Multiple sequence alignment - TraesCS1D01G075800

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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 TraesCS1D01G075800 chr1D 100.000 3104 0 0 1 3104 58443208 58446311 0.000000e+00 5733.0
1 TraesCS1D01G075800 chr1D 92.927 2050 118 13 956 2997 58623051 58621021 0.000000e+00 2957.0
2 TraesCS1D01G075800 chr1D 81.028 1070 182 17 1008 2062 49426354 49425291 0.000000e+00 832.0
3 TraesCS1D01G075800 chr1D 81.413 1033 175 13 1042 2062 36618198 36617171 0.000000e+00 828.0
4 TraesCS1D01G075800 chr1D 80.076 1049 190 14 1024 2062 38584026 38582987 0.000000e+00 761.0
5 TraesCS1D01G075800 chr1D 82.239 518 90 2 2102 2618 36622707 36622191 2.200000e-121 446.0
6 TraesCS1D01G075800 chr1D 82.046 518 87 5 2106 2620 36616291 36615777 1.320000e-118 436.0
7 TraesCS1D01G075800 chr1A 92.528 2168 129 16 956 3104 57400154 57398001 0.000000e+00 3075.0
8 TraesCS1D01G075800 chr1A 93.307 1748 100 4 993 2740 57185036 57186766 0.000000e+00 2564.0
9 TraesCS1D01G075800 chr1A 81.704 1033 173 11 1042 2062 36188324 36187296 0.000000e+00 846.0
10 TraesCS1D01G075800 chr1A 82.308 520 90 2 2102 2620 36606744 36607262 1.700000e-122 449.0
11 TraesCS1D01G075800 chr1A 82.432 518 85 6 2106 2620 36637449 36637963 6.110000e-122 448.0
12 TraesCS1D01G075800 chr1A 87.871 371 31 8 2739 3104 57187538 57187899 1.030000e-114 424.0
13 TraesCS1D01G075800 chr1A 88.976 127 14 0 426 552 372284307 372284433 1.150000e-34 158.0
14 TraesCS1D01G075800 chr1A 88.550 131 10 4 426 553 518539355 518539227 1.490000e-33 154.0
15 TraesCS1D01G075800 chr1B 94.337 777 36 5 2331 3104 94211311 94210540 0.000000e+00 1184.0
16 TraesCS1D01G075800 chr1B 81.564 1036 175 11 1039 2062 56501805 56500774 0.000000e+00 841.0
17 TraesCS1D01G075800 chr1B 80.117 1026 178 18 1042 2053 57015900 57016913 0.000000e+00 741.0
18 TraesCS1D01G075800 chr1B 81.853 518 90 3 2102 2618 56499901 56499387 1.710000e-117 433.0
19 TraesCS1D01G075800 chr3B 86.257 553 51 16 1 540 535516409 535516949 7.460000e-161 577.0
20 TraesCS1D01G075800 chr3B 88.717 452 37 6 1 440 98022471 98022022 9.790000e-150 540.0
21 TraesCS1D01G075800 chr3B 89.209 417 41 4 28 442 554571396 554570982 4.590000e-143 518.0
22 TraesCS1D01G075800 chr6B 90.112 445 38 4 1 442 551973273 551972832 9.660000e-160 573.0
23 TraesCS1D01G075800 chr6B 89.083 458 29 13 1 442 606060752 606061204 1.630000e-152 549.0
24 TraesCS1D01G075800 chr6B 90.833 120 11 0 426 545 196071388 196071507 8.910000e-36 161.0
25 TraesCS1D01G075800 chr7D 87.417 453 50 5 1 448 1533246 1532796 5.940000e-142 514.0
26 TraesCS1D01G075800 chr7D 87.982 441 43 8 10 442 36260782 36261220 2.130000e-141 512.0
27 TraesCS1D01G075800 chrUn 87.615 436 42 9 22 448 349853946 349853514 2.150000e-136 496.0
28 TraesCS1D01G075800 chr5B 87.615 436 42 9 22 448 480803850 480803418 2.150000e-136 496.0
29 TraesCS1D01G075800 chr7A 89.764 127 13 0 426 552 644460147 644460273 2.480000e-36 163.0
30 TraesCS1D01G075800 chr6A 89.062 128 14 0 426 553 542407365 542407238 3.200000e-35 159.0
31 TraesCS1D01G075800 chr6A 88.281 128 15 0 426 553 91807278 91807405 1.490000e-33 154.0
32 TraesCS1D01G075800 chr6A 88.281 128 15 0 426 553 329083296 329083423 1.490000e-33 154.0
33 TraesCS1D01G075800 chr2A 88.976 127 14 0 426 552 774467605 774467479 1.150000e-34 158.0
34 TraesCS1D01G075800 chr4A 88.800 125 14 0 429 553 595870705 595870581 1.490000e-33 154.0
35 TraesCS1D01G075800 chr3A 96.970 33 1 0 643 675 513522809 513522841 4.320000e-04 56.5


