Multiple sequence alignment - TraesCS2A01G573800

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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 TraesCS2A01G573800 chr2A 100.000 2396 0 0 1 2396 769101542 769099147 0.000000e+00 4425.0
1 TraesCS2A01G573800 chr2A 92.576 458 32 2 1940 2396 528783526 528783070 0.000000e+00 656.0
2 TraesCS2A01G573800 chr2A 91.921 458 35 2 1940 2396 482545919 482546375 7.220000e-180 640.0
3 TraesCS2A01G573800 chr2A 97.849 93 2 0 1 93 190071915 190071823 6.850000e-36 161.0
4 TraesCS2A01G573800 chr1A 96.462 1837 40 3 582 2396 230306062 230307895 0.000000e+00 3009.0
5 TraesCS2A01G573800 chr1A 94.286 1785 87 12 622 2396 288304985 288306764 0.000000e+00 2717.0
6 TraesCS2A01G573800 chr1A 92.358 458 31 4 1940 2396 534671549 534672003 0.000000e+00 649.0
7 TraesCS2A01G573800 chr1A 94.801 327 15 2 209 533 288304310 288304636 2.120000e-140 508.0
8 TraesCS2A01G573800 chr1A 96.218 238 7 1 208 443 230305227 230305464 2.890000e-104 388.0
9 TraesCS2A01G573800 chr1A 96.774 93 3 0 2 94 10609175 10609083 3.190000e-34 156.0
10 TraesCS2A01G573800 chr1A 96.774 93 3 0 1 93 130620646 130620738 3.190000e-34 156.0
11 TraesCS2A01G573800 chr1A 96.774 93 3 0 1 93 315248707 315248615 3.190000e-34 156.0
12 TraesCS2A01G573800 chr1A 96.774 93 3 0 1 93 461507707 461507799 3.190000e-34 156.0
13 TraesCS2A01G573800 chr1A 97.826 46 1 0 875 920 230306315 230306360 1.970000e-11 80.5
14 TraesCS2A01G573800 chr6B 88.435 1297 99 17 724 1985 502462063 502463343 0.000000e+00 1517.0
15 TraesCS2A01G573800 chr6B 83.871 1302 168 23 926 2191 89967902 89966607 0.000000e+00 1203.0
16 TraesCS2A01G573800 chr6B 89.548 354 31 5 1281 1629 349962462 349962814 6.080000e-121 444.0
17 TraesCS2A01G573800 chr6B 83.957 374 30 14 207 559 658358016 658358380 4.940000e-87 331.0
18 TraesCS2A01G573800 chr6B 82.014 278 39 10 210 480 62538844 62539117 2.400000e-55 226.0
19 TraesCS2A01G573800 chr6B 83.105 219 31 5 1416 1629 471103176 471102959 6.760000e-46 195.0
20 TraesCS2A01G573800 chr1B 88.204 1297 102 19 724 1985 224799487 224798207 0.000000e+00 1500.0
21 TraesCS2A01G573800 chr1B 81.773 203 31 5 1416 1614 580014592 580014792 5.300000e-37 165.0
22 TraesCS2A01G573800 chr1B 91.111 45 4 0 1882 1926 477288319 477288363 7.150000e-06 62.1
23 TraesCS2A01G573800 chr2B 87.403 1294 115 18 724 1985 156238890 156237613 0.000000e+00 1443.0
24 TraesCS2A01G573800 chr2B 97.059 34 1 0 835 868 156238736 156238703 9.250000e-05 58.4
25 TraesCS2A01G573800 chr2B 85.246 61 4 1 802 857 187503712 187503772 9.250000e-05 58.4
26 TraesCS2A01G573800 chr3B 87.350 751 68 7 1275 1999 827119533 827118784 0.000000e+00 835.0
27 TraesCS2A01G573800 chr3B 87.217 751 69 7 1275 1999 827664865 827664116 0.000000e+00 830.0
28 TraesCS2A01G573800 chr3B 90.928 485 33 7 724 1200 827120054 827119573 2.010000e-180 641.0
29 TraesCS2A01G573800 chr3B 90.722 485 34 7 724 1200 827665386 827664905 9.340000e-179 636.0
30 TraesCS2A01G573800 chr4D 93.458 535 25 6 216 746 440274765 440275293 0.000000e+00 785.0
31 TraesCS2A01G573800 chr4D 87.671 73 7 2 148 220 12630806 12630876 1.530000e-12 84.2
32 TraesCS2A01G573800 chr3D 94.714 454 20 2 208 657 400422705 400422252 0.000000e+00 702.0
33 TraesCS2A01G573800 chr3D 92.557 309 20 3 421 728 462468355 462468661 7.860000e-120 440.0
34 TraesCS2A01G573800 chr3D 85.014 347 32 13 200 544 462468098 462468426 3.820000e-88 335.0
