Multiple sequence alignment - TraesCS5B01G419900

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 TraesCS5B01G419900 chr5B 100.000 4107 0 0 1 4107 595634244 595630138 0.000000e+00 7585.0
1 TraesCS5B01G419900 chr5B 85.433 2135 231 39 1691 3786 595645975 595643882 0.000000e+00 2146.0
2 TraesCS5B01G419900 chr5B 85.864 1719 185 33 1 1693 595651278 595649592 0.000000e+00 1775.0
3 TraesCS5B01G419900 chr5B 85.228 1205 146 21 2032 3213 541499466 541500661 0.000000e+00 1210.0
4 TraesCS5B01G419900 chr5B 84.232 1205 154 24 2032 3213 541528370 541529561 0.000000e+00 1140.0
5 TraesCS5B01G419900 chr5B 83.488 539 79 4 892 1421 541498357 541498894 1.030000e-135 494.0
6 TraesCS5B01G419900 chr5B 82.785 395 58 5 892 1277 541527151 541527544 1.090000e-90 344.0
7 TraesCS5B01G419900 chr5B 82.090 134 19 4 41 172 595640483 595640353 4.340000e-20 110.0
8 TraesCS5B01G419900 chr5D 87.396 3721 373 43 224 3890 484429625 484425947 0.000000e+00 4185.0
9 TraesCS5B01G419900 chr5D 84.577 1193 151 21 2045 3213 444711806 444712989 0.000000e+00 1153.0
10 TraesCS5B01G419900 chr5D 84.787 539 72 5 892 1421 444710542 444711079 2.170000e-147 532.0
11 TraesCS5B01G419900 chr5D 86.730 211 16 4 14 221 484566234 484566033 1.490000e-54 224.0
12 TraesCS5B01G419900 chr5A 88.809 2234 181 19 1890 4106 606059635 606057454 0.000000e+00 2676.0
13 TraesCS5B01G419900 chr5A 85.636 1469 159 23 94 1538 606061500 606060060 0.000000e+00 1496.0
14 TraesCS5B01G419900 chr5A 84.041 1178 155 19 2062 3218 561554064 561555229 0.000000e+00 1103.0
15 TraesCS5B01G419900 chr5A 90.089 676 46 12 1 671 606062517 606061858 0.000000e+00 857.0
16 TraesCS5B01G419900 chr5A 89.142 571 45 5 90 654 606061968 606061409 0.000000e+00 695.0
17 TraesCS5B01G419900 chr5A 84.658 541 70 9 892 1421 561553213 561553751 1.010000e-145 527.0
18 TraesCS5B01G419900 chr5A 90.385 52 5 0 1543 1594 561553884 561553935 7.370000e-08 69.4
19 TraesCS5B01G419900 chr4D 80.765 915 142 23 2304 3201 52468995 52469892 0.000000e+00 684.0
20 TraesCS5B01G419900 chr4D 77.932 503 89 15 1017 1502 52467530 52468027 1.120000e-75 294.0
21 TraesCS5B01G419900 chr4B 80.241 911 155 20 2304 3201 76814925 76815823 0.000000e+00 662.0
22 TraesCS5B01G419900 chr4B 77.976 504 86 18 1017 1502 76813455 76813951 4.020000e-75 292.0
23 TraesCS5B01G419900 chr4B 78.947 171 29 5 86 254 612500018 612500183 4.340000e-20 110.0
24 TraesCS5B01G419900 chr4B 77.465 142 24 6 79 215 612501903 612502041 1.220000e-10 78.7
25 TraesCS5B01G419900 chr4A 78.049 656 136 8 2308 2959 544390193 544389542 1.370000e-109 407.0
26 TraesCS5B01G419900 chr4A 77.075 506 90 17 1017 1502 544204235 544203736 6.770000e-68 268.0


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 TraesCS5B01G419900 chr5B 595630138 595634244 4106 True 7585.000000 7585 100.000000 1 4107 1 chr5B.!!$R1 4106
1 TraesCS5B01G419900 chr5B 595640353 595651278 10925 True 1343.666667 2146 84.462333 1 3786 3 chr5B.!!$R2 3785
2 TraesCS5B01G419900 chr5B 541498357 541500661 2304 False 852.000000 1210 84.358000 892 3213 2 chr5B.!!$F1 2321
3 TraesCS5B01G419900 chr5B 541527151 541529561 2410 False 742.000000 1140 83.508500 892 3213 2 chr5B.!!$F2 2321
4 TraesCS5B01G419900 chr5D 484425947 484429625 3678 True 4185.000000 4185 87.396000 224 3890 1 chr5D.!!$R1 3666
5 TraesCS5B01G419900 chr5D 444710542 444712989 2447 False 842.500000 1153 84.682000 892 3213 2 chr5D.!!$F1 2321
