Multiple sequence alignment - TraesCS7B01G095500

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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 TraesCS7B01G095500 chr7B 100.000 4843 0 0 1 4843 109701313 109706155 0.000000e+00 8944.0
1 TraesCS7B01G095500 chr7B 89.933 149 12 3 2412 2559 664108597 664108743 6.400000e-44 189.0
2 TraesCS7B01G095500 chr7B 97.917 48 1 0 2088 2135 664108178 664108225 3.110000e-12 84.2
3 TraesCS7B01G095500 chr7D 93.265 4855 185 73 1 4804 146861841 146866604 0.000000e+00 7023.0
4 TraesCS7B01G095500 chr7D 89.933 149 12 3 2412 2559 589514278 589514424 6.400000e-44 189.0
5 TraesCS7B01G095500 chr7A 92.882 3793 139 57 333 4061 148414361 148418086 0.000000e+00 5387.0
6 TraesCS7B01G095500 chr7A 91.943 422 19 4 4150 4570 148418095 148418502 1.170000e-160 577.0
7 TraesCS7B01G095500 chr7A 91.740 339 21 4 1 337 148412316 148412649 9.490000e-127 464.0
8 TraesCS7B01G095500 chr7A 84.034 238 13 9 4568 4803 148418738 148418952 6.350000e-49 206.0
9 TraesCS7B01G095500 chr7A 89.262 149 13 3 2412 2559 681013372 681013226 2.980000e-42 183.0
10 TraesCS7B01G095500 chr7A 94.118 51 3 0 2088 2138 681013794 681013744 1.450000e-10 78.7
11 TraesCS7B01G095500 chr7A 97.561 41 1 0 1758 1798 637052827 637052787 2.420000e-08 71.3
12 TraesCS7B01G095500 chr6A 88.998 1118 95 15 1078 2184 543394799 543395899 0.000000e+00 1358.0
13 TraesCS7B01G095500 chr6A 84.490 245 23 7 2326 2558 543396053 543396294 1.360000e-55 228.0
14 TraesCS7B01G095500 chr6A 90.419 167 16 0 2861 3027 543396588 543396754 2.270000e-53 220.0
15 TraesCS7B01G095500 chr6A 97.674 86 2 0 3320 3405 543396943 543397028 1.090000e-31 148.0
16 TraesCS7B01G095500 chr6D 88.503 1122 96 20 1077 2184 397082337 397083439 0.000000e+00 1327.0
17 TraesCS7B01G095500 chr6D 84.490 245 26 3 2326 2558 397083590 397083834 1.050000e-56 231.0
18 TraesCS7B01G095500 chr6D 89.820 167 17 0 2861 3027 397084136 397084302 1.060000e-51 215.0
19 TraesCS7B01G095500 chr6D 98.837 86 1 0 3320 3405 397084502 397084587 2.330000e-33 154.0
20 TraesCS7B01G095500 chr6B 88.220 1129 108 18 1065 2184 593711916 593713028 0.000000e+00 1325.0
21 TraesCS7B01G095500 chr6B 90.419 167 16 0 2861 3027 593713726 593713892 2.270000e-53 220.0
22 TraesCS7B01G095500 chr6B 83.265 245 26 7 2326 2558 593713179 593713420 1.370000e-50 211.0
23 TraesCS7B01G095500 chr6B 95.349 86 4 0 3320 3405 593714083 593714168 2.350000e-28 137.0
24 TraesCS7B01G095500 chr4B 82.316 803 116 19 1084 1867 170927034 170927829 0.000000e+00 673.0
25 TraesCS7B01G095500 chr4D 82.192 803 117 21 1084 1867 109469594 109470389 0.000000e+00 667.0
26 TraesCS7B01G095500 chr4A 81.841 804 118 22 1084 1867 466941639 466940844 0.000000e+00 651.0
27 TraesCS7B01G095500 chr3D 79.658 644 108 18 1077 1713 302850186 302849559 4.450000e-120 442.0
28 TraesCS7B01G095500 chr3A 79.966 584 94 20 1077 1641 432040436 432041015 4.510000e-110 409.0
29 TraesCS7B01G095500 chr3A 90.984 122 11 0 2438 2559 432041807 432041928 1.080000e-36 165.0
30 TraesCS7B01G095500 chr3A 93.333 45 3 0 2088 2132 432041390 432041434 3.130000e-07 67.6
31 TraesCS7B01G095500 chr5B 97.561 41 1 0 1758 1798 447194713 447194753 2.420000e-08 71.3
32 TraesCS7B01G095500 chr2A 97.561 41 1 0 1758 1798 662251092 662251132 2.420000e-08 71.3
