Multiple sequence alignment - TraesCS2B01G404800

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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 TraesCS2B01G404800 chr2B 100.000 4039 0 0 1 4039 572707421 572703383 0.000000e+00 7459
1 TraesCS2B01G404800 chr2B 85.862 1832 181 37 1949 3773 133980073 133981833 0.000000e+00 1877
2 TraesCS2B01G404800 chr2B 85.906 1270 91 37 604 1805 133978668 133979917 0.000000e+00 1273
3 TraesCS2B01G404800 chr2B 89.044 1004 73 13 922 1888 531129411 531130414 0.000000e+00 1210
4 TraesCS2B01G404800 chr2B 95.935 246 9 1 3794 4038 572695679 572695434 8.130000e-107 398
5 TraesCS2B01G404800 chr2B 95.122 246 12 0 3794 4039 29665187 29665432 4.900000e-104 388
6 TraesCS2B01G404800 chr2B 95.142 247 10 2 3794 4038 799125960 799126206 4.900000e-104 388
7 TraesCS2B01G404800 chr2B 87.043 301 36 3 2118 2415 531131194 531131494 1.800000e-88 337
8 TraesCS2B01G404800 chr2B 88.889 144 12 3 1 140 133948411 133948554 1.490000e-39 174
9 TraesCS2B01G404800 chr2B 94.624 93 5 0 1 93 572756741 572756649 1.170000e-30 145
10 TraesCS2B01G404800 chr2B 96.053 76 2 1 1844 1918 133979914 133979989 5.480000e-24 122
11 TraesCS2B01G404800 chr2D 95.259 3206 109 22 533 3733 489371390 489368223 0.000000e+00 5038
12 TraesCS2B01G404800 chr2D 96.158 3019 99 9 770 3773 488555022 488552006 0.000000e+00 4916
13 TraesCS2B01G404800 chr2D 94.863 2453 94 5 1352 3773 488455085 488452634 0.000000e+00 3803
14 TraesCS2B01G404800 chr2D 86.134 1803 169 37 1949 3743 82143569 82145298 0.000000e+00 1869
15 TraesCS2B01G404800 chr2D 89.492 1399 84 29 604 1953 82142131 82143515 0.000000e+00 1711
16 TraesCS2B01G404800 chr2D 84.542 1365 156 35 2434 3773 450992708 450994042 0.000000e+00 1301
17 TraesCS2B01G404800 chr2D 89.044 1004 73 13 922 1888 450990588 450991591 0.000000e+00 1210
18 TraesCS2B01G404800 chr2D 94.351 478 20 6 1 474 489371919 489371445 0.000000e+00 726
19 TraesCS2B01G404800 chr2D 97.647 340 7 1 988 1327 488455409 488455071 2.090000e-162 582
20 TraesCS2B01G404800 chr2D 83.051 472 56 13 1959 2415 450992179 450992641 1.350000e-109 407
21 TraesCS2B01G404800 chr2D 81.638 403 50 11 83 470 488464473 488464080 3.030000e-81 313
22 TraesCS2B01G404800 chr2D 88.462 260 19 3 146 394 488555511 488555252 1.820000e-78 303
23 TraesCS2B01G404800 chr2D 82.569 327 40 4 20 329 82140170 82140496 5.140000e-69 272
24 TraesCS2B01G404800 chr2D 82.578 287 46 3 2437 2719 450984838 450985124 2.410000e-62 250
25 TraesCS2B01G404800 chr2D 94.805 154 8 0 1 154 488470220 488470067 1.450000e-59 241
26 TraesCS2B01G404800 chr2D 88.205 195 22 1 1 194 489380124 489379930 8.730000e-57 231
27 TraesCS2B01G404800 chr2D 93.960 149 6 2 1 147 488555752 488555605 5.250000e-54 222
28 TraesCS2B01G404800 chr2D 89.937 159 6 5 4 155 82139732 82139887 3.180000e-46 196
29 TraesCS2B01G404800 chr2D 93.077 130 9 0 3604 3733 489368218 489368089 1.480000e-44 191
30 TraesCS2B01G404800 chr2D 80.952 147 25 1 12 155 82139958 82140104 3.300000e-21 113
31 TraesCS2B01G404800 chr2A 86.572 1199 128 22 2434 3610 598621591 598620404 0.000000e+00 1291
32 TraesCS2B01G404800 chr2A 90.811 925 65 8 987 1891 598623590 598622666 0.000000e+00 1219
33 TraesCS2B01G404800 chr2A 83.263 472 55 14 1959 2415 598622120 598621658 2.900000e-111 412
34 TraesCS2B01G404800 chr2A 77.428 381 37 19 572 925 598624062 598623704 8.920000e-42 182
35 TraesCS2B01G404800 chr5B 96.721 244 7 1 3794 4036 256231662 256231905 4.860000e-109 405
36 TraesCS2B01G404800 chr5B 95.547 247 9 2 3794 4038 434466991 434467237 1.050000e-105 394