6 TraesCS5B01G419900 chr5A 606057454 606062517 5063 True 1431.000000 2676 88.419000 1 4106 4 chr5A.!!$R1 4105
7 TraesCS5B01G419900 chr5A 561553213 561555229 2016 False 566.466667 1103 86.361333 892 3218 3 chr5A.!!$F1 2326
8 TraesCS5B01G419900 chr4D 52467530 52469892 2362 False 489.000000 684 79.348500 1017 3201 2 chr4D.!!$F1 2184
9 TraesCS5B01G419900 chr4B 76813455 76815823 2368 False 477.000000 662 79.108500 1017 3201 2 chr4B.!!$F1 2184
10 TraesCS5B01G419900 chr4A 544389542 544390193 651 True 407.000000 407 78.049000 2308 2959 1 chr4A.!!$R2 651

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
708 1635 0.321919 ACGAGGCGTGTAGTGGTCTA 60.322 55.0 0.0 0.0 39.18 2.59 F
1128 2086 0.537188 ATGTCGCATTCTCTCCGGTT 59.463 50.0 0.0 0.0 0.00 4.44 F
1386 2353 0.811281 GCAAATACAAGGCCGAAGCT 59.189 50.0 0.0 0.0 39.73 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 2596 1.678101 GGGAGAAACAGTGGCATATGC 59.322 52.381 19.79 19.79 41.14 3.14 R
2810 8116 0.037975 GGCAGTTGCAGACCCAAATG 60.038 55.000 6.43 0.00 44.36 2.32 R
3320 8645 0.174389 TCTGCCTCTCAATCTCGCAC 59.826 55.000 0.00 0.00 0.00 5.34 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
38 39 5.934402 TTTTAACCACAAACTAAGCCCAA 57.066 34.783 0.00 0.00 0.00 4.12
39 40 4.922471 TTAACCACAAACTAAGCCCAAC 57.078 40.909 0.00 0.00 0.00 3.77
88 91 7.814107 CCAATTTGGTATATGGTGCAATATCAC 59.186 37.037 7.31 0.00 32.78 3.06
189 196 9.349713 AGTTGTGTGATCTTAAGAAAATACCAA 57.650 29.630 9.71 6.09 0.00 3.67
221 696 8.710835 AAATTAAACAACAAAAAGGTCACGAT 57.289 26.923 0.00 0.00 0.00 3.73
288 763 5.005740 AGCAGAAGTGATGAAAAGCACATA 58.994 37.500 0.00 0.00 37.48 2.29
289 764 5.651139 AGCAGAAGTGATGAAAAGCACATAT 59.349 36.000 0.00 0.00 37.48 1.78
290 765 6.152323 AGCAGAAGTGATGAAAAGCACATATT 59.848 34.615 0.00 0.00 37.48 1.28
291 766 7.337689 AGCAGAAGTGATGAAAAGCACATATTA 59.662 33.333 0.00 0.00 37.48 0.98
292 767 7.970061 GCAGAAGTGATGAAAAGCACATATTAA 59.030 33.333 0.00 0.00 37.48 1.40
425 1352 4.870636 AGTGATGCAAATCCCAATTAGGA 58.129 39.130 0.00 0.00 41.22 2.94
441 1368 7.816031 CCCAATTAGGATTTGTCATGCAATATC 59.184 37.037 0.00 8.75 41.22 1.63
442 1369 8.361889 CCAATTAGGATTTGTCATGCAATATCA 58.638 33.333 0.00 0.00 41.22 2.15
506 1433 7.762159 GGTATAGCTATATCTCAAGCTTGGAAC 59.238 40.741 25.73 12.40 46.82 3.62
534 1461 8.405418 AGTACTACTAATCAGTTGTGTGAAGA 57.595 34.615 0.00 0.00 40.34 2.87
535 1462 8.516234 AGTACTACTAATCAGTTGTGTGAAGAG 58.484 37.037 0.00 0.00 40.34 2.85
579 1506 7.065803 GCCATGCACATCTTCTTTACTAGTTAA 59.934 37.037 0.00 0.00 0.00 2.01
606 1533 2.499685 GGTCGGCACCGCTATCTT 59.500 61.111 3.66 0.00 39.59 2.40
617 1544 3.309954 CACCGCTATCTTAAGCTTGGAAC 59.690 47.826 9.86 1.61 40.49 3.62
708 1635 0.321919 ACGAGGCGTGTAGTGGTCTA 60.322 55.000 0.00 0.00 39.18 2.59
774 1701 2.100631 CCGGAAGCGCCACACTAAG 61.101 63.158 2.29 0.00 35.94 2.18
775 1702 2.740714 CGGAAGCGCCACACTAAGC 61.741 63.158 2.29 0.00 35.94 3.09
796 1725 6.107901 AGCTGATAGGATAAGCTTAGGTTG 57.892 41.667 12.54 0.00 44.79 3.77
820 1749 8.222984 TGCTTACATATATACGAAATGACACG 57.777 34.615 0.00 0.00 0.00 4.49
823 1752 9.389570 CTTACATATATACGAAATGACACGACA 57.610 33.333 0.00 0.00 0.00 4.35
835 1764 7.630987 CGAAATGACACGACAATGACTAATTAC 59.369 37.037 0.00 0.00 0.00 1.89
890 1819 3.198068 GACGCAGATGCTTCAATCCTTA 58.802 45.455 6.45 0.00 38.91 2.69
