Multiple sequence alignment - TraesCS7A01G324400

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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 TraesCS7A01G324400 chr7A 100.000 2642 0 0 1 2642 471562397 471559756 0.000000e+00 4879.0
1 TraesCS7A01G324400 chr7D 90.520 1941 75 48 748 2642 410515652 410517529 0.000000e+00 2464.0
2 TraesCS7A01G324400 chr7D 92.308 182 14 0 377 558 410515140 410515321 2.610000e-65 259.0
3 TraesCS7A01G324400 chr7D 91.589 107 9 0 624 730 410515351 410515457 5.890000e-32 148.0
4 TraesCS7A01G324400 chr7D 81.699 153 22 3 2468 2619 55140568 55140421 3.570000e-24 122.0
5 TraesCS7A01G324400 chr7B 88.877 1888 103 47 730 2535 425230309 425228447 0.000000e+00 2224.0
6 TraesCS7A01G324400 chr7B 89.630 540 46 5 72 607 425231062 425230529 0.000000e+00 678.0
7 TraesCS7A01G324400 chr7B 90.083 121 3 5 2523 2642 425227564 425227452 5.890000e-32 148.0
8 TraesCS7A01G324400 chrUn 81.884 138 21 1 2482 2619 368385244 368385377 2.150000e-21 113.0
9 TraesCS7A01G324400 chrUn 79.825 114 15 5 2212 2324 368384986 368385092 2.820000e-10 76.8
10 TraesCS7A01G324400 chr2A 81.884 138 21 1 2482 2619 6275175 6275042 2.150000e-21 113.0
11 TraesCS7A01G324400 chr2A 83.333 84 12 2 2242 2324 6275409 6275327 2.820000e-10 76.8
12 TraesCS7A01G324400 chr1A 80.921 152 21 4 2469 2619 403390144 403390000 2.150000e-21 113.0


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 TraesCS7A01G324400 chr7A 471559756 471562397 2641 True 4879.000000 4879 100.000000 1 2642 1 chr7A.!!$R1 2641
1 TraesCS7A01G324400 chr7D 410515140 410517529 2389 False 957.000000 2464 91.472333 377 2642 3 chr7D.!!$F1 2265
2 TraesCS7A01G324400 chr7B 425227452 425231062 3610 True 1016.666667 2224 89.530000 72 2642 3 chr7B.!!$R1 2570

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
744 925 0.036306 ACTCAAGTCGGGCCGAAAAT 59.964 50.0 32.91 17.16 37.72 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2247 0.829182 TGAGTCTGCAGCTGAGTGGA 60.829 55.0 20.43 6.08 0.0 4.02 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
20 21 2.196595 CTATTGTCCCCTTGACCCTCA 58.803 52.381 0.00 0.00 43.78 3.86
21 22 1.686236 ATTGTCCCCTTGACCCTCAT 58.314 50.000 0.00 0.00 43.78 2.90
22 23 1.455822 TTGTCCCCTTGACCCTCATT 58.544 50.000 0.00 0.00 43.78 2.57
23 24 0.698238 TGTCCCCTTGACCCTCATTG 59.302 55.000 0.00 0.00 43.78 2.82
24 25 0.681243 GTCCCCTTGACCCTCATTGC 60.681 60.000 0.00 0.00 38.09 3.56
25 26 1.380380 CCCCTTGACCCTCATTGCC 60.380 63.158 0.00 0.00 0.00 4.52
26 27 1.693640 CCCTTGACCCTCATTGCCT 59.306 57.895 0.00 0.00 0.00 4.75
27 28 0.394899 CCCTTGACCCTCATTGCCTC 60.395 60.000 0.00 0.00 0.00 4.70
28 29 0.622665 CCTTGACCCTCATTGCCTCT 59.377 55.000 0.00 0.00 0.00 3.69
29 30 1.839994 CCTTGACCCTCATTGCCTCTA 59.160 52.381 0.00 0.00 0.00 2.43
30 31 2.158842 CCTTGACCCTCATTGCCTCTAG 60.159 54.545 0.00 0.00 0.00 2.43
31 32 0.833287 TGACCCTCATTGCCTCTAGC 59.167 55.000 0.00 0.00 44.14 3.42
32 33 0.107643 GACCCTCATTGCCTCTAGCC 59.892 60.000 0.00 0.00 42.71 3.93
33 34 1.348775 ACCCTCATTGCCTCTAGCCC 61.349 60.000 0.00 0.00 42.71 5.19
34 35 1.453669 CCTCATTGCCTCTAGCCCC 59.546 63.158 0.00 0.00 42.71 5.80
35 36 1.453669 CTCATTGCCTCTAGCCCCC 59.546 63.158 0.00 0.00 42.71 5.40
36 37 1.004758 TCATTGCCTCTAGCCCCCT 59.995 57.895 0.00 0.00 42.71 4.79
37 38 1.056700 TCATTGCCTCTAGCCCCCTC 61.057 60.000 0.00 0.00 42.71 4.30
38 39 1.772156 ATTGCCTCTAGCCCCCTCC 60.772 63.158 0.00 0.00 42.71 4.30
