Multiple sequence alignment - TraesCS2B01G095000

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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 TraesCS2B01G095000 chr2B 100.000 4066 0 0 1 4066 55033651 55029586 0.000000e+00 7509
1 TraesCS2B01G095000 chr2B 78.977 1584 178 73 791 2279 122926368 122927891 0.000000e+00 937
2 TraesCS2B01G095000 chr2B 78.760 1549 183 75 828 2286 122992210 122993702 0.000000e+00 904
3 TraesCS2B01G095000 chr2B 87.386 769 52 18 2675 3423 54785780 54785037 0.000000e+00 841
4 TraesCS2B01G095000 chr2B 85.345 812 69 21 2627 3409 54885845 54885055 0.000000e+00 795
5 TraesCS2B01G095000 chr2B 92.806 417 27 1 1167 1583 54887936 54887523 5.820000e-168 601
6 TraesCS2B01G095000 chr2B 85.664 572 64 13 1874 2437 54887307 54886746 1.630000e-163 586
7 TraesCS2B01G095000 chr2B 86.621 441 39 10 1186 1613 54787121 54786688 1.710000e-128 470
8 TraesCS2B01G095000 chr2B 86.408 412 38 11 1213 1607 55210047 55209637 6.240000e-118 435
9 TraesCS2B01G095000 chr2B 86.139 404 42 10 1896 2286 55513999 55513597 1.350000e-114 424
10 TraesCS2B01G095000 chr2B 86.420 405 32 15 3680 4066 54783947 54783548 4.860000e-114 422
11 TraesCS2B01G095000 chr2B 85.751 386 38 6 802 1183 54888358 54887986 3.810000e-105 392
12 TraesCS2B01G095000 chr2B 83.834 433 47 13 765 1177 54787523 54787094 1.370000e-104 390
13 TraesCS2B01G095000 chr2B 79.813 535 82 16 2717 3232 55226041 55225514 2.310000e-97 366
14 TraesCS2B01G095000 chr2B 80.922 477 74 11 2721 3188 55224725 55224257 1.070000e-95 361
15 TraesCS2B01G095000 chr2B 88.215 297 26 6 871 1159 55210336 55210041 3.010000e-91 346
16 TraesCS2B01G095000 chr2B 84.127 378 29 16 2481 2841 54886318 54885955 1.810000e-88 337
17 TraesCS2B01G095000 chr2B 84.375 352 40 7 1946 2288 54786620 54786275 8.420000e-87 331
18 TraesCS2B01G095000 chr2B 87.031 293 31 2 1993 2279 55698596 55698305 1.410000e-84 324
19 TraesCS2B01G095000 chr2B 85.358 321 32 10 849 1159 55227605 55227290 6.560000e-83 318
20 TraesCS2B01G095000 chr2D 91.115 1587 66 20 740 2286 33165527 33163976 0.000000e+00 2080
21 TraesCS2B01G095000 chr2D 90.982 1120 35 28 2312 3423 33163895 33162834 0.000000e+00 1448
22 TraesCS2B01G095000 chr2D 78.974 1560 186 72 812 2286 79084882 79086384 0.000000e+00 933
23 TraesCS2B01G095000 chr2D 84.841 818 73 26 2624 3423 33047279 33046495 0.000000e+00 776
24 TraesCS2B01G095000 chr2D 85.129 659 64 20 1167 1821 33049308 33048680 0.000000e+00 643
25 TraesCS2B01G095000 chr2D 94.344 389 18 4 3680 4066 33161167 33160781 9.730000e-166 593
26 TraesCS2B01G095000 chr2D 88.251 383 39 2 1186 1568 32992652 32992276 1.720000e-123 453
27 TraesCS2B01G095000 chr2D 87.733 375 28 8 1906 2276 33048663 33048303 4.860000e-114 422
28 TraesCS2B01G095000 chr2D 87.332 371 34 8 802 1165 33049740 33049376 2.920000e-111 412
29 TraesCS2B01G095000 chr2D 87.166 374 21 13 2481 2841 33047745 33047386 2.280000e-107 399
30 TraesCS2B01G095000 chr2D 82.571 459 52 13 1993 2437 33580389 33579945 2.970000e-101 379
31 TraesCS2B01G095000 chr2D 87.500 296 30 3 1991 2279 33373441 33373146 6.510000e-88 335
32 TraesCS2B01G095000 chr2D 85.538 325 32 5 853 1177 32992934 32992625 3.920000e-85 326
33 TraesCS2B01G095000 chr2D 86.577 298 30 7 867 1159 33581161 33580869 1.820000e-83 320
34 TraesCS2B01G095000 chr2D 95.789 190 8 0 3423 3612 33162756 33162567 1.420000e-79 307
35 TraesCS2B01G095000 chr2D 84.918 305 34 6 1993 2286 33314578 33314275 8.540000e-77 298
36 TraesCS2B01G095000 chr2D 84.158 303 33 8 871 1159 33242149 33241848 3.090000e-71 279
37 TraesCS2B01G095000 chr2D 86.111 252 27 7 3680 3929 33161931 33161686 8.670000e-67 265