35 TraesCS2A01G573800 chr3D 84.834 211 28 4 1416 1624 412972873 412972665 2.410000e-50 209.0
36 TraesCS2A01G573800 chr3D 86.301 73 8 2 148 220 589676955 589677025 7.100000e-11 78.7
37 TraesCS2A01G573800 chr4A 92.576 458 32 2 1940 2396 123476517 123476973 0.000000e+00 656.0
38 TraesCS2A01G573800 chr4A 90.810 457 40 2 1940 2394 357533709 357534165 5.660000e-171 610.0
39 TraesCS2A01G573800 chr4A 96.774 93 3 0 1 93 259167895 259167803 3.190000e-34 156.0
40 TraesCS2A01G573800 chr4A 96.774 93 3 0 1 93 599492121 599492029 3.190000e-34 156.0
41 TraesCS2A01G573800 chr6A 91.703 458 34 4 1940 2396 180952811 180952357 1.210000e-177 632.0
42 TraesCS2A01G573800 chr6A 91.314 449 38 1 1940 2387 230850792 230850344 1.570000e-171 612.0
43 TraesCS2A01G573800 chr6A 96.774 93 3 0 1 93 93467833 93467741 3.190000e-34 156.0
44 TraesCS2A01G573800 chr6A 96.774 93 3 0 1 93 460244915 460245007 3.190000e-34 156.0
45 TraesCS2A01G573800 chr6D 88.136 354 30 6 1281 1629 25436472 25436126 6.160000e-111 411.0
46 TraesCS2A01G573800 chr7B 87.966 349 36 5 1281 1624 725030052 725029705 7.970000e-110 407.0
47 TraesCS2A01G573800 chr7B 90.213 235 19 4 200 430 688447157 688446923 1.080000e-78 303.0
48 TraesCS2A01G573800 chr7B 83.732 209 30 3 1416 1622 64716946 64716740 6.760000e-46 195.0
49 TraesCS2A01G573800 chr7B 82.266 203 29 6 1416 1614 248338062 248338261 4.100000e-38 169.0
50 TraesCS2A01G573800 chr7B 86.014 143 19 1 1488 1629 290310793 290310651 4.130000e-33 152.0
51 TraesCS2A01G573800 chr2D 88.722 266 19 4 1014 1278 292718920 292719175 4.970000e-82 315.0
52 TraesCS2A01G573800 chr2D 86.301 73 8 2 148 220 13967620 13967690 7.100000e-11 78.7
53 TraesCS2A01G573800 chr5B 89.216 204 19 3 434 635 321818597 321818799 3.950000e-63 252.0
54 TraesCS2A01G573800 chr7A 89.163 203 12 5 211 412 173084507 173084700 6.620000e-61 244.0
55 TraesCS2A01G573800 chr7A 94.737 57 3 0 164 220 622503133 622503077 3.280000e-14 89.8
56 TraesCS2A01G573800 chr7A 94.737 57 3 0 164 220 671787080 671787024 3.280000e-14 89.8
57 TraesCS2A01G573800 chr5D 83.412 211 29 6 1416 1622 273653411 273653203 8.740000e-45 191.0
58 TraesCS2A01G573800 chr5D 90.164 61 4 2 160 220 489821751 489821693 7.100000e-11 78.7
59 TraesCS2A01G573800 chr4B 88.462 104 11 1 1522 1624 465960584 465960481 8.990000e-25 124.0
60 TraesCS2A01G573800 chr3A 94.737 57 3 0 164 220 38075473 38075529 3.280000e-14 89.8
61 TraesCS2A01G573800 chr5A 94.643 56 3 0 164 219 516171299 516171354 1.180000e-13 87.9
62 TraesCS2A01G573800 chr7D 87.671 73 5 3 148 220 112485491 112485559 5.490000e-12 82.4
63 TraesCS2A01G573800 chr1D 90.164 61 4 2 160 220 439644576 439644518 7.100000e-11 78.7
64 TraesCS2A01G573800 chrUn 86.301 73 6 3 148 220 24618227 24618295 2.550000e-10 76.8
65 TraesCS2A01G573800 chrUn 86.301 73 6 3 148 220 326602514 326602582 2.550000e-10 76.8
66 TraesCS2A01G573800 chrUn 90.164 61 2 3 160 220 337187365 337187309 2.550000e-10 76.8


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 TraesCS2A01G573800 chr2A 769099147 769101542 2395 True 4425.000000 4425 100.000000 1 2396 1 chr2A.!!$R3 2395
1 TraesCS2A01G573800 chr1A 288304310 288306764 2454 False 1612.500000 2717 94.543500 209 2396 2 chr1A.!!$F5 2187
2 TraesCS2A01G573800 chr1A 230305227 230307895 2668 False 1159.166667 3009 96.835333 208 2396 3 chr1A.!!$F4 2188
3 TraesCS2A01G573800 chr6B 502462063 502463343 1280 False 1517.000000 1517 88.435000 724 1985 1 chr6B.!!$F3 1261
