Multiple sequence alignment - TraesCS1D01G309700

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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 TraesCS1D01G309700 chr1D 100.000 3467 0 0 1 3467 405377300 405373834 0.000000e+00 6403
1 TraesCS1D01G309700 chr1D 85.630 508 72 1 1946 2453 405285291 405284785 1.830000e-147 532
2 TraesCS1D01G309700 chr1D 87.119 427 49 3 1048 1471 405285737 405285314 2.420000e-131 479
3 TraesCS1D01G309700 chr1D 93.814 194 11 1 434 627 405377998 405378190 1.220000e-74 291
4 TraesCS1D01G309700 chr1D 94.624 93 5 0 2968 3060 19257147 19257239 1.000000e-30 145
5 TraesCS1D01G309700 chr1A 91.707 2074 127 25 933 2973 500842873 500840812 0.000000e+00 2835
6 TraesCS1D01G309700 chr1A 92.900 662 27 1 1 642 321228400 321227739 0.000000e+00 944
7 TraesCS1D01G309700 chr1A 82.503 903 131 13 1585 2483 500822842 500821963 0.000000e+00 767
8 TraesCS1D01G309700 chr1A 93.587 421 22 3 3052 3467 500840816 500840396 1.060000e-174 623
9 TraesCS1D01G309700 chr1A 86.652 442 53 5 1033 1471 500823384 500822946 5.200000e-133 484
10 TraesCS1D01G309700 chr1A 93.750 208 13 0 432 639 321246523 321246730 2.600000e-81 313
11 TraesCS1D01G309700 chr1A 85.938 192 21 5 3132 3321 7111322 7111509 2.110000e-47 200
12 TraesCS1D01G309700 chr1A 94.017 117 7 0 792 908 500843117 500843001 9.890000e-41 178
13 TraesCS1D01G309700 chr1A 93.939 99 5 1 2965 3063 64254152 64254249 7.750000e-32 148
14 TraesCS1D01G309700 chr1B 92.416 1925 102 21 820 2723 545277783 545275882 0.000000e+00 2706
15 TraesCS1D01G309700 chr1B 83.811 488 64 9 1973 2450 545165807 545165325 1.900000e-122 449
16 TraesCS1D01G309700 chr1B 88.931 262 15 5 2714 2973 545273114 545272865 9.340000e-81 311
17 TraesCS1D01G309700 chr1B 96.970 66 2 0 3391 3456 545235426 545235361 1.020000e-20 111
18 TraesCS1D01G309700 chr2D 97.508 642 16 0 1 642 623476285 623475644 0.000000e+00 1098
19 TraesCS1D01G309700 chr2D 96.795 624 17 1 1 624 427097193 427097813 0.000000e+00 1038
20 TraesCS1D01G309700 chr2D 94.811 212 10 1 432 643 623477333 623477543 2.580000e-86 329
21 TraesCS1D01G309700 chr2D 93.365 211 13 1 432 642 427092723 427092514 9.340000e-81 311
22 TraesCS1D01G309700 chr5B 93.522 247 16 0 396 642 639227476 639227722 5.470000e-98 368
23 TraesCS1D01G309700 chr5B 93.333 210 13 1 434 643 639225384 639225176 3.360000e-80 309
24 TraesCS1D01G309700 chr5B 97.674 43 1 0 2500 2542 386528972 386528930 1.330000e-09 75
25 TraesCS1D01G309700 chr3B 82.119 302 39 11 1013 1306 574677868 574678162 9.610000e-61 244
26 TraesCS1D01G309700 chr3B 85.492 193 26 2 3130 3321 755478791 755478600 2.110000e-47 200
27 TraesCS1D01G309700 chr3B 75.986 279 48 12 1041 1302 574379155 574379431 3.630000e-25 126
28 TraesCS1D01G309700 chr3A 77.751 409 59 22 1013 1397 577559352 577559752 4.500000e-54 222
29 TraesCS1D01G309700 chr3A 85.567 194 25 3 3129 3321 560467064 560466873 2.110000e-47 200
30 TraesCS1D01G309700 chr6D 86.772 189 23 2 3134 3321 363466630 363466443 3.510000e-50 209
31 TraesCS1D01G309700 chr6D 90.741 108 7 3 2971 3075 470635708 470635601 1.300000e-29 141
32 TraesCS1D01G309700 chr3D 77.163 416 55 30 1013 1397 438566675 438567081 4.540000e-49 206
33 TraesCS1D01G309700 chr3D 76.259 278 49 10 1041 1302 438542916 438543192 7.810000e-27 132
34 TraesCS1D01G309700 chr7A 85.204 196 27 2 3127 3321 243645591 243645785 2.110000e-47 200
