Multiple sequence alignment - TraesCS6B01G380000

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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 TraesCS6B01G380000 chr6B 100.000 3680 0 0 1 3680 654916559 654920238 0.000000e+00 6796.0
1 TraesCS6B01G380000 chr6B 97.072 2083 56 3 596 2674 654853638 654855719 0.000000e+00 3504.0
2 TraesCS6B01G380000 chr6B 96.875 2080 63 2 596 2674 654887858 654889936 0.000000e+00 3480.0
3 TraesCS6B01G380000 chr6B 96.783 2083 62 3 596 2674 654877735 654879816 0.000000e+00 3470.0
4 TraesCS6B01G380000 chr6B 93.671 2228 128 5 596 2822 655053016 655055231 0.000000e+00 3321.0
5 TraesCS6B01G380000 chr6B 96.661 599 20 0 1 599 654908508 654909106 0.000000e+00 996.0
6 TraesCS6B01G380000 chr6B 96.639 595 20 0 1 595 467311108 467311702 0.000000e+00 989.0
7 TraesCS6B01G380000 chr6B 95.833 240 9 1 3441 3680 83182241 83182479 1.600000e-103 387.0
8 TraesCS6B01G380000 chr6B 90.506 158 4 6 2665 2822 654886012 654886158 8.060000e-47 198.0
9 TraesCS6B01G380000 chr6B 89.873 158 5 5 2665 2822 654902676 654902822 3.750000e-45 193.0
10 TraesCS6B01G380000 chr6D 94.207 2227 110 4 596 2822 433568005 433570212 0.000000e+00 3380.0
11 TraesCS6B01G380000 chr6D 94.073 2227 113 4 596 2822 433562304 433564511 0.000000e+00 3363.0
12 TraesCS6B01G380000 chr6D 93.848 2227 119 3 596 2822 433547178 433549386 0.000000e+00 3338.0
13 TraesCS6B01G380000 chr6A 93.893 2227 132 4 596 2822 579758574 579760796 0.000000e+00 3356.0
14 TraesCS6B01G380000 chr6A 93.046 2229 145 5 596 2822 579516680 579518900 0.000000e+00 3249.0
15 TraesCS6B01G380000 chr6A 92.998 2228 149 7 596 2822 579753559 579755780 0.000000e+00 3243.0
16 TraesCS6B01G380000 chr6A 88.889 72 5 1 2257 2328 579141776 579141708 6.550000e-13 86.1
17 TraesCS6B01G380000 chr3B 96.955 624 19 0 2819 3442 722455777 722456400 0.000000e+00 1048.0
18 TraesCS6B01G380000 chr3B 96.500 600 18 3 1 599 304949110 304948513 0.000000e+00 989.0
19 TraesCS6B01G380000 chr3B 96.321 598 22 0 1 598 497409553 497408956 0.000000e+00 983.0
20 TraesCS6B01G380000 chr3B 95.473 243 10 1 3439 3680 575873037 575873279 1.600000e-103 387.0
21 TraesCS6B01G380000 chr7B 96.945 622 19 0 2821 3442 395772057 395771436 0.000000e+00 1044.0
22 TraesCS6B01G380000 chr7B 96.921 617 19 0 2821 3437 728896782 728896166 0.000000e+00 1035.0
23 TraesCS6B01G380000 chr7B 96.474 624 21 1 2820 3442 393851676 393852299 0.000000e+00 1029.0
24 TraesCS6B01G380000 chr7B 96.995 599 18 0 1 599 533693920 533693322 0.000000e+00 1007.0
25 TraesCS6B01G380000 chr7B 96.234 239 9 0 3442 3680 525224358 525224120 3.450000e-105 392.0
26 TraesCS6B01G380000 chr5B 96.624 622 20 1 2821 3442 345340847 345341467 0.000000e+00 1031.0
27 TraesCS6B01G380000 chr5B 97.046 237 7 0 3444 3680 610818293 610818057 2.060000e-107 399.0
28 TraesCS6B01G380000 chr5B 96.639 238 8 0 3443 3680 684392878 684393115 2.660000e-106 396.0
29 TraesCS6B01G380000 chr4B 96.624 622 20 1 2821 3442 14678171 14678791 0.000000e+00 1031.0
30 TraesCS6B01G380000 chr4B 96.622 592 20 0 1 592 335594604 335595195 0.000000e+00 983.0
31 TraesCS6B01G380000 chr2B 96.624 622 20 1 2821 3442 172928516 172929136 0.000000e+00 1031.0
32 TraesCS6B01G380000 chr2B 96.661 599 20 0 1 599 175265714 175266312 0.000000e+00 996.0
33 TraesCS6B01G380000 chr2B 96.494 599 20 1 1 599 563800260 563799663 0.000000e+00 989.0
34 TraesCS6B01G380000 chr2B 96.218 238 9 0 3443 3680 453716665 453716902 1.240000e-104 390.0