4 TraesCS2A01G573800 chr6B 89966607 89967902 1295 True 1203.000000 1203 83.871000 926 2191 1 chr6B.!!$R1 1265
5 TraesCS2A01G573800 chr1B 224798207 224799487 1280 True 1500.000000 1500 88.204000 724 1985 1 chr1B.!!$R1 1261
6 TraesCS2A01G573800 chr2B 156237613 156238890 1277 True 750.700000 1443 92.231000 724 1985 2 chr2B.!!$R1 1261
7 TraesCS2A01G573800 chr3B 827118784 827120054 1270 True 738.000000 835 89.139000 724 1999 2 chr3B.!!$R1 1275
8 TraesCS2A01G573800 chr3B 827664116 827665386 1270 True 733.000000 830 88.969500 724 1999 2 chr3B.!!$R2 1275
9 TraesCS2A01G573800 chr4D 440274765 440275293 528 False 785.000000 785 93.458000 216 746 1 chr4D.!!$F2 530
10 TraesCS2A01G573800 chr3D 462468098 462468661 563 False 387.500000 440 88.785500 200 728 2 chr3D.!!$F2 528

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
23 24 0.179056 CGCCGGGGAATAATCTGTGT 60.179 55.0 14.46 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 2068 3.565307 TCACTTCACCTTTCCTGCAAAT 58.435 40.909 0.0 0.0 0.0 2.32 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
17 18 2.113139 CAGGCGCCGGGGAATAAT 59.887 61.111 24.68 0.00 0.00 1.28
18 19 1.966451 CAGGCGCCGGGGAATAATC 60.966 63.158 24.68 2.49 0.00 1.75
19 20 2.147387 AGGCGCCGGGGAATAATCT 61.147 57.895 24.68 5.95 0.00 2.40
20 21 1.966451 GGCGCCGGGGAATAATCTG 60.966 63.158 24.68 0.00 0.00 2.90
21 22 1.227853 GCGCCGGGGAATAATCTGT 60.228 57.895 24.68 0.00 0.00 3.41
22 23 1.507141 GCGCCGGGGAATAATCTGTG 61.507 60.000 24.68 0.00 0.00 3.66
23 24 0.179056 CGCCGGGGAATAATCTGTGT 60.179 55.000 14.46 0.00 0.00 3.72
24 25 1.308998 GCCGGGGAATAATCTGTGTG 58.691 55.000 2.18 0.00 0.00 3.82
25 26 1.308998 CCGGGGAATAATCTGTGTGC 58.691 55.000 0.00 0.00 0.00 4.57
26 27 1.408127 CCGGGGAATAATCTGTGTGCA 60.408 52.381 0.00 0.00 0.00 4.57
27 28 2.575532 CGGGGAATAATCTGTGTGCAT 58.424 47.619 0.00 0.00 0.00 3.96
28 29 3.495983 CCGGGGAATAATCTGTGTGCATA 60.496 47.826 0.00 0.00 0.00 3.14
29 30 3.498397 CGGGGAATAATCTGTGTGCATAC 59.502 47.826 6.65 6.65 0.00 2.39
30 31 4.718961 GGGGAATAATCTGTGTGCATACT 58.281 43.478 15.05 0.00 0.00 2.12
31 32 5.510690 CGGGGAATAATCTGTGTGCATACTA 60.511 44.000 15.05 3.54 0.00 1.82
32 33 5.701290 GGGGAATAATCTGTGTGCATACTAC 59.299 44.000 15.05 1.09 0.00 2.73
33 34 5.405571 GGGAATAATCTGTGTGCATACTACG 59.594 44.000 15.05 3.78 0.00 3.51
34 35 5.983720 GGAATAATCTGTGTGCATACTACGT 59.016 40.000 15.05 0.00 0.00 3.57
35 36 6.479001 GGAATAATCTGTGTGCATACTACGTT 59.521 38.462 15.05 7.12 0.00 3.99
36 37 7.011109 GGAATAATCTGTGTGCATACTACGTTT 59.989 37.037 15.05 7.22 0.00 3.60
37 38 5.530519 AATCTGTGTGCATACTACGTTTG 57.469 39.130 15.05 0.00 0.00 2.93
38 39 2.734606 TCTGTGTGCATACTACGTTTGC 59.265 45.455 15.05 0.00 40.05 3.68
39 40 1.457683 TGTGTGCATACTACGTTTGCG 59.542 47.619 15.05 0.00 41.91 4.85
40 41 1.722464 GTGTGCATACTACGTTTGCGA 59.278 47.619 6.31 0.00 41.91 5.10
41 42 1.989864 TGTGCATACTACGTTTGCGAG 59.010 47.619 0.00 0.00 41.91 5.03
42 43 2.256174 GTGCATACTACGTTTGCGAGA 58.744 47.619 0.00 0.00 41.91 4.04
43 44 2.664568 GTGCATACTACGTTTGCGAGAA 59.335 45.455 0.00 0.00 41.91 2.87
44 45 2.664568 TGCATACTACGTTTGCGAGAAC 59.335 45.455 0.00 0.00 41.91 3.01
45 46 2.664568 GCATACTACGTTTGCGAGAACA 59.335 45.455 0.00 0.00 42.00 3.18
46 47 3.306166 GCATACTACGTTTGCGAGAACAT 59.694 43.478 0.00 0.00 42.00 2.71
47 48 4.201685 GCATACTACGTTTGCGAGAACATT 60.202 41.667 0.00 0.00 42.00 2.71
48 49 5.481472 CATACTACGTTTGCGAGAACATTC 58.519 41.667 0.00 0.00 42.00 2.67
49 50 3.386486 ACTACGTTTGCGAGAACATTCA 58.614 40.909 0.00 0.00 42.00 2.57
