Multiple sequence alignment - TraesCS2D01G431200

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 TraesCS2D01G431200 chr2D 100.000 3335 0 0 1 3335 543590115 543586781 0.000000e+00 6159.0
1 TraesCS2D01G431200 chr2D 89.159 1771 95 41 635 2338 543532429 543530689 0.000000e+00 2117.0
2 TraesCS2D01G431200 chr2D 88.704 1620 91 47 838 2417 543762098 543760531 0.000000e+00 1893.0
3 TraesCS2D01G431200 chr2D 88.490 1642 86 50 838 2417 543813834 543812234 0.000000e+00 1890.0
4 TraesCS2D01G431200 chr2D 93.031 904 56 3 2432 3334 543809598 543808701 0.000000e+00 1314.0
5 TraesCS2D01G431200 chr2D 92.920 904 57 3 2432 3334 543757862 543756965 0.000000e+00 1308.0
6 TraesCS2D01G431200 chr2D 87.923 621 64 7 1 618 574466100 574465488 0.000000e+00 721.0
7 TraesCS2D01G431200 chr2D 86.613 620 78 4 1 618 315847185 315847801 0.000000e+00 680.0
8 TraesCS2D01G431200 chr2D 92.651 381 28 0 1 381 255313185 255312805 1.750000e-152 549.0
9 TraesCS2D01G431200 chr2D 94.167 240 13 1 3097 3335 543760370 543760131 6.800000e-97 364.0
10 TraesCS2D01G431200 chr2D 93.333 240 15 1 3097 3335 543812080 543811841 1.470000e-93 353.0
11 TraesCS2D01G431200 chr2D 92.391 92 7 0 838 929 543815124 543815033 7.510000e-27 132.0
12 TraesCS2D01G431200 chr2B 87.712 1652 103 46 644 2232 649371051 649369437 0.000000e+00 1834.0
13 TraesCS2D01G431200 chr2B 87.106 1396 107 35 961 2331 648931528 648930181 0.000000e+00 1513.0
14 TraesCS2D01G431200 chr2B 86.822 387 23 10 1968 2338 649192246 649191872 1.110000e-109 407.0
15 TraesCS2D01G431200 chr2B 89.151 212 21 2 615 826 648935336 648935127 2.550000e-66 263.0
16 TraesCS2D01G431200 chr2B 85.246 183 13 9 2248 2417 649367765 649367584 3.420000e-40 176.0
17 TraesCS2D01G431200 chr2B 96.250 80 3 0 2432 2511 649367602 649367523 7.510000e-27 132.0
18 TraesCS2D01G431200 chr2A 86.187 1419 122 42 961 2338 686523703 686522318 0.000000e+00 1467.0
19 TraesCS2D01G431200 chr2A 85.946 1416 128 40 961 2338 686614576 686613194 0.000000e+00 1447.0
20 TraesCS2D01G431200 chr2A 85.744 1424 124 47 961 2338 686297113 686295723 0.000000e+00 1432.0
21 TraesCS2D01G431200 chr2A 85.684 1425 124 42 961 2338 686322696 686321305 0.000000e+00 1428.0
22 TraesCS2D01G431200 chr2A 89.815 216 18 3 615 826 686323003 686322788 1.180000e-69 274.0
23 TraesCS2D01G431200 chr2A 89.815 216 18 3 615 826 686524010 686523795 1.180000e-69 274.0
24 TraesCS2D01G431200 chr2A 89.815 216 18 3 615 826 686614883 686614668 1.180000e-69 274.0
25 TraesCS2D01G431200 chr2A 91.489 188 14 2 615 800 686623611 686623424 1.190000e-64 257.0
26 TraesCS2D01G431200 chr2A 90.256 195 17 2 634 826 686297399 686297205 1.540000e-63 254.0
27 TraesCS2D01G431200 chr4D 92.071 618 45 2 1 618 505031394 505032007 0.000000e+00 867.0
28 TraesCS2D01G431200 chr4D 88.207 619 67 5 1 618 70603629 70603016 0.000000e+00 734.0
29 TraesCS2D01G431200 chr4A 88.169 617 69 2 1 617 465770612 465771224 0.000000e+00 732.0
30 TraesCS2D01G431200 chr1D 87.762 621 65 4 1 618 365877663 365878275 0.000000e+00 715.0
31 TraesCS2D01G431200 chr1D 95.745 47 2 0 564 610 453546809 453546763 3.570000e-10 76.8
32 TraesCS2D01G431200 chr5D 87.440 621 67 4 1 618 545717173 545716561 0.000000e+00 704.0
33 TraesCS2D01G431200 chr3D 85.251 617 86 5 1 616 611661801 611661189 6.070000e-177 630.0
34 TraesCS2D01G431200 chr3D 91.228 114 10 0 502 615 351245233 351245346 4.450000e-34 156.0
35 TraesCS2D01G431200 chr6B 97.059 34 1 0 564 597 151905061 151905094 1.290000e-04 58.4


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 TraesCS2D01G431200 chr2D 543586781 543590115 3334 True 6159.000000 6159 100.000000 1 3335 1 chr2D.!!$R3 3334
