Multiple sequence alignment - TraesCS2A01G436900

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 TraesCS2A01G436900 chr2A 100.000 4592 0 0 1 4592 688634585 688639176 0.000000e+00 8480.0
1 TraesCS2A01G436900 chr2A 97.175 531 15 0 4062 4592 672807133 672807663 0.000000e+00 898.0
2 TraesCS2A01G436900 chr2A 90.000 40 4 0 3136 3175 23958285 23958246 8.000000e-03 52.8
3 TraesCS2A01G436900 chr2A 90.000 40 4 0 3136 3175 65707270 65707231 8.000000e-03 52.8
4 TraesCS2A01G436900 chr2B 91.524 1640 80 14 627 2239 651072052 651070445 0.000000e+00 2204.0
5 TraesCS2A01G436900 chr2B 97.306 891 24 0 3175 4065 651069629 651068739 0.000000e+00 1513.0
6 TraesCS2A01G436900 chr2B 96.206 817 29 2 2316 3131 651070442 651069627 0.000000e+00 1336.0
7 TraesCS2A01G436900 chr2B 97.348 528 13 1 4066 4592 570093007 570092480 0.000000e+00 896.0
8 TraesCS2A01G436900 chr2B 87.639 631 61 12 3 627 651075140 651074521 0.000000e+00 717.0
9 TraesCS2A01G436900 chr2B 89.412 170 13 2 2155 2319 209091152 209091321 4.660000e-50 209.0
10 TraesCS2A01G436900 chr2D 87.173 1910 133 39 185 2061 544851878 544850048 0.000000e+00 2067.0
11 TraesCS2A01G436900 chr2D 97.029 1077 30 2 2057 3131 544849969 544848893 0.000000e+00 1810.0
12 TraesCS2A01G436900 chr2D 98.316 891 14 1 3175 4065 544848895 544848006 0.000000e+00 1561.0
13 TraesCS2A01G436900 chr2D 90.058 171 10 4 2155 2319 249891796 249891965 1.000000e-51 215.0
14 TraesCS2A01G436900 chr2D 88.235 119 11 3 1 118 544852075 544851959 6.200000e-29 139.0
15 TraesCS2A01G436900 chr2D 86.207 58 6 2 75 131 17844316 17844260 1.380000e-05 62.1
16 TraesCS2A01G436900 chr6A 98.674 528 7 0 4065 4592 262060250 262059723 0.000000e+00 937.0
17 TraesCS2A01G436900 chr6A 97.543 529 13 0 4064 4592 200000546 200001074 0.000000e+00 905.0
18 TraesCS2A01G436900 chr6A 91.411 163 9 2 2155 2312 381088706 381088868 7.740000e-53 219.0
19 TraesCS2A01G436900 chr6A 92.500 40 3 0 3136 3175 373206772 373206733 1.780000e-04 58.4
20 TraesCS2A01G436900 chr3A 98.482 527 8 0 4066 4592 663293691 663294217 0.000000e+00 929.0
21 TraesCS2A01G436900 chr3A 97.547 530 12 1 4064 4592 588514238 588513709 0.000000e+00 905.0
22 TraesCS2A01G436900 chr3A 97.538 528 12 1 4066 4592 721300961 721300434 0.000000e+00 902.0
23 TraesCS2A01G436900 chr3A 94.595 37 2 0 3136 3172 579052847 579052883 1.780000e-04 58.4
24 TraesCS2A01G436900 chr3A 94.595 37 2 0 3136 3172 579069067 579069103 1.780000e-04 58.4
25 TraesCS2A01G436900 chr4A 97.368 532 13 1 4062 4592 45864951 45865482 0.000000e+00 904.0
26 TraesCS2A01G436900 chr4A 90.000 170 12 2 2155 2319 146552018 146552187 1.000000e-51 215.0
27 TraesCS2A01G436900 chr4A 89.080 174 12 4 2158 2326 115567237 115567066 4.660000e-50 209.0
28 TraesCS2A01G436900 chr1A 97.348 528 13 1 4066 4592 382232855 382232328 0.000000e+00 896.0
29 TraesCS2A01G436900 chr1A 100.000 31 0 0 3136 3166 539744578 539744608 1.780000e-04 58.4
