Multiple sequence alignment - TraesCS7D01G050400

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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 TraesCS7D01G050400 chr7D 100.000 3619 0 0 1 3619 25899678 25896060 0.000000e+00 6684.0
1 TraesCS7D01G050400 chr7D 87.412 1708 178 15 993 2667 26566523 26564820 0.000000e+00 1929.0
2 TraesCS7D01G050400 chr7D 87.489 1111 133 6 1659 2766 26559472 26558365 0.000000e+00 1277.0
3 TraesCS7D01G050400 chr7D 75.519 241 50 4 3196 3435 31421718 31421950 3.820000e-20 110.0
4 TraesCS7D01G050400 chr7D 78.519 135 12 7 707 832 26560492 26560366 5.010000e-09 73.1
5 TraesCS7D01G050400 chr4A 88.937 2314 161 36 1311 3615 710272588 710270361 0.000000e+00 2767.0
6 TraesCS7D01G050400 chr4A 89.887 1948 167 18 1674 3617 710284147 710282226 0.000000e+00 2479.0
7 TraesCS7D01G050400 chr4A 88.552 1022 117 0 1646 2667 710694906 710693885 0.000000e+00 1240.0
8 TraesCS7D01G050400 chr4A 87.067 1098 137 4 1659 2756 710676695 710675603 0.000000e+00 1236.0
9 TraesCS7D01G050400 chr4A 95.833 624 25 1 971 1593 710284868 710284245 0.000000e+00 1007.0
10 TraesCS7D01G050400 chr4A 86.005 836 84 11 707 1538 710695809 710695003 0.000000e+00 865.0
11 TraesCS7D01G050400 chr4A 90.625 224 14 4 651 867 710273079 710272856 1.270000e-74 291.0
12 TraesCS7D01G050400 chr4A 90.625 224 14 4 651 867 710285317 710285094 1.270000e-74 291.0
13 TraesCS7D01G050400 chr7A 95.889 1411 39 3 1619 3024 26823275 26821879 0.000000e+00 2266.0
14 TraesCS7D01G050400 chr7A 86.350 2000 202 35 707 2666 27033226 27031258 0.000000e+00 2115.0
15 TraesCS7D01G050400 chr7A 92.880 955 37 8 669 1611 26824290 26823355 0.000000e+00 1358.0
16 TraesCS7D01G050400 chr7A 87.244 1121 136 5 1651 2766 26977652 26976534 0.000000e+00 1271.0
17 TraesCS7D01G050400 chr7A 96.452 620 20 2 1 619 553033132 553032514 0.000000e+00 1022.0
18 TraesCS7D01G050400 chr7A 94.896 627 30 2 1 626 274508607 274507982 0.000000e+00 979.0
19 TraesCS7D01G050400 chr7A 87.622 614 68 6 927 1535 27604554 27605164 0.000000e+00 706.0
20 TraesCS7D01G050400 chr6D 96.013 627 23 2 1 626 187252151 187251526 0.000000e+00 1018.0
21 TraesCS7D01G050400 chr2D 96.013 627 23 2 1 626 546935006 546934381 0.000000e+00 1018.0
22 TraesCS7D01G050400 chr2D 94.880 625 29 3 1 623 116765025 116765648 0.000000e+00 974.0
23 TraesCS7D01G050400 chr2D 92.647 68 2 2 3197 3261 606084528 606084595 1.070000e-15 95.3
24 TraesCS7D01G050400 chr3D 95.673 624 25 2 1 623 586896498 586897120 0.000000e+00 1002.0
25 TraesCS7D01G050400 chr3D 75.000 204 45 6 3206 3406 520192509 520192709 4.980000e-14 89.8
26 TraesCS7D01G050400 chr5D 95.513 624 26 2 1 623 100936808 100937430 0.000000e+00 996.0