39 40 4.499116 TGCCTCTAGCCCCCTCCC 62.499 72.222 0.00 0.00 42.71 4.30
41 42 4.583442 CCTCTAGCCCCCTCCCCC 62.583 77.778 0.00 0.00 0.00 5.40
42 43 3.779083 CTCTAGCCCCCTCCCCCA 61.779 72.222 0.00 0.00 0.00 4.96
43 44 3.297579 TCTAGCCCCCTCCCCCAA 61.298 66.667 0.00 0.00 0.00 4.12
44 45 3.097162 CTAGCCCCCTCCCCCAAC 61.097 72.222 0.00 0.00 0.00 3.77
45 46 4.771745 TAGCCCCCTCCCCCAACC 62.772 72.222 0.00 0.00 0.00 3.77
50 51 4.366684 CCCTCCCCCAACCAGCAC 62.367 72.222 0.00 0.00 0.00 4.40
51 52 4.366684 CCTCCCCCAACCAGCACC 62.367 72.222 0.00 0.00 0.00 5.01
52 53 4.722700 CTCCCCCAACCAGCACCG 62.723 72.222 0.00 0.00 0.00 4.94
55 56 4.263572 CCCCAACCAGCACCGTCA 62.264 66.667 0.00 0.00 0.00 4.35
56 57 2.203280 CCCAACCAGCACCGTCAA 60.203 61.111 0.00 0.00 0.00 3.18
57 58 2.260869 CCCAACCAGCACCGTCAAG 61.261 63.158 0.00 0.00 0.00 3.02
58 59 1.525995 CCAACCAGCACCGTCAAGT 60.526 57.895 0.00 0.00 0.00 3.16
59 60 1.101049 CCAACCAGCACCGTCAAGTT 61.101 55.000 0.00 0.00 0.00 2.66
60 61 0.738389 CAACCAGCACCGTCAAGTTT 59.262 50.000 0.00 0.00 0.00 2.66
61 62 1.021968 AACCAGCACCGTCAAGTTTC 58.978 50.000 0.00 0.00 0.00 2.78
62 63 0.180406 ACCAGCACCGTCAAGTTTCT 59.820 50.000 0.00 0.00 0.00 2.52
63 64 0.588252 CCAGCACCGTCAAGTTTCTG 59.412 55.000 0.00 0.00 0.00 3.02
64 65 0.588252 CAGCACCGTCAAGTTTCTGG 59.412 55.000 0.00 0.00 0.00 3.86
65 66 1.166531 AGCACCGTCAAGTTTCTGGC 61.167 55.000 0.00 0.00 0.00 4.85
66 67 1.166531 GCACCGTCAAGTTTCTGGCT 61.167 55.000 0.00 0.00 0.00 4.75
67 68 1.308998 CACCGTCAAGTTTCTGGCTT 58.691 50.000 0.00 0.00 0.00 4.35
68 69 1.002468 CACCGTCAAGTTTCTGGCTTG 60.002 52.381 0.00 0.00 43.26 4.01
69 70 0.040067 CCGTCAAGTTTCTGGCTTGC 60.040 55.000 0.00 0.00 42.06 4.01
70 71 0.662619 CGTCAAGTTTCTGGCTTGCA 59.337 50.000 0.00 0.00 42.06 4.08
100 101 4.039357 ACAGCCTCGTCGTGGTCG 62.039 66.667 14.41 8.51 38.55 4.79
109 110 3.371063 TCGTGGTCGGTGCTCCTC 61.371 66.667 2.85 0.00 37.69 3.71
135 136 2.752358 CCAGCCTTCAGCCTCACA 59.248 61.111 0.00 0.00 45.47 3.58
140 141 1.569479 GCCTTCAGCCTCACACGAAC 61.569 60.000 0.00 0.00 34.35 3.95
142 143 1.284982 CTTCAGCCTCACACGAACCG 61.285 60.000 0.00 0.00 0.00 4.44
153 154 0.232303 CACGAACCGAAAGTGACTGC 59.768 55.000 0.00 0.00 38.06 4.40
159 160 0.320374 CCGAAAGTGACTGCCACCTA 59.680 55.000 0.00 0.00 46.87 3.08
161 162 1.798813 CGAAAGTGACTGCCACCTAAC 59.201 52.381 0.00 0.00 46.87 2.34
167 168 3.569701 AGTGACTGCCACCTAACAAATTG 59.430 43.478 0.00 0.00 46.87 2.32
168 169 2.295909 TGACTGCCACCTAACAAATTGC 59.704 45.455 0.00 0.00 0.00 3.56
169 170 2.295909 GACTGCCACCTAACAAATTGCA 59.704 45.455 0.00 0.00 0.00 4.08
173 174 1.402720 CCACCTAACAAATTGCAGGCG 60.403 52.381 12.53 5.09 0.00 5.52
191 192 2.602217 GGCGCCTGATATTTAGCAAACG 60.602 50.000 22.15 0.00 0.00 3.60
195 196 4.588278 GCCTGATATTTAGCAAACGTGTC 58.412 43.478 0.00 0.00 0.00 3.67
200 201 6.607689 TGATATTTAGCAAACGTGTCCAAAG 58.392 36.000 0.00 0.00 0.00 2.77
205 206 1.587946 GCAAACGTGTCCAAAGCTTTG 59.412 47.619 28.69 28.69 37.90 2.77
214 215 4.278419 GTGTCCAAAGCTTTGACCACTAAT 59.722 41.667 35.25 0.00 40.55 1.73
300 301 2.638556 AGTGAGATATATGGCGCGAC 57.361 50.000 12.10 8.22 0.00 5.19
301 302 1.886542 AGTGAGATATATGGCGCGACA 59.113 47.619 21.39 21.39 0.00 4.35
312 313 1.396648 TGGCGCGACACATTCATTAAG 59.603 47.619 12.71 0.00 0.00 1.85
346 347 0.326264 AACTCTGGGTCATGACTGGC 59.674 55.000 24.50 8.80 0.00 4.85
545 548 4.742438 TTCGAGTATTTTGGAACTGTGC 57.258 40.909 0.00 0.00 0.00 4.57