38 TraesCS2B01G095000 chr2D 87.097 217 20 7 3715 3929 32989979 32989769 5.250000e-59 239
39 TraesCS2B01G095000 chr2D 90.556 180 13 2 3492 3669 33046339 33046162 6.790000e-58 235
40 TraesCS2B01G095000 chrUn 97.205 644 17 1 1 643 38952096 38952739 0.000000e+00 1088
41 TraesCS2B01G095000 chr6B 97.050 644 18 1 1 643 710067860 710067217 0.000000e+00 1083
42 TraesCS2B01G095000 chr3B 96.600 647 18 2 1 643 586748392 586749038 0.000000e+00 1070
43 TraesCS2B01G095000 chr3B 85.131 612 47 19 2812 3423 229463691 229464258 1.630000e-163 586
44 TraesCS2B01G095000 chr1B 95.975 646 22 2 1 642 15656693 15656048 0.000000e+00 1046
45 TraesCS2B01G095000 chr1B 83.871 248 34 6 2193 2437 4617805 4617561 8.790000e-57 231
46 TraesCS2B01G095000 chr2A 87.802 910 55 17 1682 2550 36234923 36234029 0.000000e+00 1014
47 TraesCS2B01G095000 chr2A 93.068 678 40 4 2625 3301 36234011 36233340 0.000000e+00 985
48 TraesCS2B01G095000 chr2A 86.744 777 75 15 2624 3383 36200659 36199894 0.000000e+00 839
49 TraesCS2B01G095000 chr2A 85.258 814 67 30 2621 3423 36189297 36188526 0.000000e+00 789
50 TraesCS2B01G095000 chr2A 89.154 544 36 12 2312 2842 1212104 1212637 0.000000e+00 656
51 TraesCS2B01G095000 chr2A 92.986 442 30 1 1186 1626 36235375 36234934 0.000000e+00 643
52 TraesCS2B01G095000 chr2A 91.415 431 34 1 1156 1586 36202814 36202387 4.530000e-164 588
53 TraesCS2B01G095000 chr2A 86.492 459 25 12 742 1182 36235782 36235343 1.710000e-128 470
54 TraesCS2B01G095000 chr2A 89.318 337 26 4 1949 2281 36202159 36201829 8.130000e-112 414
55 TraesCS2B01G095000 chr2A 87.538 329 25 7 853 1165 36203217 36202889 2.310000e-97 366
56 TraesCS2B01G095000 chr2A 84.984 313 32 8 853 1151 36190712 36190401 1.840000e-78 303
57 TraesCS2B01G095000 chr2A 85.156 256 32 6 2185 2437 780182440 780182188 1.450000e-64 257
58 TraesCS2B01G095000 chr2A 83.871 248 28 10 2050 2288 36189897 36189653 4.090000e-55 226
59 TraesCS2B01G095000 chr2A 89.855 138 14 0 1713 1850 36202320 36202183 1.160000e-40 178
60 TraesCS2B01G095000 chr1A 93.865 652 35 4 1 647 249430447 249431098 0.000000e+00 977
61 TraesCS2B01G095000 chr6D 93.991 649 28 6 1 643 397347723 397348366 0.000000e+00 972
62 TraesCS2B01G095000 chr6D 93.953 645 34 4 1 640 55387485 55386841 0.000000e+00 970
63 TraesCS2B01G095000 chr4A 93.837 649 32 6 1 643 700558166 700558812 0.000000e+00 970
64 TraesCS2B01G095000 chr5A 93.692 650 34 5 1 643 621858037 621857388 0.000000e+00 966
65 TraesCS2B01G095000 chr5A 89.338 544 35 9 2312 2842 565537305 565536772 0.000000e+00 662
66 TraesCS2B01G095000 chr5A 85.385 260 32 6 2181 2437 32013083 32013339 8.670000e-67 265
67 TraesCS2B01G095000 chr7D 89.706 544 32 13 2312 2842 239730639 239730107 0.000000e+00 673
68 TraesCS2B01G095000 chr7D 84.052 232 21 9 2481 2710 190391772 190391555 4.120000e-50 209
69 TraesCS2B01G095000 chr6A 89.154 544 36 9 2312 2842 108079716 108079183 0.000000e+00 656
70 TraesCS2B01G095000 chr7A 79.917 483 72 12 2720 3187 77733584 77734056 8.420000e-87 331
71 TraesCS2B01G095000 chr7A 90.640 203 18 1 3041 3243 649475116 649475317 6.700000e-68 268
72 TraesCS2B01G095000 chr3D 83.901 323 21 14 2481 2786 551677419 551677111 3.090000e-71 279
73 TraesCS2B01G095000 chr5B 84.681 235 30 6 2206 2437 400139853 400139622 3.160000e-56 230
74 TraesCS2B01G095000 chr7B 92.913 127 8 1 2312 2437 618519435 618519561 2.500000e-42 183


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 TraesCS2B01G095000 chr2B 55029586 55033651 4065 True 7509.000000 7509 100.000000 1 4066 1 chr2B.!!$R1 4065
1 TraesCS2B01G095000 chr2B 122926368 122927891 1523 False 937.000000 937 78.977000 791 2279 1 chr2B.!!$F1 1488
