Multiple sequence alignment - TraesCS3A01G377800

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 TraesCS3A01G377800 chr3A 100.000 4262 0 0 1 4262 627784431 627788692 0.000000e+00 7871.0
1 TraesCS3A01G377800 chr3A 86.425 2011 189 38 895 2888 627817168 627819111 0.000000e+00 2124.0
2 TraesCS3A01G377800 chr3A 85.912 362 50 1 443 803 732242382 732242021 6.690000e-103 385.0
3 TraesCS3A01G377800 chr3A 89.320 206 14 3 864 1069 627793644 627793841 7.070000e-63 252.0
4 TraesCS3A01G377800 chr3A 78.882 161 34 0 1058 1218 38136559 38136399 4.510000e-20 110.0
5 TraesCS3A01G377800 chr3A 92.157 51 1 3 3333 3383 26869147 26869100 7.650000e-08 69.4
6 TraesCS3A01G377800 chr3A 96.774 31 1 0 3048 3078 627706298 627706328 8.000000e-03 52.8
7 TraesCS3A01G377800 chr3A 96.774 31 1 0 3048 3078 627819194 627819224 8.000000e-03 52.8
8 TraesCS3A01G377800 chr3D 89.552 2345 194 26 998 3325 484726149 484728459 0.000000e+00 2926.0
9 TraesCS3A01G377800 chr3D 89.331 1912 115 33 910 2805 484804978 484806816 0.000000e+00 2318.0
10 TraesCS3A01G377800 chr3D 89.157 913 88 10 1717 2628 484735942 484736844 0.000000e+00 1127.0
11 TraesCS3A01G377800 chr3D 89.988 829 63 7 884 1702 484734360 484735178 0.000000e+00 1053.0
12 TraesCS3A01G377800 chr3D 90.558 699 59 6 2630 3325 484736871 484737565 0.000000e+00 918.0
13 TraesCS3A01G377800 chr3D 97.910 335 7 0 3928 4262 484729302 484729636 7.940000e-162 580.0
14 TraesCS3A01G377800 chr3D 89.970 329 19 10 3369 3686 484728457 484728782 3.070000e-111 412.0
15 TraesCS3A01G377800 chr3D 81.944 360 52 12 2970 3325 484675359 484675709 4.170000e-75 292.0
16 TraesCS3A01G377800 chr3D 89.394 198 6 4 3744 3927 484728947 484729143 7.120000e-58 235.0
17 TraesCS3A01G377800 chr3D 87.952 166 14 3 3369 3532 484675707 484675868 1.560000e-44 191.0
18 TraesCS3A01G377800 chr3D 96.774 31 1 0 3048 3078 484806977 484807007 8.000000e-03 52.8
19 TraesCS3A01G377800 chr3B 88.474 2117 142 52 923 3003 647542264 647544314 0.000000e+00 2464.0
20 TraesCS3A01G377800 chr3B 89.263 773 60 12 2360 3128 647472252 647473005 0.000000e+00 946.0
21 TraesCS3A01G377800 chr3B 86.325 585 58 15 3693 4262 647476210 647476787 6.050000e-173 617.0
22 TraesCS3A01G377800 chr3B 88.031 518 53 3 1849 2362 647470134 647470646 4.710000e-169 604.0
23 TraesCS3A01G377800 chr3B 82.500 360 50 12 2970 3325 647467708 647468058 1.930000e-78 303.0
24 TraesCS3A01G377800 chr3B 93.878 196 12 0 3369 3564 647475865 647476060 3.220000e-76 296.0
25 TraesCS3A01G377800 chr3B 93.103 203 11 1 3123 3325 647475668 647475867 1.160000e-75 294.0
26 TraesCS3A01G377800 chr3B 88.554 166 16 3 3369 3532 647468056 647468220 9.350000e-47 198.0
27 TraesCS3A01G377800 chr3B 91.667 84 7 0 3600 3683 647476058 647476141 2.690000e-22 117.0
28 TraesCS3A01G377800 chr3B 92.453 53 3 1 3324 3375 814801845 814801897 1.640000e-09 75.0
29 TraesCS3A01G377800 chr3B 96.774 31 1 0 3048 3078 647544317 647544347 8.000000e-03 52.8
30 TraesCS3A01G377800 chr2D 84.642 866 120 6 1 854 627643937 627643073 0.000000e+00 850.0
31 TraesCS3A01G377800 chr2D 80.992 726 121 11 86 798 71425589 71426310 1.030000e-155 560.0
32 TraesCS3A01G377800 chr2D 91.343 335 29 0 4 338 444755515 444755181 3.880000e-125 459.0
33 TraesCS3A01G377800 chr2D 80.052 381 60 11 334 701 444557776 444557399 7.020000e-68 268.0
34 TraesCS3A01G377800 chr1A 84.793 868 102 16 1 856 471885508 471886357 0.000000e+00 845.0
