Multiple sequence alignment - TraesCS2A01G386000

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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 TraesCS2A01G386000 chr2A 100.000 3223 0 0 764 3986 631860420 631857198 0.000000e+00 5952.0
1 TraesCS2A01G386000 chr2A 100.000 497 0 0 1 497 631861183 631860687 0.000000e+00 918.0
2 TraesCS2A01G386000 chr2A 82.493 714 82 34 3285 3985 632586734 632587417 1.600000e-163 586.0
3 TraesCS2A01G386000 chr2A 83.448 435 50 13 3562 3985 46337766 46337343 6.250000e-103 385.0
4 TraesCS2A01G386000 chr2D 96.096 1921 51 10 2078 3985 486394256 486392347 0.000000e+00 3110.0
5 TraesCS2A01G386000 chr2D 93.501 1231 62 8 764 1985 486395475 486394254 0.000000e+00 1814.0
6 TraesCS2A01G386000 chr2D 85.613 702 59 26 3304 3985 487932139 487932818 0.000000e+00 699.0
7 TraesCS2A01G386000 chr2D 84.274 585 55 21 3405 3985 487722800 487723351 1.630000e-148 536.0
8 TraesCS2A01G386000 chr2D 80.606 495 45 21 3492 3985 488055818 488056262 6.380000e-88 335.0
9 TraesCS2A01G386000 chr2D 94.175 103 6 0 1982 2084 445894981 445894879 1.480000e-34 158.0
10 TraesCS2A01G386000 chr2B 95.682 1922 51 11 2078 3985 571349490 571347587 0.000000e+00 3061.0
11 TraesCS2A01G386000 chr2B 95.637 1123 48 1 864 1985 571350610 571349488 0.000000e+00 1801.0
12 TraesCS2A01G386000 chr2B 85.675 719 66 22 3285 3985 572311680 572312379 0.000000e+00 723.0
13 TraesCS2A01G386000 chr2B 82.006 678 82 20 3314 3985 572177494 572178137 1.260000e-149 540.0
14 TraesCS2A01G386000 chr2B 84.585 506 51 12 3 493 571352914 571352421 1.000000e-130 477.0
15 TraesCS2A01G386000 chr2B 97.196 107 3 0 764 870 571352423 571352317 8.800000e-42 182.0
16 TraesCS2A01G386000 chr2B 84.795 171 18 4 3482 3646 548939526 548939694 8.860000e-37 165.0
17 TraesCS2A01G386000 chr6A 83.973 443 45 11 3283 3710 226334473 226334904 6.200000e-108 401.0
18 TraesCS2A01G386000 chr3D 83.218 435 53 12 3562 3985 16450136 16449711 8.080000e-102 381.0
19 TraesCS2A01G386000 chr3D 93.396 106 6 1 1980 2085 277764773 277764877 5.330000e-34 156.0
20 TraesCS2A01G386000 chr7B 96.970 99 3 0 1982 2080 562993065 562993163 2.460000e-37 167.0
21 TraesCS2A01G386000 chr7B 96.939 98 3 0 1983 2080 588874917 588875014 8.860000e-37 165.0
22 TraesCS2A01G386000 chr7B 97.895 95 2 0 1986 2080 589348412 589348318 8.860000e-37 165.0
23 TraesCS2A01G386000 chr7B 98.000 50 1 0 3661 3710 421244979 421245028 1.970000e-13 87.9
24 TraesCS2A01G386000 chr4D 95.000 100 5 0 1986 2085 26254045 26253946 1.480000e-34 158.0
25 TraesCS2A01G386000 chr1A 90.833 120 7 4 1986 2105 238655880 238655765 1.480000e-34 158.0
26 TraesCS2A01G386000 chr7A 92.661 109 6 2 1979 2086 704896117 704896224 5.330000e-34 156.0
27 TraesCS2A01G386000 chr5A 95.789 95 3 1 1986 2080 239529933 239529840 6.900000e-33 152.0
28 TraesCS2A01G386000 chr6B 96.226 53 2 0 3658 3710 699127320 699127372 1.970000e-13 87.9
29 TraesCS2A01G386000 chr3B 96.226 53 2 0 3658 3710 454138715 454138767 1.970000e-13 87.9
30 TraesCS2A01G386000 chr3B 96.226 53 2 0 3658 3710 454345986 454346038 1.970000e-13 87.9
31 TraesCS2A01G386000 chr1B 98.000 50 1 0 3661 3710 665779448 665779399 1.970000e-13 87.9


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 TraesCS2A01G386000 chr2A 631857198 631861183 3985 True 3435.00 5952 100.0000 1 3986 2 chr2A.!!$R2 3985
1 TraesCS2A01G386000 chr2A 632586734 632587417 683 False 586.00 586 82.4930 3285 3985 1 chr2A.!!$F1 700
2 TraesCS2A01G386000 chr2D 486392347 486395475 3128 True 2462.00 3110 94.7985 764 3985 2 chr2D.!!$R2 3221