35 TraesCS6B01G380000 chr1B 96.463 622 22 0 2821 3442 601194826 601194205 0.000000e+00 1027.0
36 TraesCS6B01G380000 chr1B 96.463 622 21 1 2821 3442 476012240 476011620 0.000000e+00 1026.0
37 TraesCS6B01G380000 chr1B 96.639 595 19 1 5 599 431219883 431220476 0.000000e+00 987.0
38 TraesCS6B01G380000 chr1B 96.250 240 9 0 3441 3680 41145091 41144852 9.580000e-106 394.0
39 TraesCS6B01G380000 chr1B 95.833 240 10 0 3441 3680 41183623 41183384 4.460000e-104 388.0
40 TraesCS6B01G380000 chr1B 95.455 242 11 0 3439 3680 567810315 567810074 1.600000e-103 387.0


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 TraesCS6B01G380000 chr6B 654916559 654920238 3679 False 6796.0 6796 100.0000 1 3680 1 chr6B.!!$F7 3679
1 TraesCS6B01G380000 chr6B 654853638 654855719 2081 False 3504.0 3504 97.0720 596 2674 1 chr6B.!!$F3 2078
2 TraesCS6B01G380000 chr6B 654877735 654879816 2081 False 3470.0 3470 96.7830 596 2674 1 chr6B.!!$F4 2078
3 TraesCS6B01G380000 chr6B 655053016 655055231 2215 False 3321.0 3321 93.6710 596 2822 1 chr6B.!!$F8 2226
4 TraesCS6B01G380000 chr6B 654886012 654889936 3924 False 1839.0 3480 93.6905 596 2822 2 chr6B.!!$F9 2226
5 TraesCS6B01G380000 chr6B 654908508 654909106 598 False 996.0 996 96.6610 1 599 1 chr6B.!!$F6 598
6 TraesCS6B01G380000 chr6B 467311108 467311702 594 False 989.0 989 96.6390 1 595 1 chr6B.!!$F2 594
7 TraesCS6B01G380000 chr6D 433562304 433570212 7908 False 3371.5 3380 94.1400 596 2822 2 chr6D.!!$F2 2226
8 TraesCS6B01G380000 chr6D 433547178 433549386 2208 False 3338.0 3338 93.8480 596 2822 1 chr6D.!!$F1 2226
9 TraesCS6B01G380000 chr6A 579753559 579760796 7237 False 3299.5 3356 93.4455 596 2822 2 chr6A.!!$F2 2226
10 TraesCS6B01G380000 chr6A 579516680 579518900 2220 False 3249.0 3249 93.0460 596 2822 1 chr6A.!!$F1 2226
11 TraesCS6B01G380000 chr3B 722455777 722456400 623 False 1048.0 1048 96.9550 2819 3442 1 chr3B.!!$F2 623
12 TraesCS6B01G380000 chr3B 304948513 304949110 597 True 989.0 989 96.5000 1 599 1 chr3B.!!$R1 598
13 TraesCS6B01G380000 chr3B 497408956 497409553 597 True 983.0 983 96.3210 1 598 1 chr3B.!!$R2 597
14 TraesCS6B01G380000 chr7B 395771436 395772057 621 True 1044.0 1044 96.9450 2821 3442 1 chr7B.!!$R1 621
15 TraesCS6B01G380000 chr7B 728896166 728896782 616 True 1035.0 1035 96.9210 2821 3437 1 chr7B.!!$R4 616
16 TraesCS6B01G380000 chr7B 393851676 393852299 623 False 1029.0 1029 96.4740 2820 3442 1 chr7B.!!$F1 622
17 TraesCS6B01G380000 chr7B 533693322 533693920 598 True 1007.0 1007 96.9950 1 599 1 chr7B.!!$R3 598
18 TraesCS6B01G380000 chr5B 345340847 345341467 620 False 1031.0 1031 96.6240 2821 3442 1 chr5B.!!$F1 621
19 TraesCS6B01G380000 chr4B 14678171 14678791 620 False 1031.0 1031 96.6240 2821 3442 1 chr4B.!!$F1 621
20 TraesCS6B01G380000 chr4B 335594604 335595195 591 False 983.0 983 96.6220 1 592 1 chr4B.!!$F2 591
21 TraesCS6B01G380000 chr2B 172928516 172929136 620 False 1031.0 1031 96.6240 2821 3442 1 chr2B.!!$F1 621
22 TraesCS6B01G380000 chr2B 175265714 175266312 598 False 996.0 996 96.6610 1 599 1 chr2B.!!$F2 598
23 TraesCS6B01G380000 chr2B 563799663 563800260 597 True 989.0 989 96.4940 1 599 1 chr2B.!!$R1 598
24 TraesCS6B01G380000 chr1B 601194205 601194826 621 True 1027.0 1027 96.4630 2821 3442 1 chr1B.!!$R5 621
25 TraesCS6B01G380000 chr1B 476011620 476012240 620 True 1026.0 1026 96.4630 2821 3442 1 chr1B.!!$R3 621
26 TraesCS6B01G380000 chr1B 431219883 431220476 593 False 987.0 987 96.6390 5 599 1 chr1B.!!$F1 594