27 TraesCS7D01G050400 chr5D 92.982 57 4 0 3205 3261 490019937 490019993 2.320000e-12 84.2
28 TraesCS7D01G050400 chr5D 90.196 51 4 1 3204 3254 564361468 564361517 8.390000e-07 65.8
29 TraesCS7D01G050400 chrUn 95.192 624 28 2 1 623 336390944 336391566 0.000000e+00 985.0
30 TraesCS7D01G050400 chrUn 95.056 627 29 2 1 626 350620411 350619786 0.000000e+00 985.0
31 TraesCS7D01G050400 chr2A 88.196 593 59 7 949 1540 448294941 448294359 0.000000e+00 697.0
32 TraesCS7D01G050400 chr3B 87.669 592 64 6 949 1538 224961090 224960506 0.000000e+00 680.0
33 TraesCS7D01G050400 chr2B 86.129 620 70 8 937 1552 800172563 800171956 0.000000e+00 654.0
34 TraesCS7D01G050400 chr2B 83.761 117 11 3 728 844 800173018 800172910 1.780000e-18 104.0
35 TraesCS7D01G050400 chr2B 92.308 65 5 0 3197 3261 736965103 736965167 3.850000e-15 93.5
36 TraesCS7D01G050400 chr2B 93.878 49 3 0 3211 3259 394150598 394150646 1.390000e-09 75.0
37 TraesCS7D01G050400 chr7B 77.209 215 41 6 3282 3491 86632782 86632571 6.350000e-23 119.0
38 TraesCS7D01G050400 chr7B 94.915 59 3 0 3203 3261 656285353 656285411 3.850000e-15 93.5
39 TraesCS7D01G050400 chr6A 81.618 136 21 3 3270 3404 595027942 595028074 3.820000e-20 110.0
40 TraesCS7D01G050400 chr5B 81.679 131 24 0 3286 3416 162768693 162768563 3.820000e-20 110.0
41 TraesCS7D01G050400 chr3A 89.706 68 6 1 3193 3259 636125324 636125391 6.440000e-13 86.1


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 TraesCS7D01G050400 chr7D 25896060 25899678 3618 True 6684.00 6684 100.0000 1 3619 1 chr7D.!!$R1 3618
1 TraesCS7D01G050400 chr7D 26564820 26566523 1703 True 1929.00 1929 87.4120 993 2667 1 chr7D.!!$R2 1674
2 TraesCS7D01G050400 chr7D 26558365 26560492 2127 True 675.05 1277 83.0040 707 2766 2 chr7D.!!$R3 2059
3 TraesCS7D01G050400 chr4A 710270361 710273079 2718 True 1529.00 2767 89.7810 651 3615 2 chr4A.!!$R2 2964
4 TraesCS7D01G050400 chr4A 710282226 710285317 3091 True 1259.00 2479 92.1150 651 3617 3 chr4A.!!$R3 2966
5 TraesCS7D01G050400 chr4A 710675603 710676695 1092 True 1236.00 1236 87.0670 1659 2756 1 chr4A.!!$R1 1097
6 TraesCS7D01G050400 chr4A 710693885 710695809 1924 True 1052.50 1240 87.2785 707 2667 2 chr4A.!!$R4 1960
7 TraesCS7D01G050400 chr7A 27031258 27033226 1968 True 2115.00 2115 86.3500 707 2666 1 chr7A.!!$R2 1959
8 TraesCS7D01G050400 chr7A 26821879 26824290 2411 True 1812.00 2266 94.3845 669 3024 2 chr7A.!!$R5 2355
9 TraesCS7D01G050400 chr7A 26976534 26977652 1118 True 1271.00 1271 87.2440 1651 2766 1 chr7A.!!$R1 1115
10 TraesCS7D01G050400 chr7A 553032514 553033132 618 True 1022.00 1022 96.4520 1 619 1 chr7A.!!$R4 618
11 TraesCS7D01G050400 chr7A 274507982 274508607 625 True 979.00 979 94.8960 1 626 1 chr7A.!!$R3 625
