Multiple sequence alignment - TraesCS4D01G199800

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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 TraesCS4D01G199800 chr4D 100.000 5768 0 0 1 5768 346453602 346459369 0.000000e+00 10652
1 TraesCS4D01G199800 chr4A 93.291 3160 128 32 2629 5768 119078705 119075610 0.000000e+00 4584
2 TraesCS4D01G199800 chr4A 88.157 2322 103 59 352 2535 119080983 119078696 0.000000e+00 2606
3 TraesCS4D01G199800 chr4A 85.321 109 12 3 99 207 119081291 119081187 6.110000e-20 110
4 TraesCS4D01G199800 chr4A 79.775 178 12 13 387 562 538908475 538908630 2.200000e-19 108
5 TraesCS4D01G199800 chr4B 88.556 3408 207 77 299 3622 427498682 427501990 0.000000e+00 3964
6 TraesCS4D01G199800 chr4B 93.090 1288 76 9 3614 4899 427502043 427503319 0.000000e+00 1873
7 TraesCS4D01G199800 chr4B 94.492 817 18 8 4956 5768 427503447 427504240 0.000000e+00 1234
8 TraesCS4D01G199800 chr4B 89.634 164 10 2 144 307 427498506 427498662 9.800000e-48 202
9 TraesCS4D01G199800 chr4B 92.593 135 10 0 1 135 427498276 427498410 1.640000e-45 195
10 TraesCS4D01G199800 chr4B 78.977 176 17 12 387 562 385957703 385957548 1.020000e-17 102
11 TraesCS4D01G199800 chrUn 83.814 451 66 4 3175 3619 88524503 88524054 6.910000e-114 422
12 TraesCS4D01G199800 chrUn 86.466 266 28 4 3892 4156 88520891 88520633 9.460000e-73 285
13 TraesCS4D01G199800 chr7B 80.879 455 53 12 3414 3843 736105739 736106184 1.550000e-85 327
14 TraesCS4D01G199800 chr7B 86.473 207 14 8 4819 5023 734792354 734792160 1.260000e-51 215
15 TraesCS4D01G199800 chr7D 82.319 345 42 6 3276 3618 637137795 637137468 1.220000e-71 281
16 TraesCS4D01G199800 chr5D 82.319 345 42 6 3276 3618 497175556 497175883 1.220000e-71 281
17 TraesCS4D01G199800 chr5D 90.000 80 5 3 5518 5597 497177039 497177115 3.680000e-17 100
18 TraesCS4D01G199800 chr1D 80.755 265 25 14 4671 4932 50962008 50962249 3.550000e-42 183
19 TraesCS4D01G199800 chr1D 80.377 265 25 16 4671 4932 51040219 51040459 5.940000e-40 176
20 TraesCS4D01G199800 chr5A 87.050 139 12 2 352 490 692541626 692541494 1.000000e-32 152
21 TraesCS4D01G199800 chr5A 85.612 139 14 2 352 490 692548195 692548063 2.170000e-29 141
22 TraesCS4D01G199800 chr1A 82.424 165 17 6 4671 4834 49998677 49998830 3.630000e-27 134
23 TraesCS4D01G199800 chr2B 80.682 176 14 10 387 562 17219741 17219896 1.020000e-22 119
24 TraesCS4D01G199800 chr2B 80.682 176 14 10 387 562 414953425 414953270 1.020000e-22 119
25 TraesCS4D01G199800 chr2B 83.333 132 8 6 431 562 127203064 127202947 6.110000e-20 110
26 TraesCS4D01G199800 chr1B 85.149 101 12 3 4671 4770 77545915 77546013 3.680000e-17 100


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 TraesCS4D01G199800 chr4D 346453602 346459369 5767 False 10652.000000 10652 100.000 1 5768 1 chr4D.!!$F1 5767
1 TraesCS4D01G199800 chr4A 119075610 119081291 5681 True 2433.333333 4584 88.923 99 5768 3 chr4A.!!$R1 5669
2 TraesCS4D01G199800 chr4B 427498276 427504240 5964 False 1493.600000 3964 91.673 1 5768 5 chr4B.!!$F1 5767
3 TraesCS4D01G199800 chrUn 88520633 88524503 3870 True 353.500000 422 85.140 3175 4156 2 chrUn.!!$R1 981

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
861 1085 0.108019 GGAGTCGTGGACAAAAGGGT 59.892 55.000 0.00 0.0 34.60 4.34 F
1506 1777 0.162933 TTTGCGCAATCGTTCGAGTC 59.837 50.000 25.64 0.0 38.14 3.36 F
