Multiple sequence alignment - TraesCS1B01G336200

Loading Multiple Alignment...

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 TraesCS1B01G336200 chr1B 100.000 3115 0 0 1 3115 563024033 563027147 0.000000e+00 5753.0
1 TraesCS1B01G336200 chr1B 76.699 103 20 4 468 568 591956075 591955975 2.000000e-03 54.7
2 TraesCS1B01G336200 chr1D 86.339 2562 170 61 638 3115 416468448 416470913 0.000000e+00 2627.0
3 TraesCS1B01G336200 chr1A 91.793 987 55 11 638 1603 513732541 513733522 0.000000e+00 1351.0
4 TraesCS1B01G336200 chr1A 83.827 878 79 33 1662 2514 513733548 513734387 0.000000e+00 776.0
5 TraesCS1B01G336200 chr1A 80.203 394 18 15 2737 3115 513734558 513734906 1.120000e-59 241.0
6 TraesCS1B01G336200 chr4B 89.043 575 47 8 1 566 75542990 75543557 0.000000e+00 699.0
7 TraesCS1B01G336200 chr2B 87.895 570 57 8 1 567 588160463 588161023 0.000000e+00 660.0
8 TraesCS1B01G336200 chr2B 84.348 575 71 7 1 566 572708550 572707986 2.110000e-151 545.0
9 TraesCS1B01G336200 chr5B 85.962 577 56 11 2 569 255338688 255338128 7.440000e-166 593.0
10 TraesCS1B01G336200 chr4D 88.446 502 36 10 1 487 12306386 12305892 1.240000e-163 586.0
11 TraesCS1B01G336200 chr7D 86.774 499 48 8 1 487 501797239 501796747 9.830000e-150 540.0
12 TraesCS1B01G336200 chr7D 86.869 396 38 7 4 393 626621554 626621167 6.170000e-117 431.0
13 TraesCS1B01G336200 chr7D 88.281 128 15 0 442 569 28219133 28219006 1.500000e-33 154.0
14 TraesCS1B01G336200 chr5D 87.387 444 40 7 1 435 494290474 494290910 2.160000e-136 496.0
15 TraesCS1B01G336200 chr3A 86.216 399 40 8 1 393 688022319 688022708 4.800000e-113 418.0
16 TraesCS1B01G336200 chr3A 93.750 48 3 0 1082 1129 558515671 558515718 4.310000e-09 73.1
17 TraesCS1B01G336200 chr2A 86.375 389 36 10 1 382 712182322 712182700 2.890000e-110 409.0
18 TraesCS1B01G336200 chr7B 85.122 410 38 11 1 394 543847473 543847071 6.260000e-107 398.0
19 TraesCS1B01G336200 chr2D 86.719 128 15 2 442 568 476805904 476806030 1.160000e-29 141.0
20 TraesCS1B01G336200 chr3D 94.231 52 3 0 1081 1132 427631935 427631884 2.580000e-11 80.5
21 TraesCS1B01G336200 chr3B 83.721 86 12 2 1081 1165 559109913 559109829 2.580000e-11 80.5


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 TraesCS1B01G336200 chr1B 563024033 563027147 3114 False 5753.000000 5753 100.000000 1 3115 1 chr1B.!!$F1 3114
1 TraesCS1B01G336200 chr1D 416468448 416470913 2465 False 2627.000000 2627 86.339000 638 3115 1 chr1D.!!$F1 2477
2 TraesCS1B01G336200 chr1A 513732541 513734906 2365 False 789.333333 1351 85.274333 638 3115 3 chr1A.!!$F1 2477
3 TraesCS1B01G336200 chr4B 75542990 75543557 567 False 699.000000 699 89.043000 1 566 1 chr4B.!!$F1 565
4 TraesCS1B01G336200 chr2B 588160463 588161023 560 False 660.000000 660 87.895000 1 567 1 chr2B.!!$F1 566
5 TraesCS1B01G336200 chr2B 572707986 572708550 564 True 545.000000 545 84.348000 1 566 1 chr2B.!!$R1 565
6 TraesCS1B01G336200 chr5B 255338128 255338688 560 True 593.000000 593 85.962000 2 569 1 chr5B.!!$R1 567


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
628 648 0.031994 GCACGACCAAGTTTTGCCAT 59.968 50.000 0.0 0.0 0.0 4.40 F
630 650 1.066908 CACGACCAAGTTTTGCCATGT 59.933 47.619 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 1915 0.170561 CTTACTGACGGACTCACGGG 59.829 60.0 0.00 0.0 38.39 5.28 R
2382 2485 0.179094 GATCGGCCCGTTGACATACA 60.179 55.0 1.63 0.0 0.00 2.29 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