1 TraesCS2D01G431200 chr2D 543530689 543532429 1740 True 2117.000000 2117 89.159000 635 2338 1 chr2D.!!$R2 1703
2 TraesCS2D01G431200 chr2D 543756965 543762098 5133 True 1188.333333 1893 91.930333 838 3335 3 chr2D.!!$R5 2497
3 TraesCS2D01G431200 chr2D 543808701 543815124 6423 True 922.250000 1890 91.811250 838 3335 4 chr2D.!!$R6 2497
4 TraesCS2D01G431200 chr2D 574465488 574466100 612 True 721.000000 721 87.923000 1 618 1 chr2D.!!$R4 617
5 TraesCS2D01G431200 chr2D 315847185 315847801 616 False 680.000000 680 86.613000 1 618 1 chr2D.!!$F1 617
6 TraesCS2D01G431200 chr2B 648930181 648935336 5155 True 888.000000 1513 88.128500 615 2331 2 chr2B.!!$R2 1716
7 TraesCS2D01G431200 chr2B 649367523 649371051 3528 True 714.000000 1834 89.736000 644 2511 3 chr2B.!!$R3 1867
8 TraesCS2D01G431200 chr2A 686522318 686524010 1692 True 870.500000 1467 88.001000 615 2338 2 chr2A.!!$R4 1723
9 TraesCS2D01G431200 chr2A 686613194 686614883 1689 True 860.500000 1447 87.880500 615 2338 2 chr2A.!!$R5 1723
10 TraesCS2D01G431200 chr2A 686321305 686323003 1698 True 851.000000 1428 87.749500 615 2338 2 chr2A.!!$R3 1723
11 TraesCS2D01G431200 chr2A 686295723 686297399 1676 True 843.000000 1432 88.000000 634 2338 2 chr2A.!!$R2 1704
12 TraesCS2D01G431200 chr4D 505031394 505032007 613 False 867.000000 867 92.071000 1 618 1 chr4D.!!$F1 617
13 TraesCS2D01G431200 chr4D 70603016 70603629 613 True 734.000000 734 88.207000 1 618 1 chr4D.!!$R1 617
14 TraesCS2D01G431200 chr4A 465770612 465771224 612 False 732.000000 732 88.169000 1 617 1 chr4A.!!$F1 616
15 TraesCS2D01G431200 chr1D 365877663 365878275 612 False 715.000000 715 87.762000 1 618 1 chr1D.!!$F1 617
16 TraesCS2D01G431200 chr5D 545716561 545717173 612 True 704.000000 704 87.440000 1 618 1 chr5D.!!$R1 617
17 TraesCS2D01G431200 chr3D 611661189 611661801 612 True 630.000000 630 85.251000 1 616 1 chr3D.!!$R1 615

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
347 349 0.036388 CTAAAGTTCGGGCCTCTGCA 60.036 55.0 0.84 0.00 40.13 4.41 F
1119 4976 0.179108 GGGAGTCGTGCGCTTTATCT 60.179 55.0 9.73 0.26 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 5895 1.076332 CCCTCACGTCGAAATGGTTC 58.924 55.0 0.0 0.0 0.00 3.62 R
2356 7934 0.732571 CGCCGGTGCAACAGATAATT 59.267 50.0 0.0 0.0 39.98 1.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 1.427753 TGGGACCCCTCTTCTTTTTCC 59.572 52.381 8.45 0.00 36.94 3.13
107 108 3.649502 ACCCCTCTTCTTTTTCCGAACTA 59.350 43.478 0.00 0.00 0.00 2.24
119 120 0.250513 CCGAACTAAGAGGCCTTGCT 59.749 55.000 6.77 0.00 33.94 3.91
126 127 1.362224 AAGAGGCCTTGCTAACTCCA 58.638 50.000 6.77 0.00 0.00 3.86
344 346 4.223953 TCATATCTAAAGTTCGGGCCTCT 58.776 43.478 0.84 0.00 0.00 3.69
347 349 0.036388 CTAAAGTTCGGGCCTCTGCA 60.036 55.000 0.84 0.00 40.13 4.41
496 499 0.554305 ACTTTCGGGTCCTTTGGGTT 59.446 50.000 0.00 0.00 0.00 4.11
528 532 1.519408 CCTCGTTTGGGTGTACTTGG 58.481 55.000 0.00 0.00 0.00 3.61
570 578 3.324846 TGGTGTTGTTCTATGACTCTGCT 59.675 43.478 0.00 0.00 0.00 4.24
602 611 7.307573 GCTTTATTTATAAAGTCCGGCGTATGT 60.308 37.037 18.51 0.00 46.78 2.29
610 619 2.028385 AGTCCGGCGTATGTCTTTTCTT 60.028 45.455 6.01 0.00 0.00 2.52
706 718 1.503542 CACATGCGTTGGCCTCTTC 59.496 57.895 3.32 0.00 38.85 2.87
709 721 3.645268 ATGCGTTGGCCTCTTCCCC 62.645 63.158 3.32 0.00 38.85 4.81
752 764 3.308438 CAATCTTGCCCTGAAAACCTG 57.692 47.619 0.00 0.00 0.00 4.00
754 766 0.185901 TCTTGCCCTGAAAACCTGCT 59.814 50.000 0.00 0.00 0.00 4.24
755 767 1.423541 TCTTGCCCTGAAAACCTGCTA 59.576 47.619 0.00 0.00 0.00 3.49
