Multiple sequence alignment - TraesCS3B01G555900

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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 TraesCS3B01G555900 chr3B 100.000 2813 0 0 1 2813 789324640 789321828 0.000000e+00 5195.0
1 TraesCS3B01G555900 chr3B 80.920 1457 243 28 511 1948 789622777 789621337 0.000000e+00 1118.0
2 TraesCS3B01G555900 chr3B 79.667 1441 246 33 507 1922 789333637 789335055 0.000000e+00 994.0
3 TraesCS3B01G555900 chr3D 93.262 1692 106 5 500 2189 590331608 590329923 0.000000e+00 2486.0
4 TraesCS3B01G555900 chr3D 81.427 1416 214 34 545 1925 590356977 590355576 0.000000e+00 1112.0
5 TraesCS3B01G555900 chr3D 88.225 569 32 8 2279 2813 590329812 590329245 0.000000e+00 647.0
6 TraesCS3B01G555900 chr3D 87.006 354 15 10 13 363 590332094 590331769 1.230000e-98 370.0
7 TraesCS3B01G555900 chr3A 80.641 1436 247 20 507 1922 720435639 720437063 0.000000e+00 1083.0
8 TraesCS3B01G555900 chr3A 80.546 1465 234 37 507 1935 720417192 720415743 0.000000e+00 1079.0
9 TraesCS3B01G555900 chr3A 90.238 799 77 1 1247 2044 720252605 720251807 0.000000e+00 1042.0
10 TraesCS3B01G555900 chr3A 79.560 1409 245 26 548 1930 720449733 720451124 0.000000e+00 966.0
11 TraesCS3B01G555900 chr3A 88.076 738 67 8 500 1237 720367940 720367224 0.000000e+00 856.0
12 TraesCS3B01G555900 chr3A 79.976 819 145 10 1141 1949 720393371 720392562 1.120000e-163 586.0
13 TraesCS3B01G555900 chr3A 82.398 659 93 13 505 1146 720394193 720393541 1.140000e-153 553.0
14 TraesCS3B01G555900 chr3A 80.939 362 31 16 104 437 720368328 720367977 4.650000e-63 252.0
15 TraesCS3B01G555900 chr3A 83.929 168 18 4 187 349 720394556 720394393 4.850000e-33 152.0
16 TraesCS3B01G555900 chr3A 86.538 52 6 1 2680 2731 703783199 703783149 3.910000e-04 56.5
17 TraesCS3B01G555900 chrUn 79.667 1441 246 34 507 1922 237856745 237858163 0.000000e+00 994.0
18 TraesCS3B01G555900 chrUn 79.667 1441 246 34 507 1922 297376530 297375112 0.000000e+00 994.0
19 TraesCS3B01G555900 chrUn 79.667 1441 246 33 507 1922 305637786 305636368 0.000000e+00 994.0
20 TraesCS3B01G555900 chr4A 90.559 286 24 3 2119 2403 602736320 602736037 2.650000e-100 375.0
21 TraesCS3B01G555900 chr7A 90.244 287 24 4 2119 2403 50022208 50021924 3.420000e-99 372.0
22 TraesCS3B01G555900 chr1A 90.210 286 25 3 2119 2403 526922668 526922385 1.230000e-98 370.0
23 TraesCS3B01G555900 chr6D 89.895 287 25 4 2119 2403 36066993 36066709 1.590000e-97 366.0
24 TraesCS3B01G555900 chr6A 89.547 287 26 4 2119 2403 575465726 575466010 7.410000e-96 361.0
25 TraesCS3B01G555900 chr1B 89.474 285 28 2 2119 2402 664074838 664074555 2.660000e-95 359.0
26 TraesCS3B01G555900 chr5A 89.236 288 28 3 2118 2403 512621808 512622094 9.580000e-95 357.0
27 TraesCS3B01G555900 chr7B 89.161 286 29 2 2119 2403 216345602 216345886 3.450000e-94 355.0
28 TraesCS3B01G555900 chr7B 89.003 291 27 5 2115 2403 716533374 716533087 3.450000e-94 355.0


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 TraesCS3B01G555900 chr3B 789321828 789324640 2812 True 5195.000000 5195 100.000000 1 2813 1 chr3B.!!$R1 2812
1 TraesCS3B01G555900 chr3B 789621337 789622777 1440 True 1118.000000 1118 80.920000 511 1948 1 chr3B.!!$R2 1437