949 1901 5.004922 TGAAAACAACACTTCCCAATCAC 57.995 39.130 0.00 0.00 0.00 3.06
990 1942 0.744281 CAAAAGCCCAACGAACCACT 59.256 50.000 0.00 0.00 0.00 4.00
1062 2014 2.358737 CAGACCCGCTTCGGCTTT 60.359 61.111 0.00 0.00 46.86 3.51
1095 2053 2.434336 CACTATCTCATCCAACCCCGAA 59.566 50.000 0.00 0.00 0.00 4.30
1112 2070 3.009723 CCGAATCTACTGCCAACAATGT 58.990 45.455 0.00 0.00 0.00 2.71
1128 2086 0.537188 ATGTCGCATTCTCTCCGGTT 59.463 50.000 0.00 0.00 0.00 4.44
1134 2092 1.340114 GCATTCTCTCCGGTTTCCCTT 60.340 52.381 0.00 0.00 0.00 3.95
1167 2125 4.827087 CTCATCACCGCTGGCGCT 62.827 66.667 7.64 0.00 38.24 5.92
1222 2189 3.077556 GGGAAGGCGAGGCTGAGA 61.078 66.667 0.00 0.00 0.00 3.27
1224 2191 2.498726 GAAGGCGAGGCTGAGAGG 59.501 66.667 0.00 0.00 0.00 3.69
1283 2250 4.246206 CGACGCGTCCTATGCCGA 62.246 66.667 31.84 0.00 0.00 5.54
1297 2264 2.795973 CCGATAGTCCGCGTGTCA 59.204 61.111 4.92 0.00 0.00 3.58
1383 2350 1.268352 GTGTGCAAATACAAGGCCGAA 59.732 47.619 0.00 0.00 31.36 4.30
1386 2353 0.811281 GCAAATACAAGGCCGAAGCT 59.189 50.000 0.00 0.00 39.73 3.74
1440 2407 2.419713 CCTTCTTTACCTAGCCCGTTCC 60.420 54.545 0.00 0.00 0.00 3.62
1451 2418 1.238625 GCCCGTTCCCAAAATGACGA 61.239 55.000 0.00 0.00 37.69 4.20
1461 2428 4.048504 CCCAAAATGACGACAAGGTTTTC 58.951 43.478 0.00 0.00 0.00 2.29
1480 2532 9.487790 AGGTTTTCACCATAAAACAAATACATG 57.512 29.630 12.64 0.00 46.48 3.21
1494 2552 7.722795 ACAAATACATGGTAAAAAGGTTTGC 57.277 32.000 0.00 0.00 0.00 3.68
1511 2569 4.275936 GGTTTGCTCGTTATCTATGGCATT 59.724 41.667 4.78 0.00 0.00 3.56
1514 2572 6.968131 TTGCTCGTTATCTATGGCATTATC 57.032 37.500 4.78 0.00 0.00 1.75
1590 2685 8.184192 GCTTGTTTTGTGCTGATGTAATATAGT 58.816 33.333 0.00 0.00 0.00 2.12
1647 2752 8.523658 GCCTCAAGATTTGTTATAGTCCTTTTT 58.476 33.333 0.00 0.00 0.00 1.94
1700 6428 7.982224 ACCACTGTTTTTAACACTAGAAGTTC 58.018 34.615 0.00 0.00 36.25 3.01
1726 6454 5.995897 AGCACCGTTTTCAACTTTCTATAGT 59.004 36.000 0.00 0.00 0.00 2.12
1771 6524 8.305317 CGGTTGGTTGGGTAAAATAAAATAGAA 58.695 33.333 0.00 0.00 0.00 2.10
1798 6553 8.204903 TGTCTTAATACCCTACTGTTAAACCA 57.795 34.615 0.00 0.00 0.00 3.67
1832 6592 7.975866 ATGCAATTTATTTTTGTCTAGCTCG 57.024 32.000 0.00 0.00 0.00 5.03
1833 6593 6.908825 TGCAATTTATTTTTGTCTAGCTCGT 58.091 32.000 0.00 0.00 0.00 4.18
1870 6630 6.431234 GCATGGAGTACTTATTAATCCCTTGG 59.569 42.308 0.00 0.00 43.32 3.61
1934 6854 7.061566 TCATCTGAATTTATGATACCGTGGA 57.938 36.000 0.00 0.00 0.00 4.02
1937 6857 8.786898 CATCTGAATTTATGATACCGTGGAAAT 58.213 33.333 0.00 0.00 0.00 2.17
1947 6877 5.924254 TGATACCGTGGAAATATTCATCGTC 59.076 40.000 0.00 0.00 0.00 4.20
1951 6881 3.550275 CGTGGAAATATTCATCGTCGTGT 59.450 43.478 0.00 0.00 0.00 4.49
1970 6900 4.379498 CGTGTTGTCATGTTGCTTATTGTG 59.621 41.667 0.00 0.00 0.00 3.33
1971 6901 4.681025 GTGTTGTCATGTTGCTTATTGTGG 59.319 41.667 0.00 0.00 0.00 4.17
1982 6912 3.838317 TGCTTATTGTGGTCCAGAGTAGT 59.162 43.478 0.00 0.00 0.00 2.73
2027 7187 6.000219 AGCCGATATCTATGTGCTGAATTTT 59.000 36.000 0.34 0.00 0.00 1.82
2029 7189 6.621596 GCCGATATCTATGTGCTGAATTTTCC 60.622 42.308 0.34 0.00 0.00 3.13
2039 7321 6.480763 TGTGCTGAATTTTCCTAGGTATTGA 58.519 36.000 9.08 1.37 0.00 2.57
2041 7323 7.450014 TGTGCTGAATTTTCCTAGGTATTGAAA 59.550 33.333 9.08 0.00 0.00 2.69
2114 7397 8.338259 GCACATATGAATATTTTTCTGTCGTCT 58.662 33.333 10.38 0.00 0.00 4.18
2398 7701 2.526304 TCAAAGATATTCTCCCCGCG 57.474 50.000 0.00 0.00 0.00 6.46