3 TraesCS2A01G386000 chr2D 487932139 487932818 679 False 699.00 699 85.6130 3304 3985 1 chr2D.!!$F2 681
4 TraesCS2A01G386000 chr2D 487722800 487723351 551 False 536.00 536 84.2740 3405 3985 1 chr2D.!!$F1 580
5 TraesCS2A01G386000 chr2B 571347587 571352914 5327 True 1380.25 3061 93.2750 3 3985 4 chr2B.!!$R1 3982
6 TraesCS2A01G386000 chr2B 572311680 572312379 699 False 723.00 723 85.6750 3285 3985 1 chr2B.!!$F3 700
7 TraesCS2A01G386000 chr2B 572177494 572178137 643 False 540.00 540 82.0060 3314 3985 1 chr2B.!!$F2 671

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
355 356 0.551377 TAGGAAACCCATCTGGCCCA 60.551 55.000 0.0 0.0 37.83 5.36 F
1997 3734 1.062428 ACATCTATTCCCTCCGTCCCA 60.062 52.381 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 3799 0.106167 TGATACTCCCTCCGTCCCAG 60.106 60.0 0.00 0.0 0.0 4.45 R
3716 5505 0.251354 CTGCAGTACATGGGAGCTGT 59.749 55.0 5.25 0.0 0.0 4.40 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
67 68 5.201713 TGGATACACTCATAAGCTGCTAC 57.798 43.478 0.90 0.00 46.17 3.58
107 108 2.290641 CCTCGAGGAACAAAACCAACTG 59.709 50.000 28.21 0.00 37.39 3.16
125 126 6.823689 ACCAACTGTTCAACAGGTATGATATC 59.176 38.462 21.71 0.00 45.99 1.63
126 127 6.018751 CCAACTGTTCAACAGGTATGATATCG 60.019 42.308 21.71 0.47 45.99 2.92
134 135 6.537301 TCAACAGGTATGATATCGGACAAAAC 59.463 38.462 8.57 0.00 0.00 2.43
146 147 2.031870 GGACAAAACCACCTTCAGCTT 58.968 47.619 0.00 0.00 0.00 3.74
149 150 2.831526 ACAAAACCACCTTCAGCTTGTT 59.168 40.909 0.00 0.00 0.00 2.83
157 158 2.641815 ACCTTCAGCTTGTTGGAGAGAT 59.358 45.455 0.00 0.00 0.00 2.75
163 164 5.728471 TCAGCTTGTTGGAGAGATCTTTAG 58.272 41.667 0.00 0.00 0.00 1.85
166 167 5.104982 AGCTTGTTGGAGAGATCTTTAGAGG 60.105 44.000 0.00 0.00 0.00 3.69
172 173 4.038522 TGGAGAGATCTTTAGAGGCGATTG 59.961 45.833 0.00 0.00 0.00 2.67
203 204 9.554724 AGTAATATTGCACAAAGTAATTGAACG 57.445 29.630 6.31 0.00 41.85 3.95
204 205 9.549509 GTAATATTGCACAAAGTAATTGAACGA 57.450 29.630 0.00 0.00 41.85 3.85
206 207 9.469807 AATATTGCACAAAGTAATTGAACGAAA 57.530 25.926 0.00 0.00 41.85 3.46
207 208 6.561945 TTGCACAAAGTAATTGAACGAAAC 57.438 33.333 0.00 0.00 41.85 2.78
208 209 5.885881 TGCACAAAGTAATTGAACGAAACT 58.114 33.333 0.00 0.00 41.85 2.66
209 210 7.017498 TGCACAAAGTAATTGAACGAAACTA 57.983 32.000 0.00 0.00 41.85 2.24
214 215 5.511088 AGTAATTGAACGAAACTAGCACG 57.489 39.130 0.00 0.00 0.00 5.34
215 216 2.875080 ATTGAACGAAACTAGCACGC 57.125 45.000 0.00 0.00 0.00 5.34
222 223 1.360820 GAAACTAGCACGCCTCCTTC 58.639 55.000 0.00 0.00 0.00 3.46
225 226 4.143333 TAGCACGCCTCCTTCGGC 62.143 66.667 0.00 0.00 46.68 5.54
261 262 8.782339 TGAGAATGAGCACAATATATGTATGG 57.218 34.615 0.00 0.00 41.46 2.74
264 265 9.006839 AGAATGAGCACAATATATGTATGGTTG 57.993 33.333 0.00 0.00 41.46 3.77
271 272 9.599866 GCACAATATATGTATGGTTGATAGCTA 57.400 33.333 0.00 0.00 41.46 3.32
275 276 4.537135 ATGTATGGTTGATAGCTACCGG 57.463 45.455 0.00 0.00 41.98 5.28
298 299 3.733077 CGAAGAATCGCCGTAGTAACCTT 60.733 47.826 0.00 0.00 42.96 3.50
321 322 5.109210 TGCTCCACAAATATTCTAGTGACG 58.891 41.667 13.94 7.79 33.99 4.35
330 331 7.336931 ACAAATATTCTAGTGACGCTGGAAAAT 59.663 33.333 17.33 6.25 45.63 1.82
331 332 8.826710 CAAATATTCTAGTGACGCTGGAAAATA 58.173 33.333 17.33 8.08 45.63 1.40
332 333 9.561069 AAATATTCTAGTGACGCTGGAAAATAT 57.439 29.630 17.33 9.78 45.63 1.28
333 334 6.851222 ATTCTAGTGACGCTGGAAAATATG 57.149 37.500 17.33 0.00 45.63 1.78
