Multiple sequence alignment - TraesCS7D01G083000

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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 TraesCS7D01G083000 chr7D 100.000 4658 0 0 1 4658 49829678 49825021 0.000000e+00 8602.0
1 TraesCS7D01G083000 chr7D 83.810 105 15 2 3203 3306 469032669 469032772 1.070000e-16 99.0
2 TraesCS7D01G083000 chr4A 94.765 3381 140 23 754 4111 664446345 664442979 0.000000e+00 5228.0
3 TraesCS7D01G083000 chr4A 94.022 552 26 5 4107 4654 664442425 664441877 0.000000e+00 830.0
4 TraesCS7D01G083000 chr4A 83.258 663 45 27 1 652 664446967 664446360 2.450000e-152 549.0
5 TraesCS7D01G083000 chr4A 98.864 88 1 0 819 906 712733794 712733707 1.740000e-34 158.0
6 TraesCS7D01G083000 chr4A 77.202 193 35 8 2972 3160 159112568 159112381 2.290000e-18 104.0
7 TraesCS7D01G083000 chr4A 100.000 29 0 0 2835 2863 126584525 126584553 2.000000e-03 54.7
8 TraesCS7D01G083000 chr7A 95.321 3227 121 13 900 4111 52953098 52949887 0.000000e+00 5096.0
9 TraesCS7D01G083000 chr7A 92.921 777 30 8 62 822 52953860 52953093 0.000000e+00 1107.0
10 TraesCS7D01G083000 chr7A 93.285 551 32 3 4107 4654 52949334 52948786 0.000000e+00 808.0
11 TraesCS7D01G083000 chr5B 82.438 763 110 16 1331 2088 614051078 614051821 0.000000e+00 645.0
12 TraesCS7D01G083000 chr5B 77.612 402 64 11 2311 2711 613653712 613654088 2.180000e-53 220.0
13 TraesCS7D01G083000 chr5B 78.238 193 33 8 2972 3160 291175995 291176182 1.060000e-21 115.0
14 TraesCS7D01G083000 chr5B 91.358 81 5 2 3081 3160 72168779 72168700 4.930000e-20 110.0
15 TraesCS7D01G083000 chr5B 83.333 108 17 1 1011 1118 613280982 613281088 1.070000e-16 99.0
16 TraesCS7D01G083000 chr5B 82.569 109 17 2 1011 1118 613631110 613631217 1.380000e-15 95.3
17 TraesCS7D01G083000 chr4D 78.602 472 88 10 2835 3301 340990103 340989640 2.720000e-77 300.0
18 TraesCS7D01G083000 chr5D 79.751 321 58 5 3329 3643 496155471 496155790 4.690000e-55 226.0
19 TraesCS7D01G083000 chr5D 77.506 409 65 12 2304 2711 496153286 496153668 2.180000e-53 220.0
20 TraesCS7D01G083000 chr5D 79.464 336 50 12 2988 3319 496218166 496218486 2.180000e-53 220.0
21 TraesCS7D01G083000 chr5D 96.774 93 3 0 812 904 297738433 297738341 6.240000e-34 156.0
22 TraesCS7D01G083000 chr5D 76.344 186 34 8 936 1118 496072961 496073139 1.780000e-14 91.6
23 TraesCS7D01G083000 chr5D 81.250 112 19 2 1008 1118 495906199 495906309 6.420000e-14 89.8
24 TraesCS7D01G083000 chr5D 76.608 171 30 9 951 1118 496134712 496134875 8.300000e-13 86.1
25 TraesCS7D01G083000 chr6B 95.960 99 4 0 809 907 218219330 218219428 1.340000e-35 161.0
26 TraesCS7D01G083000 chr6B 94.059 101 5 1 808 908 478479058 478479157 8.070000e-33 152.0
27 TraesCS7D01G083000 chr4B 77.241 290 54 11 2835 3119 422374955 422374673 4.820000e-35 159.0
28 TraesCS7D01G083000 chr4B 75.472 265 52 13 1406 1663 68402671 68402929 2.940000e-22 117.0
29 TraesCS7D01G083000 chrUn 96.774 93 3 0 812 904 62663395 62663487 6.240000e-34 156.0
30 TraesCS7D01G083000 chr6D 93.333 105 7 0 812 916 268067204 268067100 6.240000e-34 156.0
31 TraesCS7D01G083000 chr2D 96.774 93 3 0 812 904 25037877 25037969 6.240000e-34 156.0
32 TraesCS7D01G083000 chr2D 78.238 193 33 8 2972 3160 109266398 109266211 1.060000e-21 115.0
33 TraesCS7D01G083000 chr2D 82.906 117 18 2 3203 3318 490911370 490911255 2.290000e-18 104.0
