Multiple sequence alignment - TraesCS4D01G307700

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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 TraesCS4D01G307700 chr4D 100.000 5708 0 0 1 5708 475871636 475877343 0.000000e+00 10541.0
1 TraesCS4D01G307700 chr4B 95.252 1685 63 10 1 1671 600289639 600291320 0.000000e+00 2652.0
2 TraesCS4D01G307700 chr4B 94.965 1569 48 12 2199 3746 600293090 600294648 0.000000e+00 2431.0
3 TraesCS4D01G307700 chr4B 93.912 1232 48 10 3627 4852 600294896 600296106 0.000000e+00 1834.0
4 TraesCS4D01G307700 chr4B 95.607 387 16 1 1818 2203 600292661 600293047 2.260000e-173 619.0
5 TraesCS4D01G307700 chr4B 90.511 274 20 3 5404 5677 600299691 600299958 1.960000e-94 357.0
6 TraesCS4D01G307700 chr4B 93.293 164 7 2 1664 1823 600292312 600292475 7.390000e-59 239.0
7 TraesCS4D01G307700 chr4B 97.500 120 3 0 3627 3746 600294774 600294893 7.500000e-49 206.0
8 TraesCS4D01G307700 chr4B 95.041 121 5 1 3627 3746 600294651 600294771 7.550000e-44 189.0
9 TraesCS4D01G307700 chr4A 89.995 1869 117 33 2248 4074 682982568 682984408 0.000000e+00 2351.0
10 TraesCS4D01G307700 chr4A 92.596 1094 54 7 4076 5161 682984478 682985552 0.000000e+00 1546.0
11 TraesCS4D01G307700 chr4A 95.723 795 21 8 778 1566 682981112 682981899 0.000000e+00 1267.0
12 TraesCS4D01G307700 chr4A 92.689 807 48 6 2248 3051 51133920 51134718 0.000000e+00 1153.0
13 TraesCS4D01G307700 chr4A 96.822 472 15 0 5237 5708 682985545 682986016 0.000000e+00 789.0
14 TraesCS4D01G307700 chr4A 91.732 508 28 3 1 507 682980073 682980567 0.000000e+00 693.0
15 TraesCS4D01G307700 chr4A 93.625 251 14 2 541 790 682980566 682980815 1.940000e-99 374.0
16 TraesCS4D01G307700 chr4A 88.325 197 15 2 3050 3246 51134842 51135030 4.450000e-56 230.0
17 TraesCS4D01G307700 chr4A 96.842 95 1 2 5160 5253 723335567 723335660 2.130000e-34 158.0
18 TraesCS4D01G307700 chr7D 96.040 101 2 1 5147 5245 297632563 297632663 4.580000e-36 163.0
19 TraesCS4D01G307700 chr7D 100.000 87 0 0 5158 5244 429474345 429474259 1.650000e-35 161.0
20 TraesCS4D01G307700 chr7D 95.833 96 4 0 5152 5247 204732363 204732458 7.660000e-34 156.0
21 TraesCS4D01G307700 chr2B 97.895 95 0 2 5160 5253 428384665 428384572 4.580000e-36 163.0
22 TraesCS4D01G307700 chr6B 96.842 95 1 2 5160 5253 231315741 231315834 2.130000e-34 158.0
23 TraesCS4D01G307700 chr3B 96.842 95 1 2 5160 5253 512457505 512457412 2.130000e-34 158.0
24 TraesCS4D01G307700 chr3B 96.774 31 1 0 2173 2203 44648946 44648976 1.000000e-02 52.8
25 TraesCS4D01G307700 chr1B 94.898 98 5 0 5159 5256 234252589 234252686 2.750000e-33 154.0
26 TraesCS4D01G307700 chr1B 100.000 31 0 0 2173 2203 12831801 12831771 2.220000e-04 58.4
27 TraesCS4D01G307700 chr1B 100.000 29 0 0 2175 2203 421093271 421093243 3.000000e-03 54.7
28 TraesCS4D01G307700 chr3A 94.059 101 4 2 5160 5259 83731742 83731841 9.910000e-33 152.0
29 TraesCS4D01G307700 chr7A 96.970 33 0 1 2214 2245 581848357 581848389 3.000000e-03 54.7
30 TraesCS4D01G307700 chr7A 96.970 33 0 1 2213 2244 724488188 724488220 3.000000e-03 54.7
