Multiple sequence alignment - TraesCS2A01G292800

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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 TraesCS2A01G292800 chr2A 100.000 4471 0 0 1 4471 504272056 504276526 0.000000e+00 8257.0
1 TraesCS2A01G292800 chr2A 82.986 288 23 14 3615 3888 40762102 40762377 2.080000e-58 237.0
2 TraesCS2A01G292800 chr2D 92.908 3624 134 53 61 3616 373228885 373225317 0.000000e+00 5155.0
3 TraesCS2A01G292800 chr2D 90.046 874 38 27 3618 4471 373225283 373224439 0.000000e+00 1086.0
4 TraesCS2A01G292800 chr2B 92.701 3521 165 48 163 3616 442798940 442795445 0.000000e+00 4994.0
5 TraesCS2A01G292800 chr2B 92.415 646 20 6 3833 4471 442795167 442794544 0.000000e+00 894.0
6 TraesCS2A01G292800 chr2B 84.722 288 18 10 3615 3888 735827408 735827133 9.540000e-67 265.0
7 TraesCS2A01G292800 chr2B 95.200 125 2 1 3618 3738 442795411 442795287 1.270000e-45 195.0
8 TraesCS2A01G292800 chr6B 84.028 288 20 11 3615 3888 699126034 699126309 2.060000e-63 254.0
9 TraesCS2A01G292800 chr6B 83.333 288 22 14 3615 3888 35778902 35778627 4.470000e-60 243.0
10 TraesCS2A01G292800 chr4A 84.028 288 20 10 3615 3888 661951798 661952073 2.060000e-63 254.0
11 TraesCS2A01G292800 chr3B 84.028 288 20 10 3615 3888 456361782 456362057 2.060000e-63 254.0
12 TraesCS2A01G292800 chr3B 83.681 288 21 9 3615 3888 807584591 807584316 9.600000e-62 248.0
13 TraesCS2A01G292800 chr3B 100.000 31 0 0 24 54 812610724 812610694 1.740000e-04 58.4
14 TraesCS2A01G292800 chr3B 96.970 33 1 0 24 56 812610730 812610698 6.250000e-04 56.5
15 TraesCS2A01G292800 chr1B 83.681 288 20 13 3615 3888 665780736 665780462 3.450000e-61 246.0
16 TraesCS2A01G292800 chr1B 83.333 288 22 9 3615 3888 69432336 69432611 4.470000e-60 243.0
17 TraesCS2A01G292800 chr6A 82.624 282 18 9 3615 3877 196864 196595 2.090000e-53 220.0


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 TraesCS2A01G292800 chr2A 504272056 504276526 4470 False 8257.000000 8257 100.000000 1 4471 1 chr2A.!!$F2 4470
1 TraesCS2A01G292800 chr2D 373224439 373228885 4446 True 3120.500000 5155 91.477000 61 4471 2 chr2D.!!$R1 4410
2 TraesCS2A01G292800 chr2B 442794544 442798940 4396 True 2027.666667 4994 93.438667 163 4471 3 chr2B.!!$R2 4308

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
165 166 0.041238 TAGGTGTGAGTGAGGGGAGG 59.959 60.0 0.00 0.00 0.00 4.30 F
704 781 0.176680 TCGGCTCAAGCTCCAGATTC 59.823 55.0 1.46 0.00 41.70 2.52 F
707 784 0.254178 GCTCAAGCTCCAGATTCCCA 59.746 55.0 0.00 0.00 38.21 4.37 F
1923 2023 0.319727 CTGATGATGGCTCTCTCGGC 60.320 60.0 0.00 0.00 0.00 5.54 F
2178 2278 0.392998 CGATCCAACAAGGGACCCTG 60.393 60.0 15.76 11.04 40.44 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1912 0.106419 AACCGGAACCTTTTGGCTCA 60.106 50.000 9.46 0.0 45.59 4.26 R
2533 2633 0.382158 TGCAGTCGGTCGATGAGATC 59.618 55.000 0.00 0.0 0.00 2.75 R
2605 2705 4.379082 CGTAAAACCTGCAAAGGGACATAC 60.379 45.833 0.00 0.0 0.00 2.39 R
3131 3231 0.400213 TTTCGTCATTGCCAGGTCCT 59.600 50.000 0.00 0.0 0.00 3.85 R
4026 4236 0.313043 GCACAGCACAGCATTCACTT 59.687 50.000 0.00 0.0 0.00 3.16 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
39 40 3.442996 CGTAGCCATAGCCATAGCC 57.557 57.895 0.00 0.00 41.25 3.93
40 41 0.608130 CGTAGCCATAGCCATAGCCA 59.392 55.000 0.00 0.00 41.25 4.75
41 42 1.208052 CGTAGCCATAGCCATAGCCAT 59.792 52.381 0.00 0.00 41.25 4.40
42 43 2.430694 CGTAGCCATAGCCATAGCCATA 59.569 50.000 0.00 0.00 41.25 2.74
43 44 3.491619 CGTAGCCATAGCCATAGCCATAG 60.492 52.174 0.00 0.00 41.25 2.23