756 768 1.541588 CTTGCCCTGAAAACCTGCTAC 59.458 52.381 0.00 0.00 0.00 3.58
758 770 1.923227 GCCCTGAAAACCTGCTACGC 61.923 60.000 0.00 0.00 0.00 4.42
759 771 0.321653 CCCTGAAAACCTGCTACGCT 60.322 55.000 0.00 0.00 0.00 5.07
765 777 1.263356 AAACCTGCTACGCTAGTCCA 58.737 50.000 0.00 0.00 0.00 4.02
766 778 0.818296 AACCTGCTACGCTAGTCCAG 59.182 55.000 0.00 0.00 32.77 3.86
768 780 0.665835 CCTGCTACGCTAGTCCAGAG 59.334 60.000 0.00 0.00 34.01 3.35
770 782 1.601903 CTGCTACGCTAGTCCAGAGAG 59.398 57.143 0.00 0.00 34.01 3.20
771 783 1.065345 TGCTACGCTAGTCCAGAGAGT 60.065 52.381 0.00 0.00 0.00 3.24
773 785 1.332375 CTACGCTAGTCCAGAGAGTGC 59.668 57.143 0.00 0.00 0.00 4.40
774 786 0.609406 ACGCTAGTCCAGAGAGTGCA 60.609 55.000 0.00 0.00 0.00 4.57
775 787 0.179150 CGCTAGTCCAGAGAGTGCAC 60.179 60.000 9.40 9.40 0.00 4.57
780 792 1.889829 AGTCCAGAGAGTGCACTGTAC 59.110 52.381 27.27 15.23 31.71 2.90
781 793 1.889829 GTCCAGAGAGTGCACTGTACT 59.110 52.381 27.27 15.73 31.71 2.73
784 796 4.158764 GTCCAGAGAGTGCACTGTACTTAT 59.841 45.833 27.27 5.54 31.71 1.73
785 797 5.357314 GTCCAGAGAGTGCACTGTACTTATA 59.643 44.000 27.27 1.50 31.71 0.98
786 798 5.590663 TCCAGAGAGTGCACTGTACTTATAG 59.409 44.000 27.27 5.75 31.71 1.31
788 800 6.459024 CCAGAGAGTGCACTGTACTTATAGAC 60.459 46.154 27.27 4.67 31.71 2.59
789 801 6.317642 CAGAGAGTGCACTGTACTTATAGACT 59.682 42.308 27.27 10.19 0.00 3.24
791 803 8.047911 AGAGAGTGCACTGTACTTATAGACTTA 58.952 37.037 27.27 0.00 0.00 2.24
792 804 7.987649 AGAGTGCACTGTACTTATAGACTTAC 58.012 38.462 27.27 2.87 0.00 2.34
793 805 7.610692 AGAGTGCACTGTACTTATAGACTTACA 59.389 37.037 27.27 0.00 0.00 2.41
795 807 8.191446 AGTGCACTGTACTTATAGACTTACATG 58.809 37.037 20.97 0.00 0.00 3.21
796 808 6.978659 TGCACTGTACTTATAGACTTACATGC 59.021 38.462 0.00 0.00 33.86 4.06
797 809 6.978659 GCACTGTACTTATAGACTTACATGCA 59.021 38.462 0.00 0.00 33.68 3.96
798 810 7.653713 GCACTGTACTTATAGACTTACATGCAT 59.346 37.037 0.00 0.00 33.68 3.96
799 811 8.972349 CACTGTACTTATAGACTTACATGCATG 58.028 37.037 25.09 25.09 0.00 4.06
800 812 7.653713 ACTGTACTTATAGACTTACATGCATGC 59.346 37.037 26.53 11.82 0.00 4.06
801 813 7.496747 TGTACTTATAGACTTACATGCATGCA 58.503 34.615 26.53 25.04 0.00 3.96
803 815 9.639601 GTACTTATAGACTTACATGCATGCATA 57.360 33.333 31.73 15.92 34.91 3.14
807 819 7.783090 ATAGACTTACATGCATGCATATAGC 57.217 36.000 31.73 20.85 45.96 2.97
823 835 1.012086 TAGCACAGGAGCTACGTACG 58.988 55.000 15.01 15.01 44.50 3.67
824 836 0.959372 AGCACAGGAGCTACGTACGT 60.959 55.000 25.98 25.98 44.50 3.57
825 837 0.729116 GCACAGGAGCTACGTACGTA 59.271 55.000 25.41 25.41 0.00 3.57
828 840 2.674852 CACAGGAGCTACGTACGTAAGA 59.325 50.000 26.68 9.29 43.62 2.10
829 841 2.935201 ACAGGAGCTACGTACGTAAGAG 59.065 50.000 26.68 18.98 43.62 2.85
831 843 4.115516 CAGGAGCTACGTACGTAAGAGTA 58.884 47.826 26.68 7.81 43.62 2.59
832 844 4.208873 CAGGAGCTACGTACGTAAGAGTAG 59.791 50.000 26.68 17.61 41.92 2.57
836 848 4.449870 CTACGTACGTAAGAGTAGCAGG 57.550 50.000 26.68 9.21 43.62 4.85
837 849 1.399791 ACGTACGTAAGAGTAGCAGGC 59.600 52.381 21.41 0.00 43.62 4.85
838 850 1.669779 CGTACGTAAGAGTAGCAGGCT 59.330 52.381 7.22 0.00 43.62 4.58
839 851 2.868583 CGTACGTAAGAGTAGCAGGCTA 59.131 50.000 7.22 0.00 43.62 3.93
874 4683 4.225984 TGCACGCAAAGTATAAGCTTTTG 58.774 39.130 3.20 3.62 36.64 2.44
929 4747 4.397090 CGGCGCGGCATTGACAAA 62.397 61.111 32.60 0.00 0.00 2.83
930 4748 2.504681 GGCGCGGCATTGACAAAG 60.505 61.111 29.32 0.00 0.00 2.77
931 4749 2.255252 GCGCGGCATTGACAAAGT 59.745 55.556 8.83 0.00 0.00 2.66
983 4824 3.000322 CGATCGATCGCCTATAAATTGCC 60.000 47.826 32.34 0.00 43.84 4.52