2467 7770 2.550830 TCAAAGGAGCTTGGACAGAC 57.449 50.000 0.00 0.00 0.00 3.51
2484 7787 2.872245 CAGACCAGTTTGATTCACGTGT 59.128 45.455 16.51 0.00 0.00 4.49
2701 8007 2.031333 GGCAGAAAAGTTGAGTGCTGAG 60.031 50.000 0.00 0.00 34.46 3.35
2708 8014 1.004080 TTGAGTGCTGAGCCAGAGC 60.004 57.895 0.23 0.00 40.32 4.09
2811 8117 2.634982 GCATCCGATTTGCTCAAACA 57.365 45.000 0.00 0.00 37.14 2.83
2912 8218 4.558496 GCATCTCATCCGTTTTCCACAAAA 60.558 41.667 0.00 0.00 0.00 2.44
2998 8304 1.476845 TAAGTGCAAGTCCGCCCTCA 61.477 55.000 0.00 0.00 0.00 3.86
3000 8306 2.922503 TGCAAGTCCGCCCTCAGA 60.923 61.111 0.00 0.00 0.00 3.27
3096 8405 0.464373 CATGTGGTCAATCCCCTCCG 60.464 60.000 0.00 0.00 34.77 4.63
3102 8411 1.490910 GGTCAATCCCCTCCGATCTTT 59.509 52.381 0.00 0.00 0.00 2.52
3141 8454 2.146342 AGTGTCTTGTCATTTGCCTCG 58.854 47.619 0.00 0.00 0.00 4.63
3159 8472 1.014352 CGGCTGTTACATGTAAGGGC 58.986 55.000 23.58 23.58 0.00 5.19
3239 8554 5.122396 GCTTTTGATGAATCCTACACTCGTT 59.878 40.000 0.00 0.00 0.00 3.85
3307 8622 5.506708 GACCACCTTGACCCAAAATACTAT 58.493 41.667 0.00 0.00 0.00 2.12
3314 8629 6.147821 CCTTGACCCAAAATACTATCTATGCG 59.852 42.308 0.00 0.00 0.00 4.73
3316 8631 7.004555 TGACCCAAAATACTATCTATGCGAT 57.995 36.000 0.00 0.00 36.11 4.58
3320 8645 7.544566 ACCCAAAATACTATCTATGCGATTACG 59.455 37.037 0.00 0.00 42.93 3.18
3331 8656 1.197055 GCGATTACGTGCGAGATTGA 58.803 50.000 0.00 0.00 41.98 2.57
3341 8666 0.743688 GCGAGATTGAGAGGCAGAGA 59.256 55.000 0.00 0.00 0.00 3.10
3367 8692 5.743872 GGTTCAACACACTCATTTTGACTTC 59.256 40.000 0.00 0.00 0.00 3.01
3370 8702 6.785191 TCAACACACTCATTTTGACTTCTTC 58.215 36.000 0.00 0.00 0.00 2.87
3427 8760 9.134734 TCAAGTTAAAGTCAAAACACATGAAAC 57.865 29.630 0.00 0.00 0.00 2.78
3480 8821 3.089284 CCAAGTGGATGGTAAAGTTCCC 58.911 50.000 0.00 0.00 37.39 3.97
3522 8864 4.848562 AAAGGAATTCCGACCACTTTTC 57.151 40.909 18.82 0.00 42.08 2.29
3555 8926 8.783093 TCAATTCACTGAACCAAGTACATAAAG 58.217 33.333 0.00 0.00 0.00 1.85
3560 8931 6.147821 CACTGAACCAAGTACATAAAGAGTGG 59.852 42.308 0.00 0.00 0.00 4.00
3570 8941 4.910195 ACATAAAGAGTGGTGCTGAATGA 58.090 39.130 0.00 0.00 0.00 2.57
3571 8942 5.316167 ACATAAAGAGTGGTGCTGAATGAA 58.684 37.500 0.00 0.00 0.00 2.57
3572 8943 5.769662 ACATAAAGAGTGGTGCTGAATGAAA 59.230 36.000 0.00 0.00 0.00 2.69
3573 8944 4.843220 AAAGAGTGGTGCTGAATGAAAG 57.157 40.909 0.00 0.00 0.00 2.62
3574 8945 3.777106 AGAGTGGTGCTGAATGAAAGA 57.223 42.857 0.00 0.00 0.00 2.52
3575 8946 4.090761 AGAGTGGTGCTGAATGAAAGAA 57.909 40.909 0.00 0.00 0.00 2.52
3576 8947 4.464008 AGAGTGGTGCTGAATGAAAGAAA 58.536 39.130 0.00 0.00 0.00 2.52
3577 8948 4.518211 AGAGTGGTGCTGAATGAAAGAAAG 59.482 41.667 0.00 0.00 0.00 2.62
3578 8949 4.464008 AGTGGTGCTGAATGAAAGAAAGA 58.536 39.130 0.00 0.00 0.00 2.52
3579 8950 4.889409 AGTGGTGCTGAATGAAAGAAAGAA 59.111 37.500 0.00 0.00 0.00 2.52
3580 8951 5.360714 AGTGGTGCTGAATGAAAGAAAGAAA 59.639 36.000 0.00 0.00 0.00 2.52
3581 8952 6.041296 AGTGGTGCTGAATGAAAGAAAGAAAT 59.959 34.615 0.00 0.00 0.00 2.17
3582 8953 7.231317 AGTGGTGCTGAATGAAAGAAAGAAATA 59.769 33.333 0.00 0.00 0.00 1.40
3583 8954 7.867403 GTGGTGCTGAATGAAAGAAAGAAATAA 59.133 33.333 0.00 0.00 0.00 1.40
3584 8955 8.420222 TGGTGCTGAATGAAAGAAAGAAATAAA 58.580 29.630 0.00 0.00 0.00 1.40
3585 8956 9.260002 GGTGCTGAATGAAAGAAAGAAATAAAA 57.740 29.630 0.00 0.00 0.00 1.52
3786 9173 2.159476 CCATGACATTTCCAAGCTCGTG 60.159 50.000 0.00 0.00 0.00 4.35
