Multiple sequence alignment - TraesCS6B01G231800

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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 TraesCS6B01G231800 chr6B 100.000 5816 0 0 1 5816 384966687 384960872 0.000000e+00 10741.0
1 TraesCS6B01G231800 chr6B 89.626 588 43 3 3 572 80960088 80960675 0.000000e+00 732.0
2 TraesCS6B01G231800 chr6B 89.527 592 42 5 3 574 150776861 150776270 0.000000e+00 732.0
3 TraesCS6B01G231800 chr6B 89.304 589 44 5 3 574 478886824 478887410 0.000000e+00 721.0
4 TraesCS6B01G231800 chr6B 89.060 585 46 3 4 572 221740918 221740336 0.000000e+00 710.0
5 TraesCS6B01G231800 chr6B 88.007 592 40 11 3 576 649861970 649861392 0.000000e+00 671.0
6 TraesCS6B01G231800 chr6B 87.703 431 30 10 5388 5810 132888600 132889015 1.130000e-131 481.0
7 TraesCS6B01G231800 chr6B 95.652 46 0 1 571 616 384966076 384966033 8.080000e-09 73.1
8 TraesCS6B01G231800 chr6B 95.652 46 0 1 612 655 384966117 384966072 8.080000e-09 73.1
9 TraesCS6B01G231800 chr6A 97.015 4053 96 11 1356 5389 226067437 226071483 0.000000e+00 6791.0
10 TraesCS6B01G231800 chr6A 97.078 753 16 3 612 1358 226066712 226067464 0.000000e+00 1264.0
11 TraesCS6B01G231800 chr6A 100.000 46 0 0 571 616 226066712 226066757 1.040000e-12 86.1
12 TraesCS6B01G231800 chr6D 97.647 3910 77 9 1356 5257 170962288 170966190 0.000000e+00 6697.0
13 TraesCS6B01G231800 chr6D 96.011 752 11 4 612 1358 170961578 170962315 0.000000e+00 1205.0
14 TraesCS6B01G231800 chr6D 90.580 138 13 0 5253 5390 170996389 170996526 3.580000e-42 183.0
15 TraesCS6B01G231800 chr7D 92.787 1220 66 5 2684 3884 30286434 30287650 0.000000e+00 1746.0
16 TraesCS6B01G231800 chr7D 80.471 722 76 32 4547 5247 30289398 30290075 5.240000e-135 492.0
17 TraesCS6B01G231800 chr7D 86.111 324 30 7 4187 4509 30289088 30289397 9.340000e-88 335.0
18 TraesCS6B01G231800 chr7D 91.707 205 15 2 2487 2690 30284806 30285009 3.430000e-72 283.0
19 TraesCS6B01G231800 chr7D 85.106 235 24 5 976 1199 30284364 30284598 4.530000e-56 230.0
20 TraesCS6B01G231800 chr7D 95.050 101 4 1 2587 2687 30285671 30285770 2.170000e-34 158.0
21 TraesCS6B01G231800 chr7D 87.288 118 6 4 609 720 30284134 30284248 6.120000e-25 126.0
22 TraesCS6B01G231800 chr7A 91.184 1157 71 10 2684 3813 30675327 30676479 0.000000e+00 1543.0
23 TraesCS6B01G231800 chr7A 81.385 650 89 17 4547 5189 30683036 30683660 8.700000e-138 501.0
24 TraesCS6B01G231800 chr7A 78.686 563 54 30 615 1163 30673697 30674207 1.220000e-81 315.0
25 TraesCS6B01G231800 chr7A 84.036 332 29 9 4187 4509 30682719 30683035 1.230000e-76 298.0
26 TraesCS6B01G231800 chr7A 89.500 200 21 0 2488 2687 30674460 30674659 2.690000e-63 254.0
27 TraesCS6B01G231800 chr7A 94.318 88 5 0 3810 3897 30682646 30682733 1.020000e-27 135.0
28 TraesCS6B01G231800 chr4A 89.804 1226 72 14 2687 3893 698105491 698104300 0.000000e+00 1522.0
29 TraesCS6B01G231800 chr4A 89.242 1227 77 17 2687 3893 698887970 698886779 0.000000e+00 1483.0
30 TraesCS6B01G231800 chr4A 80.675 652 81 18 4547 5189 698886519 698885904 1.140000e-126 464.0
31 TraesCS6B01G231800 chr4A 86.038 265 25 7 927 1183 698889335 698889075 2.060000e-69 274.0
32 TraesCS6B01G231800 chr4A 88.060 201 24 0 2487 2687 698888847 698888647 7.530000e-59 239.0
33 TraesCS6B01G231800 chr4A 88.060 201 21 2 2487 2687 698106370 698106173 9.740000e-58 235.0
34 TraesCS6B01G231800 chr4A 86.036 222 23 4 938 1155 698106823 698106606 1.260000e-56 231.0
35 TraesCS6B01G231800 chr4A 83.871 217 22 6 4187 4402 698104310 698104106 1.650000e-45 195.0