37 TraesCS2B01G404800 chr1B 95.547 247 9 2 3794 4038 330552617 330552371 1.050000e-105 394
38 TraesCS2B01G404800 chr1B 95.142 247 11 1 3794 4039 361858693 361858939 4.900000e-104 388
39 TraesCS2B01G404800 chr1B 95.122 246 11 1 3794 4038 253893282 253893037 1.760000e-103 387
40 TraesCS2B01G404800 chr1B 95.102 245 12 0 3794 4038 253948554 253948310 1.760000e-103 387
41 TraesCS2B01G404800 chr3D 75.197 508 104 20 1253 1749 390658593 390659089 1.890000e-53 220


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 TraesCS2B01G404800 chr2B 572703383 572707421 4038 True 7459.000000 7459 100.000000 1 4039 1 chr2B.!!$R2 4038
1 TraesCS2B01G404800 chr2B 133978668 133981833 3165 False 1090.666667 1877 89.273667 604 3773 3 chr2B.!!$F4 3169
2 TraesCS2B01G404800 chr2B 531129411 531131494 2083 False 773.500000 1210 88.043500 922 2415 2 chr2B.!!$F5 1493
3 TraesCS2B01G404800 chr2D 488452634 488455409 2775 True 2192.500000 3803 96.255000 988 3773 2 chr2D.!!$R4 2785
4 TraesCS2B01G404800 chr2D 489368089 489371919 3830 True 1985.000000 5038 94.229000 1 3733 3 chr2D.!!$R6 3732
5 TraesCS2B01G404800 chr2D 488552006 488555752 3746 True 1813.666667 4916 92.860000 1 3773 3 chr2D.!!$R5 3772
6 TraesCS2B01G404800 chr2D 450990588 450994042 3454 False 972.666667 1301 85.545667 922 3773 3 chr2D.!!$F3 2851
7 TraesCS2B01G404800 chr2D 82139732 82145298 5566 False 832.200000 1869 85.816800 4 3743 5 chr2D.!!$F2 3739
8 TraesCS2B01G404800 chr2A 598620404 598624062 3658 True 776.000000 1291 84.518500 572 3610 4 chr2A.!!$R1 3038

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
776 2705 1.602377 GGAAGCAATTTCGATACCCCG 59.398 52.381 0.0 0.0 36.62 5.73 F
2102 4823 0.820226 TCTCACTCGCTGATTCCAGG 59.180 55.000 0.0 0.0 40.72 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 5065 1.230281 AGGGAGGCTGGGAATGGAA 60.230 57.895 0.0 0.0 0.0 3.53 R
3891 6718 0.034477 AAATCCCCAATTCGCTCCGT 60.034 50.000 0.0 0.0 0.0 4.69 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
64 65 2.711922 CGGTGAAGGAGAGGACCCG 61.712 68.421 0.00 0.00 0.00 5.28
271 708 6.734137 TGTTTGGTCTTTGTTGTGATACATC 58.266 36.000 0.00 0.00 0.00 3.06
308 754 7.820872 GCAGTATGTAGAGGGTTAAAGTACAAA 59.179 37.037 0.00 0.00 39.31 2.83
364 1357 2.652590 AGGAGAATTACCTCGCGTACT 58.347 47.619 5.77 0.00 34.08 2.73
377 1370 4.083581 TCGCGTACTCAACTTAAGGTAC 57.916 45.455 5.77 8.30 33.42 3.34
483 2065 6.514947 TCTAAGCCACGTCTAAACAACTTTA 58.485 36.000 0.00 0.00 0.00 1.85
486 2068 5.997385 AGCCACGTCTAAACAACTTTAATG 58.003 37.500 0.00 0.00 0.00 1.90
489 2071 6.793680 GCCACGTCTAAACAACTTTAATGTAC 59.206 38.462 0.00 0.00 0.00 2.90
493 2075 9.101655 ACGTCTAAACAACTTTAATGTACTGTT 57.898 29.630 5.98 5.98 0.00 3.16
603 2391 3.016736 CCAGTGGCGTTTCATAGGAAAT 58.983 45.455 5.77 0.00 44.32 2.17
604 2392 3.065371 CCAGTGGCGTTTCATAGGAAATC 59.935 47.826 5.77 1.68 44.32 2.17
605 2393 3.065371 CAGTGGCGTTTCATAGGAAATCC 59.935 47.826 5.77 10.69 44.32 3.01
610 2398 4.421058 GCGTTTCATAGGAAATCCCAAAC 58.579 43.478 5.77 0.87 44.32 2.93
611 2399 4.082463 GCGTTTCATAGGAAATCCCAAACA 60.082 41.667 5.77 0.00 44.32 2.83
612 2400 5.394115 GCGTTTCATAGGAAATCCCAAACAT 60.394 40.000 5.77 0.00 44.32 2.71
614 2402 6.127758 CGTTTCATAGGAAATCCCAAACATGA 60.128 38.462 5.77 0.00 44.32 3.07
615 2403 7.260603 GTTTCATAGGAAATCCCAAACATGAG 58.739 38.462 5.77 0.00 44.32 2.90
766 2695 1.698506 TGTTCCACGGGAAGCAATTT 58.301 45.000 5.71 0.00 42.88 1.82
776 2705 1.602377 GGAAGCAATTTCGATACCCCG 59.398 52.381 0.00 0.00 36.62 5.73