34 TraesCS7D01G083000 chr7B 95.789 95 4 0 814 908 611720250 611720344 2.240000e-33 154.0
35 TraesCS7D01G083000 chr7B 77.720 193 34 8 2972 3160 665100415 665100602 4.930000e-20 110.0
36 TraesCS7D01G083000 chr7B 85.149 101 11 4 3203 3301 413731733 413731831 2.970000e-17 100.0
37 TraesCS7D01G083000 chr5A 86.207 87 11 1 1033 1118 620166563 620166649 4.960000e-15 93.5
38 TraesCS7D01G083000 chr5A 76.344 186 34 9 936 1118 619957530 619957708 1.780000e-14 91.6
39 TraesCS7D01G083000 chr6A 81.982 111 15 5 3203 3311 470175813 470175920 6.420000e-14 89.8
40 TraesCS7D01G083000 chr1A 81.982 111 15 5 3203 3311 122318615 122318722 6.420000e-14 89.8
41 TraesCS7D01G083000 chr1A 81.579 114 15 6 3201 3311 205179642 205179532 6.420000e-14 89.8
42 TraesCS7D01G083000 chr2B 87.324 71 7 2 3085 3154 404916152 404916083 3.860000e-11 80.5


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 TraesCS7D01G083000 chr7D 49825021 49829678 4657 True 8602.000000 8602 100.000000 1 4658 1 chr7D.!!$R1 4657
1 TraesCS7D01G083000 chr4A 664441877 664446967 5090 True 2202.333333 5228 90.681667 1 4654 3 chr4A.!!$R3 4653
2 TraesCS7D01G083000 chr7A 52948786 52953860 5074 True 2337.000000 5096 93.842333 62 4654 3 chr7A.!!$R1 4592
3 TraesCS7D01G083000 chr5B 614051078 614051821 743 False 645.000000 645 82.438000 1331 2088 1 chr5B.!!$F5 757
4 TraesCS7D01G083000 chr5D 496153286 496155790 2504 False 223.000000 226 78.628500 2304 3643 2 chr5D.!!$F5 1339

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
35 37 0.179065 CATGGCTGGCTTGAGATCGA 60.179 55.000 11.04 0.0 0.00 3.59 F
42 44 0.465705 GGCTTGAGATCGATGGGTCA 59.534 55.000 0.54 0.0 0.00 4.02 F
77 79 1.002134 AGACGTGGATGCAAAGGGG 60.002 57.895 0.00 0.0 0.00 4.79 F
833 868 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.0 0.00 4.37 F
839 874 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.0 0.00 2.71 F
2584 2739 0.834687 ACCTTTGGGCTACAGACGGA 60.835 55.000 0.00 0.0 35.63 4.69 F
2588 2743 1.496060 TTGGGCTACAGACGGATGAT 58.504 50.000 0.00 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1364 3.119637 CCCCTCAACGAACGCATAAAAAT 60.120 43.478 0.00 0.0 0.00 1.82 R
1268 1411 5.184287 TGTTCCGATATCACTCTGTTGTACA 59.816 40.000 3.12 0.0 0.00 2.90 R
2062 2211 5.819379 ACATATAGTTTGTGCATGTCTCCTG 59.181 40.000 0.00 0.0 0.00 3.86 R
2553 2708 2.095212 GCCCAAAGGTTTCGATGAACTC 60.095 50.000 0.35 0.0 34.57 3.01 R
2825 2980 2.992817 TTTCCAGTTGGGCACGCCAT 62.993 55.000 10.83 0.0 37.98 4.40 R
3507 4979 0.812014 TGAGCTTTTTGTCGCCACGA 60.812 50.000 0.00 0.0 0.00 4.35 R
4563 6604 1.372582 GCATGATGCTTCAAGACGGA 58.627 50.000 10.72 0.0 40.96 4.69 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
35 37 0.179065 CATGGCTGGCTTGAGATCGA 60.179 55.000 11.04 0.00 0.00 3.59
42 44 0.465705 GGCTTGAGATCGATGGGTCA 59.534 55.000 0.54 0.00 0.00 4.02
50 52 2.692557 AGATCGATGGGTCACTTCTCAG 59.307 50.000 0.54 0.00 0.00 3.35
51 53 1.924731 TCGATGGGTCACTTCTCAGT 58.075 50.000 0.00 0.00 0.00 3.41
52 54 1.819288 TCGATGGGTCACTTCTCAGTC 59.181 52.381 0.00 0.00 0.00 3.51
53 55 1.134965 CGATGGGTCACTTCTCAGTCC 60.135 57.143 0.00 0.00 0.00 3.85
54 56 2.183679 GATGGGTCACTTCTCAGTCCT 58.816 52.381 0.00 0.00 0.00 3.85
55 57 1.633774 TGGGTCACTTCTCAGTCCTC 58.366 55.000 0.00 0.00 0.00 3.71
56 58 1.133167 TGGGTCACTTCTCAGTCCTCA 60.133 52.381 0.00 0.00 0.00 3.86
58 60 2.028567 GGGTCACTTCTCAGTCCTCAAG 60.029 54.545 0.00 0.00 0.00 3.02