12 TraesCS7D01G050400 chr7A 27604554 27605164 610 False 706.00 706 87.6220 927 1535 1 chr7A.!!$F1 608
13 TraesCS7D01G050400 chr6D 187251526 187252151 625 True 1018.00 1018 96.0130 1 626 1 chr6D.!!$R1 625
14 TraesCS7D01G050400 chr2D 546934381 546935006 625 True 1018.00 1018 96.0130 1 626 1 chr2D.!!$R1 625
15 TraesCS7D01G050400 chr2D 116765025 116765648 623 False 974.00 974 94.8800 1 623 1 chr2D.!!$F1 622
16 TraesCS7D01G050400 chr3D 586896498 586897120 622 False 1002.00 1002 95.6730 1 623 1 chr3D.!!$F2 622
17 TraesCS7D01G050400 chr5D 100936808 100937430 622 False 996.00 996 95.5130 1 623 1 chr5D.!!$F1 622
18 TraesCS7D01G050400 chrUn 336390944 336391566 622 False 985.00 985 95.1920 1 623 1 chrUn.!!$F1 622
19 TraesCS7D01G050400 chrUn 350619786 350620411 625 True 985.00 985 95.0560 1 626 1 chrUn.!!$R1 625
20 TraesCS7D01G050400 chr2A 448294359 448294941 582 True 697.00 697 88.1960 949 1540 1 chr2A.!!$R1 591
21 TraesCS7D01G050400 chr3B 224960506 224961090 584 True 680.00 680 87.6690 949 1538 1 chr3B.!!$R1 589
22 TraesCS7D01G050400 chr2B 800171956 800173018 1062 True 379.00 654 84.9450 728 1552 2 chr2B.!!$R1 824

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
660 663 0.179108 CGAAGGGAGTAGCCGGAAAG 60.179 60.0 5.05 0.0 37.63 2.62 F
667 670 0.466124 AGTAGCCGGAAAGGATGAGC 59.534 55.0 5.05 0.0 45.00 4.26 F
872 1150 0.523072 GCCAGCCATGTTATATGCCG 59.477 55.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 3022 0.965363 GGCCAACACACCATCGGAAT 60.965 55.000 0.0 0.0 0.00 3.01 R
2378 3051 4.785767 CAGTTGGTCTGCTGCTCA 57.214 55.556 0.0 0.0 37.36 4.26 R
2873 3550 7.215789 CAGATGTGAATAATGCTACTTCCTCT 58.784 38.462 0.0 0.0 0.00 3.69 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
376 379 6.303903 TCCATCAATCTTCTCACAAGATGA 57.696 37.500 0.00 0.00 39.30 2.92
410 413 2.436115 GGTTTCCGGCTAGCGCTT 60.436 61.111 18.68 0.00 36.09 4.68
511 514 2.362397 AGAAGGATATTGAAGCGCGAGA 59.638 45.455 12.10 0.00 0.00 4.04
562 565 5.392811 CCAGAATCTCGTAGAAGTACCGTTT 60.393 44.000 0.00 0.00 34.09 3.60
619 622 8.558973 CTGATTTAACTCTCATCAGTCCTTTT 57.441 34.615 6.09 0.00 39.34 2.27
621 624 7.607991 TGATTTAACTCTCATCAGTCCTTTTCC 59.392 37.037 0.00 0.00 0.00 3.13
622 625 4.982241 AACTCTCATCAGTCCTTTTCCA 57.018 40.909 0.00 0.00 0.00 3.53
623 626 5.511386 AACTCTCATCAGTCCTTTTCCAT 57.489 39.130 0.00 0.00 0.00 3.41
625 628 6.627087 ACTCTCATCAGTCCTTTTCCATAA 57.373 37.500 0.00 0.00 0.00 1.90
626 629 7.205515 ACTCTCATCAGTCCTTTTCCATAAT 57.794 36.000 0.00 0.00 0.00 1.28
627 630 7.278875 ACTCTCATCAGTCCTTTTCCATAATC 58.721 38.462 0.00 0.00 0.00 1.75
628 631 7.127032 ACTCTCATCAGTCCTTTTCCATAATCT 59.873 37.037 0.00 0.00 0.00 2.40