3835 9222 2.561419 TGGTACTACCAGCAACAGAGAC 59.439 50.000 3.57 0.00 44.79 3.36
3841 9228 0.108898 CCAGCAACAGAGACTCGAGG 60.109 60.000 18.41 0.17 0.00 4.63
3866 11009 3.769739 AGTCTCCACACAGCATACAAA 57.230 42.857 0.00 0.00 0.00 2.83
3911 11054 4.020573 ACTCCGTACCAATCAGTTGAATGA 60.021 41.667 0.00 0.00 37.53 2.57
3912 11055 4.900684 TCCGTACCAATCAGTTGAATGAA 58.099 39.130 0.00 0.00 37.53 2.57
3913 11056 5.496556 TCCGTACCAATCAGTTGAATGAAT 58.503 37.500 0.00 0.00 37.53 2.57
3914 11057 5.353956 TCCGTACCAATCAGTTGAATGAATG 59.646 40.000 0.00 0.00 37.53 2.67
3915 11058 5.030295 CGTACCAATCAGTTGAATGAATGC 58.970 41.667 0.00 0.00 37.53 3.56
3916 11059 5.391843 CGTACCAATCAGTTGAATGAATGCA 60.392 40.000 0.00 0.00 37.53 3.96
3917 11060 5.670792 ACCAATCAGTTGAATGAATGCAT 57.329 34.783 0.00 0.00 37.53 3.96
3918 11061 5.416083 ACCAATCAGTTGAATGAATGCATG 58.584 37.500 0.00 0.00 37.53 4.06
3919 11062 5.186215 ACCAATCAGTTGAATGAATGCATGA 59.814 36.000 0.00 0.00 37.53 3.07
3920 11063 6.127168 ACCAATCAGTTGAATGAATGCATGAT 60.127 34.615 0.00 0.00 37.53 2.45
3921 11064 6.420903 CCAATCAGTTGAATGAATGCATGATC 59.579 38.462 0.00 0.00 37.53 2.92
3923 11066 6.709018 TCAGTTGAATGAATGCATGATCAT 57.291 33.333 1.18 1.18 37.88 2.45
3924 11067 6.503524 TCAGTTGAATGAATGCATGATCATG 58.496 36.000 28.04 28.04 41.60 3.07
3926 11069 6.638468 CAGTTGAATGAATGCATGATCATGAG 59.362 38.462 34.65 13.68 41.20 2.90
3927 11070 5.121221 TGAATGAATGCATGATCATGAGC 57.879 39.130 34.65 22.47 41.20 4.26
3928 11071 4.827284 TGAATGAATGCATGATCATGAGCT 59.173 37.500 34.65 19.04 41.20 4.09
3929 11072 6.001460 TGAATGAATGCATGATCATGAGCTA 58.999 36.000 34.65 18.96 41.20 3.32
3930 11073 6.659242 TGAATGAATGCATGATCATGAGCTAT 59.341 34.615 34.65 20.13 41.20 2.97
3931 11074 5.880054 TGAATGCATGATCATGAGCTATG 57.120 39.130 34.65 12.43 41.20 2.23
3932 11075 4.156008 TGAATGCATGATCATGAGCTATGC 59.844 41.667 34.65 27.03 43.21 3.14
3934 11077 2.812011 TGCATGATCATGAGCTATGCAC 59.188 45.455 34.65 16.33 46.31 4.57
3935 11078 3.075148 GCATGATCATGAGCTATGCACT 58.925 45.455 34.65 2.19 42.63 4.40
4076 11219 3.634910 GCAAGGAAGTTACCAAACTGGAA 59.365 43.478 0.00 0.00 45.37 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.395435 GGTTGGGCTTAGTTTGTGGTTAAAA 60.395 40.000 0.00 0.00 0.00 1.52
38 39 1.714541 TGCATCATTTGTTGTGGGGT 58.285 45.000 0.00 0.00 0.00 4.95
39 40 2.835580 TTGCATCATTTGTTGTGGGG 57.164 45.000 0.00 0.00 0.00 4.96
117 120 0.455815 GGGATTCCAATGCCAACGTC 59.544 55.000 4.80 0.00 45.30 4.34
189 196 9.884636 ACCTTTTTGTTGTTTAATTTAGAAGCT 57.115 25.926 0.00 0.00 0.00 3.74
441 1368 9.912634 TTTAACTAGAAAAAGAGGATTTGCATG 57.087 29.630 0.00 0.00 0.00 4.06
478 1405 7.454694 TCCAAGCTTGAGATATAGCTATACCAA 59.545 37.037 28.05 16.62 46.53 3.67
479 1406 6.954102 TCCAAGCTTGAGATATAGCTATACCA 59.046 38.462 28.05 10.99 46.53 3.25
489 1416 8.312669 AGTACTAAGTTCCAAGCTTGAGATAT 57.687 34.615 28.05 12.75 0.00 1.63
490 1417 7.719871 AGTACTAAGTTCCAAGCTTGAGATA 57.280 36.000 28.05 11.56 0.00 1.98
532 1459 6.309357 TGGCATTGCATAATTAGGATTCTCT 58.691 36.000 11.39 0.00 0.00 3.10
534 1461 6.573680 GCATGGCATTGCATAATTAGGATTCT 60.574 38.462 11.39 0.00 42.31 2.40
535 1462 5.579511 GCATGGCATTGCATAATTAGGATTC 59.420 40.000 11.39 0.00 42.31 2.52
579 1506 1.605232 CGGTGCCGACCTTTAAAGTTT 59.395 47.619 14.03 0.49 40.58 2.66
587 1514 1.614241 AAGATAGCGGTGCCGACCTT 61.614 55.000 15.45 7.88 40.58 3.50