795 2724 3.581755 CCGTCTTCCATTTCGTGTTCTA 58.418 45.455 0.00 0.00 0.00 2.10
805 2734 5.120208 CCATTTCGTGTTCTATGTTCTTCGT 59.880 40.000 0.00 0.00 0.00 3.85
910 2852 3.305608 GCCCTTGCAAGCAATATACATCC 60.306 47.826 21.43 0.00 37.47 3.51
918 2897 5.922544 GCAAGCAATATACATCCAAACCATC 59.077 40.000 0.00 0.00 0.00 3.51
1281 3288 1.667830 CACGGATGACAGCCACGTT 60.668 57.895 10.94 0.00 35.36 3.99
1660 3667 1.139654 CCATGCTGGGATCTTTCTCGA 59.860 52.381 0.00 0.00 32.67 4.04
1969 4620 8.891671 TTTGTGTACGTAGAGGAAATTAACTT 57.108 30.769 0.00 0.00 0.00 2.66
2055 4708 4.751098 CACTTTGGAACCATTGAACCATTG 59.249 41.667 0.00 0.00 32.31 2.82
2093 4751 6.166279 TCTTACATTGAATTTCTCACTCGCT 58.834 36.000 0.00 0.00 32.21 4.93
2102 4823 0.820226 TCTCACTCGCTGATTCCAGG 59.180 55.000 0.00 0.00 40.72 4.45
2219 4971 5.661056 TCGATATGAAGTCTGGTGAAACT 57.339 39.130 0.00 0.00 36.74 2.66
2635 5438 4.866486 GGCAATGAAAAGGCTTGTCAATAG 59.134 41.667 23.19 16.09 0.00 1.73
2682 5485 2.158957 ACAAGTGCCCATCGTATACCAG 60.159 50.000 0.00 0.00 0.00 4.00
2792 5601 0.764890 TGAGGCACAAGCAACTACCT 59.235 50.000 0.00 0.00 44.61 3.08
2843 5652 5.741962 TGAATGATCTTTTTGGCATCCAA 57.258 34.783 0.00 0.00 42.29 3.53
2980 5800 8.546597 AACAAATGTCAACTTGCTTTTTACTT 57.453 26.923 0.00 0.00 0.00 2.24
2981 5801 7.962917 ACAAATGTCAACTTGCTTTTTACTTG 58.037 30.769 0.00 0.00 0.00 3.16
2987 5807 6.972328 GTCAACTTGCTTTTTACTTGACATGA 59.028 34.615 0.00 0.00 38.15 3.07
3027 5850 4.821260 GCCATCACAAAATTTTCAGGGTTT 59.179 37.500 0.00 0.00 0.00 3.27
3030 5853 6.541641 CCATCACAAAATTTTCAGGGTTTCAA 59.458 34.615 0.00 0.00 0.00 2.69
3043 5866 1.200020 GGTTTCAATGGACTGAAGCCG 59.800 52.381 3.86 0.00 43.83 5.52
3123 5946 4.442052 CCTTTCTGCCATCGAGTTCATAGA 60.442 45.833 0.00 0.00 0.00 1.98
3236 6059 7.736691 ACATCATGAGGGAGGAATTATCTCTTA 59.263 37.037 12.66 0.00 0.00 2.10
3241 6064 6.013898 TGAGGGAGGAATTATCTCTTAGCATG 60.014 42.308 7.83 0.00 0.00 4.06
3304 6127 0.916086 TGATGGATAAGCCCGTGGTT 59.084 50.000 0.00 0.00 34.97 3.67
3324 6147 9.840427 CGTGGTTAATCATAAGAAGTTTCAAAT 57.160 29.630 0.00 0.00 0.00 2.32
3388 6211 8.753133 TCAGACATTAGTAATCAGATTGTCAGT 58.247 33.333 5.85 0.00 0.00 3.41
3659 6485 4.536364 ACACTTCTGTTTGTGTTGATCG 57.464 40.909 0.00 0.00 43.88 3.69
3761 6588 4.447724 GCATTCGTTACAGTGACTTGAGAA 59.552 41.667 0.00 0.00 0.00 2.87
3773 6600 9.566432 ACAGTGACTTGAGAATTTCTTTCTTAT 57.434 29.630 0.00 0.00 44.88 1.73
3774 6601 9.823098 CAGTGACTTGAGAATTTCTTTCTTATG 57.177 33.333 0.00 0.00 44.88 1.90
3775 6602 9.566432 AGTGACTTGAGAATTTCTTTCTTATGT 57.434 29.630 0.00 0.00 44.88 2.29
3784 6611 9.753674 AGAATTTCTTTCTTATGTAACATCCCA 57.246 29.630 0.00 0.00 42.15 4.37
3790 6617 8.748412 TCTTTCTTATGTAACATCCCAAATTGG 58.252 33.333 4.74 4.74 37.25 3.16
3791 6618 8.657387 TTTCTTATGTAACATCCCAAATTGGA 57.343 30.769 14.62 0.00 40.96 3.53
3792 6619 7.880160 TCTTATGTAACATCCCAAATTGGAG 57.120 36.000 14.62 5.60 40.96 3.86
3793 6620 7.638444 TCTTATGTAACATCCCAAATTGGAGA 58.362 34.615 14.62 9.50 40.96 3.71
3795 6622 8.837099 TTATGTAACATCCCAAATTGGAGAAT 57.163 30.769 14.62 1.19 40.96 2.40
3798 6625 7.610865 TGTAACATCCCAAATTGGAGAATTTC 58.389 34.615 14.62 6.95 40.96 2.17
3799 6626 5.682234 ACATCCCAAATTGGAGAATTTCC 57.318 39.130 14.62 1.09 46.98 3.13
3866 6693 9.603921 ATTTTATTGCATTTTGGTTGATCCTAG 57.396 29.630 0.00 0.00 37.07 3.02
3867 6694 7.953005 TTATTGCATTTTGGTTGATCCTAGA 57.047 32.000 0.00 0.00 37.07 2.43
3868 6695 6.855763 ATTGCATTTTGGTTGATCCTAGAA 57.144 33.333 0.00 0.00 37.07 2.10