30 TraesCS2A01G436900 chr5B 90.058 171 11 3 2155 2319 410849295 410849465 2.780000e-52 217.0
31 TraesCS2A01G436900 chr4D 90.000 170 12 2 2155 2319 313574202 313574371 1.000000e-51 215.0
32 TraesCS2A01G436900 chr1D 89.474 171 12 3 2155 2319 225410192 225410022 1.290000e-50 211.0
33 TraesCS2A01G436900 chr1D 100.000 31 0 0 860 890 471859995 471860025 1.780000e-04 58.4
34 TraesCS2A01G436900 chr5A 100.000 31 0 0 3136 3166 540627185 540627215 1.780000e-04 58.4
35 TraesCS2A01G436900 chr5A 100.000 29 0 0 3135 3163 462165744 462165772 2.000000e-03 54.7
36 TraesCS2A01G436900 chr3D 97.059 34 0 1 450 483 612855445 612855477 6.420000e-04 56.5
37 TraesCS2A01G436900 chr7A 100.000 28 0 0 3136 3163 515974842 515974869 8.000000e-03 52.8


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 TraesCS2A01G436900 chr2A 688634585 688639176 4591 False 8480.00 8480 100.00000 1 4592 1 chr2A.!!$F2 4591
1 TraesCS2A01G436900 chr2A 672807133 672807663 530 False 898.00 898 97.17500 4062 4592 1 chr2A.!!$F1 530
2 TraesCS2A01G436900 chr2B 651068739 651075140 6401 True 1442.50 2204 93.16875 3 4065 4 chr2B.!!$R2 4062
3 TraesCS2A01G436900 chr2B 570092480 570093007 527 True 896.00 896 97.34800 4066 4592 1 chr2B.!!$R1 526
4 TraesCS2A01G436900 chr2D 544848006 544852075 4069 True 1394.25 2067 92.68825 1 4065 4 chr2D.!!$R2 4064
5 TraesCS2A01G436900 chr6A 262059723 262060250 527 True 937.00 937 98.67400 4065 4592 1 chr6A.!!$R1 527
6 TraesCS2A01G436900 chr6A 200000546 200001074 528 False 905.00 905 97.54300 4064 4592 1 chr6A.!!$F1 528
7 TraesCS2A01G436900 chr3A 663293691 663294217 526 False 929.00 929 98.48200 4066 4592 1 chr3A.!!$F3 526
8 TraesCS2A01G436900 chr3A 588513709 588514238 529 True 905.00 905 97.54700 4064 4592 1 chr3A.!!$R1 528
9 TraesCS2A01G436900 chr3A 721300434 721300961 527 True 902.00 902 97.53800 4066 4592 1 chr3A.!!$R2 526
10 TraesCS2A01G436900 chr4A 45864951 45865482 531 False 904.00 904 97.36800 4062 4592 1 chr4A.!!$F1 530
11 TraesCS2A01G436900 chr1A 382232328 382232855 527 True 896.00 896 97.34800 4066 4592 1 chr1A.!!$R1 526

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
315 358 0.934496 TTCCGCGAGAAACACAACTG 59.066 50.000 8.23 0.00 0.00 3.16 F
411 464 1.001633 ACAGTTTTACAGATCCGCGGT 59.998 47.619 27.15 12.96 0.00 5.68 F
1421 3977 1.291459 ATGTGGGGCCATGAGGATGT 61.291 55.000 4.39 0.00 36.89 3.06 F
2270 4909 0.034186 CAAGCTTCCATGCACCCCTA 60.034 55.000 0.00 0.00 34.99 3.53 F
2273 4912 0.538287 GCTTCCATGCACCCCTATCC 60.538 60.000 0.00 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 4900 0.401250 TAGCCATGGATAGGGGTGCA 60.401 55.000 18.40 0.00 39.12 4.57 R
2270 4909 3.266772 TCACCAAAGAACTAGCCATGGAT 59.733 43.478 18.40 13.25 0.00 3.41 R
3047 5688 1.251251 GCAGAGGAAGGCAACAACAT 58.749 50.000 0.00 0.00 41.41 2.71 R
3482 6123 0.967887 TCTGCTCTCGAGTGAAGGGG 60.968 60.000 19.91 0.00 0.00 4.79 R