31 TraesCS4D01G307700 chr7A 94.286 35 1 1 2213 2246 83530401 83530435 1.000000e-02 52.8
32 TraesCS4D01G307700 chr5B 100.000 29 0 0 2175 2203 178841066 178841094 3.000000e-03 54.7
33 TraesCS4D01G307700 chr5B 100.000 28 0 0 2176 2203 323861175 323861148 1.000000e-02 52.8
34 TraesCS4D01G307700 chr3D 100.000 29 0 0 2175 2203 505174426 505174454 3.000000e-03 54.7
35 TraesCS4D01G307700 chrUn 96.774 31 1 0 2173 2203 67407021 67407051 1.000000e-02 52.8
36 TraesCS4D01G307700 chr2A 100.000 28 0 0 2176 2203 187856439 187856412 1.000000e-02 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 TraesCS4D01G307700 chr4D 475871636 475877343 5707 False 10541.000 10541 100.000000 1 5708 1 chr4D.!!$F1 5707
1 TraesCS4D01G307700 chr4B 600289639 600299958 10319 False 1065.875 2652 94.510125 1 5677 8 chr4B.!!$F1 5676
2 TraesCS4D01G307700 chr4A 682980073 682986016 5943 False 1170.000 2351 93.415500 1 5708 6 chr4A.!!$F3 5707
3 TraesCS4D01G307700 chr4A 51133920 51135030 1110 False 691.500 1153 90.507000 2248 3246 2 chr4A.!!$F2 998

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
144 145 1.478510 GTGATCGAGGTCCTGACATGT 59.521 52.381 0.00 0.0 0.00 3.21 F
329 332 1.611673 GGTGTGTTGTGCATAGGAGCT 60.612 52.381 0.00 0.0 34.99 4.09 F
441 444 2.034053 TGAACAAAGTGCTAAAAGGGCG 59.966 45.455 0.00 0.0 0.00 6.13 F
2300 3934 6.272558 AGAGGACTGGTTTTCTTGTAACCTAT 59.727 38.462 0.00 0.0 44.32 2.57 F
2714 4351 2.038863 TTGGCTGGAAGGAGTAAGGA 57.961 50.000 0.00 0.0 0.00 3.36 F
3983 6143 0.104671 TAGCCAAATACCCGCGTACC 59.895 55.000 4.92 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 3653 0.744771 GTTCTAGGGCGGGAAAGCAG 60.745 60.000 0.00 0.0 39.27 4.24 R
2324 3959 2.094258 CCGAACACGAGACATGGATTTG 59.906 50.000 0.00 0.0 0.00 2.32 R
2338 3973 4.563337 AAAAACTCTTAAGGCCGAACAC 57.437 40.909 1.85 0.0 0.00 3.32 R
3981 6141 3.688694 TCTAACTGCACAATTACGGGT 57.311 42.857 0.00 0.0 0.00 5.28 R
4479 6726 0.460987 CGAGCACAGGGTCATCCTTC 60.461 60.000 0.00 0.0 45.47 3.46 R
4955 10149 0.038166 GTTGGGCATCCTTCTGGTCA 59.962 55.000 0.00 0.0 34.23 4.02 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
85 86 5.982890 CCATGAAGGTAATTTGGTTCACT 57.017 39.130 0.00 0.00 31.94 3.41
144 145 1.478510 GTGATCGAGGTCCTGACATGT 59.521 52.381 0.00 0.00 0.00 3.21
198 200 6.346678 GGTTTCAGTTCGTGATTCTTGAGTAC 60.347 42.308 0.00 0.00 34.17 2.73
276 279 6.881065 TCCATGTTTTTAGAGAGATTCACTGG 59.119 38.462 0.00 0.00 0.00 4.00
329 332 1.611673 GGTGTGTTGTGCATAGGAGCT 60.612 52.381 0.00 0.00 34.99 4.09
431 434 3.309410 CCACCAAACAATGAACAAAGTGC 59.691 43.478 0.00 0.00 0.00 4.40
441 444 2.034053 TGAACAAAGTGCTAAAAGGGCG 59.966 45.455 0.00 0.00 0.00 6.13
507 511 6.307776 TGGTTACCAATATCAACTGTGGAAA 58.692 36.000 0.00 0.00 35.04 3.13
682 686 8.763049 TTGTTGTGTAAAATTTGTCATGTTCA 57.237 26.923 0.00 0.00 0.00 3.18
1621 2003 9.042008 CATTTACTTGTTAGTACAGAACTGTGT 57.958 33.333 16.37 7.17 44.63 3.72
1699 3084 8.598924 GTGTGAGATGAGTGTTTAATGTAGATG 58.401 37.037 0.00 0.00 0.00 2.90