334 335 5.339008 TCTAGTGACGCTGGAAAATATGT 57.661 39.130 0.00 0.00 31.45 2.29
335 336 5.109210 TCTAGTGACGCTGGAAAATATGTG 58.891 41.667 0.00 0.00 31.45 3.21
336 337 3.674997 AGTGACGCTGGAAAATATGTGT 58.325 40.909 0.00 0.00 0.00 3.72
346 347 5.893500 TGGAAAATATGTGTAGGAAACCCA 58.106 37.500 0.00 0.00 0.00 4.51
351 352 3.652057 ATGTGTAGGAAACCCATCTGG 57.348 47.619 0.00 0.00 41.37 3.86
355 356 0.551377 TAGGAAACCCATCTGGCCCA 60.551 55.000 0.00 0.00 37.83 5.36
394 403 3.334583 AGTCGTCATAATGCTGGTGTT 57.665 42.857 0.00 0.00 0.00 3.32
411 420 6.626623 GCTGGTGTTTGATTAATTGAGAGCAT 60.627 38.462 0.00 0.00 0.00 3.79
412 421 6.855836 TGGTGTTTGATTAATTGAGAGCATC 58.144 36.000 0.00 0.00 0.00 3.91
485 499 5.438761 AGAAAGGTGAAATTACAGTGCAC 57.561 39.130 9.40 9.40 0.00 4.57
490 504 6.354794 AGGTGAAATTACAGTGCACTACTA 57.645 37.500 21.20 9.19 37.60 1.82
491 505 6.398918 AGGTGAAATTACAGTGCACTACTAG 58.601 40.000 21.20 9.88 37.60 2.57
492 506 6.014499 AGGTGAAATTACAGTGCACTACTAGT 60.014 38.462 21.20 15.67 37.60 2.57
493 507 6.649557 GGTGAAATTACAGTGCACTACTAGTT 59.350 38.462 21.20 12.40 37.60 2.24
494 508 7.172703 GGTGAAATTACAGTGCACTACTAGTTT 59.827 37.037 21.20 18.68 37.60 2.66
495 509 8.557029 GTGAAATTACAGTGCACTACTAGTTTT 58.443 33.333 21.20 14.03 37.60 2.43
496 510 9.116067 TGAAATTACAGTGCACTACTAGTTTTT 57.884 29.630 21.20 15.03 37.60 1.94
845 859 2.358737 CGCCCAGAACCACCAGTC 60.359 66.667 0.00 0.00 0.00 3.51
884 2611 3.767230 CACGCTGCCGACGACTTG 61.767 66.667 0.00 0.00 38.29 3.16
1148 2883 1.533753 TTCCGTACACCGTCCCCTT 60.534 57.895 0.00 0.00 33.66 3.95
1195 2930 3.758554 ACCTGTCGATTTGCTTGCTAAAT 59.241 39.130 0.00 0.00 0.00 1.40
1198 2933 5.119931 TGTCGATTTGCTTGCTAAATGTT 57.880 34.783 0.00 0.00 0.00 2.71
1206 2941 3.568007 TGCTTGCTAAATGTTCGACCTTT 59.432 39.130 0.00 0.00 0.00 3.11
1236 2971 1.078759 CGCAGGATGACAAGGTCGTC 61.079 60.000 9.53 9.53 44.93 4.20
1341 3077 3.134458 GGTCTAGATGTGGCATTAGCAC 58.866 50.000 0.00 0.00 44.61 4.40
1342 3078 3.432186 GGTCTAGATGTGGCATTAGCACA 60.432 47.826 0.00 0.00 44.61 4.57
1352 3088 1.863454 GCATTAGCACACCTCATCGAG 59.137 52.381 0.00 0.00 41.58 4.04
1610 3347 5.699001 AGTTGCTGTTTATCATGTCACGTAA 59.301 36.000 0.00 0.00 0.00 3.18
1949 3686 6.849502 ACATTTCATGATCAGTTAGTTGCTG 58.150 36.000 0.09 0.00 35.43 4.41
1985 3722 7.885922 TGTGTGTGGTGGTTAATAACATCTATT 59.114 33.333 5.45 0.00 0.00 1.73
1986 3723 8.395633 GTGTGTGGTGGTTAATAACATCTATTC 58.604 37.037 5.45 0.00 0.00 1.75
1987 3724 7.554835 TGTGTGGTGGTTAATAACATCTATTCC 59.445 37.037 5.45 0.00 0.00 3.01
1988 3725 7.012989 GTGTGGTGGTTAATAACATCTATTCCC 59.987 40.741 5.45 0.00 0.00 3.97
1989 3726 7.092174 TGTGGTGGTTAATAACATCTATTCCCT 60.092 37.037 5.45 0.00 0.00 4.20
1990 3727 7.444487 GTGGTGGTTAATAACATCTATTCCCTC 59.556 40.741 5.45 0.00 0.00 4.30
1991 3728 6.940867 GGTGGTTAATAACATCTATTCCCTCC 59.059 42.308 5.45 0.00 0.00 4.30
1992 3729 6.649557 GTGGTTAATAACATCTATTCCCTCCG 59.350 42.308 5.45 0.00 0.00 4.63
1993 3730 6.328148 TGGTTAATAACATCTATTCCCTCCGT 59.672 38.462 5.45 0.00 0.00 4.69
1994 3731 6.872547 GGTTAATAACATCTATTCCCTCCGTC 59.127 42.308 5.45 0.00 0.00 4.79
1995 3732 5.485209 AATAACATCTATTCCCTCCGTCC 57.515 43.478 0.00 0.00 0.00 4.79
1996 3733 1.718280 ACATCTATTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
1997 3734 1.062428 ACATCTATTCCCTCCGTCCCA 60.062 52.381 0.00 0.00 0.00 4.37
1998 3735 2.047061 CATCTATTCCCTCCGTCCCAA 58.953 52.381 0.00 0.00 0.00 4.12
1999 3736 2.257391 TCTATTCCCTCCGTCCCAAA 57.743 50.000 0.00 0.00 0.00 3.28
