Multiple sequence alignment - TraesCS6B01G133600

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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 TraesCS6B01G133600 chr6B 100.000 3245 0 0 1 3245 130323387 130326631 0.000000e+00 5993.0
1 TraesCS6B01G133600 chr6B 76.816 716 109 37 958 1663 129268651 129269319 1.850000e-92 350.0
2 TraesCS6B01G133600 chr6B 75.657 723 116 36 959 1665 129446981 129447659 4.070000e-79 305.0
3 TraesCS6B01G133600 chr6B 83.137 255 42 1 417 670 707819338 707819592 7.000000e-57 231.0
4 TraesCS6B01G133600 chr6B 83.333 252 36 5 420 670 58851034 58851280 9.060000e-56 228.0
5 TraesCS6B01G133600 chr6B 82.000 250 44 1 422 670 707819845 707820094 9.120000e-51 211.0
6 TraesCS6B01G133600 chr6B 73.485 660 130 32 1010 1663 125645128 125644508 1.180000e-49 207.0
7 TraesCS6B01G133600 chr6B 89.231 130 11 3 2543 2671 130507485 130507612 3.350000e-35 159.0
8 TraesCS6B01G133600 chr6B 75.833 240 47 8 1825 2057 129851278 129851513 9.520000e-21 111.0
9 TraesCS6B01G133600 chr6D 93.162 2413 126 18 1 2384 58094195 58096597 0.000000e+00 3506.0
10 TraesCS6B01G133600 chr6D 82.764 1317 181 27 989 2291 58242521 58243805 0.000000e+00 1133.0
11 TraesCS6B01G133600 chr6D 97.830 553 11 1 2477 3028 58096595 58097147 0.000000e+00 953.0
12 TraesCS6B01G133600 chr6D 77.622 1068 186 28 1330 2383 58230696 58231724 1.670000e-167 599.0
13 TraesCS6B01G133600 chr6D 98.624 218 3 0 3028 3245 58097182 58097399 1.410000e-103 387.0
14 TraesCS6B01G133600 chr6D 84.073 383 49 9 2535 2909 58244121 58244499 3.080000e-95 359.0
15 TraesCS6B01G133600 chr6D 76.987 717 106 39 958 1663 57215868 57216536 3.980000e-94 355.0
16 TraesCS6B01G133600 chr6D 83.529 340 44 8 959 1291 57514148 57514482 1.130000e-79 307.0
17 TraesCS6B01G133600 chr6D 82.090 335 51 7 958 1285 57158792 57159124 8.870000e-71 278.0
18 TraesCS6B01G133600 chr6D 83.730 252 32 8 4 252 71277677 71277922 2.520000e-56 230.0
19 TraesCS6B01G133600 chr6D 74.080 652 126 28 1028 1668 58047125 58047744 9.060000e-56 228.0
20 TraesCS6B01G133600 chr6D 83.465 254 33 8 1 251 109797718 109797965 9.060000e-56 228.0
21 TraesCS6B01G133600 chr6D 83.212 137 17 5 2543 2679 58231884 58232014 1.580000e-23 121.0
22 TraesCS6B01G133600 chrUn 79.959 1467 240 33 928 2376 112686714 112685284 0.000000e+00 1031.0
23 TraesCS6B01G133600 chrUn 78.786 1499 239 45 913 2376 112925599 112927053 0.000000e+00 933.0
24 TraesCS6B01G133600 chrUn 82.246 276 46 2 396 670 47560067 47560340 5.410000e-58 235.0
25 TraesCS6B01G133600 chrUn 82.246 276 45 3 396 670 47560569 47560841 5.410000e-58 235.0
26 TraesCS6B01G133600 chrUn 100.000 28 0 0 1334 1361 373622708 373622735 6.000000e-03 52.8
27 TraesCS6B01G133600 chr6A 87.529 850 81 10 1 834 73445775 73446615 0.000000e+00 959.0
28 TraesCS6B01G133600 chr6A 79.956 1357 204 29 953 2291 73559268 73560574 0.000000e+00 937.0
29 TraesCS6B01G133600 chr6A 75.978 716 115 36 958 1663 72429391 72430059 1.880000e-82 316.0
30 TraesCS6B01G133600 chr6A 73.867 662 136 25 1028 1681 73379374 73380006 2.520000e-56 230.0
31 TraesCS6B01G133600 chr6A 79.801 302 29 15 2543 2825 73511874 73512162 1.190000e-44 191.0
32 TraesCS6B01G133600 chr6A 78.365 208 38 4 1855 2057 73064510 73064715 9.450000e-26 128.0
33 TraesCS6B01G133600 chr3A 86.056 251 31 3 4 251 673143071 673143320 1.920000e-67 267.0