2 TraesCS2B01G095000 chr2B 122992210 122993702 1492 False 904.000000 904 78.760000 828 2286 1 chr2B.!!$F2 1458
3 TraesCS2B01G095000 chr2B 54885055 54888358 3303 True 542.200000 795 86.738600 802 3409 5 chr2B.!!$R5 2607
4 TraesCS2B01G095000 chr2B 54783548 54787523 3975 True 490.800000 841 85.727200 765 4066 5 chr2B.!!$R4 3301
5 TraesCS2B01G095000 chr2B 55209637 55210336 699 True 390.500000 435 87.311500 871 1607 2 chr2B.!!$R6 736
6 TraesCS2B01G095000 chr2B 55224257 55227605 3348 True 348.333333 366 82.031000 849 3232 3 chr2B.!!$R7 2383
7 TraesCS2B01G095000 chr2D 33160781 33165527 4746 True 938.600000 2080 91.668200 740 4066 5 chr2D.!!$R6 3326
8 TraesCS2B01G095000 chr2D 79084882 79086384 1502 False 933.000000 933 78.974000 812 2286 1 chr2D.!!$F1 1474
9 TraesCS2B01G095000 chr2D 33046162 33049740 3578 True 481.166667 776 87.126167 802 3669 6 chr2D.!!$R5 2867
10 TraesCS2B01G095000 chr2D 33579945 33581161 1216 True 349.500000 379 84.574000 867 2437 2 chr2D.!!$R7 1570
11 TraesCS2B01G095000 chr2D 32989769 32992934 3165 True 339.333333 453 86.962000 853 3929 3 chr2D.!!$R4 3076
12 TraesCS2B01G095000 chrUn 38952096 38952739 643 False 1088.000000 1088 97.205000 1 643 1 chrUn.!!$F1 642
13 TraesCS2B01G095000 chr6B 710067217 710067860 643 True 1083.000000 1083 97.050000 1 643 1 chr6B.!!$R1 642
14 TraesCS2B01G095000 chr3B 586748392 586749038 646 False 1070.000000 1070 96.600000 1 643 1 chr3B.!!$F2 642
15 TraesCS2B01G095000 chr3B 229463691 229464258 567 False 586.000000 586 85.131000 2812 3423 1 chr3B.!!$F1 611
16 TraesCS2B01G095000 chr1B 15656048 15656693 645 True 1046.000000 1046 95.975000 1 642 1 chr1B.!!$R2 641
17 TraesCS2B01G095000 chr2A 36233340 36235782 2442 True 778.000000 1014 90.087000 742 3301 4 chr2A.!!$R4 2559
18 TraesCS2B01G095000 chr2A 1212104 1212637 533 False 656.000000 656 89.154000 2312 2842 1 chr2A.!!$F1 530
19 TraesCS2B01G095000 chr2A 36199894 36203217 3323 True 477.000000 839 88.974000 853 3383 5 chr2A.!!$R3 2530
20 TraesCS2B01G095000 chr2A 36188526 36190712 2186 True 439.333333 789 84.704333 853 3423 3 chr2A.!!$R2 2570
21 TraesCS2B01G095000 chr1A 249430447 249431098 651 False 977.000000 977 93.865000 1 647 1 chr1A.!!$F1 646
22 TraesCS2B01G095000 chr6D 397347723 397348366 643 False 972.000000 972 93.991000 1 643 1 chr6D.!!$F1 642
23 TraesCS2B01G095000 chr6D 55386841 55387485 644 True 970.000000 970 93.953000 1 640 1 chr6D.!!$R1 639
24 TraesCS2B01G095000 chr4A 700558166 700558812 646 False 970.000000 970 93.837000 1 643 1 chr4A.!!$F1 642
25 TraesCS2B01G095000 chr5A 621857388 621858037 649 True 966.000000 966 93.692000 1 643 1 chr5A.!!$R2 642
26 TraesCS2B01G095000 chr5A 565536772 565537305 533 True 662.000000 662 89.338000 2312 2842 1 chr5A.!!$R1 530
27 TraesCS2B01G095000 chr7D 239730107 239730639 532 True 673.000000 673 89.706000 2312 2842 1 chr7D.!!$R2 530
28 TraesCS2B01G095000 chr6A 108079183 108079716 533 True 656.000000 656 89.154000 2312 2842 1 chr6A.!!$R1 530

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
678 691 0.318699 TCTCTCACTCGCAACAACGG 60.319 55.000 0.0 0.0 0.00 4.44 F
687 700 0.386731 CGCAACAACGGCCCTAAAAG 60.387 55.000 0.0 0.0 0.00 2.27 F
696 709 0.526211 GGCCCTAAAAGAAACGGCTG 59.474 55.000 0.0 0.0 39.64 4.85 F
697 710 0.526211 GCCCTAAAAGAAACGGCTGG 59.474 55.000 0.0 0.0 36.65 4.85 F
1586 1960 1.068541 GCCATGACCCGTTTCTTGAAC 60.069 52.381 0.0 0.0 34.82 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1967 0.595588 AACACAATTCGCAATCGCCA 59.404 45.000 0.00 0.00 35.26 5.69 R
1944 2381 1.576421 GGCGGTTCTGCAGTTGAAG 59.424 57.895 14.67 4.23 36.28 3.02 R
1958 2395 1.966451 GGCGGAGAATATTGGGCGG 60.966 63.158 0.00 0.00 0.00 6.13 R
