Multiple sequence alignment - TraesCS6B01G150800

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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 TraesCS6B01G150800 chr6B 100.000 3479 0 0 1 3479 152018377 152014899 0.000000e+00 6425
1 TraesCS6B01G150800 chr6B 100.000 408 0 0 3687 4094 152014691 152014284 0.000000e+00 754
2 TraesCS6B01G150800 chr6B 97.519 403 10 0 3692 4094 710925537 710925135 0.000000e+00 689
3 TraesCS6B01G150800 chr6B 96.030 403 16 0 3692 4094 710952258 710951856 0.000000e+00 656
4 TraesCS6B01G150800 chr6B 85.565 478 49 11 2064 2528 151920532 151920062 2.210000e-132 483
5 TraesCS6B01G150800 chr6B 88.263 213 25 0 2685 2897 151909577 151909365 5.250000e-64 255
6 TraesCS6B01G150800 chr6A 94.584 1237 58 3 1831 3066 96431591 96430363 0.000000e+00 1905
7 TraesCS6B01G150800 chr6A 89.674 920 61 15 896 1807 96432808 96431915 0.000000e+00 1142
8 TraesCS6B01G150800 chr6A 89.145 608 59 5 1 603 135241855 135241250 0.000000e+00 750
9 TraesCS6B01G150800 chr6A 86.615 650 83 3 1 647 183322264 183321616 0.000000e+00 715
10 TraesCS6B01G150800 chr6A 89.783 323 24 2 3064 3386 96430316 96430003 4.930000e-109 405
11 TraesCS6B01G150800 chr6A 96.552 87 3 0 3393 3479 79358275 79358361 1.190000e-30 145
12 TraesCS6B01G150800 chr6D 92.967 1237 54 3 1831 3066 79711720 79710516 0.000000e+00 1772
13 TraesCS6B01G150800 chr6D 89.110 753 37 19 1058 1802 79712625 79711910 0.000000e+00 894
14 TraesCS6B01G150800 chr6D 88.298 282 33 0 786 1067 79714073 79713792 5.070000e-89 339
15 TraesCS6B01G150800 chr6D 86.018 329 28 7 3064 3392 79710469 79710159 1.820000e-88 337
16 TraesCS6B01G150800 chr7D 87.974 765 77 14 1 761 221822615 221823368 0.000000e+00 889
17 TraesCS6B01G150800 chr3A 87.662 770 79 10 1 761 43645493 43644731 0.000000e+00 881
18 TraesCS6B01G150800 chr3A 86.991 761 83 10 10 761 43034098 43033345 0.000000e+00 843
19 TraesCS6B01G150800 chr3A 87.294 669 80 5 1 666 369494672 369494006 0.000000e+00 760
20 TraesCS6B01G150800 chr5D 88.771 659 57 10 1 648 502197679 502197027 0.000000e+00 791
21 TraesCS6B01G150800 chr5D 96.591 88 2 1 3393 3479 220689268 220689355 1.190000e-30 145
22 TraesCS6B01G150800 chr5D 95.556 90 3 1 3391 3479 220683817 220683906 4.270000e-30 143
23 TraesCS6B01G150800 chr7A 86.647 674 79 7 2 670 115856610 115855943 0.000000e+00 736
24 TraesCS6B01G150800 chr3D 86.256 633 72 11 25 648 589878796 589878170 0.000000e+00 673
25 TraesCS6B01G150800 chr3D 96.667 90 2 1 3391 3479 1138464 1138553 9.170000e-32 148
26 TraesCS6B01G150800 chr3B 96.774 403 13 0 3692 4094 747524872 747524470 0.000000e+00 673
27 TraesCS6B01G150800 chr3B 96.278 403 15 0 3692 4094 44328455 44328857 0.000000e+00 662
28 TraesCS6B01G150800 chr3B 96.278 403 15 0 3692 4094 802623446 802623848 0.000000e+00 662
29 TraesCS6B01G150800 chr3B 97.701 87 2 0 3393 3479 814786232 814786146 2.550000e-32 150
30 TraesCS6B01G150800 chr3B 96.591 88 3 0 3392 3479 802623315 802623402 3.300000e-31 147
31 TraesCS6B01G150800 chr2D 96.526 403 14 0 3692 4094 159335890 159335488 0.000000e+00 667
32 TraesCS6B01G150800 chr5B 96.509 401 14 0 3694 4094 355621522 355621922 0.000000e+00 664
33 TraesCS6B01G150800 chr5B 96.030 403 16 0 3692 4094 554767425 554767827 0.000000e+00 656
34 TraesCS6B01G150800 chr5B 97.701 87 2 0 3393 3479 554767295 554767381 2.550000e-32 150