34 TraesCS6B01G133600 chr3A 80.797 276 50 3 396 670 48650423 48650150 2.540000e-51 213.0
35 TraesCS6B01G133600 chr3B 85.317 252 31 5 4 251 712152258 712152507 4.150000e-64 255.0
36 TraesCS6B01G133600 chr2B 84.524 252 30 8 4 251 588842378 588842132 1.160000e-59 241.0
37 TraesCS6B01G133600 chr5D 83.465 254 34 7 1 251 80617447 80617695 2.520000e-56 230.0
38 TraesCS6B01G133600 chr5D 95.413 109 5 0 2383 2491 500862451 500862559 1.200000e-39 174.0
39 TraesCS6B01G133600 chr2D 83.600 250 33 7 4 251 556107572 556107329 9.060000e-56 228.0
40 TraesCS6B01G133600 chr2D 100.000 29 0 0 1334 1362 628996519 628996491 2.000000e-03 54.7
41 TraesCS6B01G133600 chr7A 81.522 276 48 3 396 670 714790382 714790655 1.170000e-54 224.0
42 TraesCS6B01G133600 chr7B 98.058 103 2 0 2380 2482 5263837 5263735 2.570000e-41 180.0
43 TraesCS6B01G133600 chr5B 99.000 100 1 0 2382 2481 36231611 36231710 2.570000e-41 180.0
44 TraesCS6B01G133600 chr5B 95.370 108 4 1 2382 2489 224321977 224322083 1.550000e-38 171.0
45 TraesCS6B01G133600 chr5B 100.000 28 0 0 2666 2693 462323444 462323417 6.000000e-03 52.8
46 TraesCS6B01G133600 chr4B 97.170 106 3 0 2380 2485 538218747 538218852 2.570000e-41 180.0
47 TraesCS6B01G133600 chr4B 98.990 99 1 0 2383 2481 524845598 524845696 9.250000e-41 178.0
48 TraesCS6B01G133600 chr4B 95.327 107 5 0 2377 2483 373996209 373996315 1.550000e-38 171.0
49 TraesCS6B01G133600 chr1B 98.039 102 2 0 2383 2484 645361041 645360940 9.250000e-41 178.0
50 TraesCS6B01G133600 chr1B 90.909 121 9 2 2361 2479 268540637 268540517 9.320000e-36 161.0


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 TraesCS6B01G133600 chr6B 130323387 130326631 3244 False 5993.000000 5993 100.000000 1 3245 1 chr6B.!!$F5 3244
1 TraesCS6B01G133600 chr6B 129268651 129269319 668 False 350.000000 350 76.816000 958 1663 1 chr6B.!!$F2 705
2 TraesCS6B01G133600 chr6B 129446981 129447659 678 False 305.000000 305 75.657000 959 1665 1 chr6B.!!$F3 706
3 TraesCS6B01G133600 chr6B 707819338 707820094 756 False 221.000000 231 82.568500 417 670 2 chr6B.!!$F7 253
4 TraesCS6B01G133600 chr6B 125644508 125645128 620 True 207.000000 207 73.485000 1010 1663 1 chr6B.!!$R1 653
5 TraesCS6B01G133600 chr6D 58094195 58097399 3204 False 1615.333333 3506 96.538667 1 3245 3 chr6D.!!$F7 3244
6 TraesCS6B01G133600 chr6D 58242521 58244499 1978 False 746.000000 1133 83.418500 989 2909 2 chr6D.!!$F9 1920
7 TraesCS6B01G133600 chr6D 58230696 58232014 1318 False 360.000000 599 80.417000 1330 2679 2 chr6D.!!$F8 1349
8 TraesCS6B01G133600 chr6D 57215868 57216536 668 False 355.000000 355 76.987000 958 1663 1 chr6D.!!$F2 705
9 TraesCS6B01G133600 chr6D 58047125 58047744 619 False 228.000000 228 74.080000 1028 1668 1 chr6D.!!$F4 640
10 TraesCS6B01G133600 chrUn 112685284 112686714 1430 True 1031.000000 1031 79.959000 928 2376 1 chrUn.!!$R1 1448
11 TraesCS6B01G133600 chrUn 112925599 112927053 1454 False 933.000000 933 78.786000 913 2376 1 chrUn.!!$F1 1463
12 TraesCS6B01G133600 chrUn 47560067 47560841 774 False 235.000000 235 82.246000 396 670 2 chrUn.!!$F3 274
13 TraesCS6B01G133600 chr6A 73445775 73446615 840 False 959.000000 959 87.529000 1 834 1 chr6A.!!$F4 833
14 TraesCS6B01G133600 chr6A 73559268 73560574 1306 False 937.000000 937 79.956000 953 2291 1 chr6A.!!$F6 1338