35 TraesCS3A01G377800 chr1A 85.335 791 108 7 55 838 584939811 584940600 0.000000e+00 811.0
36 TraesCS3A01G377800 chr1A 82.683 872 104 20 1 862 471958131 471958965 0.000000e+00 730.0
37 TraesCS3A01G377800 chr2A 83.781 857 123 8 1 845 758256547 758257399 0.000000e+00 798.0
38 TraesCS3A01G377800 chr4A 81.417 861 142 14 1 857 201596602 201595756 0.000000e+00 688.0
39 TraesCS3A01G377800 chr6A 79.720 858 168 4 1 856 376485153 376484300 2.180000e-172 616.0
40 TraesCS3A01G377800 chr6A 84.190 506 70 7 16 512 24413408 24413912 2.300000e-132 483.0
41 TraesCS3A01G377800 chr6B 80.676 740 133 9 123 858 160672541 160673274 2.220000e-157 566.0
42 TraesCS3A01G377800 chr6B 77.209 215 32 12 1011 1218 75268455 75268251 4.510000e-20 110.0
43 TraesCS3A01G377800 chr6B 93.617 47 3 0 3333 3379 673619769 673619723 2.130000e-08 71.3
44 TraesCS3A01G377800 chr5B 81.991 633 98 11 1 623 358272815 358272189 1.360000e-144 523.0
45 TraesCS3A01G377800 chr5B 93.750 48 3 0 3324 3371 617830653 617830700 5.910000e-09 73.1
46 TraesCS3A01G377800 chr1D 83.978 543 71 6 333 862 372467921 372468460 1.370000e-139 507.0
47 TraesCS3A01G377800 chr5A 100.000 41 0 0 3333 3373 558146221 558146181 4.570000e-10 76.8
48 TraesCS3A01G377800 chr7D 85.526 76 6 5 3324 3396 155627061 155626988 1.640000e-09 75.0
49 TraesCS3A01G377800 chr7B 95.652 46 2 0 3328 3373 690204444 690204489 1.640000e-09 75.0
50 TraesCS3A01G377800 chr7A 97.674 43 1 0 3333 3375 490266603 490266645 1.640000e-09 75.0
51 TraesCS3A01G377800 chr4B 90.385 52 5 0 3330 3381 631841510 631841561 7.650000e-08 69.4
52 TraesCS3A01G377800 chr5D 92.683 41 2 1 3646 3686 555894482 555894521 1.660000e-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 TraesCS3A01G377800 chr3A 627784431 627788692 4261 False 7871.000000 7871 100.000000 1 4262 1 chr3A.!!$F2 4261
1 TraesCS3A01G377800 chr3A 627817168 627819224 2056 False 1088.400000 2124 91.599500 895 3078 2 chr3A.!!$F4 2183
2 TraesCS3A01G377800 chr3D 484804978 484807007 2029 False 1185.400000 2318 93.052500 910 3078 2 chr3D.!!$F4 2168
3 TraesCS3A01G377800 chr3D 484726149 484729636 3487 False 1038.250000 2926 91.706500 998 4262 4 chr3D.!!$F2 3264
4 TraesCS3A01G377800 chr3D 484734360 484737565 3205 False 1032.666667 1127 89.901000 884 3325 3 chr3D.!!$F3 2441
5 TraesCS3A01G377800 chr3D 484675359 484675868 509 False 241.500000 292 84.948000 2970 3532 2 chr3D.!!$F1 562
6 TraesCS3A01G377800 chr3B 647542264 647544347 2083 False 1258.400000 2464 92.624000 923 3078 2 chr3B.!!$F3 2155
7 TraesCS3A01G377800 chr3B 647467708 647476787 9079 False 421.875000 946 89.165125 1849 4262 8 chr3B.!!$F2 2413
8 TraesCS3A01G377800 chr2D 627643073 627643937 864 True 850.000000 850 84.642000 1 854 1 chr2D.!!$R3 853
9 TraesCS3A01G377800 chr2D 71425589 71426310 721 False 560.000000 560 80.992000 86 798 1 chr2D.!!$F1 712
10 TraesCS3A01G377800 chr1A 471885508 471886357 849 False 845.000000 845 84.793000 1 856 1 chr1A.!!$F1 855
11 TraesCS3A01G377800 chr1A 584939811 584940600 789 False 811.000000 811 85.335000 55 838 1 chr1A.!!$F3 783
12 TraesCS3A01G377800 chr1A 471958131 471958965 834 False 730.000000 730 82.683000 1 862 1 chr1A.!!$F2 861
13 TraesCS3A01G377800 chr2A 758256547 758257399 852 False 798.000000 798 83.781000 1 845 1 chr2A.!!$F1 844
14 TraesCS3A01G377800 chr4A 201595756 201596602 846 True 688.000000 688 81.417000 1 857 1 chr4A.!!$R1 856
15 TraesCS3A01G377800 chr6A 376484300 376485153 853 True 616.000000 616 79.720000 1 856 1 chr6A.!!$R1 855