2 TraesCS3B01G555900 chr3B 789333637 789335055 1418 False 994.000000 994 79.667000 507 1922 1 chr3B.!!$F1 1415
3 TraesCS3B01G555900 chr3D 590329245 590332094 2849 True 1167.666667 2486 89.497667 13 2813 3 chr3D.!!$R2 2800
4 TraesCS3B01G555900 chr3D 590355576 590356977 1401 True 1112.000000 1112 81.427000 545 1925 1 chr3D.!!$R1 1380
5 TraesCS3B01G555900 chr3A 720435639 720437063 1424 False 1083.000000 1083 80.641000 507 1922 1 chr3A.!!$F1 1415
6 TraesCS3B01G555900 chr3A 720415743 720417192 1449 True 1079.000000 1079 80.546000 507 1935 1 chr3A.!!$R3 1428
7 TraesCS3B01G555900 chr3A 720251807 720252605 798 True 1042.000000 1042 90.238000 1247 2044 1 chr3A.!!$R2 797
8 TraesCS3B01G555900 chr3A 720449733 720451124 1391 False 966.000000 966 79.560000 548 1930 1 chr3A.!!$F2 1382
9 TraesCS3B01G555900 chr3A 720367224 720368328 1104 True 554.000000 856 84.507500 104 1237 2 chr3A.!!$R4 1133
10 TraesCS3B01G555900 chr3A 720392562 720394556 1994 True 430.333333 586 82.101000 187 1949 3 chr3A.!!$R5 1762
11 TraesCS3B01G555900 chrUn 237856745 237858163 1418 False 994.000000 994 79.667000 507 1922 1 chrUn.!!$F1 1415
12 TraesCS3B01G555900 chrUn 297375112 297376530 1418 True 994.000000 994 79.667000 507 1922 1 chrUn.!!$R1 1415
13 TraesCS3B01G555900 chrUn 305636368 305637786 1418 True 994.000000 994 79.667000 507 1922 1 chrUn.!!$R2 1415

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
84 86 0.035439 GAAAGATGCACGAGGGGGAA 60.035 55.0 0.0 0.0 0.00 3.97 F
196 203 0.243095 CAGCTTTTGAGCAGCTTCCC 59.757 55.0 0.0 0.0 45.82 3.97 F
437 490 0.315251 GCAAGGTGCCCAGAAAACTC 59.685 55.0 0.0 0.0 37.42 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1572 0.034670 GGAGAAGATTGCCAGGCACT 60.035 55.0 15.89 9.42 38.71 4.40 R
1383 1719 0.476771 GACCCTTGAACTTCACCCCA 59.523 55.0 0.00 0.00 0.00 4.96 R
1943 2289 0.526211 AGTCTACAAGCGCGTGATGA 59.474 50.0 29.85 21.40 0.00 2.92 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
21 22 1.098712 TCACGCCAAACCACTCAACC 61.099 55.000 0.00 0.00 0.00 3.77
30 31 2.671177 CCACTCAACCTTGCGCTCG 61.671 63.158 9.73 0.00 0.00 5.03
57 59 2.102588 GCGGGAATCCTACTAGCTTTCA 59.897 50.000 0.00 0.00 0.00 2.69
83 85 0.909610 AGAAAGATGCACGAGGGGGA 60.910 55.000 0.00 0.00 0.00 4.81
84 86 0.035439 GAAAGATGCACGAGGGGGAA 60.035 55.000 0.00 0.00 0.00 3.97
85 87 0.404040 AAAGATGCACGAGGGGGAAA 59.596 50.000 0.00 0.00 0.00 3.13
86 88 0.625849 AAGATGCACGAGGGGGAAAT 59.374 50.000 0.00 0.00 0.00 2.17
87 89 1.507140 AGATGCACGAGGGGGAAATA 58.493 50.000 0.00 0.00 0.00 1.40
88 90 1.843851 AGATGCACGAGGGGGAAATAA 59.156 47.619 0.00 0.00 0.00 1.40
89 91 2.241176 AGATGCACGAGGGGGAAATAAA 59.759 45.455 0.00 0.00 0.00 1.40
90 92 2.588464 TGCACGAGGGGGAAATAAAA 57.412 45.000 0.00 0.00 0.00 1.52
91 93 3.094484 TGCACGAGGGGGAAATAAAAT 57.906 42.857 0.00 0.00 0.00 1.82
92 94 2.757868 TGCACGAGGGGGAAATAAAATG 59.242 45.455 0.00 0.00 0.00 2.32
93 95 2.481276 GCACGAGGGGGAAATAAAATGC 60.481 50.000 0.00 0.00 0.00 3.56
94 96 2.757868 CACGAGGGGGAAATAAAATGCA 59.242 45.455 0.00 0.00 0.00 3.96
95 97 2.758423 ACGAGGGGGAAATAAAATGCAC 59.242 45.455 0.00 0.00 0.00 4.57