15 TraesCS6B01G133600 chr6A 72429391 72430059 668 False 316.000000 316 75.978000 958 1663 1 chr6A.!!$F1 705
16 TraesCS6B01G133600 chr6A 73379374 73380006 632 False 230.000000 230 73.867000 1028 1681 1 chr6A.!!$F3 653

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
880 899 0.249955 ATTTTGAAATGGGCCGCCTG 59.75 50.0 9.86 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2984 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.0 0.0 0.0 0.0 3.28 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
50 51 9.255304 GAAGAAGTCATATTATCTTCACTCCAC 57.745 37.037 8.95 0.00 44.49 4.02
143 144 7.553044 AGTCCTTTTATTCCCTCTCATTTAACG 59.447 37.037 0.00 0.00 0.00 3.18
294 295 5.629348 GAGTAGCACTCGAAAAAGATAGC 57.371 43.478 1.40 0.00 35.28 2.97
359 372 8.997323 CCTCTTTTTCATGTAATCCTATAGCAG 58.003 37.037 0.00 0.00 0.00 4.24
404 417 7.816945 AAATTATCTCAAAAATTGCAGACCG 57.183 32.000 0.00 0.00 0.00 4.79
486 500 1.153842 CGAAAAATGCGGGGGCTTC 60.154 57.895 0.00 0.00 0.00 3.86
526 540 2.289072 CCTCCTTTGAGAGCACGAGAAA 60.289 50.000 0.00 0.00 41.42 2.52
596 611 2.241281 TGTTCCCTCTCGATACCCAA 57.759 50.000 0.00 0.00 0.00 4.12
606 621 5.221541 CCTCTCGATACCCAAAGATTAGCTT 60.222 44.000 0.00 0.00 38.88 3.74
623 638 9.810545 AGATTAGCTTAGAGATGTTGTAGTTTC 57.189 33.333 0.00 0.00 0.00 2.78
641 656 2.032528 CAAGCGGCCTCAGGTGAA 59.967 61.111 0.00 0.00 0.00 3.18
676 691 3.187637 CGCGTCCAAACTTTTATGAAGGA 59.812 43.478 0.00 0.00 0.00 3.36
710 725 4.228317 CAATGTGATGCGTTGATCAAACA 58.772 39.130 10.35 12.06 44.68 2.83
725 740 4.688511 TCAAACAACGTTATGCCCATAC 57.311 40.909 0.00 0.00 0.00 2.39
752 767 0.534203 GGTGCGAGAGGTGTTTCCAA 60.534 55.000 0.00 0.00 39.02 3.53
757 772 1.067142 CGAGAGGTGTTTCCAATCGGA 60.067 52.381 0.00 0.00 40.39 4.55
759 774 3.181479 CGAGAGGTGTTTCCAATCGGATA 60.181 47.826 0.00 0.00 42.41 2.59
775 790 1.004595 GATAACCGACGTTGCCCTTC 58.995 55.000 0.00 0.00 33.17 3.46
780 795 2.317609 CGACGTTGCCCTTCCACAG 61.318 63.158 0.00 0.00 0.00 3.66
789 804 1.475930 GCCCTTCCACAGATAGCTTCC 60.476 57.143 0.00 0.00 0.00 3.46
802 817 2.851263 AGCTTCCGGAACATACAACA 57.149 45.000 14.35 0.00 0.00 3.33
822 837 3.888323 ACATGACACATGTGGTAAGCAAA 59.112 39.130 28.64 6.21 34.19 3.68
825 840 3.505680 TGACACATGTGGTAAGCAAATCC 59.494 43.478 28.64 4.70 34.19 3.01
828 843 4.343526 ACACATGTGGTAAGCAAATCCAAA 59.656 37.500 28.64 0.00 32.82 3.28
830 845 5.933463 CACATGTGGTAAGCAAATCCAAATT 59.067 36.000 18.51 0.00 32.82 1.82
831 846 7.095910 CACATGTGGTAAGCAAATCCAAATTA 58.904 34.615 18.51 0.00 32.82 1.40
880 899 0.249955 ATTTTGAAATGGGCCGCCTG 59.750 50.000 9.86 0.00 0.00 4.85
889 908 2.573340 GGCCGCCTGAAATTGTGG 59.427 61.111 0.71 0.00 35.21 4.17
897 916 5.451242 GCCGCCTGAAATTGTGGAATTATAA 60.451 40.000 0.00 0.00 33.93 0.98
923 942 4.767255 CTCACCTCGCACAGCCCC 62.767 72.222 0.00 0.00 0.00 5.80
940 959 1.455587 CCCCAACACACACCAAGCT 60.456 57.895 0.00 0.00 0.00 3.74
941 960 1.735360 CCCAACACACACCAAGCTG 59.265 57.895 0.00 0.00 0.00 4.24
942 961 0.751277 CCCAACACACACCAAGCTGA 60.751 55.000 0.00 0.00 0.00 4.26
943 962 0.664761 CCAACACACACCAAGCTGAG 59.335 55.000 0.00 0.00 0.00 3.35
1227 1594 1.224592 CCAAGAACCCCATCCCTCG 59.775 63.158 0.00 0.00 0.00 4.63
1307 1686 1.233019 CCCGATGATGATTGGCTCAC 58.767 55.000 0.00 0.00 36.48 3.51