3969 6610 4.074627 TGGTATGGTCGTTGACTCAAAA 57.925 40.909 0.00 0.00 32.47 2.44 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
24 25 6.220930 GTTTTTCCCTAGGTTTTGAACATCC 58.779 40.000 8.29 0.00 0.00 3.51
88 89 4.452455 AGGTACAAATTTGCTTCTCGTGAG 59.548 41.667 18.12 0.00 0.00 3.51
118 119 0.946221 CACTTCCACGAGAGGCACAC 60.946 60.000 0.00 0.00 0.00 3.82
255 298 2.222027 AGAAGCACAACTCGAAAAGGG 58.778 47.619 0.00 0.00 0.00 3.95
262 305 3.011818 ACAACTCGAAAAGGGAAAACGT 58.988 40.909 0.00 0.00 0.00 3.99
281 324 3.119637 ACGTGTTTGTTTTTCCTCCACAG 60.120 43.478 0.00 0.00 0.00 3.66
300 343 3.502211 ACAGAGGTACAATTTTGCTTCCG 59.498 43.478 0.00 0.00 0.00 4.30
306 349 1.606668 ACAATTTTGCTTCCGCGAGAA 59.393 42.857 8.23 8.88 39.65 2.87
308 351 2.331809 ATTTTGCTTCCGCGAGAAAC 57.668 45.000 8.23 5.72 39.65 2.78
315 358 0.934496 TTCCGCGAGAAACACAACTG 59.066 50.000 8.23 0.00 0.00 3.16
321 364 4.523813 CGCGAGAAACACAACTGTAAAAT 58.476 39.130 0.00 0.00 0.00 1.82
322 365 4.967575 CGCGAGAAACACAACTGTAAAATT 59.032 37.500 0.00 0.00 0.00 1.82
323 366 5.454232 CGCGAGAAACACAACTGTAAAATTT 59.546 36.000 0.00 0.00 0.00 1.82
324 367 6.629649 CGCGAGAAACACAACTGTAAAATTTA 59.370 34.615 0.00 0.00 0.00 1.40
393 437 9.569167 TTACAAATTCGTTACATTTTGTGAACA 57.431 25.926 13.72 0.00 41.13 3.18
394 438 8.114359 ACAAATTCGTTACATTTTGTGAACAG 57.886 30.769 6.53 0.00 39.94 3.16
411 464 1.001633 ACAGTTTTACAGATCCGCGGT 59.998 47.619 27.15 12.96 0.00 5.68
447 500 7.032580 AGTCGTGAACATTTTGTTGAATTCAA 58.967 30.769 16.91 16.91 41.28 2.69
448 501 7.706179 AGTCGTGAACATTTTGTTGAATTCAAT 59.294 29.630 23.05 5.30 41.28 2.57
449 502 8.327429 GTCGTGAACATTTTGTTGAATTCAATT 58.673 29.630 23.05 11.75 41.28 2.32
451 504 8.935941 CGTGAACATTTTGTTGAATTCAATTTG 58.064 29.630 23.05 16.87 41.28 2.32
771 3311 8.707839 TGAAATTCCGAACATTTTTAATGAAGC 58.292 29.630 6.42 0.00 0.00 3.86
893 3436 1.461911 GGGTCGGGGAATAGGAGTCG 61.462 65.000 0.00 0.00 0.00 4.18
983 3527 4.716977 GGTCCCCGTCCAGGTCCT 62.717 72.222 0.00 0.00 38.74 3.85
1102 3652 3.866582 GTCCCCAGATCCCCGCTG 61.867 72.222 0.00 0.00 0.00 5.18
1259 3809 2.677228 CCCCATCTTTGCCGTCCT 59.323 61.111 0.00 0.00 0.00 3.85
1288 3838 4.041049 GTGCTCGTGAGATTGTCTAGATG 58.959 47.826 0.00 0.00 40.84 2.90
1342 3898 5.610398 ACCGATGCACATGATTCTTGTATA 58.390 37.500 0.00 0.00 0.00 1.47
1343 3899 5.698089 ACCGATGCACATGATTCTTGTATAG 59.302 40.000 0.00 0.00 0.00 1.31
1344 3900 5.698089 CCGATGCACATGATTCTTGTATAGT 59.302 40.000 0.00 0.00 0.00 2.12
1345 3901 6.868339 CCGATGCACATGATTCTTGTATAGTA 59.132 38.462 0.00 0.00 0.00 1.82
1346 3902 7.148738 CCGATGCACATGATTCTTGTATAGTAC 60.149 40.741 0.00 0.00 0.00 2.73
1347 3903 7.596621 CGATGCACATGATTCTTGTATAGTACT 59.403 37.037 0.00 0.00 0.00 2.73
1348 3904 8.824159 ATGCACATGATTCTTGTATAGTACTC 57.176 34.615 0.00 0.00 0.00 2.59
1349 3905 7.210174 TGCACATGATTCTTGTATAGTACTCC 58.790 38.462 0.00 0.00 0.00 3.85
1350 3906 7.069950 TGCACATGATTCTTGTATAGTACTCCT 59.930 37.037 0.00 0.00 0.00 3.69
