Multiple sequence alignment - TraesCS1A01G123300

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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 TraesCS1A01G123300 chr1A 100.000 4639 0 0 1 4639 143279888 143275250 0.000000e+00 8567
1 TraesCS1A01G123300 chr1A 96.281 1210 41 1 749 1954 444138240 444139449 0.000000e+00 1982
2 TraesCS1A01G123300 chr7D 99.284 2654 17 2 1987 4639 394381588 394378936 0.000000e+00 4795
3 TraesCS1A01G123300 chr7D 91.026 1248 76 14 749 1981 204099918 204101144 0.000000e+00 1652
4 TraesCS1A01G123300 chr7D 99.497 596 2 1 1 595 394382168 394381573 0.000000e+00 1083
5 TraesCS1A01G123300 chr7D 95.758 165 5 2 585 748 591810729 591810566 9.900000e-67 265
6 TraesCS1A01G123300 chr7A 95.510 1225 51 4 749 1972 664891965 664890744 0.000000e+00 1954
7 TraesCS1A01G123300 chr6A 95.366 1230 53 4 749 1976 505242795 505241568 0.000000e+00 1953
8 TraesCS1A01G123300 chr3D 90.924 1245 77 13 746 1974 20700484 20701708 0.000000e+00 1640
9 TraesCS1A01G123300 chr3D 98.675 151 2 0 598 748 511662623 511662473 7.650000e-68 268
10 TraesCS1A01G123300 chr2D 90.916 1244 71 15 749 1977 41999029 41997813 0.000000e+00 1633
11 TraesCS1A01G123300 chr2D 98.693 153 1 1 594 746 16055062 16055213 2.130000e-68 270
12 TraesCS1A01G123300 chr6D 90.756 1244 75 14 749 1977 423443635 423442417 0.000000e+00 1624
13 TraesCS1A01G123300 chr6D 98.684 152 2 0 595 746 181694824 181694975 2.130000e-68 270
14 TraesCS1A01G123300 chr1D 90.434 1244 79 14 749 1977 279083927 279085145 0.000000e+00 1602
15 TraesCS1A01G123300 chr1D 98.065 155 3 0 594 748 11499618 11499772 2.130000e-68 270
16 TraesCS1A01G123300 chr6B 90.304 1248 81 14 749 1977 703324292 703323066 0.000000e+00 1598
17 TraesCS1A01G123300 chr4B 89.119 386 31 4 749 1125 629701735 629701352 1.950000e-128 470
18 TraesCS1A01G123300 chr1B 93.953 215 9 1 749 959 669037392 669037606 5.790000e-84 322
19 TraesCS1A01G123300 chr2A 98.718 156 2 0 593 748 689756893 689756738 1.270000e-70 278
20 TraesCS1A01G123300 chr7B 100.000 149 0 0 598 746 600513124 600512976 4.570000e-70 276
21 TraesCS1A01G123300 chr5A 91.457 199 15 1 747 945 2917962 2917766 5.910000e-69 272
22 TraesCS1A01G123300 chr5A 91.457 199 15 1 747 945 2922604 2922408 5.910000e-69 272
23 TraesCS1A01G123300 chr5A 91.457 199 15 1 747 945 2986531 2986335 5.910000e-69 272
24 TraesCS1A01G123300 chr5A 98.561 139 2 0 749 887 316557065 316556927 3.580000e-61 246
25 TraesCS1A01G123300 chr5D 98.684 152 2 0 595 746 88169263 88169414 2.130000e-68 270
26 TraesCS1A01G123300 chr4D 98.065 155 2 1 594 748 82737943 82737790 7.650000e-68 268


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 TraesCS1A01G123300 chr1A 143275250 143279888 4638 True 8567 8567 100.0000 1 4639 1 chr1A.!!$R1 4638
1 TraesCS1A01G123300 chr1A 444138240 444139449 1209 False 1982 1982 96.2810 749 1954 1 chr1A.!!$F1 1205
2 TraesCS1A01G123300 chr7D 394378936 394382168 3232 True 2939 4795 99.3905 1 4639 2 chr7D.!!$R2 4638
3 TraesCS1A01G123300 chr7D 204099918 204101144 1226 False 1652 1652 91.0260 749 1981 1 chr7D.!!$F1 1232
4 TraesCS1A01G123300 chr7A 664890744 664891965 1221 True 1954 1954 95.5100 749 1972 1 chr7A.!!$R1 1223