59 61 2.894126 GGTCACTTCTCAGTCCTCAAGA 59.106 50.000 0.00 0.00 0.00 3.02
60 62 3.056891 GGTCACTTCTCAGTCCTCAAGAG 60.057 52.174 0.00 0.00 0.00 2.85
77 79 1.002134 AGACGTGGATGCAAAGGGG 60.002 57.895 0.00 0.00 0.00 4.79
150 152 5.119694 GGCAACTACTGAAAGGGATCTAAG 58.880 45.833 0.00 0.00 39.30 2.18
328 334 2.210116 CCCAGATGATTTTACCGTCCG 58.790 52.381 0.00 0.00 0.00 4.79
363 369 7.332430 GGCATGATTCTTGATTCAACATCAAAA 59.668 33.333 15.59 2.83 37.55 2.44
364 370 8.166706 GCATGATTCTTGATTCAACATCAAAAC 58.833 33.333 15.59 8.32 37.55 2.43
365 371 9.198837 CATGATTCTTGATTCAACATCAAAACA 57.801 29.630 15.59 4.53 37.55 2.83
366 372 9.938280 ATGATTCTTGATTCAACATCAAAACAT 57.062 25.926 15.59 6.00 37.55 2.71
369 375 6.690530 TCTTGATTCAACATCAAAACATCCC 58.309 36.000 0.00 0.00 37.55 3.85
370 376 6.494491 TCTTGATTCAACATCAAAACATCCCT 59.506 34.615 0.00 0.00 37.55 4.20
371 377 6.669125 TGATTCAACATCAAAACATCCCTT 57.331 33.333 0.00 0.00 0.00 3.95
372 378 7.065120 TGATTCAACATCAAAACATCCCTTT 57.935 32.000 0.00 0.00 0.00 3.11
373 379 7.153985 TGATTCAACATCAAAACATCCCTTTC 58.846 34.615 0.00 0.00 0.00 2.62
374 380 6.729690 TTCAACATCAAAACATCCCTTTCT 57.270 33.333 0.00 0.00 0.00 2.52
375 381 7.831691 TTCAACATCAAAACATCCCTTTCTA 57.168 32.000 0.00 0.00 0.00 2.10
376 382 8.421249 TTCAACATCAAAACATCCCTTTCTAT 57.579 30.769 0.00 0.00 0.00 1.98
377 383 9.527157 TTCAACATCAAAACATCCCTTTCTATA 57.473 29.630 0.00 0.00 0.00 1.31
378 384 9.527157 TCAACATCAAAACATCCCTTTCTATAA 57.473 29.630 0.00 0.00 0.00 0.98
404 418 4.668576 ATGAGTAACGTCAATGCAAGTG 57.331 40.909 0.00 0.00 0.00 3.16
516 531 4.162690 GGAGAATCGGCCGCAGGT 62.163 66.667 23.51 4.67 45.51 4.00
607 635 2.125753 CCAGTGCGAGAGACAGCC 60.126 66.667 0.00 0.00 0.00 4.85
637 665 1.978361 AGGGGCAGGAGAAATCTCTT 58.022 50.000 10.09 0.00 42.48 2.85
638 666 1.843206 AGGGGCAGGAGAAATCTCTTC 59.157 52.381 10.09 0.77 42.48 2.87
658 686 7.004555 TCTTCTGAGTTTCCTTGCTACAATA 57.995 36.000 0.00 0.00 0.00 1.90
682 710 1.532868 CGGCCGATTCATGGAGAAATC 59.467 52.381 24.07 0.00 40.22 2.17
691 719 5.512753 TTCATGGAGAAATCTCTCTCTCG 57.487 43.478 10.09 0.00 46.45 4.04
695 726 7.001073 TCATGGAGAAATCTCTCTCTCGAATA 58.999 38.462 10.09 0.00 46.45 1.75
727 762 4.486125 TGTCCAATTCATCTCGAATCCA 57.514 40.909 0.00 0.00 43.83 3.41
745 780 7.595130 TCGAATCCACTTCATCGATTAGTTATG 59.405 37.037 7.11 1.45 39.19 1.90
746 781 7.148738 CGAATCCACTTCATCGATTAGTTATGG 60.149 40.741 7.11 5.74 37.48 2.74
747 782 6.724893 TCCACTTCATCGATTAGTTATGGA 57.275 37.500 7.11 7.69 0.00 3.41
748 783 6.513180 TCCACTTCATCGATTAGTTATGGAC 58.487 40.000 7.11 0.00 0.00 4.02
749 784 6.323996 TCCACTTCATCGATTAGTTATGGACT 59.676 38.462 7.11 0.00 42.55 3.85
750 785 6.986817 CCACTTCATCGATTAGTTATGGACTT 59.013 38.462 7.11 0.00 39.86 3.01
751 786 8.141909 CCACTTCATCGATTAGTTATGGACTTA 58.858 37.037 7.11 0.00 39.86 2.24
752 787 9.698309 CACTTCATCGATTAGTTATGGACTTAT 57.302 33.333 7.11 0.00 39.86 1.73
772 807 1.883275 TGGTTCGATGCAAAATTCCGT 59.117 42.857 0.00 0.00 0.00 4.69
794 829 3.005472 TCCGGATTCGCATTTAGGAGTAG 59.995 47.826 0.00 0.00 34.56 2.57
822 857 6.890979 AACCGGGTCAAGTATATAGTACTC 57.109 41.667 6.32 0.00 0.00 2.59
823 858 5.320277 ACCGGGTCAAGTATATAGTACTCC 58.680 45.833 6.32 0.00 0.00 3.85
824 859 4.704057 CCGGGTCAAGTATATAGTACTCCC 59.296 50.000 0.00 0.00 0.00 4.30
825 860 5.516238 CCGGGTCAAGTATATAGTACTCCCT 60.516 48.000 0.00 0.00 30.86 4.20