96 98 2.757868 CGAGGGGGAAATAAAATGCACA 59.242 45.455 0.00 0.00 0.00 4.57
97 99 3.428862 CGAGGGGGAAATAAAATGCACAC 60.429 47.826 0.00 0.00 0.00 3.82
98 100 2.837591 AGGGGGAAATAAAATGCACACC 59.162 45.455 0.00 0.00 0.00 4.16
99 101 2.837591 GGGGGAAATAAAATGCACACCT 59.162 45.455 0.00 0.00 0.00 4.00
100 102 3.263170 GGGGGAAATAAAATGCACACCTT 59.737 43.478 0.00 0.00 0.00 3.50
101 103 4.503910 GGGGAAATAAAATGCACACCTTC 58.496 43.478 0.00 0.00 0.00 3.46
102 104 4.020662 GGGGAAATAAAATGCACACCTTCA 60.021 41.667 0.00 0.00 0.00 3.02
111 113 1.064758 TGCACACCTTCACTTCACCTT 60.065 47.619 0.00 0.00 0.00 3.50
129 131 3.244249 ACCTTAGTGCTTGACTTGACTCC 60.244 47.826 0.00 0.00 35.96 3.85
135 142 1.805869 CTTGACTTGACTCCAGCTGG 58.194 55.000 27.87 27.87 0.00 4.85
142 149 1.937191 TGACTCCAGCTGGTATGTCA 58.063 50.000 33.27 33.27 38.00 3.58
181 188 9.784531 AAAGTGTGTCAATTATATATAGCAGCT 57.215 29.630 0.00 0.00 0.00 4.24
196 203 0.243095 CAGCTTTTGAGCAGCTTCCC 59.757 55.000 0.00 0.00 45.82 3.97
201 208 1.321474 TTTGAGCAGCTTCCCAAGTG 58.679 50.000 0.00 0.00 0.00 3.16
248 255 7.328249 GCGTGAATCTTCTATTCTTATCCTCAG 59.672 40.741 0.00 0.00 0.00 3.35
296 306 2.867109 ACATATACAGATGCCAGCCC 57.133 50.000 0.00 0.00 0.00 5.19
340 354 1.000163 GTGAACTGAGCGTTGAGAGGA 60.000 52.381 0.00 0.00 35.56 3.71
346 360 1.140816 GAGCGTTGAGAGGACAACAC 58.859 55.000 0.00 0.00 46.96 3.32
375 422 3.394836 AGGAGGCGGGAGAGCAAC 61.395 66.667 0.00 0.00 39.27 4.17
395 448 5.581605 CAACGCAATCAATTGGCTTACTAT 58.418 37.500 5.42 0.00 38.21 2.12
416 469 0.523072 CGTGGACAAGCAAATGGAGG 59.477 55.000 0.00 0.00 0.00 4.30
428 481 2.505364 AATGGAGGAGCAAGGTGCCC 62.505 60.000 0.00 0.00 46.52 5.36
437 490 0.315251 GCAAGGTGCCCAGAAAACTC 59.685 55.000 0.00 0.00 37.42 3.01
438 491 1.986882 CAAGGTGCCCAGAAAACTCT 58.013 50.000 0.00 0.00 0.00 3.24
443 553 2.430694 GGTGCCCAGAAAACTCTGTTTT 59.569 45.455 7.97 7.97 36.06 2.43
456 566 3.053455 CTCTGTTTTCTGACAGGTCGAC 58.947 50.000 7.13 7.13 45.54 4.20
457 567 1.787155 CTGTTTTCTGACAGGTCGACG 59.213 52.381 9.92 0.00 42.58 5.12
458 568 1.135527 TGTTTTCTGACAGGTCGACGT 59.864 47.619 9.92 7.31 0.00 4.34
459 569 2.199236 GTTTTCTGACAGGTCGACGTT 58.801 47.619 8.27 0.37 0.00 3.99
460 570 2.129823 TTTCTGACAGGTCGACGTTC 57.870 50.000 8.27 10.12 0.00 3.95
461 571 1.026584 TTCTGACAGGTCGACGTTCA 58.973 50.000 8.27 13.72 0.00 3.18
462 572 1.244816 TCTGACAGGTCGACGTTCAT 58.755 50.000 8.27 0.00 0.00 2.57
463 573 1.611977 TCTGACAGGTCGACGTTCATT 59.388 47.619 8.27 0.00 0.00 2.57
464 574 1.986378 CTGACAGGTCGACGTTCATTC 59.014 52.381 8.27 3.82 0.00 2.67
465 575 1.338655 TGACAGGTCGACGTTCATTCA 59.661 47.619 8.27 6.31 0.00 2.57
466 576 2.029380 TGACAGGTCGACGTTCATTCAT 60.029 45.455 8.27 0.00 0.00 2.57
467 577 3.191791 TGACAGGTCGACGTTCATTCATA 59.808 43.478 8.27 0.00 0.00 2.15
468 578 4.142249 TGACAGGTCGACGTTCATTCATAT 60.142 41.667 8.27 0.00 0.00 1.78
469 579 5.066764 TGACAGGTCGACGTTCATTCATATA 59.933 40.000 8.27 0.00 0.00 0.86
470 580 6.085555 ACAGGTCGACGTTCATTCATATAT 57.914 37.500 8.27 0.00 0.00 0.86
471 581 7.040961 TGACAGGTCGACGTTCATTCATATATA 60.041 37.037 8.27 0.00 0.00 0.86
472 582 7.827701 ACAGGTCGACGTTCATTCATATATAT 58.172 34.615 8.27 0.00 0.00 0.86
