Multiple sequence alignment - TraesCS3D01G523700

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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 TraesCS3D01G523700 chr3D 100.000 3442 0 0 1 3442 604253689 604250248 0.000000e+00 6357.0
1 TraesCS3D01G523700 chr3D 82.542 2589 337 65 488 3037 604144045 604141533 0.000000e+00 2170.0
2 TraesCS3D01G523700 chr3D 85.224 1922 247 29 545 2444 603962499 603964405 0.000000e+00 1941.0
3 TraesCS3D01G523700 chr3D 83.240 1778 258 17 678 2440 602803981 602802229 0.000000e+00 1596.0
4 TraesCS3D01G523700 chr3D 85.656 244 16 9 3182 3410 313314142 313314381 4.440000e-59 239.0
5 TraesCS3D01G523700 chr3B 95.769 2340 85 11 437 2772 811141633 811139304 0.000000e+00 3760.0
6 TraesCS3D01G523700 chr3B 84.510 1969 264 31 541 2482 811079183 811081137 0.000000e+00 1908.0
7 TraesCS3D01G523700 chr3B 83.962 2014 270 29 437 2440 811153967 811151997 0.000000e+00 1881.0
8 TraesCS3D01G523700 chr3B 83.324 1775 255 16 678 2440 810948009 810949754 0.000000e+00 1600.0
9 TraesCS3D01G523700 chr3B 82.289 1835 271 37 644 2440 810977807 810979625 0.000000e+00 1539.0
10 TraesCS3D01G523700 chr3B 93.617 329 15 5 2827 3151 811139175 811138849 1.440000e-133 486.0
11 TraesCS3D01G523700 chr3B 91.892 222 16 2 60 279 811143105 811142884 3.340000e-80 309.0
12 TraesCS3D01G523700 chr3B 82.547 212 26 6 489 697 811142481 811142278 3.530000e-40 176.0
13 TraesCS3D01G523700 chr3B 81.818 132 10 10 3197 3316 380873172 380873043 7.860000e-17 99.0
14 TraesCS3D01G523700 chr3B 95.082 61 2 1 2845 2904 811126596 811126536 1.020000e-15 95.3
15 TraesCS3D01G523700 chr3B 96.154 52 2 0 8 59 811143137 811143086 6.120000e-13 86.1
16 TraesCS3D01G523700 chr3A 85.401 2370 274 38 437 2772 733726323 733723992 0.000000e+00 2394.0
17 TraesCS3D01G523700 chr3A 83.881 1948 272 31 839 2772 733637904 733635985 0.000000e+00 1820.0
18 TraesCS3D01G523700 chr3A 82.718 2060 293 35 517 2534 733860518 733858480 0.000000e+00 1773.0
19 TraesCS3D01G523700 chr3A 83.177 1813 268 24 651 2440 733333061 733334859 0.000000e+00 1624.0
20 TraesCS3D01G523700 chr3A 83.127 1778 254 22 678 2438 733039218 733040966 0.000000e+00 1580.0
21 TraesCS3D01G523700 chr3A 84.309 427 56 5 2195 2613 733475461 733475884 1.150000e-109 407.0
22 TraesCS3D01G523700 chr3A 85.750 400 39 10 2377 2772 733655850 733655465 1.150000e-109 407.0
23 TraesCS3D01G523700 chr3A 92.424 66 4 1 2845 2909 733635849 733635784 3.660000e-15 93.5
24 TraesCS3D01G523700 chr3A 94.915 59 2 1 2852 2909 733620569 733620511 1.320000e-14 91.6
25 TraesCS3D01G523700 chr3A 97.297 37 1 0 2778 2814 733620659 733620623 2.870000e-06 63.9
26 TraesCS3D01G523700 chrUn 83.974 1872 246 31 738 2595 42260122 42261953 0.000000e+00 1746.0
27 TraesCS3D01G523700 chr5A 90.875 263 13 2 3186 3438 360020164 360019903 3.290000e-90 342.0
28 TraesCS3D01G523700 chr5A 75.936 187 33 10 3188 3371 52258233 52258056 6.120000e-13 86.1
29 TraesCS3D01G523700 chr2A 90.530 264 14 2 3185 3438 772429779 772429517 4.250000e-89 339.0
30 TraesCS3D01G523700 chr7D 86.111 216 18 5 3175 3381 213781643 213781855 4.470000e-54 222.0
31 TraesCS3D01G523700 chr7D 88.095 168 8 7 3182 3339 76595920 76596085 4.530000e-44 189.0
