.393 60.000 0.00 0.00 0.00 4.61
658 1996 0.547712 AGAAGTTCCTAGCCAGCCCA 60.548 55.000 0.00 0.00 0.00 5.36
659 1997 0.107459 CAGAAGTTCCTAGCCAGCCC 60.107 60.000 0.00 0.00 0.00 5.19
660 1998 0.746204 GCAGAAGTTCCTAGCCAGCC 60.746 60.000 0.00 0.00 0.00 4.85
661 1999 1.086634 CGCAGAAGTTCCTAGCCAGC 61.087 60.000 0.00 0.00 0.00 4.85
662 2000 1.086634 GCGCAGAAGTTCCTAGCCAG 61.087 60.000 0.30 0.00 0.00 4.85
663 2001 1.079127 GCGCAGAAGTTCCTAGCCA 60.079 57.895 0.30 0.00 0.00 4.75
664 2002 1.815840 GGCGCAGAAGTTCCTAGCC 60.816 63.158 10.83 14.60 33.96 3.93
665 2003 0.391793 AAGGCGCAGAAGTTCCTAGC 60.392 55.000 10.83 2.50 0.00 3.42
666 2004 1.363744 CAAGGCGCAGAAGTTCCTAG 58.636 55.000 10.83 0.00 0.00 3.02
667 2005 0.673644 GCAAGGCGCAGAAGTTCCTA 60.674 55.000 10.83 0.00 41.79 2.94
668 2006 1.968540 GCAAGGCGCAGAAGTTCCT 60.969 57.895 10.83 0.00 41.79 3.36
669 2007 0.673644 TAGCAAGGCGCAGAAGTTCC 60.674 55.000 10.83 0.00 46.13 3.62
670 2008 1.135944 GTTAGCAAGGCGCAGAAGTTC 60.136 52.381 10.83 0.00 46.13 3.01
671 2009 0.875059 GTTAGCAAGGCGCAGAAGTT 59.125 50.000 10.83 0.00 46.13 2.66
672 2010 0.035458 AGTTAGCAAGGCGCAGAAGT 59.965 50.000 10.83 0.00 46.13 3.01
673 2011 0.445436 CAGTTAGCAAGGCGCAGAAG 59.555 55.000 10.83 0.00 46.13 2.85
674 2012 0.034756 TCAGTTAGCAAGGCGCAGAA 59.965 50.000 10.83 0.00 46.13 3.02
675 2013 0.390340 CTCAGTTAGCAAGGCGCAGA 60.390 55.000 10.83 0.00 46.13 4.26
676 2014 2.084844 CTCAGTTAGCAAGGCGCAG 58.915 57.895 10.83 0.00 46.13 5.18
677 2015 4.284123 CTCAGTTAGCAAGGCGCA 57.716 55.556 10.83 0.00 46.13 6.09
686 2024 1.093159 ACCGGACGTAGCTCAGTTAG 58.907 55.000 9.46 0.00 0.00 2.34
687 2025 1.470098 GAACCGGACGTAGCTCAGTTA 59.530 52.381 9.46 0.00 0.00 2.24
688 2026 0.243095 GAACCGGACGTAGCTCAGTT 59.757 55.000 9.46 0.00 0.00 3.16
689 2027 0.608582 AGAACCGGACGTAGCTCAGT 60.609 55.000 9.46 0.00 0.00 3.41
690 2028 0.099082 GAGAACCGGACGTAGCTCAG 59.901 60.000 9.46 0.00 0.00 3.35
691 2029 0.322277 AGAGAACCGGACGTAGCTCA 60.322 55.000 9.46 0.00 31.60 4.26
692 2030 0.810016 AAGAGAACCGGACGTAGCTC 59.190 55.000 9.46 5.19 0.00 4.09
693 2031 2.119801 TAAGAGAACCGGACGTAGCT 57.880 50.000 9.46 0.00 0.00 3.32
694 2032 3.433513 AATAAGAGAACCGGACGTAGC 57.566 47.619 9.46 0.00 0.00 3.58
695 2033 8.295288 ACAATATAATAAGAGAACCGGACGTAG 58.705 37.037 9.46 0.00 0.00 3.51
696 2034 8.169977 ACAATATAATAAGAGAACCGGACGTA 57.830 34.615 9.46 0.00 0.00 3.57
697 2035 7.047460 ACAATATAATAAGAGAACCGGACGT 57.953 36.000 9.46 0.00 0.00 4.34
698 2036 7.568861 GCAACAATATAATAAGAGAACCGGACG 60.569 40.741 9.46 0.00 0.00 4.79
699 2037 7.225931 TGCAACAATATAATAAGAGAACCGGAC 59.774 37.037 9.46 0.99 0.00 4.79
700 2038 7.276658 TGCAACAATATAATAAGAGAACCGGA 58.723 34.615 9.46 0.00 0.00 5.14
701 2039 7.490962 TGCAACAATATAATAAGAGAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
702 2040 9.385902 CATTGCAACAATATAATAAGAGAACCG 57.614 33.333 0.00 0.00 0.00 4.44
705 2043 9.734620 GCACATTGCAACAATATAATAAGAGAA 57.265 29.630 0.00 0.00 44.26 2.87
786 2124 6.086371 GCGTTGAATTGTCTTAGTTTTGCTAC 59.914 38.462 0.00 0.00 0.00 3.58
