Multiple sequence alignment - TraesCS2A01G307500

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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 TraesCS2A01G307500 chr2A 100.000 3398 0 0 533 3930 528269651 528266254 0.000000e+00 6276
1 TraesCS2A01G307500 chr2A 100.000 240 0 0 1 240 528270183 528269944 1.000000e-120 444
2 TraesCS2A01G307500 chr2B 93.012 2991 143 33 533 3498 463212364 463209415 0.000000e+00 4305
3 TraesCS2A01G307500 chr2B 92.887 239 14 3 3694 3930 463209351 463209114 1.050000e-90 344
4 TraesCS2A01G307500 chr2B 81.301 246 36 4 1 236 463212691 463212446 1.440000e-44 191
5 TraesCS2A01G307500 chr2D 89.916 1894 142 33 533 2409 391463766 391461905 0.000000e+00 2394
6 TraesCS2A01G307500 chr2D 92.558 1075 54 5 2425 3498 391461362 391460313 0.000000e+00 1519
7 TraesCS2A01G307500 chr2D 88.710 248 20 1 1 240 391464085 391463838 2.970000e-76 296
8 TraesCS2A01G307500 chr2D 91.279 172 15 0 3489 3660 305514861 305515032 6.570000e-58 235
9 TraesCS2A01G307500 chr2D 90.533 169 16 0 3490 3658 165780068 165779900 1.420000e-54 224
10 TraesCS2A01G307500 chr2D 90.964 166 14 1 3494 3658 521564027 521564192 5.110000e-54 222
11 TraesCS2A01G307500 chr2D 88.333 180 13 5 3694 3865 391460255 391460076 3.980000e-50 209
12 TraesCS2A01G307500 chr1A 90.643 171 15 1 3492 3661 15540164 15539994 3.950000e-55 226
13 TraesCS2A01G307500 chr4B 90.964 166 15 0 3496 3661 483266541 483266376 1.420000e-54 224
14 TraesCS2A01G307500 chr4B 88.701 177 19 1 3497 3672 407061335 407061159 8.550000e-52 215
15 TraesCS2A01G307500 chr6B 90.361 166 16 0 3493 3658 131720918 131720753 6.610000e-53 219
16 TraesCS2A01G307500 chr6A 89.595 173 17 1 3489 3661 22166345 22166174 6.610000e-53 219
17 TraesCS2A01G307500 chrUn 86.911 191 21 4 3473 3661 22162881 22162693 1.110000e-50 211


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 TraesCS2A01G307500 chr2A 528266254 528270183 3929 True 3360.000000 6276 100.000000 1 3930 2 chr2A.!!$R1 3929
1 TraesCS2A01G307500 chr2B 463209114 463212691 3577 True 1613.333333 4305 89.066667 1 3930 3 chr2B.!!$R1 3929
2 TraesCS2A01G307500 chr2D 391460076 391464085 4009 True 1104.500000 2394 89.879250 1 3865 4 chr2D.!!$R2 3864

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
661 674 0.250234 CACCATCATGGACGTGACCT 59.750 55.000 11.90 0.0 40.96 3.85 F
717 735 0.544223 TGGGATGTGGTATCCAACGG 59.456 55.000 8.10 0.0 39.93 4.44 F
1019 1041 1.144057 CACCACCACCTAGATCCGC 59.856 63.158 0.00 0.0 0.00 5.54 F
2632 3202 0.839853 AGGAGGCAGCTCTGAAAGGT 60.840 55.000 0.29 0.0 35.64 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1721 1.302993 ACCACATTTCCGAACCCCG 60.303 57.895 0.00 0.0 38.18 5.73 R
2073 2112 2.264455 AGCATCAACCTCTTCAGTCCT 58.736 47.619 0.00 0.0 0.00 3.85 R
2734 3304 2.123726 GGGCAGCCATTGGGGTAG 60.124 66.667 15.19 0.0 44.97 3.18 R
3766 4377 0.320771 CCCTTCCAGACACCGACTTG 60.321 60.000 0.00 0.0 0.00 3.16 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
95 105 1.881973 GAGGAATTGTGTCTTGCTGCA 59.118 47.619 0.00 0.00 0.00 4.41
109 119 2.730069 TGCTGCAACATTTTGTCGAAG 58.270 42.857 0.00 0.00 34.90 3.79
111 121 3.313803 TGCTGCAACATTTTGTCGAAGTA 59.686 39.130 0.00 0.00 34.90 2.24
119 129 4.631813 ACATTTTGTCGAAGTAGATCTGGC 59.368 41.667 5.18 0.00 0.00 4.85
120 130 3.953712 TTTGTCGAAGTAGATCTGGCA 57.046 42.857 5.18 0.00 0.00 4.92
129 139 0.325296 TAGATCTGGCAAGACCGGGT 60.325 55.000 6.32 0.00 46.01 5.28
169 179 3.320879 CTGCGCCCACTGGATCTGT 62.321 63.158 4.18 0.00 0.00 3.41