50 51 2.663279 ACGTTTGCGAGAACATTCAC 57.337 45.000 0.00 0.00 42.00 3.18
51 52 1.937223 ACGTTTGCGAGAACATTCACA 59.063 42.857 0.00 0.00 42.00 3.58
52 53 2.548057 ACGTTTGCGAGAACATTCACAT 59.452 40.909 0.00 0.00 42.00 3.21
53 54 2.904319 CGTTTGCGAGAACATTCACATG 59.096 45.455 0.00 0.00 41.33 3.21
54 55 3.363871 CGTTTGCGAGAACATTCACATGA 60.364 43.478 0.00 0.00 41.33 3.07
55 56 4.669965 CGTTTGCGAGAACATTCACATGAT 60.670 41.667 0.00 0.00 41.33 2.45
56 57 4.345271 TTGCGAGAACATTCACATGATG 57.655 40.909 0.00 0.00 34.11 3.07
57 58 2.679336 TGCGAGAACATTCACATGATGG 59.321 45.455 0.00 0.00 34.11 3.51
58 59 2.540361 GCGAGAACATTCACATGATGGC 60.540 50.000 0.00 0.00 34.11 4.40
59 60 2.679336 CGAGAACATTCACATGATGGCA 59.321 45.455 0.00 0.00 34.11 4.92
60 61 3.314357 CGAGAACATTCACATGATGGCAT 59.686 43.478 0.00 0.00 34.11 4.40
61 62 4.554134 CGAGAACATTCACATGATGGCATC 60.554 45.833 20.52 20.52 34.11 3.91
62 63 3.635373 AGAACATTCACATGATGGCATCC 59.365 43.478 23.92 7.43 34.11 3.51
63 64 1.951602 ACATTCACATGATGGCATCCG 59.048 47.619 23.92 17.10 34.11 4.18
64 65 2.223745 CATTCACATGATGGCATCCGA 58.776 47.619 23.92 12.47 30.68 4.55
65 66 2.416680 TTCACATGATGGCATCCGAA 57.583 45.000 23.92 17.04 30.68 4.30
66 67 2.416680 TCACATGATGGCATCCGAAA 57.583 45.000 23.92 6.36 30.68 3.46
67 68 2.016318 TCACATGATGGCATCCGAAAC 58.984 47.619 23.92 0.00 30.68 2.78
68 69 1.016627 ACATGATGGCATCCGAAACG 58.983 50.000 23.92 8.77 30.68 3.60
69 70 1.298602 CATGATGGCATCCGAAACGA 58.701 50.000 23.92 4.45 30.68 3.85
70 71 1.262417 CATGATGGCATCCGAAACGAG 59.738 52.381 23.92 2.25 30.68 4.18
71 72 1.089481 TGATGGCATCCGAAACGAGC 61.089 55.000 23.92 0.00 0.00 5.03
72 73 1.078497 ATGGCATCCGAAACGAGCA 60.078 52.632 0.00 0.00 0.00 4.26
73 74 1.091771 ATGGCATCCGAAACGAGCAG 61.092 55.000 0.00 0.00 0.00 4.24
74 75 1.447838 GGCATCCGAAACGAGCAGA 60.448 57.895 0.00 0.00 0.00 4.26
75 76 0.811616 GGCATCCGAAACGAGCAGAT 60.812 55.000 0.00 0.00 0.00 2.90
76 77 0.579156 GCATCCGAAACGAGCAGATC 59.421 55.000 0.00 0.00 0.00 2.75
77 78 1.804372 GCATCCGAAACGAGCAGATCT 60.804 52.381 0.00 0.00 0.00 2.75
78 79 2.123342 CATCCGAAACGAGCAGATCTC 58.877 52.381 0.00 0.00 38.47 2.75
79 80 1.173913 TCCGAAACGAGCAGATCTCA 58.826 50.000 0.00 0.00 41.98 3.27
80 81 1.544246 TCCGAAACGAGCAGATCTCAA 59.456 47.619 0.00 0.00 41.98 3.02
81 82 2.029380 TCCGAAACGAGCAGATCTCAAA 60.029 45.455 0.00 0.00 41.98 2.69
82 83 2.346847 CCGAAACGAGCAGATCTCAAAG 59.653 50.000 0.00 0.00 41.98 2.77
83 84 3.245797 CGAAACGAGCAGATCTCAAAGA 58.754 45.455 0.00 0.00 41.98 2.52
84 85 3.060098 CGAAACGAGCAGATCTCAAAGAC 59.940 47.826 0.00 0.00 41.98 3.01
85 86 3.667497 AACGAGCAGATCTCAAAGACA 57.333 42.857 0.00 0.00 41.98 3.41
86 87 3.229276 ACGAGCAGATCTCAAAGACAG 57.771 47.619 0.00 0.00 41.98 3.51
87 88 2.094286 ACGAGCAGATCTCAAAGACAGG 60.094 50.000 0.00 0.00 41.98 4.00
88 89 2.165234 CGAGCAGATCTCAAAGACAGGA 59.835 50.000 0.00 0.00 41.98 3.86
89 90 3.734597 CGAGCAGATCTCAAAGACAGGAG 60.735 52.174 0.00 0.00 41.98 3.69
90 91 3.172339 AGCAGATCTCAAAGACAGGAGT 58.828 45.455 0.00 0.00 32.93 3.85
91 92 3.055963 AGCAGATCTCAAAGACAGGAGTG 60.056 47.826 0.00 0.00 32.93 3.51
92 93 3.859443 CAGATCTCAAAGACAGGAGTGG 58.141 50.000 0.00 0.00 32.93 4.00
93 94 3.513119 CAGATCTCAAAGACAGGAGTGGA 59.487 47.826 0.00 0.00 32.93 4.02
94 95 4.020751 CAGATCTCAAAGACAGGAGTGGAA 60.021 45.833 0.00 0.00 32.93 3.53
95 96 4.594920 AGATCTCAAAGACAGGAGTGGAAA 59.405 41.667 0.00 0.00 32.93 3.13