2000 3737 2.553464 TCTATTCCCTCCGTCCCAAAA 58.447 47.619 0.00 0.00 0.00 2.44
2001 3738 3.120108 TCTATTCCCTCCGTCCCAAAAT 58.880 45.455 0.00 0.00 0.00 1.82
2002 3739 4.300345 TCTATTCCCTCCGTCCCAAAATA 58.700 43.478 0.00 0.00 0.00 1.40
2003 3740 4.722781 TCTATTCCCTCCGTCCCAAAATAA 59.277 41.667 0.00 0.00 0.00 1.40
2004 3741 3.359695 TTCCCTCCGTCCCAAAATAAG 57.640 47.619 0.00 0.00 0.00 1.73
2005 3742 2.271777 TCCCTCCGTCCCAAAATAAGT 58.728 47.619 0.00 0.00 0.00 2.24
2006 3743 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2007 3744 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2008 3745 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2009 3746 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2010 3747 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2011 3748 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2012 3749 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2013 3750 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
2014 3751 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
2015 3752 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
2016 3753 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2017 3754 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
2018 3755 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2019 3756 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2020 3757 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2021 3758 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2022 3759 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
2023 3760 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2024 3761 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
2025 3762 4.884247 AGTGTCTCAAGCTTAGTACAACC 58.116 43.478 0.00 0.00 0.00 3.77
2026 3763 4.589374 AGTGTCTCAAGCTTAGTACAACCT 59.411 41.667 0.00 0.00 0.00 3.50
2027 3764 5.070580 AGTGTCTCAAGCTTAGTACAACCTT 59.929 40.000 0.00 0.00 0.00 3.50
2028 3765 5.177696 GTGTCTCAAGCTTAGTACAACCTTG 59.822 44.000 0.00 2.72 35.44 3.61
2029 3766 5.163343 TGTCTCAAGCTTAGTACAACCTTGT 60.163 40.000 0.00 0.00 44.86 3.16
2030 3767 6.041182 TGTCTCAAGCTTAGTACAACCTTGTA 59.959 38.462 0.00 0.00 42.35 2.41
2055 3792 8.461249 ACTAGAGTTAGTACAAAGTTGAGACA 57.539 34.615 0.00 0.00 38.35 3.41
2056 3793 8.351461 ACTAGAGTTAGTACAAAGTTGAGACAC 58.649 37.037 0.00 0.00 38.35 3.67
2057 3794 7.349412 AGAGTTAGTACAAAGTTGAGACACT 57.651 36.000 0.00 0.00 0.00 3.55
2058 3795 7.783042 AGAGTTAGTACAAAGTTGAGACACTT 58.217 34.615 0.00 0.00 38.74 3.16
2059 3796 8.910944 AGAGTTAGTACAAAGTTGAGACACTTA 58.089 33.333 0.00 0.00 35.87 2.24
2060 3797 9.694137 GAGTTAGTACAAAGTTGAGACACTTAT 57.306 33.333 0.00 0.00 35.87 1.73
2064 3801 8.594881 AGTACAAAGTTGAGACACTTATTCTG 57.405 34.615 0.00 0.00 35.87 3.02
2065 3802 6.867662 ACAAAGTTGAGACACTTATTCTGG 57.132 37.500 0.00 0.00 35.87 3.86
2066 3803 5.765182 ACAAAGTTGAGACACTTATTCTGGG 59.235 40.000 0.00 0.00 35.87 4.45
2067 3804 5.825593 AAGTTGAGACACTTATTCTGGGA 57.174 39.130 0.00 0.00 35.10 4.37
2068 3805 5.153950 AGTTGAGACACTTATTCTGGGAC 57.846 43.478 0.00 0.00 0.00 4.46
2069 3806 3.868757 TGAGACACTTATTCTGGGACG 57.131 47.619 0.00 0.00 0.00 4.79
2070 3807 2.496070 TGAGACACTTATTCTGGGACGG 59.504 50.000 0.00 0.00 0.00 4.79
2071 3808 2.758979 GAGACACTTATTCTGGGACGGA 59.241 50.000 0.00 0.00 45.11 4.69
2078 3815 3.845559 TCTGGGACGGAGGGAGTA 58.154 61.111 0.00 0.00 39.80 2.59
2079 3816 2.329111 TCTGGGACGGAGGGAGTAT 58.671 57.895 0.00 0.00 39.80 2.12
2100 3837 7.254852 AGTATCAAACATGTCAAACACGTTTT 58.745 30.769 0.00 0.00 41.00 2.43