987 4828 3.412386 GATCGCCTATAAATTGCCAGGT 58.588 45.455 0.00 0.00 0.00 4.00
1003 4846 3.351740 CCAGGTACCATGCATACAAACA 58.648 45.455 15.94 0.00 0.00 2.83
1023 4875 4.978099 ACATACCCATCTCCATCAATCAC 58.022 43.478 0.00 0.00 0.00 3.06
1041 4896 2.032799 TCACCAGCAACAAAAACGCTAG 59.967 45.455 0.00 0.00 33.82 3.42
1042 4897 2.021457 ACCAGCAACAAAAACGCTAGT 58.979 42.857 0.00 0.00 33.82 2.57
1043 4898 3.002862 CACCAGCAACAAAAACGCTAGTA 59.997 43.478 0.00 0.00 33.82 1.82
1044 4899 3.628487 ACCAGCAACAAAAACGCTAGTAA 59.372 39.130 0.00 0.00 33.82 2.24
1045 4900 3.972502 CCAGCAACAAAAACGCTAGTAAC 59.027 43.478 0.00 0.00 33.82 2.50
1046 4901 4.261031 CCAGCAACAAAAACGCTAGTAACT 60.261 41.667 0.00 0.00 33.82 2.24
1047 4902 5.049954 CCAGCAACAAAAACGCTAGTAACTA 60.050 40.000 0.00 0.00 33.82 2.24
1048 4903 6.423862 CAGCAACAAAAACGCTAGTAACTAA 58.576 36.000 0.00 0.00 33.82 2.24
1049 4904 6.908284 CAGCAACAAAAACGCTAGTAACTAAA 59.092 34.615 0.00 0.00 33.82 1.85
1050 4905 6.908820 AGCAACAAAAACGCTAGTAACTAAAC 59.091 34.615 0.00 0.00 33.25 2.01
1051 4906 6.687958 GCAACAAAAACGCTAGTAACTAAACA 59.312 34.615 0.00 0.00 0.00 2.83
1052 4907 7.305019 GCAACAAAAACGCTAGTAACTAAACAC 60.305 37.037 0.00 0.00 0.00 3.32
1053 4908 7.543947 ACAAAAACGCTAGTAACTAAACACT 57.456 32.000 0.00 0.00 0.00 3.55
1054 4909 8.647143 ACAAAAACGCTAGTAACTAAACACTA 57.353 30.769 0.00 0.00 0.00 2.74
1056 4911 9.577003 CAAAAACGCTAGTAACTAAACACTAAG 57.423 33.333 0.00 0.00 0.00 2.18
1061 4916 7.120432 ACGCTAGTAACTAAACACTAAGCTAGT 59.880 37.037 0.00 0.00 40.28 2.57
1117 4974 0.460284 CTGGGAGTCGTGCGCTTTAT 60.460 55.000 9.73 0.00 0.00 1.40
1119 4976 0.179108 GGGAGTCGTGCGCTTTATCT 60.179 55.000 9.73 0.26 0.00 1.98
1138 4995 2.962569 CTGTCGTCCTTCTCGCCA 59.037 61.111 0.00 0.00 0.00 5.69
1142 4999 4.052229 CGTCCTTCTCGCCACCGT 62.052 66.667 0.00 0.00 35.54 4.83
1178 5038 3.224007 AATCCAGGCACCCACCCAC 62.224 63.158 0.00 0.00 0.00 4.61
1198 5058 3.333219 CCCAGGGGCTGAAGCAGA 61.333 66.667 0.00 0.00 44.36 4.26
1199 5059 2.759114 CCAGGGGCTGAAGCAGAA 59.241 61.111 4.43 0.00 44.36 3.02
1200 5060 1.378250 CCAGGGGCTGAAGCAGAAG 60.378 63.158 4.43 0.00 44.36 2.85
1201 5061 2.045131 CAGGGGCTGAAGCAGAAGC 61.045 63.158 4.43 0.00 44.36 3.86
1251 5111 1.071385 AGGGTCAAGTGCACTGAGAAG 59.929 52.381 22.49 8.55 0.00 2.85
1366 5226 0.456221 CTGCGGTAACCACTCGATCT 59.544 55.000 0.00 0.00 0.00 2.75
1367 5227 0.892755 TGCGGTAACCACTCGATCTT 59.107 50.000 0.00 0.00 0.00 2.40
1369 5229 2.289195 TGCGGTAACCACTCGATCTTTT 60.289 45.455 0.00 0.00 0.00 2.27
1371 5231 3.928375 GCGGTAACCACTCGATCTTTTTA 59.072 43.478 0.00 0.00 0.00 1.52
1417 5285 3.942739 ACGTACGTTGATTTTGTTGGTG 58.057 40.909 16.72 0.00 0.00 4.17
1459 5327 2.985847 GCAGTCTGCAACACCCCC 60.986 66.667 20.16 0.00 44.26 5.40
1462 5330 3.948719 GTCTGCAACACCCCCGGA 61.949 66.667 0.73 0.00 0.00 5.14
1726 5595 1.078143 GCACCTGGACATCACCCTC 60.078 63.158 0.00 0.00 0.00 4.30
2012 5895 1.061570 GTACCGCTCCGACTACGTG 59.938 63.158 0.00 0.00 37.88 4.49
2161 6044 1.449070 TGCAATCTGAGCTCGCTGG 60.449 57.895 9.64 0.00 0.00 4.85
2162 6045 1.449246 GCAATCTGAGCTCGCTGGT 60.449 57.895 9.64 0.00 0.00 4.00
2163 6046 0.179100 GCAATCTGAGCTCGCTGGTA 60.179 55.000 9.64 0.00 0.00 3.25
2196 6079 4.120331 GTGGCATGGACGGCAAGC 62.120 66.667 0.00 0.00 43.86 4.01
2202 6085 3.529341 ATGGACGGCAAGCGTGTGA 62.529 57.895 0.59 0.00 0.00 3.58
2346 7923 8.415950 TGTGTTTGGATTTGGAAATACTATGT 57.584 30.769 0.00 0.00 30.33 2.29
2348 7926 7.759433 GTGTTTGGATTTGGAAATACTATGTGG 59.241 37.037 0.00 0.00 30.33 4.17
2350 7928 5.514169 TGGATTTGGAAATACTATGTGGCA 58.486 37.500 0.00 0.00 30.33 4.92
2356 7934 4.708909 TGGAAATACTATGTGGCATTTGCA 59.291 37.500 4.74 0.00 44.36 4.08