572 575 9.469807 GAGTAGTTACATATCTTCATCCACTTG 57.530 37.037 0.00 0.00 0.00 3.16
607 611 9.739276 AGTTACATATCTTCATCCAAAGAAACA 57.261 29.630 0.00 0.00 38.69 2.83
608 612 9.774742 GTTACATATCTTCATCCAAAGAAACAC 57.225 33.333 0.00 0.00 38.69 3.32
609 613 9.513906 TTACATATCTTCATCCAAAGAAACACA 57.486 29.630 0.00 0.00 38.69 3.72
610 614 8.585471 ACATATCTTCATCCAAAGAAACACAT 57.415 30.769 0.00 0.00 38.69 3.21
611 615 9.028284 ACATATCTTCATCCAAAGAAACACATT 57.972 29.630 0.00 0.00 38.69 2.71
612 616 9.865321 CATATCTTCATCCAAAGAAACACATTT 57.135 29.630 0.00 0.00 38.69 2.32
615 619 8.422973 TCTTCATCCAAAGAAACACATTTTTG 57.577 30.769 0.00 0.00 32.42 2.44
616 620 8.040132 TCTTCATCCAAAGAAACACATTTTTGT 58.960 29.630 0.00 0.00 32.42 2.83
617 621 8.558973 TTCATCCAAAGAAACACATTTTTGTT 57.441 26.923 0.00 0.00 41.62 2.83
618 622 7.972527 TCATCCAAAGAAACACATTTTTGTTG 58.027 30.769 0.00 0.00 39.70 3.33
619 623 6.175712 TCCAAAGAAACACATTTTTGTTGC 57.824 33.333 0.00 0.00 39.70 4.17
620 624 5.020758 CCAAAGAAACACATTTTTGTTGCG 58.979 37.500 0.00 0.00 39.71 4.85
621 625 5.163913 CCAAAGAAACACATTTTTGTTGCGA 60.164 36.000 0.00 0.00 39.71 5.10
622 626 5.701029 AAGAAACACATTTTTGTTGCGAG 57.299 34.783 0.00 0.00 39.71 5.03
623 627 4.743493 AGAAACACATTTTTGTTGCGAGT 58.257 34.783 0.00 0.00 39.71 4.18
624 628 4.798387 AGAAACACATTTTTGTTGCGAGTC 59.202 37.500 0.00 0.00 39.71 3.36
625 629 3.773860 ACACATTTTTGTTGCGAGTCA 57.226 38.095 0.00 0.00 0.00 3.41
626 630 4.305989 ACACATTTTTGTTGCGAGTCAT 57.694 36.364 0.00 0.00 0.00 3.06
627 631 4.290155 ACACATTTTTGTTGCGAGTCATC 58.710 39.130 0.00 0.00 0.00 2.92
628 632 3.670055 CACATTTTTGTTGCGAGTCATCC 59.330 43.478 0.00 0.00 0.00 3.51
629 633 2.679355 TTTTTGTTGCGAGTCATCCG 57.321 45.000 0.00 0.00 0.00 4.18
630 634 1.588674 TTTTGTTGCGAGTCATCCGT 58.411 45.000 0.00 0.00 0.00 4.69
631 635 2.442212 TTTGTTGCGAGTCATCCGTA 57.558 45.000 0.00 0.00 0.00 4.02
632 636 1.990799 TTGTTGCGAGTCATCCGTAG 58.009 50.000 0.00 0.00 0.00 3.51
633 637 1.170442 TGTTGCGAGTCATCCGTAGA 58.830 50.000 0.00 0.00 0.00 2.59
634 638 1.542472 TGTTGCGAGTCATCCGTAGAA 59.458 47.619 0.00 0.00 0.00 2.10
635 639 2.029739 TGTTGCGAGTCATCCGTAGAAA 60.030 45.455 0.00 0.00 0.00 2.52
636 640 2.273370 TGCGAGTCATCCGTAGAAAC 57.727 50.000 0.00 0.00 0.00 2.78
646 650 5.805994 GTCATCCGTAGAAACTTGAAGGTAG 59.194 44.000 0.00 0.00 0.00 3.18
697 701 3.496130 CCTGATCATCCATTCGTAACAGC 59.504 47.826 0.00 0.00 0.00 4.40
723 727 3.001939 GGTGAATCGTGGCGGTTATTTAG 59.998 47.826 0.00 0.00 27.16 1.85
733 914 4.933400 TGGCGGTTATTTAGAACTCAAGTC 59.067 41.667 0.00 0.00 0.00 3.01
739 920 0.245539 TTAGAACTCAAGTCGGGCCG 59.754 55.000 22.51 22.51 0.00 6.13
744 925 0.036306 ACTCAAGTCGGGCCGAAAAT 59.964 50.000 32.91 17.16 37.72 1.82
757 938 3.498018 GGCCGAAAATTGCAGACATTTTT 59.502 39.130 8.56 2.25 40.33 1.94
780 973 4.990543 TTTTCTGAATGTACGCAGACAG 57.009 40.909 11.10 5.93 40.57 3.51
859 1052 3.060895 GTCGTCACTCCATTCGATTCAAC 59.939 47.826 0.00 0.00 34.93 3.18
916 1109 1.866853 GCTCGCAACCCAAGGAAAGG 61.867 60.000 0.00 0.00 0.00 3.11
1278 1471 3.385749 CTATGCCGCCGGGTTCTGT 62.386 63.158 4.77 0.00 34.97 3.41
1537 1730 1.746239 CTGGTGGTGATGATGCGCA 60.746 57.895 14.96 14.96 0.00 6.09
1551 1744 0.108851 TGCGCACGCTCAAGAAGATA 60.109 50.000 16.77 0.00 42.51 1.98
1621 1814 2.124942 CCGCCTCTGCTTCTTCCC 60.125 66.667 0.00 0.00 34.43 3.97
1710 1903 6.714492 TGCACTTTATGATAAATAGCGTGTG 58.286 36.000 13.21 10.61 0.00 3.82