473 583 8.953313 ACAGGTCGACGTTCATTCATATATATA 58.047 33.333 8.27 0.00 0.00 0.86
474 584 9.952188 CAGGTCGACGTTCATTCATATATATAT 57.048 33.333 8.27 0.00 0.00 0.86
737 862 1.140375 GTACAACTACCCTCGGCCG 59.860 63.158 22.12 22.12 0.00 6.13
803 928 2.036475 GAGTCTTCACAAGGTGCTCTCA 59.964 50.000 0.00 0.00 32.98 3.27
976 1107 0.683504 ATACTCTCCCGCCTCGTTGT 60.684 55.000 0.00 0.00 0.00 3.32
989 1132 1.261619 CTCGTTGTCTTCCAAGCACAC 59.738 52.381 0.00 0.00 32.51 3.82
1043 1189 2.885644 CGTCCCATCGGCGAACAG 60.886 66.667 15.93 7.06 32.47 3.16
1117 1263 3.181474 CCAGATACCTTTCTTCGTCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
1167 1488 5.465724 GGATGGTAAGGATCGTGTGATTAAC 59.534 44.000 0.00 0.00 34.09 2.01
1278 1599 4.128643 CTGGCAATCTTCTCCATCTTCTC 58.871 47.826 0.00 0.00 0.00 2.87
1383 1719 0.169230 CGACAGAGTACAGCTTCGCT 59.831 55.000 0.00 0.00 40.77 4.93
1403 1739 0.771755 GGGGTGAAGTTCAAGGGTCT 59.228 55.000 7.25 0.00 0.00 3.85
1413 1749 3.138283 AGTTCAAGGGTCTGTCCATGAAA 59.862 43.478 11.00 0.00 41.66 2.69
1456 1798 1.421485 GACGTGAAGCTGAATGGCG 59.579 57.895 0.00 0.00 37.29 5.69
1458 1800 2.753966 CGTGAAGCTGAATGGCGGG 61.754 63.158 0.00 0.00 37.29 6.13
1461 1803 3.338250 AAGCTGAATGGCGGGGGA 61.338 61.111 0.00 0.00 37.29 4.81
1476 1818 4.767255 GGAGGCACGCTGGAGGTG 62.767 72.222 0.00 0.00 38.42 4.00
1496 1838 2.264480 CCGCCTGGACATCGACAA 59.736 61.111 0.00 0.00 37.49 3.18
1525 1867 3.127533 GGCTGCTACGCAACCTGG 61.128 66.667 0.00 0.00 41.12 4.45
1597 1939 0.320683 CTGCGTGTTCATGTCCCAGA 60.321 55.000 0.00 0.00 0.00 3.86
1755 2097 1.816835 TGCAACTACCTACAGGAGACG 59.183 52.381 1.29 0.00 38.94 4.18
1796 2138 2.035155 TCGGAGCTCCTCACGGAA 59.965 61.111 29.73 4.26 39.29 4.30
1913 2256 2.224314 GGCAGTGTACTCTGTTTTGAGC 59.776 50.000 22.29 9.09 37.58 4.26
1925 2271 4.278170 TCTGTTTTGAGCTACAAACATGGG 59.722 41.667 18.62 10.64 46.32 4.00
1943 2289 6.367983 ACATGGGTGAAGTTAGCAATATGAT 58.632 36.000 0.00 0.00 0.00 2.45
2000 2346 2.700722 TGTGTGTTGTGAGGCTTGTA 57.299 45.000 0.00 0.00 0.00 2.41
2081 2428 3.003480 GGATTGTCTACTGCCAGTCAAC 58.997 50.000 0.00 1.28 0.00 3.18
2108 2455 3.986277 TCTCACTTTGGGTTAGTCGAAC 58.014 45.455 0.00 0.00 37.31 3.95
2112 2459 3.741344 CACTTTGGGTTAGTCGAACTCTG 59.259 47.826 0.00 0.00 39.53 3.35
2126 2473 4.455533 TCGAACTCTGATCCAATGGTTTTG 59.544 41.667 0.00 0.00 0.00 2.44
2139 2486 7.983307 TCCAATGGTTTTGAATTTCAGTTTTG 58.017 30.769 0.00 0.98 0.00 2.44
2145 2492 8.510505 TGGTTTTGAATTTCAGTTTTGGAAAAG 58.489 29.630 0.00 0.00 37.74 2.27
2160 2557 2.459934 GAAAAGTTTCAGCACCAACCG 58.540 47.619 0.00 0.00 37.15 4.44
2165 2562 3.482436 AGTTTCAGCACCAACCGAAATA 58.518 40.909 0.00 0.00 30.68 1.40
2206 2603 7.467557 TTTCAGTGATTTCAGTTTGCATTTC 57.532 32.000 0.00 0.00 0.00 2.17
2207 2604 6.146601 TCAGTGATTTCAGTTTGCATTTCA 57.853 33.333 0.00 0.00 0.00 2.69
2295 2693 7.984050 TCAAAAACTATTTGAATTCCTGTGCAA 59.016 29.630 2.27 0.00 35.69 4.08
2388 2787 9.506018 TCAGTGAATTTCATTGAAATCTCACTA 57.494 29.630 34.08 27.07 45.07 2.74
2435 2834 4.092091 CGTAAGTTTCTGATGAAGACCAGC 59.908 45.833 0.00 0.00 33.46 4.85
2452 2851 2.456989 CAGCAACAACTTCAGTGCAAG 58.543 47.619 0.00 0.00 0.00 4.01