5 TraesCS1A01G123300 chr6A 505241568 505242795 1227 True 1953 1953 95.3660 749 1976 1 chr6A.!!$R1 1227
6 TraesCS1A01G123300 chr3D 20700484 20701708 1224 False 1640 1640 90.9240 746 1974 1 chr3D.!!$F1 1228
7 TraesCS1A01G123300 chr2D 41997813 41999029 1216 True 1633 1633 90.9160 749 1977 1 chr2D.!!$R1 1228
8 TraesCS1A01G123300 chr6D 423442417 423443635 1218 True 1624 1624 90.7560 749 1977 1 chr6D.!!$R1 1228
9 TraesCS1A01G123300 chr1D 279083927 279085145 1218 False 1602 1602 90.4340 749 1977 1 chr1D.!!$F2 1228
10 TraesCS1A01G123300 chr6B 703323066 703324292 1226 True 1598 1598 90.3040 749 1977 1 chr6B.!!$R1 1228

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
623 625 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.0 0.0 0.0 36.73 5.73 F
1994 2022 0.038159 CGAGTCACCAGACCCAAGAC 60.038 60.0 0.0 0.0 46.15 3.01 F
1997 2025 0.759346 GTCACCAGACCCAAGACTGT 59.241 55.0 0.0 0.0 38.89 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2120 0.107945 GAGCCCTCTAACACCTGCAG 60.108 60.0 6.78 6.78 0.00 4.41 R
3440 3469 0.309922 CAGTTGACTTGCTGCAGGTG 59.690 55.0 22.59 9.71 0.00 4.00 R
3692 3721 2.416680 AATCTTGAGCAGGCTCTTCC 57.583 50.0 20.79 0.00 43.12 3.46 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
166 167 2.184322 CCAGTGCGACGCCTACAT 59.816 61.111 18.69 0.00 0.00 2.29
592 594 3.072622 AGGAACCTTACCCAAGACTGTTC 59.927 47.826 0.00 0.00 33.33 3.18
593 595 3.181448 GGAACCTTACCCAAGACTGTTCA 60.181 47.826 0.00 0.00 34.62 3.18
594 596 4.506802 GGAACCTTACCCAAGACTGTTCAT 60.507 45.833 0.00 0.00 34.62 2.57
595 597 4.724279 ACCTTACCCAAGACTGTTCATT 57.276 40.909 0.00 0.00 33.20 2.57
596 598 4.652822 ACCTTACCCAAGACTGTTCATTC 58.347 43.478 0.00 0.00 33.20 2.67
597 599 4.351111 ACCTTACCCAAGACTGTTCATTCT 59.649 41.667 0.00 0.00 33.20 2.40
598 600 5.163088 ACCTTACCCAAGACTGTTCATTCTT 60.163 40.000 0.64 0.64 33.20 2.52
599 601 5.770162 CCTTACCCAAGACTGTTCATTCTTT 59.230 40.000 3.29 0.00 33.20 2.52
600 602 6.265422 CCTTACCCAAGACTGTTCATTCTTTT 59.735 38.462 3.29 0.00 33.20 2.27
601 603 7.201911 CCTTACCCAAGACTGTTCATTCTTTTT 60.202 37.037 3.29 0.00 33.20 1.94
621 623 4.586306 TTTAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
622 624 1.299939 AGAAAAGGAGGATGACCCCC 58.700 55.000 0.00 0.00 36.73 5.40
623 625 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
624 626 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
630 632 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
636 638 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
637 639 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
638 640 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
639 641 3.473647 CGGCCTCTGCATCTGGGA 61.474 66.667 0.00 0.00 40.13 4.37
640 642 2.509916 GGCCTCTGCATCTGGGAG 59.490 66.667 0.00 0.00 40.13 4.30
641 643 2.068821 GGCCTCTGCATCTGGGAGA 61.069 63.158 0.00 0.00 42.24 3.71
642 644 1.417288 GGCCTCTGCATCTGGGAGAT 61.417 60.000 0.00 0.00 43.58 2.75
650 652 2.090400 CATCTGGGAGATGCATACGG 57.910 55.000 0.00 0.00 44.69 4.02
651 653 0.322975 ATCTGGGAGATGCATACGGC 59.677 55.000 0.00 0.00 45.13 5.68
652 654 1.302033 CTGGGAGATGCATACGGCC 60.302 63.158 0.00 0.00 43.89 6.13
653 655 2.043604 CTGGGAGATGCATACGGCCA 62.044 60.000 2.24 0.61 43.89 5.36