3869 6696 6.662865 TTGCATTTTGGTTGATCCTAGAAA 57.337 33.333 0.00 0.00 37.07 2.52
3870 6697 6.855763 TGCATTTTGGTTGATCCTAGAAAT 57.144 33.333 0.00 0.00 37.07 2.17
3871 6698 7.243604 TGCATTTTGGTTGATCCTAGAAATT 57.756 32.000 0.00 0.00 37.07 1.82
3872 6699 7.322664 TGCATTTTGGTTGATCCTAGAAATTC 58.677 34.615 0.00 0.00 37.07 2.17
3873 6700 7.178983 TGCATTTTGGTTGATCCTAGAAATTCT 59.821 33.333 0.00 0.00 37.07 2.40
3874 6701 8.686334 GCATTTTGGTTGATCCTAGAAATTCTA 58.314 33.333 2.44 2.44 37.07 2.10
3877 6704 7.865706 TTGGTTGATCCTAGAAATTCTAAGC 57.134 36.000 4.13 0.85 37.07 3.09
3878 6705 6.957631 TGGTTGATCCTAGAAATTCTAAGCA 58.042 36.000 4.13 3.37 37.07 3.91
3879 6706 7.402054 TGGTTGATCCTAGAAATTCTAAGCAA 58.598 34.615 4.13 3.15 37.07 3.91
3880 6707 7.336931 TGGTTGATCCTAGAAATTCTAAGCAAC 59.663 37.037 19.50 19.50 37.07 4.17
3881 6708 7.554476 GGTTGATCCTAGAAATTCTAAGCAACT 59.446 37.037 23.47 2.93 32.48 3.16
3882 6709 8.608317 GTTGATCCTAGAAATTCTAAGCAACTC 58.392 37.037 20.02 7.60 31.04 3.01
3883 6710 7.851228 TGATCCTAGAAATTCTAAGCAACTCA 58.149 34.615 4.13 0.28 0.00 3.41
3884 6711 8.321353 TGATCCTAGAAATTCTAAGCAACTCAA 58.679 33.333 4.13 0.00 0.00 3.02
3885 6712 8.729805 ATCCTAGAAATTCTAAGCAACTCAAG 57.270 34.615 4.13 0.00 0.00 3.02
3886 6713 7.106239 TCCTAGAAATTCTAAGCAACTCAAGG 58.894 38.462 4.13 0.06 0.00 3.61
3887 6714 7.038302 TCCTAGAAATTCTAAGCAACTCAAGGA 60.038 37.037 4.13 2.41 0.00 3.36
3888 6715 6.809630 AGAAATTCTAAGCAACTCAAGGAC 57.190 37.500 0.00 0.00 0.00 3.85
3889 6716 5.707764 AGAAATTCTAAGCAACTCAAGGACC 59.292 40.000 0.00 0.00 0.00 4.46
3890 6717 3.418684 TTCTAAGCAACTCAAGGACCC 57.581 47.619 0.00 0.00 0.00 4.46
3891 6718 2.334977 TCTAAGCAACTCAAGGACCCA 58.665 47.619 0.00 0.00 0.00 4.51
3892 6719 2.038557 TCTAAGCAACTCAAGGACCCAC 59.961 50.000 0.00 0.00 0.00 4.61
3893 6720 0.535102 AAGCAACTCAAGGACCCACG 60.535 55.000 0.00 0.00 0.00 4.94
3894 6721 1.966451 GCAACTCAAGGACCCACGG 60.966 63.158 0.00 0.00 0.00 4.94
3895 6722 1.752198 CAACTCAAGGACCCACGGA 59.248 57.895 0.00 0.00 0.00 4.69
3896 6723 0.320771 CAACTCAAGGACCCACGGAG 60.321 60.000 0.00 0.00 0.00 4.63
3897 6724 2.113243 AACTCAAGGACCCACGGAGC 62.113 60.000 0.00 0.00 0.00 4.70
3898 6725 3.649277 CTCAAGGACCCACGGAGCG 62.649 68.421 0.00 0.00 0.00 5.03
3899 6726 3.691342 CAAGGACCCACGGAGCGA 61.691 66.667 0.00 0.00 0.00 4.93
3900 6727 2.920912 AAGGACCCACGGAGCGAA 60.921 61.111 0.00 0.00 0.00 4.70
3901 6728 2.291043 AAGGACCCACGGAGCGAAT 61.291 57.895 0.00 0.00 0.00 3.34
3902 6729 1.838073 AAGGACCCACGGAGCGAATT 61.838 55.000 0.00 0.00 0.00 2.17
3903 6730 2.106683 GGACCCACGGAGCGAATTG 61.107 63.158 0.00 0.00 0.00 2.32
3904 6731 2.046314 ACCCACGGAGCGAATTGG 60.046 61.111 0.00 0.00 0.00 3.16
3905 6732 2.824041 CCCACGGAGCGAATTGGG 60.824 66.667 2.56 2.56 42.92 4.12
3906 6733 2.824041 CCACGGAGCGAATTGGGG 60.824 66.667 0.00 0.00 0.00 4.96
3907 6734 2.267642 CACGGAGCGAATTGGGGA 59.732 61.111 0.00 0.00 0.00 4.81
3908 6735 1.153168 CACGGAGCGAATTGGGGAT 60.153 57.895 0.00 0.00 0.00 3.85
3909 6736 0.748005 CACGGAGCGAATTGGGGATT 60.748 55.000 0.00 0.00 0.00 3.01
3910 6737 0.034477 ACGGAGCGAATTGGGGATTT 60.034 50.000 0.00 0.00 0.00 2.17
3911 6738 0.663153 CGGAGCGAATTGGGGATTTC 59.337 55.000 0.00 0.00 0.00 2.17
3912 6739 0.663153 GGAGCGAATTGGGGATTTCG 59.337 55.000 1.00 1.00 0.00 3.46
3913 6740 1.379527 GAGCGAATTGGGGATTTCGT 58.620 50.000 6.88 0.00 0.00 3.85
3914 6741 1.743394 GAGCGAATTGGGGATTTCGTT 59.257 47.619 6.88 0.97 0.00 3.85
3915 6742 2.940410 GAGCGAATTGGGGATTTCGTTA 59.060 45.455 6.88 0.00 0.00 3.18