44 45 1.211457 AGCCATAGCCATAGCCATAGC 59.789 52.381 0.00 0.00 41.25 2.97
45 46 1.748591 GCCATAGCCATAGCCATAGCC 60.749 57.143 0.00 0.00 41.25 3.93
46 47 1.561076 CCATAGCCATAGCCATAGCCA 59.439 52.381 0.00 0.00 41.25 4.75
47 48 2.174210 CCATAGCCATAGCCATAGCCAT 59.826 50.000 0.00 0.00 41.25 4.40
48 49 3.392285 CCATAGCCATAGCCATAGCCATA 59.608 47.826 0.00 0.00 41.25 2.74
49 50 4.504514 CCATAGCCATAGCCATAGCCATAG 60.505 50.000 0.00 0.00 41.25 2.23
50 51 1.211457 AGCCATAGCCATAGCCATAGC 59.789 52.381 0.00 0.00 41.25 2.97
51 52 1.748591 GCCATAGCCATAGCCATAGCC 60.749 57.143 0.00 0.00 41.25 3.93
52 53 1.561076 CCATAGCCATAGCCATAGCCA 59.439 52.381 0.00 0.00 41.25 4.75
53 54 2.421107 CCATAGCCATAGCCATAGCCAG 60.421 54.545 0.00 0.00 41.25 4.85
54 55 2.325661 TAGCCATAGCCATAGCCAGA 57.674 50.000 0.00 0.00 41.25 3.86
55 56 0.982704 AGCCATAGCCATAGCCAGAG 59.017 55.000 0.00 0.00 41.25 3.35
56 57 0.979665 GCCATAGCCATAGCCAGAGA 59.020 55.000 0.00 0.00 41.25 3.10
57 58 1.066286 GCCATAGCCATAGCCAGAGAG 60.066 57.143 0.00 0.00 41.25 3.20
58 59 2.533916 CCATAGCCATAGCCAGAGAGA 58.466 52.381 0.00 0.00 41.25 3.10
59 60 2.496871 CCATAGCCATAGCCAGAGAGAG 59.503 54.545 0.00 0.00 41.25 3.20
92 93 1.151777 CGTGCGTGAGTTTGGTGAGT 61.152 55.000 0.00 0.00 0.00 3.41
101 102 2.186160 TTTGGTGAGTGTGGCAGCG 61.186 57.895 0.00 0.00 36.60 5.18
102 103 2.601194 TTTGGTGAGTGTGGCAGCGA 62.601 55.000 0.00 0.00 36.60 4.93
103 104 3.044305 GGTGAGTGTGGCAGCGAC 61.044 66.667 0.00 0.00 0.00 5.19
104 105 3.044305 GTGAGTGTGGCAGCGACC 61.044 66.667 4.94 0.00 0.00 4.79
105 106 3.545574 TGAGTGTGGCAGCGACCA 61.546 61.111 4.94 0.00 37.38 4.02
106 107 2.740055 GAGTGTGGCAGCGACCAG 60.740 66.667 4.94 0.00 41.46 4.00
147 148 4.080356 GCATCCATACTTCCATAGCCCATA 60.080 45.833 0.00 0.00 0.00 2.74
148 149 5.678583 CATCCATACTTCCATAGCCCATAG 58.321 45.833 0.00 0.00 0.00 2.23
149 150 4.104086 TCCATACTTCCATAGCCCATAGG 58.896 47.826 0.00 0.00 0.00 2.57
150 151 3.846588 CCATACTTCCATAGCCCATAGGT 59.153 47.826 0.00 0.00 34.57 3.08
152 153 2.776665 ACTTCCATAGCCCATAGGTGT 58.223 47.619 0.00 0.00 34.57 4.16
153 154 2.439507 ACTTCCATAGCCCATAGGTGTG 59.560 50.000 0.00 0.00 35.08 3.82
154 155 2.487746 TCCATAGCCCATAGGTGTGA 57.512 50.000 0.00 0.00 37.27 3.58
155 156 2.329267 TCCATAGCCCATAGGTGTGAG 58.671 52.381 0.00 0.00 37.27 3.51
157 158 2.224378 CCATAGCCCATAGGTGTGAGTG 60.224 54.545 0.00 0.00 37.27 3.51
158 159 2.543037 TAGCCCATAGGTGTGAGTGA 57.457 50.000 0.00 0.00 34.57 3.41
159 160 1.198713 AGCCCATAGGTGTGAGTGAG 58.801 55.000 0.00 0.00 34.57 3.51
160 161 0.179000 GCCCATAGGTGTGAGTGAGG 59.821 60.000 0.00 0.00 34.57 3.86
161 162 0.833287 CCCATAGGTGTGAGTGAGGG 59.167 60.000 0.00 0.00 0.00 4.30
165 166 0.041238 TAGGTGTGAGTGAGGGGAGG 59.959 60.000 0.00 0.00 0.00 4.30
203 205 5.006386 TCTCATTTCTCTTCCTCTTTTGCC 58.994 41.667 0.00 0.00 0.00 4.52
210 212 1.002544 CTTCCTCTTTTGCCTCCTCGT 59.997 52.381 0.00 0.00 0.00 4.18
211 213 0.608640 TCCTCTTTTGCCTCCTCGTC 59.391 55.000 0.00 0.00 0.00 4.20
305 334 2.351336 CTAAATCTCGCCTCCGCCGT 62.351 60.000 0.00 0.00 0.00 5.68
346 375 2.409948 AAGATTCTCCCGCTCCAAAG 57.590 50.000 0.00 0.00 0.00 2.77
364 393 1.753078 GTCCAAATCCCCCGCTTCC 60.753 63.158 0.00 0.00 0.00 3.46
367 396 1.453928 CAAATCCCCCGCTTCCCTC 60.454 63.158 0.00 0.00 0.00 4.30
391 448 2.099062 CTCGTGCGCAAATCTGGC 59.901 61.111 14.00 0.00 0.00 4.85
480 541 2.362120 GCCCATCTGGTGCTTGCT 60.362 61.111 0.00 0.00 36.04 3.91
481 542 1.980772 GCCCATCTGGTGCTTGCTT 60.981 57.895 0.00 0.00 36.04 3.91