1980 2304 0.984995 GAACTTGTGGTCCTAGGGCT 59.015 55.000 14.34 0.0 0.00 5.19 F
2093 2452 1.227704 CTACACAACCACCGTGGCA 60.228 57.895 17.99 0.0 42.67 4.92 F
3769 4255 1.355971 GCCTGAAGCATTTGCATGTG 58.644 50.000 5.20 0.0 45.16 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2334 0.855349 CTGTGCTCTGACGTGTGTTC 59.145 55.000 0.0 0.0 0.00 3.18 R
2968 3363 1.686325 GCGGACCAGGGCTTGAGATA 61.686 60.000 0.0 0.0 0.00 1.98 R
3739 4225 2.359107 TTCAGGCCTTGAGCTGCG 60.359 61.111 0.0 0.0 43.05 5.18 R
4060 7433 2.877097 TGCTTACCCATTCAGCAAGA 57.123 45.000 0.0 0.0 40.61 3.02 R
4873 8247 0.032515 TCGGAATGGGGAGTAGAGCA 60.033 55.000 0.0 0.0 0.00 4.26 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
33 34 3.749609 CAGCAGTGAAACATCATCAGTCA 59.250 43.478 0.00 0.00 41.43 3.41
38 39 6.676456 GCAGTGAAACATCATCAGTCATAACC 60.676 42.308 0.00 0.00 41.43 2.85
44 45 5.111989 ACATCATCAGTCATAACCGTGAAG 58.888 41.667 0.00 0.00 0.00 3.02
74 75 6.492087 CCCAGTCCAACCTATTTAAACTTTCA 59.508 38.462 0.00 0.00 0.00 2.69
83 84 7.360361 ACCTATTTAAACTTTCAAAGTGCGAG 58.640 34.615 2.78 0.00 41.91 5.03
89 90 3.758300 ACTTTCAAAGTGCGAGTGTTTG 58.242 40.909 0.68 0.00 41.01 2.93
101 102 2.607635 CGAGTGTTTGGTATGGGATTCG 59.392 50.000 0.00 0.00 0.00 3.34
178 266 5.221501 ACCCAGATCACCTTGTCAAATTTTG 60.222 40.000 2.59 2.59 0.00 2.44
212 300 8.224389 TGTCACCCATTTATTTACAGATGATG 57.776 34.615 0.00 0.00 0.00 3.07
250 369 7.307632 GCATGAGCACGATTACATAATTTCTCT 60.308 37.037 0.00 0.00 41.58 3.10
291 410 6.503589 AGTCTGCAGTACTCACTAAGTAAG 57.496 41.667 14.67 0.00 42.11 2.34
292 411 6.005198 AGTCTGCAGTACTCACTAAGTAAGT 58.995 40.000 14.67 0.00 42.11 2.24
294 413 7.664731 AGTCTGCAGTACTCACTAAGTAAGTAA 59.335 37.037 14.67 0.00 42.11 2.24
295 414 7.750014 GTCTGCAGTACTCACTAAGTAAGTAAC 59.250 40.741 14.67 0.00 42.11 2.50
296 415 7.446319 TCTGCAGTACTCACTAAGTAAGTAACA 59.554 37.037 14.67 0.00 42.11 2.41
297 416 7.944061 TGCAGTACTCACTAAGTAAGTAACAA 58.056 34.615 0.00 0.00 42.11 2.83
316 459 3.181482 ACAAGTGTGTGTGAGACAGAGAG 60.181 47.826 0.00 0.00 36.31 3.20
342 485 3.434596 GGTTAGGTTATGGTAAGGCTGGG 60.435 52.174 0.00 0.00 0.00 4.45
620 825 2.034066 CGGCAGCCAAGGAAGGAA 59.966 61.111 13.30 0.00 0.00 3.36
642 847 0.678048 GGAGGTGCCTGAGCGAATTT 60.678 55.000 0.00 0.00 44.31 1.82
651 856 2.928757 CCTGAGCGAATTTCACAGAGAG 59.071 50.000 13.23 0.00 0.00 3.20
682 891 1.003233 AAAGTCCAGAGGAAGGCGC 60.003 57.895 0.00 0.00 31.38 6.53
861 1085 0.108019 GGAGTCGTGGACAAAAGGGT 59.892 55.000 0.00 0.00 34.60 4.34
883 1107 2.378084 CGGAGTCGTCTCGTGTCGA 61.378 63.158 2.82 2.82 41.26 4.20
972 1223 1.690985 CACTTCCCTCCCTCCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
986 1237 2.825836 CTCCCCACTGCATTCCGC 60.826 66.667 0.00 0.00 42.89 5.54
1199 1459 6.597672 GGAATTCTTCTCCTTCTTCTTCTTCC 59.402 42.308 5.23 0.00 0.00 3.46
1202 1462 3.275848 TCTCCTTCTTCTTCTTCCCCA 57.724 47.619 0.00 0.00 0.00 4.96
1375 1646 1.669760 CCGTGGTTTCTTGGCGCTA 60.670 57.895 7.64 0.00 0.00 4.26
1417 1688 6.193514 TCGTGAAATGTGTACGGAATAGTA 57.806 37.500 0.00 0.00 38.29 1.82
1491 1762 4.664891 GCAATGCTTTCTCGTGATTTTTGC 60.665 41.667 0.00 0.00 0.00 3.68
1492 1763 2.649516 TGCTTTCTCGTGATTTTTGCG 58.350 42.857 0.00 0.00 0.00 4.85
1493 1764 1.383412 GCTTTCTCGTGATTTTTGCGC 59.617 47.619 0.00 0.00 0.00 6.09
1494 1765 2.649516 CTTTCTCGTGATTTTTGCGCA 58.350 42.857 5.66 5.66 0.00 6.09
1495 1766 2.765108 TTCTCGTGATTTTTGCGCAA 57.235 40.000 21.02 21.02 0.00 4.85