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
284 285 0.533308 TCAACGAAAACCTGGGTCGG 60.533 55.0 17.26 4.82 39.07 4.79 F
569 570 0.948623 CGTGCTTCGACACATGGGAA 60.949 55.0 0.00 0.00 40.73 3.97 F
1213 5659 1.210538 AGGATGATGCTGAGAAGGCA 58.789 50.0 0.00 0.00 44.05 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 5659 0.107081 TGAACACCCCGAATCGTTGT 59.893 50.0 0.82 0.0 0.0 3.32 R
1962 12110 0.250234 GTCTGTGCCACATGAGCCTA 59.750 55.0 0.00 0.0 0.0 3.93 R
2687 12841 0.182775 GGACCCCCACGATGCTAATT 59.817 55.0 0.00 0.0 0.0 1.40 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
160 161 6.155475 AGCTTAAATAGTCTTGATCTCGCT 57.845 37.500 0.00 0.00 0.00 4.93
284 285 0.533308 TCAACGAAAACCTGGGTCGG 60.533 55.000 17.26 4.82 39.07 4.79
481 482 5.163612 GCCAACTCTTTATCCCATTCTTGTC 60.164 44.000 0.00 0.00 0.00 3.18
569 570 0.948623 CGTGCTTCGACACATGGGAA 60.949 55.000 0.00 0.00 40.73 3.97
602 5048 1.712401 GTGGGCGTTACATGTTACGA 58.288 50.000 34.05 15.69 37.76 3.43
983 5429 6.420008 GCAACTATATAAGACACCAAGTACCG 59.580 42.308 0.00 0.00 0.00 4.02
987 5433 2.538512 AAGACACCAAGTACCGTTCC 57.461 50.000 0.00 0.00 0.00 3.62
1159 5605 1.750399 GTCGATGGTGGCAAGGCAT 60.750 57.895 0.00 0.00 0.00 4.40
1213 5659 1.210538 AGGATGATGCTGAGAAGGCA 58.789 50.000 0.00 0.00 44.05 4.75
1242 5688 1.293179 GGGTGTTCAAGGCCAATGC 59.707 57.895 5.01 0.00 0.00 3.56
1857 12005 4.851639 AAAGCTATGAGGATGTTCCAGT 57.148 40.909 0.00 0.00 39.61 4.00
1962 12110 7.309990 CCAATTTTACAAAGGTGGAGTGATGAT 60.310 37.037 0.00 0.00 0.00 2.45
2128 12276 1.068055 CCTGACAAGAAAGGCATGTGC 60.068 52.381 0.00 0.00 41.14 4.57
2165 12313 2.158755 CCTTCTTACCCCACTGCATAGG 60.159 54.545 0.00 0.00 0.00 2.57
2184 12332 2.103771 AGGATGAGCGTCATATGCAACT 59.896 45.455 0.00 0.00 37.20 3.16
2571 12725 0.611200 AATTCCCGTCGTCATGGTCA 59.389 50.000 0.00 0.00 0.00 4.02
2579 12733 0.955905 TCGTCATGGTCACTCAACGA 59.044 50.000 0.00 0.00 36.86 3.85
2633 12787 5.221362 ACACCAACCTTAATTTTACACTGGC 60.221 40.000 0.00 0.00 0.00 4.85
2728 12882 4.220821 CCATACCTCAATACGGTAGAGCAT 59.779 45.833 0.00 0.00 40.14 3.79
2783 12937 3.889815 AGTAATGAGCATGCAGGCTAAA 58.110 40.909 27.90 18.14 45.99 1.85
2920 13074 8.567948 CATGCTAGAATTGTATTAACCGGAAAT 58.432 33.333 9.46 10.35 0.00 2.17
3030 13184 4.534500 TCCTAGCCATGGACAAAAGAGTTA 59.466 41.667 18.40 0.00 0.00 2.24
3124 13279 6.620733 GCACTTGATCGTTTAGTATGTTGCTT 60.621 38.462 0.00 0.00 0.00 3.91
3296 13451 3.246936 GGGTTGGCGTATTTCGAGATTAC 59.753 47.826 0.00 0.00 42.86 1.89
3442 13597 3.996480 AGAGACTTGCCAGTAACAAGAC 58.004 45.455 10.26 4.42 45.99 3.01
3443 13598 3.388024 AGAGACTTGCCAGTAACAAGACA 59.612 43.478 10.26 0.00 45.99 3.41
3444 13599 3.467803 AGACTTGCCAGTAACAAGACAC 58.532 45.455 10.26 2.40 45.99 3.67
3445 13600 3.134804 AGACTTGCCAGTAACAAGACACT 59.865 43.478 10.26 4.32 45.99 3.55
3446 13601 4.344102 AGACTTGCCAGTAACAAGACACTA 59.656 41.667 10.26 0.00 45.99 2.74
3447 13602 4.377897 ACTTGCCAGTAACAAGACACTAC 58.622 43.478 10.26 0.00 45.99 2.73
3448 13603 4.101119 ACTTGCCAGTAACAAGACACTACT 59.899 41.667 10.26 0.00 45.99 2.57
3449 13604 5.303589 ACTTGCCAGTAACAAGACACTACTA 59.696 40.000 10.26 0.00 45.99 1.82
3450 13605 5.386958 TGCCAGTAACAAGACACTACTAG 57.613 43.478 0.00 0.00 0.00 2.57
3451 13606 4.219944 TGCCAGTAACAAGACACTACTAGG 59.780 45.833 0.00 0.00 0.00 3.02
3452 13607 4.381718 GCCAGTAACAAGACACTACTAGGG 60.382 50.000 0.00 0.00 0.00 3.53
3453 13608 5.014858 CCAGTAACAAGACACTACTAGGGA 58.985 45.833 0.00 0.00 0.00 4.20