592 1519 0.249489 AGCTTAAGATAGCGGTGCCG 60.249 55.000 6.67 6.22 45.82 5.69
606 1533 5.165961 AGCAATACTGAGTTCCAAGCTTA 57.834 39.130 0.00 0.00 0.00 3.09
617 1544 6.591448 TCACACAACTGATTAGCAATACTGAG 59.409 38.462 0.00 0.00 0.00 3.35
654 1581 7.493367 ACCGGTCATTTTAAAAGAATTGTTCA 58.507 30.769 0.00 0.00 0.00 3.18
662 1589 8.009622 ACCTTTTAACCGGTCATTTTAAAAGA 57.990 30.769 31.64 12.24 46.45 2.52
672 1599 3.554752 CCTCGTAACCTTTTAACCGGTCA 60.555 47.826 8.04 0.00 31.87 4.02
675 1602 1.733912 GCCTCGTAACCTTTTAACCGG 59.266 52.381 0.00 0.00 0.00 5.28
677 1604 2.158254 CACGCCTCGTAACCTTTTAACC 59.842 50.000 0.00 0.00 38.32 2.85
708 1635 4.020573 TCTGTAGAACATCGGATTTGTGGT 60.021 41.667 0.00 0.00 0.00 4.16
774 1701 4.693095 GCAACCTAAGCTTATCCTATCAGC 59.307 45.833 6.64 0.56 0.00 4.26
775 1702 6.107901 AGCAACCTAAGCTTATCCTATCAG 57.892 41.667 6.64 0.00 39.87 2.90
796 1725 8.363755 GTCGTGTCATTTCGTATATATGTAAGC 58.636 37.037 1.91 0.00 0.00 3.09
820 1749 8.534333 TGTCTCTTGTGTAATTAGTCATTGTC 57.466 34.615 0.00 0.00 0.00 3.18
823 1752 8.902540 TGTTGTCTCTTGTGTAATTAGTCATT 57.097 30.769 0.00 0.00 0.00 2.57
835 1764 4.701956 AAGTGGTTTGTTGTCTCTTGTG 57.298 40.909 0.00 0.00 0.00 3.33
949 1901 6.042638 TGTTAGAGTTGAGAGAAAGATGGG 57.957 41.667 0.00 0.00 0.00 4.00
990 1942 2.358619 GTTGCCATGGCTGGGGTA 59.641 61.111 35.53 13.42 43.36 3.69
1062 2014 2.123854 ATAGTGGAGGCGAGGCGA 60.124 61.111 0.00 0.00 0.00 5.54
1095 2053 2.009774 GCGACATTGTTGGCAGTAGAT 58.990 47.619 6.18 0.00 0.00 1.98
1128 2086 3.909258 GAGCGCGACGTGAAGGGAA 62.909 63.158 12.10 0.00 0.00 3.97
1182 2140 0.039798 GTGTAGCGACGAGTTGGTCA 60.040 55.000 0.00 0.00 36.73 4.02
1263 2230 4.865761 GCATAGGACGCGTCGGCA 62.866 66.667 30.99 19.22 36.10 5.69
1283 2250 0.172803 GAAGGTGACACGCGGACTAT 59.827 55.000 12.47 0.00 0.00 2.12
1305 2272 1.081242 GTCCACGAAGACGCCGTTA 60.081 57.895 0.00 0.00 43.96 3.18
1371 2338 0.905357 ACTGAGCTTCGGCCTTGTAT 59.095 50.000 0.00 0.00 43.01 2.29
1424 2391 1.360185 TTGGGAACGGGCTAGGTAAA 58.640 50.000 0.00 0.00 0.00 2.01
1428 2395 1.102978 CATTTTGGGAACGGGCTAGG 58.897 55.000 0.00 0.00 0.00 3.02
1434 2401 1.231221 TGTCGTCATTTTGGGAACGG 58.769 50.000 0.00 0.00 0.00 4.44
1440 2407 4.502645 GTGAAAACCTTGTCGTCATTTTGG 59.497 41.667 0.00 0.00 0.00 3.28
1451 2418 9.320352 GTATTTGTTTTATGGTGAAAACCTTGT 57.680 29.630 8.77 0.00 44.97 3.16
1480 2532 6.250344 AGATAACGAGCAAACCTTTTTACC 57.750 37.500 0.00 0.00 0.00 2.85
1488 2540 3.202906 TGCCATAGATAACGAGCAAACC 58.797 45.455 0.00 0.00 0.00 3.27
1489 2547 5.424121 AATGCCATAGATAACGAGCAAAC 57.576 39.130 0.00 0.00 33.35 2.93
1494 2552 9.025020 GTACATGATAATGCCATAGATAACGAG 57.975 37.037 0.00 0.00 0.00 4.18
1538 2596 1.678101 GGGAGAAACAGTGGCATATGC 59.322 52.381 19.79 19.79 41.14 3.14
1617 2712 7.890655 AGGACTATAACAAATCTTGAGGCTTTT 59.109 33.333 0.00 0.00 0.00 2.27
1618 2713 7.406104 AGGACTATAACAAATCTTGAGGCTTT 58.594 34.615 0.00 0.00 0.00 3.51
1669 2774 8.426489 TCTAGTGTTAAAAACAGTGGTACAGAT 58.574 33.333 9.78 0.00 44.42 2.90
1726 6454 9.524496 ACCAACCGAGATACTATATGTATGTAA 57.476 33.333 3.48 0.00 41.55 2.41
1743 6471 5.708877 TTTATTTTACCCAACCAACCGAG 57.291 39.130 0.00 0.00 0.00 4.63
1771 6524 8.316946 GGTTTAACAGTAGGGTATTAAGACAGT 58.683 37.037 2.17 0.00 0.00 3.55
1807 6562 8.673711 ACGAGCTAGACAAAAATAAATTGCATA 58.326 29.630 0.00 0.00 0.00 3.14
1808 6563 7.538575 ACGAGCTAGACAAAAATAAATTGCAT 58.461 30.769 0.00 0.00 0.00 3.96
