Multiple sequence alignment - TraesCS3B01G389000

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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 TraesCS3B01G389000 chr3B 100.000 2627 0 0 1 2627 612105329 612102703 0.000000e+00 4852.0
1 TraesCS3B01G389000 chr3B 87.967 615 60 7 998 1602 612360319 612359709 0.000000e+00 713.0
2 TraesCS3B01G389000 chr3B 81.562 781 98 30 846 1607 612296196 612295443 1.040000e-168 603.0
3 TraesCS3B01G389000 chr3B 73.842 367 38 30 566 907 612360768 612360435 2.780000e-15 93.5
4 TraesCS3B01G389000 chr3D 91.357 1643 81 25 426 2037 461314295 461312683 0.000000e+00 2191.0
5 TraesCS3B01G389000 chr3D 88.508 1166 79 25 449 1590 461373617 461372483 0.000000e+00 1360.0
6 TraesCS3B01G389000 chr3D 86.145 729 63 17 1932 2627 461312731 461312008 0.000000e+00 752.0
7 TraesCS3B01G389000 chr3D 82.684 924 82 47 549 1434 461427268 461426385 0.000000e+00 749.0
8 TraesCS3B01G389000 chr3D 87.500 616 61 8 998 1602 461589540 461588930 0.000000e+00 697.0
9 TraesCS3B01G389000 chr3D 90.476 273 19 3 106 373 461381165 461380895 1.160000e-93 353.0
10 TraesCS3B01G389000 chr3D 88.213 263 20 5 123 375 461314724 461314463 1.180000e-78 303.0
11 TraesCS3B01G389000 chr3D 91.304 92 7 1 19 109 468698801 468698892 9.870000e-25 124.0
12 TraesCS3B01G389000 chr3D 76.389 216 21 17 713 907 461589865 461589659 3.600000e-14 89.8
13 TraesCS3B01G389000 chr3A 88.781 1854 118 48 123 1934 603814964 603813159 0.000000e+00 2189.0
14 TraesCS3B01G389000 chr3A 87.414 723 60 15 1931 2627 603812814 603812097 0.000000e+00 802.0
15 TraesCS3B01G389000 chr3A 83.660 765 82 27 854 1602 603847479 603846742 0.000000e+00 680.0
16 TraesCS3B01G389000 chr3A 87.154 615 58 9 997 1602 603895863 603895261 0.000000e+00 678.0
17 TraesCS3B01G389000 chr3A 82.407 216 15 13 566 771 603847754 603847552 1.620000e-37 167.0
18 TraesCS3B01G389000 chr3A 75.814 215 23 18 714 907 603896177 603895971 6.030000e-12 82.4
19 TraesCS3B01G389000 chr5B 95.122 82 4 0 35 116 215614008 215614089 2.120000e-26 130.0
20 TraesCS3B01G389000 chr5B 93.103 87 5 1 24 109 517190270 517190356 2.740000e-25 126.0
21 TraesCS3B01G389000 chr5B 92.135 89 6 1 20 107 254349202 254349114 9.870000e-25 124.0
22 TraesCS3B01G389000 chr7B 92.308 91 6 1 20 109 572078113 572078023 7.630000e-26 128.0
23 TraesCS3B01G389000 chr6D 92.222 90 6 1 20 108 62726413 62726324 2.740000e-25 126.0
24 TraesCS3B01G389000 chr6D 92.308 52 4 0 2471 2522 422072117 422072066 1.010000e-09 75.0
25 TraesCS3B01G389000 chr5A 92.222 90 6 1 20 108 547595322 547595411 2.740000e-25 126.0
26 TraesCS3B01G389000 chrUn 91.209 91 7 1 20 109 126990501 126990411 3.550000e-24 122.0
27 TraesCS3B01G389000 chrUn 91.209 91 7 1 20 109 239444608 239444698 3.550000e-24 122.0
28 TraesCS3B01G389000 chr4A 86.239 109 13 1 1315 1421 113505708 113505600 1.650000e-22 117.0
29 TraesCS3B01G389000 chr2D 100.000 42 0 0 2481 2522 164389777 164389736 7.800000e-11 78.7
30 TraesCS3B01G389000 chr1B 94.118 51 3 0 2472 2522 394410664 394410714 7.800000e-11 78.7
31 TraesCS3B01G389000 chr4D 90.164 61 2 4 2481 2541 73385879 73385823 2.800000e-10 76.8
32 TraesCS3B01G389000 chr1D 90.164 61 2 4 2481 2541 20971933 20971877 2.800000e-10 76.8
33 TraesCS3B01G389000 chr4B 90.385 52 5 0 2481 2532 255392202 255392151 4.690000e-08 69.4
34 TraesCS3B01G389000 chr2B 88.136 59 5 2 2464 2521 451828165 451828108 4.690000e-08 69.4