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 TraesCS1D01G075800 chr1D 58443208 58446311 3103 False 5733 5733 100.000000 1 3104 1 chr1D.!!$F1 3103
1 TraesCS1D01G075800 chr1D 58621021 58623051 2030 True 2957 2957 92.927000 956 2997 1 chr1D.!!$R3 2041
2 TraesCS1D01G075800 chr1D 49425291 49426354 1063 True 832 832 81.028000 1008 2062 1 chr1D.!!$R2 1054
3 TraesCS1D01G075800 chr1D 38582987 38584026 1039 True 761 761 80.076000 1024 2062 1 chr1D.!!$R1 1038
4 TraesCS1D01G075800 chr1D 36615777 36622707 6930 True 570 828 81.899333 1042 2620 3 chr1D.!!$R4 1578
5 TraesCS1D01G075800 chr1A 57398001 57400154 2153 True 3075 3075 92.528000 956 3104 1 chr1A.!!$R2 2148
6 TraesCS1D01G075800 chr1A 57185036 57187899 2863 False 1494 2564 90.589000 993 3104 2 chr1A.!!$F4 2111
7 TraesCS1D01G075800 chr1A 36187296 36188324 1028 True 846 846 81.704000 1042 2062 1 chr1A.!!$R1 1020
8 TraesCS1D01G075800 chr1A 36606744 36607262 518 False 449 449 82.308000 2102 2620 1 chr1A.!!$F1 518
9 TraesCS1D01G075800 chr1A 36637449 36637963 514 False 448 448 82.432000 2106 2620 1 chr1A.!!$F2 514
10 TraesCS1D01G075800 chr1B 94210540 94211311 771 True 1184 1184 94.337000 2331 3104 1 chr1B.!!$R1 773
11 TraesCS1D01G075800 chr1B 57015900 57016913 1013 False 741 741 80.117000 1042 2053 1 chr1B.!!$F1 1011
12 TraesCS1D01G075800 chr1B 56499387 56501805 2418 True 637 841 81.708500 1039 2618 2 chr1B.!!$R2 1579
13 TraesCS1D01G075800 chr3B 535516409 535516949 540 False 577 577 86.257000 1 540 1 chr3B.!!$F1 539

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
648 683 0.027324 GTGCTATTGCGAGCTCAAGC 59.973 55.0 15.4 10.64 43.27 4.01 F
649 684 0.107993 TGCTATTGCGAGCTCAAGCT 60.108 50.0 15.4 3.71 45.57 3.74 F
804 839 0.179004 TTTGCCCACACCTCATTCGT 60.179 50.0 0.0 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 5233 0.178924 ACTCCTTGCTGCCCCATTTT 60.179 50.000 0.0 0.0 0.00 1.82 R
1760 5240 0.322906 AGGCTTAACTCCTTGCTGCC 60.323 55.000 0.0 0.0 39.19 4.85 R
2409 6734 1.522580 GAACGGAGCTGGGAGCATC 60.523 63.158 0.0 0.0 45.56 3.91 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
25 26 5.397240 CGAACCGAAAAACCATACAGAAAAC 59.603 40.000 0.00 0.00 0.00 2.43
26 27 5.838531 ACCGAAAAACCATACAGAAAACA 57.161 34.783 0.00 0.00 0.00 2.83
36 37 6.110033 ACCATACAGAAAACAAAACCAAACC 58.890 36.000 0.00 0.00 0.00 3.27
79 80 7.730364 ATGGTTTCGATATGGTATGAACTTC 57.270 36.000 0.00 0.00 0.00 3.01
81 82 7.335627 TGGTTTCGATATGGTATGAACTTCTT 58.664 34.615 0.00 0.00 0.00 2.52
145 147 4.908966 CCGAACGGTTTACGAATAAACT 57.091 40.909 4.99 0.00 46.42 2.66
277 281 8.038492 AGTCATACTTCTCTTCAAAAGAATGC 57.962 34.615 0.00 0.00 37.02 3.56
285 289 5.034554 TCTTCAAAAGAATGCTAAGCACG 57.965 39.130 0.00 0.00 35.13 5.34
295 299 1.553248 TGCTAAGCACGTCCATAACCT 59.447 47.619 0.00 0.00 31.71 3.50
297 301 3.007635 GCTAAGCACGTCCATAACCTTT 58.992 45.455 0.00 0.00 0.00 3.11
528 563 6.258287 CCGTATAAATCGAACCATGTAAACCA 59.742 38.462 0.00 0.00 0.00 3.67
540 575 8.880878 AACCATGTAAACCAAATAAACAGAAC 57.119 30.769 0.00 0.00 0.00 3.01
541 576 8.012957 ACCATGTAAACCAAATAAACAGAACA 57.987 30.769 0.00 0.00 0.00 3.18
542 577 7.923878 ACCATGTAAACCAAATAAACAGAACAC 59.076 33.333 0.00 0.00 0.00 3.32
543 578 7.923344 CCATGTAAACCAAATAAACAGAACACA 59.077 33.333 0.00 0.00 0.00 3.72
544 579 8.751335 CATGTAAACCAAATAAACAGAACACAC 58.249 33.333 0.00 0.00 0.00 3.82
545 580 6.967767 TGTAAACCAAATAAACAGAACACACG 59.032 34.615 0.00 0.00 0.00 4.49
546 581 4.561735 ACCAAATAAACAGAACACACGG 57.438 40.909 0.00 0.00 0.00 4.94