1388 3944 1.627864 GCCCTGGTTAACATGTGGTT 58.372 50.000 8.10 0.00 43.62 3.67
1421 3977 1.291459 ATGTGGGGCCATGAGGATGT 61.291 55.000 4.39 0.00 36.89 3.06
1449 4005 2.993899 GTGTCGTTTCGTCTGATCCAAT 59.006 45.455 0.00 0.00 0.00 3.16
1550 4106 4.344968 GGCAGTTCCCCTATTTGCATAATT 59.655 41.667 0.00 0.00 36.53 1.40
1560 4116 6.429692 CCCTATTTGCATAATTATCGGTGTCA 59.570 38.462 0.00 0.00 0.00 3.58
1578 4134 2.749621 GTCATGGTCTCGGCAATTTCTT 59.250 45.455 0.00 0.00 0.00 2.52
1579 4135 3.009723 TCATGGTCTCGGCAATTTCTTC 58.990 45.455 0.00 0.00 0.00 2.87
1580 4136 2.859165 TGGTCTCGGCAATTTCTTCT 57.141 45.000 0.00 0.00 0.00 2.85
1581 4137 3.140325 TGGTCTCGGCAATTTCTTCTT 57.860 42.857 0.00 0.00 0.00 2.52
1599 4155 9.787435 TTTCTTCTTACCTAGCATTTAACTGAA 57.213 29.630 0.00 0.00 0.00 3.02
1619 4175 6.208599 ACTGAAAAACAACCATGGTATACCTG 59.791 38.462 20.12 14.95 36.82 4.00
1620 4176 5.047660 TGAAAAACAACCATGGTATACCTGC 60.048 40.000 20.12 6.98 36.82 4.85
1681 4237 7.916552 TGTTTAGCTTAAGAACTCAACAGAAC 58.083 34.615 6.67 0.00 29.27 3.01
1734 4290 3.289407 AGGGGATAAGAAAGAGCAAGC 57.711 47.619 0.00 0.00 0.00 4.01
1739 4295 4.886489 GGGATAAGAAAGAGCAAGCATCTT 59.114 41.667 0.00 1.87 38.65 2.40
1799 4355 6.331369 CCTTTTAGAAGAAACAAGGCATCA 57.669 37.500 0.00 0.00 34.71 3.07
1867 4423 1.888436 CTCTAGCCAACCGAGCACCA 61.888 60.000 0.00 0.00 0.00 4.17
1886 4442 4.752101 CACCACTCGTTTCTCAGAAAGAAT 59.248 41.667 0.00 0.00 43.50 2.40
1907 4463 2.292267 GAGTACCAATGGGCTGACATG 58.708 52.381 3.55 0.00 37.90 3.21
1922 4478 4.136796 CTGACATGAAGGTTGAGGTCAAA 58.863 43.478 0.00 0.00 37.63 2.69
1940 4496 7.060421 AGGTCAAACTCCAAAATCAGAAAGTA 58.940 34.615 0.00 0.00 0.00 2.24
2190 4829 3.487372 AGCCTTTAGTCCCAAACAAGTC 58.513 45.455 0.00 0.00 0.00 3.01
2218 4857 4.561752 AGGCTAGATCTGAAACCCATAGT 58.438 43.478 5.18 0.00 0.00 2.12
2223 4862 7.363443 GGCTAGATCTGAAACCCATAGTATCTC 60.363 44.444 5.18 0.00 0.00 2.75
2261 4900 2.507058 TCTGGTGATAGCAAGCTTCCAT 59.493 45.455 0.00 0.00 0.00 3.41
2270 4909 0.034186 CAAGCTTCCATGCACCCCTA 60.034 55.000 0.00 0.00 34.99 3.53
2273 4912 0.538287 GCTTCCATGCACCCCTATCC 60.538 60.000 0.00 0.00 0.00 2.59
2328 4967 9.434420 CCTTCAGATCTCTATTTGATTGGATAC 57.566 37.037 0.00 0.00 29.35 2.24
2497 5136 1.586154 CGTCTCACCCATGGTTTGGC 61.586 60.000 11.73 0.00 44.97 4.52
2508 5147 1.464734 TGGTTTGGCGTGAAAGTGAA 58.535 45.000 0.00 0.00 0.00 3.18
2639 5280 2.278332 AAGAGCCCCTGAAAGAACAC 57.722 50.000 0.00 0.00 34.07 3.32
2658 5299 3.117926 ACACTACCATGCATAGATTGGCA 60.118 43.478 0.00 0.00 45.23 4.92
2731 5372 2.675844 GCATTATGTAACTGCGTGACCA 59.324 45.455 0.00 0.00 0.00 4.02
3083 5724 3.076621 TCTGCATGTGCTCCAACTTAAG 58.923 45.455 6.55 0.00 42.66 1.85
3128 5769 6.594788 AAAAACATGGTGATAGTTCTGCAT 57.405 33.333 0.00 0.00 0.00 3.96
3129 5770 7.701539 AAAAACATGGTGATAGTTCTGCATA 57.298 32.000 0.00 0.00 0.00 3.14
3130 5771 7.701539 AAAACATGGTGATAGTTCTGCATAA 57.298 32.000 0.00 0.00 0.00 1.90