16 TraesCS3A01G377800 chr6A 24413408 24413912 504 False 483.000000 483 84.190000 16 512 1 chr6A.!!$F1 496
17 TraesCS3A01G377800 chr6B 160672541 160673274 733 False 566.000000 566 80.676000 123 858 1 chr6B.!!$F1 735
18 TraesCS3A01G377800 chr5B 358272189 358272815 626 True 523.000000 523 81.991000 1 623 1 chr5B.!!$R1 622
19 TraesCS3A01G377800 chr1D 372467921 372468460 539 False 507.000000 507 83.978000 333 862 1 chr1D.!!$F1 529

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
132 133 0.167908 GGTCGTCGCATCATGCAAAA 59.832 50.000 11.00 0.0 45.36 2.44 F
940 969 0.314935 CACACATTTCACACTGCCCC 59.685 55.000 0.00 0.0 0.00 5.80 F
943 972 0.540365 ACATTTCACACTGCCCCCAG 60.540 55.000 0.00 0.0 44.80 4.45 F
1178 1213 0.546747 ATCGACCCCAAGTTCCTCCA 60.547 55.000 0.00 0.0 0.00 3.86 F
2715 5198 2.173519 CCATGAATTCTGTGGTTGCCT 58.826 47.619 17.34 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1601 0.989890 CGAAGACGACGGTTTCATCC 59.010 55.000 0.00 0.00 42.66 3.51 R
1952 2742 1.002544 ACCCAAGTAGCTTCTGCAGTC 59.997 52.381 14.67 4.48 42.74 3.51 R
2556 5000 2.415893 CGGTGCAGAAATCAATTGGTCC 60.416 50.000 5.42 0.00 0.00 4.46 R
3133 8298 3.433343 ACCAGATCATTTCACCATTGCA 58.567 40.909 0.00 0.00 0.00 4.08 R
3599 8768 0.251354 ACAGGTGAGCAAGCGATCAT 59.749 50.000 0.00 0.00 40.26 2.45 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
115 116 2.481104 CCAACATTTGCACAAAGTCGGT 60.481 45.455 1.92 0.00 33.32 4.69
132 133 0.167908 GGTCGTCGCATCATGCAAAA 59.832 50.000 11.00 0.00 45.36 2.44
149 150 2.123988 AAACGGCGCTGCAATTTCGA 62.124 50.000 18.15 0.00 0.00 3.71
178 179 1.673993 ATGAACACGCGCAATGGGA 60.674 52.632 5.73 0.00 0.00 4.37
344 350 2.288825 CGCTCTTGTGGTGGTCTTCTTA 60.289 50.000 0.00 0.00 0.00 2.10
385 391 1.667830 CTTTCTTCGCCGGCACAGA 60.668 57.895 28.98 23.13 0.00 3.41
388 394 2.652382 TTCTTCGCCGGCACAGAACA 62.652 55.000 28.98 9.62 0.00 3.18
432 449 2.356278 GGGAGCACATGCCTTCCA 59.644 61.111 12.67 0.00 43.38 3.53
492 509 2.970324 GTGACGTTTGCAGGGCGA 60.970 61.111 12.33 0.00 0.00 5.54
516 533 1.372499 CGGAGCCTTGAACGACGAA 60.372 57.895 0.00 0.00 0.00 3.85
523 540 0.600255 CTTGAACGACGAAGGGTGCT 60.600 55.000 0.00 0.00 0.00 4.40
603 620 2.357517 CGACGGCTGTGAGGCTTT 60.358 61.111 0.80 0.00 38.85 3.51
630 647 4.111053 GGAGGGAAGCCGGGGAAC 62.111 72.222 2.18 0.00 0.00 3.62
871 896 4.794278 TTTTCGCATAGAGTACACCAGA 57.206 40.909 0.00 0.00 0.00 3.86
872 897 5.339008 TTTTCGCATAGAGTACACCAGAT 57.661 39.130 0.00 0.00 0.00 2.90
873 898 6.459670 TTTTCGCATAGAGTACACCAGATA 57.540 37.500 0.00 0.00 0.00 1.98
874 899 6.650427 TTTCGCATAGAGTACACCAGATAT 57.350 37.500 0.00 0.00 0.00 1.63
875 900 7.754851 TTTCGCATAGAGTACACCAGATATA 57.245 36.000 0.00 0.00 0.00 0.86
876 901 7.754851 TTCGCATAGAGTACACCAGATATAA 57.245 36.000 0.00 0.00 0.00 0.98
877 902 7.379098 TCGCATAGAGTACACCAGATATAAG 57.621 40.000 0.00 0.00 0.00 1.73
879 904 6.127869 CGCATAGAGTACACCAGATATAAGCT 60.128 42.308 0.00 0.00 0.00 3.74
880 905 7.254852 GCATAGAGTACACCAGATATAAGCTC 58.745 42.308 0.00 0.00 0.00 4.09
881 906 7.094162 GCATAGAGTACACCAGATATAAGCTCA 60.094 40.741 0.00 0.00 0.00 4.26
882 907 8.965819 CATAGAGTACACCAGATATAAGCTCAT 58.034 37.037 0.00 0.00 0.00 2.90
936 965 8.854979 TTTTCTAAATCACACATTTCACACTG 57.145 30.769 0.00 0.00 0.00 3.66
937 966 6.000891 TCTAAATCACACATTTCACACTGC 57.999 37.500 0.00 0.00 0.00 4.40
940 969 0.314935 CACACATTTCACACTGCCCC 59.685 55.000 0.00 0.00 0.00 5.80
