Multiple sequence alignment - TraesCS7B01G435400

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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 TraesCS7B01G435400 chr7B 100.000 4278 0 0 1 4278 702224046 702228323 0.000000e+00 7901.0
1 TraesCS7B01G435400 chr7B 92.369 629 39 4 1 622 594980636 594981262 0.000000e+00 887.0
2 TraesCS7B01G435400 chr7B 87.317 615 47 15 3351 3948 715924000 715923400 0.000000e+00 675.0
3 TraesCS7B01G435400 chr7B 84.804 612 48 23 3351 3948 715958932 715958352 1.330000e-159 573.0
4 TraesCS7B01G435400 chr7B 76.077 209 37 9 3013 3212 700959570 700959366 3.520000e-16 97.1
5 TraesCS7B01G435400 chr7B 74.107 224 46 7 3033 3247 701038053 701038273 9.860000e-12 82.4
6 TraesCS7B01G435400 chrUn 98.846 1647 17 2 1362 3008 76049080 76047436 0.000000e+00 2935.0
7 TraesCS7B01G435400 chrUn 87.317 615 47 15 3351 3948 335665032 335665632 0.000000e+00 675.0
8 TraesCS7B01G435400 chr7A 98.000 1650 24 4 1359 3008 39140754 39142394 0.000000e+00 2856.0
9 TraesCS7B01G435400 chr7A 91.717 1002 71 10 1420 2416 166279440 166278446 0.000000e+00 1380.0
10 TraesCS7B01G435400 chr7A 94.251 574 29 3 1 573 157168215 157168785 0.000000e+00 874.0
11 TraesCS7B01G435400 chr7A 85.857 700 78 13 676 1357 703557880 703558576 0.000000e+00 725.0
12 TraesCS7B01G435400 chr7A 77.647 425 64 20 737 1144 704234814 704235224 3.330000e-56 230.0
13 TraesCS7B01G435400 chr7A 86.869 198 26 0 742 939 702610848 702611045 5.570000e-54 222.0
14 TraesCS7B01G435400 chr7A 85.321 218 14 6 3148 3357 703560422 703560629 4.330000e-50 209.0
15 TraesCS7B01G435400 chr7A 82.927 82 12 2 3153 3233 703602775 703602855 5.930000e-09 73.1
16 TraesCS7B01G435400 chr7A 73.894 226 40 14 3019 3233 703651444 703651661 5.930000e-09 73.1
17 TraesCS7B01G435400 chr7A 97.368 38 1 0 1107 1144 703550009 703550046 9.930000e-07 65.8
18 TraesCS7B01G435400 chr3B 98.539 1574 22 1 1362 2935 651531949 651530377 0.000000e+00 2778.0
19 TraesCS7B01G435400 chr3B 90.331 393 33 3 2600 2991 770114511 770114899 1.060000e-140 510.0
20 TraesCS7B01G435400 chr6B 97.080 1644 41 2 1359 3001 129751716 129753353 0.000000e+00 2763.0
21 TraesCS7B01G435400 chr6B 91.557 379 25 6 2604 2976 637882043 637881666 2.280000e-142 516.0
22 TraesCS7B01G435400 chr1B 98.281 1338 21 2 1643 2979 175642369 175641033 0.000000e+00 2342.0
23 TraesCS7B01G435400 chr1B 92.564 659 37 4 1 648 48768666 48769323 0.000000e+00 935.0
24 TraesCS7B01G435400 chr1B 89.724 399 35 6 2600 2993 641136596 641136993 4.940000e-139 505.0
25 TraesCS7B01G435400 chr1B 78.207 647 99 25 738 1363 10048456 10047831 4.040000e-100 375.0
26 TraesCS7B01G435400 chr3D 90.267 1161 94 13 1362 2516 587511655 587510508 0.000000e+00 1500.0
27 TraesCS7B01G435400 chr6D 92.552 1007 57 9 1362 2367 143675920 143674931 0.000000e+00 1428.0
28 TraesCS7B01G435400 chr2B 89.252 1163 96 16 1362 2517 731559286 731558146 0.000000e+00 1428.0