1717 3102 9.995003 ATGTAGATGGATCTCTCTTAATTGAAC 57.005 33.333 3.45 0.00 38.32 3.18
1745 3133 9.586435 GGCATAAAATATATAAATCAAGCCACC 57.414 33.333 0.00 0.00 36.03 4.61
1836 3419 7.765695 ATCATATTGTCATGGTGGTAAATCC 57.234 36.000 0.00 0.00 0.00 3.01
1884 3469 9.803507 ACATTGTCATGGTAGAATCATATTGAT 57.196 29.630 0.00 0.00 34.98 2.57
2068 3653 6.317391 AGCTTTCCATCATGCTACTTTACTTC 59.683 38.462 0.00 0.00 33.64 3.01
2300 3934 6.272558 AGAGGACTGGTTTTCTTGTAACCTAT 59.727 38.462 0.00 0.00 44.32 2.57
2319 3953 7.585579 ACCTATAGCTTAGGAAGTAGAACAC 57.414 40.000 21.60 0.00 38.09 3.32
2324 3959 6.862711 AGCTTAGGAAGTAGAACACAAAAC 57.137 37.500 0.00 0.00 0.00 2.43
2338 3973 4.858935 ACACAAAACAAATCCATGTCTCG 58.141 39.130 0.00 0.00 31.81 4.04
2344 3979 2.736721 ACAAATCCATGTCTCGTGTTCG 59.263 45.455 0.00 0.00 38.55 3.95
2386 4022 3.472283 TTTCACATGCATTGGCTTTGT 57.528 38.095 0.00 0.00 41.91 2.83
2454 4091 5.604650 AGAGTCTTGCTATTGCTTATAGGGT 59.395 40.000 0.00 0.00 37.32 4.34
2455 4092 6.100424 AGAGTCTTGCTATTGCTTATAGGGTT 59.900 38.462 0.00 0.00 37.32 4.11
2456 4093 6.663734 AGTCTTGCTATTGCTTATAGGGTTT 58.336 36.000 0.00 0.00 37.32 3.27
2457 4094 6.768381 AGTCTTGCTATTGCTTATAGGGTTTC 59.232 38.462 0.00 0.00 37.32 2.78
2458 4095 6.768381 GTCTTGCTATTGCTTATAGGGTTTCT 59.232 38.462 0.00 0.00 37.32 2.52
2459 4096 7.931948 GTCTTGCTATTGCTTATAGGGTTTCTA 59.068 37.037 0.00 0.00 37.32 2.10
2460 4097 7.931948 TCTTGCTATTGCTTATAGGGTTTCTAC 59.068 37.037 0.00 0.00 37.32 2.59
2591 4228 9.810545 GAAGCTTAATCTGTACTCTGTAAATCT 57.189 33.333 0.00 0.00 0.00 2.40
2699 4336 6.430925 TCATTCAGCATACCAGTTATATTGGC 59.569 38.462 4.19 0.00 39.39 4.52
2714 4351 2.038863 TTGGCTGGAAGGAGTAAGGA 57.961 50.000 0.00 0.00 0.00 3.36
2715 4352 2.270434 TGGCTGGAAGGAGTAAGGAT 57.730 50.000 0.00 0.00 0.00 3.24
2782 4419 7.014615 GGGAGTTCAAGATATTGGCATTGTATT 59.985 37.037 0.00 0.00 0.00 1.89
2951 4588 8.563123 TCTATATTTGTCAGTAGATACTCCCG 57.437 38.462 0.00 0.00 33.46 5.14
3125 4888 6.200286 GCATGGCATTATATTATCAAGCATGC 59.800 38.462 10.51 10.51 35.79 4.06
3135 4898 8.945481 ATATTATCAAGCATGCTCTCATAGTC 57.055 34.615 22.93 0.00 0.00 2.59
3141 4904 3.642377 AGCATGCTCTCATAGTCTGTCAT 59.358 43.478 16.30 0.00 0.00 3.06
3237 5000 9.232473 GATTCATGGTACTTTCTTTTAGAAGGT 57.768 33.333 8.85 8.85 44.99 3.50
3267 5031 6.928492 AGTATGTTTGGGTTGTAATTGCTTTG 59.072 34.615 0.00 0.00 0.00 2.77
3274 5046 5.163513 GGGTTGTAATTGCTTTGTCTGATG 58.836 41.667 0.00 0.00 0.00 3.07
3310 5082 7.869937 ACACCATCACTTTATGATAAGATCTCG 59.130 37.037 0.00 0.00 46.96 4.04
3585 5375 7.550712 CAGAATAAAGGAAGGAAAAGAATGGG 58.449 38.462 0.00 0.00 0.00 4.00
3641 5677 7.055378 TGCAAACTAAGTTAAACCTTAGACCA 58.945 34.615 15.97 7.25 44.36 4.02
3663 5699 9.431887 GACCATACAGTAGATTCTTGTGTTAAA 57.568 33.333 6.06 0.00 0.00 1.52
3708 5744 3.945285 ACTTTACCCTTGTGTGTGAACAG 59.055 43.478 0.00 0.00 0.00 3.16
3979 6139 2.132762 CTAACTAGCCAAATACCCGCG 58.867 52.381 0.00 0.00 0.00 6.46
3980 6140 0.251073 AACTAGCCAAATACCCGCGT 59.749 50.000 4.92 0.00 0.00 6.01
3981 6141 1.113788 ACTAGCCAAATACCCGCGTA 58.886 50.000 4.92 0.00 0.00 4.42