629 632 7.865820 TCTCATCAGTCCTTTTCCATAATCTT 58.134 34.615 0.00 0.00 0.00 2.40
630 633 7.772292 TCTCATCAGTCCTTTTCCATAATCTTG 59.228 37.037 0.00 0.00 0.00 3.02
631 634 7.405292 TCATCAGTCCTTTTCCATAATCTTGT 58.595 34.615 0.00 0.00 0.00 3.16
632 635 8.548025 TCATCAGTCCTTTTCCATAATCTTGTA 58.452 33.333 0.00 0.00 0.00 2.41
633 636 8.616076 CATCAGTCCTTTTCCATAATCTTGTAC 58.384 37.037 0.00 0.00 0.00 2.90
634 637 7.685481 TCAGTCCTTTTCCATAATCTTGTACA 58.315 34.615 0.00 0.00 0.00 2.90
635 638 7.606456 TCAGTCCTTTTCCATAATCTTGTACAC 59.394 37.037 0.00 0.00 0.00 2.90
636 639 6.884836 AGTCCTTTTCCATAATCTTGTACACC 59.115 38.462 0.00 0.00 0.00 4.16
637 640 6.884836 GTCCTTTTCCATAATCTTGTACACCT 59.115 38.462 0.00 0.00 0.00 4.00
638 641 8.044908 GTCCTTTTCCATAATCTTGTACACCTA 58.955 37.037 0.00 0.00 0.00 3.08
639 642 8.778059 TCCTTTTCCATAATCTTGTACACCTAT 58.222 33.333 0.00 0.00 0.00 2.57
642 645 9.537192 TTTTCCATAATCTTGTACACCTATACG 57.463 33.333 0.00 0.00 0.00 3.06
643 646 8.467963 TTCCATAATCTTGTACACCTATACGA 57.532 34.615 0.00 0.00 0.00 3.43
644 647 8.467963 TCCATAATCTTGTACACCTATACGAA 57.532 34.615 0.00 0.00 0.00 3.85
645 648 8.573885 TCCATAATCTTGTACACCTATACGAAG 58.426 37.037 0.00 0.00 0.00 3.79
646 649 7.813148 CCATAATCTTGTACACCTATACGAAGG 59.187 40.741 0.00 0.00 42.82 3.46
647 650 5.786264 ATCTTGTACACCTATACGAAGGG 57.214 43.478 0.00 0.00 41.32 3.95
648 651 4.858850 TCTTGTACACCTATACGAAGGGA 58.141 43.478 0.00 0.00 41.32 4.20
649 652 4.885907 TCTTGTACACCTATACGAAGGGAG 59.114 45.833 0.00 3.42 41.32 4.30
660 663 0.179108 CGAAGGGAGTAGCCGGAAAG 60.179 60.000 5.05 0.00 37.63 2.62
667 670 0.466124 AGTAGCCGGAAAGGATGAGC 59.534 55.000 5.05 0.00 45.00 4.26
672 675 1.517832 CGGAAAGGATGAGCGGTCT 59.482 57.895 16.64 0.97 0.00 3.85
725 730 1.333524 CGATCTCATGCATTGTTCCGC 60.334 52.381 0.00 0.00 0.00 5.54
726 732 1.672363 GATCTCATGCATTGTTCCGCA 59.328 47.619 0.00 0.00 43.45 5.69
872 1150 0.523072 GCCAGCCATGTTATATGCCG 59.477 55.000 0.00 0.00 0.00 5.69
881 1323 1.292061 GTTATATGCCGACACGCCAA 58.708 50.000 0.00 0.00 0.00 4.52
889 1331 2.375766 CGACACGCCAAGAGCTCAC 61.376 63.158 17.77 1.07 40.39 3.51
897 1339 4.070552 AAGAGCTCACGGCCGGAC 62.071 66.667 31.76 15.43 43.05 4.79
941 1383 1.654137 GAACACAACGTTGCGGCTG 60.654 57.895 27.61 19.74 38.19 4.85
1158 1619 3.047877 GAGTTCAACCACCGCCGG 61.048 66.667 0.00 0.00 0.00 6.13
1538 2011 4.442753 GCTCTTCCCTCTCAAAGGTAGATG 60.443 50.000 0.00 0.00 44.56 2.90
1545 2018 4.574013 CCTCTCAAAGGTAGATGTTCATGC 59.426 45.833 0.00 0.00 40.67 4.06
1574 2052 8.542497 TCTATGTACATACACAAGAAAACCAC 57.458 34.615 11.62 0.00 39.30 4.16
1594 2185 1.264288 CCTTTCTTCAACTGCACGTCC 59.736 52.381 0.00 0.00 0.00 4.79