942 971 0.827089 CACATTTCACACTGCCCCCA 60.827 55.000 0.00 0.00 0.00 4.96
943 972 0.540365 ACATTTCACACTGCCCCCAG 60.540 55.000 0.00 0.00 44.80 4.45
969 998 2.680352 GCCCGTCTCCACTCTCCA 60.680 66.667 0.00 0.00 0.00 3.86
973 1002 1.479709 CCGTCTCCACTCTCCAAGAT 58.520 55.000 0.00 0.00 0.00 2.40
1178 1213 0.546747 ATCGACCCCAAGTTCCTCCA 60.547 55.000 0.00 0.00 0.00 3.86
1227 1262 2.302019 CCTCCTTGGGGACTTCTCC 58.698 63.158 0.00 0.00 36.57 3.71
1542 1583 3.677190 CCCATTTAAAGTGGTCGTGGTA 58.323 45.455 12.67 0.00 34.87 3.25
1663 1704 6.668645 TCTATGGGTATTGCTGTTGGTAATT 58.331 36.000 0.00 0.00 32.68 1.40
1952 2742 2.497273 GGGTGTTGAGGAAATCCATTGG 59.503 50.000 1.67 0.00 38.89 3.16
2122 2912 8.665685 AGCTTTTTAAAAGTGATCCTATGTACG 58.334 33.333 17.30 0.00 0.00 3.67
2232 3029 5.109662 TGACTCTACTTCTGAAGTGTTCG 57.890 43.478 28.46 17.28 42.84 3.95
2401 4812 6.418057 AGGAGATGGAATGATACTTCTGTC 57.582 41.667 0.00 0.00 0.00 3.51
2410 4821 7.544566 TGGAATGATACTTCTGTCGTTAGTTTC 59.455 37.037 0.00 0.00 0.00 2.78
2413 4824 7.869016 TGATACTTCTGTCGTTAGTTTCTTG 57.131 36.000 0.00 0.00 0.00 3.02
2465 4904 7.869429 CCCTGCAATTTTATATGTCTGATTTCC 59.131 37.037 0.00 0.00 0.00 3.13
2521 4964 7.148137 TGTGTACAGTACAATCACGTCATATCT 60.148 37.037 15.24 0.00 40.93 1.98
2715 5198 2.173519 CCATGAATTCTGTGGTTGCCT 58.826 47.619 17.34 0.00 0.00 4.75
2735 5218 8.613482 GTTGCCTCCAGATTTAATAAACTACTC 58.387 37.037 0.00 0.00 0.00 2.59
2764 5250 8.217111 TGCCTAATAGATGTAAAATGGTGATGA 58.783 33.333 0.00 0.00 0.00 2.92
2910 5406 7.255381 GCATTCTTAGGTTGAAGCATGATATGT 60.255 37.037 0.00 0.00 33.46 2.29
2923 5419 9.188588 GAAGCATGATATGTCCAATTTGTAATG 57.811 33.333 0.00 0.00 0.00 1.90
3009 5505 5.179555 AGTCCATTCAAGCTTAAAACGAGTC 59.820 40.000 0.00 0.00 0.00 3.36
3078 5574 7.848223 TGTATTTCAGGTAGATCATGTGTTG 57.152 36.000 0.00 0.00 0.00 3.33
3079 5575 6.823182 TGTATTTCAGGTAGATCATGTGTTGG 59.177 38.462 0.00 0.00 0.00 3.77
3082 5578 5.339008 TCAGGTAGATCATGTGTTGGTAC 57.661 43.478 0.00 0.00 0.00 3.34
3084 5580 5.127194 TCAGGTAGATCATGTGTTGGTACTC 59.873 44.000 0.00 0.00 0.00 2.59
3093 5590 2.775384 TGTGTTGGTACTCACCTTCCTT 59.225 45.455 11.50 0.00 45.98 3.36
3098 5595 4.781775 TGGTACTCACCTTCCTTTTTCA 57.218 40.909 0.00 0.00 45.98 2.69
3135 8300 9.353999 CCATTTTCTAGTTGTAATTTACCTTGC 57.646 33.333 4.17 0.00 0.00 4.01
3333 8499 2.877866 CCATCTATGGTACTCCCTCGT 58.122 52.381 0.49 0.00 43.05 4.18
3334 8500 2.558795 CCATCTATGGTACTCCCTCGTG 59.441 54.545 0.49 0.00 43.05 4.35
3335 8501 3.223435 CATCTATGGTACTCCCTCGTGT 58.777 50.000 0.00 0.00 0.00 4.49
3336 8502 4.395625 CATCTATGGTACTCCCTCGTGTA 58.604 47.826 0.00 0.00 0.00 2.90
3337 8503 4.508551 TCTATGGTACTCCCTCGTGTAA 57.491 45.455 0.00 0.00 0.00 2.41
3338 8504 4.858850 TCTATGGTACTCCCTCGTGTAAA 58.141 43.478 0.00 0.00 0.00 2.01
3339 8505 5.263599 TCTATGGTACTCCCTCGTGTAAAA 58.736 41.667 0.00 0.00 0.00 1.52
3340 8506 4.895668 ATGGTACTCCCTCGTGTAAAAA 57.104 40.909 0.00 0.00 0.00 1.94
3364 8530 9.799106 AAAACACTCTTATATTATGGGATGGAG 57.201 33.333 0.00 0.00 0.00 3.86
3365 8531 7.502060 ACACTCTTATATTATGGGATGGAGG 57.498 40.000 0.00 0.00 0.00 4.30
3366 8532 6.445139 ACACTCTTATATTATGGGATGGAGGG 59.555 42.308 0.00 0.00 0.00 4.30
3367 8533 6.673978 CACTCTTATATTATGGGATGGAGGGA 59.326 42.308 0.00 0.00 0.00 4.20
3443 8609 9.440773 TGTTATTTTCAGCTATCCTATATGCAG 57.559 33.333 0.00 0.00 0.00 4.41
3536 8703 6.932356 GAATCTCTTCCAGTTTGATATGCA 57.068 37.500 0.00 0.00 0.00 3.96
