Multiple sequence alignment - TraesCS5D01G568900

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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 TraesCS5D01G568900 chr5D 100.000 2828 0 0 1 2828 565729080 565726253 0.000000e+00 5223
1 TraesCS5D01G568900 chr5D 81.814 2062 332 33 1 2024 565712873 565710817 0.000000e+00 1690
2 TraesCS5D01G568900 chr5D 81.503 2049 333 35 1 2027 565735414 565733390 0.000000e+00 1642
3 TraesCS5D01G568900 chr5D 80.546 2051 356 28 3 2024 565719572 565717536 0.000000e+00 1537
4 TraesCS5D01G568900 chr5D 81.394 1306 181 40 756 2027 565824732 565823455 0.000000e+00 1009
5 TraesCS5D01G568900 chr5D 85.577 104 14 1 1914 2016 565716497 565716394 1.070000e-19 108
6 TraesCS5D01G568900 chr5B 82.822 2055 306 33 1 2018 707421274 707423318 0.000000e+00 1796
7 TraesCS5D01G568900 chr5B 82.554 2052 313 30 1 2021 707191954 707193991 0.000000e+00 1764
8 TraesCS5D01G568900 chr5B 85.448 1718 187 24 969 2652 707430400 707432088 0.000000e+00 1729
9 TraesCS5D01G568900 chr5B 81.090 1872 311 29 169 2013 707415555 707417410 0.000000e+00 1456
10 TraesCS5D01G568900 chr5B 82.836 1072 169 12 1 1067 707408993 707410054 0.000000e+00 946
11 TraesCS5D01G568900 chr5B 84.104 887 114 20 1146 2008 707410172 707411055 0.000000e+00 832
12 TraesCS5D01G568900 chr5B 78.729 409 70 16 341 737 707404520 707404923 1.010000e-64 257
13 TraesCS5D01G568900 chr5B 88.889 90 10 0 2738 2827 707413624 707413713 8.280000e-21 111
14 TraesCS5D01G568900 chr5B 83.962 106 15 1 2154 2257 707387849 707387954 1.790000e-17 100
15 TraesCS5D01G568900 chr4A 81.623 2046 326 41 1 2013 607278877 607276849 0.000000e+00 1650
16 TraesCS5D01G568900 chr4A 80.936 2072 342 33 1 2024 607273044 607270978 0.000000e+00 1589


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 TraesCS5D01G568900 chr5D 565726253 565729080 2827 True 5223.000000 5223 100.000000 1 2828 1 chr5D.!!$R1 2827
1 TraesCS5D01G568900 chr5D 565733390 565735414 2024 True 1642.000000 1642 81.503000 1 2027 1 chr5D.!!$R2 2026
2 TraesCS5D01G568900 chr5D 565710817 565719572 8755 True 1111.666667 1690 82.645667 1 2024 3 chr5D.!!$R4 2023
3 TraesCS5D01G568900 chr5D 565823455 565824732 1277 True 1009.000000 1009 81.394000 756 2027 1 chr5D.!!$R3 1271
4 TraesCS5D01G568900 chr5B 707191954 707193991 2037 False 1764.000000 1764 82.554000 1 2021 1 chr5B.!!$F1 2020
5 TraesCS5D01G568900 chr5B 707430400 707432088 1688 False 1729.000000 1729 85.448000 969 2652 1 chr5B.!!$F4 1683
6 TraesCS5D01G568900 chr5B 707408993 707423318 14325 False 1028.200000 1796 83.948200 1 2827 5 chr5B.!!$F5 2826
7 TraesCS5D01G568900 chr4A 607270978 607278877 7899 True 1619.500000 1650 81.279500 1 2024 2 chr4A.!!$R1 2023

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
591 593 0.032416 ACGGGCCACTACCACTAGAT 60.032 55.0 4.39 0.0 0.0 1.98 F
847 855 0.527817 CCGATACTGCCGACAACTCC 60.528 60.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 8424 0.107214 ACCCAGACGCCCATTACATG 60.107 55.0 0.0 0.0 0.0 3.21 R
2676 11090 0.530870 GGTTCTATGACTCCTGCGGC 60.531 60.0 0.0 0.0 0.0 6.53 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