3454 13609 5.479375 CCAGTAACAAGACACTACTAGGGAA 59.521 44.000 0.00 0.00 0.00 3.97
3455 13610 6.014840 CCAGTAACAAGACACTACTAGGGAAA 60.015 42.308 0.00 0.00 0.00 3.13
3456 13611 7.439381 CAGTAACAAGACACTACTAGGGAAAA 58.561 38.462 0.00 0.00 0.00 2.29
3457 13612 7.599245 CAGTAACAAGACACTACTAGGGAAAAG 59.401 40.741 0.00 0.00 0.00 2.27
3458 13613 5.485209 ACAAGACACTACTAGGGAAAAGG 57.515 43.478 0.00 0.00 0.00 3.11
3459 13614 4.254492 CAAGACACTACTAGGGAAAAGGC 58.746 47.826 0.00 0.00 0.00 4.35
3460 13615 3.792515 AGACACTACTAGGGAAAAGGCT 58.207 45.455 0.00 0.00 0.00 4.58
3461 13616 4.944177 AGACACTACTAGGGAAAAGGCTA 58.056 43.478 0.00 0.00 0.00 3.93
3462 13617 4.957327 AGACACTACTAGGGAAAAGGCTAG 59.043 45.833 0.00 0.00 0.00 3.42
3463 13618 3.451540 ACACTACTAGGGAAAAGGCTAGC 59.548 47.826 6.04 6.04 0.00 3.42
3464 13619 3.451178 CACTACTAGGGAAAAGGCTAGCA 59.549 47.826 18.24 0.00 0.00 3.49
3465 13620 3.707102 ACTACTAGGGAAAAGGCTAGCAG 59.293 47.826 18.24 4.16 0.00 4.24
3466 13621 1.210722 ACTAGGGAAAAGGCTAGCAGC 59.789 52.381 18.24 0.00 41.46 5.25
3467 13622 1.210478 CTAGGGAAAAGGCTAGCAGCA 59.790 52.381 18.24 0.00 44.75 4.41
3468 13623 0.034670 AGGGAAAAGGCTAGCAGCAG 60.035 55.000 18.24 0.00 44.75 4.24
3469 13624 1.661498 GGGAAAAGGCTAGCAGCAGC 61.661 60.000 18.24 7.98 44.75 5.25
3470 13625 1.427020 GAAAAGGCTAGCAGCAGCG 59.573 57.895 18.24 0.00 44.75 5.18
3471 13626 2.589636 GAAAAGGCTAGCAGCAGCGC 62.590 60.000 18.24 0.00 44.75 5.92
3472 13627 3.907260 AAAGGCTAGCAGCAGCGCA 62.907 57.895 18.24 0.00 44.75 6.09
3473 13628 4.834453 AGGCTAGCAGCAGCGCAG 62.834 66.667 18.24 1.31 44.75 5.18
3479 13634 2.953821 GCAGCAGCGCAGGTTTTA 59.046 55.556 11.47 0.00 33.74 1.52
3480 13635 1.154150 GCAGCAGCGCAGGTTTTAG 60.154 57.895 11.47 0.00 33.74 1.85
3481 13636 1.577328 GCAGCAGCGCAGGTTTTAGA 61.577 55.000 11.47 0.00 33.74 2.10
3482 13637 1.089920 CAGCAGCGCAGGTTTTAGAT 58.910 50.000 11.47 0.00 33.74 1.98
3483 13638 1.089920 AGCAGCGCAGGTTTTAGATG 58.910 50.000 11.47 0.00 33.74 2.90
3484 13639 0.524180 GCAGCGCAGGTTTTAGATGC 60.524 55.000 11.47 2.03 38.81 3.91
3485 13640 0.804364 CAGCGCAGGTTTTAGATGCA 59.196 50.000 11.47 0.00 39.97 3.96
3486 13641 1.402968 CAGCGCAGGTTTTAGATGCAT 59.597 47.619 11.47 0.00 39.97 3.96
3487 13642 1.672881 AGCGCAGGTTTTAGATGCATC 59.327 47.619 19.37 19.37 39.97 3.91
3488 13643 1.401552 GCGCAGGTTTTAGATGCATCA 59.598 47.619 27.81 11.65 39.97 3.07
3489 13644 2.540361 GCGCAGGTTTTAGATGCATCAG 60.540 50.000 27.81 8.38 39.97 2.90
3490 13645 2.679837 CGCAGGTTTTAGATGCATCAGT 59.320 45.455 27.81 11.41 39.97 3.41
3491 13646 3.871006 CGCAGGTTTTAGATGCATCAGTA 59.129 43.478 27.81 10.36 39.97 2.74
3492 13647 4.025396 CGCAGGTTTTAGATGCATCAGTAG 60.025 45.833 27.81 10.29 39.97 2.57
3493 13648 4.260948 GCAGGTTTTAGATGCATCAGTAGC 60.261 45.833 27.81 17.80 39.75 3.58
3494 13649 4.025396 CAGGTTTTAGATGCATCAGTAGCG 60.025 45.833 27.81 11.61 33.85 4.26
3495 13650 3.303395 GGTTTTAGATGCATCAGTAGCGC 60.303 47.826 27.81 0.00 33.85 5.92
3496 13651 1.770957 TTAGATGCATCAGTAGCGCG 58.229 50.000 27.81 0.00 33.85 6.86
3497 13652 0.039165 TAGATGCATCAGTAGCGCGG 60.039 55.000 27.81 0.00 33.85 6.46
3498 13653 2.280389 ATGCATCAGTAGCGCGGG 60.280 61.111 8.83 0.00 33.85 6.13
3499 13654 3.814615 ATGCATCAGTAGCGCGGGG 62.815 63.158 8.83 0.00 33.85 5.73
3501 13656 3.849951 CATCAGTAGCGCGGGGGT 61.850 66.667 8.83 1.54 0.00 4.95
3502 13657 3.537874 ATCAGTAGCGCGGGGGTC 61.538 66.667 8.83 0.00 0.00 4.46