29 TraesCS7B01G435400 chr2B 96.378 497 17 1 3782 4278 51071946 51071451 0.000000e+00 817.0
30 TraesCS7B01G435400 chr2B 97.483 437 11 0 3352 3788 51077834 51077398 0.000000e+00 747.0
31 TraesCS7B01G435400 chr2B 77.103 428 77 15 740 1149 666399058 666399482 1.200000e-55 228.0
32 TraesCS7B01G435400 chr5B 94.226 866 21 6 3352 4206 694224817 694223970 0.000000e+00 1295.0
33 TraesCS7B01G435400 chr5B 80.973 946 121 38 3352 4278 594611856 594612761 0.000000e+00 695.0
34 TraesCS7B01G435400 chr5B 96.512 86 3 0 4191 4276 694204885 694204800 4.460000e-30 143.0
35 TraesCS7B01G435400 chr1A 88.946 968 66 7 3352 4278 514202863 514203830 0.000000e+00 1157.0
36 TraesCS7B01G435400 chr6A 94.557 643 28 4 1 640 530140175 530139537 0.000000e+00 987.0
37 TraesCS7B01G435400 chr6A 93.356 587 32 4 1 586 58828832 58828252 0.000000e+00 861.0
38 TraesCS7B01G435400 chr6A 83.333 612 47 16 3675 4260 37835431 37834849 8.200000e-142 514.0
39 TraesCS7B01G435400 chr4B 85.623 939 93 11 3363 4277 103164197 103163277 0.000000e+00 948.0
40 TraesCS7B01G435400 chr4B 91.800 561 29 4 3350 3893 527739670 527740230 0.000000e+00 765.0
41 TraesCS7B01G435400 chr2A 94.498 618 29 3 1 617 711650343 711649730 0.000000e+00 948.0
42 TraesCS7B01G435400 chr2A 82.416 836 100 26 3477 4277 391915596 391916419 0.000000e+00 686.0
43 TraesCS7B01G435400 chr5A 85.991 928 79 18 3353 4260 565718718 565717822 0.000000e+00 946.0
44 TraesCS7B01G435400 chr3A 93.178 645 36 5 1 643 456460048 456460686 0.000000e+00 941.0
45 TraesCS7B01G435400 chr3A 93.034 646 34 5 1 640 80125640 80126280 0.000000e+00 933.0
46 TraesCS7B01G435400 chr4A 92.956 653 31 4 1 638 718515156 718515808 0.000000e+00 937.0
47 TraesCS7B01G435400 chr4A 83.958 960 91 30 3348 4278 692453272 692452347 0.000000e+00 861.0
48 TraesCS7B01G435400 chr4A 90.667 75 3 3 568 638 663258681 663258607 3.520000e-16 97.1
49 TraesCS7B01G435400 chr7D 92.361 576 31 2 3348 3911 37839040 37838466 0.000000e+00 808.0
50 TraesCS7B01G435400 chr7D 86.798 712 63 16 676 1363 612772798 612773502 0.000000e+00 765.0
51 TraesCS7B01G435400 chr7D 88.754 578 50 3 3351 3916 606436169 606436743 0.000000e+00 693.0
52 TraesCS7B01G435400 chr7D 91.573 356 14 4 3014 3361 612773487 612773834 1.080000e-130 477.0
53 TraesCS7B01G435400 chr7D 87.179 195 25 0 740 934 612427864 612428058 5.570000e-54 222.0
54 TraesCS7B01G435400 chr7D 82.174 230 39 2 741 969 612965674 612965446 3.370000e-46 196.0
55 TraesCS7B01G435400 chr7D 74.949 487 89 23 757 1225 611613841 611613370 4.370000e-45 193.0
56 TraesCS7B01G435400 chr7D 76.695 236 35 14 3074 3297 612404502 612404729 3.500000e-21 113.0
57 TraesCS7B01G435400 chr7D 75.463 216 34 10 3085 3288 612428582 612428790 2.120000e-13 87.9
58 TraesCS7B01G435400 chr2D 90.641 577 40 3 3345 3908 18029482 18030057 0.000000e+00 754.0
59 TraesCS7B01G435400 chr1D 91.667 384 30 2 2600 2982 345417307 345416925 8.150000e-147 531.0


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 TraesCS7B01G435400 chr7B 702224046 702228323 4277 False 7901 7901 100.0000 1 4278 1 chr7B.!!$F3 4277