1530 1922 0.533755 CCATTGGCGAGGATGAGGAC 60.534 60.000 0.00 0.00 0.00 3.85
1535 1927 2.122167 GCGAGGATGAGGACGAGGT 61.122 63.158 0.00 0.00 0.00 3.85
1701 2109 4.607293 GAAAGGCTTTTCCCATTTCAGT 57.393 40.909 14.66 0.00 37.34 3.41
1758 2166 1.789506 AAGACAAGCTTCTCGTGCTC 58.210 50.000 0.00 0.00 40.22 4.26
1970 2378 3.622060 ATGGCGGACCTTCCAACGG 62.622 63.158 6.45 0.00 35.91 4.44
2032 2440 3.572682 TCTCTATTATACCGTGGGTGCAG 59.427 47.826 0.00 0.00 36.19 4.41
2088 2496 2.361104 CGGTGGGGTGACAATGGG 60.361 66.667 0.00 0.00 0.00 4.00
2100 2514 2.176798 TGACAATGGGGTCTTTCCTGTT 59.823 45.455 0.00 0.00 38.61 3.16
2107 2524 3.849574 TGGGGTCTTTCCTGTTGATGATA 59.150 43.478 0.00 0.00 36.25 2.15
2179 2602 3.507233 CAGCTGCAGGGAAACAATCTTTA 59.493 43.478 17.12 0.00 0.00 1.85
2198 2621 1.586422 AATCATCCCAATCGTGCTCG 58.414 50.000 0.81 0.81 38.55 5.03
2358 2881 6.984474 TCTGTTCGTCCTTATGAATTATGGAC 59.016 38.462 0.00 0.00 45.37 4.02
2384 2907 8.398665 CCTTTGCTGTCCTAATTTAGAATGTAC 58.601 37.037 4.96 0.00 0.00 2.90
2385 2908 9.167311 CTTTGCTGTCCTAATTTAGAATGTACT 57.833 33.333 4.96 0.00 0.00 2.73
2386 2909 8.718102 TTGCTGTCCTAATTTAGAATGTACTC 57.282 34.615 4.96 0.00 0.00 2.59
2387 2910 7.272978 TGCTGTCCTAATTTAGAATGTACTCC 58.727 38.462 4.96 0.00 0.00 3.85
2388 2911 6.706716 GCTGTCCTAATTTAGAATGTACTCCC 59.293 42.308 4.96 0.00 0.00 4.30
2389 2912 7.419172 GCTGTCCTAATTTAGAATGTACTCCCT 60.419 40.741 4.96 0.00 0.00 4.20
2390 2913 8.019656 TGTCCTAATTTAGAATGTACTCCCTC 57.980 38.462 4.96 0.00 0.00 4.30
2391 2914 7.070821 TGTCCTAATTTAGAATGTACTCCCTCC 59.929 40.741 4.96 0.00 0.00 4.30
2392 2915 6.267014 TCCTAATTTAGAATGTACTCCCTCCG 59.733 42.308 4.96 0.00 0.00 4.63
2393 2916 5.952347 AATTTAGAATGTACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
2394 2917 4.996788 TTTAGAATGTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
2395 2918 1.777941 AGAATGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2396 2919 0.751452 GAATGTACTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
2397 2920 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2398 2921 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2399 2922 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2400 2923 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2401 2924 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2402 2925 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2403 2926 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2404 2927 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
2405 2928 2.238898 CTCCCTCCGTCCCAAAATAACT 59.761 50.000 0.00 0.00 0.00 2.24
2406 2929 2.026636 TCCCTCCGTCCCAAAATAACTG 60.027 50.000 0.00 0.00 0.00 3.16
2407 2930 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
2408 2931 3.007635 CCTCCGTCCCAAAATAACTGTC 58.992 50.000 0.00 0.00 0.00 3.51
2409 2932 3.307480 CCTCCGTCCCAAAATAACTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2410 2933 3.933332 CTCCGTCCCAAAATAACTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2411 2934 3.325425 TCCGTCCCAAAATAACTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2412 2935 4.069304 CCGTCCCAAAATAACTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2413 2936 4.083484 CCGTCCCAAAATAACTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2414 2937 4.755123 CGTCCCAAAATAACTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2415 2938 5.238650 CGTCCCAAAATAACTGTCTCAACTT 59.761 40.000 0.00 0.00 0.00 2.66