826 861 5.647225 CGGGTCAAGTATATAGTACTCCCTC 59.353 48.000 0.00 0.00 30.86 4.30
827 862 5.951148 GGGTCAAGTATATAGTACTCCCTCC 59.049 48.000 0.00 0.00 30.57 4.30
828 863 5.647225 GGTCAAGTATATAGTACTCCCTCCG 59.353 48.000 0.00 0.00 0.00 4.63
829 864 6.237154 GTCAAGTATATAGTACTCCCTCCGT 58.763 44.000 0.00 0.00 0.00 4.69
830 865 6.371271 GTCAAGTATATAGTACTCCCTCCGTC 59.629 46.154 0.00 0.00 0.00 4.79
831 866 5.434182 AGTATATAGTACTCCCTCCGTCC 57.566 47.826 0.00 0.00 0.00 4.79
832 867 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
833 868 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
834 869 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
835 870 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
836 871 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
837 872 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
838 873 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
839 874 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
840 875 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
841 876 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
842 877 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
843 878 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
844 879 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
846 881 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
847 882 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
848 883 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
849 884 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
850 885 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
898 933 4.377897 GTCTTACATTATGGGACGAAGGG 58.622 47.826 0.00 0.00 0.00 3.95
899 934 4.100498 GTCTTACATTATGGGACGAAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
900 935 4.344102 TCTTACATTATGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
901 936 2.478292 ACATTATGGGACGAAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
902 937 3.649843 ACATTATGGGACGAAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
903 938 3.387050 ACATTATGGGACGAAGGGAGTAC 59.613 47.826 0.00 0.00 0.00 2.73
904 939 3.393426 TTATGGGACGAAGGGAGTACT 57.607 47.619 0.00 0.00 0.00 2.73
1043 1172 2.014128 CAAACGGCGGGATGAGTATTT 58.986 47.619 13.24 0.00 0.00 1.40
1177 1313 3.955650 TTGTAAGACCACTAGACCAGC 57.044 47.619 0.00 0.00 0.00 4.85
1192 1328 6.996879 ACTAGACCAGCGATGTTTCTACTATA 59.003 38.462 0.00 0.00 0.00 1.31
1193 1329 6.902771 AGACCAGCGATGTTTCTACTATAT 57.097 37.500 0.00 0.00 0.00 0.86
1218 1354 7.695055 TCTATCCAGATTGGTTTTTGGTAAGA 58.305 34.615 0.00 0.00 39.03 2.10
1219 1355 6.590234 ATCCAGATTGGTTTTTGGTAAGAC 57.410 37.500 0.00 0.00 39.03 3.01
1220 1356 4.517453 TCCAGATTGGTTTTTGGTAAGACG 59.483 41.667 0.00 0.00 39.03 4.18
1222 1358 5.009210 CCAGATTGGTTTTTGGTAAGACGAA 59.991 40.000 0.00 0.00 31.35 3.85
1223 1359 6.294508 CCAGATTGGTTTTTGGTAAGACGAAT 60.295 38.462 0.00 0.00 32.18 3.34
1224 1360 6.582295 CAGATTGGTTTTTGGTAAGACGAATG 59.418 38.462 0.00 0.00 30.52 2.67
1227 1363 4.098044 TGGTTTTTGGTAAGACGAATGCAA 59.902 37.500 0.00 0.00 0.00 4.08
1228 1364 5.044558 GGTTTTTGGTAAGACGAATGCAAA 58.955 37.500 0.00 0.00 0.00 3.68
1268 1411 5.044328 TGAGGGGCGGACTATTCTATATAGT 60.044 44.000 9.58 0.00 37.53 2.12
1273 1416 6.600822 GGGCGGACTATTCTATATAGTGTACA 59.399 42.308 9.58 0.00 35.20 2.90