36 TraesCS6B01G231800 chr4A 82.028 217 25 7 4187 4401 698886789 698886585 7.750000e-39 172.0
37 TraesCS6B01G231800 chr4A 84.553 123 8 5 604 720 698107064 698106947 1.710000e-20 111.0
38 TraesCS6B01G231800 chr4A 85.714 112 8 3 614 720 698889558 698889450 1.710000e-20 111.0
39 TraesCS6B01G231800 chr2B 89.713 593 41 10 3 576 796286028 796286619 0.000000e+00 739.0
40 TraesCS6B01G231800 chr2B 81.293 433 38 20 5390 5811 87539975 87540375 1.570000e-80 311.0
41 TraesCS6B01G231800 chr7B 89.779 587 42 3 3 572 369876328 369876913 0.000000e+00 736.0
42 TraesCS6B01G231800 chr7B 86.177 586 51 11 4 572 668398730 668399302 1.790000e-169 606.0
43 TraesCS6B01G231800 chr1B 89.060 585 41 7 3 569 669807769 669808348 0.000000e+00 704.0
44 TraesCS6B01G231800 chr1B 87.690 593 43 10 3 577 10370545 10371125 0.000000e+00 664.0
45 TraesCS6B01G231800 chr1B 90.625 384 31 2 5438 5816 268823064 268823447 6.730000e-139 505.0
46 TraesCS6B01G231800 chr1B 88.276 435 27 9 5388 5816 573070727 573070311 3.130000e-137 499.0
47 TraesCS6B01G231800 chr1B 87.816 435 29 9 5388 5816 573066363 573065947 6.770000e-134 488.0
48 TraesCS6B01G231800 chr1B 76.250 240 40 10 3945 4177 633046635 633046406 1.710000e-20 111.0
49 TraesCS6B01G231800 chr3A 88.305 590 48 6 3 572 663280255 663279667 0.000000e+00 688.0
50 TraesCS6B01G231800 chr1A 87.858 593 50 7 3 576 489642756 489643345 0.000000e+00 676.0
51 TraesCS6B01G231800 chr1A 85.739 589 65 13 3 576 513364851 513364267 6.450000e-169 604.0
52 TraesCS6B01G231800 chrUn 83.589 652 74 17 4547 5189 380100575 380101202 1.090000e-161 580.0
53 TraesCS6B01G231800 chrUn 93.805 113 5 1 4397 4509 380100464 380100574 1.000000e-37 169.0
54 TraesCS6B01G231800 chr4B 93.351 376 18 3 5447 5816 576152381 576152007 3.060000e-152 549.0
55 TraesCS6B01G231800 chr4B 87.844 436 31 9 5388 5816 445262138 445262558 5.240000e-135 492.0
56 TraesCS6B01G231800 chr5B 92.493 373 20 2 5449 5816 116664815 116665184 1.440000e-145 527.0
57 TraesCS6B01G231800 chr5B 89.019 428 30 6 5390 5812 29331612 29331197 1.120000e-141 514.0
58 TraesCS6B01G231800 chr5B 82.407 108 19 0 3945 4052 43132003 43132110 1.730000e-15 95.3
59 TraesCS6B01G231800 chr5B 82.407 108 19 0 3945 4052 43132650 43132757 1.730000e-15 95.3
60 TraesCS6B01G231800 chr3B 91.957 373 20 5 5450 5816 507295478 507295110 1.120000e-141 514.0
61 TraesCS6B01G231800 chr3D 81.678 584 73 18 3 572 563986899 563986336 6.870000e-124 455.0


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 TraesCS6B01G231800 chr6B 384960872 384966687 5815 True 3629.066667 10741 97.101333 1 5816 3 chr6B.!!$R4 5815
1 TraesCS6B01G231800 chr6B 80960088 80960675 587 False 732.000000 732 89.626000 3 572 1 chr6B.!!$F1 569
2 TraesCS6B01G231800 chr6B 150776270 150776861 591 True 732.000000 732 89.527000 3 574 1 chr6B.!!$R1 571
3 TraesCS6B01G231800 chr6B 478886824 478887410 586 False 721.000000 721 89.304000 3 574 1 chr6B.!!$F3 571
4 TraesCS6B01G231800 chr6B 221740336 221740918 582 True 710.000000 710 89.060000 4 572 1 chr6B.!!$R2 568
5 TraesCS6B01G231800 chr6B 649861392 649861970 578 True 671.000000 671 88.007000 3 576 1 chr6B.!!$R3 573
6 TraesCS6B01G231800 chr6A 226066712 226071483 4771 False 2713.700000 6791 98.031000 571 5389 3 chr6A.!!$F1 4818
7 TraesCS6B01G231800 chr6D 170961578 170966190 4612 False 3951.000000 6697 96.829000 612 5257 2 chr6D.!!$F2 4645
8 TraesCS6B01G231800 chr7D 30284134 30290075 5941 False 481.428571 1746 88.360000 609 5247 7 chr7D.!!$F1 4638
9 TraesCS6B01G231800 chr7A 30673697 30676479 2782 False 704.000000 1543 86.456667 615 3813 3 chr7A.!!$F1 3198