176 186 1.607801 CCACTGGATCTGTGGCGAGA 61.608 60.000 19.80 0.00 44.09 4.04
199 209 1.304547 CACCGTCTCCAGACCCTCT 60.305 63.158 1.01 0.00 41.86 3.69
229 240 2.444140 CCGTCCGGAATCCCTCCT 60.444 66.667 5.23 0.00 42.85 3.69
237 248 0.398318 GGAATCCCTCCTCATTCGGG 59.602 60.000 0.00 0.00 41.61 5.14
587 599 0.608130 CGATGTTGACCACCTCCTCA 59.392 55.000 0.00 0.00 0.00 3.86
603 615 0.603707 CTCAGCCGCAACTTCCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
615 627 4.697756 CCTTCACCGCCGCTTCCA 62.698 66.667 0.00 0.00 0.00 3.53
631 643 0.682852 TCCACCGGATGACGTTCTTT 59.317 50.000 9.46 0.00 42.24 2.52
656 669 1.745087 GCAATTCACCATCATGGACGT 59.255 47.619 11.90 0.00 40.96 4.34
659 672 2.093306 TTCACCATCATGGACGTGAC 57.907 50.000 11.90 0.00 40.96 3.67
661 674 0.250234 CACCATCATGGACGTGACCT 59.750 55.000 11.90 0.00 40.96 3.85
705 723 4.524802 TCCATATTGCTCTTTGGGATGT 57.475 40.909 0.00 0.00 0.00 3.06
713 731 2.092429 GCTCTTTGGGATGTGGTATCCA 60.092 50.000 8.10 0.00 39.93 3.41
717 735 0.544223 TGGGATGTGGTATCCAACGG 59.456 55.000 8.10 0.00 39.93 4.44
740 762 6.428799 GGCGATATCTATAACGGTAGATGAC 58.571 44.000 14.00 8.80 40.64 3.06
741 763 6.428799 GCGATATCTATAACGGTAGATGACC 58.571 44.000 14.00 0.00 45.91 4.02
802 824 3.280030 ATGGGACCATGGCTCCATA 57.720 52.632 28.22 18.66 38.14 2.74
863 885 2.235402 CACGGCTAGACTTTTTCCCCTA 59.765 50.000 0.00 0.00 0.00 3.53
1019 1041 1.144057 CACCACCACCTAGATCCGC 59.856 63.158 0.00 0.00 0.00 5.54
1274 1296 3.311110 TCCTTCGGGCTGAGCGTT 61.311 61.111 0.00 0.00 34.44 4.84
1406 1428 1.726791 CATTCGATATACACCAGCGCC 59.273 52.381 2.29 0.00 0.00 6.53
1610 1632 3.904586 GCAGAGCTACTGGGCTATC 57.095 57.895 12.98 0.00 45.82 2.08
1735 1757 4.887071 TGTGGTGCTGATTAGTCTTTTTGT 59.113 37.500 0.00 0.00 0.00 2.83
1766 1788 6.709018 TCGTCATATGTATCCTGAACTTGA 57.291 37.500 1.90 0.00 0.00 3.02
1776 1798 6.826231 TGTATCCTGAACTTGAAACAACAAGA 59.174 34.615 14.00 0.00 46.85 3.02
1987 2026 1.276989 ACATTTTGCAGAGGCCATTGG 59.723 47.619 5.01 0.00 40.13 3.16
2073 2112 8.539544 TCTGAAACATGGATAGTCAGAATGTAA 58.460 33.333 11.35 0.00 41.22 2.41
2077 2116 6.821388 ACATGGATAGTCAGAATGTAAGGAC 58.179 40.000 0.00 0.00 37.40 3.85
2116 2155 6.620089 GCTTCCTGAAGTTTATCGTGTTTACC 60.620 42.308 8.57 0.00 40.45 2.85
2129 2168 3.614616 CGTGTTTACCTTCTCATCTCAGC 59.385 47.826 0.00 0.00 0.00 4.26
2170 2209 6.103997 TGTTTATGTATCCAGTTCGAGTTCC 58.896 40.000 0.00 0.00 0.00 3.62
2446 3016 9.643693 ATGCATTTTTCTGTACTTCCAATTAAG 57.356 29.630 0.00 0.00 0.00 1.85
2448 3018 9.476202 GCATTTTTCTGTACTTCCAATTAAGTT 57.524 29.630 0.00 0.00 40.20 2.66
2503 3073 6.096846 ACTCTGAACATTTTGTTGCTTAGGTT 59.903 34.615 0.00 0.00 41.28 3.50
2540 3110 2.962859 AGGAGGAAAGGTTTGCACAAT 58.037 42.857 0.00 0.00 0.00 2.71
2557 3127 2.889045 ACAATTGCACAGATCTGCACTT 59.111 40.909 22.83 13.70 46.90 3.16
2632 3202 0.839853 AGGAGGCAGCTCTGAAAGGT 60.840 55.000 0.29 0.00 35.64 3.50
2734 3304 1.081094 CGTTTCACCGTACCATTCCC 58.919 55.000 0.00 0.00 0.00 3.97
2832 3406 1.732809 GACTCAGTAGCGGAAAAAGGC 59.267 52.381 0.00 0.00 0.00 4.35
2833 3407 1.071699 ACTCAGTAGCGGAAAAAGGCA 59.928 47.619 0.00 0.00 0.00 4.75
2834 3408 2.290323 ACTCAGTAGCGGAAAAAGGCAT 60.290 45.455 0.00 0.00 0.00 4.40
2835 3409 2.083774 TCAGTAGCGGAAAAAGGCATG 58.916 47.619 0.00 0.00 0.00 4.06
2922 3497 5.398603 AAGCTGACAGAATAGATATCCCG 57.601 43.478 6.65 0.00 0.00 5.14
3014 3590 2.486982 GCTTGCCACATGCTCCATATAG 59.513 50.000 0.00 0.00 42.00 1.31
3026 3602 8.874156 ACATGCTCCATATAGACAGATTTTCTA 58.126 33.333 0.00 0.00 0.00 2.10
3044 3620 2.243994 TCTATTTCTCACTCCTCCCGGA 59.756 50.000 0.73 0.00 37.82 5.14