33 TraesCS7B01G095500 chr1B 97.561 41 1 0 1758 1798 269297763 269297723 2.420000e-08 71.3


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 TraesCS7B01G095500 chr7B 109701313 109706155 4842 False 8944.000000 8944 100.000000 1 4843 1 chr7B.!!$F1 4842
1 TraesCS7B01G095500 chr7D 146861841 146866604 4763 False 7023.000000 7023 93.265000 1 4804 1 chr7D.!!$F1 4803
2 TraesCS7B01G095500 chr7A 148412316 148418952 6636 False 1658.500000 5387 90.149750 1 4803 4 chr7A.!!$F1 4802
3 TraesCS7B01G095500 chr6A 543394799 543397028 2229 False 488.500000 1358 90.395250 1078 3405 4 chr6A.!!$F1 2327
4 TraesCS7B01G095500 chr6D 397082337 397084587 2250 False 481.750000 1327 90.412500 1077 3405 4 chr6D.!!$F1 2328
5 TraesCS7B01G095500 chr6B 593711916 593714168 2252 False 473.250000 1325 89.313250 1065 3405 4 chr6B.!!$F1 2340
6 TraesCS7B01G095500 chr4B 170927034 170927829 795 False 673.000000 673 82.316000 1084 1867 1 chr4B.!!$F1 783
7 TraesCS7B01G095500 chr4D 109469594 109470389 795 False 667.000000 667 82.192000 1084 1867 1 chr4D.!!$F1 783
8 TraesCS7B01G095500 chr4A 466940844 466941639 795 True 651.000000 651 81.841000 1084 1867 1 chr4A.!!$R1 783
9 TraesCS7B01G095500 chr3D 302849559 302850186 627 True 442.000000 442 79.658000 1077 1713 1 chr3D.!!$R1 636
10 TraesCS7B01G095500 chr3A 432040436 432041928 1492 False 213.866667 409 88.094333 1077 2559 3 chr3A.!!$F1 1482

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
312 315 0.107945 ATGCTTCCGCCTCAGTTCTC 60.108 55.0 0.00 0.0 34.43 2.87 F
1041 2787 0.248702 GCGTAGGAAGGAAGAGCGAG 60.249 60.0 0.00 0.0 0.00 5.03 F
1042 2788 0.248702 CGTAGGAAGGAAGAGCGAGC 60.249 60.0 0.00 0.0 0.00 5.03 F
1044 2790 0.393944 TAGGAAGGAAGAGCGAGCGA 60.394 55.0 0.00 0.0 0.00 4.93 F
2285 4146 1.226746 GCCCGCGCTAATTAATCTGT 58.773 50.0 5.56 0.0 0.00 3.41 F
3430 5414 0.395311 AGCCAGCCTGCGTACTAGTA 60.395 55.0 0.00 0.0 36.02 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 3746 0.679002 CCTCCTCGTAGTTGGACGGA 60.679 60.0 0.00 0.00 43.12 4.69 R
2601 4557 0.241749 TAACTGACGGACGCGTTCAT 59.758 50.0 19.39 0.15 0.00 2.57 R
2609 4565 0.456312 CTGCTCGGTAACTGACGGAC 60.456 60.0 0.00 0.00 34.04 4.79 R
2669 4625 0.952010 TCATGATGATCGCCGGCATG 60.952 55.0 28.98 19.97 38.09 4.06 R
3722 5715 0.179009 TTAGCCTCCCTCATGCATGC 60.179 55.0 22.25 11.82 0.00 4.06 R
4805 7060 0.319405 AACCTACGAACCGAACAGGG 59.681 55.0 0.00 0.00 46.96 4.45 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
25 26 4.933064 GCCGTCATCCTCGCCGAG 62.933 72.222 7.25 7.25 0.00 4.63
37 38 0.606096 TCGCCGAGTGATTCCTTTGA 59.394 50.000 0.00 0.00 0.00 2.69
99 100 5.006386 GGAGAAGACAATGGATCTTTGTGT 58.994 41.667 16.03 11.04 37.43 3.72
149 152 1.819288 TGTCCTCCTGTCATTCGTCTC 59.181 52.381 0.00 0.00 0.00 3.36
215 218 1.632920 TCATGGTGGTGCTGGTTATGA 59.367 47.619 0.00 0.00 0.00 2.15
264 267 1.704628 TCTCTCCAAAATCCACCTGCA 59.295 47.619 0.00 0.00 0.00 4.41
267 270 0.109532 TCCAAAATCCACCTGCACGA 59.890 50.000 0.00 0.00 0.00 4.35
283 286 2.039418 CACGATTATGGGGGAGAGTCA 58.961 52.381 0.00 0.00 0.00 3.41
298 301 2.027745 AGAGTCATCGACCACAATGCTT 60.028 45.455 0.00 0.00 32.18 3.91
312 315 0.107945 ATGCTTCCGCCTCAGTTCTC 60.108 55.000 0.00 0.00 34.43 2.87
314 317 1.153745 CTTCCGCCTCAGTTCTCGG 60.154 63.158 0.00 0.00 42.96 4.63