10 TraesCS6B01G231800 chr7A 30682646 30683660 1014 False 311.333333 501 86.579667 3810 5189 3 chr7A.!!$F2 1379
11 TraesCS6B01G231800 chr4A 698104106 698107064 2958 True 458.800000 1522 86.464800 604 4402 5 chr4A.!!$R1 3798
12 TraesCS6B01G231800 chr4A 698885904 698889558 3654 True 457.166667 1483 85.292833 614 5189 6 chr4A.!!$R2 4575
13 TraesCS6B01G231800 chr2B 796286028 796286619 591 False 739.000000 739 89.713000 3 576 1 chr2B.!!$F2 573
14 TraesCS6B01G231800 chr7B 369876328 369876913 585 False 736.000000 736 89.779000 3 572 1 chr7B.!!$F1 569
15 TraesCS6B01G231800 chr7B 668398730 668399302 572 False 606.000000 606 86.177000 4 572 1 chr7B.!!$F2 568
16 TraesCS6B01G231800 chr1B 669807769 669808348 579 False 704.000000 704 89.060000 3 569 1 chr1B.!!$F3 566
17 TraesCS6B01G231800 chr1B 10370545 10371125 580 False 664.000000 664 87.690000 3 577 1 chr1B.!!$F1 574
18 TraesCS6B01G231800 chr1B 573065947 573070727 4780 True 493.500000 499 88.046000 5388 5816 2 chr1B.!!$R2 428
19 TraesCS6B01G231800 chr3A 663279667 663280255 588 True 688.000000 688 88.305000 3 572 1 chr3A.!!$R1 569
20 TraesCS6B01G231800 chr1A 489642756 489643345 589 False 676.000000 676 87.858000 3 576 1 chr1A.!!$F1 573
21 TraesCS6B01G231800 chr1A 513364267 513364851 584 True 604.000000 604 85.739000 3 576 1 chr1A.!!$R1 573
22 TraesCS6B01G231800 chrUn 380100464 380101202 738 False 374.500000 580 88.697000 4397 5189 2 chrUn.!!$F1 792
23 TraesCS6B01G231800 chr3D 563986336 563986899 563 True 455.000000 455 81.678000 3 572 1 chr3D.!!$R1 569

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
188 189 0.094387 GACTACGTCGACCTCGTCAC 59.906 60.0 10.58 0.0 41.72 3.67 F
438 486 0.248289 CTACCCCGGACACGATTTGT 59.752 55.0 0.73 0.0 44.60 2.83 F
1362 1500 0.036164 TTCTTTCTTGCTAGGGCGCA 59.964 50.0 10.83 0.0 42.25 6.09 F
2028 2176 0.178873 AAGAAGTCCCTGGGGCTACA 60.179 55.0 22.45 0.0 34.68 2.74 F
2854 4483 0.595095 GCCGATGGATCATTCTTGGC 59.405 55.0 0.00 0.0 0.00 4.52 F
3186 4850 5.235616 TCATTTCGTTCAGTTTGTGGTACTC 59.764 40.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1495 0.807496 AAGAAAGAAGAGCATGCGCC 59.193 50.000 18.40 11.27 39.83 6.53 R
1381 1519 1.130561 GGCGACAAGAACTGCATAACC 59.869 52.381 0.00 0.00 0.00 2.85 R
2777 4406 1.152383 GGAACGATCCTAGCAACGCC 61.152 60.000 4.14 0.00 42.93 5.68 R
3376 5041 2.638855 TGGCCTTGAGCAAAATTTGGAT 59.361 40.909 3.32 0.00 46.50 3.41 R
3768 5436 3.840078 CCAAATGTTCCTTTCCCCTTCAT 59.160 43.478 0.00 0.00 0.00 2.57 R
4905 7737 1.202417 CGAGCCTAAGAATTGCGAGGA 60.202 52.381 0.00 0.00 0.00 3.71 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
53 54 1.770110 TGAACTGGTGCCCCACTCT 60.770 57.895 0.00 0.00 35.17 3.24
188 189 0.094387 GACTACGTCGACCTCGTCAC 59.906 60.000 10.58 0.00 41.72 3.67
343 382 1.134491 GTGGCCGACCCCTATATATGC 60.134 57.143 0.00 0.00 33.59 3.14
438 486 0.248289 CTACCCCGGACACGATTTGT 59.752 55.000 0.73 0.00 44.60 2.83
507 555 2.264480 CGAGTGAACCCATCGGCA 59.736 61.111 0.00 0.00 32.93 5.69
518 566 1.750399 CATCGGCACCCCAAAGAGG 60.750 63.158 0.00 0.00 37.03 3.69
528 576 1.340017 CCCCAAAGAGGCGAATTCTGA 60.340 52.381 3.52 0.00 35.39 3.27
548 596 1.000731 ACCAATCCGGACGTTCGTTTA 59.999 47.619 16.40 0.05 38.63 2.01
577 625 1.743394 CGGTGAAGTTGGCCTTAATCC 59.257 52.381 3.32 0.00 32.03 3.01
578 626 1.743394 GGTGAAGTTGGCCTTAATCCG 59.257 52.381 3.32 0.00 32.03 4.18
579 627 1.132453 GTGAAGTTGGCCTTAATCCGC 59.868 52.381 3.32 0.00 32.03 5.54
580 628 1.271652 TGAAGTTGGCCTTAATCCGCA 60.272 47.619 3.32 0.00 32.03 5.69