547 582 4.200874 ACCAAATAAACAGAACACACGGA 58.799 39.130 0.00 0.00 0.00 4.69
567 602 4.505217 GACGAGCGGCGCATGTTG 62.505 66.667 35.02 19.49 46.04 3.33
576 611 2.050168 CGCATGTTGGGTGCACAC 60.050 61.111 20.43 17.25 42.62 3.82
577 612 2.554636 CGCATGTTGGGTGCACACT 61.555 57.895 21.89 0.00 42.62 3.55
578 613 1.741525 GCATGTTGGGTGCACACTT 59.258 52.632 21.89 4.51 42.08 3.16
579 614 0.598158 GCATGTTGGGTGCACACTTG 60.598 55.000 21.89 17.05 42.08 3.16
601 636 2.475187 CGGAGCAAGAAGAAAATGAGCG 60.475 50.000 0.00 0.00 0.00 5.03
602 637 2.513893 GAGCAAGAAGAAAATGAGCGC 58.486 47.619 0.00 0.00 0.00 5.92
603 638 1.135859 AGCAAGAAGAAAATGAGCGCG 60.136 47.619 0.00 0.00 0.00 6.86
604 639 1.887320 CAAGAAGAAAATGAGCGCGG 58.113 50.000 8.83 0.00 0.00 6.46
605 640 1.464608 CAAGAAGAAAATGAGCGCGGA 59.535 47.619 8.83 0.00 0.00 5.54
606 641 2.029838 AGAAGAAAATGAGCGCGGAT 57.970 45.000 8.83 0.00 0.00 4.18
607 642 1.667724 AGAAGAAAATGAGCGCGGATG 59.332 47.619 8.83 0.00 0.00 3.51
608 643 1.665679 GAAGAAAATGAGCGCGGATGA 59.334 47.619 8.83 0.00 0.00 2.92
609 644 1.737838 AGAAAATGAGCGCGGATGAA 58.262 45.000 8.83 0.00 0.00 2.57
610 645 2.083774 AGAAAATGAGCGCGGATGAAA 58.916 42.857 8.83 0.00 0.00 2.69
611 646 2.159517 AGAAAATGAGCGCGGATGAAAC 60.160 45.455 8.83 0.00 0.00 2.78
612 647 0.451783 AAATGAGCGCGGATGAAACC 59.548 50.000 8.83 0.00 0.00 3.27
623 658 2.985896 GGATGAAACCGATTGAGGTGA 58.014 47.619 0.00 0.00 45.21 4.02
624 659 2.678336 GGATGAAACCGATTGAGGTGAC 59.322 50.000 0.00 0.00 45.21 3.67
626 661 1.418264 TGAAACCGATTGAGGTGACCA 59.582 47.619 3.63 0.00 45.21 4.02
627 662 2.158740 TGAAACCGATTGAGGTGACCAA 60.159 45.455 3.63 0.00 45.21 3.67
628 663 2.649531 AACCGATTGAGGTGACCAAA 57.350 45.000 3.63 0.00 45.21 3.28
630 665 1.420138 ACCGATTGAGGTGACCAAAGT 59.580 47.619 3.63 0.00 44.07 2.66
632 667 1.197721 CGATTGAGGTGACCAAAGTGC 59.802 52.381 3.63 0.00 0.00 4.40
634 669 3.674997 GATTGAGGTGACCAAAGTGCTA 58.325 45.455 3.63 0.00 0.00 3.49
636 671 3.788227 TGAGGTGACCAAAGTGCTATT 57.212 42.857 3.63 0.00 0.00 1.73
637 672 3.411446 TGAGGTGACCAAAGTGCTATTG 58.589 45.455 3.63 0.00 0.00 1.90
639 674 1.135689 GGTGACCAAAGTGCTATTGCG 60.136 52.381 0.00 0.00 43.34 4.85
640 675 1.804151 GTGACCAAAGTGCTATTGCGA 59.196 47.619 0.00 0.00 43.34 5.10
642 677 0.804989 ACCAAAGTGCTATTGCGAGC 59.195 50.000 0.00 0.00 43.34 5.03
646 681 2.099141 AAGTGCTATTGCGAGCTCAA 57.901 45.000 15.40 1.93 43.27 3.02
647 682 1.649664 AGTGCTATTGCGAGCTCAAG 58.350 50.000 15.40 0.00 43.27 3.02
648 683 0.027324 GTGCTATTGCGAGCTCAAGC 59.973 55.000 15.40 10.64 43.27 4.01
649 684 0.107993 TGCTATTGCGAGCTCAAGCT 60.108 50.000 15.40 3.71 45.57 3.74
671 706 6.057627 CTCATATGAGCTTGGATGAACAAC 57.942 41.667 19.47 0.00 35.13 3.32
672 707 5.499313 TCATATGAGCTTGGATGAACAACA 58.501 37.500 0.00 0.00 0.00 3.33
673 708 5.945191 TCATATGAGCTTGGATGAACAACAA 59.055 36.000 0.00 0.00 0.00 2.83
674 709 6.433716 TCATATGAGCTTGGATGAACAACAAA 59.566 34.615 0.00 0.00 0.00 2.83
675 710 5.733620 ATGAGCTTGGATGAACAACAAAT 57.266 34.783 0.00 0.00 0.00 2.32
676 711 5.534207 TGAGCTTGGATGAACAACAAATT 57.466 34.783 0.00 0.00 0.00 1.82
679 714 4.984161 AGCTTGGATGAACAACAAATTTCG 59.016 37.500 0.00 0.00 0.00 3.46
680 715 4.981674 GCTTGGATGAACAACAAATTTCGA 59.018 37.500 0.00 0.00 0.00 3.71
681 716 5.461737 GCTTGGATGAACAACAAATTTCGAA 59.538 36.000 0.00 0.00 0.00 3.71
682 717 6.019156 GCTTGGATGAACAACAAATTTCGAAA 60.019 34.615 13.91 13.91 0.00 3.46
684 719 7.834068 TGGATGAACAACAAATTTCGAAAAA 57.166 28.000 15.66 0.00 0.00 1.94