338 2057 2.225019 GCATCAATGGCCTCGTCAATAG 59.775 50.000 3.32 0.00 0.00 1.73
363 2083 3.009033 TCCCATGACGAGTTTTTCCATCT 59.991 43.478 0.00 0.00 0.00 2.90
380 2100 3.309121 CCATCTACATGGGGTTGGTTCTT 60.309 47.826 0.00 0.00 45.63 2.52
387 2107 5.506708 ACATGGGGTTGGTTCTTATAGTTC 58.493 41.667 0.00 0.00 0.00 3.01
400 2123 7.067981 GGTTCTTATAGTTCGTCCTTCTCCTTA 59.932 40.741 0.00 0.00 0.00 2.69
412 2135 1.299165 CTCCTTATCCCACGCGACG 60.299 63.158 15.93 2.53 0.00 5.12
455 2185 1.394917 GTTCACATCTCATGTCACCGC 59.605 52.381 0.00 0.00 42.70 5.68
468 2198 3.239253 ACCGCCGGACAACTTCCT 61.239 61.111 11.71 0.00 43.25 3.36
470 2200 2.342279 CGCCGGACAACTTCCTGA 59.658 61.111 5.05 0.00 43.25 3.86
499 2229 0.599558 CAACGACTCCCTTACACCGA 59.400 55.000 0.00 0.00 0.00 4.69
501 2231 0.538057 ACGACTCCCTTACACCGACA 60.538 55.000 0.00 0.00 0.00 4.35
521 2251 4.643387 GCGGAGTGGGTGTGGCTT 62.643 66.667 0.00 0.00 0.00 4.35
528 2258 2.743928 GGGTGTGGCTTCGAGCTG 60.744 66.667 0.00 0.00 41.99 4.24
536 2266 0.319900 GGCTTCGAGCTGAACTCACA 60.320 55.000 0.00 0.00 46.63 3.58
589 2319 4.088056 TCGACTATTCCCTCTTCGATCT 57.912 45.455 0.00 0.00 33.95 2.75
590 2320 3.815962 TCGACTATTCCCTCTTCGATCTG 59.184 47.826 0.00 0.00 33.95 2.90
602 2332 6.402550 CCCTCTTCGATCTGTTTGTACATTTG 60.403 42.308 0.00 0.00 32.86 2.32
640 2371 7.329471 GGATGTTCTTGTAAGGCTCAAAAATTC 59.671 37.037 0.00 0.00 0.00 2.17
679 2410 9.225436 TCTGAAATTGTACTGCATTACACAATA 57.775 29.630 15.74 2.92 39.92 1.90
688 2422 9.931210 GTACTGCATTACACAATATTTTAGTCC 57.069 33.333 9.19 0.00 0.00 3.85
690 2424 8.893727 ACTGCATTACACAATATTTTAGTCCTC 58.106 33.333 0.00 0.00 0.00 3.71
750 2485 5.208121 GGTATTTCCTCAATCCCCATTTCA 58.792 41.667 0.00 0.00 0.00 2.69
766 2501 0.987294 TTCAGCTCCCCCTTTCTCTG 59.013 55.000 0.00 0.00 0.00 3.35
775 2512 1.362224 CCCTTTCTCTGTCCTTCCCA 58.638 55.000 0.00 0.00 0.00 4.37
777 2514 1.339535 CCTTTCTCTGTCCTTCCCAGC 60.340 57.143 0.00 0.00 0.00 4.85
1036 2782 1.544691 GTGACAGCGTAGGAAGGAAGA 59.455 52.381 0.00 0.00 0.00 2.87
1037 2783 1.819288 TGACAGCGTAGGAAGGAAGAG 59.181 52.381 0.00 0.00 0.00 2.85
1038 2784 0.533032 ACAGCGTAGGAAGGAAGAGC 59.467 55.000 0.00 0.00 0.00 4.09
1039 2785 0.526524 CAGCGTAGGAAGGAAGAGCG 60.527 60.000 0.00 0.00 0.00 5.03
1040 2786 0.680280 AGCGTAGGAAGGAAGAGCGA 60.680 55.000 0.00 0.00 0.00 4.93
1041 2787 0.248702 GCGTAGGAAGGAAGAGCGAG 60.249 60.000 0.00 0.00 0.00 5.03
1042 2788 0.248702 CGTAGGAAGGAAGAGCGAGC 60.249 60.000 0.00 0.00 0.00 5.03
1043 2789 0.248702 GTAGGAAGGAAGAGCGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
1044 2790 0.393944 TAGGAAGGAAGAGCGAGCGA 60.394 55.000 0.00 0.00 0.00 4.93
1045 2791 1.226831 GGAAGGAAGAGCGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
1046 2792 1.876263 GAAGGAAGAGCGAGCGAGC 60.876 63.158 0.00 0.00 37.41 5.03
1047 2793 3.691744 AAGGAAGAGCGAGCGAGCG 62.692 63.158 0.00 0.00 43.00 5.03
1048 2794 4.484258 GGAAGAGCGAGCGAGCGT 62.484 66.667 0.00 0.00 43.00 5.07
1049 2795 2.505118 GAAGAGCGAGCGAGCGTT 60.505 61.111 0.00 0.00 43.00 4.84
1050 2796 2.049063 AAGAGCGAGCGAGCGTTT 60.049 55.556 0.00 0.00 43.00 3.60
1051 2797 2.272293 GAAGAGCGAGCGAGCGTTTG 62.272 60.000 0.00 0.00 43.00 2.93
1052 2798 3.106407 GAGCGAGCGAGCGTTTGT 61.106 61.111 0.00 0.00 43.00 2.83
1053 2799 2.658707 GAGCGAGCGAGCGTTTGTT 61.659 57.895 0.00 0.00 43.00 2.83