3916 6743 3.551846 AGCGAATTGGGGATTTCGTTAT 58.448 40.909 6.88 0.00 0.00 1.89
3917 6744 3.951680 AGCGAATTGGGGATTTCGTTATT 59.048 39.130 6.88 0.00 0.00 1.40
3918 6745 4.401202 AGCGAATTGGGGATTTCGTTATTT 59.599 37.500 6.88 0.00 0.00 1.40
3919 6746 5.105513 AGCGAATTGGGGATTTCGTTATTTT 60.106 36.000 6.88 0.00 0.00 1.82
3920 6747 5.231357 GCGAATTGGGGATTTCGTTATTTTC 59.769 40.000 6.88 0.00 0.00 2.29
3921 6748 6.326375 CGAATTGGGGATTTCGTTATTTTCA 58.674 36.000 0.00 0.00 0.00 2.69
3922 6749 6.978080 CGAATTGGGGATTTCGTTATTTTCAT 59.022 34.615 0.00 0.00 0.00 2.57
3923 6750 8.132362 CGAATTGGGGATTTCGTTATTTTCATA 58.868 33.333 0.00 0.00 0.00 2.15
3924 6751 9.981114 GAATTGGGGATTTCGTTATTTTCATAT 57.019 29.630 0.00 0.00 0.00 1.78
3927 6754 9.593134 TTGGGGATTTCGTTATTTTCATATTTG 57.407 29.630 0.00 0.00 0.00 2.32
3928 6755 8.972127 TGGGGATTTCGTTATTTTCATATTTGA 58.028 29.630 0.00 0.00 0.00 2.69
3929 6756 9.463443 GGGGATTTCGTTATTTTCATATTTGAG 57.537 33.333 0.00 0.00 32.27 3.02
3961 6788 9.709495 TCAAATTTTACAAAGAGGATCATTTGG 57.291 29.630 16.77 0.76 37.47 3.28
3962 6789 9.492973 CAAATTTTACAAAGAGGATCATTTGGT 57.507 29.630 16.77 5.65 37.47 3.67
3995 6822 7.753309 TTTTTCTCTCCGAATATTTCCAACA 57.247 32.000 0.00 0.00 0.00 3.33
3996 6823 7.938140 TTTTCTCTCCGAATATTTCCAACAT 57.062 32.000 0.00 0.00 0.00 2.71
3997 6824 6.925610 TTCTCTCCGAATATTTCCAACATG 57.074 37.500 0.00 0.00 0.00 3.21
3998 6825 6.233905 TCTCTCCGAATATTTCCAACATGA 57.766 37.500 0.00 0.00 0.00 3.07
3999 6826 6.649155 TCTCTCCGAATATTTCCAACATGAA 58.351 36.000 0.00 0.00 0.00 2.57
4000 6827 7.109501 TCTCTCCGAATATTTCCAACATGAAA 58.890 34.615 0.00 0.00 38.51 2.69
4001 6828 7.609918 TCTCTCCGAATATTTCCAACATGAAAA 59.390 33.333 0.00 0.00 37.74 2.29
4002 6829 8.292444 TCTCCGAATATTTCCAACATGAAAAT 57.708 30.769 0.00 2.86 37.74 1.82
4003 6830 9.402320 TCTCCGAATATTTCCAACATGAAAATA 57.598 29.630 0.00 4.96 37.74 1.40
4012 6839 9.933723 ATTTCCAACATGAAAATAAAAGAGAGG 57.066 29.630 0.00 0.00 37.74 3.69
4013 6840 7.466746 TCCAACATGAAAATAAAAGAGAGGG 57.533 36.000 0.00 0.00 0.00 4.30
4014 6841 6.437162 TCCAACATGAAAATAAAAGAGAGGGG 59.563 38.462 0.00 0.00 0.00 4.79
4015 6842 6.437162 CCAACATGAAAATAAAAGAGAGGGGA 59.563 38.462 0.00 0.00 0.00 4.81
4016 6843 7.124750 CCAACATGAAAATAAAAGAGAGGGGAT 59.875 37.037 0.00 0.00 0.00 3.85
4017 6844 9.189156 CAACATGAAAATAAAAGAGAGGGGATA 57.811 33.333 0.00 0.00 0.00 2.59
4018 6845 9.768215 AACATGAAAATAAAAGAGAGGGGATAA 57.232 29.630 0.00 0.00 0.00 1.75
4019 6846 9.768215 ACATGAAAATAAAAGAGAGGGGATAAA 57.232 29.630 0.00 0.00 0.00 1.40
4025 6852 9.997172 AAATAAAAGAGAGGGGATAAAATGACT 57.003 29.630 0.00 0.00 0.00 3.41
4026 6853 9.997172 AATAAAAGAGAGGGGATAAAATGACTT 57.003 29.630 0.00 0.00 0.00 3.01
4027 6854 7.946381 AAAAGAGAGGGGATAAAATGACTTC 57.054 36.000 0.00 0.00 0.00 3.01
4028 6855 6.899892 AAGAGAGGGGATAAAATGACTTCT 57.100 37.500 0.00 0.00 0.00 2.85
4029 6856 6.493189 AGAGAGGGGATAAAATGACTTCTC 57.507 41.667 0.00 0.00 0.00 2.87
4030 6857 5.368230 AGAGAGGGGATAAAATGACTTCTCC 59.632 44.000 0.00 0.00 0.00 3.71
4031 6858 5.039645 AGAGGGGATAAAATGACTTCTCCA 58.960 41.667 0.00 0.00 30.67 3.86
4032 6859 5.492524 AGAGGGGATAAAATGACTTCTCCAA 59.507 40.000 0.00 0.00 30.67 3.53
4033 6860 6.011628 AGAGGGGATAAAATGACTTCTCCAAA 60.012 38.462 0.00 0.00 30.67 3.28
4034 6861 6.561294 AGGGGATAAAATGACTTCTCCAAAA 58.439 36.000 0.00 0.00 30.67 2.44
4035 6862 7.016296 AGGGGATAAAATGACTTCTCCAAAAA 58.984 34.615 0.00 0.00 30.67 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.068024 TGGGTGCATTTGTTTCTCACTTC 59.932 43.478 0.00 0.00 0.00 3.01