3982 6142 1.202452 ACTAGCCAAATACCCGCGTAC 60.202 52.381 4.92 0.00 0.00 3.67
3983 6143 0.104671 TAGCCAAATACCCGCGTACC 59.895 55.000 4.92 0.00 0.00 3.34
4392 6639 1.372683 CTACTGGGCATCGGATGGG 59.627 63.158 18.96 0.00 0.00 4.00
4455 6702 2.187599 AAAACATGACCGCGAGCAGC 62.188 55.000 8.23 0.00 43.95 5.25
4479 6726 1.209275 CCTTCGGCACTAGATTCGCG 61.209 60.000 0.00 0.00 0.00 5.87
4506 6753 1.003355 CCCTGTGCTCGACCACATT 60.003 57.895 13.71 0.00 44.05 2.71
4519 6766 3.600388 GACCACATTGACGAGGAGATTT 58.400 45.455 0.00 0.00 0.00 2.17
4563 6810 2.196776 CCAGGGGGATGGTGCATC 59.803 66.667 0.00 0.00 39.87 3.91
4696 6943 5.705441 CCAGGTTTTTATTCTCAGCAGTGTA 59.295 40.000 0.00 0.00 0.00 2.90
4715 6962 4.752101 GTGTATATGGGACTGATGAGTTGC 59.248 45.833 0.00 0.00 30.16 4.17
4733 6980 6.658816 TGAGTTGCTGTAAATTGTATCACCAT 59.341 34.615 0.00 0.00 0.00 3.55
4816 7064 1.001746 AGTGCCGCTCCTGATATGATG 59.998 52.381 0.00 0.00 0.00 3.07
4887 10081 0.179150 CAGAGCGAGGAAGAAGACCG 60.179 60.000 0.00 0.00 0.00 4.79
4913 10107 0.107703 TTCGGGATCAGCATGTCACC 60.108 55.000 0.00 0.00 37.40 4.02
4927 10121 1.955778 TGTCACCTGGAAATGCAACAG 59.044 47.619 0.00 0.00 0.00 3.16
4951 10145 7.531871 CAGAATTTCAGAAGTCATTGTTACACG 59.468 37.037 0.00 0.00 32.49 4.49
4952 10146 4.725556 TTCAGAAGTCATTGTTACACGC 57.274 40.909 0.00 0.00 0.00 5.34
4953 10147 3.990092 TCAGAAGTCATTGTTACACGCT 58.010 40.909 0.00 0.00 0.00 5.07
4954 10148 3.987868 TCAGAAGTCATTGTTACACGCTC 59.012 43.478 0.00 0.00 0.00 5.03
4955 10149 3.990469 CAGAAGTCATTGTTACACGCTCT 59.010 43.478 0.00 0.00 0.00 4.09
4956 10150 3.990469 AGAAGTCATTGTTACACGCTCTG 59.010 43.478 0.00 0.00 0.00 3.35
4957 10151 3.660501 AGTCATTGTTACACGCTCTGA 57.339 42.857 0.00 0.00 0.00 3.27
4958 10152 3.318017 AGTCATTGTTACACGCTCTGAC 58.682 45.455 0.00 0.00 33.46 3.51
4959 10153 2.412089 GTCATTGTTACACGCTCTGACC 59.588 50.000 0.00 0.00 0.00 4.02
4960 10154 2.036604 TCATTGTTACACGCTCTGACCA 59.963 45.455 0.00 0.00 0.00 4.02
4961 10155 2.148916 TTGTTACACGCTCTGACCAG 57.851 50.000 0.00 0.00 0.00 4.00
4962 10156 1.324383 TGTTACACGCTCTGACCAGA 58.676 50.000 0.00 0.00 35.85 3.86
4963 10157 1.684450 TGTTACACGCTCTGACCAGAA 59.316 47.619 1.08 0.00 36.94 3.02
4964 10158 2.288213 TGTTACACGCTCTGACCAGAAG 60.288 50.000 1.08 1.68 36.94 2.85
4965 10159 0.888619 TACACGCTCTGACCAGAAGG 59.111 55.000 1.08 0.00 36.94 3.46
4966 10160 0.827925 ACACGCTCTGACCAGAAGGA 60.828 55.000 1.08 0.00 36.94 3.36
4967 10161 0.534412 CACGCTCTGACCAGAAGGAT 59.466 55.000 1.08 0.00 36.94 3.24
5051 10245 1.160329 AATAGGTTGCTGATCGGCGC 61.160 55.000 21.30 15.81 34.52 6.53
5086 10280 2.537143 TGACTACAAGGAGGGAGAACC 58.463 52.381 0.00 0.00 40.67 3.62
5087 10281 2.158219 TGACTACAAGGAGGGAGAACCA 60.158 50.000 0.00 0.00 43.89 3.67
5088 10282 2.904434 GACTACAAGGAGGGAGAACCAA 59.096 50.000 0.00 0.00 43.89 3.67
5161 10355 5.131475 TCATGGATTTAGGGTTAGGGTGTAC 59.869 44.000 0.00 0.00 0.00 2.90
5162 10356 4.702196 TGGATTTAGGGTTAGGGTGTACT 58.298 43.478 0.00 0.00 0.00 2.73