1615 2206 6.150474 CGTCCAAACTAAAATGGAGGTAACAT 59.850 38.462 6.39 0.00 46.01 2.71
1640 2303 4.939052 TTTTTCGGCAAAGGGTGAATTA 57.061 36.364 0.00 0.00 0.00 1.40
1641 2304 4.939052 TTTTCGGCAAAGGGTGAATTAA 57.061 36.364 0.00 0.00 0.00 1.40
1642 2305 3.926821 TTCGGCAAAGGGTGAATTAAC 57.073 42.857 0.00 0.00 0.00 2.01
1644 2307 3.078837 TCGGCAAAGGGTGAATTAACTC 58.921 45.455 0.00 0.00 0.00 3.01
1776 2449 1.605058 GCGTGACCTCCCTAGCTTCA 61.605 60.000 0.00 0.00 0.00 3.02
1919 2592 1.751927 CATGTCCAAGCTCCTGCCC 60.752 63.158 0.00 0.00 40.80 5.36
1920 2593 1.927527 ATGTCCAAGCTCCTGCCCT 60.928 57.895 0.00 0.00 40.80 5.19
2378 3051 0.396974 TGTGTTGGCCCTTCTTTGCT 60.397 50.000 0.00 0.00 0.00 3.91
2736 3413 8.609176 GTCATATTTTGAGCGGTTAGTTGAATA 58.391 33.333 0.00 0.00 34.17 1.75
2743 3420 6.869695 TGAGCGGTTAGTTGAATAGATTACA 58.130 36.000 0.00 0.00 0.00 2.41
2747 3424 7.280205 AGCGGTTAGTTGAATAGATTACAAAGG 59.720 37.037 0.00 0.00 0.00 3.11
2820 3497 0.254178 AGCTCCTTCCACGCATGATT 59.746 50.000 0.00 0.00 0.00 2.57
2873 3550 0.037590 ACGCCCTATGCACCTGAAAA 59.962 50.000 0.00 0.00 41.33 2.29
3066 3770 8.970859 AGTATTAGCAGTGCTCATTTATTTCT 57.029 30.769 23.64 6.26 40.44 2.52
3067 3771 9.050601 AGTATTAGCAGTGCTCATTTATTTCTC 57.949 33.333 23.64 1.41 40.44 2.87
3068 3772 7.870509 ATTAGCAGTGCTCATTTATTTCTCA 57.129 32.000 23.64 0.00 40.44 3.27
3069 3773 7.686438 TTAGCAGTGCTCATTTATTTCTCAA 57.314 32.000 23.64 2.11 40.44 3.02
3070 3774 6.579666 AGCAGTGCTCATTTATTTCTCAAA 57.420 33.333 13.14 0.00 30.62 2.69
3071 3775 6.985117 AGCAGTGCTCATTTATTTCTCAAAA 58.015 32.000 13.14 0.00 30.62 2.44
3072 3776 7.436118 AGCAGTGCTCATTTATTTCTCAAAAA 58.564 30.769 13.14 0.00 30.62 1.94
3136 3840 3.469899 TGCAAATGATTGTACACGCTC 57.530 42.857 0.00 0.00 38.85 5.03
3156 3860 4.421948 CTCGTATTTCTTGTAGACCGCTT 58.578 43.478 0.00 0.00 0.00 4.68
3201 3905 4.097892 AGTTGGAAAGCAAATGACGAACTT 59.902 37.500 0.00 0.00 0.00 2.66
3205 3909 3.455619 AAGCAAATGACGAACTTAGCG 57.544 42.857 0.00 0.00 0.00 4.26
3232 3936 5.551233 CTCAGATGGTTAGGTTCTTTGTGA 58.449 41.667 0.00 0.00 0.00 3.58
3257 3961 0.250901 CCAGTCCACCAGGGTTCAAG 60.251 60.000 0.00 0.00 38.11 3.02
3266 3970 0.179056 CAGGGTTCAAGTCCGTGTGT 60.179 55.000 0.00 0.00 36.48 3.72
3276 3980 0.665835 GTCCGTGTGTGCATTTTCCA 59.334 50.000 0.00 0.00 0.00 3.53
3289 3993 6.041409 TGTGCATTTTCCAGGATTTACTTCAA 59.959 34.615 0.00 0.00 0.00 2.69
3314 4018 7.544622 AGCTATTCGGCGATATTTATTCACTA 58.455 34.615 11.76 0.00 37.29 2.74
3324 4028 7.271653 GCGATATTTATTCACTAGGAGAAGACG 59.728 40.741 0.00 0.00 0.00 4.18
3343 4047 2.159057 ACGTTTCCGTCAACTACAAGGT 60.159 45.455 0.00 0.00 46.28 3.50
3346 4050 0.034337 TCCGTCAACTACAAGGTGCC 59.966 55.000 0.00 0.00 31.59 5.01