581 629 2.024414 GAAGTTGGCCTTAATCCGCAT 58.976 47.619 3.32 0.00 32.03 4.73
582 630 3.211045 GAAGTTGGCCTTAATCCGCATA 58.789 45.455 3.32 0.00 32.03 3.14
583 631 2.572290 AGTTGGCCTTAATCCGCATAC 58.428 47.619 3.32 0.00 0.00 2.39
584 632 2.092646 AGTTGGCCTTAATCCGCATACA 60.093 45.455 3.32 0.00 0.00 2.29
585 633 2.685897 GTTGGCCTTAATCCGCATACAA 59.314 45.455 3.32 0.00 0.00 2.41
586 634 3.006112 TGGCCTTAATCCGCATACAAA 57.994 42.857 3.32 0.00 0.00 2.83
587 635 3.357203 TGGCCTTAATCCGCATACAAAA 58.643 40.909 3.32 0.00 0.00 2.44
588 636 3.957497 TGGCCTTAATCCGCATACAAAAT 59.043 39.130 3.32 0.00 0.00 1.82
589 637 4.037446 TGGCCTTAATCCGCATACAAAATC 59.963 41.667 3.32 0.00 0.00 2.17
590 638 4.037446 GGCCTTAATCCGCATACAAAATCA 59.963 41.667 0.00 0.00 0.00 2.57
591 639 5.278957 GGCCTTAATCCGCATACAAAATCAT 60.279 40.000 0.00 0.00 0.00 2.45
592 640 5.630680 GCCTTAATCCGCATACAAAATCATG 59.369 40.000 0.00 0.00 0.00 3.07
593 641 6.735694 GCCTTAATCCGCATACAAAATCATGT 60.736 38.462 0.00 0.00 37.32 3.21
594 642 7.521423 GCCTTAATCCGCATACAAAATCATGTA 60.521 37.037 0.00 0.00 39.91 2.29
595 643 7.803189 CCTTAATCCGCATACAAAATCATGTAC 59.197 37.037 0.00 0.00 38.53 2.90
596 644 6.691754 AATCCGCATACAAAATCATGTACA 57.308 33.333 0.00 0.00 38.53 2.90
597 645 5.478233 TCCGCATACAAAATCATGTACAC 57.522 39.130 0.00 0.00 38.53 2.90
598 646 4.938226 TCCGCATACAAAATCATGTACACA 59.062 37.500 0.00 0.00 38.53 3.72
599 647 5.027737 CCGCATACAAAATCATGTACACAC 58.972 41.667 0.00 0.00 38.53 3.82
600 648 5.391416 CCGCATACAAAATCATGTACACACA 60.391 40.000 0.00 0.00 38.53 3.72
601 649 5.507876 CGCATACAAAATCATGTACACACAC 59.492 40.000 0.00 0.00 38.53 3.82
602 650 5.799936 GCATACAAAATCATGTACACACACC 59.200 40.000 0.00 0.00 38.53 4.16
603 651 4.846779 ACAAAATCATGTACACACACCC 57.153 40.909 0.00 0.00 37.54 4.61
604 652 3.252215 ACAAAATCATGTACACACACCCG 59.748 43.478 0.00 0.00 37.54 5.28
605 653 2.851263 AATCATGTACACACACCCGT 57.149 45.000 0.00 0.00 37.54 5.28
606 654 7.942375 TACAAAATCATGTACACACACCCGTG 61.942 42.308 0.00 0.00 40.65 4.94
634 686 6.183360 TGCTTAATCCGCATACAAAATCATGT 60.183 34.615 0.00 0.00 33.24 3.21
752 804 4.517952 TCCGTAACAACTAACGATTCCA 57.482 40.909 0.00 0.00 41.55 3.53
1170 1301 3.280197 TCTCCATCGCAATTCATTCCA 57.720 42.857 0.00 0.00 0.00 3.53
1296 1434 1.956297 TTGTGAGGTTGGTGTTACCG 58.044 50.000 0.00 0.00 42.58 4.02
1357 1495 3.065095 GCATGCTCTTCTTTCTTGCTAGG 59.935 47.826 11.37 0.00 0.00 3.02
1358 1496 3.340814 TGCTCTTCTTTCTTGCTAGGG 57.659 47.619 0.00 0.00 0.00 3.53
1359 1497 2.013400 GCTCTTCTTTCTTGCTAGGGC 58.987 52.381 0.00 0.00 39.26 5.19
1360 1498 2.275318 CTCTTCTTTCTTGCTAGGGCG 58.725 52.381 0.00 0.00 42.25 6.13
1361 1499 0.729690 CTTCTTTCTTGCTAGGGCGC 59.270 55.000 0.00 0.00 42.25 6.53
1362 1500 0.036164 TTCTTTCTTGCTAGGGCGCA 59.964 50.000 10.83 0.00 42.25 6.09
1363 1501 0.253044 TCTTTCTTGCTAGGGCGCAT 59.747 50.000 10.83 0.00 40.04 4.73
1364 1502 0.379669 CTTTCTTGCTAGGGCGCATG 59.620 55.000 10.83 0.00 40.04 4.06
1365 1503 1.656818 TTTCTTGCTAGGGCGCATGC 61.657 55.000 10.83 7.91 40.04 4.06
1366 1504 2.515523 CTTGCTAGGGCGCATGCT 60.516 61.111 17.13 0.00 40.04 3.79
1367 1505 2.514592 TTGCTAGGGCGCATGCTC 60.515 61.111 17.13 7.82 44.16 4.26
1373 1511 3.595819 GGGCGCATGCTCTTCTTT 58.404 55.556 17.13 0.00 39.08 2.52
1374 1512 1.431036 GGGCGCATGCTCTTCTTTC 59.569 57.895 17.13 0.00 39.08 2.62
1375 1513 1.028868 GGGCGCATGCTCTTCTTTCT 61.029 55.000 17.13 0.00 39.08 2.52
1376 1514 0.807496 GGCGCATGCTCTTCTTTCTT 59.193 50.000 17.13 0.00 42.25 2.52