35 TraesCS1D01G309700 chr5A 85.641 195 22 5 3130 3321 444536924 444536733 2.110000e-47 200
36 TraesCS1D01G309700 chr5A 90.476 105 9 1 2967 3071 641680857 641680754 1.680000e-28 137
37 TraesCS1D01G309700 chr5A 88.991 109 11 1 2947 3055 31448298 31448191 2.170000e-27 134
38 TraesCS1D01G309700 chr7B 85.052 194 27 2 3129 3321 559265055 559264863 2.730000e-46 196
39 TraesCS1D01G309700 chr7B 87.826 115 11 3 2952 3064 544134577 544134464 7.810000e-27 132
40 TraesCS1D01G309700 chr4A 85.052 194 27 2 3129 3321 541366917 541367109 2.730000e-46 196
41 TraesCS1D01G309700 chr2B 94.505 91 5 0 2968 3058 558937397 558937307 1.300000e-29 141
42 TraesCS1D01G309700 chr2B 76.241 282 56 7 1025 1299 727317472 727317195 4.670000e-29 139
43 TraesCS1D01G309700 chr2A 91.346 104 7 2 2968 3070 750532389 750532491 1.300000e-29 141
44 TraesCS1D01G309700 chr7D 88.393 112 10 2 2967 3078 611241715 611241823 7.810000e-27 132


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 TraesCS1D01G309700 chr1D 405373834 405377300 3466 True 6403.0 6403 100.000000 1 3467 1 chr1D.!!$R1 3466
1 TraesCS1D01G309700 chr1D 405284785 405285737 952 True 505.5 532 86.374500 1048 2453 2 chr1D.!!$R2 1405
2 TraesCS1D01G309700 chr1A 500840396 500843117 2721 True 1212.0 2835 93.103667 792 3467 3 chr1A.!!$R3 2675
3 TraesCS1D01G309700 chr1A 321227739 321228400 661 True 944.0 944 92.900000 1 642 1 chr1A.!!$R1 641
4 TraesCS1D01G309700 chr1A 500821963 500823384 1421 True 625.5 767 84.577500 1033 2483 2 chr1A.!!$R2 1450
5 TraesCS1D01G309700 chr1B 545272865 545277783 4918 True 1508.5 2706 90.673500 820 2973 2 chr1B.!!$R3 2153
6 TraesCS1D01G309700 chr2D 623475644 623476285 641 True 1098.0 1098 97.508000 1 642 1 chr2D.!!$R2 641
7 TraesCS1D01G309700 chr2D 427097193 427097813 620 False 1038.0 1038 96.795000 1 624 1 chr2D.!!$F1 623

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
713 734 0.037590 TGCAGGACCCAACATGGTAC 59.962 55.0 0.00 0.00 39.24 3.34 F
851 872 0.380733 TCACACTATAGCCTGACGCG 59.619 55.0 3.53 3.53 44.76 6.01 F
1951 2138 0.108898 CAGCTTCCTCTCAGTGTCGG 60.109 60.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1897 0.453282 CACATTGCGCTTTCCTCACG 60.453 55.000 9.73 0.00 0.00 4.35 R
2326 2520 0.602638 TCGCCATCACCACAGTTCAC 60.603 55.000 0.00 0.00 0.00 3.18 R
3386 6366 1.139734 CTCTTCGAGCGCTTGCCTA 59.860 57.895 20.39 6.76 40.41 3.93 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
163 164 8.275040 AGCCCTAAGAAATAGAATGTACATTGT 58.725 33.333 25.42 22.83 33.04 2.71
468 489 0.963856 AGCTACGTGTCCATCGTCCA 60.964 55.000 0.00 0.00 41.72 4.02
487 508 0.949105 ATTGCCACGTCGACCTGAAC 60.949 55.000 15.05 8.00 0.00 3.18
630 651 2.446435 CCCCAAATGTGGTAGTTCTGG 58.554 52.381 0.00 0.00 44.30 3.86
631 652 2.041081 CCCCAAATGTGGTAGTTCTGGA 59.959 50.000 0.00 0.00 44.30 3.86
642 663 6.212589 TGTGGTAGTTCTGGATCATTTACTCA 59.787 38.462 0.00 0.00 0.00 3.41
643 664 7.103641 GTGGTAGTTCTGGATCATTTACTCAA 58.896 38.462 0.00 0.00 0.00 3.02
644 665 7.064728 GTGGTAGTTCTGGATCATTTACTCAAC 59.935 40.741 0.00 0.00 0.00 3.18
645 666 7.038302 TGGTAGTTCTGGATCATTTACTCAACT 60.038 37.037 0.00 0.00 0.00 3.16
646 667 7.492994 GGTAGTTCTGGATCATTTACTCAACTC 59.507 40.741 0.00 0.00 0.00 3.01
647 668 6.102663 AGTTCTGGATCATTTACTCAACTCG 58.897 40.000 0.00 0.00 0.00 4.18
648 669 5.661056 TCTGGATCATTTACTCAACTCGT 57.339 39.130 0.00 0.00 0.00 4.18
649 670 5.410924 TCTGGATCATTTACTCAACTCGTG 58.589 41.667 0.00 0.00 0.00 4.35