271 708 7.336931 ACCCTCTACATACTGCATTTTTGTTAG 59.663 37.037 0.00 0.00 0.00 2.34
377 1370 8.522830 TGAATTCAAGGCCTAAAGAATTTACAG 58.477 33.333 27.67 0.00 39.88 2.74
486 2068 9.649167 ACAACACCATATAGACTTTAACAGTAC 57.351 33.333 0.00 0.00 35.01 2.73
493 2075 6.874664 TGCGAAACAACACCATATAGACTTTA 59.125 34.615 0.00 0.00 0.00 1.85
525 2289 3.769739 ATTTGCTTTGTCCCCCTTTTC 57.230 42.857 0.00 0.00 0.00 2.29
530 2294 3.513515 TGTATCAATTTGCTTTGTCCCCC 59.486 43.478 0.00 0.00 0.00 5.40
531 2295 4.021544 TGTGTATCAATTTGCTTTGTCCCC 60.022 41.667 0.00 0.00 0.00 4.81
603 2391 3.874383 TCTTTCCACTCATGTTTGGGA 57.126 42.857 13.34 4.29 33.25 4.37
604 2392 4.281688 ACATTCTTTCCACTCATGTTTGGG 59.718 41.667 13.34 3.11 33.25 4.12
605 2393 5.242393 AGACATTCTTTCCACTCATGTTTGG 59.758 40.000 8.57 8.57 0.00 3.28
611 2399 5.813383 ACATGAGACATTCTTTCCACTCAT 58.187 37.500 0.00 0.00 43.00 2.90
612 2400 5.233083 ACATGAGACATTCTTTCCACTCA 57.767 39.130 0.00 0.00 38.44 3.41
614 2402 5.380043 ACAACATGAGACATTCTTTCCACT 58.620 37.500 0.00 0.00 0.00 4.00
615 2403 5.695851 ACAACATGAGACATTCTTTCCAC 57.304 39.130 0.00 0.00 0.00 4.02
755 2684 1.954382 GGGGTATCGAAATTGCTTCCC 59.046 52.381 0.00 0.00 0.00 3.97
766 2695 1.784358 AATGGAAGACGGGGTATCGA 58.216 50.000 0.00 0.00 0.00 3.59
776 2705 6.369065 AGAACATAGAACACGAAATGGAAGAC 59.631 38.462 0.00 0.00 0.00 3.01
910 2852 0.394216 TGGCGATGGGAGATGGTTTG 60.394 55.000 0.00 0.00 0.00 2.93
918 2897 1.753848 TGGCAAATGGCGATGGGAG 60.754 57.895 2.36 0.00 46.16 4.30
1092 3099 2.062070 GAGCCACTCCACCTTGTCT 58.938 57.895 0.00 0.00 0.00 3.41
1281 3288 4.717629 CGCGTCGTCTTGCTCCCA 62.718 66.667 0.00 0.00 0.00 4.37
1611 3618 1.655329 GTACTCTGGCGATCCGAGG 59.345 63.158 0.00 0.00 37.34 4.63
2093 4751 2.655090 TGAAGCACAACCTGGAATCA 57.345 45.000 0.00 0.00 0.00 2.57
2102 4823 9.282247 CATGAAATAGTAGAAATGAAGCACAAC 57.718 33.333 0.00 0.00 0.00 3.32
2219 4971 2.727123 AAACGGCATCATACCCATCA 57.273 45.000 0.00 0.00 0.00 3.07
2279 5031 3.726557 TTGTTCATGAGAAGGATGCCT 57.273 42.857 0.00 0.00 33.63 4.75
2313 5065 1.230281 AGGGAGGCTGGGAATGGAA 60.230 57.895 0.00 0.00 0.00 3.53
2635 5438 3.279434 CCTAGCACCCTAACATTTGGAC 58.721 50.000 0.00 0.00 0.00 4.02
2682 5485 7.993183 TGATGGGTAAATTAGGAATGAGAAGAC 59.007 37.037 0.00 0.00 0.00 3.01
2792 5601 2.104111 AGTCACAAAACGACCATGGAGA 59.896 45.455 21.47 0.00 33.70 3.71
2843 5652 2.520536 AAGCACAACCTCCCTCGCT 61.521 57.895 0.00 0.00 0.00 4.93
2869 5679 1.394266 GCAATGTGTGGCCATAGGGG 61.394 60.000 9.72 0.00 40.85 4.79
2980 5800 9.964303 GGCAAACATAACATTAATATCATGTCA 57.036 29.630 7.88 0.00 33.54 3.58
2981 5801 9.964303 TGGCAAACATAACATTAATATCATGTC 57.036 29.630 7.88 0.00 33.54 3.06
3027 5850 1.198094 TCCCGGCTTCAGTCCATTGA 61.198 55.000 0.00 0.00 0.00 2.57
3030 5853 1.528824 CATCCCGGCTTCAGTCCAT 59.471 57.895 0.00 0.00 0.00 3.41
3043 5866 0.842635 AGCTCAATCTGGTCCATCCC 59.157 55.000 0.00 0.00 34.77 3.85
3236 6059 4.686191 TTTGTTTCAATGGTTCCATGCT 57.314 36.364 5.02 0.00 0.00 3.79
3241 6064 7.659390 TGGTCATTATTTTGTTTCAATGGTTCC 59.341 33.333 0.00 0.00 0.00 3.62
3324 6147 9.383519 CAATTTTATTGGCACTCTCTAAGTAGA 57.616 33.333 0.00 0.00 36.07 2.59
3388 6211 1.897802 GGGTCTACTCCTTTCGGAACA 59.102 52.381 0.00 0.00 39.29 3.18
3450 6273 3.672781 GCGAGACACTCTACCAAGTTACC 60.673 52.174 0.00 0.00 0.00 2.85
3644 6469 7.576236 AGAAATAAGTCGATCAACACAAACAG 58.424 34.615 0.00 0.00 0.00 3.16
3743 6570 6.771188 AGAAATTCTCAAGTCACTGTAACG 57.229 37.500 0.00 0.00 0.00 3.18
3773 6600 7.310361 GGAAATTCTCCAATTTGGGATGTTACA 60.310 37.037 15.37 0.00 44.67 2.41