3513 13668 3.149648 GGGGGTCGGCGCTACTAA 61.150 66.667 7.64 0.00 0.00 2.24
3514 13669 2.505167 GGGGGTCGGCGCTACTAAT 61.505 63.158 7.64 0.00 0.00 1.73
3515 13670 1.181098 GGGGGTCGGCGCTACTAATA 61.181 60.000 7.64 0.00 0.00 0.98
3516 13671 0.675633 GGGGTCGGCGCTACTAATAA 59.324 55.000 7.64 0.00 0.00 1.40
3517 13672 1.336609 GGGGTCGGCGCTACTAATAAG 60.337 57.143 7.64 0.00 0.00 1.73
3518 13673 1.336609 GGGTCGGCGCTACTAATAAGG 60.337 57.143 7.64 0.00 0.00 2.69
3519 13674 1.416373 GTCGGCGCTACTAATAAGGC 58.584 55.000 7.64 0.00 0.00 4.35
3525 13680 3.278367 CGCTACTAATAAGGCGCTACA 57.722 47.619 7.64 0.00 41.08 2.74
3526 13681 3.235195 CGCTACTAATAAGGCGCTACAG 58.765 50.000 7.64 0.00 41.08 2.74
3527 13682 2.987821 GCTACTAATAAGGCGCTACAGC 59.012 50.000 7.64 0.00 37.78 4.40
3528 13683 3.305471 GCTACTAATAAGGCGCTACAGCT 60.305 47.826 7.64 0.00 39.32 4.24
3529 13684 4.082895 GCTACTAATAAGGCGCTACAGCTA 60.083 45.833 7.64 0.00 39.32 3.32
3530 13685 4.931661 ACTAATAAGGCGCTACAGCTAA 57.068 40.909 7.64 0.00 39.32 3.09
3531 13686 4.618965 ACTAATAAGGCGCTACAGCTAAC 58.381 43.478 7.64 0.00 39.32 2.34
3532 13687 3.536956 AATAAGGCGCTACAGCTAACA 57.463 42.857 7.64 0.00 39.32 2.41
3533 13688 2.579207 TAAGGCGCTACAGCTAACAG 57.421 50.000 7.64 0.00 39.32 3.16
3534 13689 0.895530 AAGGCGCTACAGCTAACAGA 59.104 50.000 7.64 0.00 39.32 3.41
3535 13690 1.115467 AGGCGCTACAGCTAACAGAT 58.885 50.000 7.64 0.00 39.32 2.90
3536 13691 2.307768 AGGCGCTACAGCTAACAGATA 58.692 47.619 7.64 0.00 39.32 1.98
3537 13692 2.294791 AGGCGCTACAGCTAACAGATAG 59.705 50.000 7.64 0.00 39.32 2.08
3564 13719 4.436998 GTGCTCACCGGCGCTACT 62.437 66.667 7.64 0.00 39.35 2.57
3565 13720 4.435436 TGCTCACCGGCGCTACTG 62.435 66.667 7.64 0.00 34.52 2.74
3567 13722 4.135153 CTCACCGGCGCTACTGCT 62.135 66.667 7.64 0.00 36.97 4.24
3568 13723 2.752640 TCACCGGCGCTACTGCTA 60.753 61.111 7.64 0.00 36.97 3.49
3569 13724 2.582498 CACCGGCGCTACTGCTAC 60.582 66.667 7.64 0.00 36.97 3.58
3570 13725 3.066190 ACCGGCGCTACTGCTACA 61.066 61.111 7.64 0.00 36.97 2.74
3571 13726 2.582498 CCGGCGCTACTGCTACAC 60.582 66.667 7.64 0.00 36.97 2.90
3572 13727 2.180769 CGGCGCTACTGCTACACA 59.819 61.111 7.64 0.00 36.97 3.72
3573 13728 1.445410 CGGCGCTACTGCTACACAA 60.445 57.895 7.64 0.00 36.97 3.33
3574 13729 1.413767 CGGCGCTACTGCTACACAAG 61.414 60.000 7.64 0.00 36.97 3.16
3575 13730 0.389948 GGCGCTACTGCTACACAAGT 60.390 55.000 7.64 0.00 36.97 3.16
3576 13731 0.716108 GCGCTACTGCTACACAAGTG 59.284 55.000 0.00 0.00 36.97 3.16
3577 13732 1.935300 GCGCTACTGCTACACAAGTGT 60.935 52.381 11.00 11.00 46.87 3.55
3578 13733 2.670229 GCGCTACTGCTACACAAGTGTA 60.670 50.000 12.09 12.09 44.42 2.90
3586 13741 1.795768 TACACAAGTGTAGCAGCAGC 58.204 50.000 8.88 0.00 44.42 5.25
3587 13742 1.224069 ACACAAGTGTAGCAGCAGCG 61.224 55.000 3.64 0.00 42.90 5.18
3612 13767 2.492090 CGGAAGCTCGCTACTGCT 59.508 61.111 0.00 0.00 41.82 4.24
3613 13768 1.728069 CGGAAGCTCGCTACTGCTA 59.272 57.895 0.00 0.00 38.75 3.49
3614 13769 0.312416 CGGAAGCTCGCTACTGCTAT 59.688 55.000 0.00 0.00 38.75 2.97
3615 13770 1.269309 CGGAAGCTCGCTACTGCTATT 60.269 52.381 0.00 0.00 38.75 1.73
3616 13771 2.031069 CGGAAGCTCGCTACTGCTATTA 60.031 50.000 0.00 0.00 38.75 0.98
3617 13772 3.570559 GGAAGCTCGCTACTGCTATTAG 58.429 50.000 0.00 0.00 38.75 1.73
3618 13773 2.715737 AGCTCGCTACTGCTATTAGC 57.284 50.000 8.80 8.80 42.82 3.09
3619 13774 2.235016 AGCTCGCTACTGCTATTAGCT 58.765 47.619 16.29 0.00 42.97 3.32
3620 13775 2.227865 AGCTCGCTACTGCTATTAGCTC 59.772 50.000 16.29 1.10 42.97 4.09