1832 6592 8.888579 AAGTACTCCATGCATATTACAAGTAC 57.111 34.615 0.00 10.72 38.59 2.73
1870 6630 9.638239 TTCAATAATTAAGTTGGACAGAAATGC 57.362 29.630 0.00 0.00 0.00 3.56
1911 6831 7.728847 TTCCACGGTATCATAAATTCAGATG 57.271 36.000 0.00 0.00 0.00 2.90
1929 6849 3.550275 ACACGACGATGAATATTTCCACG 59.450 43.478 0.00 0.00 34.90 4.94
1934 6854 6.092122 ACATGACAACACGACGATGAATATTT 59.908 34.615 0.00 0.00 0.00 1.40
1937 6857 4.490743 ACATGACAACACGACGATGAATA 58.509 39.130 0.00 0.00 0.00 1.75
1947 6877 4.379498 CACAATAAGCAACATGACAACACG 59.621 41.667 0.00 0.00 0.00 4.49
1951 6881 4.022416 GGACCACAATAAGCAACATGACAA 60.022 41.667 0.00 0.00 0.00 3.18
1970 6900 6.540995 TCCTATATGTACACTACTCTGGACC 58.459 44.000 0.00 0.00 0.00 4.46
1971 6901 7.225725 ACTCCTATATGTACACTACTCTGGAC 58.774 42.308 0.00 0.00 0.00 4.02
1982 6912 8.488668 TCGGCTATACATACTCCTATATGTACA 58.511 37.037 0.00 0.00 46.00 2.90
2027 7187 5.826643 AGCACCATTTTTCAATACCTAGGA 58.173 37.500 17.98 0.00 0.00 2.94
2029 7189 6.093495 TCGAAGCACCATTTTTCAATACCTAG 59.907 38.462 0.00 0.00 0.00 3.02
2039 7321 4.037923 ACAACATCTCGAAGCACCATTTTT 59.962 37.500 0.00 0.00 0.00 1.94
2041 7323 3.058016 CACAACATCTCGAAGCACCATTT 60.058 43.478 0.00 0.00 0.00 2.32
2111 7394 6.500684 AAATCATCACATACAACCACAGAC 57.499 37.500 0.00 0.00 0.00 3.51
2114 7397 7.994425 AGTAAAATCATCACATACAACCACA 57.006 32.000 0.00 0.00 0.00 4.17
2161 7446 9.607285 ACTAACGTTTTACAAAGCATTTCTATG 57.393 29.630 5.91 0.00 35.03 2.23
2244 7541 4.685169 CACTATTGTGCTACCCAGTTTG 57.315 45.455 0.00 0.00 37.38 2.93
2295 7596 6.512297 TGGACCAAGTCAAAATAAAGAAAGC 58.488 36.000 0.00 0.00 33.68 3.51
2398 7701 2.238898 AGTGGTGTTGCTAATAGACCCC 59.761 50.000 0.00 0.00 0.00 4.95
2467 7770 4.804608 TGTTACACGTGAATCAAACTGG 57.195 40.909 25.01 0.00 0.00 4.00
2484 7787 6.752168 AGGTAGAAGTAGTCGCTTTTTGTTA 58.248 36.000 0.00 0.00 0.00 2.41
2810 8116 0.037975 GGCAGTTGCAGACCCAAATG 60.038 55.000 6.43 0.00 44.36 2.32
2811 8117 0.469705 TGGCAGTTGCAGACCCAAAT 60.470 50.000 6.43 0.00 44.36 2.32
2912 8218 4.093703 TGTTTCATTCACTTCGACAAACGT 59.906 37.500 0.00 0.00 43.13 3.99
2982 8288 2.743928 CTGAGGGCGGACTTGCAC 60.744 66.667 0.00 0.00 39.04 4.57
2983 8289 2.922503 TCTGAGGGCGGACTTGCA 60.923 61.111 0.00 0.00 36.28 4.08
2989 8295 0.982852 AATCCATGTCTGAGGGCGGA 60.983 55.000 0.00 0.00 0.00 5.54
2998 8304 1.138859 TCCGCGATGAAATCCATGTCT 59.861 47.619 8.23 0.00 41.39 3.41
3000 8306 2.146342 GATCCGCGATGAAATCCATGT 58.854 47.619 8.23 0.00 41.39 3.21
3096 8405 6.902341 TCAGAGCAAACACATTACAAAGATC 58.098 36.000 0.00 0.00 0.00 2.75
3102 8411 4.881273 ACACTTCAGAGCAAACACATTACA 59.119 37.500 0.00 0.00 0.00 2.41
3141 8454 2.017049 CTGCCCTTACATGTAACAGCC 58.983 52.381 22.98 11.06 0.00 4.85
3159 8472 4.751060 CATGATTGATTGTCCAAACCCTG 58.249 43.478 0.00 0.00 0.00 4.45
3228 8543 0.319211 TGCCGACAAACGAGTGTAGG 60.319 55.000 14.62 14.62 44.58 3.18
3239 8554 5.419155 TCCCACAAAAATAATATGCCGACAA 59.581 36.000 0.00 0.00 0.00 3.18
3307 8622 1.600485 TCTCGCACGTAATCGCATAGA 59.400 47.619 0.00 0.00 41.18 1.98
3314 8629 3.046390 CCTCTCAATCTCGCACGTAATC 58.954 50.000 0.00 0.00 0.00 1.75
3316 8631 1.469251 GCCTCTCAATCTCGCACGTAA 60.469 52.381 0.00 0.00 0.00 3.18
3320 8645 0.174389 TCTGCCTCTCAATCTCGCAC 59.826 55.000 0.00 0.00 0.00 5.34
3331 8656 0.318762 GTTGAACCGTCTCTGCCTCT 59.681 55.000 0.00 0.00 0.00 3.69