32 TraesCS3D01G523700 chr6A 81.439 264 24 11 3184 3437 534662643 534662395 3.510000e-45 193.0
33 TraesCS3D01G523700 chr6A 97.500 40 1 0 3184 3223 585478269 585478308 6.160000e-08 69.4
34 TraesCS3D01G523700 chr5B 83.105 219 24 4 3183 3389 35498804 35498587 1.630000e-43 187.0
35 TraesCS3D01G523700 chr6B 80.788 203 24 10 3185 3374 569875474 569875274 9.960000e-31 145.0
36 TraesCS3D01G523700 chr2D 78.061 196 27 12 3188 3371 577624289 577624098 3.630000e-20 110.0
37 TraesCS3D01G523700 chr2D 86.207 87 6 4 3227 3312 97625435 97625516 4.730000e-14 89.8
38 TraesCS3D01G523700 chr4D 85.057 87 7 3 3227 3312 439254719 439254800 2.200000e-12 84.2


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 TraesCS3D01G523700 chr3D 604250248 604253689 3441 True 6357.00 6357 100.0000 1 3442 1 chr3D.!!$R3 3441
1 TraesCS3D01G523700 chr3D 604141533 604144045 2512 True 2170.00 2170 82.5420 488 3037 1 chr3D.!!$R2 2549
2 TraesCS3D01G523700 chr3D 603962499 603964405 1906 False 1941.00 1941 85.2240 545 2444 1 chr3D.!!$F2 1899
3 TraesCS3D01G523700 chr3D 602802229 602803981 1752 True 1596.00 1596 83.2400 678 2440 1 chr3D.!!$R1 1762
4 TraesCS3D01G523700 chr3B 811079183 811081137 1954 False 1908.00 1908 84.5100 541 2482 1 chr3B.!!$F3 1941
5 TraesCS3D01G523700 chr3B 811151997 811153967 1970 True 1881.00 1881 83.9620 437 2440 1 chr3B.!!$R3 2003
6 TraesCS3D01G523700 chr3B 810948009 810949754 1745 False 1600.00 1600 83.3240 678 2440 1 chr3B.!!$F1 1762
7 TraesCS3D01G523700 chr3B 810977807 810979625 1818 False 1539.00 1539 82.2890 644 2440 1 chr3B.!!$F2 1796
8 TraesCS3D01G523700 chr3B 811138849 811143137 4288 True 963.42 3760 91.9958 8 3151 5 chr3B.!!$R4 3143
9 TraesCS3D01G523700 chr3A 733723992 733726323 2331 True 2394.00 2394 85.4010 437 2772 1 chr3A.!!$R2 2335
10 TraesCS3D01G523700 chr3A 733858480 733860518 2038 True 1773.00 1773 82.7180 517 2534 1 chr3A.!!$R3 2017
11 TraesCS3D01G523700 chr3A 733333061 733334859 1798 False 1624.00 1624 83.1770 651 2440 1 chr3A.!!$F2 1789
12 TraesCS3D01G523700 chr3A 733039218 733040966 1748 False 1580.00 1580 83.1270 678 2438 1 chr3A.!!$F1 1760
13 TraesCS3D01G523700 chr3A 733635784 733637904 2120 True 956.75 1820 88.1525 839 2909 2 chr3A.!!$R5 2070
14 TraesCS3D01G523700 chrUn 42260122 42261953 1831 False 1746.00 1746 83.9740 738 2595 1 chrUn.!!$F1 1857

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
683 1823 0.112412 AACCCCTTTCCGACTTGCAT 59.888 50.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 3735 0.690192 TCGGCAAAGTGATGAGGGAA 59.31 50.0 0.0 0.0 0.0 3.97 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
62 63 2.435586 CTCCTGCAGCAACTCCGG 60.436 66.667 8.66 0.00 0.00 5.14
63 64 4.704833 TCCTGCAGCAACTCCGGC 62.705 66.667 8.66 0.00 0.00 6.13
64 65 4.711949 CCTGCAGCAACTCCGGCT 62.712 66.667 8.66 0.00 43.77 5.52
65 66 3.123620 CTGCAGCAACTCCGGCTC 61.124 66.667 0.00 0.00 40.23 4.70
66 67 3.602513 CTGCAGCAACTCCGGCTCT 62.603 63.158 0.00 0.00 40.23 4.09
67 68 2.817396 GCAGCAACTCCGGCTCTC 60.817 66.667 0.00 0.00 40.23 3.20
68 69 2.507992 CAGCAACTCCGGCTCTCG 60.508 66.667 0.00 0.00 40.23 4.04
69 70 2.992114 AGCAACTCCGGCTCTCGT 60.992 61.111 0.00 0.00 36.81 4.18