1496 1767 2.987413 TCTCGTGATTTTTGCGCAAT 57.013 40.000 25.64 9.44 0.00 3.56
1497 1768 2.850321 TCTCGTGATTTTTGCGCAATC 58.150 42.857 25.64 18.97 0.00 2.67
1498 1769 1.574477 CTCGTGATTTTTGCGCAATCG 59.426 47.619 25.64 19.43 33.91 3.34
1499 1770 1.069568 TCGTGATTTTTGCGCAATCGT 60.070 42.857 25.64 12.48 38.14 3.73
1500 1771 1.713404 CGTGATTTTTGCGCAATCGTT 59.287 42.857 25.64 9.38 38.14 3.85
1501 1772 2.222050 CGTGATTTTTGCGCAATCGTTC 60.222 45.455 25.64 17.80 38.14 3.95
1502 1773 1.975362 TGATTTTTGCGCAATCGTTCG 59.025 42.857 25.64 0.00 38.14 3.95
1503 1774 2.238363 GATTTTTGCGCAATCGTTCGA 58.762 42.857 25.64 3.58 38.14 3.71
1504 1775 1.669184 TTTTTGCGCAATCGTTCGAG 58.331 45.000 25.64 0.00 38.14 4.04
1505 1776 0.584396 TTTTGCGCAATCGTTCGAGT 59.416 45.000 25.64 0.00 38.14 4.18
1506 1777 0.162933 TTTGCGCAATCGTTCGAGTC 59.837 50.000 25.64 0.00 38.14 3.36
1507 1778 1.940404 TTGCGCAATCGTTCGAGTCG 61.940 55.000 21.02 6.09 38.14 4.18
1508 1779 2.434134 GCGCAATCGTTCGAGTCGT 61.434 57.895 13.12 0.00 38.14 4.34
1509 1780 1.941476 GCGCAATCGTTCGAGTCGTT 61.941 55.000 13.12 0.00 38.14 3.85
1533 1833 6.197168 TGCATTCTTGGGAATTAGGATTTCT 58.803 36.000 0.00 0.00 39.87 2.52
1564 1864 7.042658 AGTCCATTTCTTCGCGATTAAGTAATC 60.043 37.037 10.88 0.00 38.89 1.75
1624 1929 1.126846 CACAAGATTCACGCGTTCCTC 59.873 52.381 10.22 6.28 0.00 3.71
1663 1978 7.571983 GCATGTGCACATCTTTGGATATACTAC 60.572 40.741 29.23 0.64 41.59 2.73
1675 1990 7.817418 TTGGATATACTACCAAGAAATTGCC 57.183 36.000 0.00 0.00 40.59 4.52
1785 2100 4.195225 TGTTCGCTAATGTACCATGACA 57.805 40.909 0.00 0.00 0.00 3.58
1918 2241 2.408050 CAGGACAAGATATACTGGCGC 58.592 52.381 0.00 0.00 0.00 6.53
1925 2248 5.710984 ACAAGATATACTGGCGCTATACAC 58.289 41.667 7.64 0.87 0.00 2.90
1980 2304 0.984995 GAACTTGTGGTCCTAGGGCT 59.015 55.000 14.34 0.00 0.00 5.19
1981 2305 1.351350 GAACTTGTGGTCCTAGGGCTT 59.649 52.381 14.34 0.00 0.00 4.35
1982 2306 0.984995 ACTTGTGGTCCTAGGGCTTC 59.015 55.000 14.34 7.34 0.00 3.86
1983 2307 1.280457 CTTGTGGTCCTAGGGCTTCT 58.720 55.000 14.34 0.00 0.00 2.85
1984 2308 1.630878 CTTGTGGTCCTAGGGCTTCTT 59.369 52.381 14.34 0.00 0.00 2.52
1985 2309 1.276622 TGTGGTCCTAGGGCTTCTTC 58.723 55.000 14.34 0.00 0.00 2.87
2003 2334 9.313118 GGCTTCTTCTTCTTCTTCTTTCTATAG 57.687 37.037 0.00 0.00 0.00 1.31
2093 2452 1.227704 CTACACAACCACCGTGGCA 60.228 57.895 17.99 0.00 42.67 4.92
2127 2486 1.537990 GCCGACCAAAACAGTGCAAAT 60.538 47.619 0.00 0.00 0.00 2.32
2134 2493 3.937706 CCAAAACAGTGCAAATGTCCAAA 59.062 39.130 6.30 0.00 44.85 3.28
2138 2497 7.041235 CCAAAACAGTGCAAATGTCCAAATAAT 60.041 33.333 6.30 0.00 44.85 1.28
2141 2500 6.996509 ACAGTGCAAATGTCCAAATAATCTT 58.003 32.000 0.03 0.00 44.85 2.40
2186 2545 3.429410 GGGCCTTGAAACTGCACATTATC 60.429 47.826 0.84 0.00 0.00 1.75
2191 2550 6.555315 CCTTGAAACTGCACATTATCTTACC 58.445 40.000 0.00 0.00 0.00 2.85
2285 2672 4.030641 CGCGATGCTATGTGTGATGTATAC 59.969 45.833 0.00 0.00 0.00 1.47
2286 2673 5.164233 GCGATGCTATGTGTGATGTATACT 58.836 41.667 4.17 0.00 0.00 2.12
2287 2674 5.635280 GCGATGCTATGTGTGATGTATACTT 59.365 40.000 4.17 0.00 0.00 2.24
2288 2675 6.806739 GCGATGCTATGTGTGATGTATACTTA 59.193 38.462 4.17 0.00 0.00 2.24
2289 2676 7.328493 GCGATGCTATGTGTGATGTATACTTAA 59.672 37.037 4.17 0.00 0.00 1.85
2290 2677 9.358872 CGATGCTATGTGTGATGTATACTTAAT 57.641 33.333 4.17 0.00 0.00 1.40