3081 3657 7.202016 ACTGTGAATTTGTTAGTACACATGG 57.798 36.000 0.00 0.00 37.56 3.66
3234 3810 3.020984 AGGCTGTTTTCGTTTTTGAGGA 58.979 40.909 0.00 0.00 0.00 3.71
3251 3827 3.591527 TGAGGAAGGAGCTTTGGGAATAA 59.408 43.478 0.00 0.00 0.00 1.40
3340 3916 3.749609 GTGTCCATGGTTGTGTACTAACC 59.250 47.826 12.58 19.49 46.13 2.85
3486 4062 5.177511 GGGCACTTTTTAAGATGCAACTTTC 59.822 40.000 14.90 0.00 37.31 2.62
3488 4064 6.424812 GGCACTTTTTAAGATGCAACTTTCAT 59.575 34.615 14.90 0.00 37.31 2.57
3500 4076 9.846248 AGATGCAACTTTCATTGTTATTTACTC 57.154 29.630 0.00 0.00 31.83 2.59
3501 4077 8.986477 ATGCAACTTTCATTGTTATTTACTCC 57.014 30.769 0.00 0.00 31.83 3.85
3502 4078 7.375053 TGCAACTTTCATTGTTATTTACTCCC 58.625 34.615 0.00 0.00 31.83 4.30
3503 4079 7.232534 TGCAACTTTCATTGTTATTTACTCCCT 59.767 33.333 0.00 0.00 31.83 4.20
3504 4080 7.755373 GCAACTTTCATTGTTATTTACTCCCTC 59.245 37.037 0.00 0.00 31.83 4.30
3505 4081 9.014297 CAACTTTCATTGTTATTTACTCCCTCT 57.986 33.333 0.00 0.00 0.00 3.69
3506 4082 8.567285 ACTTTCATTGTTATTTACTCCCTCTG 57.433 34.615 0.00 0.00 0.00 3.35
3507 4083 8.164070 ACTTTCATTGTTATTTACTCCCTCTGT 58.836 33.333 0.00 0.00 0.00 3.41
3508 4084 8.934023 TTTCATTGTTATTTACTCCCTCTGTT 57.066 30.769 0.00 0.00 0.00 3.16
3509 4085 8.561738 TTCATTGTTATTTACTCCCTCTGTTC 57.438 34.615 0.00 0.00 0.00 3.18
3510 4086 7.110155 TCATTGTTATTTACTCCCTCTGTTCC 58.890 38.462 0.00 0.00 0.00 3.62
3511 4087 5.431179 TGTTATTTACTCCCTCTGTTCCC 57.569 43.478 0.00 0.00 0.00 3.97
3512 4088 4.847512 TGTTATTTACTCCCTCTGTTCCCA 59.152 41.667 0.00 0.00 0.00 4.37
3513 4089 5.311121 TGTTATTTACTCCCTCTGTTCCCAA 59.689 40.000 0.00 0.00 0.00 4.12
3514 4090 6.183361 TGTTATTTACTCCCTCTGTTCCCAAA 60.183 38.462 0.00 0.00 0.00 3.28
3515 4091 5.536497 ATTTACTCCCTCTGTTCCCAAAT 57.464 39.130 0.00 0.00 0.00 2.32
3516 4092 6.652205 ATTTACTCCCTCTGTTCCCAAATA 57.348 37.500 0.00 0.00 0.00 1.40
3517 4093 6.652205 TTTACTCCCTCTGTTCCCAAATAT 57.348 37.500 0.00 0.00 0.00 1.28
3518 4094 7.758820 TTTACTCCCTCTGTTCCCAAATATA 57.241 36.000 0.00 0.00 0.00 0.86
3519 4095 7.758820 TTACTCCCTCTGTTCCCAAATATAA 57.241 36.000 0.00 0.00 0.00 0.98
3520 4096 6.253946 ACTCCCTCTGTTCCCAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
3521 4097 5.731678 ACTCCCTCTGTTCCCAAATATAAGT 59.268 40.000 0.00 0.00 0.00 2.24
3522 4098 6.126739 ACTCCCTCTGTTCCCAAATATAAGTC 60.127 42.308 0.00 0.00 0.00 3.01
3523 4099 5.970640 TCCCTCTGTTCCCAAATATAAGTCT 59.029 40.000 0.00 0.00 0.00 3.24
3524 4100 6.447084 TCCCTCTGTTCCCAAATATAAGTCTT 59.553 38.462 0.00 0.00 0.00 3.01
3525 4101 7.036863 TCCCTCTGTTCCCAAATATAAGTCTTT 60.037 37.037 0.00 0.00 0.00 2.52
3526 4102 7.067494 CCCTCTGTTCCCAAATATAAGTCTTTG 59.933 40.741 0.00 0.00 33.20 2.77
3527 4103 7.611855 CCTCTGTTCCCAAATATAAGTCTTTGT 59.388 37.037 0.00 0.00 31.83 2.83
3528 4104 9.667107 CTCTGTTCCCAAATATAAGTCTTTGTA 57.333 33.333 0.00 0.00 31.83 2.41
3529 4105 9.667107 TCTGTTCCCAAATATAAGTCTTTGTAG 57.333 33.333 0.00 0.00 31.83 2.74
3530 4106 9.667107 CTGTTCCCAAATATAAGTCTTTGTAGA 57.333 33.333 0.00 0.00 31.83 2.59
3531 4107 9.667107 TGTTCCCAAATATAAGTCTTTGTAGAG 57.333 33.333 0.00 0.00 31.83 2.43
3532 4108 9.886132 GTTCCCAAATATAAGTCTTTGTAGAGA 57.114 33.333 0.00 0.00 31.83 3.10
3544 4120 8.367660 AGTCTTTGTAGAGATTTCACTATGGA 57.632 34.615 0.00 0.00 0.00 3.41
3545 4121 8.254508 AGTCTTTGTAGAGATTTCACTATGGAC 58.745 37.037 0.00 0.00 0.00 4.02
3546 4122 7.492994 GTCTTTGTAGAGATTTCACTATGGACC 59.507 40.741 0.00 0.00 0.00 4.46
3547 4123 6.867519 TTGTAGAGATTTCACTATGGACCA 57.132 37.500 0.00 0.00 0.00 4.02