685 720 8.430801 TGGATGAACAACAAATTTCGAAAAAT 57.569 26.923 15.66 4.14 36.64 1.82
686 721 9.534565 TGGATGAACAACAAATTTCGAAAAATA 57.465 25.926 15.66 0.00 33.93 1.40
734 769 6.808008 TTTGGCAAGAAAATTGAAAACACA 57.192 29.167 0.00 0.00 0.00 3.72
735 770 5.793026 TGGCAAGAAAATTGAAAACACAC 57.207 34.783 0.00 0.00 0.00 3.82
736 771 5.486526 TGGCAAGAAAATTGAAAACACACT 58.513 33.333 0.00 0.00 0.00 3.55
738 773 6.429385 TGGCAAGAAAATTGAAAACACACTTT 59.571 30.769 0.00 0.00 0.00 2.66
739 774 7.040823 TGGCAAGAAAATTGAAAACACACTTTT 60.041 29.630 0.00 0.00 36.10 2.27
765 800 6.279513 TGAACCAATTCAAAACACACTTCT 57.720 33.333 0.00 0.00 41.99 2.85
767 802 6.589523 TGAACCAATTCAAAACACACTTCTTG 59.410 34.615 0.00 0.00 41.99 3.02
768 803 5.418676 ACCAATTCAAAACACACTTCTTGG 58.581 37.500 0.00 0.00 37.29 3.61
770 805 5.750067 CCAATTCAAAACACACTTCTTGGAG 59.250 40.000 0.00 0.00 33.99 3.86
771 806 4.370364 TTCAAAACACACTTCTTGGAGC 57.630 40.909 0.00 0.00 0.00 4.70
775 810 1.800805 ACACACTTCTTGGAGCATCG 58.199 50.000 0.00 0.00 34.37 3.84
776 811 1.344438 ACACACTTCTTGGAGCATCGA 59.656 47.619 0.00 0.00 34.37 3.59
780 815 3.438087 ACACTTCTTGGAGCATCGATTTG 59.562 43.478 0.00 0.00 34.37 2.32
782 817 4.074970 ACTTCTTGGAGCATCGATTTGTT 58.925 39.130 0.00 0.00 34.37 2.83
783 818 4.520492 ACTTCTTGGAGCATCGATTTGTTT 59.480 37.500 0.00 0.00 34.37 2.83
785 820 5.452078 TCTTGGAGCATCGATTTGTTTTT 57.548 34.783 0.00 0.00 34.37 1.94
804 839 0.179004 TTTGCCCACACCTCATTCGT 60.179 50.000 0.00 0.00 0.00 3.85
811 846 3.747099 CACACCTCATTCGTGGATTTC 57.253 47.619 0.00 0.00 35.46 2.17
812 847 3.073678 CACACCTCATTCGTGGATTTCA 58.926 45.455 0.00 0.00 35.46 2.69
814 849 3.941483 ACACCTCATTCGTGGATTTCATC 59.059 43.478 0.00 0.00 35.46 2.92
815 850 3.001634 CACCTCATTCGTGGATTTCATCG 59.998 47.826 0.00 0.00 0.00 3.84
816 851 2.032549 CCTCATTCGTGGATTTCATCGC 60.033 50.000 0.00 0.00 0.00 4.58
817 852 2.609002 CTCATTCGTGGATTTCATCGCA 59.391 45.455 0.00 0.00 0.00 5.10
819 854 3.438434 TCATTCGTGGATTTCATCGCAAA 59.562 39.130 0.00 0.00 0.00 3.68
820 855 3.906014 TTCGTGGATTTCATCGCAAAA 57.094 38.095 0.00 0.00 0.00 2.44
821 856 3.906014 TCGTGGATTTCATCGCAAAAA 57.094 38.095 0.00 0.00 0.00 1.94
861 896 3.791973 AAAACATCAACGTTTCCTGCA 57.208 38.095 0.00 0.00 38.13 4.41
862 897 3.791973 AAACATCAACGTTTCCTGCAA 57.208 38.095 0.00 0.00 33.90 4.08
863 898 3.791973 AACATCAACGTTTCCTGCAAA 57.208 38.095 0.00 0.00 0.00 3.68
864 899 3.791973 ACATCAACGTTTCCTGCAAAA 57.208 38.095 0.00 0.00 0.00 2.44
865 900 4.116747 ACATCAACGTTTCCTGCAAAAA 57.883 36.364 0.00 0.00 0.00 1.94
927 962 6.827586 TTTAAAATTTGCTATCCACGAGGT 57.172 33.333 0.00 0.00 35.89 3.85
928 963 7.925043 TTTAAAATTTGCTATCCACGAGGTA 57.075 32.000 0.00 0.00 35.89 3.08
930 965 6.827586 AAAATTTGCTATCCACGAGGTAAA 57.172 33.333 0.00 0.00 35.89 2.01
931 966 7.404671 AAAATTTGCTATCCACGAGGTAAAT 57.595 32.000 0.00 0.00 35.89 1.40
932 967 6.619801 AATTTGCTATCCACGAGGTAAATC 57.380 37.500 0.00 0.00 35.89 2.17
957 992 2.125753 CAGGCGCCTGACTCTGTC 60.126 66.667 46.72 7.85 46.30 3.51
959 994 3.695606 GGCGCCTGACTCTGTCCA 61.696 66.667 22.15 0.00 0.00 4.02
962 997 0.884704 GCGCCTGACTCTGTCCAAAA 60.885 55.000 0.00 0.00 0.00 2.44
969 1004 4.884164 CCTGACTCTGTCCAAAAGAAAACT 59.116 41.667 0.00 0.00 0.00 2.66
972 1007 6.180472 TGACTCTGTCCAAAAGAAAACTCTT 58.820 36.000 0.00 0.00 0.00 2.85
990 1029 1.808945 CTTAGCCACTCCACAAGCAAG 59.191 52.381 0.00 0.00 0.00 4.01
997 1036 0.249868 CTCCACAAGCAAGACGGTGA 60.250 55.000 0.00 0.00 33.16 4.02