70 71 2.811317 GCAACTCCGGCTCTCGTG 60.811 66.667 0.00 0.00 37.11 4.35
83 84 2.666190 TCGTGCAGCAACTGAGCC 60.666 61.111 0.00 0.00 32.44 4.70
84 85 2.974148 CGTGCAGCAACTGAGCCA 60.974 61.111 0.00 0.00 32.44 4.75
85 86 2.641559 GTGCAGCAACTGAGCCAC 59.358 61.111 0.00 0.00 32.44 5.01
86 87 1.895707 GTGCAGCAACTGAGCCACT 60.896 57.895 0.00 0.00 32.44 4.00
87 88 1.598962 TGCAGCAACTGAGCCACTC 60.599 57.895 0.00 0.00 32.44 3.51
88 89 2.331132 GCAGCAACTGAGCCACTCC 61.331 63.158 0.00 0.00 32.44 3.85
89 90 2.031516 CAGCAACTGAGCCACTCCG 61.032 63.158 0.00 0.00 32.44 4.63
90 91 2.031163 GCAACTGAGCCACTCCGT 59.969 61.111 0.00 0.00 29.55 4.69
91 92 1.185618 AGCAACTGAGCCACTCCGTA 61.186 55.000 0.00 0.00 34.23 4.02
93 94 1.714794 CAACTGAGCCACTCCGTAAG 58.285 55.000 0.00 0.00 28.38 2.34
94 95 1.000955 CAACTGAGCCACTCCGTAAGT 59.999 52.381 0.00 0.00 39.44 2.24
138 140 5.695851 AATGCTTGAAATTCGAGACTTGT 57.304 34.783 14.13 0.00 29.08 3.16
156 158 8.006298 AGACTTGTTTTGGTTCATGAATTGTA 57.994 30.769 12.12 0.00 0.00 2.41
188 190 2.440796 CATGAGGCCCGCATGGTT 60.441 61.111 18.67 0.00 37.86 3.67
196 198 2.440253 AGGCCCGCATGGTTAAGTTATA 59.560 45.455 0.00 0.00 36.04 0.98
243 245 4.213700 GCGACTAGCGAGATTCGG 57.786 61.111 0.00 0.00 44.57 4.30
244 246 1.370657 GCGACTAGCGAGATTCGGG 60.371 63.158 0.00 0.00 44.57 5.14
253 255 2.431057 AGCGAGATTCGGGTGTTTAGAT 59.569 45.455 0.34 0.00 40.84 1.98
262 265 4.817517 TCGGGTGTTTAGATTCAGTTCTC 58.182 43.478 0.00 0.00 0.00 2.87
322 493 7.646548 TTATTCTCTAGCTCTTCAGTGCTAA 57.353 36.000 10.87 0.61 43.68 3.09
330 501 3.064545 GCTCTTCAGTGCTAATTTCGCAT 59.935 43.478 5.55 0.00 39.89 4.73
391 596 7.974482 AAGATTAGTACACGGCTTTAAGTTT 57.026 32.000 0.00 0.00 0.00 2.66
392 597 9.492973 AAAGATTAGTACACGGCTTTAAGTTTA 57.507 29.630 0.00 0.00 0.00 2.01
393 598 9.492973 AAGATTAGTACACGGCTTTAAGTTTAA 57.507 29.630 0.00 0.00 0.00 1.52
394 599 9.148104 AGATTAGTACACGGCTTTAAGTTTAAG 57.852 33.333 0.00 0.00 0.00 1.85
395 600 8.837788 ATTAGTACACGGCTTTAAGTTTAAGT 57.162 30.769 3.75 0.00 0.00 2.24
396 601 6.775939 AGTACACGGCTTTAAGTTTAAGTC 57.224 37.500 3.75 0.08 0.00 3.01
397 602 6.519382 AGTACACGGCTTTAAGTTTAAGTCT 58.481 36.000 4.86 0.00 0.00 3.24
398 603 7.661040 AGTACACGGCTTTAAGTTTAAGTCTA 58.339 34.615 4.86 0.00 0.00 2.59
399 604 8.143835 AGTACACGGCTTTAAGTTTAAGTCTAA 58.856 33.333 4.86 0.00 0.00 2.10
400 605 7.417496 ACACGGCTTTAAGTTTAAGTCTAAG 57.583 36.000 4.86 0.00 0.00 2.18
401 606 7.212274 ACACGGCTTTAAGTTTAAGTCTAAGA 58.788 34.615 4.86 0.00 0.00 2.10
402 607 7.712205 ACACGGCTTTAAGTTTAAGTCTAAGAA 59.288 33.333 4.86 0.00 0.00 2.52
403 608 8.553696 CACGGCTTTAAGTTTAAGTCTAAGAAA 58.446 33.333 4.86 0.00 0.00 2.52
404 609 8.771766 ACGGCTTTAAGTTTAAGTCTAAGAAAG 58.228 33.333 4.86 0.00 0.00 2.62
405 610 8.985805 CGGCTTTAAGTTTAAGTCTAAGAAAGA 58.014 33.333 4.86 0.00 0.00 2.52
455 1568 7.118723 AGTGAATGTGGCTCCTGAATAATTTA 58.881 34.615 0.00 0.00 0.00 1.40
460 1573 6.721318 TGTGGCTCCTGAATAATTTAAGTCT 58.279 36.000 0.00 0.00 0.00 3.24
521 1634 4.730966 ACTCTGTCCTGAACTAGAGTTGA 58.269 43.478 0.00 0.00 40.43 3.18
552 1665 2.125912 CCCACGTTGAGAGCCTCG 60.126 66.667 0.00 0.00 32.35 4.63
556 1677 0.798771 CACGTTGAGAGCCTCGTAGC 60.799 60.000 0.00 0.00 35.13 3.58