35 TraesCS6B01G150800 chr1B 96.030 403 16 0 3692 4094 542604985 542605387 0.000000e+00 656
36 TraesCS6B01G150800 chr7B 96.667 90 1 2 3391 3479 718073482 718073394 9.170000e-32 148
37 TraesCS6B01G150800 chr2A 96.552 87 3 0 3393 3479 33322393 33322479 1.190000e-30 145


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 TraesCS6B01G150800 chr6B 152014284 152018377 4093 True 3589.500000 6425 100.00000 1 4094 2 chr6B.!!$R5 4093
1 TraesCS6B01G150800 chr6A 96430003 96432808 2805 True 1150.666667 1905 91.34700 896 3386 3 chr6A.!!$R3 2490
2 TraesCS6B01G150800 chr6A 135241250 135241855 605 True 750.000000 750 89.14500 1 603 1 chr6A.!!$R1 602
3 TraesCS6B01G150800 chr6A 183321616 183322264 648 True 715.000000 715 86.61500 1 647 1 chr6A.!!$R2 646
4 TraesCS6B01G150800 chr6D 79710159 79714073 3914 True 835.500000 1772 89.09825 786 3392 4 chr6D.!!$R1 2606
5 TraesCS6B01G150800 chr7D 221822615 221823368 753 False 889.000000 889 87.97400 1 761 1 chr7D.!!$F1 760
6 TraesCS6B01G150800 chr3A 43644731 43645493 762 True 881.000000 881 87.66200 1 761 1 chr3A.!!$R2 760
7 TraesCS6B01G150800 chr3A 43033345 43034098 753 True 843.000000 843 86.99100 10 761 1 chr3A.!!$R1 751
8 TraesCS6B01G150800 chr3A 369494006 369494672 666 True 760.000000 760 87.29400 1 666 1 chr3A.!!$R3 665
9 TraesCS6B01G150800 chr5D 502197027 502197679 652 True 791.000000 791 88.77100 1 648 1 chr5D.!!$R1 647
10 TraesCS6B01G150800 chr7A 115855943 115856610 667 True 736.000000 736 86.64700 2 670 1 chr7A.!!$R1 668
11 TraesCS6B01G150800 chr3D 589878170 589878796 626 True 673.000000 673 86.25600 25 648 1 chr3D.!!$R1 623
12 TraesCS6B01G150800 chr3B 802623315 802623848 533 False 404.500000 662 96.43450 3392 4094 2 chr3B.!!$F2 702
13 TraesCS6B01G150800 chr5B 554767295 554767827 532 False 403.000000 656 96.86550 3393 4094 2 chr5B.!!$F2 701

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
672 708 0.391263 AAATCCGCGTCTGAAGGGTC 60.391 55.0 4.92 0.0 0.00 4.46 F
1454 2681 0.323629 GACGGGACAAGGTGAATCCA 59.676 55.0 0.00 0.0 39.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 3059 0.548031 ATGTGTAGGGGCATGGTGAG 59.452 55.0 0.0 0.0 0.00 3.51 R
3222 4807 0.110238 CACACACATAACGCACCTGC 60.110 55.0 0.0 0.0 37.78 4.85 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
58 59 2.867855 TTCAGCGTGAAGGCCGAGT 61.868 57.895 0.00 0.00 31.83 4.18
60 61 2.992114 AGCGTGAAGGCCGAGTCT 60.992 61.111 0.00 0.00 0.00 3.24
62 63 2.125912 CGTGAAGGCCGAGTCTGG 60.126 66.667 0.00 0.00 0.00 3.86
83 84 4.176851 GGAGACGTCGCTCGGTCC 62.177 72.222 18.88 11.10 44.69 4.46
123 124 2.264794 GTCATCAACGAGGGCGGT 59.735 61.111 0.00 0.00 43.17 5.68
608 639 1.524848 TTGCCGAATTTAGCCGAACA 58.475 45.000 0.00 0.00 0.00 3.18
641 672 1.892209 ACCGAACTTTGCCGAATTCT 58.108 45.000 3.52 0.00 0.00 2.40
648 679 5.554324 CGAACTTTGCCGAATTCTGTTTTTG 60.554 40.000 3.52 0.00 0.00 2.44
652 683 6.148645 ACTTTGCCGAATTCTGTTTTTGTTTT 59.851 30.769 3.52 0.00 0.00 2.43
656 687 8.202745 TGCCGAATTCTGTTTTTGTTTTAAAT 57.797 26.923 3.52 0.00 0.00 1.40
666 702 4.815040 TTTGTTTTAAATCCGCGTCTGA 57.185 36.364 4.92 0.00 0.00 3.27
667 703 4.815040 TTGTTTTAAATCCGCGTCTGAA 57.185 36.364 4.92 0.00 0.00 3.02
668 704 4.398549 TGTTTTAAATCCGCGTCTGAAG 57.601 40.909 4.92 0.00 0.00 3.02
669 705 3.187637 TGTTTTAAATCCGCGTCTGAAGG 59.812 43.478 4.92 0.00 0.00 3.46