3548 4124 6.222038 TGTAGAGATTTCACTATGGACCAC 57.778 41.667 0.00 0.00 0.00 4.16
3549 4125 5.719563 TGTAGAGATTTCACTATGGACCACA 59.280 40.000 0.00 0.00 0.00 4.17
3550 4126 5.965033 AGAGATTTCACTATGGACCACAT 57.035 39.130 0.00 0.00 43.68 3.21
3551 4127 7.563556 TGTAGAGATTTCACTATGGACCACATA 59.436 37.037 0.00 0.00 41.03 2.29
3552 4128 7.623999 AGAGATTTCACTATGGACCACATAT 57.376 36.000 0.00 0.00 41.07 1.78
3553 4129 7.448420 AGAGATTTCACTATGGACCACATATG 58.552 38.462 0.00 0.00 41.07 1.78
3566 4142 4.974645 CCACATATGGGTGTATGTAGGT 57.025 45.455 7.80 0.00 41.96 3.08
3567 4143 4.641396 CCACATATGGGTGTATGTAGGTG 58.359 47.826 7.80 0.00 41.96 4.00
3568 4144 4.065088 CACATATGGGTGTATGTAGGTGC 58.935 47.826 7.80 0.00 41.96 5.01
3569 4145 3.714280 ACATATGGGTGTATGTAGGTGCA 59.286 43.478 7.80 0.00 42.03 4.57
3570 4146 4.350816 ACATATGGGTGTATGTAGGTGCAT 59.649 41.667 7.80 0.00 42.03 3.96
3571 4147 3.951563 ATGGGTGTATGTAGGTGCATT 57.048 42.857 0.00 0.00 0.00 3.56
3572 4148 3.730215 TGGGTGTATGTAGGTGCATTT 57.270 42.857 0.00 0.00 0.00 2.32
3573 4149 4.040936 TGGGTGTATGTAGGTGCATTTT 57.959 40.909 0.00 0.00 0.00 1.82
3574 4150 5.180810 TGGGTGTATGTAGGTGCATTTTA 57.819 39.130 0.00 0.00 0.00 1.52
3575 4151 5.189928 TGGGTGTATGTAGGTGCATTTTAG 58.810 41.667 0.00 0.00 0.00 1.85
3576 4152 5.045505 TGGGTGTATGTAGGTGCATTTTAGA 60.046 40.000 0.00 0.00 0.00 2.10
3577 4153 5.527582 GGGTGTATGTAGGTGCATTTTAGAG 59.472 44.000 0.00 0.00 0.00 2.43
3578 4154 6.113411 GGTGTATGTAGGTGCATTTTAGAGT 58.887 40.000 0.00 0.00 0.00 3.24
3579 4155 6.037172 GGTGTATGTAGGTGCATTTTAGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
3580 4156 6.594159 GTGTATGTAGGTGCATTTTAGAGTGT 59.406 38.462 0.00 0.00 0.00 3.55
3581 4157 7.762615 GTGTATGTAGGTGCATTTTAGAGTGTA 59.237 37.037 0.00 0.00 0.00 2.90
3582 4158 7.979537 TGTATGTAGGTGCATTTTAGAGTGTAG 59.020 37.037 0.00 0.00 0.00 2.74
3583 4159 6.599356 TGTAGGTGCATTTTAGAGTGTAGA 57.401 37.500 0.00 0.00 0.00 2.59
3584 4160 7.182817 TGTAGGTGCATTTTAGAGTGTAGAT 57.817 36.000 0.00 0.00 0.00 1.98
3585 4161 7.620880 TGTAGGTGCATTTTAGAGTGTAGATT 58.379 34.615 0.00 0.00 0.00 2.40
3586 4162 7.764443 TGTAGGTGCATTTTAGAGTGTAGATTC 59.236 37.037 0.00 0.00 0.00 2.52
3587 4163 6.711277 AGGTGCATTTTAGAGTGTAGATTCA 58.289 36.000 0.00 0.00 0.00 2.57
3588 4164 6.595716 AGGTGCATTTTAGAGTGTAGATTCAC 59.404 38.462 0.00 0.00 38.46 3.18
3599 4175 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3600 4176 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3601 4177 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3602 4178 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3603 4179 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3604 4180 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3605 4181 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3606 4182 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3607 4183 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3608 4184 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3609 4185 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3610 4186 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3611 4187 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
3612 4188 6.096423 ACTCATTTTGCTCCGTATGTAGTCTA 59.904 38.462 0.00 0.00 0.00 2.59
3613 4189 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
3614 4190 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
3615 4191 8.297426 TCATTTTGCTCCGTATGTAGTCTATAG 58.703 37.037 0.00 0.00 0.00 1.31