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 TraesCS3B01G389000 chr3B 612102703 612105329 2626 True 4852.00 4852 100.000000 1 2627 1 chr3B.!!$R1 2626
1 TraesCS3B01G389000 chr3B 612295443 612296196 753 True 603.00 603 81.562000 846 1607 1 chr3B.!!$R2 761
2 TraesCS3B01G389000 chr3B 612359709 612360768 1059 True 403.25 713 80.904500 566 1602 2 chr3B.!!$R3 1036
3 TraesCS3B01G389000 chr3D 461372483 461373617 1134 True 1360.00 1360 88.508000 449 1590 1 chr3D.!!$R1 1141
4 TraesCS3B01G389000 chr3D 461312008 461314724 2716 True 1082.00 2191 88.571667 123 2627 3 chr3D.!!$R4 2504
5 TraesCS3B01G389000 chr3D 461426385 461427268 883 True 749.00 749 82.684000 549 1434 1 chr3D.!!$R3 885
6 TraesCS3B01G389000 chr3D 461588930 461589865 935 True 393.40 697 81.944500 713 1602 2 chr3D.!!$R5 889
7 TraesCS3B01G389000 chr3A 603812097 603814964 2867 True 1495.50 2189 88.097500 123 2627 2 chr3A.!!$R1 2504
8 TraesCS3B01G389000 chr3A 603846742 603847754 1012 True 423.50 680 83.033500 566 1602 2 chr3A.!!$R2 1036
9 TraesCS3B01G389000 chr3A 603895261 603896177 916 True 380.20 678 81.484000 714 1602 2 chr3A.!!$R3 888

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
726 910 0.535102 ACCAAGCGGTCAAACTCCAG 60.535 55.0 0.0 0.0 44.71 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2955 0.109597 GCAAGCAGAATGGGTTGACG 60.11 55.0 9.05 0.0 46.36 4.35 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
18 19 3.798794 CATTGGCATACCCTCGGAA 57.201 52.632 0.00 0.00 33.59 4.30
19 20 2.051334 CATTGGCATACCCTCGGAAA 57.949 50.000 0.00 0.00 33.59 3.13
20 21 2.374184 CATTGGCATACCCTCGGAAAA 58.626 47.619 0.00 0.00 33.59 2.29
21 22 2.588464 TTGGCATACCCTCGGAAAAA 57.412 45.000 0.00 0.00 33.59 1.94
51 52 5.516059 AAAGGACTTTTTAGGGACTAGGG 57.484 43.478 0.00 0.00 44.25 3.53
52 53 4.431158 AGGACTTTTTAGGGACTAGGGA 57.569 45.455 0.00 0.00 44.25 4.20
53 54 4.102598 AGGACTTTTTAGGGACTAGGGAC 58.897 47.826 0.00 0.00 44.25 4.46
54 55 4.102598 GGACTTTTTAGGGACTAGGGACT 58.897 47.826 0.00 0.00 44.25 3.85
55 56 4.535294 GGACTTTTTAGGGACTAGGGACTT 59.465 45.833 0.00 0.00 44.25 3.01
56 57 5.013913 GGACTTTTTAGGGACTAGGGACTTT 59.986 44.000 0.00 0.00 44.25 2.66
57 58 6.466904 GGACTTTTTAGGGACTAGGGACTTTT 60.467 42.308 0.00 0.00 44.25 2.27
58 59 6.919158 ACTTTTTAGGGACTAGGGACTTTTT 58.081 36.000 0.00 0.00 44.25 1.94
59 60 8.049165 ACTTTTTAGGGACTAGGGACTTTTTA 57.951 34.615 0.00 0.00 44.25 1.52
60 61 8.162085 ACTTTTTAGGGACTAGGGACTTTTTAG 58.838 37.037 0.00 0.00 44.25 1.85
61 62 7.637548 TTTTAGGGACTAGGGACTTTTTAGT 57.362 36.000 0.00 0.00 44.25 2.24
62 63 7.637548 TTTAGGGACTAGGGACTTTTTAGTT 57.362 36.000 0.00 0.00 44.25 2.24
63 64 5.500546 AGGGACTAGGGACTTTTTAGTTG 57.499 43.478 0.00 0.00 41.75 3.16
64 65 4.288887 AGGGACTAGGGACTTTTTAGTTGG 59.711 45.833 0.00 0.00 41.75 3.77
65 66 4.567116 GGGACTAGGGACTTTTTAGTTGGG 60.567 50.000 0.00 0.00 41.75 4.12
66 67 4.287845 GGACTAGGGACTTTTTAGTTGGGA 59.712 45.833 0.00 0.00 41.75 4.37
67 68 5.045066 GGACTAGGGACTTTTTAGTTGGGAT 60.045 44.000 0.00 0.00 41.75 3.85
68 69 6.464530 ACTAGGGACTTTTTAGTTGGGATT 57.535 37.500 0.00 0.00 41.75 3.01
69 70 7.311486 GGACTAGGGACTTTTTAGTTGGGATTA 60.311 40.741 0.00 0.00 41.75 1.75
70 71 7.631007 ACTAGGGACTTTTTAGTTGGGATTAG 58.369 38.462 0.00 0.00 41.75 1.73
71 72 6.713731 AGGGACTTTTTAGTTGGGATTAGA 57.286 37.500 0.00 0.00 27.25 2.10
72 73 7.098845 AGGGACTTTTTAGTTGGGATTAGAA 57.901 36.000 0.00 0.00 27.25 2.10