2541 5434 4.133820 ACTGACATTCATCGTGTTGGAAA 58.866 39.130 0.00 0.00 0.00 3.13 R
3534 7427 0.868406 GCCTCACCGTATTAGCATGC 59.132 55.000 10.51 10.51 0.00 4.06 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
96 98 1.375908 CGCTGCTCCTGTTGCCTAA 60.376 57.895 0.00 0.00 0.00 2.69
298 302 1.451936 GGTGACACCTGAGGTTGCT 59.548 57.895 17.84 0.00 34.73 3.91
471 478 1.418264 TCTGTGGTGGGTCAATTTCGA 59.582 47.619 0.00 0.00 0.00 3.71
505 514 2.435938 GGGTCATCCGCGCTTTCA 60.436 61.111 5.56 0.00 33.83 2.69
564 574 5.319043 TCTTTCTCCTTCTTTTGGGCTTA 57.681 39.130 0.00 0.00 0.00 3.09
578 588 1.373570 GGCTTATTGTGCTTCTCGCT 58.626 50.000 0.00 0.00 40.11 4.93
604 614 3.438781 GCATTCCTTTGTATCGGTGTTGA 59.561 43.478 0.00 0.00 0.00 3.18
647 660 3.581755 GAAACCCTTTTTCGGTATTGCC 58.418 45.455 0.00 0.00 31.69 4.52
648 661 1.552578 ACCCTTTTTCGGTATTGCCC 58.447 50.000 0.00 0.00 0.00 5.36
649 662 1.203075 ACCCTTTTTCGGTATTGCCCA 60.203 47.619 0.00 0.00 0.00 5.36
650 663 1.896465 CCCTTTTTCGGTATTGCCCAA 59.104 47.619 0.00 0.00 0.00 4.12
651 664 2.300437 CCCTTTTTCGGTATTGCCCAAA 59.700 45.455 0.00 0.00 0.00 3.28
652 665 3.244249 CCCTTTTTCGGTATTGCCCAAAA 60.244 43.478 0.00 0.00 0.00 2.44
653 666 3.993736 CCTTTTTCGGTATTGCCCAAAAG 59.006 43.478 12.41 12.41 40.42 2.27
654 667 4.502431 CCTTTTTCGGTATTGCCCAAAAGT 60.502 41.667 15.68 0.00 39.79 2.66
655 668 4.674281 TTTTCGGTATTGCCCAAAAGTT 57.326 36.364 0.00 0.00 0.00 2.66
656 669 4.674281 TTTCGGTATTGCCCAAAAGTTT 57.326 36.364 0.00 0.00 0.00 2.66
657 670 3.651803 TCGGTATTGCCCAAAAGTTTG 57.348 42.857 0.00 0.00 37.90 2.93
669 682 4.458951 CAAAAGTTTGGTCTCTCACTCG 57.541 45.455 0.00 0.00 34.59 4.18
670 683 2.156343 AAGTTTGGTCTCTCACTCGC 57.844 50.000 0.00 0.00 0.00 5.03
671 684 1.040646 AGTTTGGTCTCTCACTCGCA 58.959 50.000 0.00 0.00 0.00 5.10
672 685 1.412710 AGTTTGGTCTCTCACTCGCAA 59.587 47.619 0.00 0.00 0.00 4.85
673 686 1.527311 GTTTGGTCTCTCACTCGCAAC 59.473 52.381 0.00 0.00 0.00 4.17
674 687 0.750249 TTGGTCTCTCACTCGCAACA 59.250 50.000 0.00 0.00 0.00 3.33
675 688 0.750249 TGGTCTCTCACTCGCAACAA 59.250 50.000 0.00 0.00 0.00 2.83
676 689 1.140816 GGTCTCTCACTCGCAACAAC 58.859 55.000 0.00 0.00 0.00 3.32
677 690 0.778815 GTCTCTCACTCGCAACAACG 59.221 55.000 0.00 0.00 0.00 4.10
678 691 0.318699 TCTCTCACTCGCAACAACGG 60.319 55.000 0.00 0.00 0.00 4.44
679 692 1.891060 CTCTCACTCGCAACAACGGC 61.891 60.000 0.00 0.00 0.00 5.68
680 693 2.954753 CTCACTCGCAACAACGGCC 61.955 63.158 0.00 0.00 0.00 6.13
681 694 4.025401 CACTCGCAACAACGGCCC 62.025 66.667 0.00 0.00 0.00 5.80
682 695 4.250305 ACTCGCAACAACGGCCCT 62.250 61.111 0.00 0.00 0.00 5.19
683 696 2.047655 CTCGCAACAACGGCCCTA 60.048 61.111 0.00 0.00 0.00 3.53
684 697 1.669760 CTCGCAACAACGGCCCTAA 60.670 57.895 0.00 0.00 0.00 2.69
685 698 1.227883 TCGCAACAACGGCCCTAAA 60.228 52.632 0.00 0.00 0.00 1.85
686 699 0.818445 TCGCAACAACGGCCCTAAAA 60.818 50.000 0.00 0.00 0.00 1.52
687 700 0.386731 CGCAACAACGGCCCTAAAAG 60.387 55.000 0.00 0.00 0.00 2.27
688 701 0.955905 GCAACAACGGCCCTAAAAGA 59.044 50.000 0.00 0.00 0.00 2.52
689 702 1.338655 GCAACAACGGCCCTAAAAGAA 59.661 47.619 0.00 0.00 0.00 2.52
690 703 2.223852 GCAACAACGGCCCTAAAAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
691 704 3.377439 CAACAACGGCCCTAAAAGAAAC 58.623 45.455 0.00 0.00 0.00 2.78
692 705 1.605232 ACAACGGCCCTAAAAGAAACG 59.395 47.619 0.00 0.00 0.00 3.60
693 706 1.068816 CAACGGCCCTAAAAGAAACGG 60.069 52.381 0.00 0.00 0.00 4.44
694 707 1.239296 ACGGCCCTAAAAGAAACGGC 61.239 55.000 0.00 0.00 38.96 5.68
695 708 0.958876 CGGCCCTAAAAGAAACGGCT 60.959 55.000 0.00 0.00 39.64 5.52
696 709 0.526211 GGCCCTAAAAGAAACGGCTG 59.474 55.000 0.00 0.00 39.64 4.85