1377 1515 1.467035 GGCGCATGCTCTTCTTTCTTG 60.467 52.381 17.13 0.00 42.25 3.02
1378 1516 1.198637 GCGCATGCTCTTCTTTCTTGT 59.801 47.619 17.13 0.00 38.39 3.16
1379 1517 2.351157 GCGCATGCTCTTCTTTCTTGTT 60.351 45.455 17.13 0.00 38.39 2.83
1380 1518 3.120199 GCGCATGCTCTTCTTTCTTGTTA 60.120 43.478 17.13 0.00 38.39 2.41
1381 1519 4.645956 CGCATGCTCTTCTTTCTTGTTAG 58.354 43.478 17.13 0.00 0.00 2.34
1436 1574 2.939103 CGAGGGTTTTGAGTCATCATCC 59.061 50.000 0.00 0.00 34.73 3.51
1558 1696 6.432162 ACTGTTACAGATCATGTGCAGAATTT 59.568 34.615 20.07 9.77 43.24 1.82
1686 1824 6.972328 TCTTCAAGTTTTTGACACAAGTATGC 59.028 34.615 0.00 0.00 42.79 3.14
1759 1897 4.348168 ACTGTGACCTCAGTTAATTCCTGT 59.652 41.667 5.29 0.00 44.92 4.00
1795 1933 8.904099 ATTAAGTTCGGACCTCTAATAAATGG 57.096 34.615 0.00 0.00 0.00 3.16
2004 2152 9.940166 ATCAATTCTTGAAATGAAAAACTTTGC 57.060 25.926 5.38 0.00 43.95 3.68
2028 2176 0.178873 AAGAAGTCCCTGGGGCTACA 60.179 55.000 22.45 0.00 34.68 2.74
2371 2531 7.801547 AGAATGTTGCATTATGAGTTTTTCG 57.198 32.000 0.00 0.00 0.00 3.46
2388 2548 6.144402 AGTTTTTCGAACAGCAGCATAAATTG 59.856 34.615 0.00 0.00 0.00 2.32
2854 4483 0.595095 GCCGATGGATCATTCTTGGC 59.405 55.000 0.00 0.00 0.00 4.52
3186 4850 5.235616 TCATTTCGTTCAGTTTGTGGTACTC 59.764 40.000 0.00 0.00 0.00 2.59
3768 5436 1.067846 CGTTCTCATCGTCCAACCTCA 60.068 52.381 0.00 0.00 0.00 3.86
3813 5481 5.239525 GGAAGCCTTGTTATGATAGCGAAAT 59.760 40.000 0.00 0.00 0.00 2.17
3839 5507 2.430694 AGGTTGGAAGCAACTGTTTTCC 59.569 45.455 14.34 14.34 40.59 3.13
3888 5556 8.958506 AGGTGAGACACTTATAACACTAGTAAG 58.041 37.037 0.00 0.00 34.40 2.34
3923 5591 5.412526 ACGCCCATTGTACGTTAATATTG 57.587 39.130 0.00 0.00 36.46 1.90
4044 5712 4.692625 ACGCTGACATTGATATTAGGCATC 59.307 41.667 0.00 0.00 0.00 3.91
4877 7709 4.885413 TGCCTTATATTCAATTGGCATGC 58.115 39.130 9.90 9.90 44.35 4.06
4905 7737 4.853007 AGTATTCTTTCTTGGAGCTGCAT 58.147 39.130 9.39 0.00 0.00 3.96
5264 8113 1.542492 AGTATGGGACCGGCTATACG 58.458 55.000 0.00 0.00 32.67 3.06
5295 8144 8.655901 TCCTTGAAATTTTATTTTGGGTAAGCT 58.344 29.630 0.00 0.00 0.00 3.74
5328 8177 5.856156 AGCCATTAGATTGAGATCTGACAG 58.144 41.667 0.00 0.00 42.55 3.51
5330 8179 5.608449 CCATTAGATTGAGATCTGACAGCA 58.392 41.667 0.00 0.00 42.55 4.41
5357 8209 7.119992 GTCCTTTCTTCTTCCTCCTACAAAATC 59.880 40.741 0.00 0.00 0.00 2.17
5364 8216 3.596214 TCCTCCTACAAAATCGACTTGC 58.404 45.455 8.60 0.00 0.00 4.01
5369 8221 3.254657 CCTACAAAATCGACTTGCCCAAA 59.745 43.478 8.60 0.00 0.00 3.28
5378 8230 7.595311 AATCGACTTGCCCAAATTTTAAATC 57.405 32.000 0.00 0.00 0.00 2.17
5407 8259 1.668826 TAGAGCAACTCCAATGGGGT 58.331 50.000 0.00 0.00 38.11 4.95
5409 8261 0.038166 GAGCAACTCCAATGGGGTGA 59.962 55.000 5.14 0.00 38.11 4.02
5411 8263 0.251341 GCAACTCCAATGGGGTGACT 60.251 55.000 5.14 0.00 38.11 3.41
5424 8276 2.355363 TGACTCAAACGGACGGCG 60.355 61.111 4.80 4.80 0.00 6.46
5425 8277 2.049802 GACTCAAACGGACGGCGA 60.050 61.111 16.62 0.00 0.00 5.54
5426 8278 1.445582 GACTCAAACGGACGGCGAT 60.446 57.895 16.62 0.00 0.00 4.58
5427 8279 1.005394 ACTCAAACGGACGGCGATT 60.005 52.632 16.62 0.00 0.00 3.34
5428 8280 0.601841 ACTCAAACGGACGGCGATTT 60.602 50.000 16.62 5.62 0.00 2.17
5429 8281 0.094730 CTCAAACGGACGGCGATTTC 59.905 55.000 16.62 0.00 0.00 2.17
5430 8282 0.600518 TCAAACGGACGGCGATTTCA 60.601 50.000 16.62 0.00 0.00 2.69
5431 8283 0.452122 CAAACGGACGGCGATTTCAC 60.452 55.000 16.62 0.00 0.00 3.18
5432 8284 1.571215 AAACGGACGGCGATTTCACC 61.571 55.000 16.62 5.95 0.00 4.02
5433 8285 3.192922 CGGACGGCGATTTCACCC 61.193 66.667 16.62 1.73 0.00 4.61