3621 13776 2.227865 GCTCGCTACTGCTATTAGCTCT 59.772 50.000 16.29 4.42 42.97 4.09
3622 13777 3.437395 GCTCGCTACTGCTATTAGCTCTA 59.563 47.826 16.29 5.27 42.97 2.43
3623 13778 4.436852 GCTCGCTACTGCTATTAGCTCTAG 60.437 50.000 16.29 13.99 42.97 2.43
3624 13779 3.437395 TCGCTACTGCTATTAGCTCTAGC 59.563 47.826 22.55 22.55 42.97 3.42
3625 13780 3.189495 CGCTACTGCTATTAGCTCTAGCA 59.811 47.826 27.04 22.63 46.97 3.49
3626 13781 4.481463 GCTACTGCTATTAGCTCTAGCAC 58.519 47.826 25.05 11.60 44.94 4.40
3627 13782 3.634568 ACTGCTATTAGCTCTAGCACG 57.365 47.619 21.08 18.69 44.94 5.34
3628 13783 2.287909 ACTGCTATTAGCTCTAGCACGC 60.288 50.000 21.08 4.97 44.94 5.34
3629 13784 1.957177 TGCTATTAGCTCTAGCACGCT 59.043 47.619 21.08 0.00 44.94 5.07
3630 13785 2.362397 TGCTATTAGCTCTAGCACGCTT 59.638 45.455 21.08 0.00 44.94 4.68
3631 13786 3.181475 TGCTATTAGCTCTAGCACGCTTT 60.181 43.478 21.08 0.00 44.94 3.51
3632 13787 3.183373 GCTATTAGCTCTAGCACGCTTTG 59.817 47.826 18.60 0.00 45.16 2.77
3633 13788 6.353354 GCTATTAGCTCTAGCACGCTTTGC 62.353 50.000 18.60 0.00 44.64 3.68
3641 13796 3.440267 CACGCTTTGCATTGACGC 58.560 55.556 0.00 0.00 0.00 5.19
3643 13798 3.526536 CGCTTTGCATTGACGCGC 61.527 61.111 5.73 0.00 37.29 6.86
3644 13799 2.126734 GCTTTGCATTGACGCGCT 60.127 55.556 5.73 0.00 33.35 5.92
3645 13800 1.134487 GCTTTGCATTGACGCGCTA 59.866 52.632 5.73 0.00 33.35 4.26
3646 13801 1.128147 GCTTTGCATTGACGCGCTAC 61.128 55.000 5.73 0.00 33.35 3.58
3647 13802 0.521242 CTTTGCATTGACGCGCTACC 60.521 55.000 5.73 0.00 33.35 3.18
3648 13803 2.234271 TTTGCATTGACGCGCTACCG 62.234 55.000 5.73 0.00 37.57 4.02
3672 13827 3.121030 CGGCGCTGCTGCTAACTT 61.121 61.111 14.03 0.00 36.97 2.66
3673 13828 2.680913 CGGCGCTGCTGCTAACTTT 61.681 57.895 14.03 0.00 36.97 2.66
3674 13829 1.581447 GGCGCTGCTGCTAACTTTT 59.419 52.632 14.03 0.00 36.97 2.27
3675 13830 0.802494 GGCGCTGCTGCTAACTTTTA 59.198 50.000 14.03 0.00 36.97 1.52
3676 13831 1.401905 GGCGCTGCTGCTAACTTTTAT 59.598 47.619 14.03 0.00 36.97 1.40
3677 13832 2.612212 GGCGCTGCTGCTAACTTTTATA 59.388 45.455 14.03 0.00 36.97 0.98
3678 13833 3.546218 GGCGCTGCTGCTAACTTTTATAC 60.546 47.826 14.03 0.00 36.97 1.47
3679 13834 3.063452 GCGCTGCTGCTAACTTTTATACA 59.937 43.478 14.03 0.00 36.97 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 4.792068 AGGACTCAACAATCTCAAAACCA 58.208 39.130 0.00 0.00 0.00 3.67
284 285 5.448438 TCAACATGAAACGAAACATAGCAC 58.552 37.500 0.00 0.00 0.00 4.40
569 570 0.673644 GCCCACGATGCGGCTATATT 60.674 55.000 0.00 0.00 42.21 1.28
983 5429 2.483013 GCTCTGGTTTGGTTTTGGGAAC 60.483 50.000 0.00 0.00 0.00 3.62
987 5433 1.480137 TGTGCTCTGGTTTGGTTTTGG 59.520 47.619 0.00 0.00 0.00 3.28
1159 5605 1.196766 ACTGCACCATCCAGCTCTCA 61.197 55.000 0.00 0.00 33.65 3.27
1213 5659 0.107081 TGAACACCCCGAATCGTTGT 59.893 50.000 0.82 0.00 0.00 3.32
1242 5688 0.389426 AAACGACTCGATGAACCCGG 60.389 55.000 5.20 0.00 0.00 5.73
1532 5979 9.742144 TGTAGATACTATAAGAGGACATTCTCC 57.258 37.037 0.00 0.00 39.81 3.71
1581 6028 2.235898 ACAGCAGAAAAAGCCCAACAAA 59.764 40.909 0.00 0.00 0.00 2.83
1688 6135 0.468226 TCGCAACCTTGGTCTTCACT 59.532 50.000 0.00 0.00 0.00 3.41
1857 12005 0.603569 GAGAGCTCCCTCGTTGTTGA 59.396 55.000 10.93 0.00 43.05 3.18
1962 12110 0.250234 GTCTGTGCCACATGAGCCTA 59.750 55.000 0.00 0.00 0.00 3.93
2165 12313 5.406477 TGATAAGTTGCATATGACGCTCATC 59.594 40.000 6.97 2.47 38.26 2.92
2460 12612 6.020916 CGCTTCAACATTTATCTGCAAATCAG 60.021 38.462 0.00 0.00 44.21 2.90