670 706 2.018542 TTAAATCCGCGTCTGAAGGG 57.981 50.000 4.92 0.80 0.00 3.95
671 707 0.899720 TAAATCCGCGTCTGAAGGGT 59.100 50.000 4.92 0.00 0.00 4.34
672 708 0.391263 AAATCCGCGTCTGAAGGGTC 60.391 55.000 4.92 0.00 0.00 4.46
673 709 1.258445 AATCCGCGTCTGAAGGGTCT 61.258 55.000 4.92 0.00 0.00 3.85
678 714 1.913762 CGTCTGAAGGGTCTGGGGT 60.914 63.158 0.00 0.00 0.00 4.95
695 736 3.940480 TGACCCTGGGAGGCTGGA 61.940 66.667 22.23 0.00 32.73 3.86
706 747 4.388499 GGCTGGAAACCCGCTCGA 62.388 66.667 0.00 0.00 0.00 4.04
707 748 2.815647 GCTGGAAACCCGCTCGAG 60.816 66.667 8.45 8.45 0.00 4.04
708 749 2.657237 CTGGAAACCCGCTCGAGT 59.343 61.111 15.13 0.00 0.00 4.18
724 765 1.927174 CGAGTCCGTGCTGATTTTAGG 59.073 52.381 0.00 0.00 0.00 2.69
732 773 1.037579 GCTGATTTTAGGGCCGGCTT 61.038 55.000 28.56 17.66 0.00 4.35
763 806 3.788817 CGTAAATCGCCGCCTTGA 58.211 55.556 0.00 0.00 0.00 3.02
764 807 1.636340 CGTAAATCGCCGCCTTGAG 59.364 57.895 0.00 0.00 0.00 3.02
765 808 1.762222 CGTAAATCGCCGCCTTGAGG 61.762 60.000 0.00 0.00 38.53 3.86
766 809 1.153249 TAAATCGCCGCCTTGAGGG 60.153 57.895 0.00 0.00 35.18 4.30
774 817 3.329093 GCCTTGAGGGGAGATGCT 58.671 61.111 0.00 0.00 35.18 3.79
775 818 1.148048 GCCTTGAGGGGAGATGCTC 59.852 63.158 0.00 0.00 35.18 4.26
776 819 1.344191 GCCTTGAGGGGAGATGCTCT 61.344 60.000 0.00 0.00 35.18 4.09
777 820 2.036929 GCCTTGAGGGGAGATGCTCTA 61.037 57.143 0.00 0.00 35.18 2.43
778 821 2.402564 CCTTGAGGGGAGATGCTCTAA 58.597 52.381 0.00 0.00 0.00 2.10
779 822 2.368221 CCTTGAGGGGAGATGCTCTAAG 59.632 54.545 0.00 0.00 0.00 2.18
780 823 2.094100 TGAGGGGAGATGCTCTAAGG 57.906 55.000 0.00 0.00 0.00 2.69
781 824 1.575788 TGAGGGGAGATGCTCTAAGGA 59.424 52.381 0.00 0.00 0.00 3.36
782 825 1.967779 GAGGGGAGATGCTCTAAGGAC 59.032 57.143 0.00 0.00 0.00 3.85
783 826 1.292242 AGGGGAGATGCTCTAAGGACA 59.708 52.381 0.00 0.00 0.00 4.02
784 827 1.414550 GGGGAGATGCTCTAAGGACAC 59.585 57.143 0.00 0.00 0.00 3.67
785 828 1.414550 GGGAGATGCTCTAAGGACACC 59.585 57.143 0.00 0.00 0.00 4.16
786 829 2.111384 GGAGATGCTCTAAGGACACCA 58.889 52.381 0.00 0.00 0.00 4.17
787 830 2.102252 GGAGATGCTCTAAGGACACCAG 59.898 54.545 0.00 0.00 0.00 4.00
788 831 2.102252 GAGATGCTCTAAGGACACCAGG 59.898 54.545 0.00 0.00 0.00 4.45
789 832 0.543749 ATGCTCTAAGGACACCAGGC 59.456 55.000 0.00 0.00 0.00 4.85
790 833 1.153549 GCTCTAAGGACACCAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
791 834 1.153549 CTCTAAGGACACCAGGCGC 60.154 63.158 0.00 0.00 0.00 6.53
792 835 1.608717 CTCTAAGGACACCAGGCGCT 61.609 60.000 7.64 0.00 0.00 5.92
793 836 1.153549 CTAAGGACACCAGGCGCTC 60.154 63.158 7.64 0.00 0.00 5.03
794 837 1.888436 CTAAGGACACCAGGCGCTCA 61.888 60.000 7.64 0.00 0.00 4.26
795 838 1.264749 TAAGGACACCAGGCGCTCAT 61.265 55.000 7.64 0.00 0.00 2.90
796 839 2.045926 GGACACCAGGCGCTCATT 60.046 61.111 7.64 0.00 0.00 2.57
797 840 2.401766 GGACACCAGGCGCTCATTG 61.402 63.158 7.64 2.48 0.00 2.82
798 841 3.044059 GACACCAGGCGCTCATTGC 62.044 63.158 7.64 0.00 38.57 3.56
808 851 2.046023 CTCATTGCACGAGCCCCA 60.046 61.111 1.39 0.00 41.13 4.96
814 857 4.468689 GCACGAGCCCCACCTACC 62.469 72.222 0.00 0.00 33.58 3.18
817 860 3.528370 CGAGCCCCACCTACCGAG 61.528 72.222 0.00 0.00 0.00 4.63
859 902 2.019249 CAACCCTGGTGTATGCTGATG 58.981 52.381 0.00 0.00 0.00 3.07
866 909 3.346315 TGGTGTATGCTGATGAAACAGG 58.654 45.455 0.00 0.00 38.22 4.00