52 53 3.247173 CGTTAAGCAATCTGATCAGCCTC 59.753 47.826 18.36 6.88 0.00 4.70
61 62 0.672889 TGATCAGCCTCGATCTCAGC 59.327 55.000 9.14 0.00 42.01 4.26
62 63 0.961019 GATCAGCCTCGATCTCAGCT 59.039 55.000 0.00 0.00 39.02 4.24
68 69 1.855360 GCCTCGATCTCAGCTTTAACG 59.145 52.381 0.00 0.00 0.00 3.18
76 77 4.111375 TCTCAGCTTTAACGATCTCACC 57.889 45.455 0.00 0.00 0.00 4.02
83 84 1.843368 TAACGATCTCACCGGTCCTT 58.157 50.000 2.59 0.00 0.00 3.36
103 104 4.288105 CCTTTGCCACTATGGATAGGAGAT 59.712 45.833 0.00 0.00 40.96 2.75
121 122 4.754114 GGAGATCTCGCAAAGCTAATTGAT 59.246 41.667 16.46 0.00 31.84 2.57
136 137 5.279910 GCTAATTGATCTGGACCTGAGCTAT 60.280 44.000 16.40 11.92 0.00 2.97
146 147 5.716979 TGGACCTGAGCTATAATAACCTCT 58.283 41.667 0.00 0.00 0.00 3.69
147 148 5.775701 TGGACCTGAGCTATAATAACCTCTC 59.224 44.000 0.00 0.00 0.00 3.20
175 176 8.352942 GGTTTGATACATGAAGGTCATTTATCC 58.647 37.037 16.29 6.39 41.97 2.59
209 210 1.490490 TGGAGAAGTTGTGGCTGTCTT 59.510 47.619 0.00 0.00 0.00 3.01
228 229 7.039644 GCTGTCTTATAACTCTATAGCCCTCAA 60.040 40.741 0.00 0.00 0.00 3.02
236 237 6.168270 ACTCTATAGCCCTCAAAGTGAATC 57.832 41.667 0.00 0.00 0.00 2.52
239 240 0.035056 AGCCCTCAAAGTGAATCCGG 60.035 55.000 0.00 0.00 0.00 5.14
251 252 2.902457 AATCCGGCGTGGGTTCCTT 61.902 57.895 6.01 0.00 35.61 3.36
263 264 4.384208 CGTGGGTTCCTTCTTCCAATCTAT 60.384 45.833 0.00 0.00 0.00 1.98
328 329 2.309528 TGTGGCTTAGATGGCTAACG 57.690 50.000 0.00 0.00 33.24 3.18
331 332 1.565106 GCTTAGATGGCTAACGCGC 59.435 57.895 5.73 0.00 36.88 6.86
367 369 9.702494 CTTGATATCTCAACACAAGCATATCTA 57.298 33.333 3.98 0.00 36.46 1.98
429 431 5.529581 TGGACTATCTGAATATGCGACAA 57.470 39.130 0.00 0.00 0.00 3.18
448 450 4.866921 ACAAAACCAAATTAGCGGTTCTC 58.133 39.130 7.18 0.00 44.80 2.87
455 457 3.838244 AATTAGCGGTTCTCTGCCATA 57.162 42.857 0.00 0.00 46.23 2.74
462 464 3.815401 GCGGTTCTCTGCCATATACAATT 59.185 43.478 0.00 0.00 39.82 2.32
484 486 3.999001 TGAACTTATGAGAGCAGTTGCAG 59.001 43.478 6.90 0.00 45.16 4.41
486 488 3.594134 ACTTATGAGAGCAGTTGCAGTC 58.406 45.455 6.90 3.13 45.16 3.51
502 504 5.638596 TGCAGTCGATCTTAGTTCTAACA 57.361 39.130 0.00 0.00 0.00 2.41
504 506 5.862323 TGCAGTCGATCTTAGTTCTAACAAC 59.138 40.000 0.00 0.00 0.00 3.32
507 509 7.410942 GCAGTCGATCTTAGTTCTAACAACTTG 60.411 40.741 0.00 0.00 0.00 3.16
534 536 3.756117 CCCAATACCTAAGCTTCCCATC 58.244 50.000 0.00 0.00 0.00 3.51
536 538 4.137543 CCAATACCTAAGCTTCCCATCAC 58.862 47.826 0.00 0.00 0.00 3.06
541 543 4.561752 ACCTAAGCTTCCCATCACTCTAT 58.438 43.478 0.00 0.00 0.00 1.98
542 544 4.971924 ACCTAAGCTTCCCATCACTCTATT 59.028 41.667 0.00 0.00 0.00 1.73
544 546 4.851639 AAGCTTCCCATCACTCTATTGT 57.148 40.909 0.00 0.00 0.00 2.71
561 563 9.357161 ACTCTATTGTACTTGGATCTTAGTAGG 57.643 37.037 7.45 0.12 0.00 3.18
586 588 0.609662 TTTAGACGGGCCACTACCAC 59.390 55.000 4.39 0.00 0.00 4.16
591 593 0.032416 ACGGGCCACTACCACTAGAT 60.032 55.000 4.39 0.00 0.00 1.98
696 698 4.807304 CGTTTACTACGCCTGTTGGATATT 59.193 41.667 0.00 0.00 44.26 1.28