1 TraesCS7B01G435400 chr7B 594980636 594981262 626 False 887 887 92.3690 1 622 1 chr7B.!!$F1 621
2 TraesCS7B01G435400 chr7B 715923400 715924000 600 True 675 675 87.3170 3351 3948 1 chr7B.!!$R2 597
3 TraesCS7B01G435400 chr7B 715958352 715958932 580 True 573 573 84.8040 3351 3948 1 chr7B.!!$R3 597
4 TraesCS7B01G435400 chrUn 76047436 76049080 1644 True 2935 2935 98.8460 1362 3008 1 chrUn.!!$R1 1646
5 TraesCS7B01G435400 chrUn 335665032 335665632 600 False 675 675 87.3170 3351 3948 1 chrUn.!!$F1 597
6 TraesCS7B01G435400 chr7A 39140754 39142394 1640 False 2856 2856 98.0000 1359 3008 1 chr7A.!!$F1 1649
7 TraesCS7B01G435400 chr7A 166278446 166279440 994 True 1380 1380 91.7170 1420 2416 1 chr7A.!!$R1 996
8 TraesCS7B01G435400 chr7A 157168215 157168785 570 False 874 874 94.2510 1 573 1 chr7A.!!$F2 572
9 TraesCS7B01G435400 chr7A 703557880 703560629 2749 False 467 725 85.5890 676 3357 2 chr7A.!!$F8 2681
10 TraesCS7B01G435400 chr3B 651530377 651531949 1572 True 2778 2778 98.5390 1362 2935 1 chr3B.!!$R1 1573
11 TraesCS7B01G435400 chr6B 129751716 129753353 1637 False 2763 2763 97.0800 1359 3001 1 chr6B.!!$F1 1642
12 TraesCS7B01G435400 chr1B 175641033 175642369 1336 True 2342 2342 98.2810 1643 2979 1 chr1B.!!$R2 1336
13 TraesCS7B01G435400 chr1B 48768666 48769323 657 False 935 935 92.5640 1 648 1 chr1B.!!$F1 647
14 TraesCS7B01G435400 chr1B 10047831 10048456 625 True 375 375 78.2070 738 1363 1 chr1B.!!$R1 625
15 TraesCS7B01G435400 chr3D 587510508 587511655 1147 True 1500 1500 90.2670 1362 2516 1 chr3D.!!$R1 1154
16 TraesCS7B01G435400 chr6D 143674931 143675920 989 True 1428 1428 92.5520 1362 2367 1 chr6D.!!$R1 1005
17 TraesCS7B01G435400 chr2B 731558146 731559286 1140 True 1428 1428 89.2520 1362 2517 1 chr2B.!!$R3 1155
18 TraesCS7B01G435400 chr5B 694223970 694224817 847 True 1295 1295 94.2260 3352 4206 1 chr5B.!!$R2 854
19 TraesCS7B01G435400 chr5B 594611856 594612761 905 False 695 695 80.9730 3352 4278 1 chr5B.!!$F1 926
20 TraesCS7B01G435400 chr1A 514202863 514203830 967 False 1157 1157 88.9460 3352 4278 1 chr1A.!!$F1 926
21 TraesCS7B01G435400 chr6A 530139537 530140175 638 True 987 987 94.5570 1 640 1 chr6A.!!$R3 639
22 TraesCS7B01G435400 chr6A 58828252 58828832 580 True 861 861 93.3560 1 586 1 chr6A.!!$R2 585
23 TraesCS7B01G435400 chr6A 37834849 37835431 582 True 514 514 83.3330 3675 4260 1 chr6A.!!$R1 585
24 TraesCS7B01G435400 chr4B 103163277 103164197 920 True 948 948 85.6230 3363 4277 1 chr4B.!!$R1 914
25 TraesCS7B01G435400 chr4B 527739670 527740230 560 False 765 765 91.8000 3350 3893 1 chr4B.!!$F1 543
26 TraesCS7B01G435400 chr2A 711649730 711650343 613 True 948 948 94.4980 1 617 1 chr2A.!!$R1 616
27 TraesCS7B01G435400 chr2A 391915596 391916419 823 False 686 686 82.4160 3477 4277 1 chr2A.!!$F1 800
28 TraesCS7B01G435400 chr5A 565717822 565718718 896 True 946 946 85.9910 3353 4260 1 chr5A.!!$R1 907