3131 5772 6.932356 AACATGGTGATAGTTCTGCATAAG 57.068 37.500 0.00 0.00 0.00 1.73
3132 5773 6.239217 ACATGGTGATAGTTCTGCATAAGA 57.761 37.500 0.00 0.00 0.00 2.10
3133 5774 6.051717 ACATGGTGATAGTTCTGCATAAGAC 58.948 40.000 0.00 0.00 33.46 3.01
3134 5775 5.023533 TGGTGATAGTTCTGCATAAGACC 57.976 43.478 0.00 0.00 33.46 3.85
3135 5776 4.716784 TGGTGATAGTTCTGCATAAGACCT 59.283 41.667 0.00 0.00 33.46 3.85
3136 5777 5.189736 TGGTGATAGTTCTGCATAAGACCTT 59.810 40.000 0.00 0.00 33.46 3.50
3137 5778 6.116126 GGTGATAGTTCTGCATAAGACCTTT 58.884 40.000 0.00 0.00 33.46 3.11
3138 5779 6.037610 GGTGATAGTTCTGCATAAGACCTTTG 59.962 42.308 0.00 0.00 33.46 2.77
3139 5780 6.037610 GTGATAGTTCTGCATAAGACCTTTGG 59.962 42.308 0.00 0.00 33.46 3.28
3140 5781 4.373156 AGTTCTGCATAAGACCTTTGGT 57.627 40.909 0.00 0.00 39.44 3.67
3141 5782 4.729868 AGTTCTGCATAAGACCTTTGGTT 58.270 39.130 0.00 0.00 35.25 3.67
3142 5783 4.762251 AGTTCTGCATAAGACCTTTGGTTC 59.238 41.667 0.00 0.00 35.25 3.62
3143 5784 4.365514 TCTGCATAAGACCTTTGGTTCA 57.634 40.909 0.00 0.00 35.25 3.18
3144 5785 4.922206 TCTGCATAAGACCTTTGGTTCAT 58.078 39.130 0.00 0.00 35.25 2.57
3145 5786 6.061022 TCTGCATAAGACCTTTGGTTCATA 57.939 37.500 0.00 0.00 35.25 2.15
3146 5787 6.115446 TCTGCATAAGACCTTTGGTTCATAG 58.885 40.000 0.00 0.00 35.25 2.23
3147 5788 5.192927 TGCATAAGACCTTTGGTTCATAGG 58.807 41.667 3.44 3.44 38.30 2.57
3148 5789 5.045213 TGCATAAGACCTTTGGTTCATAGGA 60.045 40.000 10.54 0.00 36.36 2.94
3149 5790 6.064717 GCATAAGACCTTTGGTTCATAGGAT 58.935 40.000 10.54 1.34 36.36 3.24
3150 5791 7.147391 TGCATAAGACCTTTGGTTCATAGGATA 60.147 37.037 10.54 3.06 36.36 2.59
3151 5792 7.885399 GCATAAGACCTTTGGTTCATAGGATAT 59.115 37.037 10.54 4.74 36.36 1.63
3152 5793 9.224267 CATAAGACCTTTGGTTCATAGGATATG 57.776 37.037 10.54 10.80 36.36 1.78
3153 5794 7.451731 AAGACCTTTGGTTCATAGGATATGA 57.548 36.000 10.54 0.00 36.36 2.15
3154 5795 7.639062 AGACCTTTGGTTCATAGGATATGAT 57.361 36.000 10.54 0.00 36.36 2.45
3155 5796 8.050316 AGACCTTTGGTTCATAGGATATGATT 57.950 34.615 10.54 0.00 36.36 2.57
3156 5797 9.170890 AGACCTTTGGTTCATAGGATATGATTA 57.829 33.333 10.54 0.00 36.36 1.75
3157 5798 9.965902 GACCTTTGGTTCATAGGATATGATTAT 57.034 33.333 10.54 0.00 36.36 1.28
3158 5799 9.965902 ACCTTTGGTTCATAGGATATGATTATC 57.034 33.333 10.54 0.00 36.36 1.75
3159 5800 9.964354 CCTTTGGTTCATAGGATATGATTATCA 57.036 33.333 0.00 0.00 35.14 2.15
3334 5975 1.996191 GTTGTGGCGTTTCTTTGCAAA 59.004 42.857 12.14 12.14 0.00 3.68
3363 6004 5.750352 ACCGTATCCTTCTAAAAGAACCA 57.250 39.130 0.00 0.00 34.14 3.67
3396 6037 4.624913 TCTATATCCTAGGCTCCCCATTG 58.375 47.826 2.96 0.00 0.00 2.82
3482 6123 8.342634 TGCTTCTTCTACAGTTTTTATTGTGAC 58.657 33.333 0.00 0.00 0.00 3.67
3652 6293 0.813610 CCAGCGTTCTGTTCACACCA 60.814 55.000 0.00 0.00 38.66 4.17
3694 6335 8.671384 AGTTAACAGACTGCTTTGTTACATTA 57.329 30.769 8.61 0.00 38.94 1.90
3969 6610 8.739972 ACTTTCACACTAGTTTTGAGAATTGTT 58.260 29.630 0.00 0.00 0.00 2.83