3577 8746 6.424509 GCCTCATTCATGTAGAGAGAGAATTG 59.575 42.308 11.54 0.00 33.36 2.32
3582 8751 5.668471 TCATGTAGAGAGAGAATTGCCTTG 58.332 41.667 0.00 0.00 0.00 3.61
3594 8763 1.757682 TTGCCTTGTTCTGAAACCGT 58.242 45.000 0.00 0.00 34.28 4.83
3595 8764 1.305201 TGCCTTGTTCTGAAACCGTC 58.695 50.000 0.00 0.00 34.28 4.79
3597 8766 1.814248 GCCTTGTTCTGAAACCGTCCT 60.814 52.381 0.00 0.00 34.28 3.85
3598 8767 2.549349 GCCTTGTTCTGAAACCGTCCTA 60.549 50.000 0.00 0.00 34.28 2.94
3599 8768 3.735591 CCTTGTTCTGAAACCGTCCTAA 58.264 45.455 0.00 0.00 34.28 2.69
3600 8769 4.324267 CCTTGTTCTGAAACCGTCCTAAT 58.676 43.478 0.00 0.00 34.28 1.73
3601 8770 4.154195 CCTTGTTCTGAAACCGTCCTAATG 59.846 45.833 0.00 0.00 34.28 1.90
3608 8786 2.981859 AACCGTCCTAATGATCGCTT 57.018 45.000 0.00 0.00 0.00 4.68
3609 8787 2.225068 ACCGTCCTAATGATCGCTTG 57.775 50.000 0.00 0.00 0.00 4.01
3622 8800 2.661566 CGCTTGCTCACCTGTGACG 61.662 63.158 0.00 0.00 35.46 4.35
3686 8864 2.190313 CGCATCAGCCTGCCCTTA 59.810 61.111 0.00 0.00 39.00 2.69
3687 8865 1.228063 CGCATCAGCCTGCCCTTAT 60.228 57.895 0.00 0.00 39.00 1.73
3688 8866 0.035317 CGCATCAGCCTGCCCTTATA 59.965 55.000 0.00 0.00 39.00 0.98
3689 8867 1.339438 CGCATCAGCCTGCCCTTATAT 60.339 52.381 0.00 0.00 39.00 0.86
3690 8868 2.363683 GCATCAGCCTGCCCTTATATC 58.636 52.381 0.00 0.00 36.10 1.63
3691 8869 2.026449 GCATCAGCCTGCCCTTATATCT 60.026 50.000 0.00 0.00 36.10 1.98
3699 8936 4.504340 GCCTGCCCTTATATCTCGGTTTAA 60.504 45.833 0.00 0.00 0.00 1.52
3714 8952 6.487331 TCTCGGTTTAACTTATTTTTGCCAGA 59.513 34.615 0.00 0.00 0.00 3.86
3719 8957 8.708742 GGTTTAACTTATTTTTGCCAGAATGAC 58.291 33.333 0.00 0.00 39.69 3.06
3908 9233 4.993028 ACCATAACCAGTTGCTAAAGGAA 58.007 39.130 0.00 0.00 0.00 3.36
3911 9236 3.595190 AACCAGTTGCTAAAGGAACCT 57.405 42.857 10.33 0.00 45.80 3.50
4024 9511 0.652592 GATCGACAATGTCAAGGCCG 59.347 55.000 14.24 0.00 32.09 6.13
4092 9579 2.056906 AACAGCTTCTTCCAGCCGGT 62.057 55.000 1.90 0.00 41.12 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.309764 GATCGAAATTGCAGCGCCGT 62.310 55.000 2.29 0.00 0.00 5.68
149 150 1.726791 GCGTGTTCATGACTTGTCGAT 59.273 47.619 0.00 0.00 0.00 3.59
178 179 6.740411 TTGCTTGCAATTCTTTCACTTTTT 57.260 29.167 0.00 0.00 0.00 1.94
271 276 3.157252 GAGCTGCCCCGAGGATGA 61.157 66.667 0.00 0.00 33.47 2.92
344 350 3.276846 GTTGCCGGTGTGAAGCGT 61.277 61.111 1.90 0.00 0.00 5.07
385 391 1.862123 CGCTGCGAATCAGTGTGTT 59.138 52.632 18.66 0.00 45.73 3.32
475 492 2.970324 TCGCCCTGCAAACGTCAC 60.970 61.111 0.00 0.00 0.00 3.67
492 509 3.986006 TTCAAGGCTCCGTCGCGT 61.986 61.111 5.77 0.00 0.00 6.01
497 514 2.049433 CGTCGTTCAAGGCTCCGT 60.049 61.111 0.00 0.00 0.00 4.69
516 533 3.849951 CCGGCGATGTAGCACCCT 61.850 66.667 9.30 0.00 39.27 4.34
523 540 1.099295 ATCTCGTCACCGGCGATGTA 61.099 55.000 9.30 2.27 37.74 2.29
595 612 1.675310 CGCCACCATGAAAGCCTCA 60.675 57.895 0.00 0.00 38.81 3.86
603 620 2.609299 TTCCCTCCGCCACCATGA 60.609 61.111 0.00 0.00 0.00 3.07
804 829 2.415357 CGGCCTGCGACATGTAATTTTT 60.415 45.455 0.00 0.00 0.00 1.94
806 831 0.732571 CGGCCTGCGACATGTAATTT 59.267 50.000 0.00 0.00 0.00 1.82
807 832 0.107897 TCGGCCTGCGACATGTAATT 60.108 50.000 0.00 0.00 0.00 1.40
808 833 0.106708 ATCGGCCTGCGACATGTAAT 59.893 50.000 0.00 0.00 0.00 1.89
814 839 2.421314 CCATATCGGCCTGCGACA 59.579 61.111 0.00 0.00 0.00 4.35
858 883 9.674068 CTATGAGCTTATATCTGGTGTACTCTA 57.326 37.037 0.00 0.00 0.00 2.43
860 885 7.629652 GCCTATGAGCTTATATCTGGTGTACTC 60.630 44.444 0.00 0.00 0.00 2.59