2312 2706 2.890311 ACATGTTCCCGCTCAAATTTGA 59.110 40.909 19.45 19.45 35.57 2.69
2365 2759 3.693411 GGCAAAGCCCGGATTTCA 58.307 55.556 0.73 0.00 44.06 2.69
2520 2914 7.981789 ACAACTGTATACATCTATGTGTTCCTG 59.018 37.037 5.91 0.00 41.89 3.86
2549 2943 9.334947 GTATTACTAGGTGTACATGTCTGTCTA 57.665 37.037 0.00 0.34 36.79 2.59
2550 2944 8.818622 ATTACTAGGTGTACATGTCTGTCTAA 57.181 34.615 0.00 0.00 36.79 2.10
2558 2952 9.988350 GGTGTACATGTCTGTCTAAATTTATTG 57.012 33.333 0.00 0.00 36.79 1.90
2581 2975 5.943416 TGATTTACTGTGTCCAATTACTGGG 59.057 40.000 0.00 0.00 46.44 4.45
2586 2980 5.697067 ACTGTGTCCAATTACTGGGTTTTA 58.303 37.500 0.00 0.00 46.44 1.52
2587 2981 6.130569 ACTGTGTCCAATTACTGGGTTTTAA 58.869 36.000 0.00 0.00 46.44 1.52
2588 2982 6.608002 ACTGTGTCCAATTACTGGGTTTTAAA 59.392 34.615 0.00 0.00 46.44 1.52
2822 3217 9.002600 GGTTCCTTTTTGCTGATTCATAATTTT 57.997 29.630 0.00 0.00 0.00 1.82
2853 3248 3.008594 ACGGGTGTTGTTCTGGATAATGA 59.991 43.478 0.00 0.00 0.00 2.57
2893 3288 6.225981 TCATGTGATAGCTGACAACTACAT 57.774 37.500 0.00 0.00 0.00 2.29
2926 3321 7.094075 TGCATCTATTTTGTTTCTGCAGAGATT 60.094 33.333 17.43 1.99 33.59 2.40
2929 3324 8.627208 TCTATTTTGTTTCTGCAGAGATTTCT 57.373 30.769 17.43 3.47 0.00 2.52
2968 3363 2.613506 GGCCGTGCGCACTAAGTTT 61.614 57.895 35.27 0.00 40.31 2.66
3128 3523 4.055360 CAACGAGGTGAGTTCATGTGTTA 58.945 43.478 0.00 0.00 0.00 2.41
3129 3524 3.650139 ACGAGGTGAGTTCATGTGTTAC 58.350 45.455 0.00 0.00 0.00 2.50
3130 3525 2.661675 CGAGGTGAGTTCATGTGTTACG 59.338 50.000 0.00 0.00 0.00 3.18
3133 3528 4.448210 AGGTGAGTTCATGTGTTACGTTT 58.552 39.130 0.00 0.00 0.00 3.60
3134 3529 4.879545 AGGTGAGTTCATGTGTTACGTTTT 59.120 37.500 0.00 0.00 0.00 2.43
3135 3530 6.050432 AGGTGAGTTCATGTGTTACGTTTTA 58.950 36.000 0.00 0.00 0.00 1.52
3136 3531 6.708949 AGGTGAGTTCATGTGTTACGTTTTAT 59.291 34.615 0.00 0.00 0.00 1.40
3138 3533 6.795114 GTGAGTTCATGTGTTACGTTTTATGG 59.205 38.462 0.00 0.00 0.00 2.74
3139 3534 6.072948 TGAGTTCATGTGTTACGTTTTATGGG 60.073 38.462 0.00 0.00 0.00 4.00
3140 3535 5.766174 AGTTCATGTGTTACGTTTTATGGGT 59.234 36.000 0.00 0.00 0.00 4.51
3141 3536 6.935771 AGTTCATGTGTTACGTTTTATGGGTA 59.064 34.615 0.00 0.00 0.00 3.69
3142 3537 6.971527 TCATGTGTTACGTTTTATGGGTAG 57.028 37.500 0.00 0.00 0.00 3.18
3237 3632 3.436359 TCACATGAACGACAATGTGATGG 59.564 43.478 20.08 3.98 45.61 3.51
3248 3643 5.619086 CGACAATGTGATGGGAAGTTAAACC 60.619 44.000 0.00 0.00 0.00 3.27
3271 3669 4.872124 CGATGTGAGTTCAAGAATGGATCA 59.128 41.667 0.00 0.00 0.00 2.92
3272 3670 5.526479 CGATGTGAGTTCAAGAATGGATCAT 59.474 40.000 0.00 0.00 0.00 2.45
3567 3968 7.229506 GGCTTTTAGTCTATGAATACATGCCTT 59.770 37.037 9.34 0.00 33.48 4.35
3651 4137 8.040716 AGAATAATCAGAACCTTGTTTAACCG 57.959 34.615 0.00 0.00 0.00 4.44
3769 4255 1.355971 GCCTGAAGCATTTGCATGTG 58.644 50.000 5.20 0.00 45.16 3.21
3775 4261 3.068448 TGAAGCATTTGCATGTGAACTGT 59.932 39.130 5.20 0.00 45.16 3.55
4001 7374 6.264292 TGTTTACAGCTTTGGTGTTGTCATAT 59.736 34.615 7.70 0.00 41.72 1.78
4060 7433 2.094700 TCGAATCAAAGCTGAGCGTAGT 60.095 45.455 0.00 0.00 35.77 2.73
4086 7459 3.445096 GCTGAATGGGTAAGCATCACTTT 59.555 43.478 0.00 0.00 39.97 2.66
4091 7464 2.224744 TGGGTAAGCATCACTTTCTGCA 60.225 45.455 0.00 0.00 40.88 4.41
4147 7520 6.520742 GCTTCTCCCCAATGCTATAATGTCTA 60.521 42.308 0.00 0.00 0.00 2.59
4160 7533 8.148351 TGCTATAATGTCTATACCAAGGACAAC 58.852 37.037 0.00 0.00 42.14 3.32