1275 1418 7.967303 GGCGGACTATTCTATATAGTGTACAAC 59.033 40.741 9.58 0.00 35.20 3.32
1386 1529 3.325870 TGCGAATAAACAGTCTGACCAG 58.674 45.455 6.91 0.05 0.00 4.00
2009 2155 8.696410 TTTGTTGTTTTCTTTCATAGACCAAC 57.304 30.769 0.00 0.00 37.07 3.77
2062 2211 9.929180 TGTGGATATATTTATTGCTGTAGACTC 57.071 33.333 0.00 0.00 0.00 3.36
2063 2212 9.929180 GTGGATATATTTATTGCTGTAGACTCA 57.071 33.333 0.00 0.00 0.00 3.41
2178 2331 6.867662 AGCACATTAATTCAGGTATGCTAC 57.132 37.500 0.00 0.00 40.25 3.58
2218 2371 7.292356 TCCTCATATTCAAAGATACCAGGCTTA 59.708 37.037 0.00 0.00 0.00 3.09
2230 2383 2.897326 ACCAGGCTTATTGGTTTTCACC 59.103 45.455 0.00 0.00 46.57 4.02
2584 2739 0.834687 ACCTTTGGGCTACAGACGGA 60.835 55.000 0.00 0.00 35.63 4.69
2588 2743 1.496060 TTGGGCTACAGACGGATGAT 58.504 50.000 0.00 0.00 0.00 2.45
2590 2745 2.889512 TGGGCTACAGACGGATGATAT 58.110 47.619 0.00 0.00 0.00 1.63
2591 2746 2.562738 TGGGCTACAGACGGATGATATG 59.437 50.000 0.00 0.00 0.00 1.78
2869 3024 1.816835 CAAGTCATGTCAAGGCAGCAT 59.183 47.619 0.00 0.00 0.00 3.79
3112 4488 1.558756 CAGAAGGAGCAGTTGAGGGAT 59.441 52.381 0.00 0.00 0.00 3.85
3124 4500 5.745227 CAGTTGAGGGATGGTTACATTACT 58.255 41.667 0.00 0.00 37.47 2.24
3149 4525 4.335315 CACACAAGACCAAGCTAACTTCAA 59.665 41.667 0.00 0.00 32.29 2.69
3160 4536 6.015940 CCAAGCTAACTTCAACTCAAAAGGAT 60.016 38.462 0.00 0.00 32.29 3.24
3198 4574 6.410540 AGGTCCAATCTATTGAGTCAAAGAC 58.589 40.000 10.14 8.05 40.14 3.01
3313 4689 4.100963 TCATGTAGGTGTCTGTGTGAAGTT 59.899 41.667 0.00 0.00 0.00 2.66
3390 4862 9.679661 TTCATGCCATTATCAAGTAACTCTTTA 57.320 29.630 0.00 0.00 33.63 1.85
3432 4904 4.288626 ACTTTCCCCAACTACTATGCTCAA 59.711 41.667 0.00 0.00 0.00 3.02
3507 4979 1.608590 CAAGTGCGGTTTCCAGACAAT 59.391 47.619 0.00 0.00 0.00 2.71
3541 5013 3.726557 AGCTCAAACATGGATGGAGAA 57.273 42.857 8.85 0.00 0.00 2.87
3838 5318 8.343366 TGACTACTACTTAACTCGCATAATGAG 58.657 37.037 0.00 0.00 39.40 2.90
3873 5353 9.844790 CATACTTTTGATGCAAGACTGAATAAA 57.155 29.630 0.00 0.00 0.00 1.40
3922 5402 8.421249 TTTATGTTCATTGGATTTTGGACTCT 57.579 30.769 0.00 0.00 0.00 3.24
3930 5410 3.009473 TGGATTTTGGACTCTCTCCCTTG 59.991 47.826 0.00 0.00 38.49 3.61
3949 5429 5.130477 CCCTTGAAATTAGGTCTAGCAGGTA 59.870 44.000 0.00 0.00 0.00 3.08
3951 5431 6.127026 CCTTGAAATTAGGTCTAGCAGGTACT 60.127 42.308 0.00 0.00 43.88 2.73
4029 5510 3.689347 TGGAACAATGAGTTGGATCCAG 58.311 45.455 15.53 3.83 44.04 3.86
4052 5533 4.698947 CATCTTATCGTGATGTTGGTCG 57.301 45.455 0.00 0.00 37.22 4.79
4065 5546 5.645929 TGATGTTGGTCGTGCTTTATATTGT 59.354 36.000 0.00 0.00 0.00 2.71
4066 5547 5.950758 TGTTGGTCGTGCTTTATATTGTT 57.049 34.783 0.00 0.00 0.00 2.83
4121 6159 7.768582 AGTAGAGGACATATCTGATCGTCTATG 59.231 40.741 15.60 7.61 40.21 2.23
4145 6183 1.348036 GGCCGAGCCTACCTAATCAAT 59.652 52.381 7.58 0.00 46.69 2.57
4146 6184 2.224548 GGCCGAGCCTACCTAATCAATT 60.225 50.000 7.58 0.00 46.69 2.32
4215 6253 6.132791 ACTTTCATCTTGATAGCATGCTTG 57.867 37.500 28.02 16.12 30.07 4.01
4407 6445 8.939929 TGATACAATTTCTCTTTGATGAGTGAC 58.060 33.333 0.00 0.00 35.68 3.67
4562 6603 3.537874 GCCTACATCGGGCCTCGT 61.538 66.667 0.84 0.00 43.49 4.18
4563 6604 3.090219 GCCTACATCGGGCCTCGTT 62.090 63.158 0.84 0.00 43.49 3.85
4584 6625 0.379669 CGTCTTGAAGCATCATGCCC 59.620 55.000 5.84 0.00 46.52 5.36
4586 6627 0.035152 TCTTGAAGCATCATGCCCGT 60.035 50.000 5.84 0.00 46.52 5.28