2145 3882 1.808945 CAGGCGATGTTGAGCTCTTTT 59.191 47.619 16.19 0.00 0.00 2.27
2222 3959 9.049523 TGATTTTACTCTTAGCAGCAATATGAG 57.950 33.333 0.00 0.00 33.09 2.90
2234 3971 5.353678 GCAGCAATATGAGTTCAGTTCTTCT 59.646 40.000 0.00 0.00 0.00 2.85
2281 4018 1.655484 TGATCAGCTTGTGCATACCG 58.345 50.000 0.00 0.00 42.74 4.02
2285 4022 1.804151 TCAGCTTGTGCATACCGTTTC 59.196 47.619 0.00 0.00 42.74 2.78
2600 4337 8.276252 TGAGGAACATAGGTATTGCTAAAAAC 57.724 34.615 0.00 0.00 0.00 2.43
2907 4646 6.068461 TGGAGGCAAGTAAAATATACACCA 57.932 37.500 0.00 0.00 0.00 4.17
3020 4759 3.031736 GACTGGTACTGGCTATTCCTGA 58.968 50.000 0.00 0.00 37.25 3.86
3290 5030 1.594862 GCATGGTCCGAAGAAGATTCG 59.405 52.381 3.13 3.13 41.21 3.34
3380 5131 4.653341 AGGAGGATCACTACCAAATCAGAG 59.347 45.833 0.00 0.00 36.25 3.35
3542 5313 5.465532 TTGCCTTTCAATTGATTGCAGTA 57.534 34.783 19.73 9.48 37.68 2.74
3710 5499 1.985159 ACCTCTGGAGCATTTGGTACA 59.015 47.619 0.00 0.00 34.79 2.90
3713 5502 3.264574 TGGAGCATTTGGTACAGGC 57.735 52.632 0.00 0.00 42.39 4.85
3714 5503 0.676466 TGGAGCATTTGGTACAGGCG 60.676 55.000 0.00 0.00 42.39 5.52
3715 5504 0.676782 GGAGCATTTGGTACAGGCGT 60.677 55.000 0.00 0.00 42.39 5.68
3716 5505 1.406341 GGAGCATTTGGTACAGGCGTA 60.406 52.381 0.00 0.00 42.39 4.42
3717 5506 1.664151 GAGCATTTGGTACAGGCGTAC 59.336 52.381 9.98 9.98 46.18 3.67
3921 5725 1.272490 TCCGCACTGAGACTCGAAAAT 59.728 47.619 0.00 0.00 0.00 1.82
3985 5791 1.801178 CAACCGGAAGCAGAAAGAGTC 59.199 52.381 9.46 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.482436 AGTGCGATAAGTTTTGTTCCCA 58.518 40.909 0.00 0.00 0.00 4.37
2 3 4.226761 CCAAGTGCGATAAGTTTTGTTCC 58.773 43.478 0.00 0.00 0.00 3.62
3 4 3.668656 GCCAAGTGCGATAAGTTTTGTTC 59.331 43.478 0.00 0.00 0.00 3.18
5 6 2.030274 GGCCAAGTGCGATAAGTTTTGT 60.030 45.455 0.00 0.00 42.61 2.83
6 7 2.228822 AGGCCAAGTGCGATAAGTTTTG 59.771 45.455 5.01 0.00 42.61 2.44
16 17 2.359900 AGAGAAATAAGGCCAAGTGCG 58.640 47.619 5.01 0.00 42.61 5.34
19 20 5.505181 TCTGAAGAGAAATAAGGCCAAGT 57.495 39.130 5.01 0.00 0.00 3.16
46 47 5.201713 TGTAGCAGCTTATGAGTGTATCC 57.798 43.478 0.00 0.00 0.00 2.59
47 48 8.994429 ATATTGTAGCAGCTTATGAGTGTATC 57.006 34.615 0.00 0.00 0.00 2.24
76 77 5.677319 TTGTTCCTCGAGGATCATAACTT 57.323 39.130 34.71 0.00 44.98 2.66
84 85 3.146847 GTTGGTTTTGTTCCTCGAGGAT 58.853 45.455 33.97 0.00 44.98 3.24
87 88 2.943033 ACAGTTGGTTTTGTTCCTCGAG 59.057 45.455 5.13 5.13 0.00 4.04
96 97 4.186856 ACCTGTTGAACAGTTGGTTTTG 57.813 40.909 22.40 8.24 44.50 2.44
100 101 4.431416 TCATACCTGTTGAACAGTTGGT 57.569 40.909 22.40 16.80 44.50 3.67
102 103 6.018751 CCGATATCATACCTGTTGAACAGTTG 60.019 42.308 22.40 16.33 44.50 3.16
103 104 6.049149 CCGATATCATACCTGTTGAACAGTT 58.951 40.000 22.40 12.42 44.50 3.16
107 108 5.597806 TGTCCGATATCATACCTGTTGAAC 58.402 41.667 3.12 0.00 0.00 3.18
125 126 0.310854 GCTGAAGGTGGTTTTGTCCG 59.689 55.000 0.00 0.00 0.00 4.79
126 127 1.692411 AGCTGAAGGTGGTTTTGTCC 58.308 50.000 0.00 0.00 0.00 4.02
134 135 1.202806 TCTCCAACAAGCTGAAGGTGG 60.203 52.381 10.98 10.98 0.00 4.61
146 147 3.131223 CGCCTCTAAAGATCTCTCCAACA 59.869 47.826 0.00 0.00 0.00 3.33
149 150 3.298686 TCGCCTCTAAAGATCTCTCCA 57.701 47.619 0.00 0.00 0.00 3.86
157 158 5.401531 ACTTACACAATCGCCTCTAAAGA 57.598 39.130 0.00 0.00 0.00 2.52
163 164 6.018262 TGCAATATTACTTACACAATCGCCTC 60.018 38.462 0.00 0.00 0.00 4.70
166 167 6.482835 TGTGCAATATTACTTACACAATCGC 58.517 36.000 0.00 0.00 35.28 4.58
193 194 4.079710 GCGTGCTAGTTTCGTTCAATTAC 58.920 43.478 0.00 0.00 0.00 1.89