5163 10357 4.718276 TGGATTTAGGGTTAGGGTGTACTC 59.282 45.833 0.00 0.00 0.00 2.59
5164 10358 4.102210 GGATTTAGGGTTAGGGTGTACTCC 59.898 50.000 5.35 5.35 0.00 3.85
5174 10368 3.606595 GGGTGTACTCCCTCTGTAAAC 57.393 52.381 23.22 0.00 43.85 2.01
5175 10369 3.171528 GGGTGTACTCCCTCTGTAAACT 58.828 50.000 23.22 0.00 43.85 2.66
5176 10370 4.347607 GGGTGTACTCCCTCTGTAAACTA 58.652 47.826 23.22 0.00 43.85 2.24
5177 10371 4.774200 GGGTGTACTCCCTCTGTAAACTAA 59.226 45.833 23.22 0.00 43.85 2.24
5178 10372 5.424573 GGGTGTACTCCCTCTGTAAACTAAT 59.575 44.000 23.22 0.00 43.85 1.73
5179 10373 6.608808 GGGTGTACTCCCTCTGTAAACTAATA 59.391 42.308 23.22 0.00 43.85 0.98
5180 10374 7.289549 GGGTGTACTCCCTCTGTAAACTAATAT 59.710 40.741 23.22 0.00 43.85 1.28
5181 10375 9.359653 GGTGTACTCCCTCTGTAAACTAATATA 57.640 37.037 2.33 0.00 30.92 0.86
5186 10380 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5187 10381 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
5188 10382 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
5218 10412 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
5219 10413 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
5220 10414 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
5221 10415 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
5222 10416 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
5223 10417 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
5235 10429 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5236 10430 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5237 10431 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5238 10432 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5239 10433 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5240 10434 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
5241 10435 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5242 10436 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
5243 10437 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
5426 11018 9.691362 CAGTAACAAATAAGCAACAAATTAGGT 57.309 29.630 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.499693 TCAACCATGATCACGCCTCTTA 59.500 45.455 0.00 0.00 0.00 2.10
44 45 0.539986 GTCGCTAAGAACCCCCATCA 59.460 55.000 0.00 0.00 0.00 3.07
144 145 1.004161 TCCATTTGAGCAACATCCCGA 59.996 47.619 0.00 0.00 0.00 5.14
198 200 6.934645 ACATATTCACAATATCCTGGTTACCG 59.065 38.462 0.00 0.00 31.83 4.02
239 242 5.813513 AAAAACATGGAAGCCAGATCTTT 57.186 34.783 0.00 0.00 36.75 2.52
329 332 2.472695 ATCGACTTGTGGCTTAAGCA 57.527 45.000 27.83 12.09 44.36 3.91
592 596 2.095415 GGCAAACGCTAAAAATCCGACT 60.095 45.455 0.00 0.00 0.00 4.18
682 686 4.990426 GCACTACATGGCAATTTCACTTTT 59.010 37.500 0.00 0.00 0.00 2.27
723 730 9.801873 ATGGTTATTACTATGCAACATGAAAAC 57.198 29.630 0.00 0.00 0.00 2.43
1545 1870 2.818751 AGTAGGTGTGGAGAGAGGAG 57.181 55.000 0.00 0.00 0.00 3.69
1621 2003 5.726793 AGAAGAGGAAAAGGGCAACTAGATA 59.273 40.000 0.00 0.00 0.00 1.98
1699 3084 3.810386 GCCCGTTCAATTAAGAGAGATCC 59.190 47.826 0.00 0.00 0.00 3.36