482 543 1.888018 CCCATCTGGTGCTTGCTTG 59.112 57.895 0.00 0.00 0.00 4.01
483 544 0.896940 CCCATCTGGTGCTTGCTTGT 60.897 55.000 0.00 0.00 0.00 3.16
540 601 2.741759 TCTTGCATCAGTTCGCTACA 57.258 45.000 0.00 0.00 0.00 2.74
542 603 2.995939 TCTTGCATCAGTTCGCTACAAG 59.004 45.455 0.00 0.00 35.51 3.16
546 607 3.812609 TGCATCAGTTCGCTACAAGAAAA 59.187 39.130 0.00 0.00 0.00 2.29
552 621 5.009710 TCAGTTCGCTACAAGAAAAGAGAGA 59.990 40.000 0.00 0.00 0.00 3.10
701 778 0.685785 AGATCGGCTCAAGCTCCAGA 60.686 55.000 1.46 0.00 41.70 3.86
704 781 0.176680 TCGGCTCAAGCTCCAGATTC 59.823 55.000 1.46 0.00 41.70 2.52
705 782 0.813210 CGGCTCAAGCTCCAGATTCC 60.813 60.000 1.46 0.00 41.70 3.01
707 784 0.254178 GCTCAAGCTCCAGATTCCCA 59.746 55.000 0.00 0.00 38.21 4.37
708 785 2.016096 GCTCAAGCTCCAGATTCCCAC 61.016 57.143 0.00 0.00 38.21 4.61
710 787 0.622665 CAAGCTCCAGATTCCCACCT 59.377 55.000 0.00 0.00 0.00 4.00
765 858 4.661222 TCTTTCTTGTGCATGAATACCCA 58.339 39.130 0.00 0.00 0.00 4.51
770 863 0.732571 GTGCATGAATACCCACACCG 59.267 55.000 0.00 0.00 0.00 4.94
784 877 2.069273 CACACCGTCTGATCCAGTTTC 58.931 52.381 0.00 0.00 32.61 2.78
794 887 4.081420 TCTGATCCAGTTTCTGCTTACTCC 60.081 45.833 0.00 0.00 32.61 3.85
826 919 1.880340 CCTCGTGATGCCGCTTCTC 60.880 63.158 7.69 3.52 0.00 2.87
840 933 0.461961 CTTCTCGATCCGGGAAAGCT 59.538 55.000 0.00 0.00 45.88 3.74
843 936 2.897350 CGATCCGGGAAAGCTGCC 60.897 66.667 0.00 0.00 0.00 4.85
849 942 1.589716 CCGGGAAAGCTGCCTCTTTG 61.590 60.000 0.00 0.00 36.50 2.77
850 943 1.588597 GGGAAAGCTGCCTCTTTGC 59.411 57.895 9.69 9.69 41.68 3.68
854 947 0.957362 AAAGCTGCCTCTTTGCTCAC 59.043 50.000 0.00 0.00 35.18 3.51
856 949 1.303155 GCTGCCTCTTTGCTCACCT 60.303 57.895 0.00 0.00 0.00 4.00
867 961 2.103042 GCTCACCTAACTGCAGGCG 61.103 63.158 19.93 5.42 39.53 5.52
938 1038 1.227943 TTGCAGAGCTCCGCAAGTT 60.228 52.632 29.08 0.00 42.93 2.66
950 1050 2.028112 TCCGCAAGTTCAATACTCTGCT 60.028 45.455 0.00 0.00 38.06 4.24
951 1051 3.194755 TCCGCAAGTTCAATACTCTGCTA 59.805 43.478 0.00 0.00 38.06 3.49
952 1052 3.553511 CCGCAAGTTCAATACTCTGCTAG 59.446 47.826 0.00 0.00 38.06 3.42
953 1053 3.553511 CGCAAGTTCAATACTCTGCTAGG 59.446 47.826 0.00 0.00 38.06 3.02
954 1054 3.311048 GCAAGTTCAATACTCTGCTAGGC 59.689 47.826 0.00 0.00 37.63 3.93
955 1055 3.444703 AGTTCAATACTCTGCTAGGCG 57.555 47.619 0.00 0.00 28.23 5.52
956 1056 1.861575 GTTCAATACTCTGCTAGGCGC 59.138 52.381 0.00 0.00 39.77 6.53
957 1057 0.389391 TCAATACTCTGCTAGGCGCC 59.611 55.000 21.89 21.89 38.05 6.53
1407 1507 6.510799 CGATTAAGAAGCTTTATGCCTCTGTG 60.511 42.308 0.00 0.00 41.26 3.66
1442 1542 1.555075 CGAGGACCAAGATGGGAAGAA 59.445 52.381 0.87 0.00 43.37 2.52
1515 1615 3.365969 CGGTTAAGTTGGTTGAATCAGGC 60.366 47.826 0.00 0.00 0.00 4.85
1518 1618 5.222631 GTTAAGTTGGTTGAATCAGGCAAG 58.777 41.667 0.00 0.00 0.00 4.01
1535 1635 1.537202 CAAGAAGGTGCACAGTAAGGC 59.463 52.381 20.43 0.00 0.00 4.35
1543 1643 1.082690 GCACAGTAAGGCTTCAGCTC 58.917 55.000 1.30 0.00 41.70 4.09
1576 1676 0.976641 ATCAGCGTCTCCAACCAAGA 59.023 50.000 0.00 0.00 0.00 3.02
1644 1744 1.884926 GGAGGCAAGCGAAGATCCG 60.885 63.158 0.00 0.00 0.00 4.18
1645 1745 1.141881 GAGGCAAGCGAAGATCCGA 59.858 57.895 0.00 0.00 0.00 4.55
1650 1750 0.737367 CAAGCGAAGATCCGACTGCA 60.737 55.000 0.00 0.00 0.00 4.41
1701 1801 6.069381 AGGGTAAATCTCCAAAAGCATCTAGT 60.069 38.462 0.00 0.00 0.00 2.57
1719 1819 2.357517 CCGCGAGCTGTTCCAGTT 60.358 61.111 8.23 0.00 33.43 3.16
1731 1831 2.046892 CCAGTTGGAGGCTCACGG 60.047 66.667 17.69 7.46 37.39 4.94
1776 1876 6.293790 CCTCCACTAAAAAGAAGGTTAAACCG 60.294 42.308 0.00 0.00 44.90 4.44