4169 7543 7.001674 TCTATACCAAGGACAACATTGTGTTT 58.998 34.615 1.07 0.00 42.43 2.83
4170 7544 8.158132 TCTATACCAAGGACAACATTGTGTTTA 58.842 33.333 1.07 0.00 42.43 2.01
4172 7546 4.098807 ACCAAGGACAACATTGTGTTTACC 59.901 41.667 1.07 0.00 42.43 2.85
4173 7547 4.340950 CCAAGGACAACATTGTGTTTACCT 59.659 41.667 1.07 0.72 41.62 3.08
4175 7549 4.787551 AGGACAACATTGTGTTTACCTGA 58.212 39.130 1.07 0.00 42.43 3.86
4176 7550 4.821805 AGGACAACATTGTGTTTACCTGAG 59.178 41.667 1.07 0.00 42.43 3.35
4200 7574 9.823647 GAGATATCTTTGGTGAGTTCTGATTTA 57.176 33.333 6.70 0.00 0.00 1.40
4242 7616 5.237127 TGGCAGAAGCATCATAAGTTTATCG 59.763 40.000 0.00 0.00 44.61 2.92
4269 7643 9.722056 GTAGTTTTTAACCATCTGATTAGCATG 57.278 33.333 0.00 0.00 0.00 4.06
4280 7654 8.582437 CCATCTGATTAGCATGGATTTGTTATT 58.418 33.333 9.11 0.00 39.73 1.40
4437 7811 8.053355 CCCTTTAATGTACATCTTAAGAACCCT 58.947 37.037 9.71 0.00 0.00 4.34
4549 7923 3.173953 TCAACAGGAGGGATTTTGCAT 57.826 42.857 0.00 0.00 0.00 3.96
4634 8008 2.984562 TGCTCGAATGTGCCTGAATAA 58.015 42.857 0.00 0.00 33.71 1.40
4698 8072 2.822561 TCTCGCTCACATCTCAAAGTCT 59.177 45.455 0.00 0.00 0.00 3.24
4715 8089 1.136984 CTAGAAGAACGCGGCGACT 59.863 57.895 30.94 22.77 0.00 4.18
4845 8219 6.749118 GTGTTTCTGGCTTTGTTATGATGATC 59.251 38.462 0.00 0.00 0.00 2.92
4846 8220 6.433716 TGTTTCTGGCTTTGTTATGATGATCA 59.566 34.615 0.00 0.00 0.00 2.92
4847 8221 7.123098 TGTTTCTGGCTTTGTTATGATGATCAT 59.877 33.333 13.10 13.10 40.72 2.45
4848 8222 6.628919 TCTGGCTTTGTTATGATGATCATG 57.371 37.500 17.74 1.27 37.70 3.07
4849 8223 6.358991 TCTGGCTTTGTTATGATGATCATGA 58.641 36.000 17.74 4.76 37.70 3.07
4850 8224 7.002276 TCTGGCTTTGTTATGATGATCATGAT 58.998 34.615 17.74 13.26 37.70 2.45
4871 8245 8.496751 CATGATGATGATACTGTGATCAAGAAC 58.503 37.037 0.00 0.00 39.25 3.01
4873 8247 8.208903 TGATGATGATACTGTGATCAAGAACAT 58.791 33.333 0.00 0.00 39.25 2.71
4934 8308 5.601583 GGGGGAAGTTTTGTTTGTAGAAA 57.398 39.130 0.00 0.00 0.00 2.52
4938 8312 7.423199 GGGGAAGTTTTGTTTGTAGAAACTAG 58.577 38.462 15.66 0.00 41.36 2.57
4981 8426 2.689983 CAAATATCCCTGTGTCCCTTGC 59.310 50.000 0.00 0.00 0.00 4.01
4983 8428 0.911769 TATCCCTGTGTCCCTTGCTG 59.088 55.000 0.00 0.00 0.00 4.41
5071 8517 2.930682 GACGCTTAATCTTCGCTTCCTT 59.069 45.455 0.00 0.00 0.00 3.36
5098 8544 1.147473 TGACATGTTGCTGCTGTACG 58.853 50.000 0.00 0.00 0.00 3.67
5110 8560 1.202475 TGCTGTACGTGTGCTCTTCAA 60.202 47.619 0.00 0.00 0.00 2.69
5148 8601 1.205893 TGGTTTTGTTGAGGTTGTGCC 59.794 47.619 0.00 0.00 37.58 5.01
5175 8628 7.212274 CACAAATTTTGGTTCAATCTCTTCCT 58.788 34.615 13.42 0.00 34.12 3.36
5176 8629 7.712205 CACAAATTTTGGTTCAATCTCTTCCTT 59.288 33.333 13.42 0.00 34.12 3.36
5378 8832 4.379813 GGCATGACAGGTCACAAAATGTAG 60.380 45.833 3.92 0.00 43.11 2.74
5405 8859 9.371136 ACGAACACAAATATAGATGCCATATAG 57.629 33.333 0.00 0.00 0.00 1.31
5577 9031 3.381272 TGCAAAACTCTTTCCACAAGAGG 59.619 43.478 14.55 0.37 46.05 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 7.646130 TCGCACTTTGAAAGTTTAAATAGGTTG 59.354 33.333 8.03 0.00 40.46 3.77
74 75 2.552315 CCATACCAAACACTCGCACTTT 59.448 45.455 0.00 0.00 0.00 2.66
83 84 2.681344 GACCGAATCCCATACCAAACAC 59.319 50.000 0.00 0.00 0.00 3.32
101 102 5.489792 TGCTCTAATCTGAATATGGGACC 57.510 43.478 0.00 0.00 0.00 4.46
139 189 6.433404 GTGATCTGGGTATAGAATCTACGGAA 59.567 42.308 0.00 0.00 0.00 4.30
178 266 2.496899 AATGGGTGACAGTCCATCAC 57.503 50.000 9.85 0.00 42.43 3.06