22 23 0.260816 AAGCTCACCATGGCATCCAT 59.739 50.000 13.04 0.00 46.37 3.41
63 64 2.741092 GGTTCTGACGGCTCCACA 59.259 61.111 0.00 0.00 0.00 4.17
178 179 0.386113 GATTCGTCCCCTCTCCTTCG 59.614 60.000 0.00 0.00 0.00 3.79
180 181 2.044252 CGTCCCCTCTCCTTCGGA 60.044 66.667 0.00 0.00 0.00 4.55
196 199 2.507324 GAGGTCGACGGAAGCTGC 60.507 66.667 9.92 0.00 0.00 5.25
238 242 1.671054 ACGACATTGCCTTGGACGG 60.671 57.895 0.00 0.00 0.00 4.79
291 301 4.489771 CCGGCCCGCTCAGGAATT 62.490 66.667 0.00 0.00 45.00 2.17
299 309 2.476320 GCTCAGGAATTGCCTCCGC 61.476 63.158 0.00 0.00 46.97 5.54
300 310 1.821332 CTCAGGAATTGCCTCCGCC 60.821 63.158 0.00 0.00 46.97 6.13
301 311 2.262774 CTCAGGAATTGCCTCCGCCT 62.263 60.000 0.00 0.00 46.97 5.52
302 312 1.821332 CAGGAATTGCCTCCGCCTC 60.821 63.158 0.00 0.00 46.97 4.70
303 313 2.517166 GGAATTGCCTCCGCCTCC 60.517 66.667 0.00 0.00 0.00 4.30
304 314 2.897350 GAATTGCCTCCGCCTCCG 60.897 66.667 0.00 0.00 0.00 4.63
346 356 0.857681 TCCCCCAAATCCCCAATCCA 60.858 55.000 0.00 0.00 0.00 3.41
426 446 1.092921 GTTGACACTGGCCACGTCAA 61.093 55.000 29.61 29.61 44.95 3.18
468 488 3.572255 GCACTAAGGTTTGATTTGGACCA 59.428 43.478 0.00 0.00 35.89 4.02
485 505 6.884472 TGGACCAGGATTCATTAGTTTAGA 57.116 37.500 0.00 0.00 0.00 2.10
494 514 8.816894 AGGATTCATTAGTTTAGAGTGAGAACA 58.183 33.333 0.00 0.00 0.00 3.18
506 526 4.103153 AGAGTGAGAACAACAGGGATTTCA 59.897 41.667 0.00 0.00 0.00 2.69
511 531 5.656416 TGAGAACAACAGGGATTTCAACTTT 59.344 36.000 0.00 0.00 0.00 2.66
523 543 7.292356 AGGGATTTCAACTTTAGGGTTTGATTT 59.708 33.333 0.00 0.00 0.00 2.17
536 556 3.004944 GGTTTGATTTGCCGAACACCTAA 59.995 43.478 0.00 0.00 33.20 2.69
569 589 7.959175 AGGTTTAAAATGGACTTTTTCCCTAC 58.041 34.615 0.00 0.00 45.17 3.18
570 590 7.565768 AGGTTTAAAATGGACTTTTTCCCTACA 59.434 33.333 0.00 0.00 45.17 2.74
571 591 7.870954 GGTTTAAAATGGACTTTTTCCCTACAG 59.129 37.037 0.00 0.00 45.17 2.74
572 592 8.635328 GTTTAAAATGGACTTTTTCCCTACAGA 58.365 33.333 0.00 0.00 45.17 3.41
573 593 6.650427 AAAATGGACTTTTTCCCTACAGAC 57.350 37.500 0.00 0.00 45.17 3.51
574 594 4.993705 ATGGACTTTTTCCCTACAGACA 57.006 40.909 0.00 0.00 45.17 3.41
575 595 4.993705 TGGACTTTTTCCCTACAGACAT 57.006 40.909 0.00 0.00 45.17 3.06
576 596 6.636454 ATGGACTTTTTCCCTACAGACATA 57.364 37.500 0.00 0.00 45.17 2.29
577 597 6.049955 TGGACTTTTTCCCTACAGACATAG 57.950 41.667 0.00 0.00 45.17 2.23
578 598 4.876679 GGACTTTTTCCCTACAGACATAGC 59.123 45.833 0.00 0.00 38.70 2.97
579 599 4.844884 ACTTTTTCCCTACAGACATAGCC 58.155 43.478 0.00 0.00 0.00 3.93
580 600 4.288626 ACTTTTTCCCTACAGACATAGCCA 59.711 41.667 0.00 0.00 0.00 4.75
581 601 5.044846 ACTTTTTCCCTACAGACATAGCCAT 60.045 40.000 0.00 0.00 0.00 4.40
582 602 4.422073 TTTCCCTACAGACATAGCCATG 57.578 45.455 0.00 0.00 38.21 3.66
584 604 3.384168 TCCCTACAGACATAGCCATGTT 58.616 45.455 0.00 0.00 45.58 2.71
585 605 4.552674 TCCCTACAGACATAGCCATGTTA 58.447 43.478 0.00 0.00 45.58 2.41
586 606 4.344102 TCCCTACAGACATAGCCATGTTAC 59.656 45.833 0.00 0.00 45.58 2.50
587 607 4.100963 CCCTACAGACATAGCCATGTTACA 59.899 45.833 0.00 0.00 45.58 2.41
588 608 5.396324 CCCTACAGACATAGCCATGTTACAA 60.396 44.000 0.00 0.00 45.58 2.41
589 609 6.291377 CCTACAGACATAGCCATGTTACAAT 58.709 40.000 0.00 0.00 45.58 2.71
590 610 6.203530 CCTACAGACATAGCCATGTTACAATG 59.796 42.308 0.00 0.00 45.58 2.82
591 611 5.500234 ACAGACATAGCCATGTTACAATGT 58.500 37.500 0.00 0.00 45.58 2.71