809 2156 2.076100 TGCAGAACAAATAGTCAGGCG 58.924 47.619 0.00 0.00 0.00 5.52
943 2291 6.271488 AGAGAGAGATATGCATGAAGCTAC 57.729 41.667 10.16 0.00 45.94 3.58
984 2332 1.093972 TGGTGGATTTGCATAGCGTG 58.906 50.000 0.00 0.00 0.00 5.34
998 2346 1.608590 CTGTTAGGTGTTGCTTGGTGG 59.391 52.381 0.00 0.00 0.00 4.61
999 2347 1.001378 GCTGTTAGGTGTTGCTTGGTG 60.001 52.381 0.00 0.00 0.00 4.17
1000 2348 1.133792 AGCTGTTAGGTGTTGCTTGGT 60.134 47.619 0.00 0.00 0.00 3.67
1001 2349 1.609208 AGCTGTTAGGTGTTGCTTGG 58.391 50.000 0.00 0.00 0.00 3.61
1002 2350 3.403038 AGTAGCTGTTAGGTGTTGCTTG 58.597 45.455 0.00 0.00 35.47 4.01
1003 2351 3.771577 AGTAGCTGTTAGGTGTTGCTT 57.228 42.857 0.00 0.00 35.47 3.91
1004 2352 3.368531 GCTAGTAGCTGTTAGGTGTTGCT 60.369 47.826 15.16 0.00 38.45 3.91
1005 2353 2.930682 GCTAGTAGCTGTTAGGTGTTGC 59.069 50.000 15.16 0.00 38.45 4.17
1288 2653 3.932710 CGACAAGCAAGGCTAGTTATGAA 59.067 43.478 0.00 0.00 38.25 2.57
1302 2667 1.067213 TCGATCCATCAACGACAAGCA 60.067 47.619 0.00 0.00 0.00 3.91
1421 2786 7.849515 CAGTGTACACAGTACATATACACGTAG 59.150 40.741 27.06 11.25 46.56 3.51
1501 2866 5.469479 CAAATACGCATCATTAATTCCCCC 58.531 41.667 0.00 0.00 0.00 5.40
1502 2867 5.469479 CCAAATACGCATCATTAATTCCCC 58.531 41.667 0.00 0.00 0.00 4.81
1503 2868 4.923281 GCCAAATACGCATCATTAATTCCC 59.077 41.667 0.00 0.00 0.00 3.97
1504 2869 4.616802 CGCCAAATACGCATCATTAATTCC 59.383 41.667 0.00 0.00 0.00 3.01
1517 2882 4.965062 ACAATAACTTGACGCCAAATACG 58.035 39.130 0.00 0.00 36.20 3.06
1612 3020 8.124823 CAGGCAGTTCACATGTATACTTAAATG 58.875 37.037 0.00 2.12 0.00 2.32
1632 3040 0.824109 TCACGAATAGGGTCAGGCAG 59.176 55.000 0.00 0.00 0.00 4.85
1787 3200 6.895782 TGATATATACCCATTTCGATTCCCC 58.104 40.000 0.00 0.00 0.00 4.81
1926 3349 5.053978 ACCTGTCTCCTTGAGAACAAAAT 57.946 39.130 0.00 0.00 40.59 1.82
1931 3354 6.378848 ACTTATCTACCTGTCTCCTTGAGAAC 59.621 42.308 0.00 0.00 40.59 3.01
1932 3355 6.494952 ACTTATCTACCTGTCTCCTTGAGAA 58.505 40.000 0.00 0.00 40.59 2.87
1945 3371 7.991084 AAACGGCTTTTAAACTTATCTACCT 57.009 32.000 0.00 0.00 0.00 3.08
2006 3433 7.889469 TGATCTTAGTTAACTTTGACGGTACT 58.111 34.615 14.49 0.00 0.00 2.73
2082 3543 5.222079 TCTTTAGTATGTGTTGCTGGACA 57.778 39.130 0.00 0.00 0.00 4.02
2083 3544 6.743575 AATCTTTAGTATGTGTTGCTGGAC 57.256 37.500 0.00 0.00 0.00 4.02
2153 6193 8.960591 TCTTTTTCTTGAATGAAAGAGAGTTGT 58.039 29.630 6.25 0.00 40.14 3.32
2183 6223 4.379082 GGCTTTTCGTTCCATCGTAACATT 60.379 41.667 0.00 0.00 0.00 2.71
2191 6231 2.814336 AGTCTTGGCTTTTCGTTCCATC 59.186 45.455 0.00 0.00 0.00 3.51
2196 6236 4.450082 ACAAAAGTCTTGGCTTTTCGTT 57.550 36.364 9.64 0.00 44.13 3.85
2226 6266 6.099341 AGCCAAACAGTGTTTTCTTTTACTG 58.901 36.000 18.59 5.14 44.52 2.74
2233 6273 4.578928 ACGATAAGCCAAACAGTGTTTTCT 59.421 37.500 18.59 14.89 0.00 2.52
2234 6274 4.855531 ACGATAAGCCAAACAGTGTTTTC 58.144 39.130 18.59 12.98 0.00 2.29
2272 6312 9.274065 CGTGGAAGAATAGTTATTTTAACTTGC 57.726 33.333 5.33 0.00 0.00 4.01
2297 6337 4.925054 TGACTATTTTCGTTTGGGACTACG 59.075 41.667 0.00 0.00 38.13 3.51


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

AutoCloner maintained by Alex Coulton.