73 74 7.532199 AGGGACTTTTTAGTTGGGATTAGAAA 58.468 34.615 0.00 0.00 27.25 2.52
74 75 8.008332 AGGGACTTTTTAGTTGGGATTAGAAAA 58.992 33.333 0.00 0.00 27.25 2.29
75 76 8.644216 GGGACTTTTTAGTTGGGATTAGAAAAA 58.356 33.333 0.00 0.00 0.00 1.94
76 77 9.692749 GGACTTTTTAGTTGGGATTAGAAAAAG 57.307 33.333 13.35 13.35 44.04 2.27
85 86 8.857098 AGTTGGGATTAGAAAAAGTTTTAGGAC 58.143 33.333 0.24 0.00 0.00 3.85
86 87 8.857098 GTTGGGATTAGAAAAAGTTTTAGGACT 58.143 33.333 0.24 2.61 0.00 3.85
87 88 9.429109 TTGGGATTAGAAAAAGTTTTAGGACTT 57.571 29.630 0.24 0.00 41.44 3.01
95 96 9.416284 AGAAAAAGTTTTAGGACTTATGAACCA 57.584 29.630 0.24 0.00 38.86 3.67
98 99 9.811995 AAAAGTTTTAGGACTTATGAACCAAAC 57.188 29.630 0.00 0.00 38.86 2.93
99 100 8.528044 AAGTTTTAGGACTTATGAACCAAACA 57.472 30.769 0.00 0.00 38.06 2.83
100 101 8.166422 AGTTTTAGGACTTATGAACCAAACAG 57.834 34.615 0.00 0.00 0.00 3.16
101 102 7.230712 AGTTTTAGGACTTATGAACCAAACAGG 59.769 37.037 0.00 0.00 45.67 4.00
102 103 4.034285 AGGACTTATGAACCAAACAGGG 57.966 45.455 0.00 0.00 43.89 4.45
103 104 2.492088 GGACTTATGAACCAAACAGGGC 59.508 50.000 0.00 0.00 43.89 5.19
104 105 2.492088 GACTTATGAACCAAACAGGGCC 59.508 50.000 0.00 0.00 43.89 5.80
105 106 2.110011 ACTTATGAACCAAACAGGGCCT 59.890 45.455 0.00 0.00 43.89 5.19
106 107 3.332485 ACTTATGAACCAAACAGGGCCTA 59.668 43.478 5.28 0.00 43.89 3.93
107 108 2.990740 ATGAACCAAACAGGGCCTAA 57.009 45.000 5.28 0.00 43.89 2.69
108 109 2.286365 TGAACCAAACAGGGCCTAAG 57.714 50.000 5.28 0.00 43.89 2.18
109 110 0.888619 GAACCAAACAGGGCCTAAGC 59.111 55.000 5.28 0.00 43.89 3.09
160 161 8.095452 AGTGGTATGAATTTCTAGATTCCACT 57.905 34.615 15.14 15.14 35.61 4.00
177 178 1.302033 CTGAGGCAACAACGGAGCT 60.302 57.895 0.00 0.00 41.41 4.09
178 179 1.294659 CTGAGGCAACAACGGAGCTC 61.295 60.000 4.71 4.71 41.41 4.09
179 180 2.357517 AGGCAACAACGGAGCTCG 60.358 61.111 7.83 5.83 42.43 5.03
219 224 1.692296 GCCGCTCGTTCTAGATGATC 58.308 55.000 0.00 0.00 0.00 2.92
249 254 3.130516 AGCTATTCGTGTCGATCTCCAAA 59.869 43.478 0.00 0.00 35.23 3.28
275 285 2.608546 CGTTCGCCCGGTCAATAAATTA 59.391 45.455 0.00 0.00 0.00 1.40
319 332 0.963962 TACACCAACCGGAGAGTGTC 59.036 55.000 24.20 0.00 42.25 3.67
346 359 3.056328 GAAACCCGTGCAGAGGCC 61.056 66.667 0.00 0.00 40.13 5.19
347 360 4.660938 AAACCCGTGCAGAGGCCC 62.661 66.667 0.00 0.00 40.13 5.80
395 408 3.868661 GTGTATAACACGCACCATGATGA 59.131 43.478 0.00 0.00 39.53 2.92
397 410 5.007626 GTGTATAACACGCACCATGATGAAT 59.992 40.000 0.00 0.00 39.53 2.57
399 412 2.112380 ACACGCACCATGATGAATGA 57.888 45.000 0.00 0.00 38.72 2.57
400 413 2.435422 ACACGCACCATGATGAATGAA 58.565 42.857 0.00 0.00 38.72 2.57
405 418 4.340097 ACGCACCATGATGAATGAATGAAT 59.660 37.500 0.00 0.00 38.72 2.57
408 421 6.277605 GCACCATGATGAATGAATGAATCAA 58.722 36.000 0.00 0.00 42.54 2.57
411 424 7.979537 CACCATGATGAATGAATGAATCAAAGT 59.020 33.333 0.00 0.00 42.54 2.66
414 427 9.237846 CATGATGAATGAATGAATCAAAGTCAG 57.762 33.333 0.00 0.00 42.54 3.51
416 429 9.016438 TGATGAATGAATGAATCAAAGTCAGAA 57.984 29.630 0.00 0.00 42.54 3.02
418 431 7.300320 TGAATGAATGAATCAAAGTCAGAACG 58.700 34.615 0.00 0.00 42.54 3.95
419 432 5.034554 TGAATGAATCAAAGTCAGAACGC 57.965 39.130 0.00 0.00 34.30 4.84
420 433 4.083324 TGAATGAATCAAAGTCAGAACGCC 60.083 41.667 0.00 0.00 34.30 5.68
423 436 1.148310 ATCAAAGTCAGAACGCCACG 58.852 50.000 0.00 0.00 0.00 4.94
447 580 4.748679 ACACGCTACGGACGTCGC 62.749 66.667 9.92 10.78 42.96 5.19