3347 4051 0.953960 CCGTCAACTACAAGGTGCCC 60.954 60.000 0.00 0.00 31.59 5.36
3350 4054 0.250124 TCAACTACAAGGTGCCCGTG 60.250 55.000 5.79 5.79 38.88 4.94
3351 4055 0.250124 CAACTACAAGGTGCCCGTGA 60.250 55.000 12.63 0.00 36.54 4.35
3361 4065 0.949105 GTGCCCGTGATGACTTCGTT 60.949 55.000 0.00 0.00 0.00 3.85
3364 4068 2.277084 GCCCGTGATGACTTCGTTAAT 58.723 47.619 0.00 0.00 0.00 1.40
3373 4077 7.644157 CGTGATGACTTCGTTAATCTCAAGATA 59.356 37.037 0.00 0.00 33.73 1.98
3381 4085 7.679659 TCGTTAATCTCAAGATATTGTGTCG 57.320 36.000 0.00 1.58 33.73 4.35
3393 4097 9.599322 CAAGATATTGTGTCGGCTTAATATTTC 57.401 33.333 9.56 2.05 0.00 2.17
3410 4115 6.867662 ATATTTCGAAGGTGCTCATAAAGG 57.132 37.500 0.00 0.00 0.00 3.11
3427 4132 4.722526 AAAGGTAGGGTATGCATGCATA 57.277 40.909 31.75 31.75 37.82 3.14
3439 4144 6.037940 GGTATGCATGCATATGTTCATAGGAG 59.962 42.308 36.01 0.12 40.49 3.69
3443 4148 5.471116 GCATGCATATGTTCATAGGAGTGAA 59.529 40.000 14.21 0.00 36.65 3.18
3445 4150 7.625817 GCATGCATATGTTCATAGGAGTGAATC 60.626 40.741 14.21 0.00 39.99 2.52
3473 4178 5.063438 GTGCATTTGTGAGCGTCTCTAATTA 59.937 40.000 0.00 0.00 0.00 1.40
3476 4181 7.042725 TGCATTTGTGAGCGTCTCTAATTATAC 60.043 37.037 8.07 0.00 0.00 1.47
3519 4224 0.803117 GCCCCGAGAAGTTTAAGCAC 59.197 55.000 0.00 0.00 0.00 4.40
3527 4232 2.039879 AGAAGTTTAAGCACGGGTGGAT 59.960 45.455 0.43 0.00 0.00 3.41
3560 4265 2.699846 ACAATCAACCTTGTGGCACATT 59.300 40.909 22.73 10.30 44.52 2.71
3566 4271 2.165167 ACCTTGTGGCACATTCATGAG 58.835 47.619 22.73 14.15 44.52 2.90
3568 4273 0.889994 TTGTGGCACATTCATGAGGC 59.110 50.000 22.73 4.16 44.52 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 201 6.887545 TGTCAAAGTTCCCTTGAGAGTTAAAA 59.112 34.615 0.00 0.00 0.00 1.52
280 283 8.560903 AGGAATGGAGAGTTTATGGTTAAATCT 58.439 33.333 0.00 0.00 30.34 2.40
410 413 6.049149 CGCCTCTTAATATTCACTTCAGGAA 58.951 40.000 0.00 0.00 0.00 3.36
511 514 1.745320 CGTGGCTAGGGAATACGCCT 61.745 60.000 0.00 0.00 42.90 5.52
519 522 0.178970 GGAGGATACGTGGCTAGGGA 60.179 60.000 0.00 0.00 46.39 4.20
619 622 8.467963 TTCGTATAGGTGTACAAGATTATGGA 57.532 34.615 0.00 0.00 0.00 3.41
621 624 7.813148 CCCTTCGTATAGGTGTACAAGATTATG 59.187 40.741 0.00 0.00 33.17 1.90
622 625 7.727186 TCCCTTCGTATAGGTGTACAAGATTAT 59.273 37.037 0.00 0.00 33.17 1.28
623 626 7.062322 TCCCTTCGTATAGGTGTACAAGATTA 58.938 38.462 0.00 0.00 33.17 1.75
625 628 5.452255 TCCCTTCGTATAGGTGTACAAGAT 58.548 41.667 0.00 0.00 33.17 2.40
626 629 4.858850 TCCCTTCGTATAGGTGTACAAGA 58.141 43.478 0.00 0.00 33.17 3.02
627 630 4.643784 ACTCCCTTCGTATAGGTGTACAAG 59.356 45.833 0.00 0.00 33.17 3.16
628 631 4.603131 ACTCCCTTCGTATAGGTGTACAA 58.397 43.478 0.00 0.00 33.17 2.41