3616 4192 7.578310 TTTTGCTCCGTATGTAGTCTATAGT 57.422 36.000 0.00 0.00 0.00 2.12
3617 4193 6.555812 TTGCTCCGTATGTAGTCTATAGTG 57.444 41.667 0.00 0.00 0.00 2.74
3618 4194 5.001874 TGCTCCGTATGTAGTCTATAGTGG 58.998 45.833 0.00 0.00 0.00 4.00
3619 4195 5.221783 TGCTCCGTATGTAGTCTATAGTGGA 60.222 44.000 0.00 0.00 0.00 4.02
3620 4196 5.704515 GCTCCGTATGTAGTCTATAGTGGAA 59.295 44.000 0.00 0.00 0.00 3.53
3621 4197 6.374894 GCTCCGTATGTAGTCTATAGTGGAAT 59.625 42.308 0.00 0.00 0.00 3.01
3622 4198 7.551974 GCTCCGTATGTAGTCTATAGTGGAATA 59.448 40.741 0.00 0.00 0.00 1.75
3623 4199 9.616156 CTCCGTATGTAGTCTATAGTGGAATAT 57.384 37.037 0.00 0.00 0.00 1.28
3624 4200 9.970553 TCCGTATGTAGTCTATAGTGGAATATT 57.029 33.333 0.00 0.00 0.00 1.28
3793 4405 2.258109 GTGTCTGGAAGGGAGGTAGTT 58.742 52.381 0.00 0.00 0.00 2.24
3810 4422 8.578151 GGAGGTAGTTGTATACTTTAGGATCAG 58.422 40.741 4.17 0.00 38.33 2.90
3828 4440 3.743521 TCAGAGGATCAAAGTTGTGTGG 58.256 45.455 0.00 0.00 37.82 4.17
3874 4486 1.004044 AGCAGCACTGTCCAGCTATTT 59.996 47.619 0.00 0.00 39.50 1.40
3885 4497 1.293924 CAGCTATTTGGTCCAGAGCG 58.706 55.000 13.79 7.80 38.20 5.03
3889 4501 0.546122 TATTTGGTCCAGAGCGCCAT 59.454 50.000 2.29 0.00 31.71 4.40
3904 4516 4.389374 AGCGCCATAGTATTTTGTATGCT 58.611 39.130 2.29 0.00 0.00 3.79
3916 4528 6.916360 ATTTTGTATGCTTTCCTTCCTCAA 57.084 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.440525 GCCATTGGACCAACTTGATACATG 60.441 45.833 9.67 0.18 0.00 3.21
95 105 5.122396 GCCAGATCTACTTCGACAAAATGTT 59.878 40.000 0.00 0.00 0.00 2.71
109 119 0.105039 CCCGGTCTTGCCAGATCTAC 59.895 60.000 0.00 0.00 36.97 2.59
111 121 1.613630 ACCCGGTCTTGCCAGATCT 60.614 57.895 0.00 0.00 36.97 2.75
119 129 2.027625 GCTTCGACACCCGGTCTTG 61.028 63.158 0.00 0.00 44.68 3.02
120 130 2.207924 AGCTTCGACACCCGGTCTT 61.208 57.895 0.00 0.00 44.68 3.01
149 159 2.068821 AGATCCAGTGGGCGCAGAT 61.069 57.895 10.83 3.42 0.00 2.90
176 186 2.910479 TCTGGAGACGGTGCGTGT 60.910 61.111 0.00 0.00 41.37 4.49
542 553 0.401738 ATGTGTCCCCTCTGTTGTGG 59.598 55.000 0.00 0.00 0.00 4.17
548 559 1.219124 CGTGGATGTGTCCCCTCTG 59.781 63.158 0.00 0.00 44.41 3.35
566 578 0.608640 AGGAGGTGGTCAACATCGAC 59.391 55.000 0.00 0.00 40.58 4.20
587 599 1.600916 GGTGAAGGAAGTTGCGGCT 60.601 57.895 0.00 0.00 0.00 5.52
615 627 1.289109 CGCAAAGAACGTCATCCGGT 61.289 55.000 0.00 0.00 41.02 5.28
621 633 0.660488 ATTGCACGCAAAGAACGTCA 59.340 45.000 8.76 0.00 42.96 4.35
674 688 7.446319 CCAAAGAGCAATATGGATGATGTCTTA 59.554 37.037 0.00 0.00 34.82 2.10
678 692 4.831155 CCCAAAGAGCAATATGGATGATGT 59.169 41.667 0.00 0.00 34.82 3.06
705 723 2.244695 AGATATCGCCGTTGGATACCA 58.755 47.619 0.00 0.00 0.00 3.25
713 731 4.937620 TCTACCGTTATAGATATCGCCGTT 59.062 41.667 0.00 0.00 0.00 4.44
717 735 6.428799 GGTCATCTACCGTTATAGATATCGC 58.571 44.000 0.00 0.00 39.44 4.58
743 765 4.838152 CCTCCATCCGCACCACCG 62.838 72.222 0.00 0.00 0.00 4.94
751 773 0.745845 CAACCTTGCTCCTCCATCCG 60.746 60.000 0.00 0.00 0.00 4.18
802 824 0.324943 AGTTGGCTACTTCGTGGCAT 59.675 50.000 4.78 0.00 41.80 4.40
838 860 2.483106 GGAAAAAGTCTAGCCGTGGAAC 59.517 50.000 0.00 0.00 0.00 3.62
863 885 1.295423 GTACCGTGCAGGATGGTGT 59.705 57.895 15.97 0.00 44.44 4.16
1204 1226 1.950909 CCTCGTAGAAGAAGCGGATCT 59.049 52.381 0.00 0.00 34.09 2.75
1274 1296 0.039764 ACACGGACAGGAGGATCAGA 59.960 55.000 0.00 0.00 36.25 3.27
1406 1428 1.880340 GTCGATCTTCCCGCAGCTG 60.880 63.158 10.11 10.11 0.00 4.24
1610 1632 2.507992 CAGCCTTCCGACTCTGCG 60.508 66.667 0.00 0.00 0.00 5.18
1696 1718 1.611148 CCACATTTCCGAACCCCGTTA 60.611 52.381 0.00 0.00 36.31 3.18