96 97 4.982241 TCTCAAAGACAGGAGTGGAAAT 57.018 40.909 0.00 0.00 32.93 2.17
97 98 5.310409 TCTCAAAGACAGGAGTGGAAATT 57.690 39.130 0.00 0.00 32.93 1.82
98 99 5.065914 TCTCAAAGACAGGAGTGGAAATTG 58.934 41.667 0.00 0.00 32.93 2.32
99 100 4.144297 TCAAAGACAGGAGTGGAAATTGG 58.856 43.478 0.00 0.00 0.00 3.16
100 101 3.884037 AAGACAGGAGTGGAAATTGGT 57.116 42.857 0.00 0.00 0.00 3.67
101 102 3.146104 AGACAGGAGTGGAAATTGGTG 57.854 47.619 0.00 0.00 0.00 4.17
102 103 2.711009 AGACAGGAGTGGAAATTGGTGA 59.289 45.455 0.00 0.00 0.00 4.02
103 104 3.138283 AGACAGGAGTGGAAATTGGTGAA 59.862 43.478 0.00 0.00 0.00 3.18
104 105 3.888930 GACAGGAGTGGAAATTGGTGAAA 59.111 43.478 0.00 0.00 0.00 2.69
105 106 4.482990 ACAGGAGTGGAAATTGGTGAAAT 58.517 39.130 0.00 0.00 0.00 2.17
106 107 4.901250 ACAGGAGTGGAAATTGGTGAAATT 59.099 37.500 0.00 0.00 40.32 1.82
107 108 5.221501 ACAGGAGTGGAAATTGGTGAAATTG 60.222 40.000 0.00 0.00 38.52 2.32
108 109 4.901250 AGGAGTGGAAATTGGTGAAATTGT 59.099 37.500 0.00 0.00 38.52 2.71
109 110 6.015519 CAGGAGTGGAAATTGGTGAAATTGTA 60.016 38.462 0.00 0.00 38.52 2.41
110 111 6.725834 AGGAGTGGAAATTGGTGAAATTGTAT 59.274 34.615 0.00 0.00 38.52 2.29
111 112 7.893302 AGGAGTGGAAATTGGTGAAATTGTATA 59.107 33.333 0.00 0.00 38.52 1.47
112 113 8.695456 GGAGTGGAAATTGGTGAAATTGTATAT 58.305 33.333 0.00 0.00 38.52 0.86
115 116 9.965824 GTGGAAATTGGTGAAATTGTATATAGG 57.034 33.333 0.00 0.00 38.52 2.57
116 117 9.928618 TGGAAATTGGTGAAATTGTATATAGGA 57.071 29.630 0.00 0.00 38.52 2.94
138 139 8.986929 AGGAGAAATTTCCATTCTTGTATAGG 57.013 34.615 14.61 0.00 39.84 2.57
139 140 8.781951 AGGAGAAATTTCCATTCTTGTATAGGA 58.218 33.333 14.61 0.00 39.84 2.94
140 141 9.061435 GGAGAAATTTCCATTCTTGTATAGGAG 57.939 37.037 14.61 0.00 37.26 3.69
141 142 9.838339 GAGAAATTTCCATTCTTGTATAGGAGA 57.162 33.333 14.61 0.00 37.26 3.71
147 148 9.753674 TTTCCATTCTTGTATAGGAGAAATTGT 57.246 29.630 2.75 0.00 35.69 2.71
174 175 5.521906 AGCTAGCTAATTCGAATGTCTCA 57.478 39.130 17.69 0.00 0.00 3.27
175 176 5.285651 AGCTAGCTAATTCGAATGTCTCAC 58.714 41.667 17.69 5.33 0.00 3.51
176 177 5.043903 GCTAGCTAATTCGAATGTCTCACA 58.956 41.667 12.25 0.00 0.00 3.58
177 178 5.520288 GCTAGCTAATTCGAATGTCTCACAA 59.480 40.000 12.25 0.00 0.00 3.33
178 179 5.786401 AGCTAATTCGAATGTCTCACAAC 57.214 39.130 12.25 0.00 0.00 3.32
179 180 4.631813 AGCTAATTCGAATGTCTCACAACC 59.368 41.667 12.25 0.00 0.00 3.77
180 181 4.391830 GCTAATTCGAATGTCTCACAACCA 59.608 41.667 12.25 0.00 0.00 3.67
181 182 5.065218 GCTAATTCGAATGTCTCACAACCAT 59.935 40.000 12.25 0.00 0.00 3.55
182 183 5.551760 AATTCGAATGTCTCACAACCATC 57.448 39.130 12.25 0.00 0.00 3.51
183 184 3.676291 TCGAATGTCTCACAACCATCA 57.324 42.857 0.00 0.00 0.00 3.07
184 185 4.206477 TCGAATGTCTCACAACCATCAT 57.794 40.909 0.00 0.00 0.00 2.45
185 186 4.578871 TCGAATGTCTCACAACCATCATT 58.421 39.130 0.00 0.00 0.00 2.57
186 187 5.729510 TCGAATGTCTCACAACCATCATTA 58.270 37.500 0.00 0.00 0.00 1.90
187 188 6.169800 TCGAATGTCTCACAACCATCATTAA 58.830 36.000 0.00 0.00 0.00 1.40
188 189 6.823182 TCGAATGTCTCACAACCATCATTAAT 59.177 34.615 0.00 0.00 0.00 1.40
189 190 7.336679 TCGAATGTCTCACAACCATCATTAATT 59.663 33.333 0.00 0.00 0.00 1.40
190 191 8.611757 CGAATGTCTCACAACCATCATTAATTA 58.388 33.333 0.00 0.00 0.00 1.40
198 199 9.853555 TCACAACCATCATTAATTAATTCACAC 57.146 29.630 8.01 0.00 0.00 3.82
242 243 8.923838 ATAGGATGGGTCTATTCTGATAACAT 57.076 34.615 0.00 0.00 0.00 2.71
713 1218 2.594303 CAGCACTTTCCCGTGGCA 60.594 61.111 0.00 0.00 35.47 4.92