1054 2800 2.497628 GCGAGCGAGCGTTTGTTG 60.498 61.111 0.00 0.00 0.00 3.33
1733 3503 3.224324 GCCTCCCGCTCCGACATA 61.224 66.667 0.00 0.00 0.00 2.29
2285 4146 1.226746 GCCCGCGCTAATTAATCTGT 58.773 50.000 5.56 0.00 0.00 3.41
2570 4510 2.094182 GCTTCCGGTAATCACTCACTCA 60.094 50.000 0.00 0.00 0.00 3.41
2575 4515 2.478031 CGGTAATCACTCACTCACTCCG 60.478 54.545 0.00 0.00 0.00 4.63
2576 4516 2.531206 GTAATCACTCACTCACTCCGC 58.469 52.381 0.00 0.00 0.00 5.54
2582 4522 4.087892 CACTCACTCCGCCCCCAG 62.088 72.222 0.00 0.00 0.00 4.45
2609 4565 4.946766 GCGAGGTTAATGAACGCG 57.053 55.556 3.53 3.53 39.90 6.01
2639 4595 5.640357 CAGTTACCGAGCAGTTAATTAACCA 59.360 40.000 21.92 0.00 36.88 3.67
2669 4625 0.798776 CATGCAGGTGGAACTTCGTC 59.201 55.000 0.00 0.00 36.74 4.20
2840 4800 2.026822 AGTAGAGTGGGGCTGACATTTG 60.027 50.000 0.00 0.00 0.00 2.32
2841 4801 0.773644 AGAGTGGGGCTGACATTTGT 59.226 50.000 0.00 0.00 0.00 2.83
2842 4802 0.883833 GAGTGGGGCTGACATTTGTG 59.116 55.000 0.00 0.00 0.00 3.33
2848 4808 1.403249 GGGCTGACATTTGTGTGCATC 60.403 52.381 0.00 0.00 0.00 3.91
3028 5000 2.890474 GCCATCGTGCAGGTACGG 60.890 66.667 9.90 6.71 43.85 4.02
3084 5057 1.131771 CGAGCACACACAGTACACAG 58.868 55.000 0.00 0.00 0.00 3.66
3265 5239 4.134187 CGCTTTCGCACGCACGAT 62.134 61.111 0.89 0.00 42.54 3.73
3272 5246 3.716006 GCACGCACGATGCACAGT 61.716 61.111 9.95 0.00 45.36 3.55
3281 5255 1.603802 ACGATGCACAGTTTGGTTCTG 59.396 47.619 0.00 0.00 38.68 3.02
3411 5389 2.358125 ACGGCGTAAGTGCATGCA 60.358 55.556 18.46 18.46 41.68 3.96
3419 5397 2.488771 TAAGTGCATGCAGCCAGCCT 62.489 55.000 23.41 10.78 44.83 4.58
3430 5414 0.395311 AGCCAGCCTGCGTACTAGTA 60.395 55.000 0.00 0.00 36.02 1.82
3449 5433 6.719370 ACTAGTAAAAACCATGAAATCTGGCA 59.281 34.615 0.00 0.00 37.27 4.92
3716 5709 2.475466 GGGGACATGATGCGTGCTG 61.475 63.158 0.00 0.00 0.00 4.41
3718 5711 2.110967 GGACATGATGCGTGCTGCT 61.111 57.895 0.00 0.00 46.63 4.24
3719 5712 1.351012 GACATGATGCGTGCTGCTC 59.649 57.895 0.00 0.00 46.63 4.26
3720 5713 2.044832 GACATGATGCGTGCTGCTCC 62.045 60.000 0.00 0.00 46.63 4.70
3721 5714 1.818363 CATGATGCGTGCTGCTCCT 60.818 57.895 0.00 0.00 46.63 3.69
3722 5715 1.818363 ATGATGCGTGCTGCTCCTG 60.818 57.895 0.00 0.00 46.63 3.86
3723 5716 3.873883 GATGCGTGCTGCTCCTGC 61.874 66.667 0.00 0.08 46.63 4.85
3835 5833 9.629878 TTCAGTTGTTGGTAAATTAAAGGACTA 57.370 29.630 0.00 0.00 0.00 2.59
3891 5896 6.330278 GTTTGGGGTTTTAGAAGATGTATGC 58.670 40.000 0.00 0.00 0.00 3.14
3897 5905 5.594317 GGTTTTAGAAGATGTATGCCCATGT 59.406 40.000 0.00 0.00 0.00 3.21
3928 5939 2.639839 CAGAGGTTTCTTTCCCTGGAGA 59.360 50.000 0.00 0.00 0.00 3.71
3935 5946 3.498614 TCTTTCCCTGGAGAGAGGATT 57.501 47.619 2.45 0.00 34.69 3.01
3939 5950 0.469070 CCCTGGAGAGAGGATTGCTG 59.531 60.000 0.00 0.00 34.69 4.41
3940 5951 1.202330 CCTGGAGAGAGGATTGCTGT 58.798 55.000 0.00 0.00 34.69 4.40
3941 5952 1.134461 CCTGGAGAGAGGATTGCTGTG 60.134 57.143 0.00 0.00 34.69 3.66
3942 5953 0.251354 TGGAGAGAGGATTGCTGTGC 59.749 55.000 0.00 0.00 0.00 4.57
3943 5954 0.540923 GGAGAGAGGATTGCTGTGCT 59.459 55.000 0.00 0.00 0.00 4.40
3944 5955 1.654317 GAGAGAGGATTGCTGTGCTG 58.346 55.000 0.00 0.00 0.00 4.41
4063 6074 9.186837 TCTATATATTACTAGTACTTGGCAGGC 57.813 37.037 0.00 0.00 0.00 4.85
4064 6075 9.191479 CTATATATTACTAGTACTTGGCAGGCT 57.809 37.037 0.00 0.00 0.00 4.58