738 740 3.482156 TCTATTCCTGATTGCTCTGCC 57.518 47.619 0.00 0.00 0.00 4.85
761 763 6.623986 GCCGATACATCCACAACAAACATAAA 60.624 38.462 0.00 0.00 0.00 1.40
800 808 8.870075 ATTAATCTAAGCTTGAGAAACAACCT 57.130 30.769 9.86 0.00 34.56 3.50
813 821 2.334006 ACAACCTCCTCTCAGGTGAT 57.666 50.000 0.00 0.00 46.97 3.06
830 838 4.702131 AGGTGATTTTCCTTCATTTCTCCG 59.298 41.667 0.00 0.00 30.18 4.63
839 847 2.509052 TCATTTCTCCGATACTGCCG 57.491 50.000 0.00 0.00 0.00 5.69
847 855 0.527817 CCGATACTGCCGACAACTCC 60.528 60.000 0.00 0.00 0.00 3.85
855 863 1.000955 TGCCGACAACTCCTCTTTCTC 59.999 52.381 0.00 0.00 0.00 2.87
858 866 2.586900 CGACAACTCCTCTTTCTCGAC 58.413 52.381 0.00 0.00 0.00 4.20
888 896 5.659079 ACACAACCATTTCTTTGGGACTTTA 59.341 36.000 0.00 0.00 41.35 1.85
892 900 4.832823 ACCATTTCTTTGGGACTTTACCAG 59.167 41.667 0.00 0.00 41.35 4.00
942 950 3.056322 TGGCTTTCTTAAGACTACGGTCC 60.056 47.826 4.18 1.05 40.30 4.46
954 962 9.941325 TTAAGACTACGGTCCAATATGTTTTAA 57.059 29.630 0.00 0.00 43.05 1.52
1029 1037 3.881220 TGCCTACAATAACCTAACAGGC 58.119 45.455 2.77 2.77 45.82 4.85
1031 7745 4.266714 GCCTACAATAACCTAACAGGCAA 58.733 43.478 4.88 0.00 45.13 4.52
1043 7757 5.047377 ACCTAACAGGCAACATACCAAAATG 60.047 40.000 0.00 0.00 39.63 2.32
1044 7758 3.959535 ACAGGCAACATACCAAAATGG 57.040 42.857 0.00 0.00 41.65 3.16
1076 7802 4.693283 TGCAAAGGGATGATACTAACGAG 58.307 43.478 0.00 0.00 0.00 4.18
1081 7807 7.309255 GCAAAGGGATGATACTAACGAGAGATA 60.309 40.741 0.00 0.00 0.00 1.98
1082 7808 8.577296 CAAAGGGATGATACTAACGAGAGATAA 58.423 37.037 0.00 0.00 0.00 1.75
1083 7809 7.931578 AGGGATGATACTAACGAGAGATAAG 57.068 40.000 0.00 0.00 0.00 1.73
1084 7810 6.887545 AGGGATGATACTAACGAGAGATAAGG 59.112 42.308 0.00 0.00 0.00 2.69
1085 7811 6.095720 GGGATGATACTAACGAGAGATAAGGG 59.904 46.154 0.00 0.00 0.00 3.95
1086 7812 6.660094 GGATGATACTAACGAGAGATAAGGGT 59.340 42.308 0.00 0.00 0.00 4.34
1087 7813 7.177041 GGATGATACTAACGAGAGATAAGGGTT 59.823 40.741 0.00 0.00 0.00 4.11
1088 7814 9.228949 GATGATACTAACGAGAGATAAGGGTTA 57.771 37.037 0.00 0.00 0.00 2.85
1089 7815 9.756571 ATGATACTAACGAGAGATAAGGGTTAT 57.243 33.333 0.00 0.00 0.00 1.89
1092 7818 7.893124 ACTAACGAGAGATAAGGGTTATGAA 57.107 36.000 0.00 0.00 0.00 2.57
1097 7823 9.930693 AACGAGAGATAAGGGTTATGAATATTC 57.069 33.333 8.60 8.60 0.00 1.75
1102 7828 9.507329 GAGATAAGGGTTATGAATATTCTGCAA 57.493 33.333 16.24 5.19 0.00 4.08
1108 7834 9.151177 AGGGTTATGAATATTCTGCAATTCATT 57.849 29.630 22.80 11.68 45.90 2.57
1109 7835 9.768662 GGGTTATGAATATTCTGCAATTCATTT 57.231 29.630 22.80 9.04 45.90 2.32
1165 7930 4.579454 TTCACCTATACCGAGAATTCCG 57.421 45.455 0.65 5.63 0.00 4.30
1203 7968 6.957020 AGGGTCAAGAGAGATTATATACAGGG 59.043 42.308 0.00 0.00 0.00 4.45
1210 7975 6.887545 AGAGAGATTATATACAGGGGAAGTCG 59.112 42.308 0.00 0.00 0.00 4.18
1305 8070 5.123820 TGTCAAACTGAAGAACCTGAACTTG 59.876 40.000 0.00 0.00 0.00 3.16
1349 8114 6.530019 AAAAATTCCAGAGAATATTGGCGT 57.470 33.333 0.00 0.00 42.03 5.68
1408 8173 3.244561 TGAGTTGTCTGGTGAAATCCCTC 60.245 47.826 0.00 0.00 0.00 4.30
1418 8183 4.264352 TGGTGAAATCCCTCCAAGCTTATT 60.264 41.667 0.00 0.00 0.00 1.40