1090 1611 4.379243 CAGGTGCCGCCGAGTTCT 62.379 66.667 0.00 0.00 43.70 3.01
1414 1966 2.034878 AGAGCATCAGGAGACGCATAA 58.965 47.619 0.00 0.00 37.82 1.90
1571 2127 2.224185 GGCCCGTTCCTCAATTTTGTTT 60.224 45.455 0.00 0.00 0.00 2.83
1831 2405 2.697654 ACATCTCAAAGCAGCTCACTC 58.302 47.619 0.00 0.00 0.00 3.51
1857 2431 4.634184 TTAGATGTAGTTCACTCGCTCC 57.366 45.455 0.00 0.00 0.00 4.70
1908 2482 3.881795 CTTGATGTCAAGTGCACTTCAC 58.118 45.455 28.97 26.87 46.11 3.18
1911 2485 1.953559 TGTCAAGTGCACTTCACCTC 58.046 50.000 27.82 16.70 46.81 3.85
1927 2501 5.584253 TCACCTCGTTTTGGAAAATTTGA 57.416 34.783 0.00 0.00 0.00 2.69
1958 2532 2.417586 GGTAGTATTGCGGTTCACCAAC 59.582 50.000 0.00 0.00 35.14 3.77
1984 2558 1.354040 CGTGAAGTGCACTCCATCTC 58.646 55.000 21.95 14.14 45.49 2.75
1990 2564 1.070758 AGTGCACTCCATCTCGTTTGT 59.929 47.619 15.25 0.00 0.00 2.83
2007 2581 6.197981 TCGTTTGTAAAAATTTACGTCCCAC 58.802 36.000 10.51 3.53 44.52 4.61
2156 2730 5.830912 TGTCCAATGAAGTGCAGTTTTTAG 58.169 37.500 8.48 0.00 0.00 1.85
2169 2743 9.338622 AGTGCAGTTTTTAGTCTAAATAAGTGT 57.661 29.630 21.06 10.31 30.58 3.55
2170 2744 9.382244 GTGCAGTTTTTAGTCTAAATAAGTGTG 57.618 33.333 21.06 11.26 30.58 3.82
2344 3197 7.994425 TGATAGTGTTGTGGTTCATTTACAT 57.006 32.000 0.00 0.00 0.00 2.29
2378 3231 5.703130 AGTGCACTCTAATTTCTTGTCCTTC 59.297 40.000 15.25 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.966451 GATTATTCCCCGGCGCCTG 60.966 63.158 26.68 19.17 0.00 4.85
1 2 2.147387 AGATTATTCCCCGGCGCCT 61.147 57.895 26.68 6.90 0.00 5.52
2 3 1.966451 CAGATTATTCCCCGGCGCC 60.966 63.158 19.07 19.07 0.00 6.53
3 4 1.227853 ACAGATTATTCCCCGGCGC 60.228 57.895 0.00 0.00 0.00 6.53
5 6 1.308998 CACACAGATTATTCCCCGGC 58.691 55.000 0.00 0.00 0.00 6.13
7 8 2.036958 TGCACACAGATTATTCCCCG 57.963 50.000 0.00 0.00 0.00 5.73
8 9 4.718961 AGTATGCACACAGATTATTCCCC 58.281 43.478 0.00 0.00 0.00 4.81
9 10 5.405571 CGTAGTATGCACACAGATTATTCCC 59.594 44.000 0.00 0.00 0.00 3.97
10 11 5.983720 ACGTAGTATGCACACAGATTATTCC 59.016 40.000 0.00 0.00 41.94 3.01
11 12 7.464830 AACGTAGTATGCACACAGATTATTC 57.535 36.000 0.00 0.00 45.00 1.75
12 13 7.676338 GCAAACGTAGTATGCACACAGATTATT 60.676 37.037 0.00 0.00 45.00 1.40
13 14 6.238103 GCAAACGTAGTATGCACACAGATTAT 60.238 38.462 0.00 0.00 45.00 1.28
14 15 5.062934 GCAAACGTAGTATGCACACAGATTA 59.937 40.000 0.00 0.00 45.00 1.75
15 16 4.142902 GCAAACGTAGTATGCACACAGATT 60.143 41.667 0.00 0.00 45.00 2.40
16 17 3.370978 GCAAACGTAGTATGCACACAGAT 59.629 43.478 0.00 0.00 45.00 2.90
17 18 2.734606 GCAAACGTAGTATGCACACAGA 59.265 45.455 0.00 0.00 45.00 3.41
18 19 2.472235 CGCAAACGTAGTATGCACACAG 60.472 50.000 0.00 0.00 45.00 3.66
19 20 1.457683 CGCAAACGTAGTATGCACACA 59.542 47.619 0.00 0.00 45.00 3.72
20 21 1.722464 TCGCAAACGTAGTATGCACAC 59.278 47.619 13.57 0.00 45.00 3.82
21 22 1.989864 CTCGCAAACGTAGTATGCACA 59.010 47.619 13.57 0.00 45.00 4.57
22 23 2.256174 TCTCGCAAACGTAGTATGCAC 58.744 47.619 13.57 0.00 45.00 4.57
23 24 2.640346 TCTCGCAAACGTAGTATGCA 57.360 45.000 13.57 0.00 45.00 3.96
24 25 2.664568 TGTTCTCGCAAACGTAGTATGC 59.335 45.455 0.00 0.00 45.00 3.14
25 26 5.061684 TGAATGTTCTCGCAAACGTAGTATG 59.938 40.000 0.00 0.00 45.00 2.39
26 27 5.061808 GTGAATGTTCTCGCAAACGTAGTAT 59.938 40.000 0.00 0.00 45.00 2.12
27 28 4.383649 GTGAATGTTCTCGCAAACGTAGTA 59.616 41.667 0.00 0.00 45.00 1.82
28 29 5.265760 TGTGAATGTTCTCGCAAACGTAGT 61.266 41.667 0.00 0.00 41.18 2.73
29 30 3.183574 TGTGAATGTTCTCGCAAACGTAG 59.816 43.478 0.00 0.00 41.18 3.51