194 195 3.123959 GGCGTGCTAGTTTCGTTCAATTA 59.876 43.478 0.00 0.00 0.00 1.40
196 197 1.463444 GGCGTGCTAGTTTCGTTCAAT 59.537 47.619 0.00 0.00 0.00 2.57
197 198 0.863144 GGCGTGCTAGTTTCGTTCAA 59.137 50.000 0.00 0.00 0.00 2.69
200 201 0.669625 GGAGGCGTGCTAGTTTCGTT 60.670 55.000 0.00 0.00 0.00 3.85
201 202 1.080025 GGAGGCGTGCTAGTTTCGT 60.080 57.895 0.00 0.00 0.00 3.85
202 203 0.389948 AAGGAGGCGTGCTAGTTTCG 60.390 55.000 0.00 0.00 0.00 3.46
203 204 1.360820 GAAGGAGGCGTGCTAGTTTC 58.639 55.000 0.00 0.00 0.00 2.78
204 205 0.389948 CGAAGGAGGCGTGCTAGTTT 60.390 55.000 0.00 0.00 0.00 2.66
205 206 1.215647 CGAAGGAGGCGTGCTAGTT 59.784 57.895 0.00 0.00 0.00 2.24
206 207 2.885861 CGAAGGAGGCGTGCTAGT 59.114 61.111 0.00 0.00 0.00 2.57
225 226 2.941720 GCTCATTCTCAAAGTGGCTAGG 59.058 50.000 0.00 0.00 0.00 3.02
228 229 2.157738 GTGCTCATTCTCAAAGTGGCT 58.842 47.619 0.00 0.00 0.00 4.75
261 262 1.066605 TCTTCGCCGGTAGCTATCAAC 59.933 52.381 1.90 0.00 40.39 3.18
264 265 2.597520 GATTCTTCGCCGGTAGCTATC 58.402 52.381 1.90 0.00 40.39 2.08
277 278 3.433513 AGGTTACTACGGCGATTCTTC 57.566 47.619 16.62 0.00 0.00 2.87
285 286 0.248289 TGGAGCAAGGTTACTACGGC 59.752 55.000 0.00 0.00 0.00 5.68
298 299 5.109210 CGTCACTAGAATATTTGTGGAGCA 58.891 41.667 0.00 0.00 0.00 4.26
321 322 5.163550 GGGTTTCCTACACATATTTTCCAGC 60.164 44.000 0.00 0.00 0.00 4.85
332 333 1.004277 GCCAGATGGGTTTCCTACACA 59.996 52.381 0.12 0.00 46.14 3.72
333 334 1.682087 GGCCAGATGGGTTTCCTACAC 60.682 57.143 0.00 0.00 39.65 2.90
334 335 0.623723 GGCCAGATGGGTTTCCTACA 59.376 55.000 0.00 0.00 39.65 2.74
335 336 0.106669 GGGCCAGATGGGTTTCCTAC 60.107 60.000 4.39 0.00 39.65 3.18
336 337 0.551377 TGGGCCAGATGGGTTTCCTA 60.551 55.000 0.00 0.00 39.65 2.94
355 356 1.561542 CTAATTCACCACCAGAGCCCT 59.438 52.381 0.00 0.00 0.00 5.19
453 462 8.744652 TGTAATTTCACCTTTCTTTCTGTTTGA 58.255 29.630 0.00 0.00 0.00 2.69
454 463 8.925161 TGTAATTTCACCTTTCTTTCTGTTTG 57.075 30.769 0.00 0.00 0.00 2.93
458 467 6.638468 GCACTGTAATTTCACCTTTCTTTCTG 59.362 38.462 0.00 0.00 0.00 3.02
469 483 7.653767 AACTAGTAGTGCACTGTAATTTCAC 57.346 36.000 29.57 16.16 38.24 3.18
870 884 3.112709 GTCCAAGTCGTCGGCAGC 61.113 66.667 0.00 0.00 0.00 5.25
873 2600 2.804090 GTCGTCCAAGTCGTCGGC 60.804 66.667 0.00 0.00 0.00 5.54
1148 2883 3.288964 GGAGTTCAGATCGGAGAAGGTA 58.711 50.000 0.00 0.00 43.58 3.08
1195 2930 2.088423 ACAACAGCAAAAGGTCGAACA 58.912 42.857 1.87 0.00 0.00 3.18
1198 2933 0.380378 GCACAACAGCAAAAGGTCGA 59.620 50.000 0.00 0.00 0.00 4.20
1206 2941 1.898094 ATCCTGCGCACAACAGCAA 60.898 52.632 5.66 0.00 43.31 3.91
1236 2971 0.652592 GATTGATGTCCTGGAACGCG 59.347 55.000 3.53 3.53 0.00 6.01
1260 2995 1.626654 CCAGCAAGTACCTGAACGCG 61.627 60.000 3.53 3.53 32.03 6.01
1317 3052 3.812053 GCTAATGCCACATCTAGACCAAG 59.188 47.826 0.00 0.00 0.00 3.61
1352 3088 5.062308 CGAAATGAACAAGAGCACTACTACC 59.938 44.000 0.00 0.00 0.00 3.18
1447 3183 8.967664 AGAGTATAAGACTACAAGAGTACCAG 57.032 38.462 0.00 0.00 39.06 4.00
1552 3289 7.428020 TGATAAACACTAACTACACGACAGTT 58.572 34.615 0.00 0.00 39.50 3.16
1610 3347 5.288804 CAAACATTGAAAGGAAACACCGAT 58.711 37.500 0.00 0.00 44.74 4.18
1985 3722 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
1986 3723 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1987 3724 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1988 3725 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
1989 3726 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