212 300 1.399440 TGCTCATGCTTGCTTCGATTC 59.601 47.619 0.00 0.00 40.48 2.52
250 369 8.344446 TGCAGACTTGTAGTATGTTCTTAGTA 57.656 34.615 3.73 0.00 39.48 1.82
263 382 4.775058 AGTGAGTACTGCAGACTTGTAG 57.225 45.455 23.35 0.00 42.11 2.74
269 388 6.256912 ACTTACTTAGTGAGTACTGCAGAC 57.743 41.667 23.35 14.11 40.51 3.51
291 410 4.430007 TCTGTCTCACACACACTTGTTAC 58.570 43.478 0.00 0.00 31.66 2.50
292 411 4.401202 TCTCTGTCTCACACACACTTGTTA 59.599 41.667 0.00 0.00 31.66 2.41
294 413 2.760650 TCTCTGTCTCACACACACTTGT 59.239 45.455 0.00 0.00 35.84 3.16
295 414 3.379240 CTCTCTGTCTCACACACACTTG 58.621 50.000 0.00 0.00 0.00 3.16
296 415 2.223923 GCTCTCTGTCTCACACACACTT 60.224 50.000 0.00 0.00 0.00 3.16
297 416 1.339610 GCTCTCTGTCTCACACACACT 59.660 52.381 0.00 0.00 0.00 3.55
316 459 3.200483 CCTTACCATAACCTAACCACGC 58.800 50.000 0.00 0.00 0.00 5.34
607 812 1.076187 CCTCCTTTTCCTTCCTTGGCT 59.924 52.381 0.00 0.00 0.00 4.75
620 825 1.768684 TTCGCTCAGGCACCTCCTTT 61.769 55.000 0.00 0.00 44.75 3.11
672 881 1.743252 CTCCAAGTGCGCCTTCCTC 60.743 63.158 4.18 0.00 0.00 3.71
682 891 3.240069 CGTTACGTACTTCCTCCAAGTG 58.760 50.000 0.00 0.00 45.60 3.16
879 1103 0.454117 GGAGAAACGGACGAGTCGAC 60.454 60.000 21.50 13.62 0.00 4.20
883 1107 1.532316 TGGGGAGAAACGGACGAGT 60.532 57.895 0.00 0.00 0.00 4.18
1115 1373 2.603473 ACGTACCAGCTGAGGGCA 60.603 61.111 17.39 0.00 44.79 5.36
1267 1537 2.541178 CGCACGATACCAAGAGACTACC 60.541 54.545 0.00 0.00 0.00 3.18
1375 1646 3.945285 ACGAACCAAACATCAAGTGAAGT 59.055 39.130 0.00 0.00 0.00 3.01
1491 1762 0.246374 CAACGACTCGAACGATTGCG 60.246 55.000 16.43 4.95 44.79 4.85
1492 1763 0.516524 GCAACGACTCGAACGATTGC 60.517 55.000 21.72 21.72 38.89 3.56
1493 1764 0.781787 TGCAACGACTCGAACGATTG 59.218 50.000 16.43 15.68 34.70 2.67
1494 1765 1.710013 ATGCAACGACTCGAACGATT 58.290 45.000 16.43 6.29 34.70 3.34
1495 1766 1.654105 GAATGCAACGACTCGAACGAT 59.346 47.619 16.43 4.03 34.70 3.73
1496 1767 1.057636 GAATGCAACGACTCGAACGA 58.942 50.000 16.43 0.00 34.70 3.85
1497 1768 1.060713 AGAATGCAACGACTCGAACG 58.939 50.000 5.20 9.55 0.00 3.95
1498 1769 2.411547 CCAAGAATGCAACGACTCGAAC 60.412 50.000 5.20 0.00 0.00 3.95
1499 1770 1.798223 CCAAGAATGCAACGACTCGAA 59.202 47.619 5.20 0.00 0.00 3.71
1500 1771 1.428448 CCAAGAATGCAACGACTCGA 58.572 50.000 5.20 0.00 0.00 4.04
1501 1772 0.443869 CCCAAGAATGCAACGACTCG 59.556 55.000 0.00 0.00 0.00 4.18
1502 1773 1.808411 TCCCAAGAATGCAACGACTC 58.192 50.000 0.00 0.00 0.00 3.36
1503 1774 2.270352 TTCCCAAGAATGCAACGACT 57.730 45.000 0.00 0.00 0.00 4.18
1504 1775 3.575965 AATTCCCAAGAATGCAACGAC 57.424 42.857 0.00 0.00 42.03 4.34
1505 1776 3.694072 CCTAATTCCCAAGAATGCAACGA 59.306 43.478 0.00 0.00 42.03 3.85
1506 1777 3.694072 TCCTAATTCCCAAGAATGCAACG 59.306 43.478 0.00 0.00 42.03 4.10
1507 1778 5.859205 ATCCTAATTCCCAAGAATGCAAC 57.141 39.130 0.00 0.00 42.03 4.17
1508 1779 6.669154 AGAAATCCTAATTCCCAAGAATGCAA 59.331 34.615 0.00 0.00 42.03 4.08
1509 1780 6.197168 AGAAATCCTAATTCCCAAGAATGCA 58.803 36.000 0.00 0.00 42.03 3.96
1533 1833 1.069296 CGCGAAGAAATGGACTTGCAA 60.069 47.619 0.00 0.00 0.00 4.08
1564 1864 1.135972 CACACTTTCTTGGCGGAATCG 60.136 52.381 0.00 0.00 39.81 3.34
1624 1929 2.325761 GCACATGCAAAGCAGAAAGAG 58.674 47.619 0.00 0.00 43.65 2.85
1663 1978 2.660189 AAGATGCGGCAATTTCTTGG 57.340 45.000 14.62 0.00 32.72 3.61
1675 1990 5.967674 GTGAATTGAAGTATCCAAAGATGCG 59.032 40.000 0.00 0.00 39.84 4.73