560 1681 2.603412 CGTTGAGAGCCTCGTAGCTATG 60.603 54.545 6.62 6.62 45.15 2.23
563 1684 4.022413 TGAGAGCCTCGTAGCTATGTAT 57.978 45.455 12.66 0.00 45.15 2.29
569 1690 4.884744 AGCCTCGTAGCTATGTATCCTATG 59.115 45.833 12.66 0.00 42.70 2.23
596 1717 4.678509 TGTCCAGTCGATATTTTGCAAC 57.321 40.909 0.00 0.00 0.00 4.17
675 1815 3.131400 TCAACAAAAGAAACCCCTTTCCG 59.869 43.478 0.00 0.00 37.12 4.30
683 1823 0.112412 AACCCCTTTCCGACTTGCAT 59.888 50.000 0.00 0.00 0.00 3.96
708 1848 1.067354 GGGCATGTTTGCTCTTCAAGG 60.067 52.381 0.00 0.00 46.44 3.61
774 1922 4.627035 GCTTTTCACCTTACCAATGCAATC 59.373 41.667 0.00 0.00 0.00 2.67
1026 2230 0.541764 CCTGTAAAAAGGCCAGGGCA 60.542 55.000 16.94 0.00 44.11 5.36
1047 2251 3.812053 CAGAAGCTACATCTATTGTGGGC 59.188 47.826 0.00 0.00 39.48 5.36
1092 2296 4.530875 CTCCAGAGATAAAGGGCAACATT 58.469 43.478 0.00 0.00 46.79 2.71
1222 2430 4.483476 ACAAGAACCAAGTTCATTACGC 57.517 40.909 9.92 0.00 44.11 4.42
1745 2956 4.507710 TCTGTTCCTATTGCTCATGACAC 58.492 43.478 0.00 0.00 0.00 3.67
1758 2969 4.682787 CTCATGACACGGAAAGCTATGTA 58.317 43.478 0.00 0.00 0.00 2.29
1781 2992 3.333680 AGGAAGTCATTGGGAAGCCTAAA 59.666 43.478 0.00 0.00 0.00 1.85
1792 3004 4.706476 TGGGAAGCCTAAATGACATCAAAG 59.294 41.667 0.00 0.00 0.00 2.77
1884 3104 5.871524 TCTGCATTCTGACTAATCTGTGTTC 59.128 40.000 0.00 0.00 0.00 3.18
2266 3548 0.732880 CTCGTAACGGCCAGTGTGAG 60.733 60.000 2.24 6.64 0.00 3.51
2484 3771 1.581934 CCGATCTAATTTGCTGCGGA 58.418 50.000 0.00 0.00 39.62 5.54
2493 3780 2.472695 TTTGCTGCGGATAGAGTTGT 57.527 45.000 0.00 0.00 0.00 3.32
2494 3781 2.472695 TTGCTGCGGATAGAGTTGTT 57.527 45.000 0.00 0.00 0.00 2.83
2495 3782 2.472695 TGCTGCGGATAGAGTTGTTT 57.527 45.000 0.00 0.00 0.00 2.83
2538 3825 5.280779 GGATCTACCAGCTAGGACTATCTGA 60.281 48.000 10.81 0.00 41.22 3.27
2772 4066 4.622260 TGTGTCCATGAGAAGTGATCAA 57.378 40.909 0.00 0.00 0.00 2.57
2774 4068 4.999311 TGTGTCCATGAGAAGTGATCAAAG 59.001 41.667 0.00 0.00 0.00 2.77
2775 4069 4.394300 GTGTCCATGAGAAGTGATCAAAGG 59.606 45.833 0.00 0.00 0.00 3.11
2776 4070 3.944015 GTCCATGAGAAGTGATCAAAGGG 59.056 47.826 0.00 0.00 30.82 3.95
2820 4159 2.156917 ACATTCTGCATGTGTGGACAG 58.843 47.619 0.00 0.00 45.12 3.51
2821 4160 2.156917 CATTCTGCATGTGTGGACAGT 58.843 47.619 0.00 0.00 34.87 3.55
2823 4162 2.346766 TCTGCATGTGTGGACAGTTT 57.653 45.000 0.00 0.00 34.87 2.66
2824 4163 2.653726 TCTGCATGTGTGGACAGTTTT 58.346 42.857 0.00 0.00 34.87 2.43
2825 4164 3.814625 TCTGCATGTGTGGACAGTTTTA 58.185 40.909 0.00 0.00 34.87 1.52
2917 4286 5.128205 TGGAATGAATGTCTAATGCTCCTG 58.872 41.667 0.00 0.00 0.00 3.86
2986 4357 3.058293 TGTCACTTTAAAATGCTGCTCCG 60.058 43.478 0.00 0.00 0.00 4.63
2996 4367 5.536554 AAATGCTGCTCCGATATTATTCG 57.463 39.130 0.00 0.00 38.83 3.34
3046 4418 5.472478 CAGGAACCAGTTTTTACTTCTACCC 59.528 44.000 0.00 0.00 0.00 3.69
3054 4426 8.905850 CCAGTTTTTACTTCTACCCACTTTAAA 58.094 33.333 0.00 0.00 0.00 1.52
3062 4434 8.528044 ACTTCTACCCACTTTAAACAATTCAA 57.472 30.769 0.00 0.00 0.00 2.69
3095 4468 2.614057 CTGGTGTTAATCAATCCCGCTC 59.386 50.000 0.00 0.00 0.00 5.03
3159 4532 9.436957 CACCATTAGTGTCTACAAATAGTTTCT 57.563 33.333 0.00 0.00 41.93 2.52