5434 8286 3.192922 GGACGGCGATTTCACCCG 61.193 66.667 16.62 0.00 46.97 5.28
5441 8293 2.844122 GCGATTTCACCCGCTATTTT 57.156 45.000 0.00 0.00 46.96 1.82
5443 8295 2.096819 GCGATTTCACCCGCTATTTTGA 59.903 45.455 0.00 0.00 46.96 2.69
5462 8314 2.750166 TGACTGCTTTTTGTCCGTTTGA 59.250 40.909 0.00 0.00 32.67 2.69
5511 8363 2.543777 TTTAGATATGGGTCGGCAGC 57.456 50.000 0.00 0.00 0.00 5.25
5543 8400 0.532862 CCGACTCATATGTGGTGGCC 60.533 60.000 9.45 0.00 0.00 5.36
5545 8402 0.532862 GACTCATATGTGGTGGCCGG 60.533 60.000 9.45 0.00 0.00 6.13
5716 8574 8.388484 AGAAGATACATCTATTGATTGCCAAC 57.612 34.615 0.00 0.00 35.15 3.77
5722 8580 5.889853 ACATCTATTGATTGCCAACATGAGT 59.110 36.000 0.00 0.00 37.63 3.41
5733 8591 3.281158 CCAACATGAGTCCACATATGCA 58.719 45.455 1.58 0.00 0.00 3.96
5767 8625 3.148823 GCAGTTGCACGTGAGTTTC 57.851 52.632 22.23 0.69 46.40 2.78
5772 8630 0.736053 TTGCACGTGAGTTTCCCAAC 59.264 50.000 22.23 0.00 46.40 3.77
5801 8659 6.457355 CATGTCTTGATGAAATTGGGTGAAA 58.543 36.000 0.00 0.00 0.00 2.69
5812 8670 2.500509 TGGGTGAAATGTTCAAACGC 57.499 45.000 0.00 0.00 42.15 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.169789 CCATCTCCGAAGCAGTGCG 61.170 63.158 10.00 0.00 0.00 5.34
289 323 2.351706 TCAACGGCCACTTAAAAGGT 57.648 45.000 2.24 0.00 0.00 3.50
518 566 0.657840 CCGGATTGGTCAGAATTCGC 59.342 55.000 0.00 0.00 33.63 4.70
520 568 1.933853 CGTCCGGATTGGTCAGAATTC 59.066 52.381 7.81 0.00 39.52 2.17
528 576 0.249996 AAACGAACGTCCGGATTGGT 60.250 50.000 7.81 3.09 39.52 3.67
577 625 5.507876 GTGTGTGTACATGATTTTGTATGCG 59.492 40.000 0.00 0.00 39.39 4.73
578 626 5.799936 GGTGTGTGTACATGATTTTGTATGC 59.200 40.000 0.00 0.00 39.39 3.14
579 627 6.321717 GGGTGTGTGTACATGATTTTGTATG 58.678 40.000 0.00 0.00 39.39 2.39
580 628 5.123186 CGGGTGTGTGTACATGATTTTGTAT 59.877 40.000 0.00 0.00 39.39 2.29
581 629 4.452795 CGGGTGTGTGTACATGATTTTGTA 59.547 41.667 0.00 0.00 39.39 2.41
582 630 3.252215 CGGGTGTGTGTACATGATTTTGT 59.748 43.478 0.00 0.00 39.39 2.83
583 631 3.252215 ACGGGTGTGTGTACATGATTTTG 59.748 43.478 0.00 0.00 39.39 2.44
584 632 3.252215 CACGGGTGTGTGTACATGATTTT 59.748 43.478 0.00 0.00 41.34 1.82
585 633 2.811431 CACGGGTGTGTGTACATGATTT 59.189 45.455 0.00 0.00 41.34 2.17
586 634 2.422597 CACGGGTGTGTGTACATGATT 58.577 47.619 0.00 0.00 41.34 2.57
587 635 2.093306 CACGGGTGTGTGTACATGAT 57.907 50.000 0.00 0.00 41.34 2.45
588 636 3.597550 CACGGGTGTGTGTACATGA 57.402 52.632 0.00 0.00 41.34 3.07
598 646 1.094785 GATTAAGCATGCACGGGTGT 58.905 50.000 21.98 0.00 0.00 4.16
599 647 0.381801 GGATTAAGCATGCACGGGTG 59.618 55.000 21.98 0.00 0.00 4.61
600 648 1.095228 CGGATTAAGCATGCACGGGT 61.095 55.000 21.98 0.98 0.00 5.28
601 649 1.648720 CGGATTAAGCATGCACGGG 59.351 57.895 21.98 0.00 0.00 5.28
602 650 1.009675 GCGGATTAAGCATGCACGG 60.010 57.895 21.98 10.48 34.19 4.94
603 651 1.720894 TGCGGATTAAGCATGCACG 59.279 52.632 21.98 14.37 40.01 5.34
610 658 6.208644 ACATGATTTTGTATGCGGATTAAGC 58.791 36.000 0.00 0.00 0.00 3.09
786 839 4.973055 TTTCGGCGACCACGTGGG 62.973 66.667 36.47 21.73 44.81 4.61
1170 1301 1.953686 GAGAGAGCGTAATCAGGAGCT 59.046 52.381 0.00 0.00 43.33 4.09
1296 1434 1.641577 CCGACCGTCCAAGATTCTTC 58.358 55.000 0.00 0.00 0.00 2.87
1357 1495 0.807496 AAGAAAGAAGAGCATGCGCC 59.193 50.000 18.40 11.27 39.83 6.53
1358 1496 1.198637 ACAAGAAAGAAGAGCATGCGC 59.801 47.619 14.17 14.17 38.99 6.09
1359 1497 3.549299 AACAAGAAAGAAGAGCATGCG 57.451 42.857 13.01 0.00 0.00 4.73
1360 1498 4.457257 ACCTAACAAGAAAGAAGAGCATGC 59.543 41.667 10.51 10.51 0.00 4.06
1361 1499 6.566197 AACCTAACAAGAAAGAAGAGCATG 57.434 37.500 0.00 0.00 0.00 4.06