1500 8265 1.879380 TCAGGGAATCAACTGCAAACG 59.121 47.619 0.00 0.00 34.76 3.60
1577 8344 1.610522 GCCACAGAAATGTTCACAGCT 59.389 47.619 0.00 0.00 0.00 4.24
1578 8345 2.606308 GCCACAGAAATGTTCACAGCTG 60.606 50.000 13.48 13.48 32.96 4.24
1657 8424 1.412710 TCATCGCTATGGGTTCTGGAC 59.587 52.381 0.00 0.00 33.61 4.02
1743 8510 0.104304 ACTCCGTCTGCGACAAGTTT 59.896 50.000 8.91 0.00 41.33 2.66
1820 8587 2.110901 ATTGCAGAAGCTGAGAGTGG 57.889 50.000 0.00 0.00 42.74 4.00
1880 8653 3.932710 AGTGTGTGGCTTTACATGTATCG 59.067 43.478 6.36 2.10 32.43 2.92
1897 8670 8.814235 ACATGTATCGTTGTTATTAAGTACTGC 58.186 33.333 0.00 0.00 0.00 4.40
1938 8731 7.553881 TTGAGGATTATGCTGTAAAGTAAGC 57.446 36.000 0.00 0.00 39.96 3.09
1942 8735 8.581253 AGGATTATGCTGTAAAGTAAGCTTTT 57.419 30.769 3.20 0.00 41.78 2.27
1973 8769 7.975058 TGTAAGTTGATGTGCAATGAATAATGG 59.025 33.333 0.00 0.00 39.03 3.16
2000 8796 1.062488 AGCACCAAGTCCCCTGTTCT 61.062 55.000 0.00 0.00 0.00 3.01
2056 8868 3.596214 CCACGAAAGCTGTATAAGGTGT 58.404 45.455 0.00 0.00 36.51 4.16
2058 8870 3.000727 ACGAAAGCTGTATAAGGTGTGC 58.999 45.455 0.00 0.00 36.51 4.57
2121 8945 4.097286 GCACAAACACAGTTTCTTCCCTAA 59.903 41.667 0.00 0.00 0.00 2.69
2122 8946 5.733373 GCACAAACACAGTTTCTTCCCTAAG 60.733 44.000 0.00 0.00 0.00 2.18
2157 8982 5.163754 ACGGTTTCAGAGTTTTTCAGACAAG 60.164 40.000 0.00 0.00 0.00 3.16
2172 8997 3.254166 CAGACAAGCTAGTTTTGCCACAT 59.746 43.478 8.47 0.00 0.00 3.21
2173 8998 3.503748 AGACAAGCTAGTTTTGCCACATC 59.496 43.478 8.47 0.98 0.00 3.06
2223 9060 4.517285 TCATGTCTGTTCAAATAGGGCTC 58.483 43.478 0.00 0.00 0.00 4.70
2224 9061 4.019411 TCATGTCTGTTCAAATAGGGCTCA 60.019 41.667 0.00 0.00 0.00 4.26
2227 9064 3.935828 GTCTGTTCAAATAGGGCTCAGAC 59.064 47.826 0.00 0.00 41.70 3.51
2258 9095 7.483307 ACAGCCATAATTAAGTATGTGCAAAG 58.517 34.615 24.77 19.19 33.57 2.77
2293 9130 7.855904 ACACAAGTGAATTTACTTTGTCGATTC 59.144 33.333 12.58 0.00 38.78 2.52
2300 9137 8.073768 TGAATTTACTTTGTCGATTCTTTCACC 58.926 33.333 0.00 0.00 0.00 4.02
2302 9139 3.146847 ACTTTGTCGATTCTTTCACCCC 58.853 45.455 0.00 0.00 0.00 4.95
2304 9141 2.178912 TGTCGATTCTTTCACCCCAC 57.821 50.000 0.00 0.00 0.00 4.61
2318 9155 1.227556 CCCACGCACTATACTGGGC 60.228 63.158 0.00 0.00 37.13 5.36
2344 9949 3.492313 CCGCAATTACTTCAGTTTCAGC 58.508 45.455 0.00 0.00 0.00 4.26
2345 9950 3.058293 CCGCAATTACTTCAGTTTCAGCA 60.058 43.478 0.00 0.00 0.00 4.41
2347 9952 4.083855 CGCAATTACTTCAGTTTCAGCAGA 60.084 41.667 0.00 0.00 0.00 4.26
2348 9953 5.391310 CGCAATTACTTCAGTTTCAGCAGAT 60.391 40.000 0.00 0.00 0.00 2.90
2349 9954 6.385033 GCAATTACTTCAGTTTCAGCAGATT 58.615 36.000 0.00 0.00 0.00 2.40
2350 9955 6.525976 GCAATTACTTCAGTTTCAGCAGATTC 59.474 38.462 0.00 0.00 0.00 2.52
2351 9956 7.574592 GCAATTACTTCAGTTTCAGCAGATTCT 60.575 37.037 0.00 0.00 0.00 2.40
2352 9957 7.992754 ATTACTTCAGTTTCAGCAGATTCTT 57.007 32.000 0.00 0.00 0.00 2.52
2354 9959 6.311055 ACTTCAGTTTCAGCAGATTCTTTC 57.689 37.500 0.00 0.00 0.00 2.62
2355 9960 5.824624 ACTTCAGTTTCAGCAGATTCTTTCA 59.175 36.000 0.00 0.00 0.00 2.69