3173 4546 9.066892 ACAAATAGTTTCTTAAATCAGTGAGCA 57.933 29.630 0.00 0.00 0.00 4.26
3174 4547 9.897744 CAAATAGTTTCTTAAATCAGTGAGCAA 57.102 29.630 0.00 0.00 0.00 3.91
3178 4551 6.920210 AGTTTCTTAAATCAGTGAGCAAAAGC 59.080 34.615 0.00 0.00 0.00 3.51
3179 4552 6.389830 TTCTTAAATCAGTGAGCAAAAGCA 57.610 33.333 0.00 0.00 0.00 3.91
3180 4553 6.005583 TCTTAAATCAGTGAGCAAAAGCAG 57.994 37.500 0.00 0.00 0.00 4.24
3181 4554 3.655276 AAATCAGTGAGCAAAAGCAGG 57.345 42.857 0.00 0.00 0.00 4.85
3182 4555 2.283145 ATCAGTGAGCAAAAGCAGGT 57.717 45.000 0.00 0.00 0.00 4.00
3183 4556 1.597742 TCAGTGAGCAAAAGCAGGTC 58.402 50.000 0.00 0.00 0.00 3.85
3184 4557 0.236711 CAGTGAGCAAAAGCAGGTCG 59.763 55.000 0.00 0.00 36.34 4.79
3185 4558 1.081840 GTGAGCAAAAGCAGGTCGC 60.082 57.895 0.00 0.00 42.91 5.19
3225 4598 4.413565 GGCCCGGGCGAAACCTTA 62.414 66.667 38.22 0.00 43.06 2.69
3226 4599 2.822701 GCCCGGGCGAAACCTTAG 60.823 66.667 33.60 0.00 39.10 2.18
3227 4600 2.822701 CCCGGGCGAAACCTTAGC 60.823 66.667 8.08 0.00 39.10 3.09
3232 4605 2.744709 GCGAAACCTTAGCCGCCA 60.745 61.111 0.00 0.00 41.59 5.69
3233 4606 3.035576 GCGAAACCTTAGCCGCCAC 62.036 63.158 0.00 0.00 41.59 5.01
3234 4607 1.375523 CGAAACCTTAGCCGCCACT 60.376 57.895 0.00 0.00 0.00 4.00
3235 4608 1.359459 CGAAACCTTAGCCGCCACTC 61.359 60.000 0.00 0.00 0.00 3.51
3236 4609 1.002502 AAACCTTAGCCGCCACTCC 60.003 57.895 0.00 0.00 0.00 3.85
3237 4610 1.774894 AAACCTTAGCCGCCACTCCA 61.775 55.000 0.00 0.00 0.00 3.86
3238 4611 2.185310 AACCTTAGCCGCCACTCCAG 62.185 60.000 0.00 0.00 0.00 3.86
3239 4612 2.512515 CTTAGCCGCCACTCCAGC 60.513 66.667 0.00 0.00 0.00 4.85
3240 4613 4.096003 TTAGCCGCCACTCCAGCC 62.096 66.667 0.00 0.00 0.00 4.85
3257 4630 2.122189 CCCCCTCCCAGATCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
3258 4631 2.122189 CCCCTCCCAGATCTCCCC 60.122 72.222 0.00 0.00 0.00 4.81
3259 4632 2.122189 CCCTCCCAGATCTCCCCC 60.122 72.222 0.00 0.00 0.00 5.40
3260 4633 2.731461 CCCTCCCAGATCTCCCCCT 61.731 68.421 0.00 0.00 0.00 4.79
3261 4634 1.152139 CCTCCCAGATCTCCCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
3262 4635 1.152139 CTCCCAGATCTCCCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
3263 4636 2.122189 CCCAGATCTCCCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
3264 4637 2.122189 CCAGATCTCCCCCTCCCC 60.122 72.222 0.00 0.00 0.00 4.81
3265 4638 2.731461 CCAGATCTCCCCCTCCCCT 61.731 68.421 0.00 0.00 0.00 4.79
3266 4639 1.152139 CAGATCTCCCCCTCCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
3267 4640 2.203714 GATCTCCCCCTCCCCTCG 60.204 72.222 0.00 0.00 0.00 4.63
3268 4641 4.565850 ATCTCCCCCTCCCCTCGC 62.566 72.222 0.00 0.00 0.00 5.03
3369 4742 4.344865 GGGTTGCTCGGCCAAGGA 62.345 66.667 2.24 0.00 0.00 3.36
3370 4743 2.747855 GGTTGCTCGGCCAAGGAG 60.748 66.667 2.24 2.08 34.62 3.69
3371 4744 2.347490 GTTGCTCGGCCAAGGAGA 59.653 61.111 10.05 0.00 33.27 3.71
3372 4745 1.743252 GTTGCTCGGCCAAGGAGAG 60.743 63.158 10.05 5.35 33.27 3.20
3373 4746 2.959484 TTGCTCGGCCAAGGAGAGG 61.959 63.158 10.05 0.00 33.27 3.69
3374 4747 3.077556 GCTCGGCCAAGGAGAGGA 61.078 66.667 10.05 0.00 33.27 3.71
3375 4748 3.087666 GCTCGGCCAAGGAGAGGAG 62.088 68.421 10.05 3.23 33.27 3.69
3376 4749 1.684049 CTCGGCCAAGGAGAGGAGT 60.684 63.158 2.24 0.00 33.27 3.85