3774 6601 7.041721 GGAAATTCTCCAATTTGGGATGTTAC 58.958 38.462 15.37 6.21 44.67 2.50
3775 6602 7.181569 GGAAATTCTCCAATTTGGGATGTTA 57.818 36.000 15.37 0.00 44.67 2.41
3776 6603 6.053632 GGAAATTCTCCAATTTGGGATGTT 57.946 37.500 15.37 8.35 44.67 2.71
3777 6604 5.682234 GGAAATTCTCCAATTTGGGATGT 57.318 39.130 15.37 3.18 44.67 3.06
3840 6667 9.603921 CTAGGATCAACCAAAATGCAATAAAAT 57.396 29.630 0.00 0.00 42.04 1.82
3841 6668 8.811017 TCTAGGATCAACCAAAATGCAATAAAA 58.189 29.630 0.00 0.00 42.04 1.52
3846 6673 6.662865 TTTCTAGGATCAACCAAAATGCAA 57.337 33.333 0.00 0.00 42.04 4.08
3847 6674 6.855763 ATTTCTAGGATCAACCAAAATGCA 57.144 33.333 0.00 0.00 42.04 3.96
3848 6675 7.550712 AGAATTTCTAGGATCAACCAAAATGC 58.449 34.615 0.00 0.00 42.04 3.56
3851 6678 8.739972 GCTTAGAATTTCTAGGATCAACCAAAA 58.260 33.333 17.14 0.00 42.04 2.44
3852 6679 7.888021 TGCTTAGAATTTCTAGGATCAACCAAA 59.112 33.333 17.14 0.00 42.04 3.28
3854 6681 6.957631 TGCTTAGAATTTCTAGGATCAACCA 58.042 36.000 17.14 4.18 42.04 3.67
3855 6682 7.554476 AGTTGCTTAGAATTTCTAGGATCAACC 59.446 37.037 21.66 12.44 32.54 3.77
3856 6683 8.499403 AGTTGCTTAGAATTTCTAGGATCAAC 57.501 34.615 17.14 18.70 32.44 3.18
3857 6684 8.321353 TGAGTTGCTTAGAATTTCTAGGATCAA 58.679 33.333 17.14 10.61 28.51 2.57
3858 6685 7.851228 TGAGTTGCTTAGAATTTCTAGGATCA 58.149 34.615 17.14 11.89 28.51 2.92
3859 6686 8.723942 TTGAGTTGCTTAGAATTTCTAGGATC 57.276 34.615 17.14 10.04 28.51 3.36
3860 6687 7.772757 CCTTGAGTTGCTTAGAATTTCTAGGAT 59.227 37.037 17.14 2.44 28.51 3.24
3862 6689 7.065204 GTCCTTGAGTTGCTTAGAATTTCTAGG 59.935 40.741 10.39 10.39 29.56 3.02
3863 6690 7.065204 GGTCCTTGAGTTGCTTAGAATTTCTAG 59.935 40.741 6.26 3.26 29.56 2.43
3864 6691 6.879458 GGTCCTTGAGTTGCTTAGAATTTCTA 59.121 38.462 1.90 1.90 0.00 2.10
3865 6692 5.707764 GGTCCTTGAGTTGCTTAGAATTTCT 59.292 40.000 4.03 4.03 0.00 2.52
3866 6693 5.106118 GGGTCCTTGAGTTGCTTAGAATTTC 60.106 44.000 0.00 0.00 0.00 2.17
3867 6694 4.767409 GGGTCCTTGAGTTGCTTAGAATTT 59.233 41.667 0.00 0.00 0.00 1.82
3868 6695 4.202567 TGGGTCCTTGAGTTGCTTAGAATT 60.203 41.667 0.00 0.00 0.00 2.17
3869 6696 3.330701 TGGGTCCTTGAGTTGCTTAGAAT 59.669 43.478 0.00 0.00 0.00 2.40
3870 6697 2.708861 TGGGTCCTTGAGTTGCTTAGAA 59.291 45.455 0.00 0.00 0.00 2.10
3871 6698 2.038557 GTGGGTCCTTGAGTTGCTTAGA 59.961 50.000 0.00 0.00 0.00 2.10
3872 6699 2.427506 GTGGGTCCTTGAGTTGCTTAG 58.572 52.381 0.00 0.00 0.00 2.18
3873 6700 1.270625 CGTGGGTCCTTGAGTTGCTTA 60.271 52.381 0.00 0.00 0.00 3.09
3874 6701 0.535102 CGTGGGTCCTTGAGTTGCTT 60.535 55.000 0.00 0.00 0.00 3.91
3875 6702 1.071471 CGTGGGTCCTTGAGTTGCT 59.929 57.895 0.00 0.00 0.00 3.91
3876 6703 1.966451 CCGTGGGTCCTTGAGTTGC 60.966 63.158 0.00 0.00 0.00 4.17
3877 6704 0.320771 CTCCGTGGGTCCTTGAGTTG 60.321 60.000 0.00 0.00 0.00 3.16
3878 6705 2.058675 CTCCGTGGGTCCTTGAGTT 58.941 57.895 0.00 0.00 0.00 3.01
3879 6706 2.584391 GCTCCGTGGGTCCTTGAGT 61.584 63.158 0.00 0.00 0.00 3.41
3880 6707 2.266055 GCTCCGTGGGTCCTTGAG 59.734 66.667 0.00 0.00 0.00 3.02
3881 6708 3.691342 CGCTCCGTGGGTCCTTGA 61.691 66.667 0.00 0.00 0.00 3.02
3882 6709 2.521958 ATTCGCTCCGTGGGTCCTTG 62.522 60.000 0.00 0.00 0.00 3.61
3883 6710 1.838073 AATTCGCTCCGTGGGTCCTT 61.838 55.000 0.00 0.00 0.00 3.36
3884 6711 2.291043 AATTCGCTCCGTGGGTCCT 61.291 57.895 0.00 0.00 0.00 3.85
3885 6712 2.106683 CAATTCGCTCCGTGGGTCC 61.107 63.158 0.00 0.00 0.00 4.46
3886 6713 2.106683 CCAATTCGCTCCGTGGGTC 61.107 63.158 0.00 0.00 0.00 4.46
3887 6714 2.046314 CCAATTCGCTCCGTGGGT 60.046 61.111 0.00 0.00 0.00 4.51