1717 3102 8.465999 TGGCTTGATTTATATATTTTATGCCCG 58.534 33.333 0.00 0.00 33.89 6.13
1745 3133 7.710907 TGAAGTTTATGTAGCTAATGCCTACTG 59.289 37.037 0.00 0.00 40.80 2.74
1836 3419 6.791303 TGTAGTTGCCAAAGTTAAACAAGAG 58.209 36.000 0.00 0.00 0.00 2.85
1884 3469 3.945981 TGACGTAGGATACAACAAGCA 57.054 42.857 0.00 0.00 43.24 3.91
2030 3615 5.655974 TGATGGAAAGCTATTTATGTTGCCA 59.344 36.000 0.00 0.00 0.00 4.92
2044 3629 6.317391 AGAAGTAAAGTAGCATGATGGAAAGC 59.683 38.462 0.00 0.00 0.00 3.51
2068 3653 0.744771 GTTCTAGGGCGGGAAAGCAG 60.745 60.000 0.00 0.00 39.27 4.24
2170 3756 7.862675 AGTTTACAGAGGGAGTAGCAATTATT 58.137 34.615 0.00 0.00 0.00 1.40
2289 3923 9.352191 TCTACTTCCTAAGCTATAGGTTACAAG 57.648 37.037 22.87 22.87 37.00 3.16
2300 3934 7.502696 TGTTTTGTGTTCTACTTCCTAAGCTA 58.497 34.615 0.00 0.00 0.00 3.32
2319 3953 4.858935 ACACGAGACATGGATTTGTTTTG 58.141 39.130 0.00 0.00 0.00 2.44
2324 3959 2.094258 CCGAACACGAGACATGGATTTG 59.906 50.000 0.00 0.00 0.00 2.32
2338 3973 4.563337 AAAAACTCTTAAGGCCGAACAC 57.437 40.909 1.85 0.00 0.00 3.32
2344 3979 6.748333 AATACCGTAAAAACTCTTAAGGCC 57.252 37.500 1.85 0.00 34.75 5.19
2386 4022 5.888691 TGCACTGTTTCAACTTCAACTAA 57.111 34.783 0.00 0.00 0.00 2.24
2421 4057 8.572855 AGCAATAGCAAGACTCTTTTAGAAAT 57.427 30.769 0.00 0.00 45.49 2.17
2591 4228 7.220030 AGTCAAATCAGCTCAGAAGAGTTAAA 58.780 34.615 0.00 0.00 44.00 1.52
2699 4336 6.678568 ATGACATATCCTTACTCCTTCCAG 57.321 41.667 0.00 0.00 0.00 3.86
2714 4351 8.613060 AGCGACAATTCAGAATTATGACATAT 57.387 30.769 8.12 0.00 0.00 1.78
2715 4352 8.437360 AAGCGACAATTCAGAATTATGACATA 57.563 30.769 8.12 0.00 0.00 2.29
2782 4419 2.936919 ATGTCTTGACCTGCACAGAA 57.063 45.000 0.00 0.00 0.00 3.02
3051 4814 6.788930 CAGGTCAACGAAATAAACTAAACGAC 59.211 38.462 0.00 0.00 0.00 4.34
3135 4898 9.672086 GTAGTAGAGCAAAGATAACTATGACAG 57.328 37.037 0.00 0.00 0.00 3.51
3141 4904 9.902684 AGTACAGTAGTAGAGCAAAGATAACTA 57.097 33.333 0.00 0.00 0.00 2.24
3310 5082 8.669243 CCCTAGAAACAACAGTTTAATCTGATC 58.331 37.037 18.30 9.11 35.71 2.92
3615 5405 7.722285 TGGTCTAAGGTTTAACTTAGTTTGCAT 59.278 33.333 12.87 0.00 46.33 3.96
3663 5699 8.691661 AGTTGCATAGAAATATACCCGAAAAT 57.308 30.769 0.00 0.00 0.00 1.82
3979 6139 4.497300 TCTAACTGCACAATTACGGGTAC 58.503 43.478 0.00 0.00 0.00 3.34
3980 6140 4.804868 TCTAACTGCACAATTACGGGTA 57.195 40.909 0.00 0.00 0.00 3.69
3981 6141 3.688694 TCTAACTGCACAATTACGGGT 57.311 42.857 0.00 0.00 0.00 5.28
3982 6142 6.861065 AATATCTAACTGCACAATTACGGG 57.139 37.500 0.00 0.00 0.00 5.28
3983 6143 8.360325 TGTAATATCTAACTGCACAATTACGG 57.640 34.615 0.00 0.00 33.24 4.02
4074 6244 7.221645 CCATCATCATATACGTGCAGATTAGTC 59.778 40.741 0.00 0.00 0.00 2.59
4239 6486 6.703319 TCTTGGTAGATTATTTGTTCCGACA 58.297 36.000 0.00 0.00 0.00 4.35
4392 6639 1.572941 GGGCTCGTTTTTGGACGTC 59.427 57.895 7.13 7.13 43.23 4.34
4479 6726 0.460987 CGAGCACAGGGTCATCCTTC 60.461 60.000 0.00 0.00 45.47 3.46
4506 6753 1.798223 CGTTGCAAAATCTCCTCGTCA 59.202 47.619 0.00 0.00 0.00 4.35
4545 6792 3.432335 ATGCACCATCCCCCTGGG 61.432 66.667 5.50 5.50 46.11 4.45