654 656 1.598130 GGGAGATGCATACGGCCAC 60.598 63.158 2.24 0.00 43.89 5.01
655 657 1.447643 GGAGATGCATACGGCCACT 59.552 57.895 2.24 0.00 43.89 4.00
656 658 0.179045 GGAGATGCATACGGCCACTT 60.179 55.000 2.24 0.00 43.89 3.16
657 659 1.668419 GAGATGCATACGGCCACTTT 58.332 50.000 2.24 0.00 43.89 2.66
658 660 2.484770 GGAGATGCATACGGCCACTTTA 60.485 50.000 2.24 0.00 43.89 1.85
659 661 3.403038 GAGATGCATACGGCCACTTTAT 58.597 45.455 2.24 0.00 43.89 1.40
660 662 3.815401 GAGATGCATACGGCCACTTTATT 59.185 43.478 2.24 0.00 43.89 1.40
661 663 3.565482 AGATGCATACGGCCACTTTATTG 59.435 43.478 2.24 0.00 43.89 1.90
662 664 2.992593 TGCATACGGCCACTTTATTGA 58.007 42.857 2.24 0.00 43.89 2.57
663 665 3.550820 TGCATACGGCCACTTTATTGAT 58.449 40.909 2.24 0.00 43.89 2.57
664 666 3.951037 TGCATACGGCCACTTTATTGATT 59.049 39.130 2.24 0.00 43.89 2.57
665 667 5.126779 TGCATACGGCCACTTTATTGATTA 58.873 37.500 2.24 0.00 43.89 1.75
666 668 5.767665 TGCATACGGCCACTTTATTGATTAT 59.232 36.000 2.24 0.00 43.89 1.28
667 669 6.264292 TGCATACGGCCACTTTATTGATTATT 59.736 34.615 2.24 0.00 43.89 1.40
668 670 6.801862 GCATACGGCCACTTTATTGATTATTC 59.198 38.462 2.24 0.00 36.11 1.75
669 671 7.308589 GCATACGGCCACTTTATTGATTATTCT 60.309 37.037 2.24 0.00 36.11 2.40
670 672 6.619801 ACGGCCACTTTATTGATTATTCTC 57.380 37.500 2.24 0.00 0.00 2.87
671 673 5.236478 ACGGCCACTTTATTGATTATTCTCG 59.764 40.000 2.24 0.00 0.00 4.04
672 674 5.465390 CGGCCACTTTATTGATTATTCTCGA 59.535 40.000 2.24 0.00 0.00 4.04
673 675 6.346919 CGGCCACTTTATTGATTATTCTCGAG 60.347 42.308 5.93 5.93 0.00 4.04
674 676 6.073003 GGCCACTTTATTGATTATTCTCGAGG 60.073 42.308 13.56 0.00 0.00 4.63
675 677 6.706270 GCCACTTTATTGATTATTCTCGAGGA 59.294 38.462 13.56 3.44 0.00 3.71
676 678 7.307455 GCCACTTTATTGATTATTCTCGAGGAC 60.307 40.741 13.56 0.00 0.00 3.85
677 679 7.171678 CCACTTTATTGATTATTCTCGAGGACC 59.828 40.741 13.56 0.00 0.00 4.46
678 680 7.928706 CACTTTATTGATTATTCTCGAGGACCT 59.071 37.037 13.56 0.00 0.00 3.85
679 681 8.487028 ACTTTATTGATTATTCTCGAGGACCTT 58.513 33.333 13.56 0.00 0.00 3.50
680 682 9.982651 CTTTATTGATTATTCTCGAGGACCTTA 57.017 33.333 13.56 0.00 0.00 2.69
681 683 9.760077 TTTATTGATTATTCTCGAGGACCTTAC 57.240 33.333 13.56 0.40 0.00 2.34
682 684 6.785337 TTGATTATTCTCGAGGACCTTACA 57.215 37.500 13.56 3.04 0.00 2.41
683 685 6.785337 TGATTATTCTCGAGGACCTTACAA 57.215 37.500 13.56 0.00 0.00 2.41
684 686 7.177832 TGATTATTCTCGAGGACCTTACAAA 57.822 36.000 13.56 0.00 0.00 2.83
685 687 7.265673 TGATTATTCTCGAGGACCTTACAAAG 58.734 38.462 13.56 0.00 0.00 2.77
686 688 6.600882 TTATTCTCGAGGACCTTACAAAGT 57.399 37.500 13.56 0.00 0.00 2.66
687 689 7.707624 TTATTCTCGAGGACCTTACAAAGTA 57.292 36.000 13.56 0.00 0.00 2.24
688 690 6.793505 ATTCTCGAGGACCTTACAAAGTAT 57.206 37.500 13.56 0.00 0.00 2.12
689 691 6.600882 TTCTCGAGGACCTTACAAAGTATT 57.399 37.500 13.56 0.00 0.00 1.89
690 692 7.707624 TTCTCGAGGACCTTACAAAGTATTA 57.292 36.000 13.56 0.00 0.00 0.98
691 693 7.093322 TCTCGAGGACCTTACAAAGTATTAC 57.907 40.000 13.56 0.00 0.00 1.89
692 694 6.660521 TCTCGAGGACCTTACAAAGTATTACA 59.339 38.462 13.56 0.00 0.00 2.41
693 695 7.177216 TCTCGAGGACCTTACAAAGTATTACAA 59.823 37.037 13.56 0.00 0.00 2.41