1990 3727 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
1991 3728 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
1992 3729 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
1993 3730 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
1994 3731 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
1995 3732 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
1996 3733 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
1997 3734 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
1998 3735 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
1999 3736 7.603024 GGTTGTACTAAGCTTGAGACACTTATT 59.397 37.037 9.86 0.00 0.00 1.40
2000 3737 7.038941 AGGTTGTACTAAGCTTGAGACACTTAT 60.039 37.037 9.86 0.00 0.00 1.73
2001 3738 6.267014 AGGTTGTACTAAGCTTGAGACACTTA 59.733 38.462 9.86 0.00 0.00 2.24
2002 3739 5.070580 AGGTTGTACTAAGCTTGAGACACTT 59.929 40.000 9.86 0.00 0.00 3.16
2003 3740 4.589374 AGGTTGTACTAAGCTTGAGACACT 59.411 41.667 9.86 2.08 0.00 3.55
2004 3741 4.884247 AGGTTGTACTAAGCTTGAGACAC 58.116 43.478 9.86 7.18 0.00 3.67
2005 3742 5.546621 AAGGTTGTACTAAGCTTGAGACA 57.453 39.130 9.86 7.12 36.71 3.41
2029 3766 9.565090 TGTCTCAACTTTGTACTAACTCTAGTA 57.435 33.333 0.00 0.00 39.23 1.82
2030 3767 8.351461 GTGTCTCAACTTTGTACTAACTCTAGT 58.649 37.037 0.00 0.00 41.43 2.57
2031 3768 8.569641 AGTGTCTCAACTTTGTACTAACTCTAG 58.430 37.037 0.00 0.00 0.00 2.43
2032 3769 8.461249 AGTGTCTCAACTTTGTACTAACTCTA 57.539 34.615 0.00 0.00 0.00 2.43
2033 3770 7.349412 AGTGTCTCAACTTTGTACTAACTCT 57.651 36.000 0.00 0.00 0.00 3.24
2034 3771 9.694137 ATAAGTGTCTCAACTTTGTACTAACTC 57.306 33.333 0.00 0.00 40.77 3.01
2038 3775 9.692749 CAGAATAAGTGTCTCAACTTTGTACTA 57.307 33.333 0.00 0.00 40.77 1.82
2039 3776 7.657761 CCAGAATAAGTGTCTCAACTTTGTACT 59.342 37.037 0.00 0.00 40.77 2.73
2040 3777 7.095187 CCCAGAATAAGTGTCTCAACTTTGTAC 60.095 40.741 0.00 0.00 40.77 2.90
2041 3778 6.934645 CCCAGAATAAGTGTCTCAACTTTGTA 59.065 38.462 0.00 0.00 40.77 2.41
2042 3779 5.765182 CCCAGAATAAGTGTCTCAACTTTGT 59.235 40.000 0.00 0.00 40.77 2.83
2043 3780 5.997746 TCCCAGAATAAGTGTCTCAACTTTG 59.002 40.000 0.00 0.00 40.77 2.77
2044 3781 5.998363 GTCCCAGAATAAGTGTCTCAACTTT 59.002 40.000 0.00 0.00 40.77 2.66
2045 3782 5.552178 GTCCCAGAATAAGTGTCTCAACTT 58.448 41.667 0.00 0.00 42.89 2.66
2046 3783 4.322049 CGTCCCAGAATAAGTGTCTCAACT 60.322 45.833 0.00 0.00 0.00 3.16
2047 3784 3.927142 CGTCCCAGAATAAGTGTCTCAAC 59.073 47.826 0.00 0.00 0.00 3.18
2048 3785 3.056107 CCGTCCCAGAATAAGTGTCTCAA 60.056 47.826 0.00 0.00 0.00 3.02
2049 3786 2.496070 CCGTCCCAGAATAAGTGTCTCA 59.504 50.000 0.00 0.00 0.00 3.27
2050 3787 2.758979 TCCGTCCCAGAATAAGTGTCTC 59.241 50.000 0.00 0.00 0.00 3.36
2051 3788 2.761208 CTCCGTCCCAGAATAAGTGTCT 59.239 50.000 0.00 0.00 0.00 3.41
2052 3789 2.159085 CCTCCGTCCCAGAATAAGTGTC 60.159 54.545 0.00 0.00 0.00 3.67
2053 3790 1.831736 CCTCCGTCCCAGAATAAGTGT 59.168 52.381 0.00 0.00 0.00 3.55
2054 3791 1.139058 CCCTCCGTCCCAGAATAAGTG 59.861 57.143 0.00 0.00 0.00 3.16
2055 3792 1.007963 TCCCTCCGTCCCAGAATAAGT 59.992 52.381 0.00 0.00 0.00 2.24
2056 3793 1.689273 CTCCCTCCGTCCCAGAATAAG 59.311 57.143 0.00 0.00 0.00 1.73
2057 3794 1.007963 ACTCCCTCCGTCCCAGAATAA 59.992 52.381 0.00 0.00 0.00 1.40
2058 3795 0.635009 ACTCCCTCCGTCCCAGAATA 59.365 55.000 0.00 0.00 0.00 1.75
2059 3796 0.635009 TACTCCCTCCGTCCCAGAAT 59.365 55.000 0.00 0.00 0.00 2.40
2060 3797 0.635009 ATACTCCCTCCGTCCCAGAA 59.365 55.000 0.00 0.00 0.00 3.02
2061 3798 0.185416 GATACTCCCTCCGTCCCAGA 59.815 60.000 0.00 0.00 0.00 3.86