650 671 5.047306 TCTGGATCATTTACTCAACTCGTGT 60.047 40.000 0.00 0.00 0.00 4.49
651 672 4.929211 TGGATCATTTACTCAACTCGTGTG 59.071 41.667 0.00 0.00 0.00 3.82
652 673 4.330074 GGATCATTTACTCAACTCGTGTGG 59.670 45.833 0.00 0.00 0.00 4.17
653 674 4.594123 TCATTTACTCAACTCGTGTGGA 57.406 40.909 0.00 0.00 0.00 4.02
654 675 4.556233 TCATTTACTCAACTCGTGTGGAG 58.444 43.478 18.29 18.29 46.96 3.86
668 689 5.813717 TCGTGTGGAGTATACTGTATTTCG 58.186 41.667 10.90 8.12 0.00 3.46
669 690 5.585844 TCGTGTGGAGTATACTGTATTTCGA 59.414 40.000 10.90 10.17 0.00 3.71
670 691 6.093909 TCGTGTGGAGTATACTGTATTTCGAA 59.906 38.462 10.90 0.00 0.00 3.71
671 692 6.748658 CGTGTGGAGTATACTGTATTTCGAAA 59.251 38.462 13.91 13.91 0.00 3.46
672 693 7.274033 CGTGTGGAGTATACTGTATTTCGAAAA 59.726 37.037 15.66 1.71 0.00 2.29
673 694 8.928733 GTGTGGAGTATACTGTATTTCGAAAAA 58.071 33.333 15.66 3.00 0.00 1.94
693 714 2.131776 AAAACGACTGGAACAACCCA 57.868 45.000 0.00 0.00 38.70 4.51
694 715 2.358322 AAACGACTGGAACAACCCAT 57.642 45.000 0.00 0.00 38.70 4.00
695 716 1.604604 AACGACTGGAACAACCCATG 58.395 50.000 0.00 0.00 38.70 3.66
696 717 0.889186 ACGACTGGAACAACCCATGC 60.889 55.000 0.00 0.00 38.70 4.06
697 718 0.888736 CGACTGGAACAACCCATGCA 60.889 55.000 0.00 0.00 38.70 3.96
698 719 0.883833 GACTGGAACAACCCATGCAG 59.116 55.000 0.00 0.00 38.70 4.41
699 720 0.540365 ACTGGAACAACCCATGCAGG 60.540 55.000 0.00 0.00 38.70 4.85
700 721 0.251297 CTGGAACAACCCATGCAGGA 60.251 55.000 0.00 0.00 37.52 3.86
701 722 0.539438 TGGAACAACCCATGCAGGAC 60.539 55.000 0.00 0.00 34.88 3.85
702 723 1.250840 GGAACAACCCATGCAGGACC 61.251 60.000 0.00 0.00 41.22 4.46
703 724 1.228862 AACAACCCATGCAGGACCC 60.229 57.895 0.00 0.00 41.22 4.46
704 725 2.017668 AACAACCCATGCAGGACCCA 62.018 55.000 0.00 0.00 41.22 4.51
705 726 1.228831 CAACCCATGCAGGACCCAA 60.229 57.895 0.00 0.00 41.22 4.12
706 727 1.228862 AACCCATGCAGGACCCAAC 60.229 57.895 0.00 0.00 41.22 3.77
707 728 2.017668 AACCCATGCAGGACCCAACA 62.018 55.000 0.00 0.00 41.22 3.33
708 729 1.000739 CCCATGCAGGACCCAACAT 59.999 57.895 0.00 0.00 41.22 2.71
709 730 1.324740 CCCATGCAGGACCCAACATG 61.325 60.000 0.00 10.60 41.22 3.21
710 731 2.195389 CATGCAGGACCCAACATGG 58.805 57.895 9.95 0.00 36.98 3.66
711 732 0.612732 CATGCAGGACCCAACATGGT 60.613 55.000 9.95 0.00 42.79 3.55
712 733 0.998928 ATGCAGGACCCAACATGGTA 59.001 50.000 0.00 0.00 39.24 3.25
713 734 0.037590 TGCAGGACCCAACATGGTAC 59.962 55.000 0.00 0.00 39.24 3.34
714 735 1.024579 GCAGGACCCAACATGGTACG 61.025 60.000 0.00 0.00 44.61 3.67
715 736 1.024579 CAGGACCCAACATGGTACGC 61.025 60.000 0.00 0.00 44.61 4.42
716 737 1.003112 GGACCCAACATGGTACGCA 60.003 57.895 0.00 0.00 39.24 5.24
717 738 0.393808 GGACCCAACATGGTACGCAT 60.394 55.000 0.00 0.00 39.24 4.73
718 739 1.134340 GGACCCAACATGGTACGCATA 60.134 52.381 0.00 0.00 39.24 3.14
719 740 2.210116 GACCCAACATGGTACGCATAG 58.790 52.381 0.00 0.00 39.24 2.23
720 741 1.134220 ACCCAACATGGTACGCATAGG 60.134 52.381 0.00 0.00 36.67 2.57
721 742 1.134220 CCCAACATGGTACGCATAGGT 60.134 52.381 0.00 0.00 35.17 3.08
722 743 2.639065 CCAACATGGTACGCATAGGTT 58.361 47.619 0.00 0.00 31.35 3.50
723 744 3.013921 CCAACATGGTACGCATAGGTTT 58.986 45.455 0.00 0.00 31.35 3.27
724 745 3.442273 CCAACATGGTACGCATAGGTTTT 59.558 43.478 0.00 0.00 31.35 2.43
725 746 4.082463 CCAACATGGTACGCATAGGTTTTT 60.082 41.667 0.00 0.00 31.35 1.94
806 827 2.749076 TCATAGGTTGCAACTCATGTGC 59.251 45.455 27.64 10.31 0.00 4.57