2453 2852 1.406539 AGCAACAACTTCAGTGCAAGG 59.593 47.619 0.00 0.00 0.00 3.61
2454 2853 1.536709 GCAACAACTTCAGTGCAAGGG 60.537 52.381 0.00 0.00 0.00 3.95
2455 2854 1.750778 CAACAACTTCAGTGCAAGGGT 59.249 47.619 0.00 3.25 0.00 4.34
2456 2855 1.680338 ACAACTTCAGTGCAAGGGTC 58.320 50.000 0.00 0.00 0.00 4.46
2459 2858 2.624838 CAACTTCAGTGCAAGGGTCATT 59.375 45.455 0.00 0.00 0.00 2.57
2460 2859 2.949447 ACTTCAGTGCAAGGGTCATTT 58.051 42.857 0.00 0.00 0.00 2.32
2461 2860 2.624838 ACTTCAGTGCAAGGGTCATTTG 59.375 45.455 0.00 0.00 0.00 2.32
2462 2861 2.655090 TCAGTGCAAGGGTCATTTGA 57.345 45.000 0.00 0.00 0.00 2.69
2464 2863 3.084039 TCAGTGCAAGGGTCATTTGATC 58.916 45.455 0.00 0.00 0.00 2.92
2466 2865 3.256383 CAGTGCAAGGGTCATTTGATCAA 59.744 43.478 3.38 3.38 0.00 2.57
2473 2896 1.133025 GGTCATTTGATCAACCCAGCG 59.867 52.381 7.89 0.00 0.00 5.18
2512 2935 2.093711 GTGCCCTTTGTCCACAAAAACT 60.094 45.455 6.35 0.00 44.24 2.66
2517 2940 4.142049 CCCTTTGTCCACAAAAACTAAGCA 60.142 41.667 6.35 0.00 44.24 3.91
2534 2957 1.956477 AGCACAACTAAAACAGGCCAG 59.044 47.619 5.01 0.00 0.00 4.85
2587 3010 6.289064 CCTTTAGTGTTCTCTAACAACCACT 58.711 40.000 0.00 0.00 46.84 4.00
2588 3011 6.202954 CCTTTAGTGTTCTCTAACAACCACTG 59.797 42.308 0.00 0.00 46.84 3.66
2634 3057 1.274126 CCTCTTCTTCCTCCCTTCCCT 60.274 57.143 0.00 0.00 0.00 4.20
2635 3058 2.115427 CTCTTCTTCCTCCCTTCCCTC 58.885 57.143 0.00 0.00 0.00 4.30
2636 3059 0.827368 CTTCTTCCTCCCTTCCCTCG 59.173 60.000 0.00 0.00 0.00 4.63
2662 3085 2.203139 CCGGCGCCACCATGAATA 60.203 61.111 28.98 0.00 39.03 1.75
2682 3111 8.633075 TGAATAAAGAAGAAAACACAAAGCAG 57.367 30.769 0.00 0.00 0.00 4.24
2689 3118 5.841957 AGAAAACACAAAGCAGAACAGAT 57.158 34.783 0.00 0.00 0.00 2.90
2716 3145 6.989759 TGGGACAAAAATTAAAGGAAAGAAGC 59.010 34.615 0.00 0.00 31.92 3.86
2717 3146 6.989759 GGGACAAAAATTAAAGGAAAGAAGCA 59.010 34.615 0.00 0.00 0.00 3.91
2747 3177 0.960861 CCTGGGCGGTTTCTCCTTTC 60.961 60.000 0.00 0.00 0.00 2.62
2749 3179 2.038837 GGGCGGTTTCTCCTTTCGG 61.039 63.158 0.00 0.00 0.00 4.30
2772 3202 3.141398 CCACCCTCGGTAAATCATCATG 58.859 50.000 0.00 0.00 32.11 3.07
2800 3230 6.039047 CCCATCAAAATTCCTACTCATCACTG 59.961 42.308 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.098712 TTGAGTGGTTTGGCGTGACC 61.099 55.000 0.00 0.00 39.84 4.02
1 2 0.028902 GTTGAGTGGTTTGGCGTGAC 59.971 55.000 0.00 0.00 0.00 3.67
2 3 1.098712 GGTTGAGTGGTTTGGCGTGA 61.099 55.000 0.00 0.00 0.00 4.35
3 4 1.101049 AGGTTGAGTGGTTTGGCGTG 61.101 55.000 0.00 0.00 0.00 5.34
4 5 0.395173 AAGGTTGAGTGGTTTGGCGT 60.395 50.000 0.00 0.00 0.00 5.68
5 6 0.030638 CAAGGTTGAGTGGTTTGGCG 59.969 55.000 0.00 0.00 0.00 5.69
6 7 0.249447 GCAAGGTTGAGTGGTTTGGC 60.249 55.000 0.00 0.00 0.00 4.52
7 8 0.030638 CGCAAGGTTGAGTGGTTTGG 59.969 55.000 0.00 0.00 0.00 3.28
8 9 0.594796 GCGCAAGGTTGAGTGGTTTG 60.595 55.000 0.30 0.00 38.28 2.93
9 10 1.733526 GCGCAAGGTTGAGTGGTTT 59.266 52.632 0.30 0.00 38.28 3.27
10 11 3.432186 GCGCAAGGTTGAGTGGTT 58.568 55.556 0.30 0.00 38.28 3.67
30 31 3.615351 GCTAGTAGGATTCCCGCTTGATC 60.615 52.174 0.00 0.00 37.58 2.92
57 59 3.499918 CCTCGTGCATCTTTCTGAAAAGT 59.500 43.478 4.18 0.00 42.17 2.66
83 85 6.701400 GTGAAGTGAAGGTGTGCATTTTATTT 59.299 34.615 0.00 0.00 0.00 1.40