4065 6076 3.887621 TTACTAGTACTTGGCAGGCTG 57.112 47.619 10.94 10.94 0.00 4.85
4066 6077 1.938585 ACTAGTACTTGGCAGGCTGA 58.061 50.000 20.86 0.00 0.00 4.26
4067 6078 2.472029 ACTAGTACTTGGCAGGCTGAT 58.528 47.619 20.86 0.00 0.00 2.90
4076 6087 0.681175 GGCAGGCTGATGGTTGTTTT 59.319 50.000 20.86 0.00 0.00 2.43
4098 6109 1.337821 CGTCTAGTCGTGCCTTCAAC 58.662 55.000 0.93 0.00 0.00 3.18
4128 6139 2.785357 TTTCCCTTGTGAATTGGGGT 57.215 45.000 0.00 0.00 41.22 4.95
4136 6147 4.283212 CCTTGTGAATTGGGGTTGTAATGT 59.717 41.667 0.00 0.00 0.00 2.71
4140 6151 6.653989 TGTGAATTGGGGTTGTAATGTTTTT 58.346 32.000 0.00 0.00 0.00 1.94
4307 6320 3.312421 ACCGAAATACCAATCGCTCAATG 59.688 43.478 0.00 0.00 37.73 2.82
4359 6372 5.009631 TGGACTTACACAATTGAATCTGGG 58.990 41.667 13.59 0.00 0.00 4.45
4375 6388 8.225603 TGAATCTGGGTATTTATTTCTTCTGC 57.774 34.615 0.00 0.00 0.00 4.26
4385 6398 2.370281 TTTCTTCTGCGGCAGAGTAG 57.630 50.000 29.29 24.61 41.75 2.57
4406 6419 3.060602 GCTAAATCTCGAGCCGCTTAAT 58.939 45.455 7.81 0.00 32.25 1.40
4407 6420 3.120854 GCTAAATCTCGAGCCGCTTAATG 60.121 47.826 7.81 0.00 32.25 1.90
4408 6421 1.221414 AATCTCGAGCCGCTTAATGC 58.779 50.000 7.81 0.00 38.57 3.56
4633 6885 2.355412 CCACCTCATGATTGCTCAGACA 60.355 50.000 0.00 0.00 34.12 3.41
4656 6908 7.755591 ACACATTTAGACTCATGCATAAACTG 58.244 34.615 0.00 0.00 0.00 3.16
4721 6974 7.936847 TCCATATAATCGTAAAAGAATGTGGCT 59.063 33.333 0.00 0.00 0.00 4.75
4809 7064 5.467035 TTTCTCAAAACATTAAGGCCCTG 57.533 39.130 0.00 0.00 0.00 4.45
4810 7065 4.112634 TCTCAAAACATTAAGGCCCTGT 57.887 40.909 0.00 0.00 0.00 4.00
4811 7066 4.479158 TCTCAAAACATTAAGGCCCTGTT 58.521 39.130 0.00 1.53 34.71 3.16
4812 7067 4.522789 TCTCAAAACATTAAGGCCCTGTTC 59.477 41.667 0.00 0.00 32.18 3.18
4813 7068 3.254657 TCAAAACATTAAGGCCCTGTTCG 59.745 43.478 0.00 0.71 32.18 3.95
4814 7069 1.834188 AACATTAAGGCCCTGTTCGG 58.166 50.000 0.00 0.00 0.00 4.30
4815 7070 0.696501 ACATTAAGGCCCTGTTCGGT 59.303 50.000 0.00 0.00 0.00 4.69
4816 7071 1.074889 ACATTAAGGCCCTGTTCGGTT 59.925 47.619 0.00 0.00 0.00 4.44
4817 7072 1.743394 CATTAAGGCCCTGTTCGGTTC 59.257 52.381 0.00 0.00 0.00 3.62
4818 7073 0.320946 TTAAGGCCCTGTTCGGTTCG 60.321 55.000 0.00 0.00 0.00 3.95
4819 7074 1.474332 TAAGGCCCTGTTCGGTTCGT 61.474 55.000 0.00 0.00 0.00 3.85
4820 7075 1.474332 AAGGCCCTGTTCGGTTCGTA 61.474 55.000 0.00 0.00 0.00 3.43
4821 7076 1.447314 GGCCCTGTTCGGTTCGTAG 60.447 63.158 0.00 0.00 0.00 3.51
4822 7077 1.447314 GCCCTGTTCGGTTCGTAGG 60.447 63.158 0.00 0.00 0.00 3.18
4823 7078 1.969862 CCCTGTTCGGTTCGTAGGT 59.030 57.895 0.00 0.00 0.00 3.08
4824 7079 0.319405 CCCTGTTCGGTTCGTAGGTT 59.681 55.000 0.00 0.00 0.00 3.50
4825 7080 1.270465 CCCTGTTCGGTTCGTAGGTTT 60.270 52.381 0.00 0.00 0.00 3.27
4826 7081 2.486918 CCTGTTCGGTTCGTAGGTTTT 58.513 47.619 0.00 0.00 0.00 2.43
4827 7082 2.222445 CCTGTTCGGTTCGTAGGTTTTG 59.778 50.000 0.00 0.00 0.00 2.44
4828 7083 1.598601 TGTTCGGTTCGTAGGTTTTGC 59.401 47.619 0.00 0.00 0.00 3.68
4829 7084 1.598601 GTTCGGTTCGTAGGTTTTGCA 59.401 47.619 0.00 0.00 0.00 4.08
4830 7085 1.950828 TCGGTTCGTAGGTTTTGCAA 58.049 45.000 0.00 0.00 0.00 4.08
4831 7086 2.286872 TCGGTTCGTAGGTTTTGCAAA 58.713 42.857 8.05 8.05 0.00 3.68
4832 7087 2.288458 TCGGTTCGTAGGTTTTGCAAAG 59.712 45.455 12.41 0.00 0.00 2.77
4833 7088 2.603652 CGGTTCGTAGGTTTTGCAAAGG 60.604 50.000 12.41 0.00 0.00 3.11