1699 1721 1.302993 ACCACATTTCCGAACCCCG 60.303 57.895 0.00 0.00 38.18 5.73
1766 1788 8.691661 AATTGTACATCTAGGTCTTGTTGTTT 57.308 30.769 0.00 0.00 0.00 2.83
1776 1798 9.036980 ACTCAGAAAGTAATTGTACATCTAGGT 57.963 33.333 0.00 0.00 36.07 3.08
1911 1949 9.019764 CAGCCATTTTAATTATTTACTTCCACG 57.980 33.333 0.00 0.00 0.00 4.94
1987 2026 6.992063 TTAGAGAACTCATCAGCCATTTTC 57.008 37.500 4.64 0.00 0.00 2.29
2073 2112 2.264455 AGCATCAACCTCTTCAGTCCT 58.736 47.619 0.00 0.00 0.00 3.85
2077 2116 3.008330 CAGGAAGCATCAACCTCTTCAG 58.992 50.000 0.00 0.00 38.29 3.02
2116 2155 5.982516 GGTAATACTGTGCTGAGATGAGAAG 59.017 44.000 0.00 0.00 0.00 2.85
2129 2168 6.148150 ACATAAACAACGGTGGTAATACTGTG 59.852 38.462 4.97 0.00 39.96 3.66
2170 2209 6.332630 CCAGATGGTTGCCAAAATAACTAAG 58.667 40.000 0.00 0.00 36.95 2.18
2305 2346 3.251004 GTGAGTTCTCTGAAACGGCAAAT 59.749 43.478 1.53 0.00 34.27 2.32
2446 3016 9.846248 ATTAGCAAACTATCAGACATTCAAAAC 57.154 29.630 0.00 0.00 0.00 2.43
2463 3033 4.404507 TCAGAGTCGCAAATTAGCAAAC 57.595 40.909 0.00 0.00 0.00 2.93
2503 3073 9.396022 CTTTCCTCCTTAAAATCATAGCTTACA 57.604 33.333 0.00 0.00 0.00 2.41
2557 3127 4.473142 AGAACCTTTCTTCTGGGAACCCA 61.473 47.826 12.30 12.30 43.56 4.51
2734 3304 2.123726 GGGCAGCCATTGGGGTAG 60.124 66.667 15.19 0.00 44.97 3.18
2764 3334 2.839486 TGCCGCAATAGGAGAATAGG 57.161 50.000 0.00 0.00 0.00 2.57
2851 3425 4.649674 TGGGATTTTACAGCGAGAGTAGAT 59.350 41.667 0.00 0.00 0.00 1.98
2922 3497 2.266554 CTCGCACAGAAGACAGGAATC 58.733 52.381 0.00 0.00 0.00 2.52
3014 3590 7.494298 GGAGGAGTGAGAAATAGAAAATCTGTC 59.506 40.741 0.00 0.00 0.00 3.51
3044 3620 6.322201 ACAAATTCACAGTTTTCAGTGGAGAT 59.678 34.615 0.00 0.00 37.79 2.75
3081 3657 3.680458 GCTTCCACTGCTAGTTTACAGAC 59.320 47.826 2.53 0.00 37.35 3.51
3212 3788 4.200874 TCCTCAAAAACGAAAACAGCCTA 58.799 39.130 0.00 0.00 0.00 3.93
3213 3789 3.020984 TCCTCAAAAACGAAAACAGCCT 58.979 40.909 0.00 0.00 0.00 4.58
3229 3805 1.444933 TTCCCAAAGCTCCTTCCTCA 58.555 50.000 0.00 0.00 0.00 3.86
3234 3810 6.381133 CCATTAACTTATTCCCAAAGCTCCTT 59.619 38.462 0.00 0.00 0.00 3.36
3251 3827 5.072329 AGCCAGCACATATAGACCATTAACT 59.928 40.000 0.00 0.00 0.00 2.24
3358 3934 4.159135 GGACCTTGCATCAATGTCTGAAAT 59.841 41.667 12.34 0.00 38.44 2.17
3486 4062 6.318900 GGGAACAGAGGGAGTAAATAACAATG 59.681 42.308 0.00 0.00 0.00 2.82
3488 4064 5.311121 TGGGAACAGAGGGAGTAAATAACAA 59.689 40.000 0.00 0.00 35.01 2.83
3496 4072 6.906901 ACTTATATTTGGGAACAGAGGGAGTA 59.093 38.462 0.00 0.00 44.54 2.59
3497 4073 5.731678 ACTTATATTTGGGAACAGAGGGAGT 59.268 40.000 0.00 0.00 44.54 3.85
3498 4074 6.100424 AGACTTATATTTGGGAACAGAGGGAG 59.900 42.308 0.00 0.00 44.54 4.30
3499 4075 5.970640 AGACTTATATTTGGGAACAGAGGGA 59.029 40.000 0.00 0.00 44.54 4.20
3500 4076 6.253946 AGACTTATATTTGGGAACAGAGGG 57.746 41.667 0.00 0.00 44.54 4.30
3501 4077 7.611855 ACAAAGACTTATATTTGGGAACAGAGG 59.388 37.037 3.08 0.00 40.62 3.69
3502 4078 8.567285 ACAAAGACTTATATTTGGGAACAGAG 57.433 34.615 3.08 0.00 40.62 3.35
3503 4079 9.667107 CTACAAAGACTTATATTTGGGAACAGA 57.333 33.333 3.08 0.00 40.62 3.41
3504 4080 9.667107 TCTACAAAGACTTATATTTGGGAACAG 57.333 33.333 3.08 0.00 40.62 3.16
3505 4081 9.667107 CTCTACAAAGACTTATATTTGGGAACA 57.333 33.333 3.08 0.00 40.62 3.18
3506 4082 9.886132 TCTCTACAAAGACTTATATTTGGGAAC 57.114 33.333 3.08 0.00 40.62 3.62
3518 4094 8.816894 TCCATAGTGAAATCTCTACAAAGACTT 58.183 33.333 0.00 0.00 0.00 3.01
3519 4095 8.254508 GTCCATAGTGAAATCTCTACAAAGACT 58.745 37.037 0.00 0.00 0.00 3.24