514 651 3.563808 TGCTGTTTACGATTCTGTGCTTT 59.436 39.130 0.00 0.00 0.00 3.51
563 711 3.458163 CAGCCGGCCGGTCTAGAA 61.458 66.667 42.53 0.00 37.65 2.10
564 712 3.148279 AGCCGGCCGGTCTAGAAG 61.148 66.667 42.53 17.60 37.65 2.85
655 817 4.318332 TGACAAGATTGAACGCAGATTCT 58.682 39.130 0.00 0.00 0.00 2.40
710 894 7.863722 AGACTAGTAACTAATCTCTCTCACCA 58.136 38.462 0.00 0.00 0.00 4.17
723 907 0.868406 CTCACCAAGCGGTCAAACTC 59.132 55.000 0.00 0.00 44.71 3.01
725 909 0.817634 CACCAAGCGGTCAAACTCCA 60.818 55.000 0.00 0.00 44.71 3.86
726 910 0.535102 ACCAAGCGGTCAAACTCCAG 60.535 55.000 0.00 0.00 44.71 3.86
781 1017 0.929824 CAACAAACACTTGCGAGCCG 60.930 55.000 0.00 0.00 35.84 5.52
841 1091 1.854280 ACCAAACCCCAACCTCAAGTA 59.146 47.619 0.00 0.00 0.00 2.24
846 1097 1.745489 CCCAACCTCAAGTAGCGCC 60.745 63.158 2.29 0.00 0.00 6.53
847 1098 1.745489 CCAACCTCAAGTAGCGCCC 60.745 63.158 2.29 0.00 0.00 6.13
993 1304 3.013219 CGAGAGATCAAGTCCAGACTCA 58.987 50.000 0.00 0.00 41.58 3.41
1098 1435 3.676216 CAGCACCAGCAGCATCAA 58.324 55.556 0.00 0.00 45.49 2.57
1099 1436 1.211969 CAGCACCAGCAGCATCAAC 59.788 57.895 0.00 0.00 45.49 3.18
1100 1437 1.228337 AGCACCAGCAGCATCAACA 60.228 52.632 0.00 0.00 45.49 3.33
1239 1576 2.328099 GCGACCCAGGCTTCAACAG 61.328 63.158 0.00 0.00 0.00 3.16
1249 1586 1.597854 CTTCAACAGCACCCGCAGA 60.598 57.895 0.00 0.00 42.27 4.26
1250 1587 1.153066 TTCAACAGCACCCGCAGAA 60.153 52.632 0.00 0.00 42.27 3.02
1479 1837 2.501610 GAGCCCGAGATGGTGGTC 59.498 66.667 0.00 0.00 35.15 4.02
1633 1999 1.767681 ACTGCTCCCTCTGATCATTCC 59.232 52.381 0.00 0.00 0.00 3.01
1643 2009 3.894257 GATCATTCCGATCGCTGGA 57.106 52.632 10.32 4.54 41.24 3.86
1644 2010 1.423395 GATCATTCCGATCGCTGGAC 58.577 55.000 10.32 1.81 41.24 4.02
1646 2012 1.143838 CATTCCGATCGCTGGACCA 59.856 57.895 10.32 0.00 34.56 4.02
1648 2014 1.330655 ATTCCGATCGCTGGACCACT 61.331 55.000 10.32 0.00 34.56 4.00
1650 2016 2.105128 CGATCGCTGGACCACTCC 59.895 66.667 0.26 0.00 37.04 3.85
1651 2017 2.710902 CGATCGCTGGACCACTCCA 61.711 63.158 0.26 0.00 45.11 3.86
1652 2018 1.826024 GATCGCTGGACCACTCCAT 59.174 57.895 0.00 0.00 46.18 3.41
1777 2159 5.824624 AGATGTAAATGTTCATAGGCTGGTG 59.175 40.000 0.00 0.00 0.00 4.17
1841 2223 7.488322 TGCATTTCCTTGCTGTAAATAATACC 58.512 34.615 0.00 0.00 43.18 2.73
1877 2259 3.081804 ACTTATGGTCGCCCTTTTGAAG 58.918 45.455 0.00 0.00 0.00 3.02
1882 2264 1.669795 GGTCGCCCTTTTGAAGCATTG 60.670 52.381 0.00 0.00 0.00 2.82
1936 2672 6.427150 GCTGTTCATTTCGAAAAGTAAGTCA 58.573 36.000 15.66 7.32 40.65 3.41
2012 2748 7.285788 CAAGTCAATTTGCATAAAGTTTCTGC 58.714 34.615 16.72 16.72 36.45 4.26
2084 2877 9.611284 TGACAGACATTTCAATTTATTTCTTCG 57.389 29.630 0.00 0.00 0.00 3.79
2111 2906 3.385193 AAAAGACATTTCAAAGCGGGG 57.615 42.857 0.00 0.00 0.00 5.73
2115 2910 2.156098 GACATTTCAAAGCGGGGTACA 58.844 47.619 0.00 0.00 0.00 2.90
2116 2911 2.159382 ACATTTCAAAGCGGGGTACAG 58.841 47.619 0.00 0.00 0.00 2.74
2117 2912 2.159382 CATTTCAAAGCGGGGTACAGT 58.841 47.619 0.00 0.00 0.00 3.55
2118 2913 1.886886 TTTCAAAGCGGGGTACAGTC 58.113 50.000 0.00 0.00 0.00 3.51
2204 3020 8.671921 ACTTCTGTATTGCATTCTTAACAGATG 58.328 33.333 16.08 16.08 41.94 2.90
2228 3047 4.647424 TGAAAACTGAACGCAAGGAAAT 57.353 36.364 0.00 0.00 46.39 2.17
2252 3071 5.560966 AACATTCAACAGTTCAAAGACGT 57.439 34.783 0.00 0.00 0.00 4.34
2263 3082 7.461918 ACAGTTCAAAGACGTTTTCTAACTTC 58.538 34.615 13.02 0.00 32.51 3.01