29 TraesCS7B01G435400 chr3A 456460048 456460686 638 False 941 941 93.1780 1 643 1 chr3A.!!$F2 642
30 TraesCS7B01G435400 chr3A 80125640 80126280 640 False 933 933 93.0340 1 640 1 chr3A.!!$F1 639
31 TraesCS7B01G435400 chr4A 718515156 718515808 652 False 937 937 92.9560 1 638 1 chr4A.!!$F1 637
32 TraesCS7B01G435400 chr4A 692452347 692453272 925 True 861 861 83.9580 3348 4278 1 chr4A.!!$R2 930
33 TraesCS7B01G435400 chr7D 37838466 37839040 574 True 808 808 92.3610 3348 3911 1 chr7D.!!$R1 563
34 TraesCS7B01G435400 chr7D 606436169 606436743 574 False 693 693 88.7540 3351 3916 1 chr7D.!!$F1 565
35 TraesCS7B01G435400 chr7D 612772798 612773834 1036 False 621 765 89.1855 676 3361 2 chr7D.!!$F4 2685
36 TraesCS7B01G435400 chr2D 18029482 18030057 575 False 754 754 90.6410 3345 3908 1 chr2D.!!$F1 563

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
897 916 0.527817 GGATCGTCTTCCGCGACATT 60.528 55.000 8.23 0.0 41.33 2.71 F
1159 1178 1.002366 CATCCAGCTCGGTCTTTTCG 58.998 55.000 2.68 0.0 35.57 3.46 F
1284 1327 1.202855 AGCAGCACTGAGTTGAATGGT 60.203 47.619 0.81 0.0 0.00 3.55 F
1331 1378 2.743928 GCTGGAGCTTGTCGTGGG 60.744 66.667 0.00 0.0 38.21 4.61 F
3023 3082 0.603569 AGCTACCTCCAGTGTCAACG 59.396 55.000 0.00 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2480 1.068083 CCTGCTACGATGCGGTGAT 59.932 57.895 11.00 0.00 37.61 3.06 R
3012 3071 0.248458 GGCAACAACGTTGACACTGG 60.248 55.000 33.66 10.84 0.00 4.00 R
3013 3072 0.248458 GGGCAACAACGTTGACACTG 60.248 55.000 33.66 22.67 39.74 3.66 R
3097 3156 0.329596 AGACCTTCTCCACCAATGGC 59.670 55.000 0.00 0.00 46.80 4.40 R
4079 5978 1.129058 GGGGTTAGTCGTGGGATGAT 58.871 55.000 0.00 0.00 0.00 2.45 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
63 64 7.555965 TGTGTGACTAATATCAACTAGCATGT 58.444 34.615 0.00 0.00 0.00 3.21
66 67 9.529325 TGTGACTAATATCAACTAGCATGTTAC 57.471 33.333 0.00 0.00 0.00 2.50
392 397 2.357034 ACGTTCAGATGCGGCGTT 60.357 55.556 9.37 0.00 31.37 4.84
406 411 2.700773 GCGTTGGATGGGGTTCAGC 61.701 63.158 0.00 0.00 0.00 4.26
410 415 4.506255 GGATGGGGTTCAGCCGGG 62.506 72.222 2.18 0.00 42.55 5.73
566 580 4.574013 GTCGGTCTATACGGTATGATAGGG 59.426 50.000 10.86 0.00 0.00 3.53
606 620 3.904965 TCCGTATGACCATTATGCCCTTA 59.095 43.478 0.00 0.00 0.00 2.69
648 667 2.292267 CCGAAGCAAGCCTCATACAAT 58.708 47.619 0.00 0.00 0.00 2.71
649 668 3.118408 ACCGAAGCAAGCCTCATACAATA 60.118 43.478 0.00 0.00 0.00 1.90
650 669 4.067896 CCGAAGCAAGCCTCATACAATAT 58.932 43.478 0.00 0.00 0.00 1.28
651 670 5.221641 ACCGAAGCAAGCCTCATACAATATA 60.222 40.000 0.00 0.00 0.00 0.86
652 671 5.120830 CCGAAGCAAGCCTCATACAATATAC 59.879 44.000 0.00 0.00 0.00 1.47
653 672 5.696270 CGAAGCAAGCCTCATACAATATACA 59.304 40.000 0.00 0.00 0.00 2.29
654 673 6.369890 CGAAGCAAGCCTCATACAATATACAT 59.630 38.462 0.00 0.00 0.00 2.29
655 674 7.444629 AAGCAAGCCTCATACAATATACATG 57.555 36.000 0.00 0.00 0.00 3.21
656 675 5.413833 AGCAAGCCTCATACAATATACATGC 59.586 40.000 0.00 0.00 0.00 4.06