629 632 4.240881 ACTCCCTTCGTATAGGTGTACA 57.759 45.455 0.00 0.00 33.17 2.90
630 633 4.215185 GCTACTCCCTTCGTATAGGTGTAC 59.785 50.000 0.00 0.00 33.17 2.90
631 634 4.392940 GCTACTCCCTTCGTATAGGTGTA 58.607 47.826 0.00 0.00 33.17 2.90
632 635 3.220940 GCTACTCCCTTCGTATAGGTGT 58.779 50.000 0.00 0.00 33.17 4.16
633 636 2.557490 GGCTACTCCCTTCGTATAGGTG 59.443 54.545 0.00 0.00 33.17 4.00
634 637 2.813354 CGGCTACTCCCTTCGTATAGGT 60.813 54.545 0.00 0.00 33.17 3.08
635 638 1.811359 CGGCTACTCCCTTCGTATAGG 59.189 57.143 0.00 0.00 34.92 2.57
636 639 1.811359 CCGGCTACTCCCTTCGTATAG 59.189 57.143 0.00 0.00 0.00 1.31
637 640 1.421268 TCCGGCTACTCCCTTCGTATA 59.579 52.381 0.00 0.00 0.00 1.47
638 641 0.184451 TCCGGCTACTCCCTTCGTAT 59.816 55.000 0.00 0.00 0.00 3.06
639 642 0.034186 TTCCGGCTACTCCCTTCGTA 60.034 55.000 0.00 0.00 0.00 3.43
640 643 0.901580 TTTCCGGCTACTCCCTTCGT 60.902 55.000 0.00 0.00 0.00 3.85
641 644 0.179108 CTTTCCGGCTACTCCCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
642 645 0.178301 CCTTTCCGGCTACTCCCTTC 59.822 60.000 0.00 0.00 0.00 3.46
643 646 0.252558 TCCTTTCCGGCTACTCCCTT 60.253 55.000 0.00 0.00 0.00 3.95
644 647 0.031010 ATCCTTTCCGGCTACTCCCT 60.031 55.000 0.00 0.00 0.00 4.20
645 648 0.106894 CATCCTTTCCGGCTACTCCC 59.893 60.000 0.00 0.00 0.00 4.30
646 649 1.069358 CTCATCCTTTCCGGCTACTCC 59.931 57.143 0.00 0.00 0.00 3.85
647 650 1.539280 GCTCATCCTTTCCGGCTACTC 60.539 57.143 0.00 0.00 0.00 2.59
648 651 0.466124 GCTCATCCTTTCCGGCTACT 59.534 55.000 0.00 0.00 0.00 2.57
649 652 0.876342 CGCTCATCCTTTCCGGCTAC 60.876 60.000 0.00 0.00 0.00 3.58
660 663 1.941325 AATTTCGAGACCGCTCATCC 58.059 50.000 0.00 0.00 41.36 3.51
667 670 3.302480 CGGATTTGCTAATTTCGAGACCG 60.302 47.826 10.28 6.25 37.07 4.79
672 675 2.360844 TGGCGGATTTGCTAATTTCGA 58.639 42.857 16.61 0.00 34.52 3.71
725 730 5.920193 ATTATTGTTGTTGTGGGAGGATG 57.080 39.130 0.00 0.00 0.00 3.51
726 732 6.015918 TGAATTATTGTTGTTGTGGGAGGAT 58.984 36.000 0.00 0.00 0.00 3.24
923 1365 1.654137 CAGCCGCAACGTTGTGTTC 60.654 57.895 32.95 25.08 39.29 3.18
941 1383 1.135333 CGGTTAGCTCTCTCTTCCACC 59.865 57.143 0.00 0.00 0.00 4.61
1538 2011 6.642950 GTGTATGTACATAGAGAGGCATGAAC 59.357 42.308 15.93 2.99 38.63 3.18
1545 2018 9.088512 GTTTTCTTGTGTATGTACATAGAGAGG 57.911 37.037 15.93 13.41 38.63 3.69
1574 2052 1.264288 GGACGTGCAGTTGAAGAAAGG 59.736 52.381 0.63 0.00 0.00 3.11
1736 2409 2.879907 CGCAGGTCTTTGGGCATG 59.120 61.111 0.00 0.00 0.00 4.06
1919 2592 1.890894 CCCCACTGTGTAGACGGAG 59.109 63.158 5.73 0.00 32.19 4.63
1920 2593 2.280552 GCCCCACTGTGTAGACGGA 61.281 63.158 5.73 0.00 32.19 4.69
2171 2844 2.282958 TCGCCCTTGACGAGGTCT 60.283 61.111 8.01 0.00 44.71 3.85