849 870 3.303197 CGTAGTCACACTATAGCCTGACG 60.303 52.174 18.20 8.95 38.45 4.35
851 872 0.380733 TCACACTATAGCCTGACGCG 59.619 55.000 3.53 3.53 44.76 6.01
857 878 2.424601 ACTATAGCCTGACGCGTTACAA 59.575 45.455 15.53 0.00 44.76 2.41
872 893 2.036958 TACAAATCACGAGGCCCATG 57.963 50.000 0.00 0.00 0.00 3.66
905 926 1.559065 CCCACCCCACCACGATACTT 61.559 60.000 0.00 0.00 0.00 2.24
959 1083 2.126965 CCGCGACGTTCGTCTCTT 60.127 61.111 20.22 0.00 42.81 2.85
963 1087 0.703466 GCGACGTTCGTCTCTTTCTG 59.297 55.000 20.22 6.75 42.81 3.02
964 1088 1.328439 CGACGTTCGTCTCTTTCTGG 58.672 55.000 20.22 1.95 34.72 3.86
968 1096 1.341606 GTTCGTCTCTTTCTGGCTCG 58.658 55.000 0.00 0.00 0.00 5.03
977 1105 3.971453 TTCTGGCTCGCTCGCTTCG 62.971 63.158 0.00 0.00 0.00 3.79
1440 1581 1.516386 CGTGCAGTACCGCTTCGAT 60.516 57.895 11.63 0.00 34.02 3.59
1569 1750 7.442364 AGTGCATTAATGGTACTGTACATGATC 59.558 37.037 18.79 9.74 30.88 2.92
1642 1826 1.475403 TCCTGGACTCAAGTCGATCC 58.525 55.000 4.17 0.00 45.65 3.36
1695 1879 5.106157 CGACAAGATTAGGCTGGACAAAATT 60.106 40.000 0.00 0.00 0.00 1.82
1710 1894 5.185828 GGACAAAATTCTTGAAGCATACCCT 59.814 40.000 7.18 0.00 0.00 4.34
1713 1897 7.602753 ACAAAATTCTTGAAGCATACCCTTAC 58.397 34.615 7.18 0.00 0.00 2.34
1797 1981 1.958288 TTCTAAGGCAAGAGCTCCCT 58.042 50.000 10.93 7.19 41.70 4.20
1861 2045 2.232208 CTCCAAGAAAACCAGGCCAATC 59.768 50.000 5.01 0.00 0.00 2.67
1944 2131 1.607756 ACTCGGCAGCTTCCTCTCA 60.608 57.895 0.00 0.00 0.00 3.27
1951 2138 0.108898 CAGCTTCCTCTCAGTGTCGG 60.109 60.000 0.00 0.00 0.00 4.79
1954 2141 1.533033 TTCCTCTCAGTGTCGGCCA 60.533 57.895 2.24 0.00 0.00 5.36
2024 2211 4.680237 CTGGGTGCTCCGCGACAA 62.680 66.667 8.23 0.00 38.76 3.18
2095 2288 3.892633 TGGTGTGACCAGCTCAAAA 57.107 47.368 0.00 0.00 44.79 2.44
2297 2491 0.527817 GACGGCGTCATTGGTAGAGG 60.528 60.000 33.07 0.00 32.09 3.69
2368 2565 0.455410 CACGAGGAGGAGAGCTTCTG 59.545 60.000 0.00 0.00 0.00 3.02
2415 2612 1.143073 GTTGAAGTGGGTGGTTCCTCT 59.857 52.381 0.00 0.00 36.25 3.69
2429 2626 3.964031 GGTTCCTCTGACAGAGATATGGT 59.036 47.826 30.22 0.00 45.07 3.55
2468 2665 6.684686 ACATTTCACATTTCAAGGACTGATG 58.315 36.000 0.00 0.00 32.78 3.07
2485 2682 4.142359 ACTGATGTGTTCTTAGAGGCTACG 60.142 45.833 0.00 0.00 0.00 3.51
2509 2706 5.779529 TCTCAAACAAACGTACTACCTCT 57.220 39.130 0.00 0.00 0.00 3.69
2526 2723 5.520748 ACCTCTGTTCCATAATTCCTGTT 57.479 39.130 0.00 0.00 0.00 3.16
2573 2770 6.666417 AGTAGGTTCGTTATCGTGATGTATC 58.334 40.000 0.00 0.00 38.33 2.24
2580 2777 6.210796 TCGTTATCGTGATGTATCCGAATTT 58.789 36.000 8.67 0.00 34.76 1.82
2615 2812 2.167693 TGCTAGTACTCCACCATTTCCG 59.832 50.000 0.00 0.00 0.00 4.30
2695 2892 9.219603 TCAGAACAATCTCTTTGGTGTAATAAG 57.780 33.333 0.00 0.00 34.61 1.73
2705 2902 4.497473 TGGTGTAATAAGCTTGCACAAC 57.503 40.909 9.86 12.88 36.87 3.32
2973 5948 5.914033 TCAGAACACTTGCAAGTAAGTACT 58.086 37.500 30.67 20.62 38.78 2.73
2974 5949 5.983720 TCAGAACACTTGCAAGTAAGTACTC 59.016 40.000 30.67 19.15 38.78 2.59
2975 5950 5.177696 CAGAACACTTGCAAGTAAGTACTCC 59.822 44.000 30.67 14.76 38.78 3.85
2976 5951 4.004196 ACACTTGCAAGTAAGTACTCCC 57.996 45.455 30.67 0.00 38.78 4.30
2977 5952 3.646637 ACACTTGCAAGTAAGTACTCCCT 59.353 43.478 30.67 1.66 38.78 4.20
2978 5953 4.246458 CACTTGCAAGTAAGTACTCCCTC 58.754 47.826 30.67 0.00 38.78 4.30
2979 5954 4.021016 CACTTGCAAGTAAGTACTCCCTCT 60.021 45.833 30.67 0.97 38.78 3.69