657 676 5.181811 GCAAGCCTCATACAATATACATGCA 59.818 40.000 0.00 0.00 0.00 3.96
658 677 6.605849 CAAGCCTCATACAATATACATGCAC 58.394 40.000 0.00 0.00 0.00 4.57
659 678 5.868454 AGCCTCATACAATATACATGCACA 58.132 37.500 0.00 0.00 0.00 4.57
660 679 6.298361 AGCCTCATACAATATACATGCACAA 58.702 36.000 0.00 0.00 0.00 3.33
661 680 6.772233 AGCCTCATACAATATACATGCACAAA 59.228 34.615 0.00 0.00 0.00 2.83
662 681 7.449395 AGCCTCATACAATATACATGCACAAAT 59.551 33.333 0.00 0.00 0.00 2.32
663 682 8.084073 GCCTCATACAATATACATGCACAAATT 58.916 33.333 0.00 0.00 0.00 1.82
680 699 6.526325 GCACAAATTATATGTTCAGCGTTGAA 59.474 34.615 10.92 10.92 40.92 2.69
681 700 7.253420 GCACAAATTATATGTTCAGCGTTGAAG 60.253 37.037 15.45 2.27 43.66 3.02
691 710 2.259204 CGTTGAAGTCGGGGCGTA 59.741 61.111 0.00 0.00 0.00 4.42
731 750 2.663196 GCTAGGTCAACCAGGCGT 59.337 61.111 1.33 0.00 38.89 5.68
763 782 2.359169 GGACCGGACCTCATCAGCA 61.359 63.158 16.26 0.00 0.00 4.41
798 817 2.124487 CTCCTCCTCGTCCTCGCT 60.124 66.667 0.00 0.00 36.96 4.93
897 916 0.527817 GGATCGTCTTCCGCGACATT 60.528 55.000 8.23 0.00 41.33 2.71
952 971 1.306997 TCTCCCGCCATTTCCCTCT 60.307 57.895 0.00 0.00 0.00 3.69
969 988 2.025037 CCTCTTGGAAATCCATGTCCCA 60.025 50.000 13.26 0.00 46.97 4.37
970 989 3.019564 CTCTTGGAAATCCATGTCCCAC 58.980 50.000 13.26 0.00 46.97 4.61
975 994 2.854300 AAATCCATGTCCCACCGCCC 62.854 60.000 0.00 0.00 0.00 6.13
997 1016 2.332362 GAATCGCCGCTGGTCGACTA 62.332 60.000 16.46 8.77 41.67 2.59
1000 1019 2.260434 GCCGCTGGTCGACTAACA 59.740 61.111 16.46 4.08 41.67 2.41
1001 1020 1.153628 GCCGCTGGTCGACTAACAT 60.154 57.895 16.46 0.00 41.67 2.71
1016 1035 2.050836 AACATGGTCGACACAGCCCA 62.051 55.000 18.91 5.14 0.00 5.36
1020 1039 2.733593 GTCGACACAGCCCACGTC 60.734 66.667 11.55 0.00 0.00 4.34
1032 1051 1.956170 CCACGTCAACTCGCTGCTT 60.956 57.895 0.00 0.00 0.00 3.91
1077 1096 1.485895 GAGGAGCTCATCTTCAGCCTT 59.514 52.381 20.76 0.00 37.63 4.35
1095 1114 2.418746 CCTTTCATCGGACTTCATCGGT 60.419 50.000 0.00 0.00 0.00 4.69
1100 1119 3.634910 TCATCGGACTTCATCGGTGATTA 59.365 43.478 0.00 0.00 40.91 1.75
1131 1150 2.129555 ATCTGCCTTGCTTCCACCGT 62.130 55.000 0.00 0.00 0.00 4.83
1152 1171 1.599047 CACTTCCATCCAGCTCGGT 59.401 57.895 2.68 0.00 35.57 4.69
1159 1178 1.002366 CATCCAGCTCGGTCTTTTCG 58.998 55.000 2.68 0.00 35.57 3.46
1222 1247 2.030412 CACTGTACCTGGCGTGCA 59.970 61.111 0.00 0.00 35.58 4.57
1243 1268 3.064987 ATTGACGCCCTCGACTCCG 62.065 63.158 0.00 0.00 39.41 4.63
1283 1326 1.531423 AGCAGCACTGAGTTGAATGG 58.469 50.000 0.81 0.00 0.00 3.16
1284 1327 1.202855 AGCAGCACTGAGTTGAATGGT 60.203 47.619 0.81 0.00 0.00 3.55
1331 1378 2.743928 GCTGGAGCTTGTCGTGGG 60.744 66.667 0.00 0.00 38.21 4.61
1417 1465 9.799106 TTTCATTGATTAAGGAGAAGAGAGTTT 57.201 29.630 0.00 0.00 0.00 2.66
2219 2273 3.936203 GACCACCACCACGCCTCA 61.936 66.667 0.00 0.00 0.00 3.86
2945 3004 2.841988 AGGAGGGAGATCAGCCGC 60.842 66.667 0.00 0.00 0.00 6.53