4595 6636 4.759782 AGCATCATGCCCGTAGTATTATC 58.240 43.478 5.84 0.00 46.52 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.131933 AGAAGTGACCCATCGATCTCAAG 59.868 47.826 0.00 0.00 0.00 3.02
26 27 3.099905 AGAAGTGACCCATCGATCTCAA 58.900 45.455 0.00 0.00 0.00 3.02
35 37 2.183679 GAGGACTGAGAAGTGACCCAT 58.816 52.381 0.00 0.00 0.00 4.00
42 44 2.817258 CGTCTCTTGAGGACTGAGAAGT 59.183 50.000 0.00 0.00 38.39 3.01
50 52 1.737363 GCATCCACGTCTCTTGAGGAC 60.737 57.143 0.00 0.00 32.88 3.85
51 53 0.532573 GCATCCACGTCTCTTGAGGA 59.467 55.000 0.00 0.00 32.88 3.71
52 54 0.247460 TGCATCCACGTCTCTTGAGG 59.753 55.000 0.00 0.00 0.00 3.86
53 55 2.084610 TTGCATCCACGTCTCTTGAG 57.915 50.000 0.00 0.00 0.00 3.02
54 56 2.416747 CTTTGCATCCACGTCTCTTGA 58.583 47.619 0.00 0.00 0.00 3.02
55 57 1.466167 CCTTTGCATCCACGTCTCTTG 59.534 52.381 0.00 0.00 0.00 3.02
56 58 1.611673 CCCTTTGCATCCACGTCTCTT 60.612 52.381 0.00 0.00 0.00 2.85
58 60 1.026718 CCCCTTTGCATCCACGTCTC 61.027 60.000 0.00 0.00 0.00 3.36
59 61 1.002134 CCCCTTTGCATCCACGTCT 60.002 57.895 0.00 0.00 0.00 4.18
60 62 2.046285 CCCCCTTTGCATCCACGTC 61.046 63.158 0.00 0.00 0.00 4.34
77 79 4.489771 CCACCCCGTGAGCCATCC 62.490 72.222 0.00 0.00 35.23 3.51
150 152 2.475487 GTCTGTTGCCTCGTCAAGTTAC 59.525 50.000 0.00 0.00 0.00 2.50
328 334 2.029838 AGAATCATGCCAAGACCGAC 57.970 50.000 0.00 0.00 0.00 4.79
374 380 9.974980 TGCATTGACGTTACTCATAGAATTATA 57.025 29.630 0.00 0.00 0.00 0.98
375 381 8.887036 TGCATTGACGTTACTCATAGAATTAT 57.113 30.769 0.00 0.00 0.00 1.28
376 382 8.710835 TTGCATTGACGTTACTCATAGAATTA 57.289 30.769 0.00 0.00 0.00 1.40
377 383 7.334421 ACTTGCATTGACGTTACTCATAGAATT 59.666 33.333 0.00 0.00 0.00 2.17
378 384 6.818644 ACTTGCATTGACGTTACTCATAGAAT 59.181 34.615 0.00 0.00 0.00 2.40
404 418 4.976731 CACAAGACGCATAGATGTACTACC 59.023 45.833 0.00 0.00 33.62 3.18
516 531 2.186644 CGATGATCACCGGCACCA 59.813 61.111 0.00 0.00 0.00 4.17
598 626 1.997874 GTCCCCATGGGCTGTCTCT 60.998 63.158 26.87 0.00 43.94 3.10
607 635 3.667217 CTGCCCCTTGTCCCCATGG 62.667 68.421 4.14 4.14 36.01 3.66
637 665 7.491372 CGTAATATTGTAGCAAGGAAACTCAGA 59.509 37.037 0.00 0.00 42.68 3.27
638 666 7.254455 CCGTAATATTGTAGCAAGGAAACTCAG 60.254 40.741 0.00 0.00 42.68 3.35
642 670 5.505159 GGCCGTAATATTGTAGCAAGGAAAC 60.505 44.000 0.00 0.00 0.00 2.78
658 686 1.691976 TCTCCATGAATCGGCCGTAAT 59.308 47.619 27.15 9.68 0.00 1.89
682 710 7.497249 ACAATGGGAAAAATATTCGAGAGAGAG 59.503 37.037 0.00 0.00 43.69 3.20
691 719 9.617523 ATGAATTGGACAATGGGAAAAATATTC 57.382 29.630 0.00 0.00 0.00 1.75
695 726 7.261688 AGATGAATTGGACAATGGGAAAAAT 57.738 32.000 0.00 0.00 0.00 1.82
727 762 9.698309 CATAAGTCCATAACTAATCGATGAAGT 57.302 33.333 0.00 2.99 37.17 3.01
745 780 4.695217 TTTTGCATCGAACCATAAGTCC 57.305 40.909 0.00 0.00 0.00 3.85
746 781 5.743872 GGAATTTTGCATCGAACCATAAGTC 59.256 40.000 0.00 0.26 0.00 3.01
747 782 5.650543 GGAATTTTGCATCGAACCATAAGT 58.349 37.500 0.00 0.00 0.00 2.24
748 783 4.734854 CGGAATTTTGCATCGAACCATAAG 59.265 41.667 0.00 0.00 0.00 1.73
749 784 4.156922 ACGGAATTTTGCATCGAACCATAA 59.843 37.500 0.00 0.00 0.00 1.90
750 785 3.692101 ACGGAATTTTGCATCGAACCATA 59.308 39.130 0.00 0.00 0.00 2.74
751 786 2.491693 ACGGAATTTTGCATCGAACCAT 59.508 40.909 0.00 0.00 0.00 3.55
752 787 1.883275 ACGGAATTTTGCATCGAACCA 59.117 42.857 0.00 0.00 0.00 3.67
772 807 1.760613 ACTCCTAAATGCGAATCCGGA 59.239 47.619 6.61 6.61 41.22 5.14