1766 1959 1.803334 TTTGAACCCTCGATCGTTGG 58.197 50.000 15.94 18.04 0.00 3.77
1787 1980 6.363577 TGGTTTCTTGATCGAAATATCTGC 57.636 37.500 0.00 0.00 35.56 4.26
1788 1981 5.879777 TGGTTTCTTGATCGAAATATCTGCA 59.120 36.000 0.00 0.00 35.56 4.41
1789 1982 6.183360 TGGTTTCTTGATCGAAATATCTGCAC 60.183 38.462 0.00 0.00 35.56 4.57
1790 1983 6.183360 GGTTTCTTGATCGAAATATCTGCACA 60.183 38.462 0.00 0.00 35.56 4.57
1791 1984 6.983474 TTCTTGATCGAAATATCTGCACAA 57.017 33.333 0.00 0.00 0.00 3.33
1796 1989 4.926860 TCGAAATATCTGCACAACACAG 57.073 40.909 0.00 0.00 36.44 3.66
1803 1996 2.212652 TCTGCACAACACAGTGATGAC 58.787 47.619 17.19 9.20 42.05 3.06
1818 2011 4.915158 TGATGACAATCACAGTTGCAAA 57.085 36.364 0.00 0.00 37.91 3.68
1819 2012 5.456548 TGATGACAATCACAGTTGCAAAT 57.543 34.783 0.00 0.00 37.91 2.32
1820 2013 5.463286 TGATGACAATCACAGTTGCAAATC 58.537 37.500 0.00 0.00 37.91 2.17
1821 2014 3.887741 TGACAATCACAGTTGCAAATCG 58.112 40.909 0.00 0.00 32.32 3.34
1823 2016 4.513318 TGACAATCACAGTTGCAAATCGTA 59.487 37.500 0.00 0.00 32.32 3.43
1824 2017 5.034554 ACAATCACAGTTGCAAATCGTAG 57.965 39.130 0.00 0.00 32.32 3.51
1825 2018 4.515191 ACAATCACAGTTGCAAATCGTAGT 59.485 37.500 0.00 0.00 32.32 2.73
1826 2019 5.008613 ACAATCACAGTTGCAAATCGTAGTT 59.991 36.000 0.00 0.00 32.32 2.24
1827 2020 4.466567 TCACAGTTGCAAATCGTAGTTG 57.533 40.909 0.00 0.00 0.00 3.16
1828 2021 3.874543 TCACAGTTGCAAATCGTAGTTGT 59.125 39.130 0.00 0.00 0.00 3.32
1829 2022 3.968096 CACAGTTGCAAATCGTAGTTGTG 59.032 43.478 0.00 0.00 0.00 3.33
1830 2023 3.625764 ACAGTTGCAAATCGTAGTTGTGT 59.374 39.130 0.00 0.00 0.00 3.72
1831 2024 3.968096 CAGTTGCAAATCGTAGTTGTGTG 59.032 43.478 0.00 0.00 0.00 3.82
1832 2025 3.874543 AGTTGCAAATCGTAGTTGTGTGA 59.125 39.130 0.00 0.00 0.00 3.58
1835 2039 5.524511 TGCAAATCGTAGTTGTGTGATAC 57.475 39.130 0.00 0.00 0.00 2.24
1839 2043 6.237755 GCAAATCGTAGTTGTGTGATACTACC 60.238 42.308 0.00 0.00 42.27 3.18
1860 2085 4.743151 ACCGTGTATCATTATGTACAAGCG 59.257 41.667 0.00 8.75 33.05 4.68
1900 2125 5.975693 AACATGGTTTACATACAGTTGGG 57.024 39.130 0.00 0.00 37.84 4.12
1949 2174 3.248363 CAGCGTGTTCTCATTTGTTCTGA 59.752 43.478 0.00 0.00 0.00 3.27
1975 2200 6.142818 TGATTCACTACTTGTGTTTTTGGG 57.857 37.500 0.00 0.00 46.27 4.12
1985 2212 6.245408 ACTTGTGTTTTTGGGCTGAGATATA 58.755 36.000 0.00 0.00 0.00 0.86
1989 2216 6.095300 TGTGTTTTTGGGCTGAGATATATGTG 59.905 38.462 0.00 0.00 0.00 3.21
1992 2219 3.690475 TGGGCTGAGATATATGTGCAG 57.310 47.619 0.00 0.00 0.00 4.41
1995 2222 3.007290 GGGCTGAGATATATGTGCAGTGA 59.993 47.826 0.00 0.00 0.00 3.41
2020 2247 6.110543 GCAATTTTGTTTTGCTGAAGAACT 57.889 33.333 1.36 0.00 44.71 3.01
2036 2263 0.034616 AACTCCACTCAGCTGCAGAC 59.965 55.000 20.43 9.11 0.00 3.51
2085 2335 9.502091 AAAGTTGCGGCTATATATTTATCAGAA 57.498 29.630 0.00 0.00 0.00 3.02
2109 2359 1.880271 CTCCTGAGATTGCGATGCAT 58.120 50.000 0.00 0.00 38.76 3.96
2110 2360 1.799403 CTCCTGAGATTGCGATGCATC 59.201 52.381 17.10 17.10 38.76 3.91
2115 2365 0.182061 AGATTGCGATGCATCCTGGT 59.818 50.000 20.87 5.13 38.76 4.00
2122 2372 2.618241 GCGATGCATCCTGGTAATGAAA 59.382 45.455 20.87 0.00 0.00 2.69
2190 2440 3.823873 AGGAGTCATCTATCATCGACCAC 59.176 47.826 0.00 0.00 0.00 4.16
2209 2459 3.743396 CCACTCATCTTCCGCTATTAAGC 59.257 47.826 0.00 0.00 45.86 3.09
2331 2582 8.686334 CAAAGTTAGTTAGGCCATGATAATTGT 58.314 33.333 5.01 0.00 0.00 2.71
2332 2583 9.914834 AAAGTTAGTTAGGCCATGATAATTGTA 57.085 29.630 5.01 0.00 0.00 2.41