84 86 6.215845 GTGAAGTGAAGGTGTGCATTTTATT 58.784 36.000 0.00 0.00 0.00 1.40
85 87 5.278957 GGTGAAGTGAAGGTGTGCATTTTAT 60.279 40.000 0.00 0.00 0.00 1.40
86 88 4.037446 GGTGAAGTGAAGGTGTGCATTTTA 59.963 41.667 0.00 0.00 0.00 1.52
87 89 3.181476 GGTGAAGTGAAGGTGTGCATTTT 60.181 43.478 0.00 0.00 0.00 1.82
88 90 2.362077 GGTGAAGTGAAGGTGTGCATTT 59.638 45.455 0.00 0.00 0.00 2.32
89 91 1.956477 GGTGAAGTGAAGGTGTGCATT 59.044 47.619 0.00 0.00 0.00 3.56
90 92 1.143684 AGGTGAAGTGAAGGTGTGCAT 59.856 47.619 0.00 0.00 0.00 3.96
91 93 0.546122 AGGTGAAGTGAAGGTGTGCA 59.454 50.000 0.00 0.00 0.00 4.57
92 94 1.680338 AAGGTGAAGTGAAGGTGTGC 58.320 50.000 0.00 0.00 0.00 4.57
93 95 3.809832 CACTAAGGTGAAGTGAAGGTGTG 59.190 47.826 0.00 0.00 45.89 3.82
94 96 3.744530 GCACTAAGGTGAAGTGAAGGTGT 60.745 47.826 7.39 0.00 45.89 4.16
95 97 2.808543 GCACTAAGGTGAAGTGAAGGTG 59.191 50.000 7.39 0.00 45.89 4.00
96 98 2.706190 AGCACTAAGGTGAAGTGAAGGT 59.294 45.455 7.39 0.00 45.89 3.50
97 99 3.409026 AGCACTAAGGTGAAGTGAAGG 57.591 47.619 7.39 0.00 45.89 3.46
98 100 4.212214 GTCAAGCACTAAGGTGAAGTGAAG 59.788 45.833 7.39 0.00 45.89 3.02
99 101 4.127171 GTCAAGCACTAAGGTGAAGTGAA 58.873 43.478 7.39 0.00 45.89 3.18
100 102 3.388024 AGTCAAGCACTAAGGTGAAGTGA 59.612 43.478 7.39 0.00 45.89 3.41
101 103 3.733337 AGTCAAGCACTAAGGTGAAGTG 58.267 45.455 0.00 0.00 45.61 3.16
102 104 4.130118 CAAGTCAAGCACTAAGGTGAAGT 58.870 43.478 0.00 0.00 45.61 3.01
111 113 2.289072 GCTGGAGTCAAGTCAAGCACTA 60.289 50.000 8.99 0.00 32.30 2.74
129 131 5.649782 AAAAGGAATTGACATACCAGCTG 57.350 39.130 6.78 6.78 0.00 4.24
135 142 7.224557 ACACTTTGCAAAAAGGAATTGACATAC 59.775 33.333 13.84 0.00 34.18 2.39
142 149 5.486526 TGACACACTTTGCAAAAAGGAATT 58.513 33.333 13.84 0.00 34.18 2.17
181 188 1.682854 CACTTGGGAAGCTGCTCAAAA 59.317 47.619 8.77 0.00 0.00 2.44
201 208 4.889345 GCGCAGGCAAGATCTGTTAGATC 61.889 52.174 0.30 10.14 44.06 2.75
248 255 5.007385 TCCTCTCCTACTTTACATTTCGC 57.993 43.478 0.00 0.00 0.00 4.70
296 306 2.163818 TGTTTCAGAGTTGGTAGCCG 57.836 50.000 0.00 0.00 0.00 5.52
340 354 2.238646 TCCTGGACTTGAGTTGTGTTGT 59.761 45.455 0.00 0.00 0.00 3.32
346 360 0.671781 CGCCTCCTGGACTTGAGTTG 60.672 60.000 0.00 0.00 34.57 3.16
372 419 3.836949 AGTAAGCCAATTGATTGCGTTG 58.163 40.909 7.12 0.00 36.48 4.10
375 422 4.905866 CGAATAGTAAGCCAATTGATTGCG 59.094 41.667 7.12 0.41 36.48 4.85
395 448 1.879380 CTCCATTTGCTTGTCCACGAA 59.121 47.619 0.00 0.00 0.00 3.85
437 490 1.787155 CGTCGACCTGTCAGAAAACAG 59.213 52.381 10.58 0.00 45.10 3.16
438 491 1.135527 ACGTCGACCTGTCAGAAAACA 59.864 47.619 10.58 0.00 0.00 2.83
443 553 1.244816 ATGAACGTCGACCTGTCAGA 58.755 50.000 10.58 0.00 0.00 3.27
485 595 9.170734 CCTGCAATGAAAGCATATACTGTATAT 57.829 33.333 13.30 13.30 41.82 0.86
486 596 7.119699 GCCTGCAATGAAAGCATATACTGTATA 59.880 37.037 9.78 9.78 41.82 1.47
487 597 6.072286 GCCTGCAATGAAAGCATATACTGTAT 60.072 38.462 5.53 5.53 41.82 2.29
488 598 5.239306 GCCTGCAATGAAAGCATATACTGTA 59.761 40.000 0.00 0.00 41.82 2.74
489 599 4.037208 GCCTGCAATGAAAGCATATACTGT 59.963 41.667 0.00 0.00 41.82 3.55
490 600 4.543692 GCCTGCAATGAAAGCATATACTG 58.456 43.478 0.00 0.00 41.82 2.74