2234 2907 2.801421 GTCGAGAGCATGCTCCGA 59.199 61.111 36.20 36.20 43.70 4.55
2349 3022 0.965363 GGCCAACACACCATCGGAAT 60.965 55.000 0.00 0.00 0.00 3.01
2378 3051 4.785767 CAGTTGGTCTGCTGCTCA 57.214 55.556 0.00 0.00 37.36 4.26
2873 3550 7.215789 CAGATGTGAATAATGCTACTTCCTCT 58.784 38.462 0.00 0.00 0.00 3.69
3024 3706 1.595311 ACTAGCCATCATGGGGTGAA 58.405 50.000 5.62 0.00 40.97 3.18
3025 3707 2.487746 TACTAGCCATCATGGGGTGA 57.512 50.000 5.62 0.00 39.43 4.02
3091 3795 9.250624 CATTAACCAACATCTTTAACCGAAAAA 57.749 29.630 0.00 0.00 0.00 1.94
3136 3840 4.171005 TCAAGCGGTCTACAAGAAATACG 58.829 43.478 0.00 0.00 0.00 3.06
3156 3860 9.040939 CAACTCGATGTATAATGTATTGGTTCA 57.959 33.333 0.00 0.00 0.00 3.18
3201 3905 2.885266 CCTAACCATCTGAGCTACGCTA 59.115 50.000 0.00 0.00 39.88 4.26
3205 3909 5.346181 AAGAACCTAACCATCTGAGCTAC 57.654 43.478 0.00 0.00 0.00 3.58
3257 3961 0.665835 TGGAAAATGCACACACGGAC 59.334 50.000 0.00 0.00 0.00 4.79
3266 3970 6.662865 TTGAAGTAAATCCTGGAAAATGCA 57.337 33.333 0.00 0.00 0.00 3.96
3276 3980 4.816925 GCCGAATAGCTTGAAGTAAATCCT 59.183 41.667 0.00 0.00 0.00 3.24
3289 3993 6.398918 AGTGAATAAATATCGCCGAATAGCT 58.601 36.000 0.00 0.00 0.00 3.32
3324 4028 2.032290 GCACCTTGTAGTTGACGGAAAC 60.032 50.000 0.00 0.00 0.00 2.78
3343 4047 0.604073 TAACGAAGTCATCACGGGCA 59.396 50.000 0.00 0.00 45.00 5.36
3346 4050 4.421058 TGAGATTAACGAAGTCATCACGG 58.579 43.478 0.00 0.00 45.00 4.94
3347 4051 5.800438 TCTTGAGATTAACGAAGTCATCACG 59.200 40.000 0.00 0.00 45.00 4.35
3351 4055 9.823647 ACAATATCTTGAGATTAACGAAGTCAT 57.176 29.630 0.00 0.00 36.33 3.06
3361 4065 6.161855 AGCCGACACAATATCTTGAGATTA 57.838 37.500 0.00 0.00 36.20 1.75
3364 4068 4.471904 AAGCCGACACAATATCTTGAGA 57.528 40.909 0.00 0.00 36.20 3.27
3373 4077 6.238374 CCTTCGAAATATTAAGCCGACACAAT 60.238 38.462 0.00 0.00 0.00 2.71
3381 4085 4.574828 TGAGCACCTTCGAAATATTAAGCC 59.425 41.667 0.00 0.00 0.00 4.35
3393 4097 3.458189 CCTACCTTTATGAGCACCTTCG 58.542 50.000 0.00 0.00 0.00 3.79
3410 4115 5.003160 TGAACATATGCATGCATACCCTAC 58.997 41.667 36.22 25.69 41.09 3.18
3427 4132 6.933521 GCACATAGATTCACTCCTATGAACAT 59.066 38.462 14.15 0.00 42.84 2.71
3439 4144 5.032863 GCTCACAAATGCACATAGATTCAC 58.967 41.667 0.00 0.00 0.00 3.18
3443 4148 3.273434 ACGCTCACAAATGCACATAGAT 58.727 40.909 0.00 0.00 0.00 1.98
3445 4150 2.674852 AGACGCTCACAAATGCACATAG 59.325 45.455 0.00 0.00 0.00 2.23
3476 4181 7.282916 GCACACACATTTGCTTTTTAATACAG 58.717 34.615 0.00 0.00 35.74 2.74
3527 4232 8.907229 ACAAGGTTGATTGTGATCCATTGGGA 62.907 42.308 2.09 0.00 43.94 4.37
3541 4246 2.964464 TGAATGTGCCACAAGGTTGATT 59.036 40.909 0.00 0.00 37.19 2.57


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

AutoCloner maintained by Alex Coulton.