1933 2256 6.475402 GGCGAAATTAATTACTCAATGGTTGG 59.525 38.462 0.01 0.00 0.00 3.77
1984 2308 9.915629 GTGTGTTCTATAGAAAGAAGAAGAAGA 57.084 33.333 16.73 0.00 36.19 2.87
1985 2309 8.855279 CGTGTGTTCTATAGAAAGAAGAAGAAG 58.145 37.037 16.73 0.00 36.19 2.85
2003 2334 0.855349 CTGTGCTCTGACGTGTGTTC 59.145 55.000 0.00 0.00 0.00 3.18
2101 2460 4.676586 GTTTTGGTCGGCGCCACG 62.677 66.667 28.98 14.07 38.42 4.94
2102 2461 3.536498 CTGTTTTGGTCGGCGCCAC 62.536 63.158 28.98 22.29 38.42 5.01
2134 2493 8.317679 ACAGCACTTTCTGTTCTAGAAGATTAT 58.682 33.333 5.12 0.00 45.66 1.28
2138 2497 5.537300 ACAGCACTTTCTGTTCTAGAAGA 57.463 39.130 5.12 3.38 45.66 2.87
2186 2545 7.324178 AGAACATTTACTCACTAGCTGGTAAG 58.676 38.462 0.95 0.00 0.00 2.34
2191 2550 7.658179 TCAAAGAACATTTACTCACTAGCTG 57.342 36.000 0.00 0.00 0.00 4.24
2285 2672 5.811399 TTTGAGCGGGAACATGTATTAAG 57.189 39.130 0.00 0.00 0.00 1.85
2286 2673 6.767524 AATTTGAGCGGGAACATGTATTAA 57.232 33.333 0.00 0.00 0.00 1.40
2287 2674 6.375736 TCAAATTTGAGCGGGAACATGTATTA 59.624 34.615 16.91 0.00 32.50 0.98
2288 2675 5.184864 TCAAATTTGAGCGGGAACATGTATT 59.815 36.000 16.91 0.00 32.50 1.89
2289 2676 4.704540 TCAAATTTGAGCGGGAACATGTAT 59.295 37.500 16.91 0.00 32.50 2.29
2290 2677 4.075682 TCAAATTTGAGCGGGAACATGTA 58.924 39.130 16.91 0.00 32.50 2.29
2291 2678 2.890311 TCAAATTTGAGCGGGAACATGT 59.110 40.909 16.91 0.00 32.50 3.21
2417 2811 5.635549 TTCATTTGACATATCGTACTGCG 57.364 39.130 0.00 0.00 43.01 5.18
2520 2914 7.147949 ACAGACATGTACACCTAGTAATACACC 60.148 40.741 0.00 0.00 38.09 4.16
2822 3217 2.642154 ACAACACCCGTTTATGTGGA 57.358 45.000 0.00 0.00 36.80 4.02
2853 3248 6.872920 TCACATGAAAAAGCCTAAACACTTT 58.127 32.000 0.00 0.00 0.00 2.66
2893 3288 5.304101 AGAAACAAAATAGATGCACCACCAA 59.696 36.000 0.00 0.00 0.00 3.67
2926 3321 4.219115 CCTGACTGGCCTCTAATCTAGAA 58.781 47.826 3.32 0.00 33.75 2.10
2929 3324 2.426414 CCCCTGACTGGCCTCTAATCTA 60.426 54.545 3.32 0.00 0.00 1.98
2968 3363 1.686325 GCGGACCAGGGCTTGAGATA 61.686 60.000 0.00 0.00 0.00 1.98
3128 3523 7.830201 TCCAATTATTGACTACCCATAAAACGT 59.170 33.333 6.50 0.00 0.00 3.99
3129 3524 8.215926 TCCAATTATTGACTACCCATAAAACG 57.784 34.615 6.50 0.00 0.00 3.60
3133 3528 8.637986 GCAATTCCAATTATTGACTACCCATAA 58.362 33.333 6.50 0.00 35.49 1.90
3134 3529 7.782168 TGCAATTCCAATTATTGACTACCCATA 59.218 33.333 6.50 0.00 35.49 2.74
3135 3530 6.610830 TGCAATTCCAATTATTGACTACCCAT 59.389 34.615 6.50 0.00 35.49 4.00
3136 3531 5.954752 TGCAATTCCAATTATTGACTACCCA 59.045 36.000 6.50 0.00 35.49 4.51
3138 3533 7.100458 ACTGCAATTCCAATTATTGACTACC 57.900 36.000 6.50 0.00 35.49 3.18
3139 3534 7.761409 TGACTGCAATTCCAATTATTGACTAC 58.239 34.615 6.50 0.00 35.49 2.73
3140 3535 7.936496 TGACTGCAATTCCAATTATTGACTA 57.064 32.000 6.50 0.00 35.49 2.59
3141 3536 6.839124 TGACTGCAATTCCAATTATTGACT 57.161 33.333 6.50 0.00 35.49 3.41
3142 3537 7.037438 ACATGACTGCAATTCCAATTATTGAC 58.963 34.615 6.50 0.00 35.49 3.18
3237 3632 4.753107 TGAACTCACATCGGTTTAACTTCC 59.247 41.667 0.00 0.00 0.00 3.46
3248 3643 4.872124 TGATCCATTCTTGAACTCACATCG 59.128 41.667 0.00 0.00 0.00 3.84
3271 3669 8.825667 AAAAATACGAAACAAAATGCTACCAT 57.174 26.923 0.00 0.00 0.00 3.55
3567 3968 7.552050 AAATATGAGTTTCCAATGAACCCAA 57.448 32.000 0.00 0.00 0.00 4.12
3739 4225 2.359107 TTCAGGCCTTGAGCTGCG 60.359 61.111 0.00 0.00 43.05 5.18