697 710 0.526211 GCCCTAAAAGAAACGGCTGG 59.474 55.000 0.00 0.00 36.65 4.85
698 711 1.905637 CCCTAAAAGAAACGGCTGGT 58.094 50.000 0.00 0.00 0.00 4.00
699 712 2.235891 CCCTAAAAGAAACGGCTGGTT 58.764 47.619 0.00 0.00 41.76 3.67
700 713 2.030274 CCCTAAAAGAAACGGCTGGTTG 60.030 50.000 0.00 0.00 39.30 3.77
701 714 2.621526 CCTAAAAGAAACGGCTGGTTGT 59.378 45.455 0.00 0.00 39.30 3.32
702 715 3.816523 CCTAAAAGAAACGGCTGGTTGTA 59.183 43.478 0.00 0.00 39.30 2.41
703 716 3.982576 AAAAGAAACGGCTGGTTGTAG 57.017 42.857 0.00 0.00 39.30 2.74
704 717 2.632987 AAGAAACGGCTGGTTGTAGT 57.367 45.000 0.00 0.00 39.30 2.73
705 718 3.756933 AAGAAACGGCTGGTTGTAGTA 57.243 42.857 0.00 0.00 39.30 1.82
706 719 3.756933 AGAAACGGCTGGTTGTAGTAA 57.243 42.857 0.00 0.00 39.30 2.24
707 720 4.281898 AGAAACGGCTGGTTGTAGTAAT 57.718 40.909 0.00 0.00 39.30 1.89
708 721 5.410355 AGAAACGGCTGGTTGTAGTAATA 57.590 39.130 0.00 0.00 39.30 0.98
709 722 5.797051 AGAAACGGCTGGTTGTAGTAATAA 58.203 37.500 0.00 0.00 39.30 1.40
710 723 6.232692 AGAAACGGCTGGTTGTAGTAATAAA 58.767 36.000 0.00 0.00 39.30 1.40
711 724 6.711645 AGAAACGGCTGGTTGTAGTAATAAAA 59.288 34.615 0.00 0.00 39.30 1.52
712 725 7.392393 AGAAACGGCTGGTTGTAGTAATAAAAT 59.608 33.333 0.00 0.00 39.30 1.82
713 726 6.431198 ACGGCTGGTTGTAGTAATAAAATG 57.569 37.500 0.00 0.00 0.00 2.32
714 727 6.174760 ACGGCTGGTTGTAGTAATAAAATGA 58.825 36.000 0.00 0.00 0.00 2.57
715 728 6.826741 ACGGCTGGTTGTAGTAATAAAATGAT 59.173 34.615 0.00 0.00 0.00 2.45
716 729 7.338449 ACGGCTGGTTGTAGTAATAAAATGATT 59.662 33.333 0.00 0.00 0.00 2.57
717 730 8.832521 CGGCTGGTTGTAGTAATAAAATGATTA 58.167 33.333 0.00 0.00 0.00 1.75
744 757 9.703892 TCAACTTTTCTTTTTGAGACAAAATGA 57.296 25.926 16.02 16.02 33.02 2.57
774 787 4.896482 ACTATGATAAGGAAAGAGGCTCGT 59.104 41.667 9.22 2.18 0.00 4.18
775 788 3.526931 TGATAAGGAAAGAGGCTCGTG 57.473 47.619 9.22 0.00 0.00 4.35
776 789 3.096852 TGATAAGGAAAGAGGCTCGTGA 58.903 45.455 9.22 0.00 0.00 4.35
825 843 2.332654 GGTAGTGTGGGCTTTGGCG 61.333 63.158 0.00 0.00 39.81 5.69
1070 1165 3.066190 CACCTACCTCCACGCCGA 61.066 66.667 0.00 0.00 0.00 5.54
1146 1271 1.227263 GGCGGTGCACATCTACGAT 60.227 57.895 20.43 0.00 0.00 3.73
1521 1855 2.922234 GAGCCCATCCCCTTCAGG 59.078 66.667 0.00 0.00 0.00 3.86
1586 1960 1.068541 GCCATGACCCGTTTCTTGAAC 60.069 52.381 0.00 0.00 34.82 3.18
1628 2016 5.243426 TGTGTTAGTTTCTTTCAGTTGCC 57.757 39.130 0.00 0.00 0.00 4.52
1630 2018 5.163663 TGTGTTAGTTTCTTTCAGTTGCCAG 60.164 40.000 0.00 0.00 0.00 4.85
1631 2019 4.338118 TGTTAGTTTCTTTCAGTTGCCAGG 59.662 41.667 0.00 0.00 0.00 4.45
1632 2020 3.297134 AGTTTCTTTCAGTTGCCAGGA 57.703 42.857 0.00 0.00 0.00 3.86
1633 2021 3.217626 AGTTTCTTTCAGTTGCCAGGAG 58.782 45.455 0.00 0.00 0.00 3.69
1670 2092 5.048991 CCCGAACATAACTATGGTTAATGGC 60.049 44.000 5.71 2.61 40.69 4.40
1671 2093 5.333798 CCGAACATAACTATGGTTAATGGCG 60.334 44.000 5.71 11.45 40.69 5.69
1672 2094 5.464057 CGAACATAACTATGGTTAATGGCGA 59.536 40.000 5.71 0.00 40.69 5.54
1673 2095 6.563381 CGAACATAACTATGGTTAATGGCGAC 60.563 42.308 5.71 0.00 40.69 5.19
1674 2096 5.925509 ACATAACTATGGTTAATGGCGACT 58.074 37.500 5.71 0.00 40.69 4.18
1675 2097 5.758296 ACATAACTATGGTTAATGGCGACTG 59.242 40.000 5.71 0.25 40.69 3.51
1676 2098 2.561569 ACTATGGTTAATGGCGACTGC 58.438 47.619 0.00 0.00 41.71 4.40
1677 2099 4.980554 TAACTATGGTTAATGGCGACTGCC 60.981 45.833 0.00 0.00 46.43 4.85
1708 2136 2.108601 CTCCCCTAATAGACCTCTCCGT 59.891 54.545 0.00 0.00 0.00 4.69
1870 2301 2.542595 GGATTATTCGGCGTCGTTCATT 59.457 45.455 10.18 0.00 37.69 2.57
1944 2381 4.752101 AGAACATAACCATATTCTCTGCGC 59.248 41.667 0.00 0.00 0.00 6.09