491 601 3.571401 GGCCTGCAATGAAAGCATATACT 59.429 43.478 0.00 0.00 41.82 2.12
492 602 3.318839 TGGCCTGCAATGAAAGCATATAC 59.681 43.478 3.32 0.00 41.82 1.47
493 603 3.564264 TGGCCTGCAATGAAAGCATATA 58.436 40.909 3.32 0.00 41.82 0.86
494 604 2.390696 TGGCCTGCAATGAAAGCATAT 58.609 42.857 3.32 0.00 41.82 1.78
495 605 1.849977 TGGCCTGCAATGAAAGCATA 58.150 45.000 3.32 0.00 41.82 3.14
496 606 0.978151 TTGGCCTGCAATGAAAGCAT 59.022 45.000 3.32 0.00 41.82 3.79
497 607 0.978151 ATTGGCCTGCAATGAAAGCA 59.022 45.000 3.32 0.00 40.19 3.91
498 608 1.206371 AGATTGGCCTGCAATGAAAGC 59.794 47.619 3.32 0.00 0.00 3.51
502 612 1.683943 GCTAGATTGGCCTGCAATGA 58.316 50.000 3.32 0.00 0.00 2.57
578 700 2.288825 TGAGTTGAGGGCGTCTAGTTTG 60.289 50.000 8.82 0.00 0.00 2.93
685 810 0.381089 GTGGTCAGGATCGTACTCGG 59.619 60.000 0.00 0.00 37.69 4.63
737 862 4.704833 TGCGGGTTCCTGCTCTGC 62.705 66.667 21.13 0.00 0.00 4.26
976 1107 2.429930 CGGGGTGTGCTTGGAAGA 59.570 61.111 0.00 0.00 0.00 2.87
1007 1153 1.795525 CGCCGACATCTACAGTCACAG 60.796 57.143 0.00 0.00 35.77 3.66
1117 1263 0.103937 GTCAGCTCCCCGATCTTCTG 59.896 60.000 0.00 0.00 0.00 3.02
1167 1488 0.039074 GGGCATACTCCGTGATCTCG 60.039 60.000 10.15 10.15 0.00 4.04
1251 1572 0.034670 GGAGAAGATTGCCAGGCACT 60.035 55.000 15.89 9.42 38.71 4.40
1278 1599 1.066605 GCAGGCTTCAAGTGCATATGG 59.933 52.381 4.56 0.00 37.16 2.74
1383 1719 0.476771 GACCCTTGAACTTCACCCCA 59.523 55.000 0.00 0.00 0.00 4.96
1403 1739 1.704628 TGCCCTTCTCTTTCATGGACA 59.295 47.619 0.00 0.00 0.00 4.02
1413 1749 2.124819 CAGCGCATGCCCTTCTCT 60.125 61.111 13.15 0.00 44.31 3.10
1496 1838 1.689243 TAGCAGCCGCCATGTCTCAT 61.689 55.000 0.00 0.00 39.83 2.90
1525 1867 1.548357 TTCCTCTGCTCCAGCTCCAC 61.548 60.000 0.00 0.00 42.66 4.02
1597 1939 2.360350 CTTCGTGGTGCAGGCCAT 60.360 61.111 5.01 0.00 41.08 4.40
1748 2090 1.944024 CTAGAATCGAGCACGTCTCCT 59.056 52.381 2.86 0.29 38.62 3.69
1755 2097 2.380660 CGCTTCTCTAGAATCGAGCAC 58.619 52.381 9.70 0.00 43.75 4.40
1796 2138 1.226542 CCTCAGCCATGCATCCACT 59.773 57.895 0.00 0.00 0.00 4.00
1862 2205 1.878953 CACAAACTAGCCCAACGACT 58.121 50.000 0.00 0.00 0.00 4.18
1913 2256 4.759693 TGCTAACTTCACCCATGTTTGTAG 59.240 41.667 0.00 0.00 0.00 2.74
1925 2271 7.286508 CGTGATGATCATATTGCTAACTTCAC 58.713 38.462 8.54 7.79 0.00 3.18
1943 2289 0.526211 AGTCTACAAGCGCGTGATGA 59.474 50.000 29.85 21.40 0.00 2.92
1989 2335 2.858745 TGGACCTTTTACAAGCCTCAC 58.141 47.619 0.00 0.00 0.00 3.51
2081 2428 5.120830 CGACTAACCCAAAGTGAGAATTCAG 59.879 44.000 8.44 0.00 32.98 3.02
2108 2455 7.380536 TGAAATTCAAAACCATTGGATCAGAG 58.619 34.615 10.37 0.00 0.00 3.35
2112 2459 7.967890 AACTGAAATTCAAAACCATTGGATC 57.032 32.000 10.37 0.00 0.00 3.36
2126 2473 7.904977 GCTGAAACTTTTCCAAAACTGAAATTC 59.095 33.333 0.00 0.00 36.36 2.17
2139 2486 2.798145 CGGTTGGTGCTGAAACTTTTCC 60.798 50.000 0.00 0.00 36.36 3.13
2145 2492 2.793278 ATTTCGGTTGGTGCTGAAAC 57.207 45.000 2.67 0.00 43.78 2.78
2206 2603 5.036737 GTGAATATTTCGGTCATTTGGCTG 58.963 41.667 0.00 0.00 0.00 4.85
2207 2604 4.949856 AGTGAATATTTCGGTCATTTGGCT 59.050 37.500 0.00 0.00 0.00 4.75
2269 2667 7.495901 TGCACAGGAATTCAAATAGTTTTTGA 58.504 30.769 7.93 4.82 36.71 2.69