2287 3106 3.938963 CACCGGCACATCTAAACAAGTAT 59.061 43.478 0.00 0.00 0.00 2.12
2288 3107 5.105269 TCACCGGCACATCTAAACAAGTATA 60.105 40.000 0.00 0.00 0.00 1.47
2290 3109 6.092944 CACCGGCACATCTAAACAAGTATAAA 59.907 38.462 0.00 0.00 0.00 1.40
2291 3110 6.093082 ACCGGCACATCTAAACAAGTATAAAC 59.907 38.462 0.00 0.00 0.00 2.01
2293 3112 7.201696 CCGGCACATCTAAACAAGTATAAACAT 60.202 37.037 0.00 0.00 0.00 2.71
2294 3113 8.822855 CGGCACATCTAAACAAGTATAAACATA 58.177 33.333 0.00 0.00 0.00 2.29
2332 3151 3.525199 AGGTCTAAAGCAGTCCATGGAAT 59.475 43.478 18.20 13.77 35.12 3.01
2338 3157 2.569059 AGCAGTCCATGGAATCATTCG 58.431 47.619 18.20 3.85 0.00 3.34
2355 3174 4.694982 TCATTCGAGCACACATAACATGTT 59.305 37.500 16.68 16.68 42.70 2.71
2370 3189 8.805175 ACATAACATGTTTTCATCATTCAGGAA 58.195 29.630 17.78 0.00 41.63 3.36
2417 3236 3.612860 CGATCAAAGACAAACTCTACCCG 59.387 47.826 0.00 0.00 0.00 5.28
2438 3257 3.201726 CCATTTACAAGGCACGAACTG 57.798 47.619 0.00 0.00 0.00 3.16
2442 3261 1.493772 TACAAGGCACGAACTGAACG 58.506 50.000 0.00 0.00 0.00 3.95
2461 3280 3.858247 ACGAAGTTGGCATAGTCTAACC 58.142 45.455 0.00 0.00 37.78 2.85
2464 3283 4.585879 GAAGTTGGCATAGTCTAACCCAA 58.414 43.478 9.41 9.41 33.47 4.12
2467 3286 5.681639 AGTTGGCATAGTCTAACCCAATAC 58.318 41.667 14.28 6.79 37.82 1.89
2468 3287 5.190925 AGTTGGCATAGTCTAACCCAATACA 59.809 40.000 14.28 0.00 37.82 2.29
2478 3297 6.899075 AGTCTAACCCAATACACATGGTACTA 59.101 38.462 0.00 0.00 36.14 1.82
2479 3298 7.567622 AGTCTAACCCAATACACATGGTACTAT 59.432 37.037 0.00 0.00 36.14 2.12
2523 3342 9.679661 AGATGTTATTACAACCAATATGTGACA 57.320 29.630 0.00 0.00 37.91 3.58
2527 3346 9.162764 GTTATTACAACCAATATGTGACAGAGT 57.837 33.333 0.00 0.00 32.27 3.24
2532 3352 7.903145 ACAACCAATATGTGACAGAGTAGTAA 58.097 34.615 0.00 0.00 0.00 2.24
2605 3427 3.751698 GGTGCTCAAATTAACTTCCTCGT 59.248 43.478 0.00 0.00 0.00 4.18
2606 3428 4.933400 GGTGCTCAAATTAACTTCCTCGTA 59.067 41.667 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.818751 TTTTCCGAGGGTATGCCAAT 57.181 45.000 1.04 0.00 36.17 3.16
2 3 2.588464 TTTTTCCGAGGGTATGCCAA 57.412 45.000 1.04 0.00 36.17 4.52
28 29 5.613973 TCCCTAGTCCCTAAAAAGTCCTTTT 59.386 40.000 0.00 0.00 43.88 2.27
29 30 5.013913 GTCCCTAGTCCCTAAAAAGTCCTTT 59.986 44.000 0.00 0.00 0.00 3.11
30 31 4.535294 GTCCCTAGTCCCTAAAAAGTCCTT 59.465 45.833 0.00 0.00 0.00 3.36
31 32 4.102598 GTCCCTAGTCCCTAAAAAGTCCT 58.897 47.826 0.00 0.00 0.00 3.85
32 33 4.102598 AGTCCCTAGTCCCTAAAAAGTCC 58.897 47.826 0.00 0.00 0.00 3.85
33 34 5.758790 AAGTCCCTAGTCCCTAAAAAGTC 57.241 43.478 0.00 0.00 0.00 3.01
34 35 6.526056 AAAAGTCCCTAGTCCCTAAAAAGT 57.474 37.500 0.00 0.00 0.00 2.66
35 36 8.162085 ACTAAAAAGTCCCTAGTCCCTAAAAAG 58.838 37.037 0.00 0.00 0.00 2.27
36 37 8.049165 ACTAAAAAGTCCCTAGTCCCTAAAAA 57.951 34.615 0.00 0.00 0.00 1.94
37 38 7.637548 ACTAAAAAGTCCCTAGTCCCTAAAA 57.362 36.000 0.00 0.00 0.00 1.52
38 39 7.455891 CAACTAAAAAGTCCCTAGTCCCTAAA 58.544 38.462 0.00 0.00 0.00 1.85
39 40 6.013119 CCAACTAAAAAGTCCCTAGTCCCTAA 60.013 42.308 0.00 0.00 0.00 2.69
40 41 5.486419 CCAACTAAAAAGTCCCTAGTCCCTA 59.514 44.000 0.00 0.00 0.00 3.53
41 42 4.288887 CCAACTAAAAAGTCCCTAGTCCCT 59.711 45.833 0.00 0.00 0.00 4.20
42 43 4.567116 CCCAACTAAAAAGTCCCTAGTCCC 60.567 50.000 0.00 0.00 0.00 4.46
43 44 4.287845 TCCCAACTAAAAAGTCCCTAGTCC 59.712 45.833 0.00 0.00 0.00 3.85
44 45 5.494390 TCCCAACTAAAAAGTCCCTAGTC 57.506 43.478 0.00 0.00 0.00 2.59