1958 2395 1.648720 TGCGCTTCAACTGCAGAAC 59.351 52.632 23.35 1.59 34.03 3.01
2461 3881 3.363970 CCGTTGATCACACTAACAGTTGC 60.364 47.826 0.00 0.00 0.00 4.17
2462 3882 3.247411 CGTTGATCACACTAACAGTTGCA 59.753 43.478 0.00 0.00 0.00 4.08
2463 3883 4.609113 CGTTGATCACACTAACAGTTGCAG 60.609 45.833 0.00 0.00 0.00 4.41
2470 3908 3.133003 ACACTAACAGTTGCAGACAGAGT 59.867 43.478 0.00 0.00 0.00 3.24
2487 5002 7.394077 CAGACAGAGTAGATGGTGATGATATCT 59.606 40.741 3.98 0.00 35.49 1.98
2541 5434 8.463930 TGAATAACCTCTGAACAAAATTCAGT 57.536 30.769 14.55 0.91 44.58 3.41
2550 5443 6.811170 TCTGAACAAAATTCAGTTTCCAACAC 59.189 34.615 14.55 0.00 44.58 3.32
2551 5444 5.574830 TGAACAAAATTCAGTTTCCAACACG 59.425 36.000 0.00 0.00 0.00 4.49
2553 5446 5.901552 ACAAAATTCAGTTTCCAACACGAT 58.098 33.333 0.00 0.00 0.00 3.73
2554 5447 5.748152 ACAAAATTCAGTTTCCAACACGATG 59.252 36.000 0.00 0.00 0.00 3.84
2555 5448 5.766150 AAATTCAGTTTCCAACACGATGA 57.234 34.783 0.00 0.00 0.00 2.92
2556 5449 5.766150 AATTCAGTTTCCAACACGATGAA 57.234 34.783 0.00 0.00 0.00 2.57
2557 5450 5.964958 ATTCAGTTTCCAACACGATGAAT 57.035 34.783 0.00 0.00 31.60 2.57
2558 5451 4.747540 TCAGTTTCCAACACGATGAATG 57.252 40.909 0.00 0.00 0.00 2.67
2559 5452 4.133820 TCAGTTTCCAACACGATGAATGT 58.866 39.130 0.00 0.00 0.00 2.71
2560 5453 4.213270 TCAGTTTCCAACACGATGAATGTC 59.787 41.667 0.00 0.00 0.00 3.06
2561 5454 4.024133 CAGTTTCCAACACGATGAATGTCA 60.024 41.667 0.00 0.00 0.00 3.58
2567 5460 5.178623 TCCAACACGATGAATGTCAGTAAAC 59.821 40.000 0.00 0.00 0.00 2.01
2616 5509 5.410132 TGTATTCAGGTTTTGTACATGACCG 59.590 40.000 17.59 13.87 46.30 4.79
2658 5682 4.301072 TCTGTTAGAACCTGGGAATTGG 57.699 45.455 0.00 0.00 0.00 3.16
2670 5694 1.203287 GGGAATTGGCTGAAACTGCTC 59.797 52.381 0.00 0.00 0.00 4.26
2678 5702 2.761208 GGCTGAAACTGCTCTAGTCCTA 59.239 50.000 0.00 0.00 39.18 2.94
2745 5875 5.703130 AGCTAGTTGGACATTTCTGTTCTTC 59.297 40.000 0.00 0.00 35.14 2.87
2749 5879 6.742109 AGTTGGACATTTCTGTTCTTCATTG 58.258 36.000 0.00 0.00 35.14 2.82
2767 5905 6.812481 TCATTGAGATAATTCAGTTCGTCG 57.188 37.500 0.00 0.00 0.00 5.12
2933 6413 9.607285 AGTGTATAAAATGTTTAGTTTCTTGCG 57.393 29.630 0.00 0.00 0.00 4.85
3330 6841 3.935203 CACTGTAGGGTACTTGCAATGAG 59.065 47.826 0.00 0.00 0.00 2.90
3349 6861 2.165030 GAGGTTGATGGTCCTGCAATTG 59.835 50.000 0.00 0.00 33.83 2.32
3425 7156 6.122964 AGCTGATGGTCCTTAATTCCTTAAC 58.877 40.000 0.00 0.00 0.00 2.01
3529 7422 5.999205 TTTACAGAATGAACCCATGCAAT 57.001 34.783 0.00 0.00 39.69 3.56
3534 7427 0.828022 ATGAACCCATGCAATGCAGG 59.172 50.000 14.98 14.18 44.97 4.85
3625 7518 3.055021 TGGTGTAGTTTGTCAGGACACAA 60.055 43.478 0.77 0.00 41.72 3.33
3646 7541 3.059352 ACCATGCTTGAGTACCTGAAC 57.941 47.619 0.22 0.00 0.00 3.18
3669 7564 2.148916 TGCGAAATCTGTCGAACACT 57.851 45.000 0.00 0.00 43.86 3.55
3670 7565 2.058798 TGCGAAATCTGTCGAACACTC 58.941 47.619 0.00 0.00 43.86 3.51
3673 7568 2.663602 CGAAATCTGTCGAACACTCAGG 59.336 50.000 0.00 0.00 43.86 3.86
3674 7569 3.611766 CGAAATCTGTCGAACACTCAGGA 60.612 47.826 0.00 0.00 43.86 3.86
3676 7571 1.687563 TCTGTCGAACACTCAGGACA 58.312 50.000 0.00 0.00 37.77 4.02
3677 7572 1.337071 TCTGTCGAACACTCAGGACAC 59.663 52.381 0.00 0.00 35.69 3.67
3705 8358 9.860898 AACATCCAGAAAATATGTTTTTCTAGC 57.139 29.630 14.33 0.00 44.30 3.42
3754 9172 4.580167 GCTCCAGCCAATATACAACATTCA 59.420 41.667 0.00 0.00 34.31 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 1.133513 AGAGGATGGAGAGAGACGCAT 60.134 52.381 0.00 0.00 0.00 4.73
157 159 2.110213 GCCACCACGGTCTTGACA 59.890 61.111 3.08 0.00 36.97 3.58
578 588 2.167693 ACCGATACAAAGGAATGCTCGA 59.832 45.455 0.00 0.00 33.23 4.04
648 661 3.303395 GCGAGTGAGAGACCAAACTTTTG 60.303 47.826 0.00 0.00 37.90 2.44