2356 9961 6.489361 ACTTCAGTTTCAGCAGATTCTTTCAT 59.511 34.615 0.00 0.00 0.00 2.57
2357 9962 6.492007 TCAGTTTCAGCAGATTCTTTCATC 57.508 37.500 0.00 0.00 0.00 2.92
2358 9963 5.999600 TCAGTTTCAGCAGATTCTTTCATCA 59.000 36.000 0.00 0.00 0.00 3.07
2360 9965 5.766670 AGTTTCAGCAGATTCTTTCATCACA 59.233 36.000 0.00 0.00 0.00 3.58
2361 9966 6.263842 AGTTTCAGCAGATTCTTTCATCACAA 59.736 34.615 0.00 0.00 0.00 3.33
2380 9993 5.592282 TCACAAACTAACTTGCCTGAATGAA 59.408 36.000 0.00 0.00 0.00 2.57
2406 10019 7.786305 CACAATTAAGTTTGTGCAGATAGTG 57.214 36.000 8.57 0.00 46.95 2.74
2421 10034 5.107298 GCAGATAGTGAAACACAAGTGAGAC 60.107 44.000 7.28 0.00 41.43 3.36
2432 10045 3.677121 CACAAGTGAGACTACTGCATGAC 59.323 47.826 0.00 0.00 0.00 3.06
2463 10076 8.484641 TTTTTATGTTGATTGCACTGTTTGAA 57.515 26.923 0.00 0.00 0.00 2.69
2472 10085 5.581126 TTGCACTGTTTGAATTCTTCACT 57.419 34.783 7.05 0.00 39.87 3.41
2488 10101 5.405797 TCTTCACTCAATCGAGATCACTTG 58.594 41.667 0.00 0.00 42.34 3.16
2509 10122 4.294232 TGCACGGTGTTTGATTTAATGTG 58.706 39.130 10.24 0.00 0.00 3.21
2529 10142 1.480137 GCAGAGTCACAGGCTAGACAT 59.520 52.381 18.01 6.61 37.23 3.06
2530 10143 2.738000 GCAGAGTCACAGGCTAGACATG 60.738 54.545 18.01 16.13 37.23 3.21
2632 11046 3.207669 CGGGGTCGTCGTAGGAGG 61.208 72.222 0.00 0.00 0.00 4.30
2699 11113 1.474143 GCAGGAGTCATAGAACCTGGC 60.474 57.143 17.10 9.77 46.71 4.85
2726 11140 2.805353 CGTGTCGCCGTCCTTGAG 60.805 66.667 0.00 0.00 0.00 3.02
2729 11143 4.070552 GTCGCCGTCCTTGAGCCT 62.071 66.667 0.00 0.00 0.00 4.58
2732 11146 2.185608 GCCGTCCTTGAGCCTCTC 59.814 66.667 0.00 0.00 0.00 3.20
2733 11147 2.355193 GCCGTCCTTGAGCCTCTCT 61.355 63.158 0.00 0.00 0.00 3.10
2734 11148 1.893919 GCCGTCCTTGAGCCTCTCTT 61.894 60.000 0.00 0.00 0.00 2.85
2735 11149 0.610687 CCGTCCTTGAGCCTCTCTTT 59.389 55.000 0.00 0.00 0.00 2.52
2775 11606 6.713903 AGTGAATGACAGTTCATCAATCAACT 59.286 34.615 0.00 0.00 42.00 3.16
2777 11608 7.864379 GTGAATGACAGTTCATCAATCAACTTT 59.136 33.333 0.00 0.00 42.00 2.66
2779 11610 5.522456 TGACAGTTCATCAATCAACTTTGC 58.478 37.500 0.00 0.00 30.06 3.68
2804 11635 4.449743 GTGTCGTTGTAAATAGCAGGTTCA 59.550 41.667 0.00 0.00 0.00 3.18
2815 11646 6.461110 AATAGCAGGTTCATGAAATTCAGG 57.539 37.500 10.35 0.64 0.00 3.86
2819 11650 4.400251 GCAGGTTCATGAAATTCAGGATCA 59.600 41.667 11.23 0.00 37.03 2.92
2823 11654 6.950041 AGGTTCATGAAATTCAGGATCAAAGA 59.050 34.615 11.23 0.00 37.03 2.52
2827 11658 6.950041 TCATGAAATTCAGGATCAAAGAGGTT 59.050 34.615 6.21 0.00 31.68 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.439449 GTGAGATCGTTAAAGCTGAGATCG 59.561 45.833 0.00 0.00 41.65 3.69
61 62 2.165845 AGGACCGGTGAGATCGTTAAAG 59.834 50.000 14.63 0.00 0.00 1.85
62 63 2.173519 AGGACCGGTGAGATCGTTAAA 58.826 47.619 14.63 0.00 0.00 1.52
68 69 0.744771 GGCAAAGGACCGGTGAGATC 60.745 60.000 14.63 0.00 0.00 2.75
76 77 0.251916 TCCATAGTGGCAAAGGACCG 59.748 55.000 0.00 0.00 37.47 4.79
83 84 4.756564 AGATCTCCTATCCATAGTGGCAA 58.243 43.478 0.00 0.00 37.47 4.52
103 104 3.873361 CCAGATCAATTAGCTTTGCGAGA 59.127 43.478 0.00 0.00 0.00 4.04
121 122 5.716979 AGGTTATTATAGCTCAGGTCCAGA 58.283 41.667 0.00 0.00 0.00 3.86