2416 2939 6.238648 CGTCCCAAAATAACTGTCTCAACTTT 60.239 38.462 0.00 0.00 0.00 2.66
2417 2940 6.918022 GTCCCAAAATAACTGTCTCAACTTTG 59.082 38.462 0.00 0.00 0.00 2.77
2418 2941 6.605594 TCCCAAAATAACTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 0.00 2.83
2419 2942 7.776030 TCCCAAAATAACTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 0.00 2.41
2420 2943 7.860872 CCCAAAATAACTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 0.00 2.90
2421 2944 8.621286 CCAAAATAACTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 0.00 2.73
2427 2950 7.768807 ACTGTCTCAACTTTGTACTATCTCT 57.231 36.000 0.00 0.00 0.00 3.10
2428 2951 8.865420 ACTGTCTCAACTTTGTACTATCTCTA 57.135 34.615 0.00 0.00 0.00 2.43
2429 2952 8.952278 ACTGTCTCAACTTTGTACTATCTCTAG 58.048 37.037 0.00 0.00 0.00 2.43
2430 2953 8.865420 TGTCTCAACTTTGTACTATCTCTAGT 57.135 34.615 0.00 0.00 41.19 2.57
2431 2954 9.955102 TGTCTCAACTTTGTACTATCTCTAGTA 57.045 33.333 0.00 0.00 39.04 1.82
2455 2978 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
2456 2979 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
2457 2980 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
2458 2981 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
2459 2982 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
2460 2983 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
2461 2984 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
2462 2985 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
2463 2986 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
2464 2987 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
2465 2988 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
2466 2989 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2467 2990 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2468 2991 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
2469 2992 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
2470 2993 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
2471 2994 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
2472 2995 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2473 2996 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2474 2997 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2475 2998 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2562 3183 7.904558 TCTGACCAATCTATGATAACACTCT 57.095 36.000 0.00 0.00 0.00 3.24
2938 3566 9.433317 GTCAAATTATATGTAACCATGTTGTCG 57.567 33.333 0.00 0.00 32.29 4.35
3059 3722 7.446106 TCATAATTCTGGCCTTAGGAGTTAA 57.554 36.000 3.32 0.00 0.00 2.01
3231 3894 5.745227 CAACAATCAATGGTCCTACCTAGT 58.255 41.667 0.00 0.00 39.58 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.928236 ATTCAAATTAATTTCAACACAAAACCG 57.072 25.926 10.53 0.00 0.00 4.44
79 80 9.230122 TCATTCTTGCATTCTGTATCTTTACAA 57.770 29.630 0.00 0.00 37.86 2.41
241 242 5.731957 TGTGCTAACCTAGTGTAACATCA 57.268 39.130 0.00 0.00 41.43 3.07
259 260 2.603560 GTGCTACTCTCGGTAAATGTGC 59.396 50.000 0.00 0.00 0.00 4.57
284 285 3.415212 TGCTCAGCACTGCTATCTTTTT 58.585 40.909 2.39 0.00 36.40 1.94
294 295 6.314648 TGAGTATTAATCTTTGCTCAGCACTG 59.685 38.462 0.00 0.00 38.71 3.66