1003 1042 1.237285 AAGCAAGACGGTGACCATGC 61.237 55.000 1.11 6.51 0.00 4.06
1029 1068 0.612174 TGCCTCGCTTCTACTCCACT 60.612 55.000 0.00 0.00 0.00 4.00
1605 5085 3.130516 TCGTTCTGAAGGTCTTATGCGAT 59.869 43.478 9.62 0.00 0.00 4.58
1664 5144 2.632996 TGATGTCGAAAGAAGGAGGTGT 59.367 45.455 0.00 0.00 45.01 4.16
1753 5233 0.804364 GGCATGCGATCTGTTCAACA 59.196 50.000 12.44 0.00 0.00 3.33
1760 5240 3.244976 GCGATCTGTTCAACAAAATGGG 58.755 45.455 0.00 0.00 0.00 4.00
1934 5416 3.117360 CAGGGATATTCCTCTTTGGGCTT 60.117 47.826 0.00 0.00 36.57 4.35
1986 5468 0.251916 TGACAAGCCGGGGTCTTATG 59.748 55.000 2.18 0.00 35.11 1.90
2084 6409 3.949754 GCCCATCAGATGATTGAAAGTGA 59.050 43.478 12.41 0.00 31.21 3.41
2088 6413 6.152323 CCCATCAGATGATTGAAAGTGAAACT 59.848 38.462 12.41 0.00 40.64 2.66
2400 6725 8.173542 TGATCATATGTTTTCATCAATGGAGG 57.826 34.615 1.90 0.00 41.25 4.30
2409 6734 0.107508 ATCAATGGAGGCGAGTGGTG 60.108 55.000 0.00 0.00 0.00 4.17
2623 6951 3.002348 GCAAGGTATCGATTTTTCGGAGG 59.998 47.826 1.71 0.00 0.00 4.30
2624 6952 4.439057 CAAGGTATCGATTTTTCGGAGGA 58.561 43.478 1.71 0.00 0.00 3.71
2625 6953 4.323553 AGGTATCGATTTTTCGGAGGAG 57.676 45.455 1.71 0.00 0.00 3.69
2640 6968 2.365617 GGAGGAGTCAGACACAGTTGAA 59.634 50.000 2.66 0.00 0.00 2.69
2722 7050 2.551270 TCTGGGTCTCTTGCTGGTATT 58.449 47.619 0.00 0.00 0.00 1.89
2905 8012 6.998802 AGGTATAGATATGTGCTCTTTCCAC 58.001 40.000 0.00 0.00 0.00 4.02
2918 8025 4.335416 CTCTTTCCACAAGAAGCCCAATA 58.665 43.478 0.00 0.00 35.40 1.90
3053 8161 3.447586 TCAGTGATGTGCTAAGGGTAGAC 59.552 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.247258 GGTTCGGTTTGGTTTTGTTTTCT 58.753 39.130 0.00 0.00 0.00 2.52
25 26 5.553290 AAAATTGGTTCGGTTTGGTTTTG 57.447 34.783 0.00 0.00 0.00 2.44
26 27 6.261158 CCATAAAATTGGTTCGGTTTGGTTTT 59.739 34.615 0.00 0.00 31.74 2.43
53 54 9.268268 GAAGTTCATACCATATCGAAACCATAA 57.732 33.333 0.00 0.00 0.00 1.90
56 57 6.884832 AGAAGTTCATACCATATCGAAACCA 58.115 36.000 5.50 0.00 0.00 3.67
57 58 7.787725 AAGAAGTTCATACCATATCGAAACC 57.212 36.000 5.50 0.00 0.00 3.27
61 62 9.304335 TGGTATAAGAAGTTCATACCATATCGA 57.696 33.333 22.35 7.13 45.81 3.59
159 162 7.234782 TGGTTGTTCTTCCCGAGATATATACAT 59.765 37.037 0.00 0.00 33.49 2.29
171 174 5.646360 ACTATTTGTATGGTTGTTCTTCCCG 59.354 40.000 0.00 0.00 0.00 5.14
229 233 7.644490 ACTACGTTACAAGAAAAATGAATGCA 58.356 30.769 0.00 0.00 0.00 3.96
262 266 5.084722 CGTGCTTAGCATTCTTTTGAAGAG 58.915 41.667 11.03 0.00 41.91 2.85
277 281 4.250464 TCAAAGGTTATGGACGTGCTTAG 58.750 43.478 8.99 0.00 0.00 2.18
285 289 4.402155 TGCATGGATTCAAAGGTTATGGAC 59.598 41.667 0.00 0.00 0.00 4.02
295 299 6.265876 AGTGTATATGCATGCATGGATTCAAA 59.734 34.615 37.43 19.51 39.62 2.69
297 301 5.318630 AGTGTATATGCATGCATGGATTCA 58.681 37.500 37.43 25.24 39.62 2.57
393 397 6.143118 CCAAAGTTGACGCGAATTTGAAAATA 59.857 34.615 15.93 0.00 33.69 1.40
504 539 7.236674 TGGTTTACATGGTTCGATTTATACG 57.763 36.000 0.00 0.00 0.00 3.06
513 548 7.364200 TCTGTTTATTTGGTTTACATGGTTCG 58.636 34.615 0.00 0.00 0.00 3.95
528 563 5.007332 GTCACTCCGTGTGTTCTGTTTATTT 59.993 40.000 5.84 0.00 46.27 1.40
541 576 4.039357 CCGCTCGTCACTCCGTGT 62.039 66.667 0.00 0.00 34.79 4.49
550 585 4.505217 CAACATGCGCCGCTCGTC 62.505 66.667 11.67 0.00 41.07 4.20
557 592 4.722855 GTGCACCCAACATGCGCC 62.723 66.667 5.22 0.00 45.75 6.53
561 596 3.573569 CAAGTGTGCACCCAACATG 57.426 52.632 15.69 5.50 0.00 3.21
577 612 2.884012 TCATTTTCTTCTTGCTCCGCAA 59.116 40.909 1.02 1.02 46.80 4.85
578 613 2.485426 CTCATTTTCTTCTTGCTCCGCA 59.515 45.455 0.00 0.00 36.47 5.69