3769 4255 6.990939 GGTTTATGATAGGAGGGTTACAGTTC 59.009 42.308 0.00 0.00 0.00 3.01
3775 4261 5.069516 GTCACGGTTTATGATAGGAGGGTTA 59.930 44.000 0.00 0.00 0.00 2.85
3964 7336 3.935203 AGCTGTAAACATCCGACTTGATG 59.065 43.478 0.00 0.00 46.10 3.07
3973 7345 4.202111 ACAACACCAAAGCTGTAAACATCC 60.202 41.667 0.00 0.00 0.00 3.51
4001 7374 5.514834 CCTTTCTTCCTGTGATTACCTCCAA 60.515 44.000 0.00 0.00 0.00 3.53
4060 7433 2.877097 TGCTTACCCATTCAGCAAGA 57.123 45.000 0.00 0.00 40.61 3.02
4147 7520 6.015772 GGTAAACACAATGTTGTCCTTGGTAT 60.016 38.462 0.00 0.00 40.14 2.73
4160 7533 8.400947 CCAAAGATATCTCAGGTAAACACAATG 58.599 37.037 5.51 0.00 0.00 2.82
4169 7543 6.897966 AGAACTCACCAAAGATATCTCAGGTA 59.102 38.462 21.96 13.11 33.49 3.08
4170 7544 5.723887 AGAACTCACCAAAGATATCTCAGGT 59.276 40.000 18.55 18.55 34.61 4.00
4172 7546 6.871844 TCAGAACTCACCAAAGATATCTCAG 58.128 40.000 5.51 1.58 0.00 3.35
4173 7547 6.857437 TCAGAACTCACCAAAGATATCTCA 57.143 37.500 5.51 0.00 0.00 3.27
4200 7574 5.477984 TCTGCCAGTTTTCAGAAGCAAATAT 59.522 36.000 0.00 0.00 36.50 1.28
4242 7616 8.276252 TGCTAATCAGATGGTTAAAAACTACC 57.724 34.615 0.00 0.00 34.93 3.18
4280 7654 8.825667 GGCAAGACCAAATGTAATAAAAGAAA 57.174 30.769 0.00 0.00 38.86 2.52
4410 7784 7.201794 GGGTTCTTAAGATGTACATTAAAGGGC 60.202 40.741 10.30 9.65 0.00 5.19
4634 8008 1.073897 GGTCTCTGGCTGGCTGTTT 59.926 57.895 2.00 0.00 0.00 2.83
4698 8072 0.376152 CTAGTCGCCGCGTTCTTCTA 59.624 55.000 13.39 8.07 0.00 2.10
4715 8089 2.959484 GCTGACTGCTGGTGGGCTA 61.959 63.158 0.00 0.00 38.95 3.93
4804 8178 3.369546 AACACTACATTGCTTTGCACC 57.630 42.857 0.00 0.00 38.71 5.01
4845 8219 8.496751 GTTCTTGATCACAGTATCATCATCATG 58.503 37.037 0.00 0.00 35.84 3.07
4846 8220 8.208903 TGTTCTTGATCACAGTATCATCATCAT 58.791 33.333 0.00 0.00 35.84 2.45
4847 8221 7.558604 TGTTCTTGATCACAGTATCATCATCA 58.441 34.615 0.00 0.00 35.84 3.07
4848 8222 8.496751 CATGTTCTTGATCACAGTATCATCATC 58.503 37.037 0.00 0.00 35.84 2.92
4849 8223 7.041303 GCATGTTCTTGATCACAGTATCATCAT 60.041 37.037 0.00 0.00 35.84 2.45
4850 8224 6.259387 GCATGTTCTTGATCACAGTATCATCA 59.741 38.462 0.00 0.00 35.84 3.07
4871 8245 1.270518 CGGAATGGGGAGTAGAGCATG 60.271 57.143 0.00 0.00 0.00 4.06
4873 8247 0.032515 TCGGAATGGGGAGTAGAGCA 60.033 55.000 0.00 0.00 0.00 4.26
4934 8308 8.755977 GCACCTACTCTACTCTATCTATCTAGT 58.244 40.741 0.00 0.00 0.00 2.57
4938 8312 8.624367 TTTGCACCTACTCTACTCTATCTATC 57.376 38.462 0.00 0.00 0.00 2.08
5046 8492 1.594862 AGCGAAGATTAAGCGTCATGC 59.405 47.619 7.41 3.39 46.98 4.06
5071 8517 2.291465 GCAGCAACATGTCAACAAGAGA 59.709 45.455 0.00 0.00 0.00 3.10
5098 8544 2.143925 GGTACAGGTTGAAGAGCACAC 58.856 52.381 0.00 0.00 0.00 3.82
5110 8560 4.783560 ACCAACACTTTTAGGTACAGGT 57.216 40.909 0.00 0.00 31.32 4.00
5148 8601 5.857268 AGAGATTGAACCAAAATTTGTGGG 58.143 37.500 10.41 11.40 40.75 4.61
5209 8662 7.340122 TGGAAATATGAAAACACAAGTGACA 57.660 32.000 7.28 2.57 0.00 3.58
5283 8737 7.054124 GGAACAGTTGGATAATAATCACCTGA 58.946 38.462 0.00 0.00 33.41 3.86
5378 8832 5.984233 TGGCATCTATATTTGTGTTCGTC 57.016 39.130 0.00 0.00 0.00 4.20
5417 8871 7.453439 TGATTATTGCCAGGAATGATCATTCAT 59.547 33.333 36.93 31.85 46.77 2.57
5483 8937 3.085533 ACCGTTGGCTTGCAACATATTA 58.914 40.909 0.00 0.00 33.13 0.98
5577 9031 2.627699 TGGGGAAGAGCATGTTTTGTTC 59.372 45.455 0.00 0.00 35.92 3.18
5712 9166 6.127366 GGCATCCATGTAAATTTTCTTCTCCA 60.127 38.462 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.