794 829 6.756221 ACTATATACTTGACCCGGTTTCATC 58.244 40.000 0.00 0.00 0.00 2.92
822 857 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
823 858 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
824 859 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
825 860 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
870 905 6.173191 CGTCCCATAATGTAAGACGTTTTT 57.827 37.500 0.00 0.00 43.89 1.94
871 906 5.789710 CGTCCCATAATGTAAGACGTTTT 57.210 39.130 0.00 0.00 43.89 2.43
876 911 4.100498 TCCCTTCGTCCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
877 912 4.291792 TCCCTTCGTCCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
878 913 4.101119 ACTCCCTTCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
879 914 4.035112 ACTCCCTTCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
880 915 3.649843 ACTCCCTTCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
881 916 2.478292 ACTCCCTTCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
882 917 3.641906 AGTACTCCCTTCGTCCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
883 918 3.924922 AGTACTCCCTTCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
884 919 3.393426 AGTACTCCCTTCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
885 920 4.736611 ATAGTACTCCCTTCGTCCCATA 57.263 45.455 0.00 0.00 0.00 2.74
886 921 3.614568 ATAGTACTCCCTTCGTCCCAT 57.385 47.619 0.00 0.00 0.00 4.00
887 922 3.202818 TGTATAGTACTCCCTTCGTCCCA 59.797 47.826 0.00 0.00 0.00 4.37
888 923 3.825328 TGTATAGTACTCCCTTCGTCCC 58.175 50.000 0.00 0.00 0.00 4.46
889 924 4.886489 ACTTGTATAGTACTCCCTTCGTCC 59.114 45.833 0.00 0.00 34.56 4.79
890 925 5.821995 AGACTTGTATAGTACTCCCTTCGTC 59.178 44.000 0.00 1.52 37.17 4.20
891 926 5.753716 AGACTTGTATAGTACTCCCTTCGT 58.246 41.667 0.00 0.00 37.17 3.85
892 927 6.543100 AGAAGACTTGTATAGTACTCCCTTCG 59.457 42.308 0.00 0.00 37.17 3.79
893 928 7.885009 AGAAGACTTGTATAGTACTCCCTTC 57.115 40.000 0.00 2.61 37.17 3.46
894 929 9.939424 ATAAGAAGACTTGTATAGTACTCCCTT 57.061 33.333 0.00 0.00 37.17 3.95
895 930 9.577222 GATAAGAAGACTTGTATAGTACTCCCT 57.423 37.037 0.00 0.00 37.17 4.20
896 931 8.505625 CGATAAGAAGACTTGTATAGTACTCCC 58.494 40.741 0.00 0.00 37.17 4.30
897 932 9.054922 ACGATAAGAAGACTTGTATAGTACTCC 57.945 37.037 0.00 0.00 37.17 3.85
902 937 9.737427 CATGAACGATAAGAAGACTTGTATAGT 57.263 33.333 0.00 0.00 40.71 2.12
903 938 9.186323 CCATGAACGATAAGAAGACTTGTATAG 57.814 37.037 0.00 0.00 37.53 1.31
904 939 7.652105 GCCATGAACGATAAGAAGACTTGTATA 59.348 37.037 0.00 0.00 37.53 1.47
924 1046 3.548770 GAGGACATGAATGAAGCCATGA 58.451 45.455 0.00 0.00 41.88 3.07
1043 1172 8.542926 TCTTCTCATCATCCAAATTTCTGTAGA 58.457 33.333 0.00 0.00 0.00 2.59
1192 1328 8.336235 TCTTACCAAAAACCAATCTGGATAGAT 58.664 33.333 0.00 0.00 45.51 1.98
1193 1329 7.610305 GTCTTACCAAAAACCAATCTGGATAGA 59.390 37.037 0.00 0.00 40.96 1.98
1203 1339 4.098044 TGCATTCGTCTTACCAAAAACCAA 59.902 37.500 0.00 0.00 0.00 3.67
1215 1351 5.633182 ACGCATAAAAATTTGCATTCGTCTT 59.367 32.000 0.00 0.00 38.80 3.01
1216 1352 5.160641 ACGCATAAAAATTTGCATTCGTCT 58.839 33.333 0.00 0.00 38.80 4.18
1218 1354 5.837586 AACGCATAAAAATTTGCATTCGT 57.162 30.435 0.00 0.00 38.80 3.85
1220 1356 5.842377 ACGAACGCATAAAAATTTGCATTC 58.158 33.333 0.00 0.00 37.61 2.67
1222 1358 5.403766 TCAACGAACGCATAAAAATTTGCAT 59.596 32.000 0.00 0.00 38.80 3.96