579 614 2.730402 GCTCATTTTCTTCTTGCTCCGC 60.730 50.000 0.00 0.00 0.00 5.54
580 615 2.475187 CGCTCATTTTCTTCTTGCTCCG 60.475 50.000 0.00 0.00 0.00 4.63
581 616 2.730402 GCGCTCATTTTCTTCTTGCTCC 60.730 50.000 0.00 0.00 0.00 4.70
582 617 2.513893 GCGCTCATTTTCTTCTTGCTC 58.486 47.619 0.00 0.00 0.00 4.26
583 618 1.135859 CGCGCTCATTTTCTTCTTGCT 60.136 47.619 5.56 0.00 0.00 3.91
585 620 1.464608 TCCGCGCTCATTTTCTTCTTG 59.535 47.619 5.56 0.00 0.00 3.02
587 622 1.667724 CATCCGCGCTCATTTTCTTCT 59.332 47.619 5.56 0.00 0.00 2.85
588 623 1.665679 TCATCCGCGCTCATTTTCTTC 59.334 47.619 5.56 0.00 0.00 2.87
590 625 1.737838 TTCATCCGCGCTCATTTTCT 58.262 45.000 5.56 0.00 0.00 2.52
591 626 2.177173 GTTTCATCCGCGCTCATTTTC 58.823 47.619 5.56 0.00 0.00 2.29
592 627 1.135402 GGTTTCATCCGCGCTCATTTT 60.135 47.619 5.56 0.00 0.00 1.82
594 629 1.705337 CGGTTTCATCCGCGCTCATT 61.705 55.000 5.56 0.00 43.96 2.57
595 630 2.173669 CGGTTTCATCCGCGCTCAT 61.174 57.895 5.56 0.00 43.96 2.90
596 631 2.813474 CGGTTTCATCCGCGCTCA 60.813 61.111 5.56 0.00 43.96 4.26
603 638 2.678336 GTCACCTCAATCGGTTTCATCC 59.322 50.000 0.00 0.00 34.29 3.51
604 639 2.678336 GGTCACCTCAATCGGTTTCATC 59.322 50.000 0.00 0.00 34.29 2.92
605 640 2.039746 TGGTCACCTCAATCGGTTTCAT 59.960 45.455 0.00 0.00 34.29 2.57
606 641 1.418264 TGGTCACCTCAATCGGTTTCA 59.582 47.619 0.00 0.00 34.29 2.69
607 642 2.178912 TGGTCACCTCAATCGGTTTC 57.821 50.000 0.00 0.00 34.29 2.78
608 643 2.649531 TTGGTCACCTCAATCGGTTT 57.350 45.000 0.00 0.00 34.29 3.27
609 644 2.158667 ACTTTGGTCACCTCAATCGGTT 60.159 45.455 0.00 0.00 34.29 4.44
610 645 1.420138 ACTTTGGTCACCTCAATCGGT 59.580 47.619 0.00 0.00 37.93 4.69
611 646 1.806542 CACTTTGGTCACCTCAATCGG 59.193 52.381 0.00 0.00 0.00 4.18
612 647 1.197721 GCACTTTGGTCACCTCAATCG 59.802 52.381 0.00 0.00 0.00 3.34
613 648 2.508526 AGCACTTTGGTCACCTCAATC 58.491 47.619 0.00 0.00 0.00 2.67
615 650 3.788227 ATAGCACTTTGGTCACCTCAA 57.212 42.857 0.00 0.00 0.00 3.02
617 652 2.162408 GCAATAGCACTTTGGTCACCTC 59.838 50.000 0.00 0.00 41.58 3.85
618 653 2.162681 GCAATAGCACTTTGGTCACCT 58.837 47.619 0.00 0.00 41.58 4.00
619 654 1.135689 CGCAATAGCACTTTGGTCACC 60.136 52.381 0.00 0.00 42.27 4.02
622 657 1.202076 GCTCGCAATAGCACTTTGGTC 60.202 52.381 0.00 0.00 42.30 4.02
623 658 0.804989 GCTCGCAATAGCACTTTGGT 59.195 50.000 0.00 0.00 42.30 3.67
624 659 1.063174 GAGCTCGCAATAGCACTTTGG 59.937 52.381 0.00 0.00 45.30 3.28
626 661 2.099141 TGAGCTCGCAATAGCACTTT 57.901 45.000 9.64 0.00 45.30 2.66
627 662 2.005451 CTTGAGCTCGCAATAGCACTT 58.995 47.619 9.64 0.00 45.30 3.16
628 663 1.649664 CTTGAGCTCGCAATAGCACT 58.350 50.000 9.64 0.00 45.30 4.40
630 665 2.387309 GCTTGAGCTCGCAATAGCA 58.613 52.632 9.64 0.00 45.30 3.49
648 683 5.587443 TGTTGTTCATCCAAGCTCATATGAG 59.413 40.000 25.64 25.64 44.75 2.90
649 684 5.499313 TGTTGTTCATCCAAGCTCATATGA 58.501 37.500 5.07 5.07 0.00 2.15
650 685 5.823209 TGTTGTTCATCCAAGCTCATATG 57.177 39.130 0.00 0.00 0.00 1.78
652 687 6.839124 ATTTGTTGTTCATCCAAGCTCATA 57.161 33.333 0.00 0.00 0.00 2.15
653 688 5.733620 ATTTGTTGTTCATCCAAGCTCAT 57.266 34.783 0.00 0.00 0.00 2.90
657 692 4.981674 TCGAAATTTGTTGTTCATCCAAGC 59.018 37.500 0.00 0.00 0.00 4.01
658 693 7.462109 TTTCGAAATTTGTTGTTCATCCAAG 57.538 32.000 6.47 0.00 0.00 3.61
660 695 7.834068 TTTTTCGAAATTTGTTGTTCATCCA 57.166 28.000 12.12 0.00 0.00 3.41
710 745 7.040823 AGTGTGTTTTCAATTTTCTTGCCAAAA 60.041 29.630 0.00 0.00 0.00 2.44
712 747 5.936956 AGTGTGTTTTCAATTTTCTTGCCAA 59.063 32.000 0.00 0.00 0.00 4.52