4403 7047 1.021390 CCATGACTCGAGGCAACACC 61.021 60.000 27.74 0.93 41.41 4.16
4576 7220 3.304911 TGGACACCATCTGGACAAAAA 57.695 42.857 2.55 0.00 38.94 1.94
4585 7229 4.218200 CCATCTGGACAAAAACAGTGCATA 59.782 41.667 0.00 0.00 36.72 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.642429 AGAAGCAAATTTGTACCTCTCGT 58.358 39.130 19.03 0.00 0.00 4.18
88 89 1.150536 TGGAAGTGAACCTGTGCCC 59.849 57.895 0.00 0.00 0.00 5.36
219 261 2.248487 CTTCTCGCAAAAGAAGCATGC 58.752 47.619 10.51 10.51 44.13 4.06
252 295 4.020928 AGGAAAAACAAACACGTTTTCCCT 60.021 37.500 17.77 10.31 45.57 4.20
255 298 4.924462 TGGAGGAAAAACAAACACGTTTTC 59.076 37.500 2.56 0.00 45.85 2.29
262 305 4.981806 CTCTGTGGAGGAAAAACAAACA 57.018 40.909 0.00 0.00 36.03 2.83
300 343 6.806120 AAATTTTACAGTTGTGTTTCTCGC 57.194 33.333 0.00 0.00 38.19 5.03
387 431 3.423123 CGCGGATCTGTAAAACTGTTCAC 60.423 47.826 0.00 0.00 0.00 3.18
391 435 1.001633 ACCGCGGATCTGTAAAACTGT 59.998 47.619 35.90 0.00 0.00 3.55
392 436 1.659098 GACCGCGGATCTGTAAAACTG 59.341 52.381 35.90 0.00 0.00 3.16
393 437 1.274167 TGACCGCGGATCTGTAAAACT 59.726 47.619 35.90 3.54 0.00 2.66
394 438 1.717194 TGACCGCGGATCTGTAAAAC 58.283 50.000 35.90 9.52 0.00 2.43
426 479 9.771915 ACAAATTGAATTCAACAAAATGTTCAC 57.228 25.926 22.71 0.00 38.77 3.18
554 607 4.568152 AAAAACGTTCATGGGTTCTGAG 57.432 40.909 0.00 0.00 0.00 3.35
582 635 6.741448 TTTCGAATTTGGAAAACATTCGTC 57.259 33.333 11.94 0.00 46.09 4.20
733 3273 6.531948 TGTTCGGAATTTCAAACAAAAATCGT 59.468 30.769 11.83 0.00 0.00 3.73
751 3291 8.425577 TTTTTGCTTCATTAAAAATGTTCGGA 57.574 26.923 0.00 0.00 32.57 4.55
799 3341 1.152839 GGGCGCCCCTGCTTTTATA 60.153 57.895 36.64 0.00 41.34 0.98
852 3394 0.955905 GCGGTGGAAAGCAAGGTAAA 59.044 50.000 0.00 0.00 0.00 2.01
893 3436 1.352687 GGGATGGATAGAGAAAGGGGC 59.647 57.143 0.00 0.00 0.00 5.80
1020 3564 3.842925 TTGGCGTTGGAGAGGTGCC 62.843 63.158 0.00 0.00 45.91 5.01
1028 3572 0.036732 AAGAGATGCTTGGCGTTGGA 59.963 50.000 0.00 0.00 34.93 3.53
1151 3701 2.125512 CGGAGCCGTGGAAGAAGG 60.126 66.667 0.00 0.00 34.35 3.46
1255 3805 2.179517 CGAGCACCGTCTCAGGAC 59.820 66.667 0.00 0.00 38.97 3.85
1288 3838 6.409524 TCTCTACTCTCTACCAGTAGTAGC 57.590 45.833 4.81 0.00 46.98 3.58
1342 3898 8.962679 GCTGTAATCTAAGCATATAGGAGTACT 58.037 37.037 0.00 0.00 39.31 2.73
1343 3899 7.911205 CGCTGTAATCTAAGCATATAGGAGTAC 59.089 40.741 0.00 0.00 39.47 2.73
1344 3900 7.415318 GCGCTGTAATCTAAGCATATAGGAGTA 60.415 40.741 0.00 0.00 39.47 2.59
1345 3901 6.626181 GCGCTGTAATCTAAGCATATAGGAGT 60.626 42.308 0.00 0.00 39.47 3.85
1346 3902 5.746245 GCGCTGTAATCTAAGCATATAGGAG 59.254 44.000 0.00 0.00 39.47 3.69
1347 3903 5.394224 GGCGCTGTAATCTAAGCATATAGGA 60.394 44.000 7.64 0.00 39.47 2.94
1348 3904 4.806247 GGCGCTGTAATCTAAGCATATAGG 59.194 45.833 7.64 0.00 39.47 2.57
1349 3905 4.806247 GGGCGCTGTAATCTAAGCATATAG 59.194 45.833 7.64 0.00 39.47 1.31