2980 5955 4.021016 ACTTGCAAGTAAGTACTCCCTCTG 60.021 45.833 30.25 0.00 39.03 3.35
2981 5956 3.507411 TGCAAGTAAGTACTCCCTCTGT 58.493 45.455 0.00 0.00 34.99 3.41
2982 5957 4.669700 TGCAAGTAAGTACTCCCTCTGTA 58.330 43.478 0.00 0.00 34.99 2.74
2983 5958 5.081728 TGCAAGTAAGTACTCCCTCTGTAA 58.918 41.667 0.00 0.00 34.99 2.41
2984 5959 5.541101 TGCAAGTAAGTACTCCCTCTGTAAA 59.459 40.000 0.00 0.00 34.99 2.01
2985 5960 5.868258 GCAAGTAAGTACTCCCTCTGTAAAC 59.132 44.000 0.00 0.00 34.99 2.01
2986 5961 6.295180 GCAAGTAAGTACTCCCTCTGTAAACT 60.295 42.308 0.00 0.00 34.99 2.66
2987 5962 7.094032 GCAAGTAAGTACTCCCTCTGTAAACTA 60.094 40.741 0.00 0.00 34.99 2.24
2988 5963 8.800332 CAAGTAAGTACTCCCTCTGTAAACTAA 58.200 37.037 0.00 0.00 34.99 2.24
2989 5964 9.544579 AAGTAAGTACTCCCTCTGTAAACTAAT 57.455 33.333 0.00 0.00 34.99 1.73
2997 5972 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2999 5974 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
3048 6023 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3049 6024 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3050 6025 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3051 6026 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3052 6027 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3053 6028 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3054 6029 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3055 6030 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
3070 6045 6.884836 GGAGGGAGTACATGACTATTTTGTTT 59.115 38.462 0.00 0.00 39.06 2.83
3134 6109 5.069119 ACAAGAAACTGGAAAAGCTTTAGGG 59.931 40.000 13.10 6.03 0.00 3.53
3139 6114 1.710809 TGGAAAAGCTTTAGGGCTCCT 59.289 47.619 21.70 2.46 42.24 3.69
3150 6125 5.105187 GCTTTAGGGCTCCTTTGATTCAAAT 60.105 40.000 12.04 0.00 34.61 2.32
3227 6202 6.214399 GGTTGTTCGATTCGTAGGATAGAAT 58.786 40.000 5.89 0.00 39.52 2.40
3228 6203 6.362820 GGTTGTTCGATTCGTAGGATAGAATC 59.637 42.308 5.89 7.81 45.45 2.52
3299 6279 3.895232 TCTAGCATCCACTCAAACCTC 57.105 47.619 0.00 0.00 0.00 3.85
3303 6283 3.152341 AGCATCCACTCAAACCTCTTTG 58.848 45.455 0.00 0.00 38.56 2.77
3308 6288 4.207165 TCCACTCAAACCTCTTTGAAAGG 58.793 43.478 4.94 0.00 44.18 3.11
3311 6291 5.048434 CCACTCAAACCTCTTTGAAAGGATC 60.048 44.000 4.94 0.00 44.18 3.36
3321 6301 8.588472 ACCTCTTTGAAAGGATCCTTTATTTTG 58.412 33.333 34.50 23.26 45.16 2.44
3351 6331 4.149571 CGAGGATTGTATCTTCTCAATGCG 59.850 45.833 0.00 0.00 43.55 4.73
3368 6348 2.837498 TGCGGACATAGTCATTGATGG 58.163 47.619 0.00 0.00 33.68 3.51
3373 6353 5.181009 CGGACATAGTCATTGATGGCATAT 58.819 41.667 0.00 0.00 32.24 1.78
3376 6356 6.093219 GGACATAGTCATTGATGGCATATGTC 59.907 42.308 22.74 22.74 43.30 3.06
3386 6366 0.250467 GGCATATGTCGAGCACCCAT 60.250 55.000 4.29 0.00 0.00 4.00
3461 6441 2.237143 TGAGTCATGGAGTGAACCCATC 59.763 50.000 0.00 0.00 42.18 3.51
3463 6443 0.107703 TCATGGAGTGAACCCATCGC 60.108 55.000 0.00 0.00 42.18 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 3.221771 GAGCTAGATCTTCTCTCAGCCA 58.778 50.000 0.00 0.00 34.11 4.75
468 489 0.949105 GTTCAGGTCGACGTGGCAAT 60.949 55.000 31.35 1.04 33.00 3.56
630 651 5.168569 TCCACACGAGTTGAGTAAATGATC 58.831 41.667 0.00 0.00 0.00 2.92
631 652 5.147330 TCCACACGAGTTGAGTAAATGAT 57.853 39.130 0.00 0.00 0.00 2.45
644 665 5.907945 CGAAATACAGTATACTCCACACGAG 59.092 44.000 1.26 0.00 44.95 4.18
645 666 5.585844 TCGAAATACAGTATACTCCACACGA 59.414 40.000 1.26 7.76 0.00 4.35