713 748 5.486526 AGTGTGTTTTCAATTTTCTTGCCA 58.513 33.333 0.00 0.00 0.00 4.92
714 749 6.421377 AAGTGTGTTTTCAATTTTCTTGCC 57.579 33.333 0.00 0.00 0.00 4.52
742 777 6.279513 AGAAGTGTGTTTTGAATTGGTTCA 57.720 33.333 0.00 0.00 42.41 3.18
743 778 6.035975 CCAAGAAGTGTGTTTTGAATTGGTTC 59.964 38.462 0.00 0.00 32.02 3.62
744 779 5.874261 CCAAGAAGTGTGTTTTGAATTGGTT 59.126 36.000 0.00 0.00 32.02 3.67
745 780 5.186797 TCCAAGAAGTGTGTTTTGAATTGGT 59.813 36.000 0.00 0.00 36.79 3.67
747 782 5.232838 GCTCCAAGAAGTGTGTTTTGAATTG 59.767 40.000 0.00 0.00 0.00 2.32
748 783 5.105392 TGCTCCAAGAAGTGTGTTTTGAATT 60.105 36.000 0.00 0.00 0.00 2.17
751 786 3.351740 TGCTCCAAGAAGTGTGTTTTGA 58.648 40.909 0.00 0.00 0.00 2.69
752 787 3.781079 TGCTCCAAGAAGTGTGTTTTG 57.219 42.857 0.00 0.00 0.00 2.44
753 788 3.003689 CGATGCTCCAAGAAGTGTGTTTT 59.996 43.478 0.00 0.00 0.00 2.43
754 789 2.549754 CGATGCTCCAAGAAGTGTGTTT 59.450 45.455 0.00 0.00 0.00 2.83
756 791 1.344438 TCGATGCTCCAAGAAGTGTGT 59.656 47.619 0.00 0.00 0.00 3.72
757 792 2.084610 TCGATGCTCCAAGAAGTGTG 57.915 50.000 0.00 0.00 0.00 3.82
758 793 3.340814 AATCGATGCTCCAAGAAGTGT 57.659 42.857 0.00 0.00 0.00 3.55
759 794 3.438087 ACAAATCGATGCTCCAAGAAGTG 59.562 43.478 0.00 0.00 0.00 3.16
760 795 3.679389 ACAAATCGATGCTCCAAGAAGT 58.321 40.909 0.00 0.00 0.00 3.01
761 796 4.691860 AACAAATCGATGCTCCAAGAAG 57.308 40.909 0.00 0.00 0.00 2.85
762 797 5.452078 AAAACAAATCGATGCTCCAAGAA 57.548 34.783 0.00 0.00 0.00 2.52
763 798 5.452078 AAAAACAAATCGATGCTCCAAGA 57.548 34.783 0.00 0.00 0.00 3.02
783 818 1.339610 CGAATGAGGTGTGGGCAAAAA 59.660 47.619 0.00 0.00 0.00 1.94
785 820 0.179004 ACGAATGAGGTGTGGGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
786 821 0.888736 CACGAATGAGGTGTGGGCAA 60.889 55.000 0.00 0.00 0.00 4.52
787 822 1.302431 CACGAATGAGGTGTGGGCA 60.302 57.895 0.00 0.00 0.00 5.36
788 823 3.578456 CACGAATGAGGTGTGGGC 58.422 61.111 0.00 0.00 0.00 5.36
792 827 3.417069 TGAAATCCACGAATGAGGTGT 57.583 42.857 0.00 0.00 33.56 4.16
793 828 3.001634 CGATGAAATCCACGAATGAGGTG 59.998 47.826 0.00 0.00 41.39 4.00
794 829 3.198068 CGATGAAATCCACGAATGAGGT 58.802 45.455 0.00 0.00 41.39 3.85
795 830 2.032549 GCGATGAAATCCACGAATGAGG 60.033 50.000 0.00 0.00 41.39 3.86
796 831 2.609002 TGCGATGAAATCCACGAATGAG 59.391 45.455 0.00 0.00 41.39 2.90
798 833 3.403613 TTGCGATGAAATCCACGAATG 57.596 42.857 0.00 0.00 41.39 2.67
799 834 4.433186 TTTTGCGATGAAATCCACGAAT 57.567 36.364 0.00 0.00 41.39 3.34
801 836 3.906014 TTTTTGCGATGAAATCCACGA 57.094 38.095 0.00 0.00 41.39 4.35
840 875 4.116747 TGCAGGAAACGTTGATGTTTTT 57.883 36.364 0.00 0.00 41.89 1.94
841 876 3.791973 TGCAGGAAACGTTGATGTTTT 57.208 38.095 0.00 0.00 41.89 2.43
842 877 3.791973 TTGCAGGAAACGTTGATGTTT 57.208 38.095 0.00 1.17 44.36 2.83
844 879 3.791973 TTTTGCAGGAAACGTTGATGT 57.208 38.095 0.00 0.00 0.00 3.06
902 937 7.662897 ACCTCGTGGATAGCAAATTTTAAAAA 58.337 30.769 11.17 0.00 37.04 1.94
903 938 7.222000 ACCTCGTGGATAGCAAATTTTAAAA 57.778 32.000 11.17 2.51 37.04 1.52
904 939 6.827586 ACCTCGTGGATAGCAAATTTTAAA 57.172 33.333 11.17 0.00 37.04 1.52
905 940 7.925043 TTACCTCGTGGATAGCAAATTTTAA 57.075 32.000 11.17 0.00 37.04 1.52
906 941 7.925043 TTTACCTCGTGGATAGCAAATTTTA 57.075 32.000 11.17 0.00 37.04 1.52
908 943 6.039382 GGATTTACCTCGTGGATAGCAAATTT 59.961 38.462 11.17 0.00 37.04 1.82
911 946 4.448210 GGATTTACCTCGTGGATAGCAAA 58.552 43.478 11.17 3.08 37.04 3.68
912 947 4.067972 GGATTTACCTCGTGGATAGCAA 57.932 45.455 11.17 0.00 37.04 3.91