3888 6715 2.824041 CCCAATTCGCTCCGTGGG 60.824 66.667 0.00 0.00 44.69 4.61
3889 6716 2.608970 ATCCCCAATTCGCTCCGTGG 62.609 60.000 0.00 0.00 0.00 4.94
3890 6717 0.748005 AATCCCCAATTCGCTCCGTG 60.748 55.000 0.00 0.00 0.00 4.94
3891 6718 0.034477 AAATCCCCAATTCGCTCCGT 60.034 50.000 0.00 0.00 0.00 4.69
3892 6719 0.663153 GAAATCCCCAATTCGCTCCG 59.337 55.000 0.00 0.00 0.00 4.63
3893 6720 0.663153 CGAAATCCCCAATTCGCTCC 59.337 55.000 0.00 0.00 41.46 4.70
3898 6725 9.981114 ATATGAAAATAACGAAATCCCCAATTC 57.019 29.630 0.00 0.00 0.00 2.17
3901 6728 9.593134 CAAATATGAAAATAACGAAATCCCCAA 57.407 29.630 0.00 0.00 0.00 4.12
3902 6729 8.972127 TCAAATATGAAAATAACGAAATCCCCA 58.028 29.630 0.00 0.00 30.99 4.96
3903 6730 9.463443 CTCAAATATGAAAATAACGAAATCCCC 57.537 33.333 0.00 0.00 34.49 4.81
3926 6753 9.801873 CCTCTTTGTAAAATTTGAGAAAACTCA 57.198 29.630 0.00 0.00 0.00 3.41
3935 6762 9.709495 CCAAATGATCCTCTTTGTAAAATTTGA 57.291 29.630 0.00 0.00 35.51 2.69
3936 6763 9.492973 ACCAAATGATCCTCTTTGTAAAATTTG 57.507 29.630 0.00 0.00 34.07 2.32
3969 6796 9.456147 TGTTGGAAATATTCGGAGAGAAAAATA 57.544 29.630 0.00 0.00 42.91 1.40
3970 6797 8.348285 TGTTGGAAATATTCGGAGAGAAAAAT 57.652 30.769 0.00 0.00 42.91 1.82
3971 6798 7.753309 TGTTGGAAATATTCGGAGAGAAAAA 57.247 32.000 0.00 0.00 42.91 1.94
3972 6799 7.609918 TCATGTTGGAAATATTCGGAGAGAAAA 59.390 33.333 0.00 0.00 42.91 2.29
3973 6800 7.109501 TCATGTTGGAAATATTCGGAGAGAAA 58.890 34.615 0.00 0.00 42.91 2.52
3974 6801 6.649155 TCATGTTGGAAATATTCGGAGAGAA 58.351 36.000 0.00 0.00 43.93 2.87
3975 6802 6.233905 TCATGTTGGAAATATTCGGAGAGA 57.766 37.500 0.00 0.00 38.43 3.10
3976 6803 6.925610 TTCATGTTGGAAATATTCGGAGAG 57.074 37.500 0.00 0.00 38.43 3.20
3977 6804 7.695480 TTTTCATGTTGGAAATATTCGGAGA 57.305 32.000 0.00 0.00 36.71 3.71
3986 6813 9.933723 CCTCTCTTTTATTTTCATGTTGGAAAT 57.066 29.630 0.00 0.00 36.71 2.17
3987 6814 8.367156 CCCTCTCTTTTATTTTCATGTTGGAAA 58.633 33.333 0.00 0.00 35.11 3.13
3988 6815 7.039082 CCCCTCTCTTTTATTTTCATGTTGGAA 60.039 37.037 0.00 0.00 0.00 3.53
3989 6816 6.437162 CCCCTCTCTTTTATTTTCATGTTGGA 59.563 38.462 0.00 0.00 0.00 3.53
3990 6817 6.437162 TCCCCTCTCTTTTATTTTCATGTTGG 59.563 38.462 0.00 0.00 0.00 3.77
3991 6818 7.466746 TCCCCTCTCTTTTATTTTCATGTTG 57.533 36.000 0.00 0.00 0.00 3.33
3992 6819 9.768215 TTATCCCCTCTCTTTTATTTTCATGTT 57.232 29.630 0.00 0.00 0.00 2.71
3993 6820 9.768215 TTTATCCCCTCTCTTTTATTTTCATGT 57.232 29.630 0.00 0.00 0.00 3.21
3999 6826 9.997172 AGTCATTTTATCCCCTCTCTTTTATTT 57.003 29.630 0.00 0.00 0.00 1.40
4000 6827 9.997172 AAGTCATTTTATCCCCTCTCTTTTATT 57.003 29.630 0.00 0.00 0.00 1.40
4001 6828 9.634021 GAAGTCATTTTATCCCCTCTCTTTTAT 57.366 33.333 0.00 0.00 0.00 1.40
4002 6829 8.836735 AGAAGTCATTTTATCCCCTCTCTTTTA 58.163 33.333 0.00 0.00 0.00 1.52
4003 6830 7.703755 AGAAGTCATTTTATCCCCTCTCTTTT 58.296 34.615 0.00 0.00 0.00 2.27
4004 6831 7.277405 AGAAGTCATTTTATCCCCTCTCTTT 57.723 36.000 0.00 0.00 0.00 2.52
4005 6832 6.126623 GGAGAAGTCATTTTATCCCCTCTCTT 60.127 42.308 0.00 0.00 0.00 2.85
4006 6833 5.368230 GGAGAAGTCATTTTATCCCCTCTCT 59.632 44.000 0.00 0.00 0.00 3.10
4007 6834 5.131142 TGGAGAAGTCATTTTATCCCCTCTC 59.869 44.000 0.00 0.00 0.00 3.20
4008 6835 5.039645 TGGAGAAGTCATTTTATCCCCTCT 58.960 41.667 0.00 0.00 0.00 3.69
4009 6836 5.373812 TGGAGAAGTCATTTTATCCCCTC 57.626 43.478 0.00 0.00 0.00 4.30
4010 6837 5.796502 TTGGAGAAGTCATTTTATCCCCT 57.203 39.130 0.00 0.00 0.00 4.79
4011 6838 6.850752 TTTTGGAGAAGTCATTTTATCCCC 57.149 37.500 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.