1806 1906 2.742372 GCGGTGGCGTCACAGAAT 60.742 61.111 24.49 0.00 45.32 2.40
1812 1912 1.806542 GTGGCGTCACAGAATCATTGT 59.193 47.619 16.80 0.00 43.13 2.71
1836 1936 2.514803 CCAAAAGGTTCCGGTTCTCAT 58.485 47.619 0.00 0.00 0.00 2.90
1838 1938 3.439129 CCAAAAGGTTCCGGTTCTCATAC 59.561 47.826 0.00 0.00 0.00 2.39
1851 1951 5.062308 CGGTTCTCATACTAAGAAGCAACAC 59.938 44.000 13.50 0.00 46.54 3.32
1859 1959 3.056328 GAAGCAACACGAGGCCCC 61.056 66.667 0.00 0.00 0.00 5.80
1892 1992 1.067516 CAAAACTCCAGCACCAACCAG 59.932 52.381 0.00 0.00 0.00 4.00
1902 2002 0.468029 CACCAACCAGCAAGAAGGGT 60.468 55.000 0.00 0.00 36.19 4.34
1923 2023 0.319727 CTGATGATGGCTCTCTCGGC 60.320 60.000 0.00 0.00 0.00 5.54
2052 2152 0.457851 AGAGCAGCATCGGTGACTAC 59.542 55.000 0.00 0.00 32.22 2.73
2154 2254 0.749454 GATGGGAAGCCATGAAGCGT 60.749 55.000 0.00 0.00 38.01 5.07
2178 2278 0.392998 CGATCCAACAAGGGACCCTG 60.393 60.000 15.76 11.04 40.44 4.45
2253 2353 2.371841 TGTGTATCTGGCTGAGTTGGTT 59.628 45.455 0.00 0.00 0.00 3.67
2334 2434 0.990374 AGATGCTGAGGGCTCAAACT 59.010 50.000 0.00 0.00 39.39 2.66
2533 2633 1.069296 CAGCCGTGGTGTTTATGTGTG 60.069 52.381 0.00 0.00 0.00 3.82
2546 2646 2.498807 ATGTGTGATCTCATCGACCG 57.501 50.000 0.02 0.00 0.00 4.79
2548 2648 1.132453 TGTGTGATCTCATCGACCGAC 59.868 52.381 0.02 0.00 0.00 4.79
2775 2875 3.262420 CTGAGGTGTTCAGTTAATCCCG 58.738 50.000 0.00 0.00 46.77 5.14
2936 3036 1.913762 ACCTTCCAGGACACGGAGG 60.914 63.158 2.83 2.83 37.67 4.30
2990 3090 2.126424 GTCGTCGAGCCCACTGAC 60.126 66.667 0.00 0.00 0.00 3.51
3131 3231 0.396435 ACGGCAAGACACCATTCAGA 59.604 50.000 0.00 0.00 0.00 3.27
3146 3246 0.615331 TCAGAGGACCTGGCAATGAC 59.385 55.000 0.00 0.00 43.12 3.06
3532 3632 5.408604 ACGTTGTGTTCTGAAGAATATCCAC 59.591 40.000 0.00 1.04 36.33 4.02
3571 3671 0.323957 GTAGTCCCACAGTTCCCCAC 59.676 60.000 0.00 0.00 0.00 4.61
3602 3702 3.118811 CCCCTGCAGTTTTTCTGTTGAAA 60.119 43.478 13.81 0.00 45.23 2.69
3742 3878 3.826637 GCAAGCAATTGCATCTGGT 57.173 47.368 30.89 7.52 46.60 4.00
3743 3879 2.088950 GCAAGCAATTGCATCTGGTT 57.911 45.000 30.89 13.37 46.60 3.67
3745 3881 1.730064 CAAGCAATTGCATCTGGTTGC 59.270 47.619 30.89 15.93 42.21 4.17
3752 3888 3.484524 GCATCTGGTTGCAGTTGTG 57.515 52.632 0.00 0.00 42.31 3.33
3782 3988 1.948104 TGCAGTAGTCGTTGTTGCTT 58.052 45.000 0.00 0.00 35.85 3.91
3787 3993 4.434330 GCAGTAGTCGTTGTTGCTTGATAC 60.434 45.833 0.00 0.00 0.00 2.24
3788 3994 4.684242 CAGTAGTCGTTGTTGCTTGATACA 59.316 41.667 0.00 0.00 0.00 2.29
3789 3995 4.923871 AGTAGTCGTTGTTGCTTGATACAG 59.076 41.667 0.00 0.00 0.00 2.74
3790 3996 3.728845 AGTCGTTGTTGCTTGATACAGT 58.271 40.909 0.00 0.00 0.00 3.55
3791 3997 4.878439 AGTCGTTGTTGCTTGATACAGTA 58.122 39.130 0.00 0.00 0.00 2.74
3792 3998 5.479306 AGTCGTTGTTGCTTGATACAGTAT 58.521 37.500 0.00 0.00 0.00 2.12
3831 4037 8.095169 ACTCAAGTAAGGTCCAGTAATAAGTTG 58.905 37.037 0.00 0.00 0.00 3.16
3902 4109 5.181748 AGGATTTAGAAGTCATGTGTCTGC 58.818 41.667 0.00 0.00 0.00 4.26
3938 4145 5.906113 ATTATGTTATGGGTTTGCGTTGA 57.094 34.783 0.00 0.00 0.00 3.18
3946 4153 1.349234 GGTTTGCGTTGATGAATGCC 58.651 50.000 6.65 0.00 42.60 4.40
3986 4193 7.322664 AGTTGCTTGGATGTAACCATTTTATG 58.677 34.615 0.00 0.00 39.82 1.90
4023 4233 2.838386 GCATAACTGTGCATCTGTGG 57.162 50.000 0.00 0.00 44.43 4.17
4026 4236 3.689161 GCATAACTGTGCATCTGTGGTAA 59.311 43.478 0.00 0.00 44.43 2.85
4033 4243 4.397420 TGTGCATCTGTGGTAAAGTGAAT 58.603 39.130 0.00 0.00 0.00 2.57
4034 4244 4.216042 TGTGCATCTGTGGTAAAGTGAATG 59.784 41.667 0.00 0.00 0.00 2.67