876 919 4.320057 GCTGATGAAACAGGAACAGTGAAG 60.320 45.833 0.00 0.00 38.22 3.02
878 921 4.816385 TGATGAAACAGGAACAGTGAAGAC 59.184 41.667 0.00 0.00 0.00 3.01
883 926 1.671379 GGAACAGTGAAGACCCCGC 60.671 63.158 0.00 0.00 0.00 6.13
1043 1086 3.072468 CCTACGGGGCGAGGTTCA 61.072 66.667 0.00 0.00 0.00 3.18
1054 1097 0.665369 CGAGGTTCACCGTAAACGCT 60.665 55.000 0.00 0.00 42.08 5.07
1193 2415 1.006805 CGCGATCTGGACATCTCCC 60.007 63.158 0.00 0.00 35.34 4.30
1454 2681 0.323629 GACGGGACAAGGTGAATCCA 59.676 55.000 0.00 0.00 39.02 3.41
1457 2684 2.574369 ACGGGACAAGGTGAATCCATTA 59.426 45.455 0.00 0.00 39.02 1.90
1556 2788 1.332375 GGACACAGTTACTTTGCGCAA 59.668 47.619 21.02 21.02 0.00 4.85
1591 2823 9.787435 TGTGTTAAATTCTGTATTAAGGTCAGT 57.213 29.630 0.00 0.00 0.00 3.41
1675 2908 7.095940 TGTCTTAGCAAACATACACGTTAAGAC 60.096 37.037 16.76 16.76 45.12 3.01
1727 2962 2.623535 TGTTGTGGATATGTACACGGC 58.376 47.619 0.00 0.00 42.45 5.68
1731 2966 2.159014 TGTGGATATGTACACGGCCTTC 60.159 50.000 0.00 0.00 42.45 3.46
1787 3022 9.331282 GAGTGAACTTTTATTATACCTGCAGAT 57.669 33.333 17.39 0.00 0.00 2.90
1798 3033 7.615582 TTATACCTGCAGATTGAAAAGAGTG 57.384 36.000 17.39 0.00 0.00 3.51
1802 3037 4.276678 CCTGCAGATTGAAAAGAGTGAACA 59.723 41.667 17.39 0.00 0.00 3.18
1807 3042 8.077991 TGCAGATTGAAAAGAGTGAACATTTAG 58.922 33.333 0.00 0.00 0.00 1.85
1808 3043 8.078596 GCAGATTGAAAAGAGTGAACATTTAGT 58.921 33.333 0.00 0.00 0.00 2.24
1834 3369 5.527582 CAGTAAAATACTACCTCACCATGCC 59.472 44.000 0.00 0.00 37.23 4.40
1837 3372 0.341961 TACTACCTCACCATGCCCCT 59.658 55.000 0.00 0.00 0.00 4.79
1840 3375 0.043485 TACCTCACCATGCCCCTACA 59.957 55.000 0.00 0.00 0.00 2.74
1897 3432 6.018262 CCTCAATCGAACGCCTATTTCAATTA 60.018 38.462 0.00 0.00 0.00 1.40
1898 3433 7.307989 CCTCAATCGAACGCCTATTTCAATTAT 60.308 37.037 0.00 0.00 0.00 1.28
1900 3435 5.090652 TCGAACGCCTATTTCAATTATGC 57.909 39.130 0.00 0.00 0.00 3.14
1924 3460 7.118101 TGCAAAAATGAACAAATATCCTTGAGC 59.882 33.333 0.00 0.00 0.00 4.26
1957 3493 5.984233 TGAACACTGTAAAGCTACACAAG 57.016 39.130 2.32 1.44 34.28 3.16
2048 3584 6.633856 ACTCTTTTGTGCAGTTCAGAAATTT 58.366 32.000 0.00 0.00 37.71 1.82
2056 3592 3.862264 GCAGTTCAGAAATTTCTTGGGGC 60.862 47.826 18.16 13.75 34.74 5.80
2106 3642 1.073177 CTACGGTTGCGGTAAACCTG 58.927 55.000 11.34 8.25 46.31 4.00
2115 3651 1.199327 GCGGTAAACCTGAAGGCTTTC 59.801 52.381 0.00 0.77 39.32 2.62
2128 3664 1.006922 GCTTTCAACCTGCCACTGC 60.007 57.895 0.00 0.00 38.26 4.40
2208 3744 6.927381 TGCACTAACAAGTACTTAGAACCTTC 59.073 38.462 8.04 0.00 0.00 3.46
2281 3817 5.202765 TGTGCCATAAAACATGATCTGGAT 58.797 37.500 0.00 0.00 0.00 3.41
2298 3834 6.505048 TCTGGATATGAACATGGACTCAAT 57.495 37.500 0.00 0.00 0.00 2.57
2310 3846 5.879223 ACATGGACTCAATCTCAGAAATCAC 59.121 40.000 0.00 0.00 0.00 3.06
2352 3888 2.172851 TACGGTGTCCATGAACCAAC 57.827 50.000 11.30 0.01 36.14 3.77
2429 3965 6.265196 TGTTTTTCCTTGTACATGAAGATGCT 59.735 34.615 10.20 0.00 32.14 3.79
2439 3975 9.783081 TTGTACATGAAGATGCTGTATTATGAT 57.217 29.630 0.00 0.00 32.14 2.45
2463 3999 3.056393 TCCAGAAGGATTTTGCTGCAATG 60.056 43.478 16.77 8.51 39.61 2.82
2514 4050 6.561519 AAGAGGGAGCTAGCTAAAATGTAA 57.438 37.500 19.38 0.00 0.00 2.41
2629 4165 5.877012 ACTCAATAACCATAGCACTGACAAG 59.123 40.000 0.00 0.00 0.00 3.16
2647 4183 5.105106 TGACAAGTCACTGGTTGAAGTTCTA 60.105 40.000 4.17 0.00 35.39 2.10