694 696 7.092716 TCGAGGACCTTACAAAGTATTACAAC 58.907 38.462 0.00 0.00 0.00 3.32
695 697 6.869913 CGAGGACCTTACAAAGTATTACAACA 59.130 38.462 0.00 0.00 0.00 3.33
696 698 7.385752 CGAGGACCTTACAAAGTATTACAACAA 59.614 37.037 0.00 0.00 0.00 2.83
697 699 9.227777 GAGGACCTTACAAAGTATTACAACAAT 57.772 33.333 0.00 0.00 0.00 2.71
698 700 9.010029 AGGACCTTACAAAGTATTACAACAATG 57.990 33.333 0.00 0.00 0.00 2.82
699 701 8.789762 GGACCTTACAAAGTATTACAACAATGT 58.210 33.333 0.00 0.00 43.74 2.71
700 702 9.607285 GACCTTACAAAGTATTACAACAATGTG 57.393 33.333 0.00 0.00 40.84 3.21
701 703 8.079809 ACCTTACAAAGTATTACAACAATGTGC 58.920 33.333 0.00 0.00 40.84 4.57
702 704 7.540745 CCTTACAAAGTATTACAACAATGTGCC 59.459 37.037 0.00 0.00 40.84 5.01
703 705 6.648879 ACAAAGTATTACAACAATGTGCCT 57.351 33.333 0.00 0.00 40.84 4.75
704 706 6.446318 ACAAAGTATTACAACAATGTGCCTG 58.554 36.000 0.00 0.00 40.84 4.85
705 707 6.264292 ACAAAGTATTACAACAATGTGCCTGA 59.736 34.615 0.00 0.00 40.84 3.86
706 708 6.892658 AAGTATTACAACAATGTGCCTGAA 57.107 33.333 0.00 0.00 40.84 3.02
707 709 7.466746 AAGTATTACAACAATGTGCCTGAAT 57.533 32.000 0.00 0.00 40.84 2.57
708 710 7.088589 AGTATTACAACAATGTGCCTGAATC 57.911 36.000 0.00 0.00 40.84 2.52
709 711 4.782019 TTACAACAATGTGCCTGAATCC 57.218 40.909 0.00 0.00 40.84 3.01
710 712 2.596346 ACAACAATGTGCCTGAATCCA 58.404 42.857 0.00 0.00 38.69 3.41
711 713 2.297033 ACAACAATGTGCCTGAATCCAC 59.703 45.455 0.00 0.00 38.69 4.02
712 714 1.549203 ACAATGTGCCTGAATCCACC 58.451 50.000 0.00 0.00 0.00 4.61
713 715 1.203038 ACAATGTGCCTGAATCCACCA 60.203 47.619 0.00 0.00 0.00 4.17
714 716 2.104967 CAATGTGCCTGAATCCACCAT 58.895 47.619 0.00 0.00 0.00 3.55
715 717 2.062971 ATGTGCCTGAATCCACCATC 57.937 50.000 0.00 0.00 0.00 3.51
716 718 0.994247 TGTGCCTGAATCCACCATCT 59.006 50.000 0.00 0.00 0.00 2.90
717 719 1.355381 TGTGCCTGAATCCACCATCTT 59.645 47.619 0.00 0.00 0.00 2.40
718 720 1.747355 GTGCCTGAATCCACCATCTTG 59.253 52.381 0.00 0.00 0.00 3.02
719 721 1.341285 TGCCTGAATCCACCATCTTGG 60.341 52.381 0.00 0.00 45.02 3.61
720 722 1.396653 CCTGAATCCACCATCTTGGC 58.603 55.000 0.00 0.00 42.67 4.52
721 723 1.341285 CCTGAATCCACCATCTTGGCA 60.341 52.381 0.00 0.00 42.67 4.92
722 724 2.449464 CTGAATCCACCATCTTGGCAA 58.551 47.619 0.00 0.00 42.67 4.52
723 725 2.165030 CTGAATCCACCATCTTGGCAAC 59.835 50.000 0.00 0.00 42.67 4.17
736 738 2.979814 TGGCAACATATGTCGCTACT 57.020 45.000 17.86 0.00 46.17 2.57
737 739 2.821546 TGGCAACATATGTCGCTACTC 58.178 47.619 17.86 2.56 46.17 2.59
738 740 2.135933 GGCAACATATGTCGCTACTCC 58.864 52.381 17.86 0.00 0.00 3.85
739 741 2.224066 GGCAACATATGTCGCTACTCCT 60.224 50.000 17.86 0.00 0.00 3.69
740 742 3.005472 GGCAACATATGTCGCTACTCCTA 59.995 47.826 17.86 0.00 0.00 2.94
741 743 4.322049 GGCAACATATGTCGCTACTCCTAT 60.322 45.833 17.86 0.00 0.00 2.57
742 744 4.859798 GCAACATATGTCGCTACTCCTATC 59.140 45.833 11.60 0.00 0.00 2.08
743 745 5.403246 CAACATATGTCGCTACTCCTATCC 58.597 45.833 9.23 0.00 0.00 2.59
744 746 4.663334 ACATATGTCGCTACTCCTATCCA 58.337 43.478 1.41 0.00 0.00 3.41
747 749 6.890268 ACATATGTCGCTACTCCTATCCAATA 59.110 38.462 1.41 0.00 0.00 1.90
1004 1015 0.530650 GCCATCGACGTCACCATGAT 60.531 55.000 17.16 6.72 0.00 2.45
1221 1236 1.067060 CACCGCCGTCATCTGATCTAA 59.933 52.381 0.00 0.00 0.00 2.10