45 46 6.464530 AATCCCAACTAAAAAGTCCCTAGT 57.535 37.500 0.00 0.00 0.00 2.57
46 47 7.858498 TCTAATCCCAACTAAAAAGTCCCTAG 58.142 38.462 0.00 0.00 0.00 3.02
47 48 7.817910 TCTAATCCCAACTAAAAAGTCCCTA 57.182 36.000 0.00 0.00 0.00 3.53
48 49 6.713731 TCTAATCCCAACTAAAAAGTCCCT 57.286 37.500 0.00 0.00 0.00 4.20
49 50 7.770366 TTTCTAATCCCAACTAAAAAGTCCC 57.230 36.000 0.00 0.00 0.00 4.46
50 51 9.692749 CTTTTTCTAATCCCAACTAAAAAGTCC 57.307 33.333 0.00 0.00 38.32 3.85
59 60 8.857098 GTCCTAAAACTTTTTCTAATCCCAACT 58.143 33.333 0.00 0.00 0.00 3.16
60 61 8.857098 AGTCCTAAAACTTTTTCTAATCCCAAC 58.143 33.333 0.00 0.00 0.00 3.77
61 62 9.429109 AAGTCCTAAAACTTTTTCTAATCCCAA 57.571 29.630 0.00 0.00 36.02 4.12
69 70 9.416284 TGGTTCATAAGTCCTAAAACTTTTTCT 57.584 29.630 0.00 0.00 40.01 2.52
72 73 9.811995 GTTTGGTTCATAAGTCCTAAAACTTTT 57.188 29.630 0.00 0.00 40.01 2.27
73 74 8.973182 TGTTTGGTTCATAAGTCCTAAAACTTT 58.027 29.630 0.00 0.00 40.01 2.66
74 75 8.528044 TGTTTGGTTCATAAGTCCTAAAACTT 57.472 30.769 0.00 0.00 42.10 2.66
75 76 7.230712 CCTGTTTGGTTCATAAGTCCTAAAACT 59.769 37.037 0.00 0.00 0.00 2.66
76 77 7.368059 CCTGTTTGGTTCATAAGTCCTAAAAC 58.632 38.462 0.00 0.00 0.00 2.43
77 78 6.492087 CCCTGTTTGGTTCATAAGTCCTAAAA 59.508 38.462 0.00 0.00 0.00 1.52
78 79 6.007703 CCCTGTTTGGTTCATAAGTCCTAAA 58.992 40.000 0.00 0.00 0.00 1.85
79 80 5.566469 CCCTGTTTGGTTCATAAGTCCTAA 58.434 41.667 0.00 0.00 0.00 2.69
80 81 4.566907 GCCCTGTTTGGTTCATAAGTCCTA 60.567 45.833 0.00 0.00 0.00 2.94
81 82 3.814316 GCCCTGTTTGGTTCATAAGTCCT 60.814 47.826 0.00 0.00 0.00 3.85
82 83 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
83 84 2.492088 GGCCCTGTTTGGTTCATAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
84 85 2.110011 AGGCCCTGTTTGGTTCATAAGT 59.890 45.455 0.00 0.00 0.00 2.24
85 86 2.807676 AGGCCCTGTTTGGTTCATAAG 58.192 47.619 0.00 0.00 0.00 1.73
86 87 2.990740 AGGCCCTGTTTGGTTCATAA 57.009 45.000 0.00 0.00 0.00 1.90
87 88 3.876156 GCTTAGGCCCTGTTTGGTTCATA 60.876 47.826 0.00 0.00 0.00 2.15
88 89 2.807676 CTTAGGCCCTGTTTGGTTCAT 58.192 47.619 0.00 0.00 0.00 2.57
89 90 1.821666 GCTTAGGCCCTGTTTGGTTCA 60.822 52.381 0.00 0.00 0.00 3.18
90 91 0.888619 GCTTAGGCCCTGTTTGGTTC 59.111 55.000 0.00 0.00 0.00 3.62
91 92 3.051617 GCTTAGGCCCTGTTTGGTT 57.948 52.632 0.00 0.00 0.00 3.67
92 93 4.843624 GCTTAGGCCCTGTTTGGT 57.156 55.556 0.00 0.00 0.00 3.67
102 103 2.986479 CGTCAAACAATTTGGCTTAGGC 59.014 45.455 0.00 0.00 42.88 3.93
103 104 4.215399 TCTCGTCAAACAATTTGGCTTAGG 59.785 41.667 4.55 0.00 42.88 2.69
104 105 5.049405 AGTCTCGTCAAACAATTTGGCTTAG 60.049 40.000 4.55 2.58 42.88 2.18
105 106 4.819630 AGTCTCGTCAAACAATTTGGCTTA 59.180 37.500 4.55 0.00 42.88 3.09
106 107 3.632145 AGTCTCGTCAAACAATTTGGCTT 59.368 39.130 4.55 0.00 42.88 4.35
107 108 3.003689 CAGTCTCGTCAAACAATTTGGCT 59.996 43.478 4.55 0.00 42.88 4.75
108 109 3.300009 CAGTCTCGTCAAACAATTTGGC 58.700 45.455 0.78 0.00 41.68 4.52
109 110 3.003689 AGCAGTCTCGTCAAACAATTTGG 59.996 43.478 0.78 0.00 40.98 3.28
110 111 4.214980 AGCAGTCTCGTCAAACAATTTG 57.785 40.909 0.00 0.00 41.96 2.32
111 112 5.057149 ACTAGCAGTCTCGTCAAACAATTT 58.943 37.500 0.00 0.00 0.00 1.82
112 113 4.632153 ACTAGCAGTCTCGTCAAACAATT 58.368 39.130 0.00 0.00 0.00 2.32
113 114 4.258702 ACTAGCAGTCTCGTCAAACAAT 57.741 40.909 0.00 0.00 0.00 2.71
114 115 3.728076 ACTAGCAGTCTCGTCAAACAA 57.272 42.857 0.00 0.00 0.00 2.83
115 116 3.819337 ACTACTAGCAGTCTCGTCAAACA 59.181 43.478 0.00 0.00 0.00 2.83