3520 4096 7.492994 GGTCCATAGTGAAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 0.00 3.01
3521 4097 7.180229 TGGTCCATAGTGAAATCTCTACAAAGA 59.820 37.037 0.00 0.00 0.00 2.52
3522 4098 7.278868 GTGGTCCATAGTGAAATCTCTACAAAG 59.721 40.741 0.00 0.00 0.00 2.77
3523 4099 7.103641 GTGGTCCATAGTGAAATCTCTACAAA 58.896 38.462 0.00 0.00 0.00 2.83
3524 4100 6.212589 TGTGGTCCATAGTGAAATCTCTACAA 59.787 38.462 0.00 0.00 0.00 2.41
3525 4101 5.719563 TGTGGTCCATAGTGAAATCTCTACA 59.280 40.000 0.00 0.00 0.00 2.74
3526 4102 6.222038 TGTGGTCCATAGTGAAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
3527 4103 8.588472 CATATGTGGTCCATAGTGAAATCTCTA 58.412 37.037 0.00 0.00 39.36 2.43
3528 4104 5.965033 ATGTGGTCCATAGTGAAATCTCT 57.035 39.130 0.00 0.00 29.82 3.10
3529 4105 6.652481 CCATATGTGGTCCATAGTGAAATCTC 59.348 42.308 0.00 0.00 39.36 2.75
3530 4106 6.466326 CCCATATGTGGTCCATAGTGAAATCT 60.466 42.308 7.81 0.00 44.48 2.40
3531 4107 5.707298 CCCATATGTGGTCCATAGTGAAATC 59.293 44.000 7.81 0.00 44.48 2.17
3532 4108 5.134339 ACCCATATGTGGTCCATAGTGAAAT 59.866 40.000 7.81 0.00 44.48 2.17
3533 4109 4.476846 ACCCATATGTGGTCCATAGTGAAA 59.523 41.667 7.81 0.00 44.48 2.69
3534 4110 4.044308 ACCCATATGTGGTCCATAGTGAA 58.956 43.478 7.81 0.00 44.48 3.18
3535 4111 3.390967 CACCCATATGTGGTCCATAGTGA 59.609 47.826 7.81 0.00 44.48 3.41
3536 4112 3.136443 ACACCCATATGTGGTCCATAGTG 59.864 47.826 7.81 9.32 44.48 2.74
3537 4113 3.393687 ACACCCATATGTGGTCCATAGT 58.606 45.455 7.81 5.56 44.48 2.12
3538 4114 5.013079 ACATACACCCATATGTGGTCCATAG 59.987 44.000 7.81 5.07 42.84 2.23
3539 4115 4.910913 ACATACACCCATATGTGGTCCATA 59.089 41.667 7.81 0.00 42.84 2.74
3540 4116 3.721575 ACATACACCCATATGTGGTCCAT 59.278 43.478 7.81 6.64 42.84 3.41
3541 4117 3.119319 ACATACACCCATATGTGGTCCA 58.881 45.455 7.81 0.00 42.84 4.02
3542 4118 3.857157 ACATACACCCATATGTGGTCC 57.143 47.619 7.81 0.00 42.84 4.46
3543 4119 4.347000 ACCTACATACACCCATATGTGGTC 59.653 45.833 7.81 0.00 43.93 4.02
3544 4120 4.102524 CACCTACATACACCCATATGTGGT 59.897 45.833 7.81 9.38 43.93 4.16
3545 4121 4.641396 CACCTACATACACCCATATGTGG 58.359 47.826 0.51 0.51 43.93 4.17
3546 4122 4.065088 GCACCTACATACACCCATATGTG 58.935 47.826 8.36 0.00 43.93 3.21
3547 4123 3.714280 TGCACCTACATACACCCATATGT 59.286 43.478 1.24 4.04 45.60 2.29
3548 4124 4.350368 TGCACCTACATACACCCATATG 57.650 45.455 0.00 0.00 38.34 1.78
3549 4125 5.582950 AATGCACCTACATACACCCATAT 57.417 39.130 0.00 0.00 0.00 1.78
3550 4126 5.381184 AAATGCACCTACATACACCCATA 57.619 39.130 0.00 0.00 0.00 2.74
3551 4127 3.951563 AATGCACCTACATACACCCAT 57.048 42.857 0.00 0.00 0.00 4.00
3552 4128 3.730215 AAATGCACCTACATACACCCA 57.270 42.857 0.00 0.00 0.00 4.51
3553 4129 5.433526 TCTAAAATGCACCTACATACACCC 58.566 41.667 0.00 0.00 0.00 4.61
3554 4130 6.037172 CACTCTAAAATGCACCTACATACACC 59.963 42.308 0.00 0.00 0.00 4.16
3555 4131 6.594159 ACACTCTAAAATGCACCTACATACAC 59.406 38.462 0.00 0.00 0.00 2.90
3556 4132 6.707290 ACACTCTAAAATGCACCTACATACA 58.293 36.000 0.00 0.00 0.00 2.29
3557 4133 8.195436 TCTACACTCTAAAATGCACCTACATAC 58.805 37.037 0.00 0.00 0.00 2.39
3558 4134 8.301252 TCTACACTCTAAAATGCACCTACATA 57.699 34.615 0.00 0.00 0.00 2.29
3559 4135 7.182817 TCTACACTCTAAAATGCACCTACAT 57.817 36.000 0.00 0.00 0.00 2.29
3560 4136 6.599356 TCTACACTCTAAAATGCACCTACA 57.401 37.500 0.00 0.00 0.00 2.74
3561 4137 7.764443 TGAATCTACACTCTAAAATGCACCTAC 59.236 37.037 0.00 0.00 0.00 3.18
3562 4138 7.764443 GTGAATCTACACTCTAAAATGCACCTA 59.236 37.037 0.00 0.00 37.73 3.08
3563 4139 6.595716 GTGAATCTACACTCTAAAATGCACCT 59.404 38.462 0.00 0.00 37.73 4.00