1825 1846 1.293179 CTGACCTCCATGCGTGACA 59.707 57.895 7.72 0.00 0.00 3.58
1989 2017 2.048127 GTGCGAGTCACCAGACCC 60.048 66.667 0.00 0.00 46.15 4.46
1990 2018 2.523168 TGCGAGTCACCAGACCCA 60.523 61.111 0.00 0.00 46.15 4.51
1991 2019 2.137528 TGCGAGTCACCAGACCCAA 61.138 57.895 0.00 0.00 46.15 4.12
1992 2020 1.374758 GCGAGTCACCAGACCCAAG 60.375 63.158 0.00 0.00 46.15 3.61
1993 2021 1.816863 GCGAGTCACCAGACCCAAGA 61.817 60.000 0.00 0.00 46.15 3.02
1994 2022 0.038159 CGAGTCACCAGACCCAAGAC 60.038 60.000 0.00 0.00 46.15 3.01
1995 2023 1.343069 GAGTCACCAGACCCAAGACT 58.657 55.000 0.00 0.00 46.15 3.24
1996 2024 1.001406 GAGTCACCAGACCCAAGACTG 59.999 57.143 0.00 0.00 46.15 3.51
1997 2025 0.759346 GTCACCAGACCCAAGACTGT 59.241 55.000 0.00 0.00 38.89 3.55
1998 2026 1.141053 GTCACCAGACCCAAGACTGTT 59.859 52.381 0.00 0.00 38.89 3.16
2007 2035 4.104102 AGACCCAAGACTGTTCATGGTAAA 59.896 41.667 0.00 0.00 38.72 2.01
2092 2120 2.609350 TGATACGCCGTCTTGGTTTAC 58.391 47.619 0.00 0.00 41.21 2.01
2100 2128 1.531149 CGTCTTGGTTTACTGCAGGTG 59.469 52.381 19.93 0.00 0.00 4.00
2140 2169 0.973632 TCCGCTTGCCGATGGTATAT 59.026 50.000 0.00 0.00 40.02 0.86
2241 2270 4.320567 GGTTTTCTTCTTTGCCTGCTCTAC 60.321 45.833 0.00 0.00 0.00 2.59
2365 2394 3.081061 TCCAGATCCAATTGTTCAACCG 58.919 45.455 4.43 0.00 0.00 4.44
3428 3457 7.939588 ACCTATTCCATTCCTATCTTAAAGTGC 59.060 37.037 0.00 0.00 0.00 4.40
3440 3469 1.593196 TAAAGTGCCGCTGCCATATC 58.407 50.000 0.00 0.00 36.33 1.63
3692 3721 1.134995 TGTGCATCTTGACTAGCCTCG 60.135 52.381 0.00 0.00 0.00 4.63
3814 3843 2.985896 TGATGTGGTTAGCTGTTAGCC 58.014 47.619 0.00 0.00 43.77 3.93
4447 4476 6.212235 TGAGAAAGAAGAGCAGATTATAGCG 58.788 40.000 0.00 0.00 35.48 4.26
4501 4530 7.148507 GGTGATTTATCTCTCTTGTGAACACAG 60.149 40.741 7.67 3.60 42.94 3.66
4588 4617 7.806690 TGTATAGAAAGCACAGAAAATGTCAC 58.193 34.615 0.00 0.00 41.41 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 6.945435 ACACAATATAACTGACCAATGAACCA 59.055 34.615 0.00 0.00 0.00 3.67
598 600 5.330233 GGGGTCATCCTCCTTTTCTAAAAA 58.670 41.667 0.00 0.00 35.33 1.94
599 601 4.930696 GGGGTCATCCTCCTTTTCTAAAA 58.069 43.478 0.00 0.00 35.33 1.52
600 602 4.586306 GGGGTCATCCTCCTTTTCTAAA 57.414 45.455 0.00 0.00 35.33 1.85
613 615 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
619 621 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
620 622 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
621 623 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
622 624 3.457625 CTCCCAGATGCAGAGGCCG 62.458 68.421 0.00 0.00 40.13 6.13
623 625 1.417288 ATCTCCCAGATGCAGAGGCC 61.417 60.000 0.00 0.00 40.13 5.19
624 626 0.250381 CATCTCCCAGATGCAGAGGC 60.250 60.000 0.61 0.00 44.69 4.70
632 634 0.322975 GCCGTATGCATCTCCCAGAT 59.677 55.000 0.19 0.00 40.77 2.90
633 635 1.748403 GCCGTATGCATCTCCCAGA 59.252 57.895 0.19 0.00 40.77 3.86
634 636 1.302033 GGCCGTATGCATCTCCCAG 60.302 63.158 0.19 0.00 43.89 4.45
635 637 2.069430 TGGCCGTATGCATCTCCCA 61.069 57.895 0.19 3.16 43.89 4.37
636 638 1.598130 GTGGCCGTATGCATCTCCC 60.598 63.158 0.19 0.17 43.89 4.30
637 639 0.179045 AAGTGGCCGTATGCATCTCC 60.179 55.000 0.19 0.71 43.89 3.71
638 640 1.668419 AAAGTGGCCGTATGCATCTC 58.332 50.000 0.19 0.00 43.89 2.75