2678 4214 5.695363 CACTATGTAGCTGATCATCTGTTGG 59.305 44.000 9.34 0.00 0.00 3.77
2739 4275 1.364721 CGCCATTCGTATGTGGACAA 58.635 50.000 1.16 0.00 37.72 3.18
2793 4329 8.871125 ACTTATAGAAGTGGTGAAGAAGAAAGA 58.129 33.333 1.03 0.00 44.50 2.52
2827 4363 4.464008 TGGAGAAGTCTGAAGCAAACAAT 58.536 39.130 0.00 0.00 0.00 2.71
2841 4377 0.322816 AACAATGCCGATGCTGAGGT 60.323 50.000 0.00 0.00 38.71 3.85
2925 4461 5.136105 ACCCCTTAACATCGGTAGTACTAG 58.864 45.833 1.87 0.00 0.00 2.57
2965 4501 7.138736 CCAAATTAACCAACAGTAACTCAGTG 58.861 38.462 0.00 0.00 0.00 3.66
3058 4594 2.082231 CAGACAGCAACAGGAAGATGG 58.918 52.381 0.00 0.00 0.00 3.51
3075 4660 0.673333 TGGACATGTTACTGGCAGCG 60.673 55.000 15.89 0.00 0.00 5.18
3105 4690 1.000896 ATCCTGAAAACTGCCCCCG 60.001 57.895 0.00 0.00 0.00 5.73
3124 4709 1.808411 GTCTCCGACATGCTGGAAAA 58.192 50.000 7.81 0.00 32.89 2.29
3150 4735 4.784177 TGCATTATGATGAAGCCTTCTCA 58.216 39.130 5.96 7.42 35.16 3.27
3154 4739 0.107993 TGATGAAGCCTTCTCAGCGG 60.108 55.000 5.96 0.00 34.64 5.52
3164 4749 2.765250 TTCTCAGCGGCGTGGAGAAC 62.765 60.000 28.58 5.91 41.38 3.01
3181 4766 5.754890 TGGAGAACACTACGGTTAAAACTTC 59.245 40.000 0.00 0.00 0.00 3.01
3199 4784 2.328989 CAGGTGTGCGTGCAACTG 59.671 61.111 10.93 10.93 46.06 3.16
3232 4817 3.289834 CAGCCTTGCAGGTGCGTT 61.290 61.111 0.00 0.00 45.83 4.84
3233 4818 1.965930 CAGCCTTGCAGGTGCGTTA 60.966 57.895 0.00 0.00 45.83 3.18
3234 4819 1.002134 AGCCTTGCAGGTGCGTTAT 60.002 52.632 0.00 0.00 45.83 1.89
3235 4820 1.137404 GCCTTGCAGGTGCGTTATG 59.863 57.895 0.00 0.00 45.83 1.90
3238 4823 0.874390 CTTGCAGGTGCGTTATGTGT 59.126 50.000 0.00 0.00 45.83 3.72
3242 4827 1.225855 CAGGTGCGTTATGTGTGTGT 58.774 50.000 0.00 0.00 0.00 3.72
3275 4860 2.612672 TCAACAAATGGACACGCGTTAA 59.387 40.909 10.22 0.00 0.00 2.01
3323 4908 1.569479 GCAGAACTGTGGGCTCGTTC 61.569 60.000 3.77 0.00 37.80 3.95
3349 4934 4.273235 TGGATATGCTTGCTAATGAACACG 59.727 41.667 0.00 0.00 0.00 4.49
3377 4962 0.032912 TCCGCCTATGAGGTGTGGTA 60.033 55.000 5.40 0.00 44.26 3.25
3386 4971 3.695830 TGAGGTGTGGTAGGATTTGTC 57.304 47.619 0.00 0.00 0.00 3.18
3388 4973 3.392947 TGAGGTGTGGTAGGATTTGTCAA 59.607 43.478 0.00 0.00 0.00 3.18
3390 4975 3.081804 GGTGTGGTAGGATTTGTCAAGG 58.918 50.000 0.00 0.00 0.00 3.61
3463 5048 8.313944 ACATATACATGTGTAGGGTAAAGTGA 57.686 34.615 16.94 0.00 43.89 3.41
3794 5379 1.414919 AGTCCGCCAACTGTAACTCAA 59.585 47.619 0.00 0.00 0.00 3.02
3949 5534 3.700038 ACAATAAGGGAGTCGAGGTAGTG 59.300 47.826 0.00 0.00 0.00 2.74
3952 5537 2.424733 GGGAGTCGAGGTAGTGGCC 61.425 68.421 0.00 0.00 0.00 5.36
4053 5638 1.878088 TGTACTCGAGCGAGAAACTGT 59.122 47.619 24.81 6.21 44.53 3.55
4072 5657 5.990668 ACTGTAGTCTGTTTCTTGGTCTTT 58.009 37.500 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 1.228894 TCCTCCTCCTTGACGCTGT 60.229 57.895 0.00 0.00 0.00 4.40
217 218 2.355193 GCTCCTCCTCCTTGACGCT 61.355 63.158 0.00 0.00 0.00 5.07
471 485 3.822192 CCGCCATCCTCGTCGTCA 61.822 66.667 0.00 0.00 0.00 4.35
608 639 7.254624 GGCAAAGTTCGGTAAATTGAACAAAAT 60.255 33.333 7.71 0.00 45.34 1.82
641 672 5.230306 CAGACGCGGATTTAAAACAAAAACA 59.770 36.000 12.47 0.00 0.00 2.83
648 679 3.425758 CCCTTCAGACGCGGATTTAAAAC 60.426 47.826 12.47 0.00 0.00 2.43
652 683 0.899720 ACCCTTCAGACGCGGATTTA 59.100 50.000 12.47 0.00 0.00 1.40
656 687 2.282958 AGACCCTTCAGACGCGGA 60.283 61.111 12.47 0.00 0.00 5.54