861 886 6.153680 GCCTATGAGCTTATATCTGGTGTACT 59.846 42.308 0.00 0.00 0.00 2.73
862 887 6.153680 AGCCTATGAGCTTATATCTGGTGTAC 59.846 42.308 0.00 0.00 41.41 2.90
863 888 6.256819 AGCCTATGAGCTTATATCTGGTGTA 58.743 40.000 0.00 0.00 41.41 2.90
867 892 5.929058 TGAGCCTATGAGCTTATATCTGG 57.071 43.478 0.00 0.00 45.15 3.86
868 893 7.014518 AGCTATGAGCCTATGAGCTTATATCTG 59.985 40.741 0.00 0.00 45.15 2.90
871 896 6.838090 TCAGCTATGAGCCTATGAGCTTATAT 59.162 38.462 0.00 0.00 45.15 0.86
872 897 6.190587 TCAGCTATGAGCCTATGAGCTTATA 58.809 40.000 0.00 0.00 45.15 0.98
873 898 5.022122 TCAGCTATGAGCCTATGAGCTTAT 58.978 41.667 0.00 0.00 45.15 1.73
874 899 4.411013 TCAGCTATGAGCCTATGAGCTTA 58.589 43.478 0.00 0.00 45.15 3.09
875 900 3.237746 TCAGCTATGAGCCTATGAGCTT 58.762 45.455 0.00 0.00 45.15 3.74
876 901 2.827322 CTCAGCTATGAGCCTATGAGCT 59.173 50.000 0.00 0.00 46.19 4.09
877 902 3.235157 CTCAGCTATGAGCCTATGAGC 57.765 52.381 4.01 0.00 46.19 4.26
969 998 0.999712 ACGGATTGGGTTGGGATCTT 59.000 50.000 0.00 0.00 0.00 2.40
973 1002 0.906775 GTCTACGGATTGGGTTGGGA 59.093 55.000 0.00 0.00 0.00 4.37
1227 1262 5.389516 CGAGAGTTTTCCGTTGATTTGTAGG 60.390 44.000 0.00 0.00 0.00 3.18
1231 1266 4.468095 ACGAGAGTTTTCCGTTGATTTG 57.532 40.909 0.00 0.00 46.40 2.32
1351 1392 2.951745 GATGAGGAGCACGCGTCG 60.952 66.667 9.86 6.55 0.00 5.12
1500 1541 2.352422 GAGTGGCAGGCACCATGA 59.648 61.111 23.00 0.00 43.01 3.07
1524 1565 5.217978 TGTCTACCACGACCACTTTAAAT 57.782 39.130 0.00 0.00 32.97 1.40
1542 1583 4.731612 CCGTGCTCGCAGCTGTCT 62.732 66.667 16.64 0.00 42.97 3.41
1560 1601 0.989890 CGAAGACGACGGTTTCATCC 59.010 55.000 0.00 0.00 42.66 3.51
1663 1704 1.403679 GTTACCAACAAGTGTGCTGCA 59.596 47.619 0.00 0.00 0.00 4.41
1952 2742 1.002544 ACCCAAGTAGCTTCTGCAGTC 59.997 52.381 14.67 4.48 42.74 3.51
2034 2824 7.615365 AGAGATGAGTGCACCCATAAAAATAAA 59.385 33.333 14.42 0.00 0.00 1.40
2122 2912 7.631717 AGAAACTTGTGAAAGGATAATAGGC 57.368 36.000 0.00 0.00 0.00 3.93
2208 3005 5.278071 CGAACACTTCAGAAGTAGAGTCAGT 60.278 44.000 15.73 5.04 40.46 3.41
2209 3006 5.049336 TCGAACACTTCAGAAGTAGAGTCAG 60.049 44.000 15.73 4.41 40.46 3.51
2210 3007 4.820173 TCGAACACTTCAGAAGTAGAGTCA 59.180 41.667 15.73 0.00 40.46 3.41
2211 3008 5.359716 TCGAACACTTCAGAAGTAGAGTC 57.640 43.478 15.73 9.39 40.46 3.36
2215 3012 6.309251 GGAGATTTCGAACACTTCAGAAGTAG 59.691 42.308 15.73 12.20 40.46 2.57
2232 3029 5.760743 GGCTATAAGTTCACTGGGAGATTTC 59.239 44.000 0.00 0.00 0.00 2.17
2390 4801 7.870588 ACAAGAAACTAACGACAGAAGTATC 57.129 36.000 0.00 0.00 0.00 2.24
2401 4812 9.068008 ACAAAAATGTTGTACAAGAAACTAACG 57.932 29.630 8.98 0.00 0.00 3.18
2413 4824 9.124807 GTCCAGCTAATAACAAAAATGTTGTAC 57.875 33.333 4.55 0.00 33.59 2.90
2465 4904 6.018507 CAGGAAAAGAAAACCAAAGCATCAAG 60.019 38.462 0.00 0.00 0.00 3.02
2508 4947 7.896811 TCTTTTATAGCCAGATATGACGTGAT 58.103 34.615 0.00 0.00 0.00 3.06
2512 4955 7.821652 TCTCTCTTTTATAGCCAGATATGACG 58.178 38.462 0.00 0.00 0.00 4.35
2556 5000 2.415893 CGGTGCAGAAATCAATTGGTCC 60.416 50.000 5.42 0.00 0.00 4.46
2628 5072 9.706691 CTGTCAAACAAGGAAACTATAGAGTTA 57.293 33.333 6.78 0.00 45.50 2.24
2630 5074 7.963532 TCTGTCAAACAAGGAAACTATAGAGT 58.036 34.615 6.78 0.00 42.68 3.24
2631 5075 9.092876 GATCTGTCAAACAAGGAAACTATAGAG 57.907 37.037 6.78 0.00 42.68 2.43
2632 5076 8.593679 TGATCTGTCAAACAAGGAAACTATAGA 58.406 33.333 6.78 0.00 42.68 1.98
2633 5077 8.777865 TGATCTGTCAAACAAGGAAACTATAG 57.222 34.615 0.00 0.00 42.68 1.31