639 641 3.492102 ATAAAGTGGCCGTATGCATCT 57.508 42.857 0.19 0.00 43.89 2.90
640 642 3.563808 TCAATAAAGTGGCCGTATGCATC 59.436 43.478 0.19 0.00 43.89 3.91
641 643 3.550820 TCAATAAAGTGGCCGTATGCAT 58.449 40.909 3.79 3.79 43.89 3.96
642 644 2.992593 TCAATAAAGTGGCCGTATGCA 58.007 42.857 0.00 0.00 43.89 3.96
643 645 4.568152 AATCAATAAAGTGGCCGTATGC 57.432 40.909 0.00 0.00 40.16 3.14
644 646 8.099364 AGAATAATCAATAAAGTGGCCGTATG 57.901 34.615 0.00 0.00 0.00 2.39
645 647 7.117812 CGAGAATAATCAATAAAGTGGCCGTAT 59.882 37.037 0.00 0.00 0.00 3.06
646 648 6.422701 CGAGAATAATCAATAAAGTGGCCGTA 59.577 38.462 0.00 0.00 0.00 4.02
647 649 5.236478 CGAGAATAATCAATAAAGTGGCCGT 59.764 40.000 0.00 0.00 0.00 5.68
648 650 5.465390 TCGAGAATAATCAATAAAGTGGCCG 59.535 40.000 0.00 0.00 0.00 6.13
649 651 6.073003 CCTCGAGAATAATCAATAAAGTGGCC 60.073 42.308 15.71 0.00 0.00 5.36
650 652 6.706270 TCCTCGAGAATAATCAATAAAGTGGC 59.294 38.462 15.71 0.00 0.00 5.01
651 653 7.171678 GGTCCTCGAGAATAATCAATAAAGTGG 59.828 40.741 15.71 0.00 0.00 4.00
652 654 7.928706 AGGTCCTCGAGAATAATCAATAAAGTG 59.071 37.037 15.71 0.00 0.00 3.16
653 655 8.024145 AGGTCCTCGAGAATAATCAATAAAGT 57.976 34.615 15.71 0.00 0.00 2.66
654 656 8.894768 AAGGTCCTCGAGAATAATCAATAAAG 57.105 34.615 15.71 0.00 0.00 1.85
655 657 9.760077 GTAAGGTCCTCGAGAATAATCAATAAA 57.240 33.333 15.71 0.00 0.00 1.40
656 658 8.920174 TGTAAGGTCCTCGAGAATAATCAATAA 58.080 33.333 15.71 0.00 0.00 1.40
657 659 8.473358 TGTAAGGTCCTCGAGAATAATCAATA 57.527 34.615 15.71 0.00 0.00 1.90
658 660 7.361457 TGTAAGGTCCTCGAGAATAATCAAT 57.639 36.000 15.71 0.00 0.00 2.57
659 661 6.785337 TGTAAGGTCCTCGAGAATAATCAA 57.215 37.500 15.71 0.00 0.00 2.57
660 662 6.785337 TTGTAAGGTCCTCGAGAATAATCA 57.215 37.500 15.71 2.16 0.00 2.57
661 663 7.266400 ACTTTGTAAGGTCCTCGAGAATAATC 58.734 38.462 15.71 0.00 0.00 1.75
662 664 7.184067 ACTTTGTAAGGTCCTCGAGAATAAT 57.816 36.000 15.71 0.00 0.00 1.28
663 665 6.600882 ACTTTGTAAGGTCCTCGAGAATAA 57.399 37.500 15.71 0.00 0.00 1.40
664 666 7.893124 ATACTTTGTAAGGTCCTCGAGAATA 57.107 36.000 15.71 0.00 0.00 1.75
665 667 6.793505 ATACTTTGTAAGGTCCTCGAGAAT 57.206 37.500 15.71 0.00 0.00 2.40
666 668 6.600882 AATACTTTGTAAGGTCCTCGAGAA 57.399 37.500 15.71 0.00 0.00 2.87
667 669 6.660521 TGTAATACTTTGTAAGGTCCTCGAGA 59.339 38.462 15.71 0.00 0.00 4.04
668 670 6.860080 TGTAATACTTTGTAAGGTCCTCGAG 58.140 40.000 5.13 5.13 0.00 4.04
669 671 6.839124 TGTAATACTTTGTAAGGTCCTCGA 57.161 37.500 0.00 0.00 0.00 4.04
670 672 6.869913 TGTTGTAATACTTTGTAAGGTCCTCG 59.130 38.462 0.00 0.00 0.00 4.63
671 673 8.611654 TTGTTGTAATACTTTGTAAGGTCCTC 57.388 34.615 0.00 0.00 0.00 3.71
672 674 9.010029 CATTGTTGTAATACTTTGTAAGGTCCT 57.990 33.333 0.00 0.00 0.00 3.85
673 675 8.789762 ACATTGTTGTAATACTTTGTAAGGTCC 58.210 33.333 0.00 0.00 33.16 4.46
674 676 9.607285 CACATTGTTGTAATACTTTGTAAGGTC 57.393 33.333 0.00 0.00 33.76 3.85
675 677 8.079809 GCACATTGTTGTAATACTTTGTAAGGT 58.920 33.333 0.00 0.00 33.76 3.50
676 678 7.540745 GGCACATTGTTGTAATACTTTGTAAGG 59.459 37.037 0.00 0.00 33.76 2.69
677 679 8.296713 AGGCACATTGTTGTAATACTTTGTAAG 58.703 33.333 0.00 0.00 33.76 2.34
678 680 8.079203 CAGGCACATTGTTGTAATACTTTGTAA 58.921 33.333 0.00 0.00 33.76 2.41