1223 1359 4.740205 TCAACGAACGCATAAAAATTTGCA 59.260 33.333 0.00 0.00 38.80 4.08
1224 1360 5.244025 TCAACGAACGCATAAAAATTTGC 57.756 34.783 0.00 0.00 35.50 3.68
1227 1363 4.481463 CCCTCAACGAACGCATAAAAATT 58.519 39.130 0.00 0.00 0.00 1.82
1228 1364 3.119637 CCCCTCAACGAACGCATAAAAAT 60.120 43.478 0.00 0.00 0.00 1.82
1268 1411 5.184287 TGTTCCGATATCACTCTGTTGTACA 59.816 40.000 3.12 0.00 0.00 2.90
1273 1416 8.041323 ACTTTAATGTTCCGATATCACTCTGTT 58.959 33.333 3.12 0.00 0.00 3.16
1275 1418 9.186323 CTACTTTAATGTTCCGATATCACTCTG 57.814 37.037 3.12 0.00 0.00 3.35
1277 1420 9.530633 AACTACTTTAATGTTCCGATATCACTC 57.469 33.333 3.12 0.00 0.00 3.51
1386 1529 9.366216 AGGAAGAAATAACAACAACAAAAAGTC 57.634 29.630 0.00 0.00 0.00 3.01
2062 2211 5.819379 ACATATAGTTTGTGCATGTCTCCTG 59.181 40.000 0.00 0.00 0.00 3.86
2063 2212 5.994250 ACATATAGTTTGTGCATGTCTCCT 58.006 37.500 0.00 0.00 0.00 3.69
2095 2248 5.236911 GCAGACATTGAGCAAATTTTGGAAA 59.763 36.000 10.96 0.00 0.00 3.13
2096 2249 4.751098 GCAGACATTGAGCAAATTTTGGAA 59.249 37.500 10.96 0.00 0.00 3.53
2097 2250 4.039488 AGCAGACATTGAGCAAATTTTGGA 59.961 37.500 10.96 0.00 0.00 3.53
2098 2251 4.312443 AGCAGACATTGAGCAAATTTTGG 58.688 39.130 10.96 0.00 0.00 3.28
2218 2371 6.716284 TCAAAGGAAAAAGGTGAAAACCAAT 58.284 32.000 0.00 0.00 0.00 3.16
2382 2537 5.891198 TGGGATGATCTGGAGAAAAAGAAA 58.109 37.500 0.00 0.00 0.00 2.52
2553 2708 2.095212 GCCCAAAGGTTTCGATGAACTC 60.095 50.000 0.35 0.00 34.57 3.01
2590 2745 8.870116 AGTTGCCATTGTATATGAGTACTATCA 58.130 33.333 0.00 0.00 0.00 2.15
2591 2746 9.360093 GAGTTGCCATTGTATATGAGTACTATC 57.640 37.037 0.00 0.00 0.00 2.08
2825 2980 2.992817 TTTCCAGTTGGGCACGCCAT 62.993 55.000 10.83 0.00 37.98 4.40
2869 3024 2.424234 GGGGGAGTATTTATTGCAGCCA 60.424 50.000 0.00 0.00 0.00 4.75
3112 4488 4.513692 GTCTTGTGTGCAGTAATGTAACCA 59.486 41.667 0.00 0.00 0.00 3.67
3124 4500 1.946768 GTTAGCTTGGTCTTGTGTGCA 59.053 47.619 0.00 0.00 0.00 4.57
3149 4525 4.277476 TGTTTCACCACATCCTTTTGAGT 58.723 39.130 0.00 0.00 0.00 3.41
3160 4536 1.562008 TGGACCTTCTGTTTCACCACA 59.438 47.619 0.00 0.00 0.00 4.17
3198 4574 2.507484 TCACAGCAACAAAGATGAGGG 58.493 47.619 0.00 0.00 0.00 4.30
3432 4904 3.198853 GTGCCTCCTCTCCAAGATACTTT 59.801 47.826 0.00 0.00 0.00 2.66
3507 4979 0.812014 TGAGCTTTTTGTCGCCACGA 60.812 50.000 0.00 0.00 0.00 4.35
3873 5353 9.906660 AAATTCGACACAACACAATTACATTAT 57.093 25.926 0.00 0.00 0.00 1.28
3893 5373 8.594687 GTCCAAAATCCAATGAACATAAATTCG 58.405 33.333 0.00 0.00 0.00 3.34
3922 5402 5.030147 TGCTAGACCTAATTTCAAGGGAGA 58.970 41.667 0.00 0.00 38.54 3.71
3930 5410 6.223351 ACAGTACCTGCTAGACCTAATTTC 57.777 41.667 0.00 0.00 34.37 2.17
3982 5463 7.475299 TCTAAACTTTCAGGGGGTAATGAAAT 58.525 34.615 1.25 0.00 42.72 2.17
4052 5533 7.723270 CAAGTTTGCTCAACAATATAAAGCAC 58.277 34.615 0.00 0.00 42.26 4.40
4215 6253 4.701765 CAGCATCCTGGCATATATACCTC 58.298 47.826 3.60 0.00 35.38 3.85
4399 6437 5.237344 GCAGTAAGTTGAAGTTGTCACTCAT 59.763 40.000 0.00 0.00 35.39 2.90
4508 6549 2.094338 GGTACCAGAACAGTCCTAACCG 60.094 54.545 7.15 0.00 0.00 4.44
4548 6589 3.213264 GGAACGAGGCCCGATGTA 58.787 61.111 18.74 0.00 41.76 2.29
4562 6603 1.739466 GCATGATGCTTCAAGACGGAA 59.261 47.619 10.72 0.00 40.96 4.30
4563 6604 1.372582 GCATGATGCTTCAAGACGGA 58.627 50.000 10.72 0.00 40.96 4.69


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

AutoCloner maintained by Alex Coulton.