3018 3077 2.875188 CGAGAGCTACCTCCAGTGT 58.125 57.895 0.00 0.00 38.96 3.55
3019 3078 0.736053 CGAGAGCTACCTCCAGTGTC 59.264 60.000 0.00 0.00 38.96 3.67
3020 3079 1.840737 GAGAGCTACCTCCAGTGTCA 58.159 55.000 0.00 0.00 38.96 3.58
3021 3080 2.171840 GAGAGCTACCTCCAGTGTCAA 58.828 52.381 0.00 0.00 38.96 3.18
3022 3081 1.896465 AGAGCTACCTCCAGTGTCAAC 59.104 52.381 0.00 0.00 38.96 3.18
3023 3082 0.603569 AGCTACCTCCAGTGTCAACG 59.396 55.000 0.00 0.00 0.00 4.10
3070 3129 2.284625 ATGTCCCTCACCGCCTCA 60.285 61.111 0.00 0.00 0.00 3.86
3083 3142 1.746727 CGCCTCAAAGATCAGCGTCG 61.747 60.000 0.00 0.00 41.78 5.12
3097 3156 2.504244 GTCGTCTCCGTCTTGGCG 60.504 66.667 0.00 0.00 37.80 5.69
3144 3203 5.336213 GGAAATGCTGCTATATGAATGGGTG 60.336 44.000 0.00 0.00 0.00 4.61
3166 4946 6.092748 GTGTATTACATTTGGTCTTTGGCTG 58.907 40.000 0.00 0.00 0.00 4.85
3215 4995 1.152030 AGACAAGGACAGCTCCCCA 60.152 57.895 3.94 0.00 37.25 4.96
3216 4996 0.548682 AGACAAGGACAGCTCCCCAT 60.549 55.000 3.94 0.00 37.25 4.00
3569 5360 2.358615 GTGACGCACTGGCCATGA 60.359 61.111 5.51 0.00 36.38 3.07
3638 5438 2.158234 AGAGATAGGGGCAAGAGGTAGG 60.158 54.545 0.00 0.00 0.00 3.18
3653 5459 1.096416 GTAGGAGACTCTGGTCACGG 58.904 60.000 1.74 0.00 44.36 4.94
3893 5779 8.051901 TCGTCAGTATCTTCAGTATTTTCAGA 57.948 34.615 0.00 0.00 0.00 3.27
3894 5780 8.520351 TCGTCAGTATCTTCAGTATTTTCAGAA 58.480 33.333 0.00 0.00 0.00 3.02
3920 5807 0.099436 GTATTTTCAGCAGCGGCAGG 59.901 55.000 12.44 2.61 44.61 4.85
3965 5864 2.938086 CGGTGGTGATCGTGGGTCA 61.938 63.158 0.00 0.00 0.00 4.02
4034 5933 6.486253 TTCCTTCTTTTCGTTGATCAGATG 57.514 37.500 0.00 0.00 0.00 2.90
4075 5974 4.766375 ACGAGGTTTGATCCGTCAATTAT 58.234 39.130 0.00 0.00 43.49 1.28
4079 5978 3.380004 GGTTTGATCCGTCAATTATGGCA 59.620 43.478 0.00 0.00 43.49 4.92
4147 6046 2.552315 CCAGGACAGTACGCACAAAATT 59.448 45.455 0.00 0.00 0.00 1.82
4167 6066 0.041312 GTTGACTCATGCACGCGTTT 60.041 50.000 10.22 0.00 0.00 3.60
4176 6075 2.971430 TGCACGCGTTTAATTGCTTA 57.029 40.000 10.22 0.00 35.91 3.09
4217 6117 0.096976 AAGAACATACGTGCGCATGC 59.903 50.000 28.93 7.91 43.20 4.06
4233 6139 4.776647 GCAACAATCACGGCCCGC 62.777 66.667 1.23 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 7.255520 GCCATCTAATCTCCTCGTCTAAAGTAA 60.256 40.741 0.00 0.00 0.00 2.24
66 67 5.010112 TGCCATCTAATCTCCTCGTCTAAAG 59.990 44.000 0.00 0.00 0.00 1.85
392 397 3.727258 CCGGCTGAACCCCATCCA 61.727 66.667 0.00 0.00 30.53 3.41
410 415 3.499737 CCAACTGTGCGATCGCCC 61.500 66.667 35.12 26.20 41.09 6.13
566 580 1.092348 GAAGAAACGTATGCCCACCC 58.908 55.000 0.00 0.00 0.00 4.61
649 668 7.804600 CGCTGAACATATAATTTGTGCATGTAT 59.195 33.333 0.00 0.00 32.23 2.29
650 669 7.131565 CGCTGAACATATAATTTGTGCATGTA 58.868 34.615 0.00 0.00 32.23 2.29
651 670 5.972973 CGCTGAACATATAATTTGTGCATGT 59.027 36.000 0.00 0.00 32.23 3.21
652 671 5.972973 ACGCTGAACATATAATTTGTGCATG 59.027 36.000 0.00 0.00 32.23 4.06
653 672 6.135290 ACGCTGAACATATAATTTGTGCAT 57.865 33.333 0.00 0.00 32.23 3.96