592 612 5.355071 ACAGACATAGCCATGTTACAATGTG 59.645 40.000 0.00 0.00 45.58 3.21
593 613 4.336433 AGACATAGCCATGTTACAATGTGC 59.664 41.667 0.00 0.00 45.58 4.57
594 614 4.272489 ACATAGCCATGTTACAATGTGCT 58.728 39.130 0.00 0.00 42.98 4.40
595 615 4.096833 ACATAGCCATGTTACAATGTGCTG 59.903 41.667 0.00 0.00 42.98 4.41
596 616 2.517959 AGCCATGTTACAATGTGCTGT 58.482 42.857 0.00 0.00 34.69 4.40
597 617 2.489329 AGCCATGTTACAATGTGCTGTC 59.511 45.455 0.00 0.00 34.69 3.51
598 618 2.415893 GCCATGTTACAATGTGCTGTCC 60.416 50.000 0.00 0.00 0.00 4.02
599 619 3.084039 CCATGTTACAATGTGCTGTCCT 58.916 45.455 0.00 0.00 0.00 3.85
600 620 3.507233 CCATGTTACAATGTGCTGTCCTT 59.493 43.478 0.00 0.00 0.00 3.36
601 621 4.379813 CCATGTTACAATGTGCTGTCCTTC 60.380 45.833 0.00 0.00 0.00 3.46
602 622 4.085357 TGTTACAATGTGCTGTCCTTCT 57.915 40.909 0.00 0.00 0.00 2.85
603 623 4.460263 TGTTACAATGTGCTGTCCTTCTT 58.540 39.130 0.00 0.00 0.00 2.52
604 624 4.887071 TGTTACAATGTGCTGTCCTTCTTT 59.113 37.500 0.00 0.00 0.00 2.52
605 625 5.008613 TGTTACAATGTGCTGTCCTTCTTTC 59.991 40.000 0.00 0.00 0.00 2.62
606 626 3.825328 ACAATGTGCTGTCCTTCTTTCT 58.175 40.909 0.00 0.00 0.00 2.52
607 627 3.567164 ACAATGTGCTGTCCTTCTTTCTG 59.433 43.478 0.00 0.00 0.00 3.02
608 628 3.498774 ATGTGCTGTCCTTCTTTCTGT 57.501 42.857 0.00 0.00 0.00 3.41
609 629 2.564771 TGTGCTGTCCTTCTTTCTGTG 58.435 47.619 0.00 0.00 0.00 3.66
610 630 1.265365 GTGCTGTCCTTCTTTCTGTGC 59.735 52.381 0.00 0.00 0.00 4.57
611 631 1.134128 TGCTGTCCTTCTTTCTGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
612 632 1.265365 GCTGTCCTTCTTTCTGTGCAC 59.735 52.381 10.75 10.75 0.00 4.57
613 633 1.528586 CTGTCCTTCTTTCTGTGCACG 59.471 52.381 13.13 7.36 0.00 5.34
614 634 1.138069 TGTCCTTCTTTCTGTGCACGA 59.862 47.619 13.13 9.76 0.00 4.35
615 635 1.527311 GTCCTTCTTTCTGTGCACGAC 59.473 52.381 13.13 6.18 0.00 4.34
616 636 0.868406 CCTTCTTTCTGTGCACGACC 59.132 55.000 13.13 0.00 0.00 4.79
617 637 1.581934 CTTCTTTCTGTGCACGACCA 58.418 50.000 13.13 0.00 0.00 4.02
618 638 1.939934 CTTCTTTCTGTGCACGACCAA 59.060 47.619 13.13 4.35 0.00 3.67
619 639 1.581934 TCTTTCTGTGCACGACCAAG 58.418 50.000 13.13 12.89 0.00 3.61
620 640 1.134521 TCTTTCTGTGCACGACCAAGT 60.135 47.619 13.13 0.00 0.00 3.16
621 641 1.670811 CTTTCTGTGCACGACCAAGTT 59.329 47.619 13.13 0.00 0.00 2.66
622 642 1.745232 TTCTGTGCACGACCAAGTTT 58.255 45.000 13.13 0.00 0.00 2.66
623 643 1.745232 TCTGTGCACGACCAAGTTTT 58.255 45.000 13.13 0.00 0.00 2.43
624 644 1.400142 TCTGTGCACGACCAAGTTTTG 59.600 47.619 13.13 0.00 0.00 2.44
625 645 0.179150 TGTGCACGACCAAGTTTTGC 60.179 50.000 13.13 0.00 0.00 3.68
626 646 0.869880 GTGCACGACCAAGTTTTGCC 60.870 55.000 0.00 0.00 31.94 4.52
627 647 1.315981 TGCACGACCAAGTTTTGCCA 61.316 50.000 0.00 0.00 31.94 4.92
628 648 0.031994 GCACGACCAAGTTTTGCCAT 59.968 50.000 0.00 0.00 0.00 4.40
629 649 1.769733 CACGACCAAGTTTTGCCATG 58.230 50.000 0.00 0.00 0.00 3.66
630 650 1.066908 CACGACCAAGTTTTGCCATGT 59.933 47.619 0.00 0.00 0.00 3.21
631 651 1.754226 ACGACCAAGTTTTGCCATGTT 59.246 42.857 0.00 0.00 0.00 2.71
632 652 2.952978 ACGACCAAGTTTTGCCATGTTA 59.047 40.909 0.00 0.00 0.00 2.41
633 653 3.243267 ACGACCAAGTTTTGCCATGTTAC 60.243 43.478 0.00 0.00 0.00 2.50
634 654 3.243234 CGACCAAGTTTTGCCATGTTACA 60.243 43.478 0.00 0.00 0.00 2.41
635 655 4.298332 GACCAAGTTTTGCCATGTTACAG 58.702 43.478 0.00 0.00 0.00 2.74