2409 2672 7.124298 AGGTTGTCTGATTCTTGCATACTACTA 59.876 37.037 0.00 0.00 0.00 1.82
2542 3711 3.317993 TGACTTGACGATGACACAAGAGA 59.682 43.478 12.04 0.00 42.12 3.10
2561 3730 6.054860 AGAGAGTGTAACAAGGCAATGTAT 57.945 37.500 0.00 0.00 41.43 2.29
2604 3773 7.716560 TCACAAATCACAATCTCTGAAGAAGAA 59.283 33.333 0.00 0.00 34.49 2.52
2605 3774 7.802251 CACAAATCACAATCTCTGAAGAAGAAC 59.198 37.037 0.00 0.00 34.49 3.01
2607 3776 7.432350 AATCACAATCTCTGAAGAAGAACAC 57.568 36.000 0.00 0.00 34.49 3.32
2608 3777 6.166984 TCACAATCTCTGAAGAAGAACACT 57.833 37.500 0.00 0.00 34.49 3.55
2609 3778 7.290110 TCACAATCTCTGAAGAAGAACACTA 57.710 36.000 0.00 0.00 34.49 2.74
2610 3779 7.901029 TCACAATCTCTGAAGAAGAACACTAT 58.099 34.615 0.00 0.00 34.49 2.12
2611 3780 7.816513 TCACAATCTCTGAAGAAGAACACTATG 59.183 37.037 0.00 0.00 34.49 2.23
2612 3781 6.593382 ACAATCTCTGAAGAAGAACACTATGC 59.407 38.462 0.00 0.00 34.49 3.14
2613 3782 5.728637 TCTCTGAAGAAGAACACTATGCA 57.271 39.130 0.00 0.00 33.37 3.96
2614 3783 5.718146 TCTCTGAAGAAGAACACTATGCAG 58.282 41.667 0.00 0.00 33.37 4.41
2615 3784 5.244851 TCTCTGAAGAAGAACACTATGCAGT 59.755 40.000 0.00 0.00 33.37 4.40
2616 3785 6.434340 TCTCTGAAGAAGAACACTATGCAGTA 59.566 38.462 0.00 0.00 33.37 2.74
2617 3786 6.390721 TCTGAAGAAGAACACTATGCAGTAC 58.609 40.000 0.00 0.00 29.21 2.73
2618 3787 6.209589 TCTGAAGAAGAACACTATGCAGTACT 59.790 38.462 0.00 0.00 29.21 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.681243 GCAATGAGGGTCAAGGGGAC 60.681 60.000 0.00 0.00 46.20 4.46
6 7 1.691219 GCAATGAGGGTCAAGGGGA 59.309 57.895 0.00 0.00 0.00 4.81
7 8 1.380380 GGCAATGAGGGTCAAGGGG 60.380 63.158 0.00 0.00 0.00 4.79
8 9 0.394899 GAGGCAATGAGGGTCAAGGG 60.395 60.000 0.00 0.00 0.00 3.95
9 10 0.622665 AGAGGCAATGAGGGTCAAGG 59.377 55.000 0.00 0.00 0.00 3.61
10 11 2.744494 GCTAGAGGCAATGAGGGTCAAG 60.744 54.545 0.00 0.00 41.35 3.02
11 12 1.210478 GCTAGAGGCAATGAGGGTCAA 59.790 52.381 0.00 0.00 41.35 3.18
12 13 0.833287 GCTAGAGGCAATGAGGGTCA 59.167 55.000 0.00 0.00 41.35 4.02
13 14 0.107643 GGCTAGAGGCAATGAGGGTC 59.892 60.000 0.00 0.00 44.01 4.46
14 15 1.348775 GGGCTAGAGGCAATGAGGGT 61.349 60.000 5.38 0.00 44.01 4.34
15 16 1.453669 GGGCTAGAGGCAATGAGGG 59.546 63.158 5.38 0.00 44.01 4.30
16 17 1.453669 GGGGCTAGAGGCAATGAGG 59.546 63.158 5.38 0.00 44.01 3.86
17 18 1.059006 AGGGGGCTAGAGGCAATGAG 61.059 60.000 5.38 0.00 44.01 2.90
18 19 1.004758 AGGGGGCTAGAGGCAATGA 59.995 57.895 5.38 0.00 44.01 2.57
19 20 1.453669 GAGGGGGCTAGAGGCAATG 59.546 63.158 5.38 0.00 44.01 2.82
20 21 1.772156 GGAGGGGGCTAGAGGCAAT 60.772 63.158 5.38 0.00 44.01 3.56
21 22 2.366972 GGAGGGGGCTAGAGGCAA 60.367 66.667 5.38 0.00 44.01 4.52
22 23 4.499116 GGGAGGGGGCTAGAGGCA 62.499 72.222 5.38 0.00 44.01 4.75
24 25 4.583442 GGGGGAGGGGGCTAGAGG 62.583 77.778 0.00 0.00 0.00 3.69
25 26 3.347562 TTGGGGGAGGGGGCTAGAG 62.348 68.421 0.00 0.00 0.00 2.43
26 27 3.297579 TTGGGGGAGGGGGCTAGA 61.298 66.667 0.00 0.00 0.00 2.43
27 28 3.097162 GTTGGGGGAGGGGGCTAG 61.097 72.222 0.00 0.00 0.00 3.42
28 29 4.771745 GGTTGGGGGAGGGGGCTA 62.772 72.222 0.00 0.00 0.00 3.93
33 34 4.366684 GTGCTGGTTGGGGGAGGG 62.367 72.222 0.00 0.00 0.00 4.30
34 35 4.366684 GGTGCTGGTTGGGGGAGG 62.367 72.222 0.00 0.00 0.00 4.30
35 36 4.722700 CGGTGCTGGTTGGGGGAG 62.723 72.222 0.00 0.00 0.00 4.30
38 39 3.783362 TTGACGGTGCTGGTTGGGG 62.783 63.158 0.00 0.00 0.00 4.96
39 40 2.203280 TTGACGGTGCTGGTTGGG 60.203 61.111 0.00 0.00 0.00 4.12