4834 7089 2.619646 GGTTCGTAGGTTTTGCAAAGGA 59.380 45.455 12.41 0.00 0.00 3.36
4835 7090 3.067040 GGTTCGTAGGTTTTGCAAAGGAA 59.933 43.478 12.41 5.60 0.00 3.36
4836 7091 4.440387 GGTTCGTAGGTTTTGCAAAGGAAA 60.440 41.667 12.41 0.00 0.00 3.13
4837 7092 4.985538 TCGTAGGTTTTGCAAAGGAAAA 57.014 36.364 12.41 0.00 0.00 2.29
4838 7093 4.674475 TCGTAGGTTTTGCAAAGGAAAAC 58.326 39.130 12.41 15.56 40.89 2.43
4841 7096 2.730183 GTTTTGCAAAGGAAAACCGC 57.270 45.000 12.41 0.00 37.34 5.68
4842 7097 2.276201 GTTTTGCAAAGGAAAACCGCT 58.724 42.857 12.41 0.00 37.34 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.827481 GCGAGGATGACGGCTTTA 57.173 55.556 0.00 0.00 0.00 1.85
25 26 5.046288 AGGATGGAGATCAAAGGAATCAC 57.954 43.478 0.00 0.00 0.00 3.06
99 100 4.538490 ACATATACCAAGACTCCCCACAAA 59.462 41.667 0.00 0.00 0.00 2.83
244 247 1.704628 TGCAGGTGGATTTTGGAGAGA 59.295 47.619 0.00 0.00 0.00 3.10
261 264 0.758734 CTCTCCCCCATAATCGTGCA 59.241 55.000 0.00 0.00 0.00 4.57
264 267 2.471815 TGACTCTCCCCCATAATCGT 57.528 50.000 0.00 0.00 0.00 3.73
267 270 2.900546 GTCGATGACTCTCCCCCATAAT 59.099 50.000 0.00 0.00 0.00 1.28
283 286 2.767536 CGGAAGCATTGTGGTCGAT 58.232 52.632 0.00 0.00 0.00 3.59
298 301 2.282958 ACCGAGAACTGAGGCGGA 60.283 61.111 7.16 0.00 46.29 5.54
328 331 3.919216 GTCATGGGATCCTATTGACGAG 58.081 50.000 19.38 5.76 0.00 4.18
338 2057 2.683362 GGAAAAACTCGTCATGGGATCC 59.317 50.000 1.92 1.92 0.00 3.36
363 2083 6.630863 CGAACTATAAGAACCAACCCCATGTA 60.631 42.308 0.00 0.00 0.00 2.29
376 2096 8.763984 ATAAGGAGAAGGACGAACTATAAGAA 57.236 34.615 0.00 0.00 0.00 2.52
380 2100 6.008960 GGGATAAGGAGAAGGACGAACTATA 58.991 44.000 0.00 0.00 0.00 1.31
387 2107 1.067212 CGTGGGATAAGGAGAAGGACG 59.933 57.143 0.00 0.00 0.00 4.79
400 2123 4.789075 CGAACCGTCGCGTGGGAT 62.789 66.667 21.65 12.06 41.08 3.85
412 2135 4.026475 CGAAGATGATCTAAAGCACGAACC 60.026 45.833 0.00 0.00 0.00 3.62
468 2198 2.426024 GGAGTCGTTGTAGCTATGGTCA 59.574 50.000 0.00 0.00 0.00 4.02
470 2200 1.755380 GGGAGTCGTTGTAGCTATGGT 59.245 52.381 0.00 0.00 0.00 3.55
499 2229 3.857038 ACACCCACTCCGCGTTGT 61.857 61.111 4.92 0.00 0.00 3.32
501 2231 4.619227 CCACACCCACTCCGCGTT 62.619 66.667 4.92 0.00 0.00 4.84
510 2240 3.241530 AGCTCGAAGCCACACCCA 61.242 61.111 3.66 0.00 43.77 4.51
513 2243 0.601311 AGTTCAGCTCGAAGCCACAC 60.601 55.000 3.66 0.00 43.77 3.82
528 2258 1.790387 GATGGCGCACTGTGAGTTC 59.210 57.895 12.86 6.07 0.00 3.01
536 2266 2.281484 ACAAACCGATGGCGCACT 60.281 55.556 10.83 0.00 35.83 4.40
575 2305 4.282449 TGTACAAACAGATCGAAGAGGGAA 59.718 41.667 0.00 0.00 43.63 3.97
589 2319 8.877779 CCTTGATGAAAAACAAATGTACAAACA 58.122 29.630 0.00 0.00 40.69 2.83
590 2320 9.092876 TCCTTGATGAAAAACAAATGTACAAAC 57.907 29.630 0.00 0.00 0.00 2.93
602 2332 9.185192 CTTACAAGAACATCCTTGATGAAAAAC 57.815 33.333 10.84 0.00 44.66 2.43
640 2371 5.807909 ACAATTTCAGAAAAATGGGGATGG 58.192 37.500 13.69 0.00 30.88 3.51
679 2410 7.709149 CTCCTGAAAATTGGAGGACTAAAAT 57.291 36.000 2.27 0.00 44.44 1.82
697 2431 7.168219 AGCAACTTCAAATTGTATACTCCTGA 58.832 34.615 4.17 0.00 0.00 3.86
750 2485 0.912006 GGACAGAGAAAGGGGGAGCT 60.912 60.000 0.00 0.00 0.00 4.09
1023 2769 0.248702 GCTCGCTCTTCCTTCCTACG 60.249 60.000 0.00 0.00 0.00 3.51
1036 2782 2.661866 AACAAACGCTCGCTCGCT 60.662 55.556 0.00 0.00 0.00 4.93