636 656 3.704061 ACCAAGTTTTGCCATGTTACAGT 59.296 39.130 0.00 0.00 0.00 3.55
670 690 3.000727 GGTCGTGAATACCACTTTCCAG 58.999 50.000 0.00 0.00 43.53 3.86
701 721 5.905331 AGAACATGACCCCTGATCAGTATTA 59.095 40.000 21.11 3.78 0.00 0.98
713 733 7.816995 CCCTGATCAGTATTATAAGCTCAACTC 59.183 40.741 21.11 0.00 0.00 3.01
724 746 8.858003 TTATAAGCTCAACTCTCAGATAAACG 57.142 34.615 0.00 0.00 0.00 3.60
787 809 3.625897 TCTCCCACCACACTGCCG 61.626 66.667 0.00 0.00 0.00 5.69
830 862 2.223782 GGCTCACACAAATCAAAGCACA 60.224 45.455 0.00 0.00 0.00 4.57
901 935 2.689034 CCCCTGTCTGTCCCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
902 936 2.452114 CCCTGTCTGTCCCTCCCT 59.548 66.667 0.00 0.00 0.00 4.20
903 937 1.687493 CCCTGTCTGTCCCTCCCTC 60.687 68.421 0.00 0.00 0.00 4.30
904 938 1.687493 CCTGTCTGTCCCTCCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
905 939 1.687493 CTGTCTGTCCCTCCCTCCC 60.687 68.421 0.00 0.00 0.00 4.30
908 942 2.041405 CTGTCCCTCCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
983 1021 1.067821 CTAGAAGCCTGGTAGAAGCGG 59.932 57.143 0.00 0.00 0.00 5.52
1695 1748 2.181021 CACGGTCCTCCTACGCAC 59.819 66.667 0.00 0.00 0.00 5.34
1701 1754 1.906333 TCCTCCTACGCACTGTGCA 60.906 57.895 29.86 12.63 45.36 4.57
1812 1871 2.359967 GGAGTCCCTGGAGAACCCG 61.360 68.421 0.00 0.00 37.93 5.28
1848 1907 5.591877 GGAATGCTTCATCTTCCTGTAACAT 59.408 40.000 0.00 0.00 36.36 2.71
1850 1909 6.690194 ATGCTTCATCTTCCTGTAACATTC 57.310 37.500 0.00 0.00 0.00 2.67
1851 1910 5.559770 TGCTTCATCTTCCTGTAACATTCA 58.440 37.500 0.00 0.00 0.00 2.57
1852 1911 6.182627 TGCTTCATCTTCCTGTAACATTCAT 58.817 36.000 0.00 0.00 0.00 2.57
1856 1915 6.586344 TCATCTTCCTGTAACATTCATCCTC 58.414 40.000 0.00 0.00 0.00 3.71
1857 1916 5.359194 TCTTCCTGTAACATTCATCCTCC 57.641 43.478 0.00 0.00 0.00 4.30
1858 1917 4.164221 TCTTCCTGTAACATTCATCCTCCC 59.836 45.833 0.00 0.00 0.00 4.30
1859 1918 2.434336 TCCTGTAACATTCATCCTCCCG 59.566 50.000 0.00 0.00 0.00 5.14
1860 1919 2.170607 CCTGTAACATTCATCCTCCCGT 59.829 50.000 0.00 0.00 0.00 5.28
1861 1920 3.198068 CTGTAACATTCATCCTCCCGTG 58.802 50.000 0.00 0.00 0.00 4.94
1864 1923 1.573108 ACATTCATCCTCCCGTGAGT 58.427 50.000 0.00 0.00 36.86 3.41
1867 1926 1.320344 TTCATCCTCCCGTGAGTCCG 61.320 60.000 0.00 0.00 36.86 4.79
1969 2039 1.301677 CTGGCAACTTCTTCTCGGGC 61.302 60.000 0.00 0.00 37.61 6.13
1994 2064 3.577805 ATTTTGTATCCCGGGGAAGAG 57.422 47.619 23.50 0.00 34.34 2.85
2021 2091 1.586541 CAGCTCTCTGGTGTACGCA 59.413 57.895 8.97 0.00 39.17 5.24
2022 2092 0.174389 CAGCTCTCTGGTGTACGCAT 59.826 55.000 8.97 0.00 39.17 4.73
2023 2093 0.457851 AGCTCTCTGGTGTACGCATC 59.542 55.000 8.97 0.00 0.00 3.91
2024 2094 0.457851 GCTCTCTGGTGTACGCATCT 59.542 55.000 8.97 0.00 0.00 2.90
2025 2095 1.800655 GCTCTCTGGTGTACGCATCTG 60.801 57.143 8.97 0.00 0.00 2.90
2026 2096 1.474478 CTCTCTGGTGTACGCATCTGT 59.526 52.381 8.97 0.00 0.00 3.41
2049 2119 3.947626 CAACTAGTTTGTTTGGTGTCCG 58.052 45.455 5.07 0.00 0.00 4.79
2050 2120 2.567985 ACTAGTTTGTTTGGTGTCCGG 58.432 47.619 0.00 0.00 0.00 5.14
2122 2205 6.017605 GGGTATCTCTGTAATGAACTGCATTG 60.018 42.308 0.00 0.00 46.38 2.82
2132 2215 5.831702 ATGAACTGCATTGATTCCTCTTC 57.168 39.130 0.00 0.00 31.73 2.87
2140 2235 4.141390 GCATTGATTCCTCTTCCCTTCCTA 60.141 45.833 0.00 0.00 0.00 2.94
2141 2236 5.372373 CATTGATTCCTCTTCCCTTCCTAC 58.628 45.833 0.00 0.00 0.00 3.18
2142 2237 4.354208 TGATTCCTCTTCCCTTCCTACT 57.646 45.455 0.00 0.00 0.00 2.57