2406 7984 7.912949 TCGATTCAAACTTTTCATTCAACTG 57.087 32.000 0.00 0.00 0.00 3.16
2407 7985 7.479980 TCGATTCAAACTTTTCATTCAACTGT 58.520 30.769 0.00 0.00 0.00 3.55
2408 7986 7.973388 TCGATTCAAACTTTTCATTCAACTGTT 59.027 29.630 0.00 0.00 0.00 3.16
2409 7987 8.051909 CGATTCAAACTTTTCATTCAACTGTTG 58.948 33.333 14.24 14.24 0.00 3.33
2410 7988 9.086336 GATTCAAACTTTTCATTCAACTGTTGA 57.914 29.630 18.69 18.69 38.04 3.18
2535 10801 1.745827 CGATGCCGGGTTTTATGGACT 60.746 52.381 2.18 0.00 0.00 3.85
2542 10808 4.202388 GCCGGGTTTTATGGACTATTAGGA 60.202 45.833 2.18 0.00 0.00 2.94
2601 10868 2.935201 TGTGGTTGCTTGTTCAAAATGC 59.065 40.909 0.00 0.00 0.00 3.56
2606 10873 2.902523 TGCTTGTTCAAAATGCTTGCA 58.097 38.095 0.00 0.00 0.00 4.08
2613 10880 5.522456 TGTTCAAAATGCTTGCACTCTTAG 58.478 37.500 0.00 0.00 0.00 2.18
2644 10911 7.384439 GCCTCTGCTTCTATTTTAGTTCTTT 57.616 36.000 0.00 0.00 33.53 2.52
2669 10936 8.918202 TCACCTACAAAAACATAACAGAATCT 57.082 30.769 0.00 0.00 0.00 2.40
2695 10962 5.415415 GCTTGTAACTCAGGCATAGAATG 57.585 43.478 0.00 0.00 46.35 2.67
2710 10977 5.108217 GCATAGAATGTGACGATACTTGTCG 60.108 44.000 0.00 0.00 46.56 4.35
2803 11070 6.073447 TCATAAGAATCCCAAACCAGCTTA 57.927 37.500 0.00 0.00 0.00 3.09
2804 11071 6.489603 TCATAAGAATCCCAAACCAGCTTAA 58.510 36.000 0.00 0.00 0.00 1.85
2805 11072 6.377146 TCATAAGAATCCCAAACCAGCTTAAC 59.623 38.462 0.00 0.00 0.00 2.01
2806 11073 3.431415 AGAATCCCAAACCAGCTTAACC 58.569 45.455 0.00 0.00 0.00 2.85
2807 11074 2.231716 ATCCCAAACCAGCTTAACCC 57.768 50.000 0.00 0.00 0.00 4.11
2933 11201 0.400213 AACACCATGTCCCACGTCAT 59.600 50.000 0.00 0.00 0.00 3.06
2935 11203 0.744414 CACCATGTCCCACGTCATCC 60.744 60.000 0.00 0.00 0.00 3.51
2942 11210 0.608130 TCCCACGTCATCCAAGACTG 59.392 55.000 0.00 0.00 36.38 3.51
2947 11215 1.000955 ACGTCATCCAAGACTGTCCAC 59.999 52.381 3.76 0.00 36.38 4.02
2948 11216 1.000843 CGTCATCCAAGACTGTCCACA 59.999 52.381 3.76 0.00 36.38 4.17
3038 11306 6.104990 AGGAGGTGGATAAGGTAAGTAGATCT 59.895 42.308 0.00 0.00 0.00 2.75
3039 11307 6.783482 GGAGGTGGATAAGGTAAGTAGATCTT 59.217 42.308 0.00 0.00 39.89 2.40
3043 11311 8.091449 GGTGGATAAGGTAAGTAGATCTTCATG 58.909 40.741 0.00 0.00 37.56 3.07
3063 11331 4.644103 TGGAAGATAGTGCCTAACGTAC 57.356 45.455 0.00 0.00 0.00 3.67
3077 11345 1.068474 ACGTACAAGCTGCAATCGAC 58.932 50.000 1.02 0.00 0.00 4.20
3095 11363 5.693769 TCGACTCCCCTAATTCAAGAAAT 57.306 39.130 0.00 0.00 0.00 2.17
3127 11395 0.179000 ATCTTCTGCCGATGTGGTCC 59.821 55.000 0.00 0.00 41.21 4.46
3153 11421 5.691754 CCAAAGGCTTTTAACTGTTGATGAC 59.308 40.000 10.36 0.00 0.00 3.06
3160 11428 7.148967 GGCTTTTAACTGTTGATGACGAAATTC 60.149 37.037 2.69 0.00 0.00 2.17
3203 11471 6.295249 TGTTACACAACTGAATCTGATTCCA 58.705 36.000 23.62 12.96 34.15 3.53
3221 11489 3.114606 TCCACTTCCTAGCATGATTGGA 58.885 45.455 10.19 10.19 0.00 3.53
3244 11512 1.064906 TCCATCTCGGTTCTCCTACGT 60.065 52.381 0.00 0.00 35.57 3.57
3311 11579 8.197988 AGAAGTGTGTGTAAACAAAAGAGTAG 57.802 34.615 0.00 0.00 0.00 2.57
3334 11602 9.106070 GTAGGGTAGTTTATATGTGGAAAACTG 57.894 37.037 9.76 0.00 42.01 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.930682 GTTAGCAAGGCCTCTTAGTTCG 59.069 50.000 5.23 0.00 0.00 3.95
107 108 1.362224 TGGAGTTAGCAAGGCCTCTT 58.638 50.000 5.23 0.00 0.00 2.85
119 120 0.906066 TAACGCCTGCCATGGAGTTA 59.094 50.000 18.40 13.39 45.74 2.24
126 127 1.453155 CTCTTTGTAACGCCTGCCAT 58.547 50.000 0.00 0.00 0.00 4.40
307 309 9.414295 CTTTAGATATGAGAAGATTCAGAGCAG 57.586 37.037 0.00 0.00 27.73 4.24
344 346 0.676184 GCCCAGATAGAGACGATGCA 59.324 55.000 0.00 0.00 0.00 3.96