40 41 1.101049 AACTTGACGGTGCTGGTTGG 61.101 55.000 0.00 0.00 0.00 3.77
41 42 0.738389 AAACTTGACGGTGCTGGTTG 59.262 50.000 0.00 0.00 0.00 3.77
42 43 1.021968 GAAACTTGACGGTGCTGGTT 58.978 50.000 0.00 0.00 0.00 3.67
43 44 0.180406 AGAAACTTGACGGTGCTGGT 59.820 50.000 0.00 0.00 0.00 4.00
44 45 0.588252 CAGAAACTTGACGGTGCTGG 59.412 55.000 0.00 0.00 0.00 4.85
45 46 0.588252 CCAGAAACTTGACGGTGCTG 59.412 55.000 0.00 0.00 0.00 4.41
46 47 1.166531 GCCAGAAACTTGACGGTGCT 61.167 55.000 0.00 0.00 0.00 4.40
47 48 1.166531 AGCCAGAAACTTGACGGTGC 61.167 55.000 0.00 0.00 0.00 5.01
48 49 1.002468 CAAGCCAGAAACTTGACGGTG 60.002 52.381 0.00 0.00 45.99 4.94
49 50 1.308998 CAAGCCAGAAACTTGACGGT 58.691 50.000 0.00 0.00 45.99 4.83
50 51 0.040067 GCAAGCCAGAAACTTGACGG 60.040 55.000 7.64 0.00 45.99 4.79
51 52 0.662619 TGCAAGCCAGAAACTTGACG 59.337 50.000 7.64 0.00 45.99 4.35
52 53 1.678101 AGTGCAAGCCAGAAACTTGAC 59.322 47.619 7.64 3.60 45.99 3.18
53 54 1.949525 GAGTGCAAGCCAGAAACTTGA 59.050 47.619 7.64 0.00 45.99 3.02
54 55 1.334419 CGAGTGCAAGCCAGAAACTTG 60.334 52.381 0.00 0.00 45.88 3.16
55 56 0.947244 CGAGTGCAAGCCAGAAACTT 59.053 50.000 0.00 0.00 0.00 2.66
56 57 0.179045 ACGAGTGCAAGCCAGAAACT 60.179 50.000 0.00 0.00 0.00 2.66
57 58 0.040958 CACGAGTGCAAGCCAGAAAC 60.041 55.000 0.00 0.00 0.00 2.78
58 59 2.320215 CACGAGTGCAAGCCAGAAA 58.680 52.632 0.00 0.00 0.00 2.52
59 60 4.047834 CACGAGTGCAAGCCAGAA 57.952 55.556 0.00 0.00 0.00 3.02
83 84 4.039357 CGACCACGACGAGGCTGT 62.039 66.667 11.51 0.00 42.66 4.40
84 85 4.778415 CCGACCACGACGAGGCTG 62.778 72.222 11.51 3.94 42.66 4.85
92 93 3.371063 GAGGAGCACCGACCACGA 61.371 66.667 0.00 0.00 42.66 4.35
93 94 3.680786 TGAGGAGCACCGACCACG 61.681 66.667 0.00 0.00 41.83 4.94
94 95 2.048127 GTGAGGAGCACCGACCAC 60.048 66.667 7.38 7.38 41.78 4.16
95 96 3.680786 CGTGAGGAGCACCGACCA 61.681 66.667 0.00 0.00 44.85 4.02
135 136 0.878961 GGCAGTCACTTTCGGTTCGT 60.879 55.000 0.00 0.00 0.00 3.85
140 141 0.320374 TAGGTGGCAGTCACTTTCGG 59.680 55.000 4.85 0.00 45.38 4.30
142 143 2.846193 TGTTAGGTGGCAGTCACTTTC 58.154 47.619 4.85 0.00 45.38 2.62
153 154 1.402720 CGCCTGCAATTTGTTAGGTGG 60.403 52.381 19.25 11.11 37.21 4.61
159 160 1.005867 CAGGCGCCTGCAATTTGTT 60.006 52.632 41.27 7.73 45.35 2.83
161 162 0.740149 TATCAGGCGCCTGCAATTTG 59.260 50.000 44.77 25.53 45.35 2.32
167 168 0.519077 GCTAAATATCAGGCGCCTGC 59.481 55.000 44.77 29.87 43.31 4.85
168 169 1.882912 TGCTAAATATCAGGCGCCTG 58.117 50.000 44.24 44.24 44.86 4.85
169 170 2.618709 GTTTGCTAAATATCAGGCGCCT 59.381 45.455 27.08 27.08 0.00 5.52
173 174 4.495844 GGACACGTTTGCTAAATATCAGGC 60.496 45.833 0.00 0.00 0.00 4.85
191 192 2.024414 AGTGGTCAAAGCTTTGGACAC 58.976 47.619 34.72 34.72 41.26 3.67
195 196 6.375455 ACTCATATTAGTGGTCAAAGCTTTGG 59.625 38.462 33.01 18.01 38.66 3.28
200 201 8.947115 AGTTTTACTCATATTAGTGGTCAAAGC 58.053 33.333 0.00 0.00 0.00 3.51
245 246 6.547880 TGACCCAGAGTTATTTTGCTACAAAA 59.452 34.615 7.84 7.84 0.00 2.44
286 287 2.993220 TGAATGTGTCGCGCCATATATC 59.007 45.455 0.00 1.86 0.00 1.63
294 295 2.806288 ACTTAATGAATGTGTCGCGC 57.194 45.000 0.00 0.00 0.00 6.86
323 324 4.141711 GCCAGTCATGACCCAGAGTTATAA 60.142 45.833 22.21 0.00 0.00 0.98
333 334 0.610232 AAAGCTGCCAGTCATGACCC 60.610 55.000 22.21 11.46 0.00 4.46
425 428 7.692908 AATGTATGCATTATTTTGGTTACGC 57.307 32.000 3.54 0.00 42.96 4.42
508 511 9.722056 AAATACTCGAATATGTGAGCAATTTTC 57.278 29.630 4.75 0.00 35.61 2.29
545 548 7.877003 AGTGGATGAAGATATGTAACTACTCG 58.123 38.462 0.00 0.00 0.00 4.18