646 667 5.813717 TCGAAATACAGTATACTCCACACG 58.186 41.667 1.26 5.63 0.00 4.49
647 668 8.470040 TTTTCGAAATACAGTATACTCCACAC 57.530 34.615 12.12 0.00 0.00 3.82
673 694 2.448453 TGGGTTGTTCCAGTCGTTTTT 58.552 42.857 0.00 0.00 38.11 1.94
674 695 2.131776 TGGGTTGTTCCAGTCGTTTT 57.868 45.000 0.00 0.00 38.11 2.43
675 696 1.953686 CATGGGTTGTTCCAGTCGTTT 59.046 47.619 0.00 0.00 40.56 3.60
676 697 1.604604 CATGGGTTGTTCCAGTCGTT 58.395 50.000 0.00 0.00 40.56 3.85
677 698 0.889186 GCATGGGTTGTTCCAGTCGT 60.889 55.000 0.00 0.00 40.56 4.34
678 699 0.888736 TGCATGGGTTGTTCCAGTCG 60.889 55.000 0.00 0.00 40.56 4.18
679 700 0.883833 CTGCATGGGTTGTTCCAGTC 59.116 55.000 0.00 0.00 40.56 3.51
680 701 0.540365 CCTGCATGGGTTGTTCCAGT 60.540 55.000 0.00 0.00 40.56 4.00
681 702 0.251297 TCCTGCATGGGTTGTTCCAG 60.251 55.000 0.00 0.00 40.56 3.86
682 703 0.539438 GTCCTGCATGGGTTGTTCCA 60.539 55.000 0.00 0.00 41.60 3.53
683 704 1.250840 GGTCCTGCATGGGTTGTTCC 61.251 60.000 0.00 0.00 36.20 3.62
684 705 1.250840 GGGTCCTGCATGGGTTGTTC 61.251 60.000 0.00 0.00 36.20 3.18
685 706 1.228862 GGGTCCTGCATGGGTTGTT 60.229 57.895 0.00 0.00 36.20 2.83
686 707 2.017668 TTGGGTCCTGCATGGGTTGT 62.018 55.000 0.00 0.00 36.20 3.32
687 708 1.228831 TTGGGTCCTGCATGGGTTG 60.229 57.895 0.00 0.00 36.20 3.77
688 709 1.228862 GTTGGGTCCTGCATGGGTT 60.229 57.895 0.00 0.00 36.20 4.11
689 710 1.803453 ATGTTGGGTCCTGCATGGGT 61.803 55.000 0.00 0.00 36.20 4.51
690 711 1.000739 ATGTTGGGTCCTGCATGGG 59.999 57.895 0.00 0.00 36.20 4.00
691 712 2.195389 CATGTTGGGTCCTGCATGG 58.805 57.895 12.80 0.00 36.15 3.66
692 713 0.612732 ACCATGTTGGGTCCTGCATG 60.613 55.000 13.33 13.33 43.37 4.06
693 714 0.998928 TACCATGTTGGGTCCTGCAT 59.001 50.000 0.00 0.00 43.37 3.96
694 715 0.037590 GTACCATGTTGGGTCCTGCA 59.962 55.000 0.00 0.00 43.37 4.41
695 716 1.024579 CGTACCATGTTGGGTCCTGC 61.025 60.000 0.00 0.00 43.37 4.85
696 717 1.024579 GCGTACCATGTTGGGTCCTG 61.025 60.000 0.00 0.00 43.37 3.86
697 718 1.298667 GCGTACCATGTTGGGTCCT 59.701 57.895 0.00 0.00 43.37 3.85
698 719 0.393808 ATGCGTACCATGTTGGGTCC 60.394 55.000 0.00 0.00 43.37 4.46
699 720 2.210116 CTATGCGTACCATGTTGGGTC 58.790 52.381 6.99 0.00 43.37 4.46
700 721 1.134220 CCTATGCGTACCATGTTGGGT 60.134 52.381 6.99 0.00 43.37 4.51
701 722 1.134220 ACCTATGCGTACCATGTTGGG 60.134 52.381 6.99 6.54 43.37 4.12
702 723 2.325583 ACCTATGCGTACCATGTTGG 57.674 50.000 6.99 8.30 45.02 3.77
703 724 4.695217 AAAACCTATGCGTACCATGTTG 57.305 40.909 6.99 0.19 35.34 3.33
773 794 9.515226 AGTTGCAACCTATGAGTAATTCTAAAA 57.485 29.630 25.62 0.00 0.00 1.52
774 795 9.162764 GAGTTGCAACCTATGAGTAATTCTAAA 57.837 33.333 25.62 0.00 0.00 1.85
775 796 8.318412 TGAGTTGCAACCTATGAGTAATTCTAA 58.682 33.333 25.62 0.00 0.00 2.10
776 797 7.847096 TGAGTTGCAACCTATGAGTAATTCTA 58.153 34.615 25.62 1.54 0.00 2.10
777 798 6.711277 TGAGTTGCAACCTATGAGTAATTCT 58.289 36.000 25.62 1.73 0.00 2.40
778 799 6.985188 TGAGTTGCAACCTATGAGTAATTC 57.015 37.500 25.62 12.27 0.00 2.17
779 800 6.886459 ACATGAGTTGCAACCTATGAGTAATT 59.114 34.615 33.01 17.37 31.29 1.40
780 801 6.317140 CACATGAGTTGCAACCTATGAGTAAT 59.683 38.462 33.01 17.87 31.29 1.89
781 802 5.643348 CACATGAGTTGCAACCTATGAGTAA 59.357 40.000 33.01 10.44 31.29 2.24
782 803 5.178061 CACATGAGTTGCAACCTATGAGTA 58.822 41.667 33.01 13.43 31.29 2.59
783 804 4.005650 CACATGAGTTGCAACCTATGAGT 58.994 43.478 33.01 20.60 31.29 3.41