347 349 1.145945 TCCTGCCCAGATAGAGACGAT 59.854 52.381 0.00 0.00 0.00 3.73
528 532 0.530431 CCAGCCAACCAAAGCAACAC 60.530 55.000 0.00 0.00 0.00 3.32
632 641 5.501897 CGTTTAGCCGTCCTTGATTACAATC 60.502 44.000 0.00 0.00 35.37 2.67
706 718 3.633986 GGATGCAACTTAATCTTCAGGGG 59.366 47.826 0.00 0.00 0.00 4.79
709 721 4.201990 GCCAGGATGCAACTTAATCTTCAG 60.202 45.833 0.00 0.00 31.97 3.02
754 766 1.339727 TGCACTCTCTGGACTAGCGTA 60.340 52.381 0.00 0.00 0.00 4.42
755 767 0.609406 TGCACTCTCTGGACTAGCGT 60.609 55.000 0.00 0.00 0.00 5.07
756 768 0.179150 GTGCACTCTCTGGACTAGCG 60.179 60.000 10.32 0.00 38.19 4.26
765 777 6.419791 AGTCTATAAGTACAGTGCACTCTCT 58.580 40.000 18.64 12.44 0.00 3.10
766 778 6.687081 AGTCTATAAGTACAGTGCACTCTC 57.313 41.667 18.64 10.23 0.00 3.20
768 780 7.759465 TGTAAGTCTATAAGTACAGTGCACTC 58.241 38.462 18.64 6.10 0.00 3.51
770 782 7.043325 GCATGTAAGTCTATAAGTACAGTGCAC 60.043 40.741 9.40 9.40 0.00 4.57
771 783 6.978659 GCATGTAAGTCTATAAGTACAGTGCA 59.021 38.462 0.00 0.00 0.00 4.57
773 785 8.972349 CATGCATGTAAGTCTATAAGTACAGTG 58.028 37.037 18.91 0.00 0.00 3.66
774 786 7.653713 GCATGCATGTAAGTCTATAAGTACAGT 59.346 37.037 26.79 0.00 0.00 3.55
775 787 7.653311 TGCATGCATGTAAGTCTATAAGTACAG 59.347 37.037 26.79 0.00 0.00 2.74
781 793 9.317936 GCTATATGCATGCATGTAAGTCTATAA 57.682 33.333 37.43 17.23 42.31 0.98
799 811 2.029828 ACGTAGCTCCTGTGCTATATGC 60.030 50.000 0.00 0.00 45.70 3.14
800 812 3.924918 ACGTAGCTCCTGTGCTATATG 57.075 47.619 0.00 1.85 45.70 1.78
801 813 3.436015 CGTACGTAGCTCCTGTGCTATAT 59.564 47.826 7.22 0.05 45.70 0.86
803 815 1.602851 CGTACGTAGCTCCTGTGCTAT 59.397 52.381 7.22 0.00 45.70 2.97
804 816 1.012086 CGTACGTAGCTCCTGTGCTA 58.988 55.000 7.22 0.00 43.74 3.49
805 817 0.959372 ACGTACGTAGCTCCTGTGCT 60.959 55.000 21.41 0.00 46.11 4.40
806 818 0.729116 TACGTACGTAGCTCCTGTGC 59.271 55.000 23.60 0.00 0.00 4.57
807 819 2.674852 TCTTACGTACGTAGCTCCTGTG 59.325 50.000 25.56 11.16 31.71 3.66
808 820 2.935201 CTCTTACGTACGTAGCTCCTGT 59.065 50.000 25.56 1.38 31.71 4.00
809 821 2.935201 ACTCTTACGTACGTAGCTCCTG 59.065 50.000 25.56 16.21 31.71 3.86
815 827 3.303001 GCCTGCTACTCTTACGTACGTAG 60.303 52.174 25.56 19.49 34.07 3.51
816 828 2.609459 GCCTGCTACTCTTACGTACGTA 59.391 50.000 23.60 23.60 0.00 3.57
817 829 1.399791 GCCTGCTACTCTTACGTACGT 59.600 52.381 25.98 25.98 0.00 3.57
819 831 4.208074 GTAGCCTGCTACTCTTACGTAC 57.792 50.000 19.46 0.00 43.92 3.67
829 841 1.069358 GGTGGATGAGTAGCCTGCTAC 59.931 57.143 19.19 19.19 46.70 3.58
831 843 0.326048 AGGTGGATGAGTAGCCTGCT 60.326 55.000 0.00 0.00 32.18 4.24
832 844 1.414158 TAGGTGGATGAGTAGCCTGC 58.586 55.000 0.00 0.00 32.18 4.85
833 845 2.289320 GCATAGGTGGATGAGTAGCCTG 60.289 54.545 0.00 0.00 32.18 4.85
834 846 1.974236 GCATAGGTGGATGAGTAGCCT 59.026 52.381 0.00 0.00 32.18 4.58
835 847 1.694150 TGCATAGGTGGATGAGTAGCC 59.306 52.381 0.00 0.00 0.00 3.93
836 848 2.760374 GTGCATAGGTGGATGAGTAGC 58.240 52.381 0.00 0.00 0.00 3.58
837 849 2.864097 GCGTGCATAGGTGGATGAGTAG 60.864 54.545 0.00 0.00 34.91 2.57
838 850 1.068588 GCGTGCATAGGTGGATGAGTA 59.931 52.381 0.00 0.00 34.91 2.59
839 851 0.179073 GCGTGCATAGGTGGATGAGT 60.179 55.000 0.00 0.00 34.91 3.41
841 853 0.251634 TTGCGTGCATAGGTGGATGA 59.748 50.000 0.00 0.00 34.91 2.92
842 854 1.064505 CTTTGCGTGCATAGGTGGATG 59.935 52.381 4.61 0.00 35.94 3.51
844 856 0.036164 ACTTTGCGTGCATAGGTGGA 59.964 50.000 15.13 0.00 30.92 4.02
845 857 1.732941 TACTTTGCGTGCATAGGTGG 58.267 50.000 15.13 0.00 30.92 4.61
846 858 4.552767 GCTTATACTTTGCGTGCATAGGTG 60.553 45.833 15.13 3.70 30.92 4.00
847 859 3.560068 GCTTATACTTTGCGTGCATAGGT 59.440 43.478 15.13 8.19 30.92 3.08