4035 4245 3.191162 TGCATCTGTGGTAAAGTGAATGC 59.809 43.478 0.00 0.00 0.00 3.56
4036 4246 3.441572 GCATCTGTGGTAAAGTGAATGCT 59.558 43.478 0.00 0.00 0.00 3.79
4037 4247 4.673580 GCATCTGTGGTAAAGTGAATGCTG 60.674 45.833 0.00 0.00 0.00 4.41
4092 4303 4.141482 ACCAACCATAAACAGAGTGACAGT 60.141 41.667 0.00 0.00 0.00 3.55
4102 4313 2.799412 CAGAGTGACAGTGTCTCAAAGC 59.201 50.000 23.29 10.91 33.15 3.51
4278 4493 3.423154 CACGCTTCCTGTTCGGGC 61.423 66.667 0.00 0.00 0.00 6.13
4337 4552 3.713858 TCCTCGTCTTCGTTGTTACAA 57.286 42.857 0.00 0.00 38.33 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.479412 CTATGGCTACGCGAGGGAGC 62.479 65.000 15.93 15.48 41.73 4.70
13 14 1.581954 CTATGGCTACGCGAGGGAG 59.418 63.158 15.93 5.35 0.00 4.30
14 15 2.561956 GCTATGGCTACGCGAGGGA 61.562 63.158 15.93 0.00 35.22 4.20
15 16 2.049063 GCTATGGCTACGCGAGGG 60.049 66.667 15.93 2.88 35.22 4.30
16 17 2.049063 GGCTATGGCTACGCGAGG 60.049 66.667 15.93 5.83 38.73 4.63
17 18 0.526211 TATGGCTATGGCTACGCGAG 59.474 55.000 15.93 7.21 38.73 5.03
18 19 0.526211 CTATGGCTATGGCTACGCGA 59.474 55.000 15.93 0.00 38.73 5.87
19 20 1.078759 GCTATGGCTATGGCTACGCG 61.079 60.000 11.26 3.53 37.75 6.01
20 21 0.741221 GGCTATGGCTATGGCTACGC 60.741 60.000 17.60 1.42 40.33 4.42
21 22 0.608130 TGGCTATGGCTATGGCTACG 59.392 55.000 17.60 0.00 40.33 3.51
22 23 4.065321 CTATGGCTATGGCTATGGCTAC 57.935 50.000 17.60 3.24 39.92 3.58
26 27 1.561076 TGGCTATGGCTATGGCTATGG 59.439 52.381 17.60 8.28 39.92 2.74
27 28 3.572632 ATGGCTATGGCTATGGCTATG 57.427 47.619 15.66 1.88 39.80 2.23
28 29 4.970860 CTATGGCTATGGCTATGGCTAT 57.029 45.455 19.55 19.55 42.87 2.97
32 33 1.561076 TGGCTATGGCTATGGCTATGG 59.439 52.381 17.60 8.28 39.92 2.74
33 34 2.502947 TCTGGCTATGGCTATGGCTATG 59.497 50.000 17.60 8.51 39.92 2.23
34 35 2.770802 CTCTGGCTATGGCTATGGCTAT 59.229 50.000 17.60 5.06 40.33 2.97
35 36 2.182827 CTCTGGCTATGGCTATGGCTA 58.817 52.381 17.60 11.19 40.33 3.93
36 37 0.982704 CTCTGGCTATGGCTATGGCT 59.017 55.000 17.60 0.00 40.33 4.75
37 38 0.979665 TCTCTGGCTATGGCTATGGC 59.020 55.000 10.06 10.06 39.80 4.40
38 39 2.496871 CTCTCTCTGGCTATGGCTATGG 59.503 54.545 0.00 0.00 38.73 2.74
39 40 3.429492 TCTCTCTCTGGCTATGGCTATG 58.571 50.000 0.00 0.00 38.73 2.23
40 41 3.333381 TCTCTCTCTCTGGCTATGGCTAT 59.667 47.826 0.00 0.00 38.73 2.97
41 42 2.713708 TCTCTCTCTCTGGCTATGGCTA 59.286 50.000 0.00 0.00 38.73 3.93
42 43 1.498576 TCTCTCTCTCTGGCTATGGCT 59.501 52.381 0.00 0.00 38.73 4.75
43 44 1.888512 CTCTCTCTCTCTGGCTATGGC 59.111 57.143 0.00 0.00 37.82 4.40
44 45 3.415212 CTCTCTCTCTCTCTGGCTATGG 58.585 54.545 0.00 0.00 0.00 2.74
45 46 3.415212 CCTCTCTCTCTCTCTGGCTATG 58.585 54.545 0.00 0.00 0.00 2.23
46 47 2.376518 CCCTCTCTCTCTCTCTGGCTAT 59.623 54.545 0.00 0.00 0.00 2.97
47 48 1.774254 CCCTCTCTCTCTCTCTGGCTA 59.226 57.143 0.00 0.00 0.00 3.93
48 49 0.552848 CCCTCTCTCTCTCTCTGGCT 59.447 60.000 0.00 0.00 0.00 4.75
49 50 0.468029 CCCCTCTCTCTCTCTCTGGC 60.468 65.000 0.00 0.00 0.00 4.85
50 51 0.185901 CCCCCTCTCTCTCTCTCTGG 59.814 65.000 0.00 0.00 0.00 3.86
51 52 0.468029 GCCCCCTCTCTCTCTCTCTG 60.468 65.000 0.00 0.00 0.00 3.35
52 53 0.923729 TGCCCCCTCTCTCTCTCTCT 60.924 60.000 0.00 0.00 0.00 3.10
53 54 0.755327 GTGCCCCCTCTCTCTCTCTC 60.755 65.000 0.00 0.00 0.00 3.20
54 55 1.309688 GTGCCCCCTCTCTCTCTCT 59.690 63.158 0.00 0.00 0.00 3.10
55 56 1.760480 GGTGCCCCCTCTCTCTCTC 60.760 68.421 0.00 0.00 0.00 3.20
56 57 2.366570 GGTGCCCCCTCTCTCTCT 59.633 66.667 0.00 0.00 0.00 3.10
57 58 3.151022 CGGTGCCCCCTCTCTCTC 61.151 72.222 0.00 0.00 0.00 3.20