2143 2238 4.699994 TGATTCCTCTTCCCTTCCTACTT 58.300 43.478 0.00 0.00 0.00 2.24
2144 2239 4.717280 TGATTCCTCTTCCCTTCCTACTTC 59.283 45.833 0.00 0.00 0.00 3.01
2145 2240 3.117552 TCCTCTTCCCTTCCTACTTCC 57.882 52.381 0.00 0.00 0.00 3.46
2146 2241 2.660556 TCCTCTTCCCTTCCTACTTCCT 59.339 50.000 0.00 0.00 0.00 3.36
2155 2250 7.229951 TCCCTTCCTACTTCCTAGTACATTA 57.770 40.000 0.00 0.00 35.78 1.90
2185 2280 2.589014 CGATCTTTCTTGTGCAAAGCC 58.411 47.619 0.00 0.00 31.85 4.35
2205 2300 1.468520 CGGAGTTGCCACTTATGTTGG 59.531 52.381 0.00 0.00 35.94 3.77
2206 2301 1.818674 GGAGTTGCCACTTATGTTGGG 59.181 52.381 0.00 0.00 36.34 4.12
2207 2302 1.818674 GAGTTGCCACTTATGTTGGGG 59.181 52.381 0.00 0.00 31.22 4.96
2208 2303 0.894835 GTTGCCACTTATGTTGGGGG 59.105 55.000 0.00 0.00 0.00 5.40
2230 2325 5.523438 GATCCGATCCAATCCTATCCTAC 57.477 47.826 0.00 0.00 0.00 3.18
2318 2421 2.601905 GCATTCAATGGCCCCTTATCT 58.398 47.619 0.00 0.00 0.00 1.98
2324 2427 2.701951 CAATGGCCCCTTATCTGCATTT 59.298 45.455 0.00 0.00 0.00 2.32
2426 2536 1.439353 CTGCGTATTCAATGCCCGCT 61.439 55.000 10.85 0.00 44.32 5.52
2468 2578 1.569493 CGGGCGTTATGCTATGCAC 59.431 57.895 0.00 0.00 43.04 4.57
2469 2579 1.157257 CGGGCGTTATGCTATGCACA 61.157 55.000 0.00 0.00 43.04 4.57
2470 2580 0.588252 GGGCGTTATGCTATGCACAG 59.412 55.000 0.00 0.00 43.04 3.66
2471 2581 0.588252 GGCGTTATGCTATGCACAGG 59.412 55.000 0.00 0.00 43.04 4.00
2506 2620 1.019278 AGTCGAACAAATGCGCCGAT 61.019 50.000 4.18 0.00 0.00 4.18
2534 2657 0.957395 AGAACATGTGCTTGCTCCGG 60.957 55.000 0.00 0.00 0.00 5.14
2535 2658 1.228245 AACATGTGCTTGCTCCGGT 60.228 52.632 0.00 0.00 0.00 5.28
2538 2661 1.228245 ATGTGCTTGCTCCGGTGTT 60.228 52.632 0.00 0.00 0.00 3.32
2540 2663 1.282875 GTGCTTGCTCCGGTGTTTC 59.717 57.895 0.00 0.00 0.00 2.78
2547 2670 1.071542 TGCTCCGGTGTTTCAGATTCA 59.928 47.619 0.00 0.00 0.00 2.57
2549 2672 3.055458 TGCTCCGGTGTTTCAGATTCATA 60.055 43.478 0.00 0.00 0.00 2.15
2820 2984 0.601576 TTTTAGCAGAGCACGGCGAA 60.602 50.000 16.62 0.00 41.73 4.70
2883 3047 2.098233 CCACGGTGCGATGGTGTAC 61.098 63.158 1.68 0.00 0.00 2.90
2884 3048 2.098233 CACGGTGCGATGGTGTACC 61.098 63.158 0.00 0.00 40.78 3.34
2886 3050 2.510691 GGTGCGATGGTGTACCGG 60.511 66.667 0.00 0.00 39.43 5.28
2897 3061 2.280552 TGTACCGGACTGGAGCACC 61.281 63.158 9.46 0.00 42.00 5.01
2907 3071 1.893801 ACTGGAGCACCTGTACTGTAC 59.106 52.381 10.93 10.98 44.49 2.90
2908 3072 2.171840 CTGGAGCACCTGTACTGTACT 58.828 52.381 17.98 0.00 37.04 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.612251 GGAGGTACTACGCCTGCA 58.388 61.111 0.00 0.00 41.55 4.41
63 64 1.690219 AAGGCGCCGAGATGGATCTT 61.690 55.000 23.20 2.00 42.00 2.40
178 179 2.182030 CAGCTTCCGTCGACCTCC 59.818 66.667 10.58 0.00 0.00 4.30
180 181 4.421479 CGCAGCTTCCGTCGACCT 62.421 66.667 10.58 0.00 0.00 3.85
182 185 3.173240 GTCGCAGCTTCCGTCGAC 61.173 66.667 5.18 5.18 43.23 4.20
196 199 1.859427 TTCGGGTCGTTCTCAGGTCG 61.859 60.000 0.00 0.00 0.00 4.79
315 325 2.045242 GGGGGAAGAAACGAGGGC 60.045 66.667 0.00 0.00 0.00 5.19
320 330 1.182667 GGGATTTGGGGGAAGAAACG 58.817 55.000 0.00 0.00 0.00 3.60
346 356 1.579429 GCGAGGGCGAACAACAAAT 59.421 52.632 0.00 0.00 40.82 2.32
372 382 1.676248 TGGTGGGCCAGGTTATAACT 58.324 50.000 6.40 0.00 40.46 2.24
439 459 3.701532 TCAAACCTTAGTGCCGTTTTG 57.298 42.857 0.00 0.00 0.00 2.44
468 488 8.816894 TGTTCTCACTCTAAACTAATGAATCCT 58.183 33.333 0.00 0.00 0.00 3.24