3564 4140 6.595716 AGTGAATCTACACTCTAAAATGCACC 59.404 38.462 0.00 0.00 46.36 5.01
3565 4141 7.602517 AGTGAATCTACACTCTAAAATGCAC 57.397 36.000 0.00 0.00 46.36 4.57
3577 4153 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3578 4154 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3579 4155 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3580 4156 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3581 4157 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3582 4158 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3583 4159 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3584 4160 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3585 4161 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3586 4162 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3587 4163 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3588 4164 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
3589 4165 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
3590 4166 8.082852 ACTATAGACTACATACGGAGCAAAATG 58.917 37.037 6.78 0.00 0.00 2.32
3591 4167 8.082852 CACTATAGACTACATACGGAGCAAAAT 58.917 37.037 6.78 0.00 0.00 1.82
3592 4168 7.423199 CACTATAGACTACATACGGAGCAAAA 58.577 38.462 6.78 0.00 0.00 2.44
3593 4169 6.016527 CCACTATAGACTACATACGGAGCAAA 60.017 42.308 6.78 0.00 0.00 3.68
3594 4170 5.472478 CCACTATAGACTACATACGGAGCAA 59.528 44.000 6.78 0.00 0.00 3.91
3595 4171 5.001874 CCACTATAGACTACATACGGAGCA 58.998 45.833 6.78 0.00 0.00 4.26
3596 4172 5.243981 TCCACTATAGACTACATACGGAGC 58.756 45.833 6.78 0.00 0.00 4.70
3597 4173 7.925043 ATTCCACTATAGACTACATACGGAG 57.075 40.000 6.78 0.00 0.00 4.63
3598 4174 9.970553 AATATTCCACTATAGACTACATACGGA 57.029 33.333 6.78 0.00 0.00 4.69
3636 4212 8.348507 CGTACTACTTCCTCCGTTTCTAAATAT 58.651 37.037 0.00 0.00 0.00 1.28
3637 4213 7.336931 ACGTACTACTTCCTCCGTTTCTAAATA 59.663 37.037 0.00 0.00 0.00 1.40
3638 4214 6.151817 ACGTACTACTTCCTCCGTTTCTAAAT 59.848 38.462 0.00 0.00 0.00 1.40
3639 4215 5.473504 ACGTACTACTTCCTCCGTTTCTAAA 59.526 40.000 0.00 0.00 0.00 1.85
3640 4216 5.003804 ACGTACTACTTCCTCCGTTTCTAA 58.996 41.667 0.00 0.00 0.00 2.10
3641 4217 4.579869 ACGTACTACTTCCTCCGTTTCTA 58.420 43.478 0.00 0.00 0.00 2.10
3642 4218 3.416156 ACGTACTACTTCCTCCGTTTCT 58.584 45.455 0.00 0.00 0.00 2.52
3643 4219 3.839051 ACGTACTACTTCCTCCGTTTC 57.161 47.619 0.00 0.00 0.00 2.78
3644 4220 5.705609 TTTACGTACTACTTCCTCCGTTT 57.294 39.130 0.00 0.00 0.00 3.60
3645 4221 5.705609 TTTTACGTACTACTTCCTCCGTT 57.294 39.130 0.00 0.00 0.00 4.44
3646 4222 5.705609 TTTTTACGTACTACTTCCTCCGT 57.294 39.130 0.00 0.00 0.00 4.69
3647 4223 6.095377 ACATTTTTACGTACTACTTCCTCCG 58.905 40.000 0.00 0.00 0.00 4.63
3648 4224 7.895975 AACATTTTTACGTACTACTTCCTCC 57.104 36.000 0.00 0.00 0.00 4.30
3649 4225 9.631452 ACTAACATTTTTACGTACTACTTCCTC 57.369 33.333 0.00 0.00 0.00 3.71
3749 4355 5.213675 CGACTTGAACTTCTCTAACTTCGT 58.786 41.667 0.00 0.00 0.00 3.85
3751 4357 5.402867 CACCGACTTGAACTTCTCTAACTTC 59.597 44.000 0.00 0.00 0.00 3.01
3766 4377 0.320771 CCCTTCCAGACACCGACTTG 60.321 60.000 0.00 0.00 0.00 3.16
3793 4405 9.434275 TTTGATCCTCTGATCCTAAAGTATACA 57.566 33.333 5.50 0.00 45.74 2.29
3810 4422 3.214328 ACACCACACAACTTTGATCCTC 58.786 45.455 0.00 0.00 0.00 3.71
3874 4486 0.396556 TACTATGGCGCTCTGGACCA 60.397 55.000 7.64 0.00 37.99 4.02
3885 4497 7.277174 AGGAAAGCATACAAAATACTATGGC 57.723 36.000 0.00 0.00 0.00 4.40
3889 4501 8.325787 TGAGGAAGGAAAGCATACAAAATACTA 58.674 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.