1037 2783 2.497628 CAACAAACGCTCGCTCGC 60.498 61.111 0.00 0.00 0.00 5.03
1038 2784 2.170985 CCAACAAACGCTCGCTCG 59.829 61.111 0.00 0.00 0.00 5.03
1039 2785 2.127232 GCCAACAAACGCTCGCTC 60.127 61.111 0.00 0.00 0.00 5.03
1040 2786 4.012895 CGCCAACAAACGCTCGCT 62.013 61.111 0.00 0.00 0.00 4.93
1733 3503 3.606662 ATGGAGCGGCGCGAGTAT 61.607 61.111 27.59 16.32 0.00 2.12
1940 3740 3.751246 TAGTTGGACGGACGCGGG 61.751 66.667 12.47 1.02 0.00 6.13
1946 3746 0.679002 CCTCCTCGTAGTTGGACGGA 60.679 60.000 0.00 0.00 43.12 4.69
2262 4123 1.602377 GATTAATTAGCGCGGGCACTT 59.398 47.619 27.20 17.43 43.41 3.16
2285 4146 9.513906 TTGATTGATCAGTTACCAATAACAGAA 57.486 29.630 0.00 0.00 42.83 3.02
2584 4524 2.803817 ATTAACCTCGCCGGCGGAT 61.804 57.895 44.95 29.86 40.25 4.18
2585 4525 3.463585 ATTAACCTCGCCGGCGGA 61.464 61.111 44.95 30.40 40.25 5.54
2601 4557 0.241749 TAACTGACGGACGCGTTCAT 59.758 50.000 19.39 0.15 0.00 2.57
2602 4558 0.661187 GTAACTGACGGACGCGTTCA 60.661 55.000 19.39 14.93 0.00 3.18
2603 4559 1.339946 GGTAACTGACGGACGCGTTC 61.340 60.000 15.53 11.52 0.00 3.95
2609 4565 0.456312 CTGCTCGGTAACTGACGGAC 60.456 60.000 0.00 0.00 34.04 4.79
2669 4625 0.952010 TCATGATGATCGCCGGCATG 60.952 55.000 28.98 19.97 38.09 4.06
2777 4736 1.904865 CCACAGTTGGCTGGCATGT 60.905 57.895 4.22 4.56 46.62 3.21
2789 4748 6.348498 TGAATGAATGATATCGAACCACAGT 58.652 36.000 0.00 0.00 0.00 3.55
2790 4749 6.849588 TGAATGAATGATATCGAACCACAG 57.150 37.500 0.00 0.00 0.00 3.66
2791 4750 8.938906 CATATGAATGAATGATATCGAACCACA 58.061 33.333 0.00 0.00 34.84 4.17
2795 4754 8.663025 ACTGCATATGAATGAATGATATCGAAC 58.337 33.333 6.97 0.00 34.84 3.95
2797 4756 9.525409 CTACTGCATATGAATGAATGATATCGA 57.475 33.333 6.97 0.00 34.84 3.59
2803 4763 6.932960 CCACTCTACTGCATATGAATGAATGA 59.067 38.462 6.97 0.00 34.84 2.57
2840 4800 2.101575 CATGCGCCAGATGCACAC 59.898 61.111 4.18 0.00 46.57 3.82
2841 4801 3.817655 GCATGCGCCAGATGCACA 61.818 61.111 22.14 0.00 46.57 4.57
3028 5000 3.371063 TCGGGTGTCGTCTCTGGC 61.371 66.667 0.00 0.00 40.32 4.85
3084 5057 2.188829 TCAGTGTGCAAGCCTGTGC 61.189 57.895 8.01 0.00 45.15 4.57
3265 5239 1.846007 AACCAGAACCAAACTGTGCA 58.154 45.000 0.00 0.00 34.04 4.57
3272 5246 6.147985 GCTTAAACAAACAAACCAGAACCAAA 59.852 34.615 0.00 0.00 0.00 3.28
3281 5255 3.555547 CCAGCAGCTTAAACAAACAAACC 59.444 43.478 0.00 0.00 0.00 3.27
3411 5389 0.395311 TACTAGTACGCAGGCTGGCT 60.395 55.000 17.64 0.00 0.00 4.75
3419 5397 7.604927 AGATTTCATGGTTTTTACTAGTACGCA 59.395 33.333 0.91 0.00 0.00 5.24
3424 5402 6.719370 TGCCAGATTTCATGGTTTTTACTAGT 59.281 34.615 0.00 0.00 40.17 2.57
3430 5414 3.667360 GCTGCCAGATTTCATGGTTTTT 58.333 40.909 0.00 0.00 40.17 1.94
3490 5478 2.035237 AACGGCGGGTGAGACAAGAA 62.035 55.000 13.24 0.00 0.00 2.52
3718 5711 1.530283 CTCCCTCATGCATGCAGGA 59.470 57.895 30.87 30.87 35.38 3.86
3719 5712 1.528542 CCTCCCTCATGCATGCAGG 60.529 63.158 25.78 25.78 0.00 4.85
3720 5713 2.194212 GCCTCCCTCATGCATGCAG 61.194 63.158 26.69 18.06 0.00 4.41
3721 5714 1.347243 TAGCCTCCCTCATGCATGCA 61.347 55.000 25.04 25.04 0.00 3.96
3722 5715 0.179009 TTAGCCTCCCTCATGCATGC 60.179 55.000 22.25 11.82 0.00 4.06
3723 5716 2.581216 ATTAGCCTCCCTCATGCATG 57.419 50.000 21.07 21.07 0.00 4.06
3724 5717 3.654806 AGTAATTAGCCTCCCTCATGCAT 59.345 43.478 0.00 0.00 0.00 3.96