3377 4750 1.954362 CTCGGCCAAGGAGAGGAGTG 61.954 65.000 2.24 0.00 33.27 3.51
3378 4751 2.993853 GGCCAAGGAGAGGAGTGG 59.006 66.667 0.00 0.00 0.00 4.00
3379 4752 2.674220 GGCCAAGGAGAGGAGTGGG 61.674 68.421 0.00 0.00 0.00 4.61
3380 4753 2.674220 GCCAAGGAGAGGAGTGGGG 61.674 68.421 0.00 0.00 0.00 4.96
3381 4754 1.081092 CCAAGGAGAGGAGTGGGGA 59.919 63.158 0.00 0.00 0.00 4.81
3382 4755 1.268283 CCAAGGAGAGGAGTGGGGAC 61.268 65.000 0.00 0.00 0.00 4.46
3383 4756 1.305381 AAGGAGAGGAGTGGGGACG 60.305 63.158 0.00 0.00 0.00 4.79
3384 4757 2.037527 GGAGAGGAGTGGGGACGT 59.962 66.667 0.00 0.00 0.00 4.34
3385 4758 2.352032 GGAGAGGAGTGGGGACGTG 61.352 68.421 0.00 0.00 0.00 4.49
3386 4759 2.283966 AGAGGAGTGGGGACGTGG 60.284 66.667 0.00 0.00 0.00 4.94
3387 4760 4.083862 GAGGAGTGGGGACGTGGC 62.084 72.222 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.507992 CGAGAGCCGGAGTTGCTG 60.508 66.667 5.05 0.00 39.69 4.41
52 53 2.992114 ACGAGAGCCGGAGTTGCT 60.992 61.111 5.05 0.00 43.93 3.91
53 54 2.811317 CACGAGAGCCGGAGTTGC 60.811 66.667 5.05 0.00 43.93 4.17
54 55 2.811317 GCACGAGAGCCGGAGTTG 60.811 66.667 5.05 0.00 43.93 3.16
55 56 3.288308 CTGCACGAGAGCCGGAGTT 62.288 63.158 5.05 0.00 43.93 3.01
56 57 3.753434 CTGCACGAGAGCCGGAGT 61.753 66.667 5.05 0.00 43.93 3.85
60 61 3.782244 GTTGCTGCACGAGAGCCG 61.782 66.667 0.00 0.00 45.44 5.52
61 62 2.358003 AGTTGCTGCACGAGAGCC 60.358 61.111 0.00 0.00 35.43 4.70
62 63 1.624865 CTCAGTTGCTGCACGAGAGC 61.625 60.000 14.53 0.00 36.95 4.09
63 64 1.624865 GCTCAGTTGCTGCACGAGAG 61.625 60.000 20.85 18.35 0.00 3.20
64 65 1.665916 GCTCAGTTGCTGCACGAGA 60.666 57.895 20.85 10.70 0.00 4.04
65 66 2.675056 GGCTCAGTTGCTGCACGAG 61.675 63.158 0.00 10.04 0.00 4.18
66 67 2.666190 GGCTCAGTTGCTGCACGA 60.666 61.111 0.00 0.00 0.00 4.35
67 68 2.974148 TGGCTCAGTTGCTGCACG 60.974 61.111 0.00 0.00 0.00 5.34
68 69 1.849976 GAGTGGCTCAGTTGCTGCAC 61.850 60.000 0.00 0.00 0.00 4.57
69 70 1.598962 GAGTGGCTCAGTTGCTGCA 60.599 57.895 0.00 0.00 0.00 4.41
70 71 2.331132 GGAGTGGCTCAGTTGCTGC 61.331 63.158 0.00 0.00 31.08 5.25
83 84 2.290641 AGCAAAGCAAACTTACGGAGTG 59.709 45.455 0.00 0.00 45.73 3.51
85 86 3.555518 GAAGCAAAGCAAACTTACGGAG 58.444 45.455 0.00 0.00 34.05 4.63
86 87 2.292292 GGAAGCAAAGCAAACTTACGGA 59.708 45.455 0.00 0.00 34.05 4.69
87 88 2.293399 AGGAAGCAAAGCAAACTTACGG 59.707 45.455 0.00 0.00 34.05 4.02
88 89 3.243068 ACAGGAAGCAAAGCAAACTTACG 60.243 43.478 0.00 0.00 34.05 3.18
89 90 4.307443 ACAGGAAGCAAAGCAAACTTAC 57.693 40.909 0.00 0.00 34.05 2.34
90 91 4.202111 GGAACAGGAAGCAAAGCAAACTTA 60.202 41.667 0.00 0.00 34.05 2.24
91 92 3.430790 GGAACAGGAAGCAAAGCAAACTT 60.431 43.478 0.00 0.00 37.90 2.66
93 94 2.473816 GGAACAGGAAGCAAAGCAAAC 58.526 47.619 0.00 0.00 0.00 2.93
94 95 1.412343 GGGAACAGGAAGCAAAGCAAA 59.588 47.619 0.00 0.00 0.00 3.68
156 158 3.687125 CCTCATGCATGGCTGATCTTAT 58.313 45.455 25.97 0.00 0.00 1.73
160 162 1.957562 GCCTCATGCATGGCTGATC 59.042 57.895 25.97 6.68 45.26 2.92
361 532 9.709495 TTAAAGCCGTGTACTAATCTTTCTTAA 57.291 29.630 0.00 0.00 0.00 1.85
415 620 7.388776 GCCACATTCACTATAAGCATGATCTAA 59.611 37.037 0.00 0.00 0.00 2.10
417 622 5.704515 GCCACATTCACTATAAGCATGATCT 59.295 40.000 0.00 0.00 0.00 2.75