30 31 3.124560 TGTGAATGTTCTCGCAAACGTA 58.875 40.909 0.00 0.00 41.18 3.57
31 32 1.937223 TGTGAATGTTCTCGCAAACGT 59.063 42.857 0.00 0.00 41.18 3.99
32 33 2.661504 TGTGAATGTTCTCGCAAACG 57.338 45.000 0.00 0.00 42.01 3.60
33 34 4.145876 TCATGTGAATGTTCTCGCAAAC 57.854 40.909 0.00 0.00 39.18 2.93
34 35 4.379708 CCATCATGTGAATGTTCTCGCAAA 60.380 41.667 0.00 0.00 39.18 3.68
35 36 3.127376 CCATCATGTGAATGTTCTCGCAA 59.873 43.478 0.00 0.00 39.18 4.85
36 37 2.679336 CCATCATGTGAATGTTCTCGCA 59.321 45.455 0.00 0.00 39.99 5.10
37 38 2.540361 GCCATCATGTGAATGTTCTCGC 60.540 50.000 0.00 0.00 0.00 5.03
38 39 2.679336 TGCCATCATGTGAATGTTCTCG 59.321 45.455 0.00 0.00 0.00 4.04
39 40 4.261489 GGATGCCATCATGTGAATGTTCTC 60.261 45.833 7.06 0.00 31.96 2.87
40 41 3.635373 GGATGCCATCATGTGAATGTTCT 59.365 43.478 7.06 0.00 31.96 3.01
41 42 3.549423 CGGATGCCATCATGTGAATGTTC 60.549 47.826 7.06 0.00 31.96 3.18
42 43 2.359848 CGGATGCCATCATGTGAATGTT 59.640 45.455 7.06 0.00 31.96 2.71
43 44 1.951602 CGGATGCCATCATGTGAATGT 59.048 47.619 7.06 0.00 31.96 2.71
44 45 2.223745 TCGGATGCCATCATGTGAATG 58.776 47.619 7.06 0.00 31.96 2.67
45 46 2.643995 TCGGATGCCATCATGTGAAT 57.356 45.000 7.06 0.00 31.96 2.57
46 47 2.416680 TTCGGATGCCATCATGTGAA 57.583 45.000 7.06 2.36 31.96 3.18
47 48 2.016318 GTTTCGGATGCCATCATGTGA 58.984 47.619 7.06 0.00 31.96 3.58
48 49 1.268184 CGTTTCGGATGCCATCATGTG 60.268 52.381 7.06 0.00 31.96 3.21
49 50 1.016627 CGTTTCGGATGCCATCATGT 58.983 50.000 7.06 0.00 31.96 3.21
50 51 1.262417 CTCGTTTCGGATGCCATCATG 59.738 52.381 7.06 0.00 31.96 3.07
51 52 1.586422 CTCGTTTCGGATGCCATCAT 58.414 50.000 7.06 0.00 35.17 2.45
52 53 1.089481 GCTCGTTTCGGATGCCATCA 61.089 55.000 7.06 0.00 0.00 3.07
53 54 1.089481 TGCTCGTTTCGGATGCCATC 61.089 55.000 0.00 0.00 0.00 3.51
54 55 1.078497 TGCTCGTTTCGGATGCCAT 60.078 52.632 0.00 0.00 0.00 4.40
55 56 1.741401 CTGCTCGTTTCGGATGCCA 60.741 57.895 0.00 0.00 0.00 4.92
56 57 0.811616 ATCTGCTCGTTTCGGATGCC 60.812 55.000 0.00 0.00 0.00 4.40
57 58 0.579156 GATCTGCTCGTTTCGGATGC 59.421 55.000 0.00 0.00 30.21 3.91
58 59 2.123342 GAGATCTGCTCGTTTCGGATG 58.877 52.381 0.00 0.00 33.17 3.51
59 60 2.500509 GAGATCTGCTCGTTTCGGAT 57.499 50.000 0.00 0.00 33.17 4.18
68 69 3.195396 ACTCCTGTCTTTGAGATCTGCTC 59.805 47.826 0.00 0.00 44.21 4.26
69 70 3.055963 CACTCCTGTCTTTGAGATCTGCT 60.056 47.826 0.00 0.00 32.84 4.24
70 71 3.260740 CACTCCTGTCTTTGAGATCTGC 58.739 50.000 0.00 0.00 32.84 4.26
71 72 3.513119 TCCACTCCTGTCTTTGAGATCTG 59.487 47.826 0.00 0.00 32.84 2.90
72 73 3.784178 TCCACTCCTGTCTTTGAGATCT 58.216 45.455 0.00 0.00 32.84 2.75
73 74 4.543590 TTCCACTCCTGTCTTTGAGATC 57.456 45.455 0.00 0.00 32.84 2.75
74 75 4.982241 TTTCCACTCCTGTCTTTGAGAT 57.018 40.909 0.00 0.00 32.84 2.75
75 76 4.982241 ATTTCCACTCCTGTCTTTGAGA 57.018 40.909 0.00 0.00 32.84 3.27
76 77 4.217118 CCAATTTCCACTCCTGTCTTTGAG 59.783 45.833 0.00 0.00 34.73 3.02
77 78 4.144297 CCAATTTCCACTCCTGTCTTTGA 58.856 43.478 0.00 0.00 0.00 2.69
78 79 3.891366 ACCAATTTCCACTCCTGTCTTTG 59.109 43.478 0.00 0.00 0.00 2.77
79 80 3.891366 CACCAATTTCCACTCCTGTCTTT 59.109 43.478 0.00 0.00 0.00 2.52
80 81 3.138283 TCACCAATTTCCACTCCTGTCTT 59.862 43.478 0.00 0.00 0.00 3.01
81 82 2.711009 TCACCAATTTCCACTCCTGTCT 59.289 45.455 0.00 0.00 0.00 3.41
82 83 3.140325 TCACCAATTTCCACTCCTGTC 57.860 47.619 0.00 0.00 0.00 3.51
83 84 3.593442 TTCACCAATTTCCACTCCTGT 57.407 42.857 0.00 0.00 0.00 4.00
84 85 5.221501 ACAATTTCACCAATTTCCACTCCTG 60.222 40.000 0.00 0.00 32.24 3.86