607 611 3.609175 CGGATGACTCGCAACAAAAATGT 60.609 43.478 0.00 0.00 0.00 2.71
608 612 2.910482 CGGATGACTCGCAACAAAAATG 59.090 45.455 0.00 0.00 0.00 2.32
609 613 2.552315 ACGGATGACTCGCAACAAAAAT 59.448 40.909 0.00 0.00 0.00 1.82
610 614 1.944024 ACGGATGACTCGCAACAAAAA 59.056 42.857 0.00 0.00 0.00 1.94
611 615 1.588674 ACGGATGACTCGCAACAAAA 58.411 45.000 0.00 0.00 0.00 2.44
612 616 2.029739 TCTACGGATGACTCGCAACAAA 60.030 45.455 0.00 0.00 0.00 2.83
613 617 1.542472 TCTACGGATGACTCGCAACAA 59.458 47.619 0.00 0.00 0.00 2.83
614 618 1.170442 TCTACGGATGACTCGCAACA 58.830 50.000 0.00 0.00 0.00 3.33
615 619 2.273370 TTCTACGGATGACTCGCAAC 57.727 50.000 0.00 0.00 0.00 4.17
616 620 2.230508 AGTTTCTACGGATGACTCGCAA 59.769 45.455 0.00 0.00 0.00 4.85
617 621 1.816835 AGTTTCTACGGATGACTCGCA 59.183 47.619 0.00 0.00 0.00 5.10
618 622 2.563471 AGTTTCTACGGATGACTCGC 57.437 50.000 0.00 0.00 0.00 5.03
619 623 4.092771 TCAAGTTTCTACGGATGACTCG 57.907 45.455 0.00 0.00 0.00 4.18
620 624 4.865365 CCTTCAAGTTTCTACGGATGACTC 59.135 45.833 0.00 0.00 0.00 3.36
621 625 4.283722 ACCTTCAAGTTTCTACGGATGACT 59.716 41.667 0.00 0.00 0.00 3.41
622 626 4.566987 ACCTTCAAGTTTCTACGGATGAC 58.433 43.478 0.00 0.00 0.00 3.06
623 627 4.884668 ACCTTCAAGTTTCTACGGATGA 57.115 40.909 0.00 0.00 0.00 2.92
624 628 5.962433 TCTACCTTCAAGTTTCTACGGATG 58.038 41.667 0.00 0.00 0.00 3.51
625 629 5.715753 ACTCTACCTTCAAGTTTCTACGGAT 59.284 40.000 0.00 0.00 0.00 4.18
626 630 5.075493 ACTCTACCTTCAAGTTTCTACGGA 58.925 41.667 0.00 0.00 0.00 4.69
627 631 5.388408 ACTCTACCTTCAAGTTTCTACGG 57.612 43.478 0.00 0.00 0.00 4.02
628 632 7.143514 AGTACTCTACCTTCAAGTTTCTACG 57.856 40.000 0.00 0.00 0.00 3.51
629 633 8.183536 GCTAGTACTCTACCTTCAAGTTTCTAC 58.816 40.741 0.00 0.00 0.00 2.59
630 634 7.886970 TGCTAGTACTCTACCTTCAAGTTTCTA 59.113 37.037 0.00 0.00 0.00 2.10
631 635 6.720288 TGCTAGTACTCTACCTTCAAGTTTCT 59.280 38.462 0.00 0.00 0.00 2.52
632 636 6.921914 TGCTAGTACTCTACCTTCAAGTTTC 58.078 40.000 0.00 0.00 0.00 2.78
633 637 6.912951 TGCTAGTACTCTACCTTCAAGTTT 57.087 37.500 0.00 0.00 0.00 2.66
634 638 6.437793 ACATGCTAGTACTCTACCTTCAAGTT 59.562 38.462 0.00 0.00 0.00 2.66
635 639 5.952947 ACATGCTAGTACTCTACCTTCAAGT 59.047 40.000 0.00 0.00 0.00 3.16
636 640 6.458232 ACATGCTAGTACTCTACCTTCAAG 57.542 41.667 0.00 0.00 0.00 3.02
646 650 4.767928 AGGCCTATGTACATGCTAGTACTC 59.232 45.833 18.81 0.24 43.65 2.59
697 701 3.853330 CGCCACGATTCACCGCAG 61.853 66.667 0.00 0.00 0.00 5.18
723 727 0.601841 TTTCGGCCCGACTTGAGTTC 60.602 55.000 4.70 0.00 34.89 3.01
733 914 1.154035 GTCTGCAATTTTCGGCCCG 60.154 57.895 0.00 0.00 0.00 6.13
758 939 4.213270 CCTGTCTGCGTACATTCAGAAAAA 59.787 41.667 10.01 1.67 40.57 1.94
759 940 3.745975 CCTGTCTGCGTACATTCAGAAAA 59.254 43.478 10.01 3.50 40.57 2.29
763 944 1.995484 CACCTGTCTGCGTACATTCAG 59.005 52.381 0.00 0.00 0.00 3.02
770 963 0.538746 TGACTCCACCTGTCTGCGTA 60.539 55.000 0.00 0.00 35.63 4.42
780 973 0.680280 TACTCCGCTCTGACTCCACC 60.680 60.000 0.00 0.00 0.00 4.61
897 1090 1.581447 CTTTCCTTGGGTTGCGAGC 59.419 57.895 0.00 0.00 0.00 5.03
904 1097 0.405973 GCCTTCTCCTTTCCTTGGGT 59.594 55.000 0.00 0.00 0.00 4.51
1293 1486 1.969923 CTGTCCATCATCTCCTCCTCC 59.030 57.143 0.00 0.00 0.00 4.30
1537 1730 3.364062 CGACGAATATCTTCTTGAGCGT 58.636 45.455 0.00 0.00 0.00 5.07
1551 1744 2.730672 GCTCTTGTGCGCGACGAAT 61.731 57.895 12.10 0.00 0.00 3.34
1621 1814 4.082571 ACCTCATTTCTTGAAGGAATTGCG 60.083 41.667 0.00 0.00 32.78 4.85