404 417 4.398358 GGTTTCAGCACCCTAGAAATTACC 59.602 45.833 0.00 0.00 34.23 2.85
486 500 1.540607 GCTATCGCATGACACGTCCG 61.541 60.000 0.00 0.00 35.78 4.79
526 540 1.745489 GCTCCGTTGGCCTCGAAAT 60.745 57.895 19.23 0.00 0.00 2.17
606 621 5.168569 CGCTTGGAAACTACAACATCTCTA 58.831 41.667 0.00 0.00 0.00 2.43
623 638 3.551496 TTCACCTGAGGCCGCTTGG 62.551 63.158 8.34 12.45 0.00 3.61
641 656 1.337074 TGGACGCGTTTCGAATAAGGT 60.337 47.619 15.53 0.00 41.67 3.50
676 691 4.414852 GCATCACATTGCGTACATCTTTT 58.585 39.130 0.00 0.00 32.06 2.27
701 716 3.149981 TGGGCATAACGTTGTTTGATCA 58.850 40.909 11.99 0.00 0.00 2.92
710 725 0.460635 ACGCGTATGGGCATAACGTT 60.461 50.000 11.67 5.88 35.90 3.99
714 729 0.872451 CGTCACGCGTATGGGCATAA 60.872 55.000 13.44 0.00 35.54 1.90
757 772 0.392060 GGAAGGGCAACGTCGGTTAT 60.392 55.000 0.00 0.00 33.72 1.89
759 774 2.281276 GGAAGGGCAACGTCGGTT 60.281 61.111 0.00 0.00 36.63 4.44
764 779 0.981183 TATCTGTGGAAGGGCAACGT 59.019 50.000 0.00 0.00 37.60 3.99
775 790 1.207089 TGTTCCGGAAGCTATCTGTGG 59.793 52.381 19.50 0.00 32.01 4.17
780 795 4.439057 TGTTGTATGTTCCGGAAGCTATC 58.561 43.478 19.50 5.91 0.00 2.08
789 804 4.154015 ACATGTGTCATGTTGTATGTTCCG 59.846 41.667 9.21 0.00 0.00 4.30
802 817 4.158394 GGATTTGCTTACCACATGTGTCAT 59.842 41.667 23.79 11.74 0.00 3.06
845 864 9.390243 CATTTCAAAATGTTCCCGAAGCTTTCG 62.390 40.741 0.00 5.87 44.53 3.46
847 866 4.664150 TTCAAAATGTTCCCGAAGCTTT 57.336 36.364 0.00 0.00 0.00 3.51
848 867 4.664150 TTTCAAAATGTTCCCGAAGCTT 57.336 36.364 0.00 0.00 0.00 3.74
849 868 4.559153 CATTTCAAAATGTTCCCGAAGCT 58.441 39.130 7.20 0.00 40.61 3.74
851 870 4.244862 CCCATTTCAAAATGTTCCCGAAG 58.755 43.478 12.99 0.00 43.24 3.79
852 871 3.556004 GCCCATTTCAAAATGTTCCCGAA 60.556 43.478 12.99 0.00 43.24 4.30
853 872 2.028567 GCCCATTTCAAAATGTTCCCGA 60.029 45.455 12.99 0.00 43.24 5.14
854 873 2.345876 GCCCATTTCAAAATGTTCCCG 58.654 47.619 12.99 0.00 43.24 5.14
855 874 2.710377 GGCCCATTTCAAAATGTTCCC 58.290 47.619 12.99 7.34 43.24 3.97
856 875 2.345876 CGGCCCATTTCAAAATGTTCC 58.654 47.619 12.99 11.70 43.24 3.62
857 876 1.731709 GCGGCCCATTTCAAAATGTTC 59.268 47.619 12.99 5.55 43.24 3.18
858 877 1.610363 GGCGGCCCATTTCAAAATGTT 60.610 47.619 8.12 0.00 43.24 2.71
859 878 0.036483 GGCGGCCCATTTCAAAATGT 60.036 50.000 8.12 0.00 43.24 2.71
860 879 0.249955 AGGCGGCCCATTTCAAAATG 59.750 50.000 17.02 8.23 44.12 2.32
861 880 0.249955 CAGGCGGCCCATTTCAAAAT 59.750 50.000 17.02 0.00 0.00 1.82
880 899 5.977129 CAGCGGGTTATAATTCCACAATTTC 59.023 40.000 8.07 0.00 33.95 2.17
889 908 2.548480 GTGAGCCAGCGGGTTATAATTC 59.452 50.000 4.36 0.00 36.17 2.17
921 940 2.498056 GCTTGGTGTGTGTTGGGGG 61.498 63.158 0.00 0.00 0.00 5.40
923 942 0.751277 TCAGCTTGGTGTGTGTTGGG 60.751 55.000 0.00 0.00 0.00 4.12
925 944 1.331756 GACTCAGCTTGGTGTGTGTTG 59.668 52.381 11.38 0.00 0.00 3.33
926 945 1.668419 GACTCAGCTTGGTGTGTGTT 58.332 50.000 11.38 0.00 0.00 3.32
927 946 0.179045 GGACTCAGCTTGGTGTGTGT 60.179 55.000 11.38 4.51 0.00 3.72
928 947 0.886490 GGGACTCAGCTTGGTGTGTG 60.886 60.000 11.38 1.81 0.00 3.82
929 948 1.451936 GGGACTCAGCTTGGTGTGT 59.548 57.895 7.15 7.15 0.00 3.72
930 949 1.302832 GGGGACTCAGCTTGGTGTG 60.303 63.158 0.00 0.45 0.00 3.82
935 954 1.303643 GGTTGGGGGACTCAGCTTG 60.304 63.158 0.00 0.00 0.00 4.01
936 955 0.178873 TAGGTTGGGGGACTCAGCTT 60.179 55.000 0.00 0.00 0.00 3.74