874 4683 4.451652 GCCGCTCGCTTGAACTGC 62.452 66.667 0.00 0.00 0.00 4.40
877 4686 3.793144 CCTGCCGCTCGCTTGAAC 61.793 66.667 0.00 0.00 38.78 3.18
921 4739 5.107065 GCTTGCTTCGTAGTACTTTGTCAAT 60.107 40.000 0.00 0.00 0.00 2.57
929 4747 4.882427 TCTATCTGCTTGCTTCGTAGTACT 59.118 41.667 0.00 0.00 0.00 2.73
930 4748 5.171147 TCTATCTGCTTGCTTCGTAGTAC 57.829 43.478 0.00 0.00 0.00 2.73
931 4749 5.763088 CATCTATCTGCTTGCTTCGTAGTA 58.237 41.667 0.00 0.00 0.00 1.82
983 4824 5.008613 GGTATGTTTGTATGCATGGTACCTG 59.991 44.000 14.36 10.00 0.00 4.00
987 4828 5.117406 TGGGTATGTTTGTATGCATGGTA 57.883 39.130 10.16 0.00 0.00 3.25
1003 4846 3.982730 TGGTGATTGATGGAGATGGGTAT 59.017 43.478 0.00 0.00 0.00 2.73
1023 4875 2.774439 ACTAGCGTTTTTGTTGCTGG 57.226 45.000 0.00 0.00 42.21 4.85
1061 4916 0.734942 GCGCCTTCACGTTGCTAGTA 60.735 55.000 0.00 0.00 34.88 1.82
1065 4920 3.044305 GAGCGCCTTCACGTTGCT 61.044 61.111 2.29 0.00 38.89 3.91
1066 4921 4.430423 CGAGCGCCTTCACGTTGC 62.430 66.667 2.29 0.00 34.88 4.17
1069 4924 4.961511 TTGCGAGCGCCTTCACGT 62.962 61.111 12.70 0.00 41.09 4.49
1094 4949 4.039357 CGCACGACTCCCAGACGT 62.039 66.667 0.00 0.00 46.38 4.34
1117 4974 1.876664 CGAGAAGGACGACAGCAGA 59.123 57.895 0.00 0.00 0.00 4.26
1119 4976 2.258591 GCGAGAAGGACGACAGCA 59.741 61.111 0.00 0.00 0.00 4.41
1188 5048 2.105466 CCTCGGCTTCTGCTTCAGC 61.105 63.158 0.00 0.00 39.59 4.26
1189 5049 2.105466 GCCTCGGCTTCTGCTTCAG 61.105 63.158 0.00 0.00 39.59 3.02
1190 5050 2.046892 GCCTCGGCTTCTGCTTCA 60.047 61.111 0.00 0.00 39.59 3.02
1191 5051 2.821810 GGCCTCGGCTTCTGCTTC 60.822 66.667 8.00 0.00 41.60 3.86
1192 5052 4.767255 CGGCCTCGGCTTCTGCTT 62.767 66.667 8.00 0.00 41.60 3.91
1194 5054 4.760047 TTCGGCCTCGGCTTCTGC 62.760 66.667 8.00 0.00 41.60 4.26
1195 5055 2.510238 CTTCGGCCTCGGCTTCTG 60.510 66.667 8.00 0.00 41.60 3.02
1196 5056 4.459089 GCTTCGGCCTCGGCTTCT 62.459 66.667 8.00 0.00 41.60 2.85
1251 5111 2.038837 GTAGGGGTTCACCTTGCGC 61.039 63.158 0.00 0.00 42.09 6.09
1366 5226 8.177119 AGCTCCATTGTTAAGACATGTAAAAA 57.823 30.769 0.00 0.00 35.29 1.94
1367 5227 7.759489 AGCTCCATTGTTAAGACATGTAAAA 57.241 32.000 0.00 0.00 35.29 1.52
1369 5229 7.620880 AGTAGCTCCATTGTTAAGACATGTAA 58.379 34.615 0.00 0.00 35.29 2.41
1371 5231 6.054860 AGTAGCTCCATTGTTAAGACATGT 57.945 37.500 0.00 0.00 35.29 3.21
1417 5285 1.339929 AGGCACGAACCAAAACCATTC 59.660 47.619 0.00 0.00 0.00 2.67
1726 5595 1.939785 GTAGACATGCTCGCCGTCG 60.940 63.158 0.00 0.00 34.80 5.12
1876 5759 2.367202 TGCACCCTCGATTCCTCCC 61.367 63.158 0.00 0.00 0.00 4.30
1958 5841 3.359523 TGGACGTCGTCGGTGAGG 61.360 66.667 18.61 0.00 41.85 3.86
2012 5895 1.076332 CCCTCACGTCGAAATGGTTC 58.924 55.000 0.00 0.00 0.00 3.62
2146 6029 1.135915 CAGTACCAGCGAGCTCAGATT 59.864 52.381 15.40 0.00 0.00 2.40
2161 6044 1.738099 CTGGCGCAGGTGACAGTAC 60.738 63.158 10.83 0.00 0.00 2.73
2162 6045 2.207229 ACTGGCGCAGGTGACAGTA 61.207 57.895 19.15 0.00 41.95 2.74
2163 6046 3.550431 ACTGGCGCAGGTGACAGT 61.550 61.111 15.30 15.30 39.20 3.55
2196 6079 4.466567 TTTACTTCTTGCACATCACACG 57.533 40.909 0.00 0.00 0.00 4.49
2202 6085 4.537015 GAAGCGTTTTACTTCTTGCACAT 58.463 39.130 0.00 0.00 40.33 3.21
2331 7895 6.105333 GCAAATGCCACATAGTATTTCCAAA 58.895 36.000 0.00 0.00 34.31 3.28
2332 7896 5.186603 TGCAAATGCCACATAGTATTTCCAA 59.813 36.000 2.46 0.00 41.18 3.53
2334 7898 5.261209 TGCAAATGCCACATAGTATTTCC 57.739 39.130 2.46 0.00 41.18 3.13
2341 7918 6.509656 ACAGATAATTGCAAATGCCACATAG 58.490 36.000 1.71 0.00 41.18 2.23
2356 7934 0.732571 CGCCGGTGCAACAGATAATT 59.267 50.000 0.00 0.00 39.98 1.40