146 147 5.497464 TGACCTTCATGTATCAAACCAGA 57.503 39.130 0.00 0.00 0.00 3.86
147 148 6.764308 AATGACCTTCATGTATCAAACCAG 57.236 37.500 0.00 0.00 37.15 4.00
154 155 5.122396 GCCGGATAAATGACCTTCATGTATC 59.878 44.000 5.05 14.39 46.29 2.24
175 176 0.537188 TCTCCAAGCTTTCTAGGCCG 59.463 55.000 0.00 0.00 0.00 6.13
209 210 8.777578 TTCACTTTGAGGGCTATAGAGTTATA 57.222 34.615 3.21 0.00 0.00 0.98
228 229 2.046314 CCCACGCCGGATTCACTT 60.046 61.111 5.05 0.00 36.56 3.16
236 237 3.546714 AAGAAGGAACCCACGCCGG 62.547 63.158 0.00 0.00 0.00 6.13
239 240 0.536460 TTGGAAGAAGGAACCCACGC 60.536 55.000 0.00 0.00 0.00 5.34
275 276 1.656652 CCGAGAAGGCATGAACGAAT 58.343 50.000 0.00 0.00 0.00 3.34
298 299 5.452356 CCATCTAAGCCACAATGGGAATTTC 60.452 44.000 0.00 0.00 38.19 2.17
328 329 7.265647 TGAGATATCAAGATATACTAGGCGC 57.734 40.000 5.32 0.00 34.36 6.53
367 369 0.467290 AACCAATCTGGCACCGTGTT 60.467 50.000 0.00 0.00 42.67 3.32
411 413 6.603237 TGGTTTTGTCGCATATTCAGATAG 57.397 37.500 0.00 0.00 0.00 2.08
413 415 5.895636 TTGGTTTTGTCGCATATTCAGAT 57.104 34.783 0.00 0.00 0.00 2.90
448 450 9.276590 TCTCATAAGTTCAATTGTATATGGCAG 57.723 33.333 5.13 5.54 0.00 4.85
455 457 8.671921 CAACTGCTCTCATAAGTTCAATTGTAT 58.328 33.333 5.13 0.00 31.88 2.29
462 464 3.999001 CTGCAACTGCTCTCATAAGTTCA 59.001 43.478 2.95 0.00 42.66 3.18
484 486 7.808856 ACTCAAGTTGTTAGAACTAAGATCGAC 59.191 37.037 2.11 0.00 0.00 4.20
486 488 7.062371 CCACTCAAGTTGTTAGAACTAAGATCG 59.938 40.741 2.11 0.00 0.00 3.69
502 504 1.710809 AGGTATTGGGCCACTCAAGTT 59.289 47.619 5.23 0.00 0.00 2.66
504 506 3.545703 CTTAGGTATTGGGCCACTCAAG 58.454 50.000 5.23 0.20 0.00 3.02
507 509 1.490910 AGCTTAGGTATTGGGCCACTC 59.509 52.381 5.23 0.00 0.00 3.51
536 538 9.575868 TCCTACTAAGATCCAAGTACAATAGAG 57.424 37.037 0.00 0.00 0.00 2.43
561 563 4.753610 GGTAGTGGCCCGTCTAAATTATTC 59.246 45.833 0.00 0.00 0.00 1.75
628 630 1.271597 GGTGCCAGAGATGGAGTTGTT 60.272 52.381 0.00 0.00 0.00 2.83
675 677 6.537301 CAGAAATATCCAACAGGCGTAGTAAA 59.463 38.462 0.00 0.00 0.00 2.01
684 686 8.689972 AGCTTATTTTCAGAAATATCCAACAGG 58.310 33.333 0.00 0.00 37.52 4.00
718 720 2.224137 CGGCAGAGCAATCAGGAATAGA 60.224 50.000 0.00 0.00 0.00 1.98
720 722 1.762370 TCGGCAGAGCAATCAGGAATA 59.238 47.619 0.00 0.00 0.00 1.75
738 740 8.735303 TTTTTATGTTTGTTGTGGATGTATCG 57.265 30.769 0.00 0.00 0.00 2.92
800 808 3.909995 TGAAGGAAAATCACCTGAGAGGA 59.090 43.478 0.00 0.00 37.67 3.71
813 821 5.354234 GCAGTATCGGAGAAATGAAGGAAAA 59.646 40.000 0.00 0.00 43.58 2.29
830 838 1.751924 AGAGGAGTTGTCGGCAGTATC 59.248 52.381 0.00 0.00 0.00 2.24
839 847 2.559231 AGGTCGAGAAAGAGGAGTTGTC 59.441 50.000 0.00 0.00 0.00 3.18
847 855 1.795286 GTGTGCAAGGTCGAGAAAGAG 59.205 52.381 0.00 0.00 0.00 2.85
855 863 0.667993 AATGGTTGTGTGCAAGGTCG 59.332 50.000 0.00 0.00 34.94 4.79
858 866 3.457610 AAGAAATGGTTGTGTGCAAGG 57.542 42.857 0.00 0.00 34.94 3.61
888 896 0.409092 TGTCCCAAATCCATGCTGGT 59.591 50.000 2.68 0.00 39.03 4.00
892 900 2.679336 GCAATTTGTCCCAAATCCATGC 59.321 45.455 8.31 8.31 0.00 4.06
916 924 5.642491 ACCGTAGTCTTAAGAAAGCCAAATC 59.358 40.000 6.78 0.00 32.36 2.17