937 956 0.178873 TTAGGTTGGGGGACTCAGCT 60.179 55.000 0.00 0.00 0.00 4.24
940 959 1.591768 GGATTAGGTTGGGGGACTCA 58.408 55.000 0.00 0.00 0.00 3.41
941 960 0.844660 GGGATTAGGTTGGGGGACTC 59.155 60.000 0.00 0.00 0.00 3.36
942 961 0.626574 GGGGATTAGGTTGGGGGACT 60.627 60.000 0.00 0.00 0.00 3.85
943 962 0.626574 AGGGGATTAGGTTGGGGGAC 60.627 60.000 0.00 0.00 0.00 4.46
1261 1628 3.703052 GGGACGAAGGAGTAGGTGAAATA 59.297 47.826 0.00 0.00 0.00 1.40
1530 1922 1.479709 AGGTCTCATCCTCAACCTCG 58.520 55.000 0.00 0.00 37.59 4.63
1701 2109 1.533625 AGAAGCAGCCACGCAAATAA 58.466 45.000 0.00 0.00 0.00 1.40
1758 2166 1.221466 ACTCCATTGTGCGTGTGTCG 61.221 55.000 0.00 0.00 43.12 4.35
1833 2241 2.029020 GGTAGACATGCACACACTCTGA 60.029 50.000 0.00 0.00 0.00 3.27
1953 2361 4.323477 CCGTTGGAAGGTCCGCCA 62.323 66.667 2.68 2.68 40.17 5.69
1970 2378 2.531522 AACATTTTTCAGCTGCCACC 57.468 45.000 9.47 0.00 0.00 4.61
2032 2440 4.061596 CGAAGGAATAAGAATCCCTCAGC 58.938 47.826 0.00 0.00 37.71 4.26
2078 2486 2.162681 CAGGAAAGACCCCATTGTCAC 58.837 52.381 0.00 0.00 40.05 3.67
2088 2496 5.601662 TCGATATCATCAACAGGAAAGACC 58.398 41.667 3.12 0.00 39.35 3.85
2168 2588 7.975616 CACGATTGGGATGATTAAAGATTGTTT 59.024 33.333 0.00 0.00 0.00 2.83
2179 2602 1.586422 CGAGCACGATTGGGATGATT 58.414 50.000 0.00 0.00 42.66 2.57
2321 2844 1.732259 ACGAACAGAATAAGCTTGCCG 59.268 47.619 9.86 2.90 0.00 5.69
2358 2881 7.396540 ACATTCTAAATTAGGACAGCAAAGG 57.603 36.000 0.00 0.00 0.00 3.11
2384 2907 2.238898 AGTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2385 2908 2.026636 CAGTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2386 2909 2.290705 ACAGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2387 2910 3.007635 GACAGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2388 2911 3.933332 GAGACAGTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2389 2912 3.325425 TGAGACAGTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2390 2913 3.670625 TGAGACAGTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2391 2914 4.755123 AGTTGAGACAGTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2392 2915 6.635030 AAGTTGAGACAGTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
2393 2916 6.605594 ACAAAGTTGAGACAGTTATTTTGGGA 59.394 34.615 0.00 0.00 0.00 4.37
2394 2917 6.805713 ACAAAGTTGAGACAGTTATTTTGGG 58.194 36.000 0.00 0.00 0.00 4.12
2395 2918 8.621286 AGTACAAAGTTGAGACAGTTATTTTGG 58.379 33.333 0.00 0.00 0.00 3.28
2401 2924 9.298250 AGAGATAGTACAAAGTTGAGACAGTTA 57.702 33.333 0.00 0.00 0.00 2.24
2402 2925 8.184304 AGAGATAGTACAAAGTTGAGACAGTT 57.816 34.615 0.00 0.00 0.00 3.16
2403 2926 7.768807 AGAGATAGTACAAAGTTGAGACAGT 57.231 36.000 0.00 0.00 0.00 3.55
2404 2927 8.952278 ACTAGAGATAGTACAAAGTTGAGACAG 58.048 37.037 0.00 0.00 0.00 3.51
2405 2928 8.865420 ACTAGAGATAGTACAAAGTTGAGACA 57.135 34.615 0.00 0.00 0.00 3.41
2430 2953 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
2431 2954 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
2432 2955 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
2433 2956 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
2434 2957 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
2435 2958 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
2436 2959 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