913 948 3.746045 GGATTTACCTCGTGGATAGCA 57.254 47.619 11.17 0.00 37.04 3.49
940 975 2.125753 GACAGAGTCAGGCGCCTG 60.126 66.667 44.24 44.24 44.86 4.85
941 976 3.386237 GGACAGAGTCAGGCGCCT 61.386 66.667 27.08 27.08 33.68 5.52
942 977 2.731691 TTTGGACAGAGTCAGGCGCC 62.732 60.000 21.89 21.89 33.68 6.53
943 978 0.884704 TTTTGGACAGAGTCAGGCGC 60.885 55.000 0.00 0.00 33.68 6.53
944 979 1.151668 CTTTTGGACAGAGTCAGGCG 58.848 55.000 0.00 0.00 33.68 5.52
945 980 2.550830 TCTTTTGGACAGAGTCAGGC 57.449 50.000 0.00 0.00 33.68 4.85
948 983 5.745227 AGAGTTTTCTTTTGGACAGAGTCA 58.255 37.500 0.00 0.00 33.68 3.41
949 984 6.685527 AAGAGTTTTCTTTTGGACAGAGTC 57.314 37.500 0.00 0.00 40.79 3.36
950 985 6.261158 GCTAAGAGTTTTCTTTTGGACAGAGT 59.739 38.462 0.00 0.00 40.79 3.24
952 987 5.531287 GGCTAAGAGTTTTCTTTTGGACAGA 59.469 40.000 0.00 0.00 40.79 3.41
953 988 5.299279 TGGCTAAGAGTTTTCTTTTGGACAG 59.701 40.000 0.00 0.00 40.79 3.51
954 989 5.067283 GTGGCTAAGAGTTTTCTTTTGGACA 59.933 40.000 0.00 0.00 40.79 4.02
955 990 5.299531 AGTGGCTAAGAGTTTTCTTTTGGAC 59.700 40.000 0.00 0.00 40.79 4.02
956 991 5.445964 AGTGGCTAAGAGTTTTCTTTTGGA 58.554 37.500 0.00 0.00 40.79 3.53
957 992 5.278512 GGAGTGGCTAAGAGTTTTCTTTTGG 60.279 44.000 0.00 0.00 40.79 3.28
959 994 5.299531 GTGGAGTGGCTAAGAGTTTTCTTTT 59.700 40.000 0.00 0.00 40.79 2.27
962 997 3.391296 TGTGGAGTGGCTAAGAGTTTTCT 59.609 43.478 0.00 0.00 34.29 2.52
969 1004 1.055849 TGCTTGTGGAGTGGCTAAGA 58.944 50.000 0.00 0.00 0.00 2.10
972 1007 1.055849 TCTTGCTTGTGGAGTGGCTA 58.944 50.000 0.00 0.00 0.00 3.93
990 1029 2.034879 CACTGGCATGGTCACCGTC 61.035 63.158 0.00 0.00 0.00 4.79
1003 1042 0.461548 TAGAAGCGAGGCATCACTGG 59.538 55.000 0.00 0.00 0.00 4.00
1605 5085 1.742324 CTCGCTGGCTCCTGCTATCA 61.742 60.000 14.41 0.00 38.49 2.15
1684 5164 2.688507 GTGGATGACCGTGCTATATGG 58.311 52.381 0.00 0.00 41.55 2.74
1753 5233 0.178924 ACTCCTTGCTGCCCCATTTT 60.179 50.000 0.00 0.00 0.00 1.82
1760 5240 0.322906 AGGCTTAACTCCTTGCTGCC 60.323 55.000 0.00 0.00 39.19 4.85
1934 5416 7.395772 TGAATATTTTTACTGCCTCATTCCACA 59.604 33.333 0.00 0.00 0.00 4.17
1986 5468 4.363999 AGTTGCGAGTAACATCATCTAGC 58.636 43.478 6.81 0.00 33.02 3.42
2093 6418 1.881973 GTGGAAATGCTCAGTTGCTCA 59.118 47.619 3.53 0.00 0.00 4.26
2094 6419 1.881973 TGTGGAAATGCTCAGTTGCTC 59.118 47.619 3.53 0.90 0.00 4.26
2095 6420 1.985473 TGTGGAAATGCTCAGTTGCT 58.015 45.000 3.53 0.00 0.00 3.91
2096 6421 3.728864 CGTATGTGGAAATGCTCAGTTGC 60.729 47.826 0.00 0.00 0.00 4.17
2097 6422 3.181507 CCGTATGTGGAAATGCTCAGTTG 60.182 47.826 0.00 0.00 0.00 3.16
2098 6423 3.009723 CCGTATGTGGAAATGCTCAGTT 58.990 45.455 0.00 0.00 0.00 3.16
2099 6424 2.027192 ACCGTATGTGGAAATGCTCAGT 60.027 45.455 0.00 0.00 0.00 3.41
2100 6425 2.632377 ACCGTATGTGGAAATGCTCAG 58.368 47.619 0.00 0.00 0.00 3.35
2400 6725 2.512515 GGGAGCATCACCACTCGC 60.513 66.667 0.00 0.00 38.47 5.03
2409 6734 1.522580 GAACGGAGCTGGGAGCATC 60.523 63.158 0.00 0.00 45.56 3.91
2623 6951 6.216569 TCAACTATTCAACTGTGTCTGACTC 58.783 40.000 9.51 6.13 0.00 3.36
2624 6952 6.161855 TCAACTATTCAACTGTGTCTGACT 57.838 37.500 9.51 0.00 0.00 3.41
2625 6953 7.426929 AATCAACTATTCAACTGTGTCTGAC 57.573 36.000 0.00 0.00 0.00 3.51
2753 7854 7.724287 TGAACTGAATGAAAAATGAATGACCA 58.276 30.769 0.00 0.00 0.00 4.02
2905 8012 4.599047 TTGGTGTTTATTGGGCTTCTTG 57.401 40.909 0.00 0.00 0.00 3.02
3053 8161 8.840321 TCAGAAATTCCTCAAACTAAAAGTGAG 58.160 33.333 0.00 0.00 38.81 3.51


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

AutoCloner maintained by Alex Coulton.