485 505 4.437682 TGAAATCCCTGTTGTTCTCACT 57.562 40.909 0.00 0.00 0.00 3.41
494 514 5.074746 ACCCTAAAGTTGAAATCCCTGTT 57.925 39.130 0.00 0.00 0.00 3.16
506 526 3.892588 TCGGCAAATCAAACCCTAAAGTT 59.107 39.130 0.00 0.00 0.00 2.66
511 531 2.554893 GTGTTCGGCAAATCAAACCCTA 59.445 45.455 0.00 0.00 0.00 3.53
540 560 8.902540 GGAAAAAGTCCATTTTAAACCTTGAT 57.097 30.769 0.00 0.00 46.97 2.57
569 589 5.731406 GCACATTGTAACATGGCTATGTCTG 60.731 44.000 16.73 11.03 46.54 3.51
570 590 4.336433 GCACATTGTAACATGGCTATGTCT 59.664 41.667 16.73 9.24 46.54 3.41
571 591 4.336433 AGCACATTGTAACATGGCTATGTC 59.664 41.667 16.73 5.57 46.54 3.06
573 593 4.096833 ACAGCACATTGTAACATGGCTATG 59.903 41.667 8.74 8.74 40.24 2.23
574 594 4.272489 ACAGCACATTGTAACATGGCTAT 58.728 39.130 0.00 0.00 0.00 2.97
575 595 3.684908 ACAGCACATTGTAACATGGCTA 58.315 40.909 0.00 0.00 0.00 3.93
576 596 2.489329 GACAGCACATTGTAACATGGCT 59.511 45.455 0.00 0.00 0.00 4.75
577 597 2.415893 GGACAGCACATTGTAACATGGC 60.416 50.000 0.00 0.00 0.00 4.40
578 598 3.084039 AGGACAGCACATTGTAACATGG 58.916 45.455 0.00 0.00 0.00 3.66
579 599 4.456911 AGAAGGACAGCACATTGTAACATG 59.543 41.667 0.00 0.00 0.00 3.21
580 600 4.655963 AGAAGGACAGCACATTGTAACAT 58.344 39.130 0.00 0.00 0.00 2.71
581 601 4.085357 AGAAGGACAGCACATTGTAACA 57.915 40.909 0.00 0.00 0.00 2.41
582 602 5.239525 AGAAAGAAGGACAGCACATTGTAAC 59.760 40.000 0.00 0.00 0.00 2.50
583 603 5.239306 CAGAAAGAAGGACAGCACATTGTAA 59.761 40.000 0.00 0.00 0.00 2.41
584 604 4.756642 CAGAAAGAAGGACAGCACATTGTA 59.243 41.667 0.00 0.00 0.00 2.41
585 605 3.567164 CAGAAAGAAGGACAGCACATTGT 59.433 43.478 0.00 0.00 0.00 2.71
586 606 3.567164 ACAGAAAGAAGGACAGCACATTG 59.433 43.478 0.00 0.00 0.00 2.82
587 607 3.567164 CACAGAAAGAAGGACAGCACATT 59.433 43.478 0.00 0.00 0.00 2.71
588 608 3.144506 CACAGAAAGAAGGACAGCACAT 58.855 45.455 0.00 0.00 0.00 3.21
589 609 2.564771 CACAGAAAGAAGGACAGCACA 58.435 47.619 0.00 0.00 0.00 4.57
590 610 1.265365 GCACAGAAAGAAGGACAGCAC 59.735 52.381 0.00 0.00 0.00 4.40
591 611 1.134128 TGCACAGAAAGAAGGACAGCA 60.134 47.619 0.00 0.00 0.00 4.41
592 612 1.265365 GTGCACAGAAAGAAGGACAGC 59.735 52.381 13.17 0.00 0.00 4.40
593 613 1.528586 CGTGCACAGAAAGAAGGACAG 59.471 52.381 18.64 0.00 0.00 3.51
594 614 1.138069 TCGTGCACAGAAAGAAGGACA 59.862 47.619 18.64 0.00 0.00 4.02
595 615 1.527311 GTCGTGCACAGAAAGAAGGAC 59.473 52.381 18.64 8.71 0.00 3.85
596 616 1.540363 GGTCGTGCACAGAAAGAAGGA 60.540 52.381 18.64 0.00 0.00 3.36
597 617 0.868406 GGTCGTGCACAGAAAGAAGG 59.132 55.000 18.64 0.00 0.00 3.46
598 618 1.581934 TGGTCGTGCACAGAAAGAAG 58.418 50.000 18.64 0.00 0.00 2.85
599 619 1.939934 CTTGGTCGTGCACAGAAAGAA 59.060 47.619 18.64 7.60 0.00 2.52
600 620 1.134521 ACTTGGTCGTGCACAGAAAGA 60.135 47.619 18.64 2.07 0.00 2.52
601 621 1.299541 ACTTGGTCGTGCACAGAAAG 58.700 50.000 18.64 15.71 0.00 2.62
602 622 1.745232 AACTTGGTCGTGCACAGAAA 58.255 45.000 18.64 4.45 0.00 2.52
603 623 1.745232 AAACTTGGTCGTGCACAGAA 58.255 45.000 18.64 2.27 0.00 3.02
604 624 1.400142 CAAAACTTGGTCGTGCACAGA 59.600 47.619 18.64 12.26 0.00 3.41
605 625 1.826327 CAAAACTTGGTCGTGCACAG 58.174 50.000 18.64 8.66 0.00 3.66
606 626 0.179150 GCAAAACTTGGTCGTGCACA 60.179 50.000 18.64 0.81 35.28 4.57
607 627 0.869880 GGCAAAACTTGGTCGTGCAC 60.870 55.000 6.82 6.82 36.93 4.57
608 628 1.315981 TGGCAAAACTTGGTCGTGCA 61.316 50.000 0.00 0.00 36.93 4.57