4563 6810 4.742201 CTGTCGTCCCCAGCACCG 62.742 72.222 0.00 0.00 0.00 4.94
4653 6900 3.492102 GGATAGGATAGCCTTTGTGCA 57.508 47.619 4.04 0.00 45.63 4.57
4696 6943 3.457380 ACAGCAACTCATCAGTCCCATAT 59.543 43.478 0.00 0.00 29.93 1.78
4715 6962 7.754924 GTGGTTTCATGGTGATACAATTTACAG 59.245 37.037 0.00 0.00 31.29 2.74
4733 6980 5.209818 AGATAACTGAACTCGTGGTTTCA 57.790 39.130 0.00 0.00 38.41 2.69
4816 7064 7.088589 ACAAGAATGTATAATTGCACAGGAC 57.911 36.000 0.00 0.00 38.24 3.85
4887 10081 2.467826 GCTGATCCCGAAGCAGTGC 61.468 63.158 7.13 7.13 39.31 4.40
4913 10107 5.775686 TCTGAAATTCTGTTGCATTTCCAG 58.224 37.500 5.91 2.27 38.23 3.86
4922 10116 9.173939 GTAACAATGACTTCTGAAATTCTGTTG 57.826 33.333 12.14 11.78 0.00 3.33
4927 10121 6.303259 GCGTGTAACAATGACTTCTGAAATTC 59.697 38.462 0.00 0.00 35.74 2.17
4951 10145 0.463474 GGCATCCTTCTGGTCAGAGC 60.463 60.000 0.75 0.00 38.88 4.09
4952 10146 0.179936 GGGCATCCTTCTGGTCAGAG 59.820 60.000 0.75 0.00 38.88 3.35
4953 10147 0.547471 TGGGCATCCTTCTGGTCAGA 60.547 55.000 0.00 0.00 35.27 3.27
4954 10148 0.329261 TTGGGCATCCTTCTGGTCAG 59.671 55.000 0.00 0.00 34.23 3.51
4955 10149 0.038166 GTTGGGCATCCTTCTGGTCA 59.962 55.000 0.00 0.00 34.23 4.02
4956 10150 0.681243 GGTTGGGCATCCTTCTGGTC 60.681 60.000 0.00 0.00 34.23 4.02
4957 10151 1.384191 GGTTGGGCATCCTTCTGGT 59.616 57.895 0.00 0.00 34.23 4.00
4958 10152 0.251742 TTGGTTGGGCATCCTTCTGG 60.252 55.000 0.00 0.00 0.00 3.86
4959 10153 0.890683 GTTGGTTGGGCATCCTTCTG 59.109 55.000 0.00 0.00 0.00 3.02
4960 10154 0.779997 AGTTGGTTGGGCATCCTTCT 59.220 50.000 0.00 0.00 0.00 2.85
4961 10155 1.632589 AAGTTGGTTGGGCATCCTTC 58.367 50.000 0.00 0.00 0.00 3.46
4962 10156 2.990740 TAAGTTGGTTGGGCATCCTT 57.009 45.000 0.00 0.00 0.00 3.36
4963 10157 2.582636 AGATAAGTTGGTTGGGCATCCT 59.417 45.455 0.00 0.00 0.00 3.24
4964 10158 2.689983 CAGATAAGTTGGTTGGGCATCC 59.310 50.000 0.00 0.00 0.00 3.51
4965 10159 3.620488 TCAGATAAGTTGGTTGGGCATC 58.380 45.455 0.00 0.00 0.00 3.91
4966 10160 3.737559 TCAGATAAGTTGGTTGGGCAT 57.262 42.857 0.00 0.00 0.00 4.40
4967 10161 3.737559 ATCAGATAAGTTGGTTGGGCA 57.262 42.857 0.00 0.00 0.00 5.36
5044 10238 4.454717 GAAAAACCGCGCGCCGAT 62.455 61.111 27.36 11.51 40.02 4.18
5046 10240 4.676586 AAGAAAAACCGCGCGCCG 62.677 61.111 27.36 22.49 0.00 6.46
5051 10245 4.344448 TGTAGTCAAAAAGAAAAACCGCG 58.656 39.130 0.00 0.00 0.00 6.46
5086 10280 9.447040 CACAGCTCAATATCATTATTTGACTTG 57.553 33.333 0.00 0.00 37.11 3.16
5087 10281 9.182214 ACACAGCTCAATATCATTATTTGACTT 57.818 29.630 0.00 0.00 37.11 3.01
5088 10282 8.618677 CACACAGCTCAATATCATTATTTGACT 58.381 33.333 0.00 0.00 37.11 3.41
5161 10355 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
5162 10356 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
5191 10385 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
5192 10386 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
5193 10387 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
5194 10388 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