678 714 3.498961 TTCCAGCCTCCCAGGGTCA 62.499 63.158 5.01 0.00 43.92 4.02
688 724 4.394712 CGAGCGGGTTTCCAGCCT 62.395 66.667 7.24 0.00 38.58 4.58
695 736 3.300765 ACGGACTCGAGCGGGTTT 61.301 61.111 13.61 0.00 40.11 3.27
706 747 1.679032 GCCCTAAAATCAGCACGGACT 60.679 52.381 0.00 0.00 0.00 3.85
707 748 0.733150 GCCCTAAAATCAGCACGGAC 59.267 55.000 0.00 0.00 0.00 4.79
708 749 0.393808 GGCCCTAAAATCAGCACGGA 60.394 55.000 0.00 0.00 0.00 4.69
715 756 1.319614 GCAAGCCGGCCCTAAAATCA 61.320 55.000 26.15 0.00 0.00 2.57
736 777 2.888534 GATTTACGCGCCCGCTGA 60.889 61.111 5.73 0.00 39.32 4.26
769 812 1.474143 GCCTGGTGTCCTTAGAGCATC 60.474 57.143 0.00 0.00 0.00 3.91
770 813 0.543749 GCCTGGTGTCCTTAGAGCAT 59.456 55.000 0.00 0.00 0.00 3.79
771 814 1.888436 CGCCTGGTGTCCTTAGAGCA 61.888 60.000 0.00 0.00 0.00 4.26
772 815 1.153549 CGCCTGGTGTCCTTAGAGC 60.154 63.158 0.00 0.00 0.00 4.09
773 816 1.153549 GCGCCTGGTGTCCTTAGAG 60.154 63.158 9.31 0.00 0.00 2.43
774 817 1.605058 GAGCGCCTGGTGTCCTTAGA 61.605 60.000 2.29 0.00 0.00 2.10
775 818 1.153549 GAGCGCCTGGTGTCCTTAG 60.154 63.158 2.29 0.00 0.00 2.18
776 819 1.264749 ATGAGCGCCTGGTGTCCTTA 61.265 55.000 2.29 0.00 0.00 2.69
777 820 2.129555 AATGAGCGCCTGGTGTCCTT 62.130 55.000 2.29 2.55 0.00 3.36
778 821 2.596851 AATGAGCGCCTGGTGTCCT 61.597 57.895 2.29 0.00 0.00 3.85
779 822 2.045926 AATGAGCGCCTGGTGTCC 60.046 61.111 2.29 1.83 0.00 4.02
780 823 3.044059 GCAATGAGCGCCTGGTGTC 62.044 63.158 2.29 6.07 0.00 3.67
781 824 3.058160 GCAATGAGCGCCTGGTGT 61.058 61.111 2.29 0.00 0.00 4.16
792 835 2.359850 GTGGGGCTCGTGCAATGA 60.360 61.111 12.07 0.00 41.91 2.57
793 836 2.535485 TAGGTGGGGCTCGTGCAATG 62.535 60.000 12.07 0.00 41.91 2.82
794 837 2.297895 TAGGTGGGGCTCGTGCAAT 61.298 57.895 12.07 0.00 41.91 3.56
795 838 2.925706 TAGGTGGGGCTCGTGCAA 60.926 61.111 12.07 0.00 41.91 4.08
796 839 3.702048 GTAGGTGGGGCTCGTGCA 61.702 66.667 12.07 0.00 41.91 4.57
797 840 4.468689 GGTAGGTGGGGCTCGTGC 62.469 72.222 0.00 0.00 38.76 5.34
798 841 4.143333 CGGTAGGTGGGGCTCGTG 62.143 72.222 0.00 0.00 0.00 4.35
838 881 0.322456 TCAGCATACACCAGGGTTGC 60.322 55.000 5.65 5.65 0.00 4.17
839 882 2.019249 CATCAGCATACACCAGGGTTG 58.981 52.381 0.00 0.00 0.00 3.77
841 884 1.583556 TCATCAGCATACACCAGGGT 58.416 50.000 0.00 0.00 0.00 4.34
847 890 4.455533 TGTTCCTGTTTCATCAGCATACAC 59.544 41.667 0.00 0.00 34.47 2.90
850 893 4.696877 CACTGTTCCTGTTTCATCAGCATA 59.303 41.667 0.00 0.00 34.47 3.14
859 902 2.879026 GGGTCTTCACTGTTCCTGTTTC 59.121 50.000 0.00 0.00 0.00 2.78
866 909 1.671379 GGCGGGGTCTTCACTGTTC 60.671 63.158 0.00 0.00 0.00 3.18
876 919 2.754254 GATTTGTGGGGCGGGGTC 60.754 66.667 0.00 0.00 0.00 4.46
878 921 1.910772 TTTGATTTGTGGGGCGGGG 60.911 57.895 0.00 0.00 0.00 5.73
883 926 1.291906 GGGCGTTTGATTTGTGGGG 59.708 57.895 0.00 0.00 0.00 4.96
1193 2415 1.443872 GACGTACCTGGTCACGCAG 60.444 63.158 20.84 5.55 41.80 5.18
1454 2681 9.155975 GCAATCCATTACTTGTAGATCGATAAT 57.844 33.333 0.00 0.00 0.00 1.28
1457 2684 6.763355 AGCAATCCATTACTTGTAGATCGAT 58.237 36.000 0.00 0.00 0.00 3.59
1474 2701 2.738314 GCCACAACAAATCAAGCAATCC 59.262 45.455 0.00 0.00 0.00 3.01
1582 2814 9.359653 GGTAGTACCTTAATCATACTGACCTTA 57.640 37.037 12.41 0.00 34.73 2.69
1600 2832 6.861144 ACTAAATCGAACAAGAGGTAGTACC 58.139 40.000 11.73 11.73 38.99 3.34