1350 3906 4.466370 AGGGCGCTGTAATCTAAGCATATA 59.534 41.667 7.64 0.00 39.47 0.86
1365 3921 0.960364 ACATGTTAACCAGGGCGCTG 60.960 55.000 23.12 23.12 0.00 5.18
1404 3960 1.152881 GACATCCTCATGGCCCCAC 60.153 63.158 0.00 0.00 30.62 4.61
1421 3977 4.800784 TCAGACGAAACGACACATATTGA 58.199 39.130 0.00 0.00 0.00 2.57
1449 4005 1.180456 CCACACCAGCAGCAATCCAA 61.180 55.000 0.00 0.00 0.00 3.53
1459 4015 3.177997 ACAAAATCAAACCACACCAGC 57.822 42.857 0.00 0.00 0.00 4.85
1460 4016 6.568869 TCTAAACAAAATCAAACCACACCAG 58.431 36.000 0.00 0.00 0.00 4.00
1500 4056 2.372264 TGCATTCTGCCAATTCCTCTC 58.628 47.619 0.00 0.00 44.23 3.20
1550 4106 1.029681 CCGAGACCATGACACCGATA 58.970 55.000 0.00 0.00 0.00 2.92
1560 4116 3.356529 AGAAGAAATTGCCGAGACCAT 57.643 42.857 0.00 0.00 0.00 3.55
1578 4134 9.344772 TGTTTTTCAGTTAAATGCTAGGTAAGA 57.655 29.630 0.00 0.00 0.00 2.10
1579 4135 9.959749 TTGTTTTTCAGTTAAATGCTAGGTAAG 57.040 29.630 0.00 0.00 0.00 2.34
1580 4136 9.738832 GTTGTTTTTCAGTTAAATGCTAGGTAA 57.261 29.630 0.00 0.00 0.00 2.85
1581 4137 8.354426 GGTTGTTTTTCAGTTAAATGCTAGGTA 58.646 33.333 0.00 0.00 0.00 3.08
1599 4155 3.442273 CGCAGGTATACCATGGTTGTTTT 59.558 43.478 25.38 3.77 38.89 2.43
1603 4159 0.944386 GCGCAGGTATACCATGGTTG 59.056 55.000 25.38 15.98 38.89 3.77
1619 4175 1.272781 GCATATAGATCGGACAGCGC 58.727 55.000 0.00 0.00 0.00 5.92
1620 4176 2.636768 TGCATATAGATCGGACAGCG 57.363 50.000 0.00 0.00 0.00 5.18
1671 4227 1.986378 CGGTAGCTTCGTTCTGTTGAG 59.014 52.381 0.00 0.00 0.00 3.02
1681 4237 4.749099 ACAGTATAGTACTCGGTAGCTTCG 59.251 45.833 0.00 0.00 36.76 3.79
1747 4303 1.781786 GAGCTAGTCTCCATGGGTCA 58.218 55.000 13.02 0.00 35.77 4.02
1816 4372 1.373748 GCTTACTCACCCGCGTTCA 60.374 57.895 4.92 0.00 0.00 3.18
1828 4384 2.296471 AGCACACGTCTGTAAGCTTACT 59.704 45.455 31.14 12.87 34.79 2.24
1867 4423 5.848406 ACTCATTCTTTCTGAGAAACGAGT 58.152 37.500 3.02 10.26 46.90 4.18
1872 4428 7.391554 CCATTGGTACTCATTCTTTCTGAGAAA 59.608 37.037 7.49 7.49 46.90 2.52
1886 4442 1.357137 TGTCAGCCCATTGGTACTCA 58.643 50.000 1.20 0.00 0.00 3.41
1907 4463 3.208747 TGGAGTTTGACCTCAACCTTC 57.791 47.619 0.00 0.00 35.28 3.46
1922 4478 8.912988 TCAAATTGTACTTTCTGATTTTGGAGT 58.087 29.630 0.00 0.00 0.00 3.85
2190 4829 0.470080 TTCAGATCTAGCCTCCCCCG 60.470 60.000 0.00 0.00 0.00 5.73
2218 4857 2.905075 CCATGAGTTGGTTGCGAGATA 58.095 47.619 0.00 0.00 40.99 1.98
2245 4884 2.019249 GTGCATGGAAGCTTGCTATCA 58.981 47.619 19.34 10.43 39.60 2.15
2261 4900 0.401250 TAGCCATGGATAGGGGTGCA 60.401 55.000 18.40 0.00 39.12 4.57
2270 4909 3.266772 TCACCAAAGAACTAGCCATGGAT 59.733 43.478 18.40 13.25 0.00 3.41
2273 4912 5.431765 AGTATCACCAAAGAACTAGCCATG 58.568 41.667 0.00 0.00 0.00 3.66
2497 5136 2.802816 CCTTCCTCAGTTCACTTTCACG 59.197 50.000 0.00 0.00 0.00 4.35
2508 5147 1.302285 CTGCATGGCCTTCCTCAGT 59.698 57.895 3.32 0.00 0.00 3.41
2713 5354 3.932822 ACATGGTCACGCAGTTACATAA 58.067 40.909 0.00 0.00 41.61 1.90
2731 5372 5.256474 AGCACCTTAATTAGCTCACAACAT 58.744 37.500 0.00 0.00 30.05 2.71