784 805 3.181503 GCACATGAGTTGCAACCTATGAG 60.182 47.826 33.01 28.41 31.29 2.90
785 806 2.749076 GCACATGAGTTGCAACCTATGA 59.251 45.455 33.01 13.10 31.29 2.15
786 807 2.751259 AGCACATGAGTTGCAACCTATG 59.249 45.455 28.31 28.31 0.00 2.23
787 808 3.077484 AGCACATGAGTTGCAACCTAT 57.923 42.857 25.62 16.86 0.00 2.57
788 809 2.566833 AGCACATGAGTTGCAACCTA 57.433 45.000 25.62 15.30 0.00 3.08
789 810 2.430465 CTAGCACATGAGTTGCAACCT 58.570 47.619 25.62 15.45 0.00 3.50
790 811 1.470098 CCTAGCACATGAGTTGCAACC 59.530 52.381 25.62 17.03 0.00 3.77
849 870 0.096454 GGCCTCGTGATTTGTAACGC 59.904 55.000 0.00 0.00 0.00 4.84
851 872 1.816074 TGGGCCTCGTGATTTGTAAC 58.184 50.000 4.53 0.00 0.00 2.50
857 878 2.514592 CGCATGGGCCTCGTGATT 60.515 61.111 15.31 0.00 36.38 2.57
905 926 2.970324 GTCCGTGCGCCAACAAGA 60.970 61.111 4.18 0.00 0.00 3.02
946 1070 1.061485 GCCAGAAAGAGACGAACGTC 58.939 55.000 17.79 17.79 44.86 4.34
947 1071 0.674534 AGCCAGAAAGAGACGAACGT 59.325 50.000 0.00 0.00 0.00 3.99
959 1083 2.125912 GAAGCGAGCGAGCCAGAA 60.126 61.111 2.87 0.00 38.01 3.02
977 1105 0.538287 AGCTGGTTGGCTTGAACCTC 60.538 55.000 12.20 6.19 45.07 3.85
984 1112 1.669440 CATTGCAGCTGGTTGGCTT 59.331 52.632 17.12 0.00 41.00 4.35
1059 1189 2.030412 AGCATGGCGTTGACGTGA 59.970 55.556 0.00 0.00 42.22 4.35
1569 1750 6.537660 TGACATCTGCATGAGATTTAAGACTG 59.462 38.462 0.00 0.00 39.64 3.51
1695 1879 3.512329 TCACGTAAGGGTATGCTTCAAGA 59.488 43.478 0.00 0.00 45.20 3.02
1710 1894 1.463056 CATTGCGCTTTCCTCACGTAA 59.537 47.619 9.73 0.00 35.93 3.18
1713 1897 0.453282 CACATTGCGCTTTCCTCACG 60.453 55.000 9.73 0.00 0.00 4.35
1797 1981 2.055042 AACGGCAAACACAGGGCAA 61.055 52.632 0.00 0.00 0.00 4.52
1861 2045 3.539604 CCATGTAGCTTTCTTCCTCTGG 58.460 50.000 0.00 0.00 0.00 3.86
1951 2138 4.803426 CTCGTCGAGCTGGGTGGC 62.803 72.222 9.74 0.00 0.00 5.01
1954 2141 3.515611 GATCTCGTCGAGCTGGGT 58.484 61.111 17.61 0.93 0.00 4.51
2023 2210 2.345244 CTGCACTCGGGAGCACTT 59.655 61.111 2.24 0.00 35.39 3.16
2024 2211 3.699894 CCTGCACTCGGGAGCACT 61.700 66.667 2.24 0.00 41.45 4.40
2187 2380 1.300233 GTCGAAGGCTATCGGCAGG 60.300 63.158 15.38 0.00 46.23 4.85
2297 2491 2.897350 CGGCTCCAGCGATTTCCC 60.897 66.667 0.00 0.00 43.26 3.97
2326 2520 0.602638 TCGCCATCACCACAGTTCAC 60.603 55.000 0.00 0.00 0.00 3.18
2415 2612 6.155049 TGATGAAAGACACCATATCTCTGTCA 59.845 38.462 0.00 0.00 37.39 3.58
2468 2665 4.082895 TGAGAACGTAGCCTCTAAGAACAC 60.083 45.833 11.94 0.00 32.85 3.32
2485 2682 5.981915 AGAGGTAGTACGTTTGTTTGAGAAC 59.018 40.000 0.00 0.00 36.29 3.01
2573 2770 7.251704 AGCAGATACTACAAATCAAATTCGG 57.748 36.000 0.00 0.00 0.00 4.30
2580 2777 7.778382 TGGAGTACTAGCAGATACTACAAATCA 59.222 37.037 0.00 0.00 38.94 2.57
2592 2789 3.451178 GGAAATGGTGGAGTACTAGCAGA 59.549 47.826 0.00 0.00 38.28 4.26
2615 2812 5.639506 TGAGAAAATCGACCAGAGTTCATTC 59.360 40.000 0.00 0.00 35.96 2.67
2695 2892 3.059461 CACCAATTGAATGTTGTGCAAGC 60.059 43.478 7.12 0.00 0.00 4.01
2705 2902 4.196626 ACAATCTGCCACCAATTGAATG 57.803 40.909 7.12 4.86 35.03 2.67
2752 5726 4.177026 GGAGTCGACTTACTACACGAGTA 58.823 47.826 21.08 0.00 39.81 2.59
2753 5727 2.999355 GGAGTCGACTTACTACACGAGT 59.001 50.000 21.08 0.00 42.69 4.18
2754 5728 2.998670 TGGAGTCGACTTACTACACGAG 59.001 50.000 21.08 0.00 35.33 4.18
2755 5729 3.044235 TGGAGTCGACTTACTACACGA 57.956 47.619 21.08 0.00 35.33 4.35
2798 5772 8.893727 GCAGAAAAAGGAGTTAATAGCTCATAA 58.106 33.333 6.47 0.00 34.83 1.90