679 681 7.445707 TCAGGCACATTGTTGTAATACTTTGTA 59.554 33.333 0.00 0.00 33.76 2.41
680 682 6.264292 TCAGGCACATTGTTGTAATACTTTGT 59.736 34.615 0.00 0.00 33.76 2.83
681 683 6.676950 TCAGGCACATTGTTGTAATACTTTG 58.323 36.000 0.00 0.00 33.76 2.77
682 684 6.892658 TCAGGCACATTGTTGTAATACTTT 57.107 33.333 0.00 0.00 33.76 2.66
683 685 6.892658 TTCAGGCACATTGTTGTAATACTT 57.107 33.333 0.00 0.00 33.76 2.24
684 686 6.095440 GGATTCAGGCACATTGTTGTAATACT 59.905 38.462 0.00 0.00 33.76 2.12
685 687 6.127758 TGGATTCAGGCACATTGTTGTAATAC 60.128 38.462 0.00 0.00 33.76 1.89
686 688 5.948758 TGGATTCAGGCACATTGTTGTAATA 59.051 36.000 0.00 0.00 33.76 0.98
687 689 4.771577 TGGATTCAGGCACATTGTTGTAAT 59.228 37.500 0.00 0.00 33.76 1.89
688 690 4.022416 GTGGATTCAGGCACATTGTTGTAA 60.022 41.667 0.00 0.00 33.76 2.41
689 691 3.505680 GTGGATTCAGGCACATTGTTGTA 59.494 43.478 0.00 0.00 33.76 2.41
690 692 2.297033 GTGGATTCAGGCACATTGTTGT 59.703 45.455 0.00 0.00 36.15 3.32
691 693 2.353011 GGTGGATTCAGGCACATTGTTG 60.353 50.000 0.00 0.00 0.00 3.33
692 694 1.895131 GGTGGATTCAGGCACATTGTT 59.105 47.619 0.00 0.00 0.00 2.83
693 695 1.203038 TGGTGGATTCAGGCACATTGT 60.203 47.619 0.00 0.00 0.00 2.71
694 696 1.548081 TGGTGGATTCAGGCACATTG 58.452 50.000 0.00 0.00 0.00 2.82
695 697 2.024655 AGATGGTGGATTCAGGCACATT 60.025 45.455 0.00 0.00 0.00 2.71
696 698 1.567649 AGATGGTGGATTCAGGCACAT 59.432 47.619 0.00 0.00 0.00 3.21
697 699 0.994247 AGATGGTGGATTCAGGCACA 59.006 50.000 0.00 0.00 0.00 4.57
698 700 1.747355 CAAGATGGTGGATTCAGGCAC 59.253 52.381 0.00 0.00 0.00 5.01
699 701 1.341285 CCAAGATGGTGGATTCAGGCA 60.341 52.381 0.00 0.00 41.65 4.75
700 702 1.396653 CCAAGATGGTGGATTCAGGC 58.603 55.000 0.00 0.00 41.65 4.85
701 703 1.341285 TGCCAAGATGGTGGATTCAGG 60.341 52.381 0.00 0.00 41.65 3.86
702 704 2.133281 TGCCAAGATGGTGGATTCAG 57.867 50.000 0.00 0.00 41.65 3.02
703 705 2.170166 GTTGCCAAGATGGTGGATTCA 58.830 47.619 0.00 0.00 41.65 2.57
704 706 2.170166 TGTTGCCAAGATGGTGGATTC 58.830 47.619 0.00 0.00 41.65 2.52
705 707 2.307496 TGTTGCCAAGATGGTGGATT 57.693 45.000 0.00 0.00 41.65 3.01
706 708 2.537633 ATGTTGCCAAGATGGTGGAT 57.462 45.000 0.00 0.00 41.65 3.41
707 709 3.289836 CATATGTTGCCAAGATGGTGGA 58.710 45.455 0.00 0.00 41.65 4.02
708 710 3.025978 ACATATGTTGCCAAGATGGTGG 58.974 45.455 1.41 0.00 40.46 4.61
709 711 3.242837 CGACATATGTTGCCAAGATGGTG 60.243 47.826 10.30 0.00 40.46 4.17
710 712 2.945008 CGACATATGTTGCCAAGATGGT 59.055 45.455 10.30 0.00 40.46 3.55
711 713 3.614159 CGACATATGTTGCCAAGATGG 57.386 47.619 10.30 0.00 41.55 3.51
720 722 5.048013 TGGATAGGAGTAGCGACATATGTTG 60.048 44.000 17.52 17.52 0.00 3.33
721 723 5.077564 TGGATAGGAGTAGCGACATATGTT 58.922 41.667 10.30 0.00 0.00 2.71
722 724 4.663334 TGGATAGGAGTAGCGACATATGT 58.337 43.478 8.43 8.43 0.00 2.29
723 725 5.644977 TTGGATAGGAGTAGCGACATATG 57.355 43.478 0.00 0.00 0.00 1.78
724 726 6.039941 GCTATTGGATAGGAGTAGCGACATAT 59.960 42.308 0.00 0.00 33.43 1.78
725 727 5.357314 GCTATTGGATAGGAGTAGCGACATA 59.643 44.000 0.00 0.00 33.43 2.29
726 728 4.158764 GCTATTGGATAGGAGTAGCGACAT 59.841 45.833 0.00 0.00 33.43 3.06
727 729 3.506455 GCTATTGGATAGGAGTAGCGACA 59.494 47.826 0.00 0.00 33.43 4.35