2437 2960 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2438 2961 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
2439 2962 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2440 2963 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2441 2964 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2442 2965 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2443 2966 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
2444 2967 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2445 2968 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
2446 2969 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
2447 2970 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
2448 2971 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
2449 2972 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
2450 2973 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2451 2974 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2452 2975 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2453 2976 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2454 2977 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2455 2978 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2456 2979 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2457 2980 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2458 2981 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2459 2982 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2460 2983 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
2461 2984 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
2462 2985 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
2463 2986 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
2464 2987 1.112950 CTTTCTACTCCCTCCGTCCC 58.887 60.000 0.00 0.00 0.00 4.46
2465 2988 1.849977 ACTTTCTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
2466 2989 4.673841 CGTTAACTTTCTACTCCCTCCGTC 60.674 50.000 3.71 0.00 0.00 4.79
2467 2990 3.192212 CGTTAACTTTCTACTCCCTCCGT 59.808 47.826 3.71 0.00 0.00 4.69
2468 2991 3.428589 CCGTTAACTTTCTACTCCCTCCG 60.429 52.174 3.71 0.00 0.00 4.63
2469 2992 3.513119 ACCGTTAACTTTCTACTCCCTCC 59.487 47.826 3.71 0.00 0.00 4.30
2470 2993 4.797800 ACCGTTAACTTTCTACTCCCTC 57.202 45.455 3.71 0.00 0.00 4.30
2471 2994 4.590222 TGAACCGTTAACTTTCTACTCCCT 59.410 41.667 14.47 0.00 0.00 4.20
2472 2995 4.886579 TGAACCGTTAACTTTCTACTCCC 58.113 43.478 14.47 0.00 0.00 4.30
2473 2996 5.930569 ACATGAACCGTTAACTTTCTACTCC 59.069 40.000 0.00 0.00 0.00 3.85
2474 2997 6.643770 TCACATGAACCGTTAACTTTCTACTC 59.356 38.462 0.00 0.42 0.00 2.59
2475 2998 6.518493 TCACATGAACCGTTAACTTTCTACT 58.482 36.000 0.00 2.11 0.00 2.57
2562 3183 6.530534 GTCTTAGCTAAAACTATGCACTCGAA 59.469 38.462 7.74 0.00 0.00 3.71
2932 3560 4.351131 AGTTTTTCACCTGTTCGACAAC 57.649 40.909 0.00 0.00 0.00 3.32
2938 3566 6.530181 CCAACAAACTAGTTTTTCACCTGTTC 59.470 38.462 18.25 0.00 0.00 3.18
3008 3636 8.025445 AGTTTTCATCAACAATCTTATCAGCAC 58.975 33.333 0.00 0.00 0.00 4.40
3059 3722 5.048013 TCAACAAGACACACGATGAGAGTAT 60.048 40.000 0.00 0.00 0.00 2.12
3116 3779 7.324935 TCTATGAAAAGACGCCTATTGTGTTA 58.675 34.615 0.00 0.00 37.96 2.41


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

AutoCloner maintained by Alex Coulton.