116 117 4.159857 CACTACTAGCAGTCTCGTCAAAC 58.840 47.826 0.00 0.00 0.00 2.93
117 118 3.190744 CCACTACTAGCAGTCTCGTCAAA 59.809 47.826 0.00 0.00 0.00 2.69
118 119 2.747989 CCACTACTAGCAGTCTCGTCAA 59.252 50.000 0.00 0.00 0.00 3.18
119 120 2.290134 ACCACTACTAGCAGTCTCGTCA 60.290 50.000 0.00 0.00 0.00 4.35
120 121 2.358015 ACCACTACTAGCAGTCTCGTC 58.642 52.381 0.00 0.00 0.00 4.20
121 122 2.493414 ACCACTACTAGCAGTCTCGT 57.507 50.000 0.00 0.00 0.00 4.18
160 161 1.301716 GAGCTCCGTTGTTGCCTCA 60.302 57.895 0.87 0.00 0.00 3.86
177 178 0.178533 ACGTCCCTGTTCAAAACCGA 59.821 50.000 0.00 0.00 0.00 4.69
178 179 0.584876 GACGTCCCTGTTCAAAACCG 59.415 55.000 3.51 0.00 0.00 4.44
179 180 0.584876 CGACGTCCCTGTTCAAAACC 59.415 55.000 10.58 0.00 0.00 3.27
219 224 2.748605 GACACGAATAGCTCCATCCAG 58.251 52.381 0.00 0.00 0.00 3.86
275 285 1.034838 TTTTGTTGCTGCCGTCACCT 61.035 50.000 0.00 0.00 0.00 4.00
319 332 1.268539 GCACGGGTTTCAGTGTTTCAG 60.269 52.381 0.00 0.00 40.26 3.02
364 377 0.648958 GTGTTATACACTTCGGCGCC 59.351 55.000 19.07 19.07 45.27 6.53
369 382 2.330286 TGGTGCGTGTTATACACTTCG 58.670 47.619 8.18 0.00 46.46 3.79
375 388 5.236263 TCATTCATCATGGTGCGTGTTATAC 59.764 40.000 0.00 0.00 33.07 1.47
376 389 5.363939 TCATTCATCATGGTGCGTGTTATA 58.636 37.500 0.00 0.00 33.07 0.98
377 390 4.198530 TCATTCATCATGGTGCGTGTTAT 58.801 39.130 0.00 0.00 33.07 1.89
378 391 3.604582 TCATTCATCATGGTGCGTGTTA 58.395 40.909 0.00 0.00 33.07 2.41
388 401 9.237846 CTGACTTTGATTCATTCATTCATCATG 57.762 33.333 0.00 0.00 33.34 3.07
390 403 8.570068 TCTGACTTTGATTCATTCATTCATCA 57.430 30.769 0.00 0.00 33.34 3.07
391 404 9.286946 GTTCTGACTTTGATTCATTCATTCATC 57.713 33.333 0.00 0.00 33.34 2.92
393 406 7.300320 CGTTCTGACTTTGATTCATTCATTCA 58.700 34.615 0.00 0.00 33.34 2.57
395 408 6.088824 GCGTTCTGACTTTGATTCATTCATT 58.911 36.000 0.00 0.00 33.34 2.57
397 410 4.083324 GGCGTTCTGACTTTGATTCATTCA 60.083 41.667 0.00 0.00 0.00 2.57
399 412 3.820467 TGGCGTTCTGACTTTGATTCATT 59.180 39.130 0.00 0.00 0.00 2.57
400 413 3.189287 GTGGCGTTCTGACTTTGATTCAT 59.811 43.478 0.00 0.00 0.00 2.57
405 418 1.495584 GCGTGGCGTTCTGACTTTGA 61.496 55.000 0.00 0.00 0.00 2.69
408 421 2.665185 GGCGTGGCGTTCTGACTT 60.665 61.111 0.00 0.00 0.00 3.01
561 709 2.540769 CGATCGAGCTGACTCTTCCTTC 60.541 54.545 10.26 0.00 41.09 3.46
562 710 1.403679 CGATCGAGCTGACTCTTCCTT 59.596 52.381 10.26 0.00 41.09 3.36
563 711 1.021202 CGATCGAGCTGACTCTTCCT 58.979 55.000 10.26 0.00 41.09 3.36
564 712 0.593773 GCGATCGAGCTGACTCTTCC 60.594 60.000 21.57 0.00 41.09 3.46
710 894 0.472471 TTCCTGGAGTTTGACCGCTT 59.528 50.000 0.00 0.00 0.00 4.68
723 907 3.189287 GTGTCTGCATGTACTTTTCCTGG 59.811 47.826 0.00 0.00 0.00 4.45
725 909 3.067106 CGTGTCTGCATGTACTTTTCCT 58.933 45.455 0.00 0.00 0.00 3.36
726 910 2.806244 ACGTGTCTGCATGTACTTTTCC 59.194 45.455 0.00 0.00 42.54 3.13
781 1017 1.855223 GCACGCACGACTACTACTAGC 60.855 57.143 0.00 0.00 0.00 3.42
841 1091 2.180276 CCTCTTATATAGTGGGGCGCT 58.820 52.381 7.64 0.00 34.50 5.92
846 1097 4.080863 GGTGGATGCCTCTTATATAGTGGG 60.081 50.000 0.00 0.00 37.87 4.61
847 1098 4.532126 TGGTGGATGCCTCTTATATAGTGG 59.468 45.833 0.00 0.00 39.94 4.00
948 1239 1.697284 CCGGTTAGGGTAGGTAGTCC 58.303 60.000 0.00 0.00 35.97 3.85
993 1304 1.209990 CCTCTCTTGCTCATGGCTCTT 59.790 52.381 7.54 0.00 42.39 2.85
1093 1430 4.465512 GGCGCGCTGGTGTTGATG 62.466 66.667 32.29 0.00 0.00 3.07