649 662 2.872858 GCGAGTGAGAGACCAAACTTTT 59.127 45.455 0.00 0.00 0.00 2.27
650 663 2.158957 TGCGAGTGAGAGACCAAACTTT 60.159 45.455 0.00 0.00 0.00 2.66
651 664 1.412710 TGCGAGTGAGAGACCAAACTT 59.587 47.619 0.00 0.00 0.00 2.66
652 665 1.040646 TGCGAGTGAGAGACCAAACT 58.959 50.000 0.00 0.00 0.00 2.66
653 666 1.527311 GTTGCGAGTGAGAGACCAAAC 59.473 52.381 0.00 0.00 0.00 2.93
654 667 1.138069 TGTTGCGAGTGAGAGACCAAA 59.862 47.619 0.00 0.00 0.00 3.28
655 668 0.750249 TGTTGCGAGTGAGAGACCAA 59.250 50.000 0.00 0.00 0.00 3.67
656 669 0.750249 TTGTTGCGAGTGAGAGACCA 59.250 50.000 0.00 0.00 0.00 4.02
657 670 1.140816 GTTGTTGCGAGTGAGAGACC 58.859 55.000 0.00 0.00 0.00 3.85
658 671 0.778815 CGTTGTTGCGAGTGAGAGAC 59.221 55.000 0.00 0.00 0.00 3.36
659 672 0.318699 CCGTTGTTGCGAGTGAGAGA 60.319 55.000 0.00 0.00 0.00 3.10
660 673 1.891060 GCCGTTGTTGCGAGTGAGAG 61.891 60.000 0.00 0.00 0.00 3.20
661 674 1.954146 GCCGTTGTTGCGAGTGAGA 60.954 57.895 0.00 0.00 0.00 3.27
662 675 2.551270 GCCGTTGTTGCGAGTGAG 59.449 61.111 0.00 0.00 0.00 3.51
663 676 2.970324 GGCCGTTGTTGCGAGTGA 60.970 61.111 0.00 0.00 0.00 3.41
664 677 4.025401 GGGCCGTTGTTGCGAGTG 62.025 66.667 0.00 0.00 0.00 3.51
665 678 2.386064 TTAGGGCCGTTGTTGCGAGT 62.386 55.000 1.81 0.00 0.00 4.18
666 679 1.231958 TTTAGGGCCGTTGTTGCGAG 61.232 55.000 1.81 0.00 0.00 5.03
667 680 0.818445 TTTTAGGGCCGTTGTTGCGA 60.818 50.000 1.81 0.00 0.00 5.10
668 681 0.386731 CTTTTAGGGCCGTTGTTGCG 60.387 55.000 1.81 0.00 0.00 4.85
669 682 0.955905 TCTTTTAGGGCCGTTGTTGC 59.044 50.000 1.81 0.00 0.00 4.17
670 683 3.377439 GTTTCTTTTAGGGCCGTTGTTG 58.623 45.455 1.81 0.00 0.00 3.33
671 684 2.033675 CGTTTCTTTTAGGGCCGTTGTT 59.966 45.455 1.81 0.00 0.00 2.83
672 685 1.605232 CGTTTCTTTTAGGGCCGTTGT 59.395 47.619 1.81 0.00 0.00 3.32
673 686 1.068816 CCGTTTCTTTTAGGGCCGTTG 60.069 52.381 1.81 0.00 0.00 4.10
674 687 1.241165 CCGTTTCTTTTAGGGCCGTT 58.759 50.000 1.81 0.00 0.00 4.44
675 688 1.239296 GCCGTTTCTTTTAGGGCCGT 61.239 55.000 2.24 2.24 39.92 5.68
676 689 0.958876 AGCCGTTTCTTTTAGGGCCG 60.959 55.000 0.00 0.00 45.32 6.13
677 690 0.526211 CAGCCGTTTCTTTTAGGGCC 59.474 55.000 0.00 0.00 45.32 5.80
678 691 0.526211 CCAGCCGTTTCTTTTAGGGC 59.474 55.000 0.00 0.00 44.72 5.19
679 692 1.905637 ACCAGCCGTTTCTTTTAGGG 58.094 50.000 0.00 0.00 0.00 3.53
680 693 2.621526 ACAACCAGCCGTTTCTTTTAGG 59.378 45.455 0.00 0.00 29.93 2.69
681 694 3.982576 ACAACCAGCCGTTTCTTTTAG 57.017 42.857 0.00 0.00 29.93 1.85
682 695 4.453751 ACTACAACCAGCCGTTTCTTTTA 58.546 39.130 0.00 0.00 29.93 1.52
683 696 3.284617 ACTACAACCAGCCGTTTCTTTT 58.715 40.909 0.00 0.00 29.93 2.27
684 697 2.927028 ACTACAACCAGCCGTTTCTTT 58.073 42.857 0.00 0.00 29.93 2.52
685 698 2.632987 ACTACAACCAGCCGTTTCTT 57.367 45.000 0.00 0.00 29.93 2.52
686 699 3.756933 TTACTACAACCAGCCGTTTCT 57.243 42.857 0.00 0.00 29.93 2.52
687 700 6.484818 TTTATTACTACAACCAGCCGTTTC 57.515 37.500 0.00 0.00 29.93 2.78
688 701 6.880942 TTTTATTACTACAACCAGCCGTTT 57.119 33.333 0.00 0.00 29.93 3.60
689 702 6.655848 TCATTTTATTACTACAACCAGCCGTT 59.344 34.615 0.00 0.00 33.90 4.44
690 703 6.174760 TCATTTTATTACTACAACCAGCCGT 58.825 36.000 0.00 0.00 0.00 5.68
691 704 6.671614 TCATTTTATTACTACAACCAGCCG 57.328 37.500 0.00 0.00 0.00 5.52
718 731 9.703892 TCATTTTGTCTCAAAAAGAAAAGTTGA 57.296 25.926 10.84 5.90 32.67 3.18
719 732 9.745323 GTCATTTTGTCTCAAAAAGAAAAGTTG 57.255 29.630 12.22 5.16 32.67 3.16
720 733 9.710900 AGTCATTTTGTCTCAAAAAGAAAAGTT 57.289 25.926 12.22 0.00 32.67 2.66
726 739 9.950680 GTTGATAGTCATTTTGTCTCAAAAAGA 57.049 29.630 10.84 9.45 32.81 2.52
727 740 9.956720 AGTTGATAGTCATTTTGTCTCAAAAAG 57.043 29.630 10.84 7.55 32.81 2.27