1636 2868 6.816134 TTGCTAAGACATTCTTACATGCAA 57.184 33.333 13.14 13.14 41.31 4.08
1727 2962 3.165058 TGCAGAGTATAACAGCGAAGG 57.835 47.619 0.00 0.00 0.00 3.46
1731 2966 8.590470 CATTTCTATATGCAGAGTATAACAGCG 58.410 37.037 0.00 0.00 0.00 5.18
1787 3022 9.391006 ACTGTACTAAATGTTCACTCTTTTCAA 57.609 29.630 0.00 0.00 0.00 2.69
1807 3042 7.224167 GCATGGTGAGGTAGTATTTTACTGTAC 59.776 40.741 0.00 0.00 39.81 2.90
1808 3043 7.270047 GCATGGTGAGGTAGTATTTTACTGTA 58.730 38.462 0.00 0.00 39.81 2.74
1810 3045 5.527582 GGCATGGTGAGGTAGTATTTTACTG 59.472 44.000 0.00 0.00 39.81 2.74
1812 3047 4.820173 GGGCATGGTGAGGTAGTATTTTAC 59.180 45.833 0.00 0.00 0.00 2.01
1814 3049 3.372675 GGGGCATGGTGAGGTAGTATTTT 60.373 47.826 0.00 0.00 0.00 1.82
1815 3050 2.174854 GGGGCATGGTGAGGTAGTATTT 59.825 50.000 0.00 0.00 0.00 1.40
1816 3051 1.774856 GGGGCATGGTGAGGTAGTATT 59.225 52.381 0.00 0.00 0.00 1.89
1820 3055 0.759346 GTAGGGGCATGGTGAGGTAG 59.241 60.000 0.00 0.00 0.00 3.18
1824 3059 0.548031 ATGTGTAGGGGCATGGTGAG 59.452 55.000 0.00 0.00 0.00 3.51
1825 3060 0.998928 AATGTGTAGGGGCATGGTGA 59.001 50.000 0.00 0.00 0.00 4.02
1826 3061 1.851304 AAATGTGTAGGGGCATGGTG 58.149 50.000 0.00 0.00 0.00 4.17
1828 3063 3.297134 ACTAAATGTGTAGGGGCATGG 57.703 47.619 0.00 0.00 0.00 3.66
1829 3064 4.275936 GCTTACTAAATGTGTAGGGGCATG 59.724 45.833 0.00 0.00 0.00 4.06
1834 3369 8.421784 TCTGAATAGCTTACTAAATGTGTAGGG 58.578 37.037 0.00 0.00 30.45 3.53
1840 3375 9.944376 TTCTGTTCTGAATAGCTTACTAAATGT 57.056 29.630 9.06 0.00 30.45 2.71
1870 3405 4.142116 TGAAATAGGCGTTCGATTGAGGTA 60.142 41.667 0.00 0.00 0.00 3.08
1897 3432 9.158233 CTCAAGGATATTTGTTCATTTTTGCAT 57.842 29.630 0.00 0.00 0.00 3.96
1898 3433 7.118101 GCTCAAGGATATTTGTTCATTTTTGCA 59.882 33.333 0.00 0.00 0.00 4.08
1900 3435 7.669098 CGCTCAAGGATATTTGTTCATTTTTG 58.331 34.615 0.00 0.00 0.00 2.44
1924 3460 4.996113 GTGTTCAACACCTGTGCG 57.004 55.556 9.76 0.00 43.05 5.34
1941 3477 8.256611 ACAATCATACTTGTGTAGCTTTACAG 57.743 34.615 0.00 0.00 37.93 2.74
1942 3478 8.503196 CAACAATCATACTTGTGTAGCTTTACA 58.497 33.333 0.00 0.00 39.25 2.41
1957 3493 4.855388 CAGCAGCAAACTCAACAATCATAC 59.145 41.667 0.00 0.00 0.00 2.39
2048 3584 3.319198 GGACGTGGAGCCCCAAGA 61.319 66.667 7.29 0.00 45.59 3.02
2281 3817 6.796785 TCTGAGATTGAGTCCATGTTCATA 57.203 37.500 0.00 0.00 0.00 2.15
2298 3834 5.702670 GTCAACCATGAAGTGATTTCTGAGA 59.297 40.000 0.00 0.00 37.30 3.27
2310 3846 8.383619 CGTATAAAGAAAGAGTCAACCATGAAG 58.616 37.037 0.00 0.00 37.30 3.02
2352 3888 3.143807 TCCAGTGCAAAAGACAAAACG 57.856 42.857 0.00 0.00 0.00 3.60
2384 3920 9.643693 AAAAACAACCTGAAATATAGCTTCATG 57.356 29.630 0.00 0.00 32.53 3.07
2429 3965 9.565090 CAAAATCCTTCTGGAGATCATAATACA 57.435 33.333 0.00 0.00 46.91 2.29
2439 3975 2.224843 TGCAGCAAAATCCTTCTGGAGA 60.225 45.455 0.00 0.00 46.91 3.71
2514 4050 5.451908 CGTCATGCATTAGTTCACAAACTT 58.548 37.500 0.00 0.00 43.28 2.66
2530 4066 4.558860 GGAAAAAGATGTAAAGCGTCATGC 59.441 41.667 0.00 0.00 46.98 4.06
2531 4067 5.942872 AGGAAAAAGATGTAAAGCGTCATG 58.057 37.500 0.00 0.00 35.60 3.07
2567 4103 6.214191 TCAAATTGTTAGTTGAAACAGCCA 57.786 33.333 0.00 0.00 40.29 4.75
2629 4165 5.467063 CCTCTTTAGAACTTCAACCAGTGAC 59.533 44.000 0.00 0.00 35.39 3.67
2647 4183 4.406972 TGATCAGCTACATAGTGCCTCTTT 59.593 41.667 0.00 0.00 0.00 2.52
2678 4214 2.613133 GCTTCTCTTGATGCTCATCACC 59.387 50.000 11.71 0.00 46.49 4.02