2470 12622 5.967674 CCATTCTCACGCTTCAACATTTATC 59.032 40.000 0.00 0.00 0.00 1.75
2571 12725 2.132762 GGTTGTTGTCGATCGTTGAGT 58.867 47.619 15.94 0.00 0.00 3.41
2579 12733 1.550976 GGAGAGGAGGTTGTTGTCGAT 59.449 52.381 0.00 0.00 0.00 3.59
2684 12838 2.357952 GACCCCCACGATGCTAATTTTC 59.642 50.000 0.00 0.00 0.00 2.29
2686 12840 1.409661 GGACCCCCACGATGCTAATTT 60.410 52.381 0.00 0.00 0.00 1.82
2687 12841 0.182775 GGACCCCCACGATGCTAATT 59.817 55.000 0.00 0.00 0.00 1.40
2718 12872 6.929049 TGTTTCTCCATTTATATGCTCTACCG 59.071 38.462 0.00 0.00 0.00 4.02
2770 12924 1.821136 AGGAGTTTTTAGCCTGCATGC 59.179 47.619 11.82 11.82 0.00 4.06
3030 13184 9.809395 ATGATGTGATCCTCTTAATCAAATGAT 57.191 29.630 0.00 0.00 32.39 2.45
3043 13197 7.002250 TCATTCTCCTAATGATGTGATCCTC 57.998 40.000 0.00 0.00 32.21 3.71
3124 13279 9.013229 ACATGTATAAGTCATGAAGAAAGCAAA 57.987 29.630 11.92 0.00 43.47 3.68
3296 13451 2.409752 CGACAATCGGAGTGACAAAACG 60.410 50.000 12.93 4.48 36.00 3.60
3442 13597 3.451178 TGCTAGCCTTTTCCCTAGTAGTG 59.549 47.826 13.29 0.00 34.81 2.74
3443 13598 3.707102 CTGCTAGCCTTTTCCCTAGTAGT 59.293 47.826 13.29 0.00 38.66 2.73
3444 13599 3.493524 GCTGCTAGCCTTTTCCCTAGTAG 60.494 52.174 13.29 7.97 43.15 2.57
3445 13600 2.434702 GCTGCTAGCCTTTTCCCTAGTA 59.565 50.000 13.29 0.00 34.48 1.82
3446 13601 1.210722 GCTGCTAGCCTTTTCCCTAGT 59.789 52.381 13.29 0.00 34.48 2.57
3447 13602 1.210478 TGCTGCTAGCCTTTTCCCTAG 59.790 52.381 13.29 0.00 41.51 3.02
3448 13603 1.210478 CTGCTGCTAGCCTTTTCCCTA 59.790 52.381 13.29 0.00 41.51 3.53
3449 13604 0.034670 CTGCTGCTAGCCTTTTCCCT 60.035 55.000 13.29 0.00 41.51 4.20
3450 13605 1.661498 GCTGCTGCTAGCCTTTTCCC 61.661 60.000 13.29 0.00 41.51 3.97
3451 13606 1.805910 GCTGCTGCTAGCCTTTTCC 59.194 57.895 13.29 0.00 41.51 3.13
3452 13607 1.427020 CGCTGCTGCTAGCCTTTTC 59.573 57.895 13.29 0.00 41.51 2.29
3453 13608 2.694760 GCGCTGCTGCTAGCCTTTT 61.695 57.895 13.29 0.00 41.51 2.27
3454 13609 3.130160 GCGCTGCTGCTAGCCTTT 61.130 61.111 13.29 0.00 41.51 3.11
3455 13610 4.399395 TGCGCTGCTGCTAGCCTT 62.399 61.111 13.29 0.00 41.51 4.35
3456 13611 4.834453 CTGCGCTGCTGCTAGCCT 62.834 66.667 13.29 0.00 41.51 4.58
3459 13614 1.580845 AAAACCTGCGCTGCTGCTAG 61.581 55.000 9.73 11.11 36.97 3.42
3460 13615 0.321210 TAAAACCTGCGCTGCTGCTA 60.321 50.000 9.73 1.85 36.97 3.49
3461 13616 1.580845 CTAAAACCTGCGCTGCTGCT 61.581 55.000 9.73 0.00 36.97 4.24
3462 13617 1.154150 CTAAAACCTGCGCTGCTGC 60.154 57.895 9.73 5.34 0.00 5.25
3463 13618 1.089920 ATCTAAAACCTGCGCTGCTG 58.910 50.000 9.73 0.00 0.00 4.41
3464 13619 1.089920 CATCTAAAACCTGCGCTGCT 58.910 50.000 9.73 0.00 0.00 4.24
3465 13620 0.524180 GCATCTAAAACCTGCGCTGC 60.524 55.000 9.73 1.38 0.00 5.25
3466 13621 0.804364 TGCATCTAAAACCTGCGCTG 59.196 50.000 9.73 8.47 38.75 5.18
3467 13622 1.672881 GATGCATCTAAAACCTGCGCT 59.327 47.619 19.70 0.00 38.75 5.92
3468 13623 1.401552 TGATGCATCTAAAACCTGCGC 59.598 47.619 26.32 0.00 38.75 6.09
3469 13624 2.679837 ACTGATGCATCTAAAACCTGCG 59.320 45.455 26.32 5.67 38.75 5.18
3470 13625 4.260948 GCTACTGATGCATCTAAAACCTGC 60.261 45.833 26.32 15.11 36.45 4.85
3471 13626 4.025396 CGCTACTGATGCATCTAAAACCTG 60.025 45.833 26.32 6.46 0.00 4.00
3472 13627 4.122776 CGCTACTGATGCATCTAAAACCT 58.877 43.478 26.32 4.75 0.00 3.50
3473 13628 3.303395 GCGCTACTGATGCATCTAAAACC 60.303 47.826 26.32 10.22 0.00 3.27
3474 13629 3.602491 CGCGCTACTGATGCATCTAAAAC 60.602 47.826 26.32 12.69 0.00 2.43
3475 13630 2.539688 CGCGCTACTGATGCATCTAAAA 59.460 45.455 26.32 6.27 0.00 1.52