3731 5724 5.983608 AGAATCCTAGTAATTAGCCTCCCT 58.016 41.667 0.00 0.00 0.00 4.20
3835 5833 2.972021 CTCCCCAACCTTTGATTTTGGT 59.028 45.455 0.00 0.00 38.53 3.67
3891 5896 0.822944 TCTGCCAACACACACATGGG 60.823 55.000 0.00 0.00 34.71 4.00
3897 5905 1.064758 AGAAACCTCTGCCAACACACA 60.065 47.619 0.00 0.00 0.00 3.72
3928 5939 1.302285 CCCAGCACAGCAATCCTCT 59.698 57.895 0.00 0.00 0.00 3.69
4050 6061 0.254178 CCATCAGCCTGCCAAGTACT 59.746 55.000 0.00 0.00 0.00 2.73
4061 6072 1.539827 ACGCTAAAACAACCATCAGCC 59.460 47.619 0.00 0.00 0.00 4.85
4062 6073 2.484264 AGACGCTAAAACAACCATCAGC 59.516 45.455 0.00 0.00 0.00 4.26
4063 6074 4.929808 ACTAGACGCTAAAACAACCATCAG 59.070 41.667 0.00 0.00 0.00 2.90
4064 6075 4.890088 ACTAGACGCTAAAACAACCATCA 58.110 39.130 0.00 0.00 0.00 3.07
4065 6076 4.031426 CGACTAGACGCTAAAACAACCATC 59.969 45.833 0.89 0.00 0.00 3.51
4066 6077 3.924686 CGACTAGACGCTAAAACAACCAT 59.075 43.478 0.89 0.00 0.00 3.55
4067 6078 3.243501 ACGACTAGACGCTAAAACAACCA 60.244 43.478 14.46 0.00 36.70 3.67
4076 6087 0.731417 GAAGGCACGACTAGACGCTA 59.269 55.000 14.46 0.00 36.70 4.26
4187 6198 2.416431 GCCAACACATTGAGAAGGATGC 60.416 50.000 0.00 0.00 38.15 3.91
4219 6230 5.279206 CCGAGCTAGGAACATCATCAATAGT 60.279 44.000 7.14 0.00 0.00 2.12
4322 6335 8.856153 TGTGTAAGTCCAAATTATGCTTAGAA 57.144 30.769 0.00 0.00 0.00 2.10
4359 6372 5.294552 ACTCTGCCGCAGAAGAAATAAATAC 59.705 40.000 23.06 0.00 40.18 1.89
4375 6388 2.290916 TCGAGATTTAGCTACTCTGCCG 59.709 50.000 9.26 8.00 0.00 5.69
4385 6398 2.135664 TAAGCGGCTCGAGATTTAGC 57.864 50.000 18.75 12.73 38.03 3.09
4444 6458 7.120923 TCCATCTACACCTCCTTATTACAAC 57.879 40.000 0.00 0.00 0.00 3.32
4612 6864 2.286872 GTCTGAGCAATCATGAGGTGG 58.713 52.381 0.09 0.00 0.00 4.61
4633 6885 8.565896 TTCAGTTTATGCATGAGTCTAAATGT 57.434 30.769 10.16 0.00 0.00 2.71
4710 6963 8.246180 CACTCAATGTTTTATAGCCACATTCTT 58.754 33.333 0.00 0.00 38.75 2.52
4762 7016 1.064017 TGGTTGAGGATGGTATTGCCC 60.064 52.381 0.00 0.00 36.04 5.36
4765 7019 2.288666 CCGTGGTTGAGGATGGTATTG 58.711 52.381 0.00 0.00 0.00 1.90
4766 7020 1.913419 ACCGTGGTTGAGGATGGTATT 59.087 47.619 0.00 0.00 29.16 1.89
4804 7059 1.447314 CCTACGAACCGAACAGGGC 60.447 63.158 0.00 0.00 46.96 5.19
4805 7060 0.319405 AACCTACGAACCGAACAGGG 59.681 55.000 0.00 0.00 46.96 4.45
4807 7062 2.349155 GCAAAACCTACGAACCGAACAG 60.349 50.000 0.00 0.00 0.00 3.16
4808 7063 1.598601 GCAAAACCTACGAACCGAACA 59.401 47.619 0.00 0.00 0.00 3.18
4809 7064 1.598601 TGCAAAACCTACGAACCGAAC 59.401 47.619 0.00 0.00 0.00 3.95
4810 7065 1.950828 TGCAAAACCTACGAACCGAA 58.049 45.000 0.00 0.00 0.00 4.30
4811 7066 1.950828 TTGCAAAACCTACGAACCGA 58.049 45.000 0.00 0.00 0.00 4.69
4812 7067 2.603652 CCTTTGCAAAACCTACGAACCG 60.604 50.000 13.84 0.00 0.00 4.44
4813 7068 2.619646 TCCTTTGCAAAACCTACGAACC 59.380 45.455 13.84 0.00 0.00 3.62
4814 7069 3.974871 TCCTTTGCAAAACCTACGAAC 57.025 42.857 13.84 0.00 0.00 3.95
4815 7070 4.985538 TTTCCTTTGCAAAACCTACGAA 57.014 36.364 13.84 5.55 0.00 3.85
4816 7071 4.674475 GTTTTCCTTTGCAAAACCTACGA 58.326 39.130 13.84 0.00 37.64 3.43
4822 7077 2.276201 AGCGGTTTTCCTTTGCAAAAC 58.724 42.857 13.84 7.83 41.23 2.43
4823 7078 2.682155 AGCGGTTTTCCTTTGCAAAA 57.318 40.000 13.84 0.00 37.95 2.44


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

AutoCloner maintained by Alex Coulton.