654 673 5.559427 ACGCTGAACATATAATTTGTGCA 57.441 34.783 0.00 0.00 31.75 4.57
655 674 6.027131 TCAACGCTGAACATATAATTTGTGC 58.973 36.000 0.00 0.00 0.00 4.57
656 675 7.750458 ACTTCAACGCTGAACATATAATTTGTG 59.250 33.333 0.00 0.00 36.62 3.33
657 676 7.816640 ACTTCAACGCTGAACATATAATTTGT 58.183 30.769 0.00 0.00 36.62 2.83
658 677 7.162546 CGACTTCAACGCTGAACATATAATTTG 59.837 37.037 0.00 0.00 36.62 2.32
659 678 7.180079 CGACTTCAACGCTGAACATATAATTT 58.820 34.615 0.00 0.00 36.62 1.82
660 679 6.238103 CCGACTTCAACGCTGAACATATAATT 60.238 38.462 0.00 0.00 36.62 1.40
661 680 5.234329 CCGACTTCAACGCTGAACATATAAT 59.766 40.000 0.00 0.00 36.62 1.28
662 681 4.565166 CCGACTTCAACGCTGAACATATAA 59.435 41.667 0.00 0.00 36.62 0.98
663 682 4.109766 CCGACTTCAACGCTGAACATATA 58.890 43.478 0.00 0.00 36.62 0.86
664 683 2.930040 CCGACTTCAACGCTGAACATAT 59.070 45.455 0.00 0.00 36.62 1.78
665 684 2.333926 CCGACTTCAACGCTGAACATA 58.666 47.619 0.00 0.00 36.62 2.29
666 685 1.148310 CCGACTTCAACGCTGAACAT 58.852 50.000 0.00 0.00 36.62 2.71
667 686 0.878523 CCCGACTTCAACGCTGAACA 60.879 55.000 0.00 0.00 36.62 3.18
668 687 1.566018 CCCCGACTTCAACGCTGAAC 61.566 60.000 0.00 0.00 36.62 3.18
669 688 1.301401 CCCCGACTTCAACGCTGAA 60.301 57.895 0.67 0.67 39.30 3.02
670 689 2.342279 CCCCGACTTCAACGCTGA 59.658 61.111 0.00 0.00 0.00 4.26
671 690 3.423154 GCCCCGACTTCAACGCTG 61.423 66.667 0.00 0.00 0.00 5.18
673 692 3.919973 TACGCCCCGACTTCAACGC 62.920 63.158 0.00 0.00 0.00 4.84
674 693 1.804326 CTACGCCCCGACTTCAACG 60.804 63.158 0.00 0.00 0.00 4.10
691 710 1.153549 GTCGCGAGAAATGGAGGCT 60.154 57.895 10.24 0.00 45.01 4.58
978 997 3.255379 GTCGACCAGCGGCGATTC 61.255 66.667 12.98 0.00 41.33 2.52
997 1016 1.302511 GGGCTGTGTCGACCATGTT 60.303 57.895 14.12 0.00 0.00 2.71
1000 1019 2.347490 GTGGGCTGTGTCGACCAT 59.653 61.111 14.12 0.00 35.13 3.55
1001 1020 4.293648 CGTGGGCTGTGTCGACCA 62.294 66.667 14.12 9.70 0.00 4.02
1011 1030 3.616721 AGCGAGTTGACGTGGGCT 61.617 61.111 0.00 0.00 35.59 5.19
1016 1035 2.016704 CGAAGCAGCGAGTTGACGT 61.017 57.895 0.00 0.00 35.59 4.34
1077 1096 1.822371 TCACCGATGAAGTCCGATGAA 59.178 47.619 0.00 0.00 0.00 2.57
1095 1114 2.357952 CAGATCGACGACTGGGTAATCA 59.642 50.000 15.39 0.00 0.00 2.57
1100 1119 2.711922 GGCAGATCGACGACTGGGT 61.712 63.158 21.03 0.00 35.05 4.51
1131 1150 1.300963 GAGCTGGATGGAAGTGGCA 59.699 57.895 0.00 0.00 0.00 4.92
1152 1171 1.407721 CGCGTATGACGGCGAAAAGA 61.408 55.000 16.62 0.00 42.82 2.52
1206 1231 2.343758 CTGCACGCCAGGTACAGT 59.656 61.111 0.00 0.00 35.64 3.55
1222 1247 2.125512 GTCGAGGGCGTCAATGCT 60.126 61.111 8.06 0.00 38.98 3.79
1243 1268 4.530857 ATGGAGCACGCGTAGGCC 62.531 66.667 13.44 14.03 35.02 5.19
1248 1291 2.182791 CTGAGATGGAGCACGCGT 59.817 61.111 5.58 5.58 0.00 6.01
1331 1378 2.743538 TGCGTGTCCATCTGCTGC 60.744 61.111 0.00 0.00 0.00 5.25
1417 1465 4.847198 GGTTTTCCTCTAATTAACCGGGA 58.153 43.478 6.32 0.00 36.94 5.14