2062 3799 0.106167 TGATACTCCCTCCGTCCCAG 60.106 60.000 0.00 0.00 0.00 4.45
2063 3800 0.337082 TTGATACTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
2064 3801 1.138464 GTTTGATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
2065 3802 1.829222 TGTTTGATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
2066 3803 3.118738 ACATGTTTGATACTCCCTCCGTC 60.119 47.826 0.00 0.00 0.00 4.79
2067 3804 2.838202 ACATGTTTGATACTCCCTCCGT 59.162 45.455 0.00 0.00 0.00 4.69
2068 3805 3.118775 TGACATGTTTGATACTCCCTCCG 60.119 47.826 0.00 0.00 0.00 4.63
2069 3806 4.487714 TGACATGTTTGATACTCCCTCC 57.512 45.455 0.00 0.00 0.00 4.30
2070 3807 5.705441 TGTTTGACATGTTTGATACTCCCTC 59.295 40.000 0.00 0.00 0.00 4.30
2071 3808 5.473504 GTGTTTGACATGTTTGATACTCCCT 59.526 40.000 0.00 0.00 0.00 4.20
2072 3809 5.616866 CGTGTTTGACATGTTTGATACTCCC 60.617 44.000 0.00 0.00 30.72 4.30
2073 3810 5.049680 ACGTGTTTGACATGTTTGATACTCC 60.050 40.000 0.00 0.00 45.33 3.85
2074 3811 5.985781 ACGTGTTTGACATGTTTGATACTC 58.014 37.500 0.00 0.00 45.33 2.59
2100 3837 8.598916 TGTTATCCCTTTCACTGAGTAAATGTA 58.401 33.333 0.00 0.00 0.00 2.29
2145 3882 4.005650 CTTATCAAAGAGGCAGACAGCAA 58.994 43.478 0.00 0.00 39.04 3.91
2222 3959 5.179555 GTGGTGGTCAATAGAAGAACTGAAC 59.820 44.000 0.00 0.00 0.00 3.18
2234 3971 4.227073 TGATGGATCTTGTGGTGGTCAATA 59.773 41.667 0.00 0.00 0.00 1.90
2285 4022 8.244494 TCGAACACAGATCTTCAAGATAAAAG 57.756 34.615 0.00 0.00 34.53 2.27
2308 4045 3.059868 ACGTTGCACAACAAGAATACTCG 60.060 43.478 13.52 0.00 39.50 4.18
2416 4153 2.821307 GCAAGAAGCTATGAGCACAC 57.179 50.000 0.64 0.00 45.56 3.82
2600 4337 7.712264 TGCCAGAACAAATGTATTTCTTTTG 57.288 32.000 0.00 0.00 42.81 2.44
2997 4736 3.452627 CAGGAATAGCCAGTACCAGTCTT 59.547 47.826 0.00 0.00 40.02 3.01
3290 5030 9.282247 CTAACAAGATGAGAATACAATGTTTGC 57.718 33.333 0.00 0.00 32.20 3.68
3380 5131 0.541392 GGGCCAAAATTGATGACCCC 59.459 55.000 4.39 5.09 0.00 4.95
3473 5240 3.884693 TGAATGTCTTTGCATGACAGTGT 59.115 39.130 21.94 12.93 45.88 3.55
3542 5313 6.073819 GCTCGTGCCTTTGTAAATCAAATTTT 60.074 34.615 0.00 0.00 43.78 1.82
3657 5436 9.462606 CTAGACCTCATATATGGTGTACATACA 57.537 37.037 12.78 1.85 44.41 2.29
3658 5437 8.407064 GCTAGACCTCATATATGGTGTACATAC 58.593 40.741 12.78 0.00 44.41 2.39
3659 5438 8.336987 AGCTAGACCTCATATATGGTGTACATA 58.663 37.037 12.78 0.00 45.60 2.29
3660 5439 7.185565 AGCTAGACCTCATATATGGTGTACAT 58.814 38.462 12.78 3.72 43.68 2.29
3661 5440 6.552932 AGCTAGACCTCATATATGGTGTACA 58.447 40.000 12.78 0.00 36.59 2.90
3662 5441 7.283580 CCTAGCTAGACCTCATATATGGTGTAC 59.716 44.444 22.70 5.34 36.59 2.90
3663 5442 7.184022 TCCTAGCTAGACCTCATATATGGTGTA 59.816 40.741 22.70 6.00 36.59 2.90
3710 5499 0.686441 TACATGGGAGCTGTACGCCT 60.686 55.000 0.00 0.00 40.39 5.52
3711 5500 0.529992 GTACATGGGAGCTGTACGCC 60.530 60.000 0.00 0.00 39.51 5.68
3712 5501 2.973420 GTACATGGGAGCTGTACGC 58.027 57.895 0.00 2.08 39.51 4.42
3714 5503 1.207089 TGCAGTACATGGGAGCTGTAC 59.793 52.381 0.00 0.00 45.99 2.90
3715 5504 1.482182 CTGCAGTACATGGGAGCTGTA 59.518 52.381 5.25 0.00 0.00 2.74
3716 5505 0.251354 CTGCAGTACATGGGAGCTGT 59.749 55.000 5.25 0.00 0.00 4.40
3717 5506 0.251354 ACTGCAGTACATGGGAGCTG 59.749 55.000 20.16 2.60 0.00 4.24
3718 5507 0.251354 CACTGCAGTACATGGGAGCT 59.749 55.000 21.20 0.00 0.00 4.09
3921 5725 2.594303 CCAACTGCCAGGTGCGAA 60.594 61.111 3.60 0.00 45.60 4.70


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

AutoCloner maintained by Alex Coulton.