609 629 0.031994 ATGGCAAAACTTGGTCGTGC 59.968 50.000 0.00 0.00 34.42 5.34
610 630 1.066908 ACATGGCAAAACTTGGTCGTG 59.933 47.619 0.00 0.00 0.00 4.35
611 631 1.398692 ACATGGCAAAACTTGGTCGT 58.601 45.000 0.00 0.00 0.00 4.34
612 632 2.507339 AACATGGCAAAACTTGGTCG 57.493 45.000 0.00 0.00 0.00 4.79
613 633 4.202111 ACTGTAACATGGCAAAACTTGGTC 60.202 41.667 0.00 0.00 0.00 4.02
614 634 3.704061 ACTGTAACATGGCAAAACTTGGT 59.296 39.130 0.00 0.00 0.00 3.67
615 635 4.050553 CACTGTAACATGGCAAAACTTGG 58.949 43.478 0.00 0.00 0.00 3.61
616 636 4.930963 TCACTGTAACATGGCAAAACTTG 58.069 39.130 0.00 0.00 0.00 3.16
617 637 5.590530 TTCACTGTAACATGGCAAAACTT 57.409 34.783 0.00 0.00 0.00 2.66
618 638 5.590530 TTTCACTGTAACATGGCAAAACT 57.409 34.783 0.00 0.00 0.00 2.66
619 639 6.654793 TTTTTCACTGTAACATGGCAAAAC 57.345 33.333 0.00 0.00 0.00 2.43
658 678 2.703536 TCTTGCTCACTGGAAAGTGGTA 59.296 45.455 6.06 0.00 40.03 3.25
670 690 1.168714 GGGGTCATGTTCTTGCTCAC 58.831 55.000 0.00 0.00 0.00 3.51
701 721 5.751028 GCGTTTATCTGAGAGTTGAGCTTAT 59.249 40.000 0.00 0.00 0.00 1.73
713 733 7.568497 GCTCTAATTAAGCTGCGTTTATCTGAG 60.568 40.741 10.54 0.00 36.80 3.35
743 765 2.027653 AGTCAAAAGGGCTCAGCTACTC 60.028 50.000 0.00 0.00 0.00 2.59
814 846 2.425312 TCCGTTGTGCTTTGATTTGTGT 59.575 40.909 0.00 0.00 0.00 3.72
830 862 0.826256 GCTTTGGGTTTCCCTCCGTT 60.826 55.000 6.38 0.00 45.70 4.44
901 935 2.664081 GGTGGTGAGCAGGAGGGAG 61.664 68.421 0.00 0.00 0.00 4.30
902 936 2.607750 GGTGGTGAGCAGGAGGGA 60.608 66.667 0.00 0.00 0.00 4.20
903 937 2.262774 GATGGTGGTGAGCAGGAGGG 62.263 65.000 0.00 0.00 31.77 4.30
904 938 1.222936 GATGGTGGTGAGCAGGAGG 59.777 63.158 0.00 0.00 31.77 4.30
905 939 0.107800 CTGATGGTGGTGAGCAGGAG 60.108 60.000 0.00 0.00 31.77 3.69
908 942 0.392193 GGTCTGATGGTGGTGAGCAG 60.392 60.000 0.00 0.00 31.77 4.24
972 1006 1.601419 CGTCCTTCCCGCTTCTACCA 61.601 60.000 0.00 0.00 0.00 3.25
1626 1667 4.065281 GGCGCCTCCTGTGTACGT 62.065 66.667 22.15 0.00 0.00 3.57
1779 1838 1.990060 CTCCTTCCCCTCGCCTTCA 60.990 63.158 0.00 0.00 0.00 3.02
1782 1841 2.364448 GACTCCTTCCCCTCGCCT 60.364 66.667 0.00 0.00 0.00 5.52
1812 1871 0.682209 AGCATTCCATGGACACCAGC 60.682 55.000 15.91 13.80 36.75 4.85
1848 1907 1.320344 CGGACTCACGGGAGGATGAA 61.320 60.000 20.91 0.00 45.81 2.57
1850 1909 2.005960 GACGGACTCACGGGAGGATG 62.006 65.000 20.91 10.15 45.81 3.51
1851 1910 1.753463 GACGGACTCACGGGAGGAT 60.753 63.158 20.91 0.00 45.81 3.24
1852 1911 2.360852 GACGGACTCACGGGAGGA 60.361 66.667 20.91 0.00 45.81 3.71
1856 1915 0.170561 CTTACTGACGGACTCACGGG 59.829 60.000 0.00 0.00 38.39 5.28
1857 1916 0.879765 ACTTACTGACGGACTCACGG 59.120 55.000 0.00 0.00 38.39 4.94
1858 1917 3.818961 TTACTTACTGACGGACTCACG 57.181 47.619 0.00 0.00 40.31 4.35
1859 1918 5.106237 ACTGATTACTTACTGACGGACTCAC 60.106 44.000 0.00 0.00 0.00 3.51
1860 1919 5.008331 ACTGATTACTTACTGACGGACTCA 58.992 41.667 0.00 0.00 0.00 3.41
1861 1920 5.333513 CACTGATTACTTACTGACGGACTC 58.666 45.833 0.00 0.00 0.00 3.36
1864 1923 3.762288 AGCACTGATTACTTACTGACGGA 59.238 43.478 0.00 0.00 0.00 4.69
1867 1926 5.073311 TGGAGCACTGATTACTTACTGAC 57.927 43.478 0.00 0.00 0.00 3.51
1969 2039 2.092103 TCCCCGGGATACAAAATTCCAG 60.092 50.000 26.32 0.00 39.74 3.86
2010 2080 2.647529 TGTACAGATGCGTACACCAG 57.352 50.000 0.00 0.00 45.18 4.00
2029 2099 2.946990 CCGGACACCAAACAAACTAGTT 59.053 45.455 1.12 1.12 0.00 2.24
2034 2104 0.812549 ACACCGGACACCAAACAAAC 59.187 50.000 9.46 0.00 0.00 2.93