5195 10389 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
5196 10390 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
5197 10391 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
5209 10403 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
5210 10404 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
5211 10405 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5212 10406 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5213 10407 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5214 10408 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5215 10409 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5216 10410 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5217 10411 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5222 10416 9.819754 AGTTATACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
5223 10417 9.071276 CAGTTATACTCCCTCCGTAAACTAATA 57.929 37.037 0.00 0.00 0.00 0.98
5224 10418 7.562821 ACAGTTATACTCCCTCCGTAAACTAAT 59.437 37.037 0.00 0.00 0.00 1.73
5225 10419 6.891908 ACAGTTATACTCCCTCCGTAAACTAA 59.108 38.462 0.00 0.00 0.00 2.24
5226 10420 6.426587 ACAGTTATACTCCCTCCGTAAACTA 58.573 40.000 0.00 0.00 0.00 2.24
5227 10421 5.267587 ACAGTTATACTCCCTCCGTAAACT 58.732 41.667 0.00 0.00 0.00 2.66
5228 10422 5.588958 ACAGTTATACTCCCTCCGTAAAC 57.411 43.478 0.00 0.00 0.00 2.01
5229 10423 6.662755 TCTACAGTTATACTCCCTCCGTAAA 58.337 40.000 0.00 0.00 0.00 2.01
5230 10424 6.252599 TCTACAGTTATACTCCCTCCGTAA 57.747 41.667 0.00 0.00 0.00 3.18
5231 10425 5.894298 TCTACAGTTATACTCCCTCCGTA 57.106 43.478 0.00 0.00 0.00 4.02
5232 10426 4.785346 TCTACAGTTATACTCCCTCCGT 57.215 45.455 0.00 0.00 0.00 4.69
5233 10427 5.768662 TGAATCTACAGTTATACTCCCTCCG 59.231 44.000 0.00 0.00 0.00 4.63
5234 10428 7.451877 TCATGAATCTACAGTTATACTCCCTCC 59.548 40.741 0.00 0.00 0.00 4.30
5235 10429 8.410673 TCATGAATCTACAGTTATACTCCCTC 57.589 38.462 0.00 0.00 0.00 4.30
5236 10430 7.453126 CCTCATGAATCTACAGTTATACTCCCT 59.547 40.741 0.00 0.00 0.00 4.20
5237 10431 7.233757 ACCTCATGAATCTACAGTTATACTCCC 59.766 40.741 0.00 0.00 0.00 4.30
5238 10432 8.085296 CACCTCATGAATCTACAGTTATACTCC 58.915 40.741 0.00 0.00 0.00 3.85
5239 10433 7.596995 GCACCTCATGAATCTACAGTTATACTC 59.403 40.741 0.00 0.00 0.00 2.59
5240 10434 7.069950 TGCACCTCATGAATCTACAGTTATACT 59.930 37.037 0.00 0.00 0.00 2.12
5241 10435 7.210174 TGCACCTCATGAATCTACAGTTATAC 58.790 38.462 0.00 0.00 0.00 1.47
5242 10436 7.360113 TGCACCTCATGAATCTACAGTTATA 57.640 36.000 0.00 0.00 0.00 0.98
5243 10437 6.239217 TGCACCTCATGAATCTACAGTTAT 57.761 37.500 0.00 0.00 0.00 1.89
5244 10438 5.675684 TGCACCTCATGAATCTACAGTTA 57.324 39.130 0.00 0.00 0.00 2.24
5342 10536 4.083431 GCATCTAGCCATAGCAGTGAATTG 60.083 45.833 0.00 0.00 43.56 2.32
5426 11018 1.557832 AGCTATGGCGGTTTGGAAGTA 59.442 47.619 0.00 0.00 44.37 2.24
5492 11084 6.553953 TGTCAACAAGGCATAGGAGTATAA 57.446 37.500 0.00 0.00 0.00 0.98
5597 11189 7.323656 CGCTTTCAAACATCTTAGTAAAACTGG 59.676 37.037 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.