3476 13631 2.127251 CGCGCTACTGATGCATCTAAA 58.873 47.619 26.32 11.04 0.00 1.85
3477 13632 1.602920 CCGCGCTACTGATGCATCTAA 60.603 52.381 26.32 11.37 0.00 2.10
3478 13633 0.039165 CCGCGCTACTGATGCATCTA 60.039 55.000 26.32 11.36 0.00 1.98
3479 13634 1.300465 CCGCGCTACTGATGCATCT 60.300 57.895 26.32 10.78 0.00 2.90
3480 13635 2.313172 CCCGCGCTACTGATGCATC 61.313 63.158 20.14 20.14 0.00 3.91
3481 13636 2.280389 CCCGCGCTACTGATGCAT 60.280 61.111 5.56 0.00 0.00 3.96
3482 13637 4.529219 CCCCGCGCTACTGATGCA 62.529 66.667 5.56 0.00 0.00 3.96
3484 13639 3.792053 GACCCCCGCGCTACTGATG 62.792 68.421 5.56 0.00 0.00 3.07
3485 13640 3.537874 GACCCCCGCGCTACTGAT 61.538 66.667 5.56 0.00 0.00 2.90
3496 13651 1.181098 TATTAGTAGCGCCGACCCCC 61.181 60.000 2.29 0.00 0.00 5.40
3497 13652 0.675633 TTATTAGTAGCGCCGACCCC 59.324 55.000 2.29 0.00 0.00 4.95
3498 13653 1.336609 CCTTATTAGTAGCGCCGACCC 60.337 57.143 2.29 0.00 0.00 4.46
3499 13654 1.933949 GCCTTATTAGTAGCGCCGACC 60.934 57.143 2.29 0.00 0.00 4.79
3500 13655 1.416373 GCCTTATTAGTAGCGCCGAC 58.584 55.000 2.29 2.03 0.00 4.79
3501 13656 0.039798 CGCCTTATTAGTAGCGCCGA 60.040 55.000 2.29 0.00 42.31 5.54
3502 13657 2.431539 CGCCTTATTAGTAGCGCCG 58.568 57.895 2.29 0.00 42.31 6.46
3506 13661 2.987821 GCTGTAGCGCCTTATTAGTAGC 59.012 50.000 2.29 0.00 0.00 3.58
3527 13682 2.287069 ACGCGCTACTGCTATCTGTTAG 60.287 50.000 5.73 0.00 36.97 2.34
3528 13683 1.674441 ACGCGCTACTGCTATCTGTTA 59.326 47.619 5.73 0.00 36.97 2.41
3529 13684 0.456221 ACGCGCTACTGCTATCTGTT 59.544 50.000 5.73 0.00 36.97 3.16
3530 13685 0.248661 CACGCGCTACTGCTATCTGT 60.249 55.000 5.73 0.00 36.97 3.41
3531 13686 1.543941 GCACGCGCTACTGCTATCTG 61.544 60.000 5.73 0.00 36.97 2.90
3532 13687 1.299468 GCACGCGCTACTGCTATCT 60.299 57.895 5.73 0.00 36.97 1.98
3533 13688 3.225758 GCACGCGCTACTGCTATC 58.774 61.111 5.73 0.00 36.97 2.08
3547 13702 4.436998 AGTAGCGCCGGTGAGCAC 62.437 66.667 21.76 12.41 40.10 4.40
3548 13703 4.435436 CAGTAGCGCCGGTGAGCA 62.435 66.667 21.76 0.00 40.10 4.26
3566 13721 1.728971 GCTGCTGCTACACTTGTGTAG 59.271 52.381 27.27 27.27 43.30 2.74
3567 13722 1.795768 GCTGCTGCTACACTTGTGTA 58.204 50.000 8.53 12.31 36.03 2.90
3568 13723 1.224069 CGCTGCTGCTACACTTGTGT 61.224 55.000 14.03 11.30 36.97 3.72
3569 13724 1.494628 CGCTGCTGCTACACTTGTG 59.505 57.895 14.03 0.00 36.97 3.33
3570 13725 2.320587 GCGCTGCTGCTACACTTGT 61.321 57.895 14.03 0.00 36.97 3.16
3571 13726 2.031516 AGCGCTGCTGCTACACTTG 61.032 57.895 10.39 0.00 45.14 3.16
3572 13727 2.345244 AGCGCTGCTGCTACACTT 59.655 55.556 10.39 0.00 45.14 3.16
3610 13765 2.715737 AGCGTGCTAGAGCTAATAGC 57.284 50.000 19.04 19.04 44.81 2.97
3611 13766 4.963237 CAAAGCGTGCTAGAGCTAATAG 57.037 45.455 7.97 0.00 43.78 1.73
3624 13779 2.419895 CGCGTCAATGCAAAGCGTG 61.420 57.895 8.71 5.91 44.96 5.34
3625 13780 2.127270 CGCGTCAATGCAAAGCGT 60.127 55.556 8.71 0.00 44.96 5.07
3627 13782 1.128147 GTAGCGCGTCAATGCAAAGC 61.128 55.000 8.43 0.00 34.15 3.51
3628 13783 0.521242 GGTAGCGCGTCAATGCAAAG 60.521 55.000 8.43 0.00 34.15 2.77
3629 13784 1.499949 GGTAGCGCGTCAATGCAAA 59.500 52.632 8.43 0.00 34.15 3.68
3630 13785 2.735677 CGGTAGCGCGTCAATGCAA 61.736 57.895 8.43 0.00 34.15 4.08
3631 13786 3.185365 CGGTAGCGCGTCAATGCA 61.185 61.111 8.43 0.00 34.15 3.96
3632 13787 4.575245 GCGGTAGCGCGTCAATGC 62.575 66.667 24.65 3.22 0.00 3.56


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

AutoCloner maintained by Alex Coulton.