2270 2668 7.712264 TGCACAGGAATTCAAATAGTTTTTG 57.288 32.000 7.93 0.03 0.00 2.44
2271 2669 8.907222 ATTGCACAGGAATTCAAATAGTTTTT 57.093 26.923 7.93 0.00 0.00 1.94
2272 2670 9.423061 GTATTGCACAGGAATTCAAATAGTTTT 57.577 29.630 7.93 0.00 0.00 2.43
2273 2671 8.806146 AGTATTGCACAGGAATTCAAATAGTTT 58.194 29.630 7.93 0.00 0.00 2.66
2274 2672 8.246180 CAGTATTGCACAGGAATTCAAATAGTT 58.754 33.333 7.93 0.00 0.00 2.24
2275 2673 7.611467 TCAGTATTGCACAGGAATTCAAATAGT 59.389 33.333 7.93 2.35 0.00 2.12
2276 2674 7.988737 TCAGTATTGCACAGGAATTCAAATAG 58.011 34.615 7.93 0.00 0.00 1.73
2277 2675 7.936496 TCAGTATTGCACAGGAATTCAAATA 57.064 32.000 7.93 0.00 0.00 1.40
2295 2693 7.712205 GGCCAAATATTTCAGCAATTTCAGTAT 59.288 33.333 17.31 0.00 0.00 2.12
2388 2787 5.453198 GGTGGATGTGATGGTTTTCACTTTT 60.453 40.000 6.20 0.00 45.07 2.27
2402 2801 3.322541 TCAGAAACTTACGGTGGATGTGA 59.677 43.478 0.00 0.00 0.00 3.58
2435 2834 1.750778 ACCCTTGCACTGAAGTTGTTG 59.249 47.619 0.00 0.00 0.00 3.33
2453 2852 1.133025 CGCTGGGTTGATCAAATGACC 59.867 52.381 10.35 7.77 0.00 4.02
2454 2853 1.468054 GCGCTGGGTTGATCAAATGAC 60.468 52.381 10.35 0.00 0.00 3.06
2455 2854 0.810648 GCGCTGGGTTGATCAAATGA 59.189 50.000 10.35 0.00 0.00 2.57
2456 2855 0.527113 TGCGCTGGGTTGATCAAATG 59.473 50.000 10.35 2.08 0.00 2.32
2459 2858 2.334946 GCTGCGCTGGGTTGATCAA 61.335 57.895 16.47 3.38 0.00 2.57
2460 2859 2.747460 GCTGCGCTGGGTTGATCA 60.747 61.111 16.47 0.00 0.00 2.92
2461 2860 2.747460 TGCTGCGCTGGGTTGATC 60.747 61.111 16.47 0.00 0.00 2.92
2462 2861 2.749044 CTGCTGCGCTGGGTTGAT 60.749 61.111 16.47 0.00 0.00 2.57
2464 2863 3.259425 GAACTGCTGCGCTGGGTTG 62.259 63.158 16.47 0.56 0.00 3.77
2466 2865 3.946201 AGAACTGCTGCGCTGGGT 61.946 61.111 16.47 0.00 0.00 4.51
2473 2896 1.288127 CCAAAGCCAGAACTGCTGC 59.712 57.895 0.00 0.00 43.50 5.25
2498 2921 5.047660 AGTTGTGCTTAGTTTTTGTGGACAA 60.048 36.000 0.00 0.00 36.81 3.18
2500 2923 4.993905 AGTTGTGCTTAGTTTTTGTGGAC 58.006 39.130 0.00 0.00 0.00 4.02
2512 2935 3.556999 TGGCCTGTTTTAGTTGTGCTTA 58.443 40.909 3.32 0.00 0.00 3.09
2517 2940 1.681264 GTGCTGGCCTGTTTTAGTTGT 59.319 47.619 11.69 0.00 0.00 3.32
2534 2957 2.094906 GGTTAATGGGTTTTCTCGGTGC 60.095 50.000 0.00 0.00 0.00 5.01
2587 3010 0.835971 TTGACCTAGGGCTCTGTGCA 60.836 55.000 17.75 0.00 45.15 4.57
2588 3011 0.107945 CTTGACCTAGGGCTCTGTGC 60.108 60.000 17.75 0.00 41.94 4.57
2659 3082 9.087424 GTTCTGCTTTGTGTTTTCTTCTTTATT 57.913 29.630 0.00 0.00 0.00 1.40
2661 3084 7.598278 TGTTCTGCTTTGTGTTTTCTTCTTTA 58.402 30.769 0.00 0.00 0.00 1.85
2662 3085 6.454795 TGTTCTGCTTTGTGTTTTCTTCTTT 58.545 32.000 0.00 0.00 0.00 2.52
2682 3111 9.586435 CCTTTAATTTTTGTCCCATATCTGTTC 57.414 33.333 0.00 0.00 0.00 3.18
2707 3136 4.339530 AGGTTCTTTCTTGTGCTTCTTTCC 59.660 41.667 0.00 0.00 0.00 3.13
2716 3145 0.593128 CGCCCAGGTTCTTTCTTGTG 59.407 55.000 0.00 0.00 0.00 3.33
2717 3146 0.537371 CCGCCCAGGTTCTTTCTTGT 60.537 55.000 0.00 0.00 34.51 3.16
2747 3177 0.179092 GATTTACCGAGGGTGGACCG 60.179 60.000 0.00 0.00 46.96 4.79
2749 3179 2.169769 TGATGATTTACCGAGGGTGGAC 59.830 50.000 0.00 0.00 36.19 4.02
2772 3202 4.855340 TGAGTAGGAATTTTGATGGGGAC 58.145 43.478 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.