58 59 3.999285 ACGGTGCCCCCTCTCTCT 61.999 66.667 0.00 0.00 0.00 3.10
59 60 3.775654 CACGGTGCCCCCTCTCTC 61.776 72.222 0.00 0.00 0.00 3.20
101 102 2.124693 CCTCTCTCCCTCGCTGGTC 61.125 68.421 0.00 0.00 0.00 4.02
102 103 2.043450 CCTCTCTCCCTCGCTGGT 60.043 66.667 0.00 0.00 0.00 4.00
103 104 1.827789 CTCCTCTCTCCCTCGCTGG 60.828 68.421 0.00 0.00 0.00 4.85
104 105 2.489275 GCTCCTCTCTCCCTCGCTG 61.489 68.421 0.00 0.00 0.00 5.18
105 106 2.123897 GCTCCTCTCTCCCTCGCT 60.124 66.667 0.00 0.00 0.00 4.93
106 107 3.591835 CGCTCCTCTCTCCCTCGC 61.592 72.222 0.00 0.00 0.00 5.03
107 108 2.904866 CCGCTCCTCTCTCCCTCG 60.905 72.222 0.00 0.00 0.00 4.63
108 109 3.223589 GCCGCTCCTCTCTCCCTC 61.224 72.222 0.00 0.00 0.00 4.30
109 110 3.387609 ATGCCGCTCCTCTCTCCCT 62.388 63.158 0.00 0.00 0.00 4.20
110 111 2.841988 ATGCCGCTCCTCTCTCCC 60.842 66.667 0.00 0.00 0.00 4.30
111 112 2.733945 GATGCCGCTCCTCTCTCC 59.266 66.667 0.00 0.00 0.00 3.71
115 116 0.470833 AGTATGGATGCCGCTCCTCT 60.471 55.000 9.42 4.37 36.20 3.69
147 148 1.229336 CCTCCCCTCACTCACACCT 60.229 63.158 0.00 0.00 0.00 4.00
148 149 2.294078 CCCTCCCCTCACTCACACC 61.294 68.421 0.00 0.00 0.00 4.16
149 150 2.294078 CCCCTCCCCTCACTCACAC 61.294 68.421 0.00 0.00 0.00 3.82
150 151 2.122729 CCCCTCCCCTCACTCACA 59.877 66.667 0.00 0.00 0.00 3.58
203 205 1.875813 GCGCACATCTGACGAGGAG 60.876 63.158 0.30 0.00 0.00 3.69
210 212 2.786584 CAATGCGCGCACATCTGA 59.213 55.556 39.05 12.65 0.00 3.27
211 213 2.947621 GCAATGCGCGCACATCTG 60.948 61.111 39.05 28.96 0.00 2.90
346 375 1.753078 GGAAGCGGGGGATTTGGAC 60.753 63.158 0.00 0.00 0.00 4.02
364 393 3.106552 CGCACGAGAGAGAGGAGG 58.893 66.667 0.00 0.00 0.00 4.30
367 396 0.459237 ATTTGCGCACGAGAGAGAGG 60.459 55.000 11.12 0.00 0.00 3.69
480 541 3.924114 TTGAGGGACAAGAAGACACAA 57.076 42.857 0.00 0.00 34.20 3.33
508 569 2.396590 TGCAAGATCCGTAAACCTCC 57.603 50.000 0.00 0.00 0.00 4.30
540 601 4.446455 GGTGGGGTTTCTCTCTCTTTTCTT 60.446 45.833 0.00 0.00 0.00 2.52
542 603 3.073209 AGGTGGGGTTTCTCTCTCTTTTC 59.927 47.826 0.00 0.00 0.00 2.29
546 607 1.150135 TGAGGTGGGGTTTCTCTCTCT 59.850 52.381 0.00 0.00 0.00 3.10
552 621 1.359168 GTAGGTGAGGTGGGGTTTCT 58.641 55.000 0.00 0.00 0.00 2.52
611 680 9.423061 CCACCCATAGTTAAAATTTGAAGAAAG 57.577 33.333 0.00 0.00 0.00 2.62
615 686 6.439058 TCCCCACCCATAGTTAAAATTTGAAG 59.561 38.462 0.00 0.00 0.00 3.02
631 702 2.051050 TAGTCACCCTTCCCCACCCA 62.051 60.000 0.00 0.00 0.00 4.51
727 815 6.775629 ACAAGAAAGAACCTTATTGGCACTAA 59.224 34.615 0.00 0.00 40.22 2.24
765 858 1.971357 AGAAACTGGATCAGACGGTGT 59.029 47.619 1.59 0.00 35.18 4.16
770 863 4.826556 AGTAAGCAGAAACTGGATCAGAC 58.173 43.478 1.59 0.00 35.18 3.51
805 898 4.827087 AGCGGCATCACGAGGCAG 62.827 66.667 6.00 2.64 40.32 4.85
806 899 4.393155 AAGCGGCATCACGAGGCA 62.393 61.111 6.00 0.00 40.32 4.75
807 900 3.567797 GAAGCGGCATCACGAGGC 61.568 66.667 1.45 0.00 37.39 4.70
808 901 1.880340 GAGAAGCGGCATCACGAGG 60.880 63.158 8.03 0.00 35.47 4.63
826 919 2.897350 GGCAGCTTTCCCGGATCG 60.897 66.667 0.73 0.00 0.00 3.69
840 933 1.699634 AGTTAGGTGAGCAAAGAGGCA 59.300 47.619 0.00 0.00 35.83 4.75
843 936 2.740981 CTGCAGTTAGGTGAGCAAAGAG 59.259 50.000 5.25 0.00 36.44 2.85
849 942 3.896479 GCCTGCAGTTAGGTGAGC 58.104 61.111 13.81 1.97 40.11 4.26
854 947 2.359850 TTGGCGCCTGCAGTTAGG 60.360 61.111 29.70 0.00 45.35 2.69
856 949 3.047280 CGTTGGCGCCTGCAGTTA 61.047 61.111 29.70 1.01 45.35 2.24
867 961 1.804748 CTTCAAGTTAGGACCGTTGGC 59.195 52.381 0.00 0.00 0.00 4.52