1362 1500 7.148171 GCATAACCTAACAAGAAAGAAGAGCAT 60.148 37.037 0.00 0.00 0.00 3.79
1363 1501 6.149474 GCATAACCTAACAAGAAAGAAGAGCA 59.851 38.462 0.00 0.00 0.00 4.26
1364 1502 6.149474 TGCATAACCTAACAAGAAAGAAGAGC 59.851 38.462 0.00 0.00 0.00 4.09
1365 1503 7.389053 ACTGCATAACCTAACAAGAAAGAAGAG 59.611 37.037 0.00 0.00 0.00 2.85
1366 1504 7.224297 ACTGCATAACCTAACAAGAAAGAAGA 58.776 34.615 0.00 0.00 0.00 2.87
1367 1505 7.440523 ACTGCATAACCTAACAAGAAAGAAG 57.559 36.000 0.00 0.00 0.00 2.85
1368 1506 7.719633 AGAACTGCATAACCTAACAAGAAAGAA 59.280 33.333 0.00 0.00 0.00 2.52
1369 1507 7.224297 AGAACTGCATAACCTAACAAGAAAGA 58.776 34.615 0.00 0.00 0.00 2.52
1370 1508 7.440523 AGAACTGCATAACCTAACAAGAAAG 57.559 36.000 0.00 0.00 0.00 2.62
1371 1509 7.284489 ACAAGAACTGCATAACCTAACAAGAAA 59.716 33.333 0.00 0.00 0.00 2.52
1372 1510 6.770785 ACAAGAACTGCATAACCTAACAAGAA 59.229 34.615 0.00 0.00 0.00 2.52
1373 1511 6.296026 ACAAGAACTGCATAACCTAACAAGA 58.704 36.000 0.00 0.00 0.00 3.02
1374 1512 6.560253 ACAAGAACTGCATAACCTAACAAG 57.440 37.500 0.00 0.00 0.00 3.16
1375 1513 5.178623 CGACAAGAACTGCATAACCTAACAA 59.821 40.000 0.00 0.00 0.00 2.83
1376 1514 4.688879 CGACAAGAACTGCATAACCTAACA 59.311 41.667 0.00 0.00 0.00 2.41
1377 1515 4.435651 GCGACAAGAACTGCATAACCTAAC 60.436 45.833 0.00 0.00 0.00 2.34
1378 1516 3.682858 GCGACAAGAACTGCATAACCTAA 59.317 43.478 0.00 0.00 0.00 2.69
1379 1517 3.259064 GCGACAAGAACTGCATAACCTA 58.741 45.455 0.00 0.00 0.00 3.08
1380 1518 2.076863 GCGACAAGAACTGCATAACCT 58.923 47.619 0.00 0.00 0.00 3.50
1381 1519 1.130561 GGCGACAAGAACTGCATAACC 59.869 52.381 0.00 0.00 0.00 2.85
1544 1682 4.826733 ACTTGTACCAAATTCTGCACATGA 59.173 37.500 0.00 0.00 0.00 3.07
1558 1696 2.729194 ACCTGCAAAACACTTGTACCA 58.271 42.857 0.00 0.00 0.00 3.25
1670 1808 6.735678 ATACATCGCATACTTGTGTCAAAA 57.264 33.333 0.00 0.00 34.86 2.44
1759 1897 6.383147 AGGTCCGAACTTAATATCCTTGAGAA 59.617 38.462 0.00 0.00 0.00 2.87
1827 1965 7.444299 AGAACCTCGGTTACAATTTAACAGTA 58.556 34.615 0.48 0.00 38.60 2.74
2105 2261 5.988561 CAGATGTTTGCTAATCTAGGTCCTC 59.011 44.000 0.00 0.00 31.87 3.71
2371 2531 5.051891 ACAGACAATTTATGCTGCTGTTC 57.948 39.130 0.00 0.00 36.44 3.18
2529 2689 3.732212 ACGAGGGTTAAACAACTACCAC 58.268 45.455 0.00 0.00 33.51 4.16
2564 2724 2.348411 AGTCTGAAACCACCAACAGG 57.652 50.000 0.00 0.00 0.00 4.00
2728 4357 8.359642 AGCAATTCAAAAGTCAGCTTATGTTTA 58.640 29.630 0.00 0.00 33.95 2.01
2733 4362 7.927629 TGAAAAGCAATTCAAAAGTCAGCTTAT 59.072 29.630 0.00 0.00 39.65 1.73
2777 4406 1.152383 GGAACGATCCTAGCAACGCC 61.152 60.000 4.14 0.00 42.93 5.68
2854 4483 3.119352 GCCCTTGCTCAACATTAGGAAAG 60.119 47.826 0.00 0.00 28.82 2.62
3074 4731 4.452825 TCAGTATCACCCAAAAACGTTGA 58.547 39.130 0.00 0.00 0.00 3.18
3186 4850 5.403766 CACTTAGTGCTGAGTTGAACAGTAG 59.596 44.000 0.00 0.00 37.64 2.57
3376 5041 2.638855 TGGCCTTGAGCAAAATTTGGAT 59.361 40.909 3.32 0.00 46.50 3.41
3768 5436 3.840078 CCAAATGTTCCTTTCCCCTTCAT 59.160 43.478 0.00 0.00 0.00 2.57
3839 5507 8.361139 ACCTTCAAATAGTTGATAGATAGTCCG 58.639 37.037 6.42 0.00 43.29 4.79
3888 5556 4.632688 ACAATGGGCGTACACAATTACTAC 59.367 41.667 0.00 0.00 0.00 2.73
4020 5688 4.058124 TGCCTAATATCAATGTCAGCGTC 58.942 43.478 0.00 0.00 0.00 5.19
4044 5712 6.207417 CACATTTACAGCCCTCCCTTAATATG 59.793 42.308 0.00 0.00 0.00 1.78
4104 5772 5.172934 GTCTATCCAATGGTTTACGTCACA 58.827 41.667 0.00 0.00 0.00 3.58
4877 7709 6.018098 CAGCTCCAAGAAAGAATACTATGCTG 60.018 42.308 0.00 0.00 36.28 4.41
4905 7737 1.202417 CGAGCCTAAGAATTGCGAGGA 60.202 52.381 0.00 0.00 0.00 3.71