2049 2119 4.463186 ACAGTCTACAGGACAGATTACACC 59.537 45.833 0.00 0.00 46.72 4.16
2050 2120 5.646577 ACAGTCTACAGGACAGATTACAC 57.353 43.478 0.00 0.00 46.72 2.90
2122 2205 4.101898 GGAAGTAGGAAGGGAAGAGGAATC 59.898 50.000 0.00 0.00 0.00 2.52
2132 2215 7.564292 AGTTAATGTACTAGGAAGTAGGAAGGG 59.436 40.741 0.00 0.00 38.89 3.95
2140 2235 4.159879 AGCGCAGTTAATGTACTAGGAAGT 59.840 41.667 11.47 0.00 39.91 3.01
2141 2236 4.683832 AGCGCAGTTAATGTACTAGGAAG 58.316 43.478 11.47 0.00 0.00 3.46
2142 2237 4.441079 GGAGCGCAGTTAATGTACTAGGAA 60.441 45.833 11.47 0.00 0.00 3.36
2143 2238 3.067742 GGAGCGCAGTTAATGTACTAGGA 59.932 47.826 11.47 0.00 0.00 2.94
2144 2239 3.381949 GGAGCGCAGTTAATGTACTAGG 58.618 50.000 11.47 0.00 0.00 3.02
2145 2240 3.043586 CGGAGCGCAGTTAATGTACTAG 58.956 50.000 11.47 0.00 0.00 2.57
2146 2241 2.684374 TCGGAGCGCAGTTAATGTACTA 59.316 45.455 11.47 0.00 0.00 1.82
2155 2250 0.247736 AGAAAGATCGGAGCGCAGTT 59.752 50.000 11.47 0.00 0.00 3.16
2185 2280 1.468520 CCAACATAAGTGGCAACTCCG 59.531 52.381 0.00 0.00 34.77 4.63
2208 2303 4.342665 GGTAGGATAGGATTGGATCGGATC 59.657 50.000 9.54 9.54 0.00 3.36
2218 2313 4.114597 CCATCCATGGGTAGGATAGGATT 58.885 47.826 13.02 0.00 43.90 3.01
2310 2413 1.684983 CTGGGCAAATGCAGATAAGGG 59.315 52.381 7.80 0.00 44.36 3.95
2314 2417 3.084536 TGAACTGGGCAAATGCAGATA 57.915 42.857 7.80 0.00 44.36 1.98
2318 2421 3.577848 AGTTATTGAACTGGGCAAATGCA 59.422 39.130 7.80 0.00 44.50 3.96
2382 2485 0.179094 GATCGGCCCGTTGACATACA 60.179 55.000 1.63 0.00 0.00 2.29
2386 2489 4.444838 CGGATCGGCCCGTTGACA 62.445 66.667 1.63 0.00 44.23 3.58
2447 2557 1.566018 GCATAGCATAACGCCCGGTC 61.566 60.000 0.00 0.00 44.04 4.79
2453 2563 1.261619 GTCCTGTGCATAGCATAACGC 59.738 52.381 4.68 0.00 41.91 4.84
2454 2564 2.285220 GTGTCCTGTGCATAGCATAACG 59.715 50.000 4.68 0.00 41.91 3.18
2456 2566 2.167487 TCGTGTCCTGTGCATAGCATAA 59.833 45.455 4.68 0.00 41.91 1.90
2488 2602 0.586502 GATCGGCGCATTTGTTCGAC 60.587 55.000 10.83 0.00 32.60 4.20
2517 2631 1.228245 ACCGGAGCAAGCACATGTT 60.228 52.632 9.46 0.00 0.00 2.71
2518 2632 1.968017 CACCGGAGCAAGCACATGT 60.968 57.895 9.46 0.00 0.00 3.21
2519 2633 1.518056 AACACCGGAGCAAGCACATG 61.518 55.000 9.46 0.00 0.00 3.21
2520 2634 0.823356 AAACACCGGAGCAAGCACAT 60.823 50.000 9.46 0.00 0.00 3.21
2521 2635 1.444119 GAAACACCGGAGCAAGCACA 61.444 55.000 9.46 0.00 0.00 4.57
2522 2636 1.282875 GAAACACCGGAGCAAGCAC 59.717 57.895 9.46 0.00 0.00 4.40
2534 2657 5.119694 GTCCCTCCTATGAATCTGAAACAC 58.880 45.833 0.00 0.00 0.00 3.32
2535 2658 4.782691 TGTCCCTCCTATGAATCTGAAACA 59.217 41.667 0.00 0.00 0.00 2.83
2538 2661 3.389329 GCTGTCCCTCCTATGAATCTGAA 59.611 47.826 0.00 0.00 0.00 3.02
2540 2663 2.288702 CGCTGTCCCTCCTATGAATCTG 60.289 54.545 0.00 0.00 0.00 2.90
2547 2670 3.227276 CGCCGCTGTCCCTCCTAT 61.227 66.667 0.00 0.00 0.00 2.57
2883 3047 1.982395 TACAGGTGCTCCAGTCCGG 60.982 63.158 6.09 0.00 35.16 5.14
2884 3048 1.215647 GTACAGGTGCTCCAGTCCG 59.784 63.158 6.09 0.00 35.16 4.79
2885 3049 0.247736 CAGTACAGGTGCTCCAGTCC 59.752 60.000 6.09 0.00 35.16 3.85
2886 3050 0.969894 ACAGTACAGGTGCTCCAGTC 59.030 55.000 6.09 0.00 35.16 3.51
2907 3071 8.102047 AGGCAGTACAGTAGTATACCAGTATAG 58.898 40.741 0.00 0.00 44.47 1.31
2908 3072 7.881751 CAGGCAGTACAGTAGTATACCAGTATA 59.118 40.741 0.00 0.00 44.47 1.47



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

AutoCloner maintained by Alex Coulton.