2634 5078 9.739276 ATTGATCTGTCAAACAAGGAAACTATA 57.261 29.630 0.00 0.00 46.67 1.31
2635 5079 8.641498 ATTGATCTGTCAAACAAGGAAACTAT 57.359 30.769 0.00 0.00 46.67 2.12
2636 5080 8.463930 AATTGATCTGTCAAACAAGGAAACTA 57.536 30.769 0.00 0.00 46.67 2.24
2637 5081 6.966534 ATTGATCTGTCAAACAAGGAAACT 57.033 33.333 0.00 0.00 46.67 2.66
2638 5082 7.168135 GTGAATTGATCTGTCAAACAAGGAAAC 59.832 37.037 0.00 0.00 46.67 2.78
2715 5198 9.120538 GGCATTGAGTAGTTTATTAAATCTGGA 57.879 33.333 0.00 0.00 0.00 3.86
2735 5218 8.849168 TCACCATTTTACATCTATTAGGCATTG 58.151 33.333 0.00 0.00 0.00 2.82
2764 5250 4.104086 TGACTGAAACTCCCCAGTATGAT 58.896 43.478 0.00 0.00 43.02 2.45
2888 5384 6.126796 TGGACATATCATGCTTCAACCTAAGA 60.127 38.462 0.00 0.00 0.00 2.10
2910 5406 4.529769 TCATGTTGCCCATTACAAATTGGA 59.470 37.500 0.00 0.00 34.81 3.53
2923 5419 5.126067 AGTATTCAGTGTATCATGTTGCCC 58.874 41.667 0.00 0.00 0.00 5.36
3009 5505 4.393062 AGATTCTTTAGATGCAACCGTGTG 59.607 41.667 0.00 0.00 0.00 3.82
3079 5575 4.762251 AGCATGAAAAAGGAAGGTGAGTAC 59.238 41.667 0.00 0.00 0.00 2.73
3082 5578 4.038402 ACAAGCATGAAAAAGGAAGGTGAG 59.962 41.667 0.00 0.00 0.00 3.51
3084 5580 4.326504 ACAAGCATGAAAAAGGAAGGTG 57.673 40.909 0.00 0.00 0.00 4.00
3093 5590 7.862512 AGAAAATGGAAAACAAGCATGAAAA 57.137 28.000 0.00 0.00 0.00 2.29
3098 5595 7.500141 ACAACTAGAAAATGGAAAACAAGCAT 58.500 30.769 0.00 0.00 0.00 3.79
3133 8298 3.433343 ACCAGATCATTTCACCATTGCA 58.567 40.909 0.00 0.00 0.00 4.08
3135 8300 6.028146 TCAAACCAGATCATTTCACCATTG 57.972 37.500 0.00 0.00 0.00 2.82
3166 8331 5.485662 AACTTCAGACTTGTGTAACTTGC 57.514 39.130 0.00 0.00 38.04 4.01
3338 8504 9.799106 CTCCATCCCATAATATAAGAGTGTTTT 57.201 33.333 0.00 0.00 0.00 2.43
3339 8505 8.386264 CCTCCATCCCATAATATAAGAGTGTTT 58.614 37.037 0.00 0.00 0.00 2.83
3340 8506 7.037297 CCCTCCATCCCATAATATAAGAGTGTT 60.037 40.741 0.00 0.00 0.00 3.32
3341 8507 6.445139 CCCTCCATCCCATAATATAAGAGTGT 59.555 42.308 0.00 0.00 0.00 3.55
3342 8508 6.673978 TCCCTCCATCCCATAATATAAGAGTG 59.326 42.308 0.00 0.00 0.00 3.51
3343 8509 6.826727 TCCCTCCATCCCATAATATAAGAGT 58.173 40.000 0.00 0.00 0.00 3.24
3344 8510 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
3345 8511 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
3346 8512 7.846823 ACTACTCCCTCCATCCCATAATATAAG 59.153 40.741 0.00 0.00 0.00 1.73
3347 8513 7.729350 ACTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
3348 8514 7.312162 ACTACTCCCTCCATCCCATAATATA 57.688 40.000 0.00 0.00 0.00 0.86
3349 8515 6.185677 ACTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
3350 8516 5.633473 ACTACTCCCTCCATCCCATAATA 57.367 43.478 0.00 0.00 0.00 0.98
3351 8517 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
3352 8518 3.973973 CAACTACTCCCTCCATCCCATAA 59.026 47.826 0.00 0.00 0.00 1.90
3353 8519 3.051341 ACAACTACTCCCTCCATCCCATA 60.051 47.826 0.00 0.00 0.00 2.74
3354 8520 2.293856 ACAACTACTCCCTCCATCCCAT 60.294 50.000 0.00 0.00 0.00 4.00
3355 8521 1.080498 ACAACTACTCCCTCCATCCCA 59.920 52.381 0.00 0.00 0.00 4.37
3356 8522 1.763545 GACAACTACTCCCTCCATCCC 59.236 57.143 0.00 0.00 0.00 3.85
3357 8523 2.432510 CTGACAACTACTCCCTCCATCC 59.567 54.545 0.00 0.00 0.00 3.51
3358 8524 2.159028 GCTGACAACTACTCCCTCCATC 60.159 54.545 0.00 0.00 0.00 3.51
3359 8525 1.834263 GCTGACAACTACTCCCTCCAT 59.166 52.381 0.00 0.00 0.00 3.41
3360 8526 1.203187 AGCTGACAACTACTCCCTCCA 60.203 52.381 0.00 0.00 0.00 3.86
3361 8527 1.562783 AGCTGACAACTACTCCCTCC 58.437 55.000 0.00 0.00 0.00 4.30