950 1050 2.521479 CTCCCTCCTAGGCGCCTA 59.479 66.667 33.24 33.24 32.73 3.93
953 1053 2.330924 AAATGCTCCCTCCTAGGCGC 62.331 60.000 2.96 0.00 32.73 6.53
954 1054 0.250081 GAAATGCTCCCTCCTAGGCG 60.250 60.000 2.96 0.00 32.73 5.52
955 1055 1.135960 AGAAATGCTCCCTCCTAGGC 58.864 55.000 2.96 0.00 32.73 3.93
956 1056 1.419387 CCAGAAATGCTCCCTCCTAGG 59.581 57.143 0.82 0.82 34.30 3.02
957 1057 2.368221 CTCCAGAAATGCTCCCTCCTAG 59.632 54.545 0.00 0.00 0.00 3.02
1326 1426 1.288188 TGGACATCCTCTTCATGGCA 58.712 50.000 0.00 0.00 36.82 4.92
1407 1507 0.602905 CCTCGTCTGTTGGAACCACC 60.603 60.000 0.00 0.00 39.54 4.61
1442 1542 0.182775 AACGGCCTTCTCAACCTTGT 59.817 50.000 0.00 0.00 0.00 3.16
1515 1615 1.537202 GCCTTACTGTGCACCTTCTTG 59.463 52.381 15.69 0.04 0.00 3.02
1518 1618 1.807142 GAAGCCTTACTGTGCACCTTC 59.193 52.381 15.69 13.47 0.00 3.46
1563 1663 1.143073 ACCTTGGTCTTGGTTGGAGAC 59.857 52.381 0.00 0.00 42.16 3.36
1596 1696 9.553064 GACTTATTACTGATGACATCTTGGATT 57.447 33.333 16.25 5.69 0.00 3.01
1644 1744 0.673022 CCACAGCTCTTCCTGCAGTC 60.673 60.000 13.81 0.00 36.29 3.51
1645 1745 1.374190 CCACAGCTCTTCCTGCAGT 59.626 57.895 13.81 0.00 36.29 4.40
1650 1750 1.322442 GTTTTGCCACAGCTCTTCCT 58.678 50.000 0.00 0.00 40.80 3.36
1749 1849 7.255381 GGTTTAACCTTCTTTTTAGTGGAGGAC 60.255 40.741 6.92 0.00 34.73 3.85
1791 1891 1.131126 CAATGATTCTGTGACGCCACC 59.869 52.381 0.00 0.00 42.53 4.61
1800 1900 4.021719 CCTTTTGGCTCACAATGATTCTGT 60.022 41.667 0.00 0.00 39.21 3.41
1806 1906 2.627699 GGAACCTTTTGGCTCACAATGA 59.372 45.455 0.00 0.00 45.59 2.57
1812 1912 0.106419 AACCGGAACCTTTTGGCTCA 60.106 50.000 9.46 0.00 45.59 4.26
1815 1915 0.596577 GAGAACCGGAACCTTTTGGC 59.403 55.000 9.46 0.00 45.59 4.52
1818 1918 4.635699 AGTATGAGAACCGGAACCTTTT 57.364 40.909 9.46 0.00 0.00 2.27
1836 1936 2.353406 GGCCTCGTGTTGCTTCTTAGTA 60.353 50.000 0.00 0.00 0.00 1.82
1838 1938 1.079503 GGCCTCGTGTTGCTTCTTAG 58.920 55.000 0.00 0.00 0.00 2.18
1851 1951 2.066393 TTCATCCTGAGGGGCCTCG 61.066 63.158 0.84 0.00 45.48 4.63
1859 1959 3.084786 GGAGTTTTGGGTTCATCCTGAG 58.915 50.000 0.00 0.00 36.25 3.35
1878 1978 1.529010 CTTGCTGGTTGGTGCTGGA 60.529 57.895 0.00 0.00 0.00 3.86
1892 1992 1.404391 CATCATCAGCACCCTTCTTGC 59.596 52.381 0.00 0.00 40.52 4.01
1902 2002 0.388294 CGAGAGAGCCATCATCAGCA 59.612 55.000 0.00 0.00 0.00 4.41
1905 2005 1.744639 GCCGAGAGAGCCATCATCA 59.255 57.895 0.00 0.00 0.00 3.07
1906 2006 1.372748 CGCCGAGAGAGCCATCATC 60.373 63.158 0.00 0.00 0.00 2.92
1907 2007 2.733301 CGCCGAGAGAGCCATCAT 59.267 61.111 0.00 0.00 0.00 2.45
1923 2023 1.135689 CCAAAATCAACTCCTTCGGCG 60.136 52.381 0.00 0.00 0.00 6.46
1989 2089 3.003378 CCTTTTCCTTCGACCTTGACAAC 59.997 47.826 0.00 0.00 0.00 3.32
2052 2152 1.211969 GATGCTGGTGCTTGTGCTG 59.788 57.895 0.00 0.00 40.48 4.41
2154 2254 2.367567 GGTCCCTTGTTGGATCGCTATA 59.632 50.000 0.00 0.00 36.63 1.31
2178 2278 4.764308 AGAAGCTTGAAGTTCTTCAATCCC 59.236 41.667 22.59 15.64 39.85 3.85
2253 2353 0.950836 CAAACATGCAGTCCGAACCA 59.049 50.000 0.00 0.00 0.00 3.67
2334 2434 3.432749 GCATTTGCAGTATCTCCCTCTCA 60.433 47.826 0.00 0.00 41.59 3.27
2533 2633 0.382158 TGCAGTCGGTCGATGAGATC 59.618 55.000 0.00 0.00 0.00 2.75
2546 2646 4.692625 TCAGCTAGAAATTCAAGTGCAGTC 59.307 41.667 0.00 0.00 0.00 3.51
2548 2648 5.618056 TTCAGCTAGAAATTCAAGTGCAG 57.382 39.130 0.00 0.00 32.05 4.41
2597 2697 5.163622 CCTGCAAAGGGACATACAATACTTG 60.164 44.000 0.00 0.00 0.00 3.16
2605 2705 4.379082 CGTAAAACCTGCAAAGGGACATAC 60.379 45.833 0.00 0.00 0.00 2.39
2775 2875 0.801251 GATGAGCACCTCACAAGCAC 59.199 55.000 0.00 0.00 43.63 4.40