439 1552 8.966069 ACTTAGACTTAAATTATTCAGGAGCC 57.034 34.615 0.00 0.00 0.00 4.70
455 1568 2.237392 GCCTGGATGTGGACTTAGACTT 59.763 50.000 0.00 0.00 0.00 3.01
460 1573 3.719871 TCTTAGCCTGGATGTGGACTTA 58.280 45.455 0.00 0.00 0.00 2.24
521 1634 3.959535 ACGTGGGCAAATGATGAAATT 57.040 38.095 0.00 0.00 0.00 1.82
552 1665 8.888579 ACAAACAACATAGGATACATAGCTAC 57.111 34.615 0.00 0.00 41.41 3.58
556 1677 7.987458 ACTGGACAAACAACATAGGATACATAG 59.013 37.037 0.00 0.00 41.41 2.23
560 1681 5.291128 CGACTGGACAAACAACATAGGATAC 59.709 44.000 0.00 0.00 0.00 2.24
563 1684 3.322541 TCGACTGGACAAACAACATAGGA 59.677 43.478 0.00 0.00 0.00 2.94
569 1690 5.342259 GCAAAATATCGACTGGACAAACAAC 59.658 40.000 0.00 0.00 0.00 3.32
623 1757 4.391830 GTGCGGTCATTTGAAGAAGATGTA 59.608 41.667 0.00 0.00 0.00 2.29
675 1815 1.076485 ATGCCCCCTGATGCAAGTC 60.076 57.895 0.00 0.00 41.50 3.01
683 1823 1.304381 GAGCAAACATGCCCCCTGA 60.304 57.895 0.00 0.00 34.90 3.86
708 1848 4.453136 TGTTACAAGACCCTAATTTGCGAC 59.547 41.667 0.00 0.00 0.00 5.19
774 1922 4.749245 ATTAACAGAACTGAACTTGGCG 57.251 40.909 8.87 0.00 0.00 5.69
1026 2230 3.713764 AGCCCACAATAGATGTAGCTTCT 59.286 43.478 0.00 0.00 44.26 2.85
1092 2296 5.940617 TCTTCAACATTCAAAAGGGAGAGA 58.059 37.500 0.00 0.00 0.00 3.10
1222 2430 5.201713 AGTGATAACACCATATCGACCAG 57.798 43.478 0.00 0.00 46.99 4.00
1351 2559 4.327680 AGCCCTGAGTTCAACTTGATTAC 58.672 43.478 0.00 0.00 0.00 1.89
1459 2667 8.437575 AGTTAGTCTCTTGAAACCTTGGAATAA 58.562 33.333 0.00 0.00 0.00 1.40
1745 2956 4.755411 TGACTTCCTTACATAGCTTTCCG 58.245 43.478 0.00 0.00 0.00 4.30
1758 2969 1.713078 AGGCTTCCCAATGACTTCCTT 59.287 47.619 0.00 0.00 0.00 3.36
1781 2992 4.530710 ATTGCAAGTGCTTTGATGTCAT 57.469 36.364 4.94 0.00 42.66 3.06
1792 3004 2.660189 ATGCCACTAATTGCAAGTGC 57.340 45.000 10.14 4.77 42.47 4.40
2126 3360 4.558178 TGATTAGGCGTCGTAAACTGAAA 58.442 39.130 0.00 0.00 0.00 2.69
2449 3735 0.690192 TCGGCAAAGTGATGAGGGAA 59.310 50.000 0.00 0.00 0.00 3.97
2538 3825 8.476064 TCCAATGCACACAAATATATAACCAT 57.524 30.769 0.00 0.00 0.00 3.55
2568 3855 6.374565 ACACACTACGTCTACCTGATAATC 57.625 41.667 0.00 0.00 0.00 1.75
2772 4066 4.918588 ACGAAGGTACAATTTGATCCCTT 58.081 39.130 14.42 14.42 0.00 3.95
2774 4068 6.317893 ACAATACGAAGGTACAATTTGATCCC 59.682 38.462 2.79 0.00 0.00 3.85
2775 4069 7.316544 ACAATACGAAGGTACAATTTGATCC 57.683 36.000 2.79 5.13 0.00 3.36
2776 4070 8.875803 TGTACAATACGAAGGTACAATTTGATC 58.124 33.333 2.79 0.00 42.99 2.92
2973 4343 5.700832 TCGAATAATATCGGAGCAGCATTTT 59.299 36.000 0.00 0.00 42.92 1.82
2979 4350 6.507900 ACCATATCGAATAATATCGGAGCAG 58.492 40.000 0.00 0.00 42.92 4.24
3152 4525 8.076178 GCTTTTGCTCACTGATTTAAGAAACTA 58.924 33.333 0.00 0.00 43.35 2.24
3153 4526 6.920210 GCTTTTGCTCACTGATTTAAGAAACT 59.080 34.615 0.00 0.00 43.35 2.66
3154 4527 7.098503 GCTTTTGCTCACTGATTTAAGAAAC 57.901 36.000 0.00 0.00 43.35 2.78
3208 4581 4.413565 TAAGGTTTCGCCCGGGCC 62.414 66.667 39.24 24.84 38.26 5.80
3209 4582 2.822701 CTAAGGTTTCGCCCGGGC 60.823 66.667 36.69 36.69 38.26 6.13
3210 4583 2.822701 GCTAAGGTTTCGCCCGGG 60.823 66.667 19.09 19.09 38.26 5.73
3211 4584 2.822701 GGCTAAGGTTTCGCCCGG 60.823 66.667 0.00 0.00 37.86 5.73