3341 8666 3.692101 TCAAAATGAGTGTGTTGAACCGT 59.308 39.130 0.00 0.00 0.00 4.83
3407 8739 9.562583 GTTACAGTTTCATGTGTTTTGACTTTA 57.437 29.630 0.00 0.00 34.56 1.85
3427 8760 6.884096 TTTGCAATGTTTGACAAGTTACAG 57.116 33.333 0.00 0.00 31.74 2.74
3512 8853 4.590850 ATTGAGCAAAGGAAAAGTGGTC 57.409 40.909 0.00 0.00 39.62 4.02
3522 8864 3.318839 TGGTTCAGTGAATTGAGCAAAGG 59.681 43.478 9.18 0.00 30.80 3.11
3555 8926 4.516698 TCTTTCTTTCATTCAGCACCACTC 59.483 41.667 0.00 0.00 0.00 3.51
3598 8969 0.033366 GCCCGTGCTTGGAAAATGTT 59.967 50.000 0.00 0.00 33.53 2.71
3599 8970 1.665442 GCCCGTGCTTGGAAAATGT 59.335 52.632 0.00 0.00 33.53 2.71
3623 8994 1.810030 GTAGTTGGCGAGCCTTCGG 60.810 63.158 15.75 0.00 46.76 4.30
3768 9154 0.874390 GCACGAGCTTGGAAATGTCA 59.126 50.000 5.79 0.00 37.91 3.58
3786 9173 0.604578 TTGGATTGCTTGGCTTGAGC 59.395 50.000 0.00 0.00 40.53 4.26
3828 9215 2.554893 GACTTCAACCTCGAGTCTCTGT 59.445 50.000 12.31 2.94 37.43 3.41
3835 9222 1.613925 TGTGGAGACTTCAACCTCGAG 59.386 52.381 5.13 5.13 0.00 4.04
3841 9228 1.953559 TGCTGTGTGGAGACTTCAAC 58.046 50.000 0.00 0.00 0.00 3.18
3866 11009 2.423538 GCTTATGCTCCGTGTTTCCATT 59.576 45.455 0.00 0.00 36.03 3.16
3911 11054 4.079253 TGCATAGCTCATGATCATGCATT 58.921 39.130 27.68 17.53 45.09 3.56
3912 11055 3.686016 TGCATAGCTCATGATCATGCAT 58.314 40.909 27.68 18.21 45.09 3.96
3914 11057 3.075148 AGTGCATAGCTCATGATCATGC 58.925 45.455 27.68 18.52 41.81 4.06
3915 11058 6.649557 TCTTTAGTGCATAGCTCATGATCATG 59.350 38.462 26.79 26.79 36.69 3.07
3916 11059 6.649973 GTCTTTAGTGCATAGCTCATGATCAT 59.350 38.462 1.18 1.18 36.69 2.45
3917 11060 5.987953 GTCTTTAGTGCATAGCTCATGATCA 59.012 40.000 0.00 0.00 36.69 2.92
3918 11061 5.987953 TGTCTTTAGTGCATAGCTCATGATC 59.012 40.000 0.00 0.00 36.69 2.92
3919 11062 5.757320 GTGTCTTTAGTGCATAGCTCATGAT 59.243 40.000 0.00 0.00 36.69 2.45
3920 11063 5.111989 GTGTCTTTAGTGCATAGCTCATGA 58.888 41.667 0.00 0.00 36.69 3.07
3921 11064 4.872124 TGTGTCTTTAGTGCATAGCTCATG 59.128 41.667 0.00 0.00 37.73 3.07
3923 11066 4.220602 TCTGTGTCTTTAGTGCATAGCTCA 59.779 41.667 0.00 0.00 0.00 4.26
3924 11067 4.748892 TCTGTGTCTTTAGTGCATAGCTC 58.251 43.478 0.00 0.00 0.00 4.09
3926 11069 4.748892 TCTCTGTGTCTTTAGTGCATAGC 58.251 43.478 0.00 0.00 0.00 2.97
3927 11070 6.201226 TCTCTCTGTGTCTTTAGTGCATAG 57.799 41.667 0.00 0.00 0.00 2.23
3928 11071 6.590234 TTCTCTCTGTGTCTTTAGTGCATA 57.410 37.500 0.00 0.00 0.00 3.14
3929 11072 5.474578 TTCTCTCTGTGTCTTTAGTGCAT 57.525 39.130 0.00 0.00 0.00 3.96
3930 11073 4.937201 TTCTCTCTGTGTCTTTAGTGCA 57.063 40.909 0.00 0.00 0.00 4.57
3931 11074 5.473931 TCATTCTCTCTGTGTCTTTAGTGC 58.526 41.667 0.00 0.00 0.00 4.40
3932 11075 7.095439 GGTTTCATTCTCTCTGTGTCTTTAGTG 60.095 40.741 0.00 0.00 0.00 2.74
3933 11076 6.931840 GGTTTCATTCTCTCTGTGTCTTTAGT 59.068 38.462 0.00 0.00 0.00 2.24
3934 11077 6.090088 CGGTTTCATTCTCTCTGTGTCTTTAG 59.910 42.308 0.00 0.00 0.00 1.85
3935 11078 5.926542 CGGTTTCATTCTCTCTGTGTCTTTA 59.073 40.000 0.00 0.00 0.00 1.85
4000 11143 2.241941 TGCTTGGCCTCATGAATAAGGA 59.758 45.455 3.32 0.00 34.35 3.36
4029 11172 3.778629 ACCTGAATAATTGTAGGACGGGT 59.221 43.478 0.00 0.00 34.42 5.28
4031 11174 4.980434 CGTACCTGAATAATTGTAGGACGG 59.020 45.833 0.00 0.00 33.89 4.79
4032 11175 4.443394 GCGTACCTGAATAATTGTAGGACG 59.557 45.833 0.00 0.00 37.14 4.79


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

AutoCloner maintained by Alex Coulton.