2799 5773 8.046708 TGCAGAAAAAGGAGTTAATAGCTCATA 58.953 33.333 6.47 0.00 34.83 2.15
2973 5948 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
3022 5997 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3023 5998 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3024 5999 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3025 6000 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3026 6001 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3027 6002 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3028 6003 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3029 6004 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3030 6005 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
3031 6006 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
3032 6007 9.017509 CATGTACTCCCTCCGTAAACTAATATA 57.982 37.037 0.00 0.00 0.00 0.86
3033 6008 7.727186 TCATGTACTCCCTCCGTAAACTAATAT 59.273 37.037 0.00 0.00 0.00 1.28
3034 6009 7.013655 GTCATGTACTCCCTCCGTAAACTAATA 59.986 40.741 0.00 0.00 0.00 0.98
3035 6010 5.895534 TCATGTACTCCCTCCGTAAACTAAT 59.104 40.000 0.00 0.00 0.00 1.73
3036 6011 5.126061 GTCATGTACTCCCTCCGTAAACTAA 59.874 44.000 0.00 0.00 0.00 2.24
3037 6012 4.641989 GTCATGTACTCCCTCCGTAAACTA 59.358 45.833 0.00 0.00 0.00 2.24
3038 6013 3.446516 GTCATGTACTCCCTCCGTAAACT 59.553 47.826 0.00 0.00 0.00 2.66
3039 6014 3.446516 AGTCATGTACTCCCTCCGTAAAC 59.553 47.826 0.00 0.00 30.33 2.01
3040 6015 3.705051 AGTCATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 30.33 2.01
3041 6016 3.377253 AGTCATGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 30.33 3.18
3042 6017 4.719026 ATAGTCATGTACTCCCTCCGTA 57.281 45.455 0.00 0.00 39.80 4.02
3043 6018 3.596940 ATAGTCATGTACTCCCTCCGT 57.403 47.619 0.00 0.00 39.80 4.69
3044 6019 4.939052 AAATAGTCATGTACTCCCTCCG 57.061 45.455 0.00 0.00 39.80 4.63
3045 6020 5.990668 ACAAAATAGTCATGTACTCCCTCC 58.009 41.667 0.00 0.00 39.80 4.30
3046 6021 7.923414 AAACAAAATAGTCATGTACTCCCTC 57.077 36.000 0.00 0.00 39.80 4.30
3047 6022 9.227777 GTTAAACAAAATAGTCATGTACTCCCT 57.772 33.333 0.00 0.00 39.80 4.20
3048 6023 9.227777 AGTTAAACAAAATAGTCATGTACTCCC 57.772 33.333 0.00 0.00 39.80 4.30
3134 6109 7.894376 TGAAAATCATTTGAATCAAAGGAGC 57.106 32.000 24.00 15.06 44.97 4.70
3199 6174 1.576246 CTACGAATCGAACAACCGACG 59.424 52.381 10.55 0.00 41.70 5.12
3202 6177 2.267188 TCCTACGAATCGAACAACCG 57.733 50.000 10.55 0.00 0.00 4.44
3299 6279 8.876790 GCATCAAAATAAAGGATCCTTTCAAAG 58.123 33.333 37.19 24.62 44.17 2.77
3303 6283 7.117285 AGGCATCAAAATAAAGGATCCTTTC 57.883 36.000 37.19 21.53 44.17 2.62
3308 6288 5.049129 CCTCGAGGCATCAAAATAAAGGATC 60.049 44.000 20.67 0.00 0.00 3.36
3311 6291 4.199310 TCCTCGAGGCATCAAAATAAAGG 58.801 43.478 27.39 0.00 34.44 3.11
3321 6301 3.951775 AGATACAATCCTCGAGGCATC 57.048 47.619 27.39 20.17 34.44 3.91
3323 6303 3.300388 AGAAGATACAATCCTCGAGGCA 58.700 45.455 27.39 15.79 34.44 4.75
3351 6331 5.942236 ACATATGCCATCAATGACTATGTCC 59.058 40.000 1.58 0.00 29.11 4.02
3368 6348 2.341257 CTATGGGTGCTCGACATATGC 58.659 52.381 1.58 0.00 0.00 3.14
3373 6353 1.549243 TTGCCTATGGGTGCTCGACA 61.549 55.000 0.00 0.00 34.45 4.35
3376 6356 2.182842 GCTTGCCTATGGGTGCTCG 61.183 63.158 0.00 0.00 34.45 5.03
3386 6366 1.139734 CTCTTCGAGCGCTTGCCTA 59.860 57.895 20.39 6.76 40.41 3.93


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

AutoCloner maintained by Alex Coulton.