3212 4585 3.192922 CGGCTAAGGTTTCGCCCG 61.193 66.667 0.00 0.00 40.70 6.13
3213 4586 3.506096 GCGGCTAAGGTTTCGCCC 61.506 66.667 0.00 0.00 42.02 6.13
3215 4588 2.744709 TGGCGGCTAAGGTTTCGC 60.745 61.111 11.43 0.00 46.35 4.70
3216 4589 1.359459 GAGTGGCGGCTAAGGTTTCG 61.359 60.000 11.43 0.00 0.00 3.46
3217 4590 1.025113 GGAGTGGCGGCTAAGGTTTC 61.025 60.000 11.43 0.00 0.00 2.78
3218 4591 1.002502 GGAGTGGCGGCTAAGGTTT 60.003 57.895 11.43 0.00 0.00 3.27
3219 4592 2.185310 CTGGAGTGGCGGCTAAGGTT 62.185 60.000 11.43 0.00 0.00 3.50
3220 4593 2.606519 TGGAGTGGCGGCTAAGGT 60.607 61.111 11.43 0.00 0.00 3.50
3221 4594 2.187946 CTGGAGTGGCGGCTAAGG 59.812 66.667 11.43 0.00 0.00 2.69
3222 4595 2.512515 GCTGGAGTGGCGGCTAAG 60.513 66.667 11.43 1.64 0.00 2.18
3223 4596 4.096003 GGCTGGAGTGGCGGCTAA 62.096 66.667 11.43 0.00 0.00 3.09
3240 4613 2.122189 GGGAGATCTGGGAGGGGG 60.122 72.222 0.00 0.00 0.00 5.40
3241 4614 2.122189 GGGGAGATCTGGGAGGGG 60.122 72.222 0.00 0.00 0.00 4.79
3242 4615 2.122189 GGGGGAGATCTGGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
3243 4616 1.152139 GAGGGGGAGATCTGGGAGG 60.152 68.421 0.00 0.00 0.00 4.30
3244 4617 1.152139 GGAGGGGGAGATCTGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
3245 4618 2.727071 GGGAGGGGGAGATCTGGGA 61.727 68.421 0.00 0.00 0.00 4.37
3246 4619 2.122189 GGGAGGGGGAGATCTGGG 60.122 72.222 0.00 0.00 0.00 4.45
3247 4620 2.122189 GGGGAGGGGGAGATCTGG 60.122 72.222 0.00 0.00 0.00 3.86
3248 4621 1.152139 GAGGGGAGGGGGAGATCTG 60.152 68.421 0.00 0.00 0.00 2.90
3249 4622 2.784654 CGAGGGGAGGGGGAGATCT 61.785 68.421 0.00 0.00 0.00 2.75
3250 4623 2.203714 CGAGGGGAGGGGGAGATC 60.204 72.222 0.00 0.00 0.00 2.75
3251 4624 4.565850 GCGAGGGGAGGGGGAGAT 62.566 72.222 0.00 0.00 0.00 2.75
3352 4725 4.344865 TCCTTGGCCGAGCAACCC 62.345 66.667 15.36 0.00 0.00 4.11
3353 4726 2.747855 CTCCTTGGCCGAGCAACC 60.748 66.667 15.36 0.00 0.00 3.77
3354 4727 1.743252 CTCTCCTTGGCCGAGCAAC 60.743 63.158 15.36 0.00 0.00 4.17
3355 4728 2.665000 CTCTCCTTGGCCGAGCAA 59.335 61.111 15.36 3.80 0.00 3.91
3356 4729 3.393970 CCTCTCCTTGGCCGAGCA 61.394 66.667 15.36 0.00 0.00 4.26
3357 4730 3.077556 TCCTCTCCTTGGCCGAGC 61.078 66.667 15.36 0.00 0.00 5.03
3358 4731 1.684049 ACTCCTCTCCTTGGCCGAG 60.684 63.158 13.75 13.75 0.00 4.63
3359 4732 1.984570 CACTCCTCTCCTTGGCCGA 60.985 63.158 0.00 0.00 0.00 5.54
3360 4733 2.581354 CACTCCTCTCCTTGGCCG 59.419 66.667 0.00 0.00 0.00 6.13
3361 4734 2.674220 CCCACTCCTCTCCTTGGCC 61.674 68.421 0.00 0.00 0.00 5.36
3362 4735 2.674220 CCCCACTCCTCTCCTTGGC 61.674 68.421 0.00 0.00 0.00 4.52
3363 4736 1.081092 TCCCCACTCCTCTCCTTGG 59.919 63.158 0.00 0.00 0.00 3.61
3364 4737 1.608717 CGTCCCCACTCCTCTCCTTG 61.609 65.000 0.00 0.00 0.00 3.61
3365 4738 1.305381 CGTCCCCACTCCTCTCCTT 60.305 63.158 0.00 0.00 0.00 3.36
3366 4739 2.360980 CGTCCCCACTCCTCTCCT 59.639 66.667 0.00 0.00 0.00 3.69
3367 4740 2.037527 ACGTCCCCACTCCTCTCC 59.962 66.667 0.00 0.00 0.00 3.71
3368 4741 2.352032 CCACGTCCCCACTCCTCTC 61.352 68.421 0.00 0.00 0.00 3.20
3369 4742 2.283966 CCACGTCCCCACTCCTCT 60.284 66.667 0.00 0.00 0.00 3.69
3370 4743 4.083862 GCCACGTCCCCACTCCTC 62.084 72.222 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.