2832 5473 7.073208 ACCCTTTTATTTCTGGGAAGAAAAGA 58.927 34.615 17.80 0.00 44.49 2.52
3047 5688 1.251251 GCAGAGGAAGGCAACAACAT 58.749 50.000 0.00 0.00 41.41 2.71
3128 5769 8.561536 TCATATCCTATGAACCAAAGGTCTTA 57.438 34.615 0.00 0.00 33.12 2.10
3129 5770 7.451731 TCATATCCTATGAACCAAAGGTCTT 57.548 36.000 0.00 0.00 33.12 3.01
3130 5771 7.639062 ATCATATCCTATGAACCAAAGGTCT 57.361 36.000 1.28 0.00 33.12 3.85
3131 5772 9.965902 ATAATCATATCCTATGAACCAAAGGTC 57.034 33.333 1.28 0.00 33.12 3.85
3132 5773 9.965902 GATAATCATATCCTATGAACCAAAGGT 57.034 33.333 1.28 0.00 33.18 3.50
3133 5774 9.964354 TGATAATCATATCCTATGAACCAAAGG 57.036 33.333 1.28 0.00 37.68 3.11
3154 5795 9.667107 CCAGTTAGTTTTCTGTTCCTATGATAA 57.333 33.333 0.00 0.00 0.00 1.75
3155 5796 8.822805 ACCAGTTAGTTTTCTGTTCCTATGATA 58.177 33.333 0.00 0.00 0.00 2.15
3156 5797 7.690256 ACCAGTTAGTTTTCTGTTCCTATGAT 58.310 34.615 0.00 0.00 0.00 2.45
3157 5798 7.074653 ACCAGTTAGTTTTCTGTTCCTATGA 57.925 36.000 0.00 0.00 0.00 2.15
3158 5799 7.745620 AACCAGTTAGTTTTCTGTTCCTATG 57.254 36.000 0.00 0.00 0.00 2.23
3161 5802 7.606839 GCTATAACCAGTTAGTTTTCTGTTCCT 59.393 37.037 0.00 0.00 0.00 3.36
3162 5803 7.606839 AGCTATAACCAGTTAGTTTTCTGTTCC 59.393 37.037 0.00 0.00 0.00 3.62
3163 5804 8.443937 CAGCTATAACCAGTTAGTTTTCTGTTC 58.556 37.037 0.00 0.00 0.00 3.18
3164 5805 7.094762 GCAGCTATAACCAGTTAGTTTTCTGTT 60.095 37.037 0.00 0.00 0.00 3.16
3165 5806 6.371825 GCAGCTATAACCAGTTAGTTTTCTGT 59.628 38.462 0.00 0.00 0.00 3.41
3166 5807 6.595716 AGCAGCTATAACCAGTTAGTTTTCTG 59.404 38.462 0.00 0.00 0.00 3.02
3167 5808 6.712276 AGCAGCTATAACCAGTTAGTTTTCT 58.288 36.000 0.00 0.00 0.00 2.52
3168 5809 6.986904 AGCAGCTATAACCAGTTAGTTTTC 57.013 37.500 0.00 0.00 0.00 2.29
3169 5810 8.857694 TTTAGCAGCTATAACCAGTTAGTTTT 57.142 30.769 2.02 0.00 0.00 2.43
3170 5811 8.101419 ACTTTAGCAGCTATAACCAGTTAGTTT 58.899 33.333 2.02 0.00 0.00 2.66
3171 5812 7.621796 ACTTTAGCAGCTATAACCAGTTAGTT 58.378 34.615 2.02 0.00 0.00 2.24
3172 5813 7.184067 ACTTTAGCAGCTATAACCAGTTAGT 57.816 36.000 2.02 0.00 0.00 2.24
3173 5814 9.197694 CATACTTTAGCAGCTATAACCAGTTAG 57.802 37.037 2.02 0.00 0.00 2.34
3396 6037 5.104374 CACATTAATTGGGCACATTCTGAC 58.896 41.667 0.00 0.00 0.00 3.51
3482 6123 0.967887 TCTGCTCTCGAGTGAAGGGG 60.968 60.000 19.91 0.00 0.00 4.79
3493 6134 9.719279 CAAGAAAAATTCTTCATATCTGCTCTC 57.281 33.333 2.47 0.00 46.62 3.20
3652 6293 9.295825 TCTGTTAACTTGATAATCCAAACACAT 57.704 29.630 7.22 0.00 0.00 3.21
3694 6335 9.791801 AAACTTTATGGTTGGAGCATTAAAAAT 57.208 25.926 0.00 0.00 37.51 1.82
3697 6338 8.207545 ACAAAACTTTATGGTTGGAGCATTAAA 58.792 29.630 0.00 0.00 37.51 1.52
3884 6525 5.528043 TTACGTACAAACAGGTGGTAAGA 57.472 39.130 0.00 0.00 0.00 2.10
3969 6610 4.074627 TGGTATGGTCGTTGACTCAAAA 57.925 40.909 0.00 0.00 32.47 2.44
4403 7047 5.068591 AGGCTTGTTTTTAGGTGTTAGGTTG 59.931 40.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.