931 939 7.046033 CCTTAAAACATATTGGACCGTAGTCT 58.954 38.462 0.00 0.00 43.05 3.24
942 950 8.739039 TCTGGAATGTGACCTTAAAACATATTG 58.261 33.333 0.00 0.00 33.48 1.90
954 962 0.908198 GCTCCTCTGGAATGTGACCT 59.092 55.000 0.00 0.00 0.00 3.85
999 1007 3.632145 GGTTATTGTAGGCAAGGTCCATG 59.368 47.826 0.00 0.00 38.10 3.66
1000 1008 3.527665 AGGTTATTGTAGGCAAGGTCCAT 59.472 43.478 0.00 0.00 38.10 3.41
1043 7757 2.802719 TCCCTTTGCAGTTACCAATCC 58.197 47.619 0.00 0.00 0.00 3.01
1044 7758 4.016444 TCATCCCTTTGCAGTTACCAATC 58.984 43.478 0.00 0.00 0.00 2.67
1049 7763 6.018994 CGTTAGTATCATCCCTTTGCAGTTAC 60.019 42.308 0.00 0.00 0.00 2.50
1076 7802 9.507329 TTGCAGAATATTCATAACCCTTATCTC 57.493 33.333 17.56 0.00 0.00 2.75
1081 7807 8.537728 TGAATTGCAGAATATTCATAACCCTT 57.462 30.769 17.56 2.54 36.22 3.95
1082 7808 8.716674 ATGAATTGCAGAATATTCATAACCCT 57.283 30.769 18.43 0.15 45.10 4.34
1083 7809 9.768662 AAATGAATTGCAGAATATTCATAACCC 57.231 29.630 19.62 5.84 45.79 4.11
1130 7856 8.627403 CGGTATAGGTGAAATCAAGACTAAGTA 58.373 37.037 0.00 0.00 0.00 2.24
1132 7858 7.713750 TCGGTATAGGTGAAATCAAGACTAAG 58.286 38.462 0.00 0.00 0.00 2.18
1142 7868 5.539048 CGGAATTCTCGGTATAGGTGAAAT 58.461 41.667 5.23 0.00 0.00 2.17
1143 7869 4.738541 GCGGAATTCTCGGTATAGGTGAAA 60.739 45.833 15.15 0.00 0.00 2.69
1165 7930 0.034337 TGACCCTTTGTGACTACCGC 59.966 55.000 0.00 0.00 0.00 5.68
1203 7968 6.342338 AGGTTCACCATATATACGACTTCC 57.658 41.667 0.00 0.00 38.89 3.46
1305 8070 5.389859 TTCCATTGAATGTGTTCCATGAC 57.610 39.130 4.27 0.00 38.91 3.06
1349 8114 0.750249 TGACTCCACTTGCGTCAAGA 59.250 50.000 21.19 4.05 43.42 3.02
1408 8173 2.715046 TGTGAGAGCCAATAAGCTTGG 58.285 47.619 9.86 3.47 45.15 3.61
1418 8183 2.417787 CGACTCAATGATGTGAGAGCCA 60.418 50.000 9.10 0.00 46.76 4.75
1577 8344 1.210478 GAGTAGCTGGAATTGGCTCCA 59.790 52.381 0.00 0.00 43.45 3.86
1578 8345 1.210478 TGAGTAGCTGGAATTGGCTCC 59.790 52.381 0.00 0.00 39.65 4.70
1657 8424 0.107214 ACCCAGACGCCCATTACATG 60.107 55.000 0.00 0.00 0.00 3.21
1669 8436 1.066787 GGTGCAGAAGACTACCCAGAC 60.067 57.143 0.00 0.00 0.00 3.51
1743 8510 3.134623 CCAGCACATAGACCCAGTCATAA 59.865 47.826 0.00 0.00 34.60 1.90
1820 8587 3.258228 GAAGAACCAGAGAGCTAGTTGC 58.742 50.000 0.00 0.00 43.29 4.17
1880 8653 7.884816 TCTGTGAGCAGTACTTAATAACAAC 57.115 36.000 0.00 0.00 43.05 3.32
1896 8669 7.792374 TCCTCAAATTTATGTATCTGTGAGC 57.208 36.000 0.00 0.00 31.87 4.26
1938 8731 8.969121 TTGCACATCAACTTACATATCAAAAG 57.031 30.769 0.00 0.00 0.00 2.27
1942 8735 7.862512 TCATTGCACATCAACTTACATATCA 57.137 32.000 0.00 0.00 37.53 2.15
1973 8769 4.982701 ACTTGGTGCTGCCCCTGC 62.983 66.667 2.15 0.00 36.04 4.85
2000 8796 1.340502 ACACATTGACACACACACCCA 60.341 47.619 0.00 0.00 0.00 4.51
2121 8945 2.028130 TGAAACCGTGCATTGTTTCCT 58.972 42.857 27.31 7.36 46.13 3.36
2122 8946 2.034053 TCTGAAACCGTGCATTGTTTCC 59.966 45.455 27.31 16.80 46.13 3.13
2133 8957 4.258543 TGTCTGAAAAACTCTGAAACCGT 58.741 39.130 0.00 0.00 34.16 4.83
2134 8958 4.875544 TGTCTGAAAAACTCTGAAACCG 57.124 40.909 0.00 0.00 34.16 4.44