2739 4275 4.022329 CCTTCAACCTTTCCATAAAAGCGT 60.022 41.667 0.00 0.00 42.63 5.07
2793 4329 7.979786 TCAGACTTCTCCAACCTTTCTATAT 57.020 36.000 0.00 0.00 0.00 0.86
2827 4363 1.960040 ATTCGACCTCAGCATCGGCA 61.960 55.000 0.00 0.00 44.61 5.69
2841 4377 2.353269 ACAACGTTTGCACTTGATTCGA 59.647 40.909 0.00 0.00 0.00 3.71
2925 4461 2.981859 TTTGGCTATCCGACCTCTTC 57.018 50.000 0.00 0.00 34.14 2.87
2965 4501 2.675348 GTGAACATAGAAGCAGGCACTC 59.325 50.000 0.00 0.00 34.60 3.51
3058 4594 0.721718 GACGCTGCCAGTAACATGTC 59.278 55.000 0.00 0.00 0.00 3.06
3075 4660 2.743636 TTCAGGATGTTGGAGACGAC 57.256 50.000 0.00 0.00 45.61 4.34
3147 4732 2.811317 GTTCTCCACGCCGCTGAG 60.811 66.667 0.00 0.00 0.00 3.35
3164 4749 4.212636 CACCTGGAAGTTTTAACCGTAGTG 59.787 45.833 0.00 0.00 0.00 2.74
3170 4755 2.287368 CGCACACCTGGAAGTTTTAACC 60.287 50.000 0.00 0.00 0.00 2.85
3181 4766 2.901840 AGTTGCACGCACACCTGG 60.902 61.111 0.00 0.00 0.00 4.45
3219 4804 0.874390 ACACATAACGCACCTGCAAG 59.126 50.000 0.00 0.00 42.21 4.01
3221 4806 0.533978 ACACACATAACGCACCTGCA 60.534 50.000 0.00 0.00 42.21 4.41
3222 4807 0.110238 CACACACATAACGCACCTGC 60.110 55.000 0.00 0.00 37.78 4.85
3223 4808 1.069973 CACACACACATAACGCACCTG 60.070 52.381 0.00 0.00 0.00 4.00
3224 4809 1.225855 CACACACACATAACGCACCT 58.774 50.000 0.00 0.00 0.00 4.00
3225 4810 0.385473 GCACACACACATAACGCACC 60.385 55.000 0.00 0.00 0.00 5.01
3226 4811 0.721155 CGCACACACACATAACGCAC 60.721 55.000 0.00 0.00 0.00 5.34
3227 4812 1.567050 CGCACACACACATAACGCA 59.433 52.632 0.00 0.00 0.00 5.24
3228 4813 1.792057 GCGCACACACACATAACGC 60.792 57.895 0.30 0.00 37.93 4.84
3229 4814 0.721155 GTGCGCACACACACATAACG 60.721 55.000 34.52 0.00 46.61 3.18
3230 4815 3.071495 GTGCGCACACACACATAAC 57.929 52.632 34.52 2.71 46.61 1.89
3275 4860 2.811431 TGCTGTGAATTTCGACCGAATT 59.189 40.909 5.65 0.00 33.79 2.17
3323 4908 3.069289 TCATTAGCAAGCATATCCAGCG 58.931 45.455 0.00 0.00 37.01 5.18
3364 4949 4.780554 TGACAAATCCTACCACACCTCATA 59.219 41.667 0.00 0.00 0.00 2.15
3377 4962 2.158475 TCCAACAGCCTTGACAAATCCT 60.158 45.455 0.00 0.00 0.00 3.24
3386 4971 3.018856 TGCTCATTATCCAACAGCCTTG 58.981 45.455 0.00 0.00 0.00 3.61
3388 4973 3.019564 GTTGCTCATTATCCAACAGCCT 58.980 45.455 0.00 0.00 38.85 4.58
3390 4975 3.733077 GCAGTTGCTCATTATCCAACAGC 60.733 47.826 4.78 4.78 42.03 4.40
3686 5271 1.340991 ACCATGAATTTGAGGGACGGG 60.341 52.381 0.00 0.00 0.00 5.28
3687 5272 1.745087 CACCATGAATTTGAGGGACGG 59.255 52.381 0.00 0.00 0.00 4.79
3688 5273 1.745087 CCACCATGAATTTGAGGGACG 59.255 52.381 0.00 0.00 0.00 4.79
3689 5274 3.085952 TCCACCATGAATTTGAGGGAC 57.914 47.619 0.00 0.00 0.00 4.46
3690 5275 3.269118 TGATCCACCATGAATTTGAGGGA 59.731 43.478 0.00 0.00 0.00 4.20
3699 5284 3.569277 CAGTGTTGTTGATCCACCATGAA 59.431 43.478 0.00 0.00 0.00 2.57
3794 5379 1.406069 CGCTCTTCACTATGTGCCCTT 60.406 52.381 0.00 0.00 32.98 3.95
3949 5534 0.893727 AGGATTTTGGTGTGTCGGCC 60.894 55.000 0.00 0.00 0.00 6.13
3952 5537 2.878406 ACTTGAGGATTTTGGTGTGTCG 59.122 45.455 0.00 0.00 0.00 4.35
4032 5617 2.292569 ACAGTTTCTCGCTCGAGTACAA 59.707 45.455 15.13 7.85 42.49 2.41
4053 5638 5.611374 CCTGAAAGACCAAGAAACAGACTA 58.389 41.667 0.00 0.00 34.07 2.59
4072 5657 1.210478 GGTGGCTCTCTTATTGCCTGA 59.790 52.381 0.00 0.00 46.23 3.86


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

AutoCloner maintained by Alex Coulton.