1710 1903 7.333528 TCAATGCTTTACAAGATTATGACCC 57.666 36.000 0.00 0.00 0.00 4.46
1745 1938 2.550606 CCAACGATCGAGGGTTCAAAAA 59.449 45.455 24.34 0.00 0.00 1.94
1746 1939 2.147958 CCAACGATCGAGGGTTCAAAA 58.852 47.619 24.34 0.00 0.00 2.44
1755 1948 4.506838 GATCAAGAAACCAACGATCGAG 57.493 45.455 24.34 13.52 0.00 4.04
1760 1953 6.816640 AGATATTTCGATCAAGAAACCAACGA 59.183 34.615 0.00 0.00 42.12 3.85
1762 1955 6.688813 GCAGATATTTCGATCAAGAAACCAAC 59.311 38.462 0.00 0.00 42.12 3.77
1766 1959 6.775088 TGTGCAGATATTTCGATCAAGAAAC 58.225 36.000 0.00 0.00 42.12 2.78
1787 1980 4.816786 TGATTGTCATCACTGTGTTGTG 57.183 40.909 16.12 10.30 34.22 3.33
1803 1996 5.034554 ACTACGATTTGCAACTGTGATTG 57.965 39.130 0.00 0.00 0.00 2.67
1815 2008 6.020916 CGGTAGTATCACACAACTACGATTTG 60.021 42.308 6.56 0.00 45.89 2.32
1816 2009 6.032094 CGGTAGTATCACACAACTACGATTT 58.968 40.000 6.56 0.00 45.89 2.17
1817 2010 5.124457 ACGGTAGTATCACACAACTACGATT 59.876 40.000 6.56 0.00 45.89 3.34
1818 2011 4.637534 ACGGTAGTATCACACAACTACGAT 59.362 41.667 6.56 0.00 45.89 3.73
1819 2012 4.002982 ACGGTAGTATCACACAACTACGA 58.997 43.478 6.56 0.00 45.89 3.43
1820 2013 4.093514 CACGGTAGTATCACACAACTACG 58.906 47.826 6.56 5.28 45.89 3.51
1821 2014 5.051891 ACACGGTAGTATCACACAACTAC 57.948 43.478 4.44 4.44 44.77 2.73
1823 2016 5.888105 GATACACGGTAGTATCACACAACT 58.112 41.667 17.89 0.00 46.10 3.16
1835 2039 6.087687 CGCTTGTACATAATGATACACGGTAG 59.912 42.308 0.00 0.00 31.09 3.18
1839 2043 4.743151 ACCGCTTGTACATAATGATACACG 59.257 41.667 0.00 0.00 31.09 4.49
1851 2055 5.549347 TCTAACCAAATAACCGCTTGTACA 58.451 37.500 0.00 0.00 0.00 2.90
1906 2131 2.167487 GCACAAAGTGGGGAAAGACAAA 59.833 45.455 0.00 0.00 33.64 2.83
1909 2134 1.338020 CTGCACAAAGTGGGGAAAGAC 59.662 52.381 0.00 0.00 33.64 3.01
1975 2200 5.781452 CATCACTGCACATATATCTCAGC 57.219 43.478 5.68 0.00 0.00 4.26
2003 2230 4.016444 AGTGGAGTTCTTCAGCAAAACAA 58.984 39.130 0.00 0.00 0.00 2.83
2020 2247 0.829182 TGAGTCTGCAGCTGAGTGGA 60.829 55.000 20.43 6.08 0.00 4.02
2060 2287 9.155975 CTTCTGATAAATATATAGCCGCAACTT 57.844 33.333 0.00 0.00 0.00 2.66
2061 2288 8.531982 TCTTCTGATAAATATATAGCCGCAACT 58.468 33.333 0.00 0.00 0.00 3.16
2067 2294 9.541143 GGAGCTTCTTCTGATAAATATATAGCC 57.459 37.037 0.00 0.00 0.00 3.93
2078 2305 5.453057 GCAATCTCAGGAGCTTCTTCTGATA 60.453 44.000 5.37 0.00 44.15 2.15
2085 2335 1.189752 TCGCAATCTCAGGAGCTTCT 58.810 50.000 0.00 0.00 0.00 2.85
2109 2359 5.815581 AGCTGTACAATTTCATTACCAGGA 58.184 37.500 0.00 0.00 0.00 3.86
2110 2360 6.515272 AAGCTGTACAATTTCATTACCAGG 57.485 37.500 0.00 0.00 0.00 4.45
2209 2459 6.188407 TCCTATATCCTCCTAATTGGTCGAG 58.812 44.000 0.00 0.00 37.07 4.04
2245 2496 1.819305 GCCCTAATTGGCCGTGATCAT 60.819 52.381 0.00 0.00 46.11 2.45
2331 2582 9.132923 ACTAGTACTTGACAGCTTTGCTATATA 57.867 33.333 11.43 0.00 36.40 0.86
2332 2583 8.012957 ACTAGTACTTGACAGCTTTGCTATAT 57.987 34.615 11.43 0.00 36.40 0.86
2409 2672 4.219919 GGCCTCTCCTCTCAAATACTAGT 58.780 47.826 0.00 0.00 0.00 2.57
2542 3711 5.935789 ACGTAATACATTGCCTTGTTACACT 59.064 36.000 0.00 0.00 0.00 3.55
2561 3730 9.478768 TGATTTGTGAAATACTCTTGTACGTAA 57.521 29.630 0.00 0.00 0.00 3.18
2613 3782 3.165875 ACTGATGTGGCAGTACAGTACT 58.834 45.455 7.48 7.48 46.67 2.73
2614 3783 3.594603 ACTGATGTGGCAGTACAGTAC 57.405 47.619 15.35 2.05 46.67 2.73


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

AutoCloner maintained by Alex Coulton.