731 744 9.942850 TCATAGTTGATAGTCATTTTGTCTCAA 57.057 29.630 0.00 0.00 0.00 3.02
744 757 8.371699 GCCTCTTTCCTTATCATAGTTGATAGT 58.628 37.037 0.00 0.00 43.82 2.12
825 843 3.809374 CTTGCGGGCCGTATCCTCC 62.809 68.421 28.82 9.29 0.00 4.30
1180 1473 4.814294 ATCGCCGTCTCCGTTGCC 62.814 66.667 0.00 0.00 0.00 4.52
1181 1474 3.554692 CATCGCCGTCTCCGTTGC 61.555 66.667 0.00 0.00 0.00 4.17
1182 1475 2.885644 CCATCGCCGTCTCCGTTG 60.886 66.667 0.00 0.00 0.00 4.10
1183 1476 4.814294 GCCATCGCCGTCTCCGTT 62.814 66.667 0.00 0.00 0.00 4.44
1314 1607 4.112341 GGCTGGTCGTAGTCGCGT 62.112 66.667 5.77 0.00 36.96 6.01
1592 1967 0.595588 AACACAATTCGCAATCGCCA 59.404 45.000 0.00 0.00 35.26 5.69
1631 2019 3.193691 TGTTCGGGAGATCAAGAACTCTC 59.806 47.826 17.25 2.69 42.29 3.20
1632 2020 3.165875 TGTTCGGGAGATCAAGAACTCT 58.834 45.455 17.25 0.00 42.29 3.24
1633 2021 3.594603 TGTTCGGGAGATCAAGAACTC 57.405 47.619 17.25 0.00 42.29 3.01
1680 2102 2.365941 GGTCTATTAGGGGAGTCTGCAC 59.634 54.545 0.00 0.00 0.00 4.57
1708 2136 2.279851 CCCGGCGCGTGAATATGA 60.280 61.111 8.43 0.00 0.00 2.15
1944 2381 1.576421 GGCGGTTCTGCAGTTGAAG 59.424 57.895 14.67 4.23 36.28 3.02
1958 2395 1.966451 GGCGGAGAATATTGGGCGG 60.966 63.158 0.00 0.00 0.00 6.13
2382 3059 6.653320 ACACTAACAGTTTCAGACTTCAACAA 59.347 34.615 0.00 0.00 36.10 2.83
2461 3881 5.787953 ATCATCACCATCTACTCTGTCTG 57.212 43.478 0.00 0.00 0.00 3.51
2462 3882 7.394077 CAGATATCATCACCATCTACTCTGTCT 59.606 40.741 5.32 0.00 0.00 3.41
2463 3883 7.176515 ACAGATATCATCACCATCTACTCTGTC 59.823 40.741 5.32 0.00 35.90 3.51
2487 5002 5.226194 AGCAAAATGGGCTAAATCAAACA 57.774 34.783 0.00 0.00 40.47 2.83
2541 5434 4.133820 ACTGACATTCATCGTGTTGGAAA 58.866 39.130 0.00 0.00 0.00 3.13
2550 5443 9.694520 CAAGATTTAGTTTACTGACATTCATCG 57.305 33.333 0.00 0.00 0.00 3.84
2557 5450 8.342634 GCAGAAACAAGATTTAGTTTACTGACA 58.657 33.333 15.14 0.00 38.01 3.58
2558 5451 8.342634 TGCAGAAACAAGATTTAGTTTACTGAC 58.657 33.333 15.14 10.12 38.01 3.51
2559 5452 8.342634 GTGCAGAAACAAGATTTAGTTTACTGA 58.657 33.333 15.14 0.00 38.01 3.41
2560 5453 8.128582 TGTGCAGAAACAAGATTTAGTTTACTG 58.871 33.333 0.00 0.00 38.01 2.74
2561 5454 8.220755 TGTGCAGAAACAAGATTTAGTTTACT 57.779 30.769 0.00 0.00 38.01 2.24
2658 5682 4.664150 ATAGGACTAGAGCAGTTTCAGC 57.336 45.455 0.00 0.00 37.72 4.26
2745 5875 6.812481 TCGACGAACTGAATTATCTCAATG 57.188 37.500 0.00 0.00 0.00 2.82
2749 5879 5.977725 TGGAATCGACGAACTGAATTATCTC 59.022 40.000 0.00 0.00 0.00 2.75
2767 5905 3.815401 ACTAGCGGCAAACATATGGAATC 59.185 43.478 7.80 0.00 0.00 2.52
2933 6413 6.018016 AGCAAAAACCTGAAACAACATAATGC 60.018 34.615 0.00 0.00 0.00 3.56
2990 6472 1.395635 TTATGAGCGAGTTAGGCGGA 58.604 50.000 0.00 0.00 35.00 5.54
3330 6841 1.895131 ACAATTGCAGGACCATCAACC 59.105 47.619 5.05 0.00 0.00 3.77
3349 6861 7.546667 AGTTATGTGAAATGCATGATCCAAAAC 59.453 33.333 0.00 1.35 0.00 2.43
3494 7387 7.731882 TCATTCTGTAAAATGACAACCGTTA 57.268 32.000 0.00 0.00 39.98 3.18
3534 7427 0.868406 GCCTCACCGTATTAGCATGC 59.132 55.000 10.51 10.51 0.00 4.06
3543 7436 1.357690 CGCTAATCGCCTCACCGTA 59.642 57.895 0.00 0.00 34.21 4.02
3625 7518 3.412386 GTTCAGGTACTCAAGCATGGTT 58.588 45.455 3.82 3.82 34.60 3.67
3646 7541 1.128692 GTTCGACAGATTTCGCAAGGG 59.871 52.381 0.00 0.00 38.95 3.95
3669 7564 3.855255 TTCTGGATGTTTGTGTCCTGA 57.145 42.857 0.00 0.00 39.69 3.86
3670 7565 4.916983 TTTTCTGGATGTTTGTGTCCTG 57.083 40.909 0.00 0.00 35.49 3.86
3673 7568 8.816640 AAACATATTTTCTGGATGTTTGTGTC 57.183 30.769 10.51 0.00 46.69 3.67
3702 8355 3.196901 ACCGGACATATCAAGTTGTGCTA 59.803 43.478 9.46 0.00 32.64 3.49
3705 8358 2.677836 CCACCGGACATATCAAGTTGTG 59.322 50.000 9.46 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.