2419 7997 2.959707 ACAGTTGAATACCCCGCAAAAA 59.040 40.909 0.00 0.00 0.00 1.94
2420 7998 2.588620 ACAGTTGAATACCCCGCAAAA 58.411 42.857 0.00 0.00 0.00 2.44
2421 7999 2.279935 ACAGTTGAATACCCCGCAAA 57.720 45.000 0.00 0.00 0.00 3.68
2422 8000 1.883275 CAACAGTTGAATACCCCGCAA 59.117 47.619 7.61 0.00 0.00 4.85
2423 8001 1.072489 TCAACAGTTGAATACCCCGCA 59.928 47.619 13.90 0.00 36.59 5.69
2424 8002 1.816074 TCAACAGTTGAATACCCCGC 58.184 50.000 13.90 0.00 36.59 6.13
2451 8029 3.423154 CCGCCACCAAACGAGAGC 61.423 66.667 0.00 0.00 0.00 4.09
2579 10846 3.560896 GCATTTTGAACAAGCAACCACAT 59.439 39.130 0.00 0.00 0.00 3.21
2581 10848 3.197265 AGCATTTTGAACAAGCAACCAC 58.803 40.909 0.00 0.00 0.00 4.16
2584 10851 3.063725 TGCAAGCATTTTGAACAAGCAAC 59.936 39.130 0.00 0.00 0.00 4.17
2601 10868 3.195396 AGGCTTCTCTCTAAGAGTGCAAG 59.805 47.826 18.43 14.75 42.83 4.01
2606 10873 3.023832 GCAGAGGCTTCTCTCTAAGAGT 58.976 50.000 0.00 0.00 45.45 3.24
2641 10908 9.965824 ATTCTGTTATGTTTTTGTAGGTGAAAG 57.034 29.630 0.00 0.00 0.00 2.62
2644 10911 8.918202 AGATTCTGTTATGTTTTTGTAGGTGA 57.082 30.769 0.00 0.00 0.00 4.02
2669 10936 1.055849 TGCCTGAGTTACAAGCTGGA 58.944 50.000 0.00 0.00 36.93 3.86
2690 10957 3.770666 CCGACAAGTATCGTCACATTCT 58.229 45.455 0.00 0.00 40.59 2.40
2691 10958 2.281762 GCCGACAAGTATCGTCACATTC 59.718 50.000 0.00 0.00 40.59 2.67
2695 10962 1.654105 CTTGCCGACAAGTATCGTCAC 59.346 52.381 2.94 0.00 46.84 3.67
2710 10977 1.142474 GCAATGTGTTCAAGCTTGCC 58.858 50.000 21.99 14.39 36.96 4.52
2761 11028 7.828717 TCTTATGATCATAACTTTGTGCCTCAA 59.171 33.333 21.67 1.48 0.00 3.02
2803 11070 2.491693 CAAGTTCAATATGCCGTGGGTT 59.508 45.455 0.00 0.00 0.00 4.11
2804 11071 2.091541 CAAGTTCAATATGCCGTGGGT 58.908 47.619 0.00 0.00 0.00 4.51
2805 11072 2.091541 ACAAGTTCAATATGCCGTGGG 58.908 47.619 0.00 0.00 0.00 4.61
2806 11073 3.190327 TCAACAAGTTCAATATGCCGTGG 59.810 43.478 0.00 0.00 0.00 4.94
2807 11074 4.418013 TCAACAAGTTCAATATGCCGTG 57.582 40.909 0.00 0.00 0.00 4.94
2933 11201 1.048601 GACCTGTGGACAGTCTTGGA 58.951 55.000 6.06 0.00 42.27 3.53
2935 11203 1.967066 AGAGACCTGTGGACAGTCTTG 59.033 52.381 6.06 0.00 42.27 3.02
2942 11210 3.056035 ACGGAATTAAGAGACCTGTGGAC 60.056 47.826 0.00 0.00 0.00 4.02
2947 11215 5.290386 GTGGATACGGAATTAAGAGACCTG 58.710 45.833 0.00 0.00 42.51 4.00
2948 11216 4.037684 CGTGGATACGGAATTAAGAGACCT 59.962 45.833 0.00 0.00 46.23 3.85
2978 11246 5.703876 AGAAAATTGAAAGGATTGAGCGAC 58.296 37.500 0.00 0.00 0.00 5.19
2979 11247 5.964958 AGAAAATTGAAAGGATTGAGCGA 57.035 34.783 0.00 0.00 0.00 4.93
3038 11306 4.161565 ACGTTAGGCACTATCTTCCATGAA 59.838 41.667 0.00 0.00 42.38 2.57
3039 11307 3.704566 ACGTTAGGCACTATCTTCCATGA 59.295 43.478 0.00 0.00 42.38 3.07
3043 11311 4.644103 TGTACGTTAGGCACTATCTTCC 57.356 45.455 0.00 0.00 42.38 3.46
3063 11331 1.372087 GGGGAGTCGATTGCAGCTTG 61.372 60.000 1.22 0.00 0.00 4.01
3077 11345 6.039829 GCACCTTATTTCTTGAATTAGGGGAG 59.960 42.308 9.53 9.24 46.33 4.30
3127 11395 5.004922 TCAACAGTTAAAAGCCTTTGGTG 57.995 39.130 0.00 0.00 0.00 4.17
3137 11405 7.646130 GTGGAATTTCGTCATCAACAGTTAAAA 59.354 33.333 0.00 0.00 0.00 1.52
3160 11428 2.224209 ACAAGTAACAACTCCGAGGTGG 60.224 50.000 17.78 1.29 37.20 4.61
3191 11459 5.028549 TGCTAGGAAGTGGAATCAGATTC 57.971 43.478 14.09 14.09 38.55 2.52
3203 11471 5.136105 GGAATTCCAATCATGCTAGGAAGT 58.864 41.667 20.04 12.98 42.84 3.01
3221 11489 3.068307 CGTAGGAGAACCGAGATGGAATT 59.932 47.826 0.00 0.00 42.00 2.17
3244 11512 8.783093 CAAAACTACTGAGATTGACAACCAATA 58.217 33.333 0.00 0.00 45.00 1.90


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

AutoCloner maintained by Alex Coulton.