3362 8528 2.933056 GCAAGCTGACAACTACTCCCTC 60.933 54.545 0.00 0.00 0.00 4.30
3363 8529 1.002544 GCAAGCTGACAACTACTCCCT 59.997 52.381 0.00 0.00 0.00 4.20
3364 8530 1.002544 AGCAAGCTGACAACTACTCCC 59.997 52.381 0.00 0.00 0.00 4.30
3365 8531 2.464157 AGCAAGCTGACAACTACTCC 57.536 50.000 0.00 0.00 0.00 3.85
3366 8532 4.991687 AGTTAAGCAAGCTGACAACTACTC 59.008 41.667 12.49 0.00 0.00 2.59
3367 8533 4.962155 AGTTAAGCAAGCTGACAACTACT 58.038 39.130 12.49 0.00 0.00 2.57
3443 8609 4.848299 GCATTTCAGAGTTCATTTGACGAC 59.152 41.667 0.00 0.00 0.00 4.34
3532 8699 5.807909 AGGCTCAAACCAAAATATTTGCAT 58.192 33.333 0.39 0.00 36.06 3.96
3534 8701 5.237048 TGAGGCTCAAACCAAAATATTTGC 58.763 37.500 16.28 0.00 36.06 3.68
3535 8702 7.603404 TGAATGAGGCTCAAACCAAAATATTTG 59.397 33.333 22.84 0.00 37.19 2.32
3536 8703 7.678837 TGAATGAGGCTCAAACCAAAATATTT 58.321 30.769 22.84 6.28 0.00 1.40
3577 8746 0.591659 GGACGGTTTCAGAACAAGGC 59.408 55.000 0.00 0.00 37.51 4.35
3582 8751 4.267928 CGATCATTAGGACGGTTTCAGAAC 59.732 45.833 0.00 0.00 34.96 3.01
3594 8763 2.483714 GGTGAGCAAGCGATCATTAGGA 60.484 50.000 0.00 0.00 40.26 2.94
3595 8764 1.869767 GGTGAGCAAGCGATCATTAGG 59.130 52.381 0.00 0.00 40.26 2.69
3597 8766 2.093500 ACAGGTGAGCAAGCGATCATTA 60.093 45.455 0.00 0.00 40.26 1.90
3598 8767 1.339438 ACAGGTGAGCAAGCGATCATT 60.339 47.619 0.00 0.00 40.26 2.57
3599 8768 0.251354 ACAGGTGAGCAAGCGATCAT 59.749 50.000 0.00 0.00 40.26 2.45
3600 8769 0.671472 CACAGGTGAGCAAGCGATCA 60.671 55.000 0.00 0.00 34.48 2.92
3601 8770 0.390340 TCACAGGTGAGCAAGCGATC 60.390 55.000 0.00 0.00 34.14 3.69
3608 8786 4.314440 GGCCGTCACAGGTGAGCA 62.314 66.667 13.46 0.00 40.75 4.26
3630 8808 4.021925 AGCCTCCGTGCTCCAACC 62.022 66.667 0.00 0.00 36.75 3.77
3679 8857 5.881923 AGTTAAACCGAGATATAAGGGCA 57.118 39.130 0.00 0.00 0.00 5.36
3686 8864 8.962679 TGGCAAAAATAAGTTAAACCGAGATAT 58.037 29.630 0.00 0.00 0.00 1.63
3687 8865 8.338072 TGGCAAAAATAAGTTAAACCGAGATA 57.662 30.769 0.00 0.00 0.00 1.98
3688 8866 7.175990 TCTGGCAAAAATAAGTTAAACCGAGAT 59.824 33.333 0.00 0.00 0.00 2.75
3689 8867 6.487331 TCTGGCAAAAATAAGTTAAACCGAGA 59.513 34.615 0.00 0.00 0.00 4.04
3690 8868 6.674066 TCTGGCAAAAATAAGTTAAACCGAG 58.326 36.000 0.00 0.00 0.00 4.63
3691 8869 6.636562 TCTGGCAAAAATAAGTTAAACCGA 57.363 33.333 0.00 0.00 0.00 4.69
3699 8936 6.369615 GCATTGTCATTCTGGCAAAAATAAGT 59.630 34.615 0.00 0.00 45.80 2.24
3709 8947 3.863142 AAGAAGCATTGTCATTCTGGC 57.137 42.857 0.00 0.00 33.67 4.85
3714 8952 4.859304 TGCAGAAAGAAGCATTGTCATT 57.141 36.364 0.00 0.00 35.51 2.57
3719 8957 8.834465 ACTAGTATATTGCAGAAAGAAGCATTG 58.166 33.333 0.00 0.00 40.94 2.82
3757 9042 5.577164 AGCACGAGATATAAGTCACAAACAC 59.423 40.000 0.00 0.00 0.00 3.32
3887 9211 4.157840 GGTTCCTTTAGCAACTGGTTATGG 59.842 45.833 0.00 0.00 0.00 2.74
3888 9212 5.010282 AGGTTCCTTTAGCAACTGGTTATG 58.990 41.667 0.00 0.00 0.00 1.90
3889 9213 5.014228 AGAGGTTCCTTTAGCAACTGGTTAT 59.986 40.000 0.00 0.00 0.00 1.89
3890 9214 4.349930 AGAGGTTCCTTTAGCAACTGGTTA 59.650 41.667 0.00 0.00 0.00 2.85
3908 9233 7.870509 TTGTACGTAATACAGATGTAGAGGT 57.129 36.000 0.00 4.21 44.68 3.85
4024 9511 2.811317 CTCGCACACCTCGAAGCC 60.811 66.667 0.00 0.00 35.38 4.35
4182 9669 0.456221 GTCGATCTTGGAAGCCGAGA 59.544 55.000 5.90 5.90 46.80 4.04
4189 9676 0.677288 ACGTGGTGTCGATCTTGGAA 59.323 50.000 0.00 0.00 34.70 3.53


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

AutoCloner maintained by Alex Coulton.