1143 1480 3.893914 CTTGCACTCGAACACGCGC 62.894 63.158 5.73 0.00 0.00 6.86
1233 1570 1.597854 CTTCTGCGGGTGCTGTTGA 60.598 57.895 0.00 0.00 43.34 3.18
1463 1821 3.461773 CGACCACCATCTCGGGCT 61.462 66.667 0.00 0.00 40.22 5.19
1579 1945 2.347490 CTTGTGTACGCCCTGCCT 59.653 61.111 3.51 0.00 0.00 4.75
1633 1999 2.105128 GGAGTGGTCCAGCGATCG 59.895 66.667 11.69 11.69 43.31 3.69
1650 2016 2.889617 CAGCCACCACCATGCATG 59.110 61.111 20.19 20.19 0.00 4.06
1651 2017 3.072468 GCAGCCACCACCATGCAT 61.072 61.111 0.00 0.00 38.54 3.96
1652 2018 4.289101 AGCAGCCACCACCATGCA 62.289 61.111 0.00 0.00 41.14 3.96
1777 2159 4.789075 TCAGAACTACGCCGGCGC 62.789 66.667 46.22 30.11 44.19 6.53
1882 2264 7.561237 ACATTATTACACGTTTTCAACATGC 57.439 32.000 0.00 0.00 0.00 4.06
1952 2688 7.195374 TGTTAGCCTTCATTAGTAGGAACAT 57.805 36.000 0.00 0.00 34.44 2.71
2006 2742 4.471386 AGCCTTCATTAGTAGGAGCAGAAA 59.529 41.667 0.00 0.00 34.44 2.52
2012 2748 8.738645 AAAATGTTAGCCTTCATTAGTAGGAG 57.261 34.615 0.00 0.00 34.44 3.69
2139 2955 0.109597 GCAAGCAGAATGGGTTGACG 60.110 55.000 9.05 0.00 46.36 4.35
2176 2992 9.719355 TCTGTTAAGAATGCAATACAGAAGTTA 57.281 29.630 3.18 0.00 39.06 2.24
2182 2998 9.447040 CATTCATCTGTTAAGAATGCAATACAG 57.553 33.333 0.00 0.00 41.24 2.74
2199 3015 4.786507 TGCGTTCAGTTTTCATTCATCTG 58.213 39.130 0.00 0.00 0.00 2.90
2204 3020 4.223320 TCCTTGCGTTCAGTTTTCATTC 57.777 40.909 0.00 0.00 0.00 2.67
2228 3047 7.079182 ACGTCTTTGAACTGTTGAATGTTTA 57.921 32.000 0.00 0.00 0.00 2.01
2252 3071 3.135994 GTGCCGGTGAGAAGTTAGAAAA 58.864 45.455 1.90 0.00 0.00 2.29
2263 3082 2.093306 TGTTTAGATGTGCCGGTGAG 57.907 50.000 1.90 0.00 0.00 3.51
2294 3113 9.000486 GCTTTAGACCTTGTTTTGTTCTACTAT 58.000 33.333 0.00 0.00 0.00 2.12
2295 3114 7.988599 TGCTTTAGACCTTGTTTTGTTCTACTA 59.011 33.333 0.00 0.00 0.00 1.82
2296 3115 6.826741 TGCTTTAGACCTTGTTTTGTTCTACT 59.173 34.615 0.00 0.00 0.00 2.57
2297 3116 7.023197 TGCTTTAGACCTTGTTTTGTTCTAC 57.977 36.000 0.00 0.00 0.00 2.59
2317 3136 2.947652 CGAATGATTCCATGGACTGCTT 59.052 45.455 15.91 6.22 32.36 3.91
2332 3151 4.252878 ACATGTTATGTGTGCTCGAATGA 58.747 39.130 0.00 0.00 43.01 2.57
2338 3157 6.380995 TGATGAAAACATGTTATGTGTGCTC 58.619 36.000 12.39 2.37 44.07 4.26
2355 3174 5.419788 CCACCTGAATTCCTGAATGATGAAA 59.580 40.000 2.27 0.00 0.00 2.69
2392 3211 4.323868 GGTAGAGTTTGTCTTTGATCGTCG 59.676 45.833 0.00 0.00 36.64 5.12
2436 3255 3.589988 AGACTATGCCAACTTCGTTCAG 58.410 45.455 0.00 0.00 0.00 3.02
2437 3256 3.678056 AGACTATGCCAACTTCGTTCA 57.322 42.857 0.00 0.00 0.00 3.18
2438 3257 4.329256 GGTTAGACTATGCCAACTTCGTTC 59.671 45.833 0.25 0.00 0.00 3.95
2442 3261 4.216411 TGGGTTAGACTATGCCAACTTC 57.784 45.455 6.11 0.00 0.00 3.01
2455 3274 7.787904 AGATAGTACCATGTGTATTGGGTTAGA 59.212 37.037 0.00 0.00 38.64 2.10
2461 3280 5.010719 ACGGAGATAGTACCATGTGTATTGG 59.989 44.000 0.00 0.00 40.26 3.16
2464 3283 4.765856 GGACGGAGATAGTACCATGTGTAT 59.234 45.833 0.00 0.00 0.00 2.29
2467 3286 2.296471 GGGACGGAGATAGTACCATGTG 59.704 54.545 0.00 0.00 42.20 3.21
2468 3287 2.091499 TGGGACGGAGATAGTACCATGT 60.091 50.000 0.00 0.00 46.98 3.21
2478 3297 7.979786 ACATCTTATATTATGGGACGGAGAT 57.020 36.000 0.00 0.00 0.00 2.75
2479 3298 7.792364 AACATCTTATATTATGGGACGGAGA 57.208 36.000 0.00 0.00 0.00 3.71
2532 3352 9.175312 TGAATTGCAAACATGCCAATAATATTT 57.825 25.926 1.71 0.00 0.00 1.40
2575 3395 6.670695 AGTTAATTTGAGCACCTTTTCCAT 57.329 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.