4992 7839 5.993106 AAAGTCGAGACCTTCTCTTTTTG 57.007 39.130 0.00 0.00 41.26 2.44
5264 8113 7.228507 ACCCAAAATAAAATTTCAAGGACTTGC 59.771 33.333 7.18 0.00 40.24 4.01
5278 8127 9.487790 CAGAAAATCAGCTTACCCAAAATAAAA 57.512 29.630 0.00 0.00 0.00 1.52
5286 8135 3.347216 GCTCAGAAAATCAGCTTACCCA 58.653 45.455 0.00 0.00 0.00 4.51
5295 8144 7.341030 TCTCAATCTAATGGCTCAGAAAATCA 58.659 34.615 0.00 0.00 0.00 2.57
5328 8177 2.304470 AGGAGGAAGAAGAAAGGACTGC 59.696 50.000 0.00 0.00 0.00 4.40
5330 8179 4.753186 TGTAGGAGGAAGAAGAAAGGACT 58.247 43.478 0.00 0.00 0.00 3.85
5357 8209 5.233988 TGGATTTAAAATTTGGGCAAGTCG 58.766 37.500 0.00 0.00 0.00 4.18
5364 8216 9.423061 CTAAGTTGACTGGATTTAAAATTTGGG 57.577 33.333 0.00 0.00 0.00 4.12
5369 8221 8.635765 TGCTCTAAGTTGACTGGATTTAAAAT 57.364 30.769 0.00 0.00 0.00 1.82
5378 8230 3.244215 TGGAGTTGCTCTAAGTTGACTGG 60.244 47.826 0.00 0.00 0.00 4.00
5407 8259 2.149803 ATCGCCGTCCGTTTGAGTCA 62.150 55.000 0.00 0.00 38.35 3.41
5409 8261 0.601841 AAATCGCCGTCCGTTTGAGT 60.602 50.000 0.00 0.00 38.35 3.41
5411 8263 0.600518 TGAAATCGCCGTCCGTTTGA 60.601 50.000 0.00 0.00 38.35 2.69
5424 8276 4.662145 CAGTCAAAATAGCGGGTGAAATC 58.338 43.478 0.00 0.00 0.00 2.17
5425 8277 3.119495 GCAGTCAAAATAGCGGGTGAAAT 60.119 43.478 0.00 0.00 0.00 2.17
5426 8278 2.227865 GCAGTCAAAATAGCGGGTGAAA 59.772 45.455 0.00 0.00 0.00 2.69
5427 8279 1.810151 GCAGTCAAAATAGCGGGTGAA 59.190 47.619 0.00 0.00 0.00 3.18
5428 8280 1.003118 AGCAGTCAAAATAGCGGGTGA 59.997 47.619 0.00 0.00 0.00 4.02
5429 8281 1.453155 AGCAGTCAAAATAGCGGGTG 58.547 50.000 0.00 0.00 0.00 4.61
5430 8282 2.200373 AAGCAGTCAAAATAGCGGGT 57.800 45.000 0.00 0.00 0.00 5.28
5431 8283 3.575965 AAAAGCAGTCAAAATAGCGGG 57.424 42.857 0.00 0.00 0.00 6.13
5432 8284 4.298332 ACAAAAAGCAGTCAAAATAGCGG 58.702 39.130 0.00 0.00 0.00 5.52
5433 8285 4.382754 GGACAAAAAGCAGTCAAAATAGCG 59.617 41.667 0.00 0.00 36.50 4.26
5434 8286 4.382754 CGGACAAAAAGCAGTCAAAATAGC 59.617 41.667 0.00 0.00 36.50 2.97
5435 8287 5.519722 ACGGACAAAAAGCAGTCAAAATAG 58.480 37.500 0.00 0.00 36.50 1.73
5436 8288 5.508200 ACGGACAAAAAGCAGTCAAAATA 57.492 34.783 0.00 0.00 36.50 1.40
5441 8293 2.750166 TCAAACGGACAAAAAGCAGTCA 59.250 40.909 0.00 0.00 36.50 3.41
5443 8295 2.752903 ACTCAAACGGACAAAAAGCAGT 59.247 40.909 0.00 0.00 0.00 4.40
5529 8381 2.191908 GCCGGCCACCACATATGA 59.808 61.111 18.11 0.00 0.00 2.15
5583 8440 8.455682 TCGGTCCAAAACTATGTTATTTGATTC 58.544 33.333 0.00 0.00 36.41 2.52
5584 8441 8.343168 TCGGTCCAAAACTATGTTATTTGATT 57.657 30.769 0.00 0.00 36.41 2.57
5585 8442 7.931578 TCGGTCCAAAACTATGTTATTTGAT 57.068 32.000 0.00 0.00 36.41 2.57
5586 8443 7.747155 TTCGGTCCAAAACTATGTTATTTGA 57.253 32.000 0.00 0.00 36.41 2.69
5594 8451 8.402472 TGCTATTTTATTCGGTCCAAAACTATG 58.598 33.333 0.00 0.00 0.00 2.23
5597 8454 6.827586 TGCTATTTTATTCGGTCCAAAACT 57.172 33.333 0.00 0.00 0.00 2.66
5669 8527 9.993881 CTTCTTTTATTCGTTTGCAAAACTATG 57.006 29.630 14.67 0.00 0.00 2.23
5708 8566 2.291209 TGTGGACTCATGTTGGCAAT 57.709 45.000 1.92 0.00 0.00 3.56
5716 8574 3.065786 GGTTGTGCATATGTGGACTCATG 59.934 47.826 14.81 0.00 45.81 3.07
5722 8580 4.085009 TGATTTGGTTGTGCATATGTGGA 58.915 39.130 4.29 0.00 0.00 4.02
5733 8591 4.035441 GCAACTGCAAAATGATTTGGTTGT 59.965 37.500 18.08 7.08 43.32 3.32
5758 8616 1.938861 CGTGGTTGGGAAACTCACG 59.061 57.895 13.88 13.88 39.22 4.35
5767 8625 0.888736 TCAAGACATGCGTGGTTGGG 60.889 55.000 18.20 2.94 0.00 4.12
5772 8630 3.770263 ATTTCATCAAGACATGCGTGG 57.230 42.857 11.36 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.