85 86 4.901250 ACAATTTCACCAATTTCCACTCCT 59.099 37.500 0.00 0.00 32.24 3.69
86 87 5.213891 ACAATTTCACCAATTTCCACTCC 57.786 39.130 0.00 0.00 32.24 3.85
89 90 9.965824 CCTATATACAATTTCACCAATTTCCAC 57.034 33.333 0.00 0.00 32.24 4.02
90 91 9.928618 TCCTATATACAATTTCACCAATTTCCA 57.071 29.630 0.00 0.00 32.24 3.53
113 114 8.781951 TCCTATACAAGAATGGAAATTTCTCCT 58.218 33.333 17.42 7.13 36.35 3.69
114 115 8.980481 TCCTATACAAGAATGGAAATTTCTCC 57.020 34.615 17.42 3.66 32.33 3.71
115 116 9.838339 TCTCCTATACAAGAATGGAAATTTCTC 57.162 33.333 17.42 7.84 32.33 2.87
121 122 9.753674 ACAATTTCTCCTATACAAGAATGGAAA 57.246 29.630 0.00 0.00 31.89 3.13
148 149 8.961634 TGAGACATTCGAATTAGCTAGCTATAT 58.038 33.333 24.69 16.20 0.00 0.86
149 150 8.237949 GTGAGACATTCGAATTAGCTAGCTATA 58.762 37.037 24.69 15.51 0.00 1.31
150 151 7.087639 GTGAGACATTCGAATTAGCTAGCTAT 58.912 38.462 24.69 11.45 0.00 2.97
151 152 6.039382 TGTGAGACATTCGAATTAGCTAGCTA 59.961 38.462 20.67 20.67 0.00 3.32
152 153 5.163509 TGTGAGACATTCGAATTAGCTAGCT 60.164 40.000 23.12 23.12 0.00 3.32
153 154 5.043903 TGTGAGACATTCGAATTAGCTAGC 58.956 41.667 8.21 6.62 0.00 3.42
154 155 6.019479 GGTTGTGAGACATTCGAATTAGCTAG 60.019 42.308 8.21 0.00 0.00 3.42
155 156 5.810587 GGTTGTGAGACATTCGAATTAGCTA 59.189 40.000 8.21 0.00 0.00 3.32
156 157 4.631813 GGTTGTGAGACATTCGAATTAGCT 59.368 41.667 8.21 5.91 0.00 3.32
157 158 4.391830 TGGTTGTGAGACATTCGAATTAGC 59.608 41.667 8.21 0.69 0.00 3.09
158 159 6.313658 TGATGGTTGTGAGACATTCGAATTAG 59.686 38.462 8.21 0.45 0.00 1.73
159 160 6.169800 TGATGGTTGTGAGACATTCGAATTA 58.830 36.000 8.21 0.00 0.00 1.40
160 161 5.003160 TGATGGTTGTGAGACATTCGAATT 58.997 37.500 8.21 0.00 0.00 2.17
161 162 4.578871 TGATGGTTGTGAGACATTCGAAT 58.421 39.130 4.39 4.39 0.00 3.34
162 163 4.001618 TGATGGTTGTGAGACATTCGAA 57.998 40.909 0.00 0.00 0.00 3.71
163 164 3.676291 TGATGGTTGTGAGACATTCGA 57.324 42.857 0.00 0.00 0.00 3.71
164 165 4.952262 AATGATGGTTGTGAGACATTCG 57.048 40.909 0.00 0.00 0.00 3.34
172 173 9.853555 GTGTGAATTAATTAATGATGGTTGTGA 57.146 29.630 11.42 0.00 0.00 3.58
173 174 9.636879 TGTGTGAATTAATTAATGATGGTTGTG 57.363 29.630 11.42 0.00 0.00 3.33
266 267 6.293462 GGGTGTTATCAAAATAAGCTCCGATC 60.293 42.308 0.00 0.00 0.00 3.69
268 269 4.879545 GGGTGTTATCAAAATAAGCTCCGA 59.120 41.667 0.00 0.00 0.00 4.55
662 1167 4.323477 GCGTGGTGGTAGGTGGCA 62.323 66.667 0.00 0.00 0.00 4.92
713 1218 2.365237 GGAGAAGTAGGGGGCGGT 60.365 66.667 0.00 0.00 0.00 5.68
1512 2068 3.565307 TCACTTCACCTTTCCTGCAAAT 58.435 40.909 0.00 0.00 0.00 2.32
1571 2127 7.319646 ACTAATGAAGTGCAGTTTTCAACAAA 58.680 30.769 8.48 0.00 36.93 2.83
1831 2405 6.740110 AGCGAGTGAACTACATCTAATAAGG 58.260 40.000 0.00 0.00 0.00 2.69
1908 2482 7.593825 AGACTATCAAATTTTCCAAAACGAGG 58.406 34.615 0.00 0.00 0.00 4.63
1911 2485 7.295201 TCGAGACTATCAAATTTTCCAAAACG 58.705 34.615 0.00 0.00 0.00 3.60
1927 2501 3.752222 CCGCAATACTACCTCGAGACTAT 59.248 47.826 15.71 0.00 0.00 2.12
1984 2558 5.970023 TGTGGGACGTAAATTTTTACAAACG 59.030 36.000 12.33 7.24 42.34 3.60
2023 2597 2.229675 TCAGACTGACAAGTGCACTG 57.770 50.000 22.49 16.62 36.52 3.66
2156 2730 8.283291 CAGACAGAAAACCACACTTATTTAGAC 58.717 37.037 0.00 0.00 0.00 2.59
2169 2743 3.213206 ACTGCATCAGACAGAAAACCA 57.787 42.857 0.29 0.00 38.55 3.67
2170 2744 3.123621 CGTACTGCATCAGACAGAAAACC 59.876 47.826 0.29 0.00 38.55 3.27


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

AutoCloner maintained by Alex Coulton.