728 730 3.506455 TGCTATTGGATAGGAGTAGCGAC 59.494 47.826 0.00 0.00 40.37 5.19
729 731 3.763057 TGCTATTGGATAGGAGTAGCGA 58.237 45.455 0.00 0.00 40.37 4.93
730 732 4.238514 GTTGCTATTGGATAGGAGTAGCG 58.761 47.826 0.00 0.00 40.37 4.26
731 733 5.215252 TGTTGCTATTGGATAGGAGTAGC 57.785 43.478 0.00 0.00 38.52 3.58
732 734 8.939201 CATATGTTGCTATTGGATAGGAGTAG 57.061 38.462 0.00 0.00 34.59 2.57
926 931 0.904865 AGACCTGTGGAAGATGGCGA 60.905 55.000 0.00 0.00 0.00 5.54
1004 1015 2.116983 GAGGAGGTTGCTGTCTGGCA 62.117 60.000 0.00 0.00 40.74 4.92
1147 1162 2.042404 TTGGAGGCGTACACGGGTTT 62.042 55.000 0.00 0.00 40.23 3.27
1311 1326 2.280524 CAAGACCGGTGTTGGCGA 60.281 61.111 31.43 0.00 31.08 5.54
1344 1359 1.065998 CGGATCCGGGTGAAAACCTAA 60.066 52.381 26.95 0.00 35.56 2.69
1486 1501 2.276740 CATGGAGGGCCTGGGTTC 59.723 66.667 12.95 0.00 34.31 3.62
1716 1737 2.187685 CAGTGGCGCTGGATGCTA 59.812 61.111 20.17 0.00 41.42 3.49
1825 1846 3.403558 GCGGGCCTTTCCTCTCCT 61.404 66.667 0.84 0.00 34.39 3.69
1977 2005 1.051812 CAGTCTTGGGTCTGGTGACT 58.948 55.000 0.00 0.00 42.54 3.41
1978 2006 0.759346 ACAGTCTTGGGTCTGGTGAC 59.241 55.000 0.00 0.00 42.22 3.67
1979 2007 1.416401 GAACAGTCTTGGGTCTGGTGA 59.584 52.381 0.00 0.00 36.17 4.02
1980 2008 1.140852 TGAACAGTCTTGGGTCTGGTG 59.859 52.381 0.00 0.00 36.17 4.17
1981 2009 1.507140 TGAACAGTCTTGGGTCTGGT 58.493 50.000 0.00 0.00 36.17 4.00
1982 2010 2.430465 CATGAACAGTCTTGGGTCTGG 58.570 52.381 0.00 0.00 36.17 3.86
1983 2011 2.430465 CCATGAACAGTCTTGGGTCTG 58.570 52.381 0.00 0.00 42.70 3.51
1984 2012 2.867109 CCATGAACAGTCTTGGGTCT 57.133 50.000 0.00 0.00 42.70 3.85
1988 2016 9.226606 TAAAGTATTTACCATGAACAGTCTTGG 57.773 33.333 0.00 7.01 44.65 3.61
1990 2018 8.947115 GCTAAAGTATTTACCATGAACAGTCTT 58.053 33.333 0.00 0.00 40.09 3.01
1991 2019 8.322091 AGCTAAAGTATTTACCATGAACAGTCT 58.678 33.333 0.00 0.00 40.09 3.24
1992 2020 8.494016 AGCTAAAGTATTTACCATGAACAGTC 57.506 34.615 0.00 0.00 40.09 3.51
1996 2024 9.665264 GCAATAGCTAAAGTATTTACCATGAAC 57.335 33.333 0.00 0.00 40.09 3.18
2092 2120 0.107945 GAGCCCTCTAACACCTGCAG 60.108 60.000 6.78 6.78 0.00 4.41
2100 2128 1.137282 GCTACCACTGAGCCCTCTAAC 59.863 57.143 0.00 0.00 33.60 2.34
2140 2169 7.971368 TTGATATCGGGTATATCCTCATGAA 57.029 36.000 0.00 0.00 44.09 2.57
2365 2394 0.888285 AGTTGAGCCAGCTGAAGCAC 60.888 55.000 17.39 10.35 45.16 4.40
3377 3406 4.452455 AGCTATATATGCACCGACAAAAGC 59.548 41.667 0.00 0.00 0.00 3.51
3428 3457 2.256591 GCAGGTGATATGGCAGCGG 61.257 63.158 0.00 0.00 40.96 5.52
3440 3469 0.309922 CAGTTGACTTGCTGCAGGTG 59.690 55.000 22.59 9.71 0.00 4.00
3692 3721 2.416680 AATCTTGAGCAGGCTCTTCC 57.583 50.000 20.79 0.00 43.12 3.46
3814 3843 6.706716 AGTACATGCTCAGATCATCAATTCTG 59.293 38.462 0.00 0.00 40.58 3.02
4258 4287 0.471191 TCCATGATCAAGCTCGCCAT 59.529 50.000 0.00 0.00 0.00 4.40
4319 4348 0.979665 TGGGGCAGTCAAAGAGAGAG 59.020 55.000 0.00 0.00 0.00 3.20
4447 4476 3.771577 TCTTCTCCACCAAACTCTTCC 57.228 47.619 0.00 0.00 0.00 3.46
4501 4530 6.681777 ACCAATTGCTCAGATTAAACTTGAC 58.318 36.000 0.00 0.00 0.00 3.18
4588 4617 0.392998 AACAGCCTGAATACAGCCCG 60.393 55.000 0.00 0.00 42.25 6.13


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

AutoCloner maintained by Alex Coulton.