3023 3123 1.335132 TGATCTCCGGGGCAAGGTAC 61.335 60.000 0.00 0.00 0.00 3.34
3131 3231 0.400213 TTTCGTCATTGCCAGGTCCT 59.600 50.000 0.00 0.00 0.00 3.85
3146 3246 5.007234 TGAGACCACATTTGTAAGTGTTTCG 59.993 40.000 0.00 0.00 33.99 3.46
3299 3399 1.000396 CAGGCCTTGGAAGAAGGGG 60.000 63.158 0.00 0.00 37.88 4.79
3532 3632 3.015327 ACTACTTCTAGCTACCACGGTG 58.985 50.000 0.00 0.00 0.00 4.94
3571 3671 3.406200 CTGCAGGGGAGTGGGGAG 61.406 72.222 5.57 0.00 0.00 4.30
3602 3702 7.013464 CCGACCTTACTCTACTGATAACTCATT 59.987 40.741 0.00 0.00 0.00 2.57
3616 3716 1.343465 CACAACACCCGACCTTACTCT 59.657 52.381 0.00 0.00 0.00 3.24
3782 3988 8.975663 AGTTACTACTGCTACATACTGTATCA 57.024 34.615 0.00 0.00 30.30 2.15
3787 3993 7.763356 ACTTGAGTTACTACTGCTACATACTG 58.237 38.462 0.00 0.00 33.84 2.74
3788 3994 7.941431 ACTTGAGTTACTACTGCTACATACT 57.059 36.000 0.00 0.00 33.84 2.12
3789 3995 9.719279 CTTACTTGAGTTACTACTGCTACATAC 57.281 37.037 0.00 0.00 33.84 2.39
3790 3996 8.900781 CCTTACTTGAGTTACTACTGCTACATA 58.099 37.037 0.00 0.00 33.84 2.29
3791 3997 7.396623 ACCTTACTTGAGTTACTACTGCTACAT 59.603 37.037 0.00 0.00 33.84 2.29
3792 3998 6.718454 ACCTTACTTGAGTTACTACTGCTACA 59.282 38.462 0.00 0.00 33.84 2.74
3796 4002 5.047519 TGGACCTTACTTGAGTTACTACTGC 60.048 44.000 0.00 0.00 33.84 4.40
3797 4003 6.208994 ACTGGACCTTACTTGAGTTACTACTG 59.791 42.308 0.00 0.00 33.84 2.74
3798 4004 6.313324 ACTGGACCTTACTTGAGTTACTACT 58.687 40.000 0.00 0.00 37.31 2.57
3799 4005 6.587206 ACTGGACCTTACTTGAGTTACTAC 57.413 41.667 0.00 0.00 0.00 2.73
3800 4006 8.890410 ATTACTGGACCTTACTTGAGTTACTA 57.110 34.615 0.00 0.00 0.00 1.82
3801 4007 7.793948 ATTACTGGACCTTACTTGAGTTACT 57.206 36.000 0.00 0.00 0.00 2.24
3802 4008 9.583765 CTTATTACTGGACCTTACTTGAGTTAC 57.416 37.037 0.00 0.00 0.00 2.50
3803 4009 9.317827 ACTTATTACTGGACCTTACTTGAGTTA 57.682 33.333 0.00 0.00 0.00 2.24
3804 4010 8.203681 ACTTATTACTGGACCTTACTTGAGTT 57.796 34.615 0.00 0.00 0.00 3.01
3805 4011 7.793948 ACTTATTACTGGACCTTACTTGAGT 57.206 36.000 0.00 0.00 0.00 3.41
3902 4109 4.963276 AACATAATTGTGATGTCCGTGG 57.037 40.909 9.40 0.00 36.50 4.94
3910 4117 6.127479 ACGCAAACCCATAACATAATTGTGAT 60.127 34.615 9.40 0.00 35.83 3.06
3938 4145 1.143481 TGATGTCCCATCGGCATTCAT 59.857 47.619 0.25 0.00 0.00 2.57
3946 4153 2.159043 AGCAACTACTGATGTCCCATCG 60.159 50.000 0.25 0.00 0.00 3.84
3962 4169 6.534793 CCATAAAATGGTTACATCCAAGCAAC 59.465 38.462 0.00 0.00 45.54 4.17
3986 4193 1.215647 CTACTCACCGGTCAGCACC 59.784 63.158 4.93 0.00 39.69 5.01
4023 4233 3.558505 CACAGCACAGCATTCACTTTAC 58.441 45.455 0.00 0.00 0.00 2.01
4026 4236 0.313043 GCACAGCACAGCATTCACTT 59.687 50.000 0.00 0.00 0.00 3.16
4033 4243 4.914388 TCGCAGCACAGCACAGCA 62.914 61.111 0.00 0.00 0.00 4.41
4034 4244 2.666715 TTTTCGCAGCACAGCACAGC 62.667 55.000 0.00 0.00 0.00 4.40
4035 4245 0.931662 GTTTTCGCAGCACAGCACAG 60.932 55.000 0.00 0.00 0.00 3.66
4036 4246 1.063972 GTTTTCGCAGCACAGCACA 59.936 52.632 0.00 0.00 0.00 4.57
4037 4247 1.658409 GGTTTTCGCAGCACAGCAC 60.658 57.895 0.00 0.00 0.00 4.40
4085 4296 0.861837 CCGCTTTGAGACACTGTCAC 59.138 55.000 11.80 5.84 34.60 3.67
4092 4303 0.881118 GAAATGCCCGCTTTGAGACA 59.119 50.000 0.00 0.00 0.00 3.41
4102 4313 2.093447 ACTTGTCTAGAGGAAATGCCCG 60.093 50.000 0.00 0.00 37.37 6.13
4278 4493 2.572290 TCTCATGGCTGATTCATGCAG 58.428 47.619 0.00 0.00 41.11 4.41
4337 4552 9.286170 GAAAACCCTGAAAAGTCTAGAATACTT 57.714 33.333 0.00 0.00 38.82 2.24


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

AutoCloner maintained by Alex Coulton.