2423 2480 1.068083 CCTGCTACGATGCGGTGAT 59.932 57.895 11.00 0.00 37.61 3.06
3004 3063 0.603569 CGTTGACACTGGAGGTAGCT 59.396 55.000 0.00 0.00 0.00 3.32
3005 3064 0.317479 ACGTTGACACTGGAGGTAGC 59.683 55.000 0.00 0.00 0.00 3.58
3006 3065 2.223971 ACAACGTTGACACTGGAGGTAG 60.224 50.000 33.66 3.06 0.00 3.18
3007 3066 1.758280 ACAACGTTGACACTGGAGGTA 59.242 47.619 33.66 0.00 0.00 3.08
3008 3067 0.539986 ACAACGTTGACACTGGAGGT 59.460 50.000 33.66 5.05 0.00 3.85
3009 3068 1.330521 CAACAACGTTGACACTGGAGG 59.669 52.381 33.66 4.29 0.00 4.30
3010 3069 1.268032 GCAACAACGTTGACACTGGAG 60.268 52.381 33.66 14.02 0.00 3.86
3011 3070 0.730265 GCAACAACGTTGACACTGGA 59.270 50.000 33.66 0.00 0.00 3.86
3012 3071 0.248458 GGCAACAACGTTGACACTGG 60.248 55.000 33.66 10.84 0.00 4.00
3013 3072 0.248458 GGGCAACAACGTTGACACTG 60.248 55.000 33.66 22.67 39.74 3.66
3014 3073 1.381165 GGGGCAACAACGTTGACACT 61.381 55.000 33.66 9.41 39.74 3.55
3015 3074 1.065109 GGGGCAACAACGTTGACAC 59.935 57.895 33.66 21.79 39.74 3.67
3016 3075 2.122167 GGGGGCAACAACGTTGACA 61.122 57.895 33.66 0.00 39.74 3.58
3017 3076 2.725641 GGGGGCAACAACGTTGAC 59.274 61.111 33.66 20.84 39.74 3.18
3018 3077 2.902846 CGGGGGCAACAACGTTGA 60.903 61.111 33.66 0.00 39.74 3.18
3019 3078 3.213402 ACGGGGGCAACAACGTTG 61.213 61.111 26.20 26.20 46.13 4.10
3020 3079 3.213402 CACGGGGGCAACAACGTT 61.213 61.111 0.00 0.00 46.13 3.99
3023 3082 1.457009 TTAAGCACGGGGGCAACAAC 61.457 55.000 0.00 0.00 39.74 3.32
3070 3129 3.723554 GGAGACGACGCTGATCTTT 57.276 52.632 0.00 0.00 0.00 2.52
3083 3142 3.665675 ATGGCGCCAAGACGGAGAC 62.666 63.158 36.33 0.00 44.60 3.36
3097 3156 0.329596 AGACCTTCTCCACCAATGGC 59.670 55.000 0.00 0.00 46.80 4.40
3144 3203 5.102313 GCAGCCAAAGACCAAATGTAATAC 58.898 41.667 0.00 0.00 0.00 1.89
3166 4946 1.079819 TAGCGTCACCTGCTCAAGC 60.080 57.895 0.00 0.00 42.85 4.01
3305 5093 3.557228 AAAAACAATTTGGCAGGAGCA 57.443 38.095 0.78 0.00 44.61 4.26
3638 5438 1.979693 AGCCCGTGACCAGAGTCTC 60.980 63.158 0.00 0.00 43.91 3.36
3653 5459 8.281212 TGAATAATAGGAAAGAAACTTCAGCC 57.719 34.615 0.00 0.00 0.00 4.85
3893 5779 4.095483 CCGCTGCTGAAAATACTGAAGATT 59.905 41.667 0.00 0.00 0.00 2.40
3894 5780 3.624861 CCGCTGCTGAAAATACTGAAGAT 59.375 43.478 0.00 0.00 0.00 2.40
3897 5783 1.468520 GCCGCTGCTGAAAATACTGAA 59.531 47.619 0.00 0.00 33.53 3.02
3920 5807 1.454663 GGGGCTTCTTCATCAGGGC 60.455 63.158 0.00 0.00 0.00 5.19
4034 5933 9.687210 AACCTCGTTTTTCTGGTTATTTTTATC 57.313 29.630 0.00 0.00 40.55 1.75
4075 5974 1.134521 GTTAGTCGTGGGATGATGCCA 60.135 52.381 0.00 0.00 34.62 4.92
4079 5978 1.129058 GGGGTTAGTCGTGGGATGAT 58.871 55.000 0.00 0.00 0.00 2.45
4147 6046 1.157257 AACGCGTGCATGAGTCAACA 61.157 50.000 14.98 0.00 0.00 3.33
4167 6066 6.745159 TTTTCCGCTACATGTAAGCAATTA 57.255 33.333 20.12 6.60 0.00 1.40
4176 6075 2.504367 AGCAGTTTTTCCGCTACATGT 58.496 42.857 2.69 2.69 33.25 3.21
4217 6117 4.114997 GGCGGGCCGTGATTGTTG 62.115 66.667 28.82 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.