2157 8982 3.923017 ACAAGATGTGGCAAAACTAGC 57.077 42.857 0.00 0.00 0.00 3.42
2223 9060 7.820648 ACTTAATTATGGCTGTCAAAAGTCTG 58.179 34.615 3.66 0.00 0.00 3.51
2224 9061 9.686683 ATACTTAATTATGGCTGTCAAAAGTCT 57.313 29.630 3.66 0.00 0.00 3.24
2227 9064 9.507280 CACATACTTAATTATGGCTGTCAAAAG 57.493 33.333 15.05 0.00 34.25 2.27
2277 9114 6.072119 GGGGTGAAAGAATCGACAAAGTAAAT 60.072 38.462 0.00 0.00 0.00 1.40
2285 9122 1.606994 CGTGGGGTGAAAGAATCGACA 60.607 52.381 0.00 0.00 0.00 4.35
2293 9130 2.093658 AGTATAGTGCGTGGGGTGAAAG 60.094 50.000 0.00 0.00 0.00 2.62
2302 9139 4.012554 CGCCCAGTATAGTGCGTG 57.987 61.111 1.67 0.00 41.95 5.34
2329 9166 7.498900 TGAAAGAATCTGCTGAAACTGAAGTAA 59.501 33.333 0.00 0.00 0.00 2.24
2344 9949 9.390795 CAAGTTAGTTTGTGATGAAAGAATCTG 57.609 33.333 0.00 0.00 0.00 2.90
2345 9950 8.078596 GCAAGTTAGTTTGTGATGAAAGAATCT 58.921 33.333 0.00 0.00 0.00 2.40
2347 9952 7.014615 AGGCAAGTTAGTTTGTGATGAAAGAAT 59.985 33.333 0.00 0.00 0.00 2.40
2348 9953 6.321181 AGGCAAGTTAGTTTGTGATGAAAGAA 59.679 34.615 0.00 0.00 0.00 2.52
2349 9954 5.827797 AGGCAAGTTAGTTTGTGATGAAAGA 59.172 36.000 0.00 0.00 0.00 2.52
2350 9955 5.916883 CAGGCAAGTTAGTTTGTGATGAAAG 59.083 40.000 0.00 0.00 0.00 2.62
2351 9956 5.592282 TCAGGCAAGTTAGTTTGTGATGAAA 59.408 36.000 0.00 0.00 0.00 2.69
2352 9957 5.129634 TCAGGCAAGTTAGTTTGTGATGAA 58.870 37.500 0.00 0.00 0.00 2.57
2354 9959 5.437289 TTCAGGCAAGTTAGTTTGTGATG 57.563 39.130 0.00 0.00 0.00 3.07
2355 9960 5.769662 TCATTCAGGCAAGTTAGTTTGTGAT 59.230 36.000 0.00 0.00 0.00 3.06
2356 9961 5.129634 TCATTCAGGCAAGTTAGTTTGTGA 58.870 37.500 0.00 0.00 0.00 3.58
2357 9962 5.437289 TCATTCAGGCAAGTTAGTTTGTG 57.563 39.130 0.00 0.00 0.00 3.33
2358 9963 5.221244 GGTTCATTCAGGCAAGTTAGTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
2360 9965 4.892934 TGGTTCATTCAGGCAAGTTAGTTT 59.107 37.500 0.00 0.00 0.00 2.66
2361 9966 4.278419 GTGGTTCATTCAGGCAAGTTAGTT 59.722 41.667 0.00 0.00 0.00 2.24
2400 10013 7.327275 CAGTAGTCTCACTTGTGTTTCACTATC 59.673 40.741 0.46 1.01 35.11 2.08
2402 10015 6.504398 CAGTAGTCTCACTTGTGTTTCACTA 58.496 40.000 0.46 1.64 35.11 2.74
2406 10019 4.119862 TGCAGTAGTCTCACTTGTGTTTC 58.880 43.478 0.46 0.00 0.00 2.78
2463 10076 6.219417 AGTGATCTCGATTGAGTGAAGAAT 57.781 37.500 9.87 0.00 43.09 2.40
2472 10085 2.262211 CGTGCAAGTGATCTCGATTGA 58.738 47.619 0.00 0.00 0.00 2.57
2488 10101 3.121113 GCACATTAAATCAAACACCGTGC 59.879 43.478 0.00 0.00 40.21 5.34
2509 10122 0.891373 TGTCTAGCCTGTGACTCTGC 59.109 55.000 0.00 0.00 34.57 4.26
2521 10134 2.854777 CGCAGTGTTCTACATGTCTAGC 59.145 50.000 0.00 0.00 0.00 3.42
2529 10142 6.448852 TCTATAACAAACGCAGTGTTCTACA 58.551 36.000 0.00 0.00 45.00 2.74
2530 10143 6.034683 CCTCTATAACAAACGCAGTGTTCTAC 59.965 42.308 0.00 0.00 45.00 2.59
2673 11087 4.221422 TATGACTCCTGCGGCGCC 62.221 66.667 30.82 19.07 0.00 6.53
2676 11090 0.530870 GGTTCTATGACTCCTGCGGC 60.531 60.000 0.00 0.00 0.00 6.53
2713 11127 3.760035 GAGGCTCAAGGACGGCGA 61.760 66.667 16.62 0.00 0.00 5.54
2718 11132 3.333804 CAGAAAAGAGAGGCTCAAGGAC 58.666 50.000 18.26 3.58 32.06 3.85
2726 11140 2.483491 CTCACTTGCAGAAAAGAGAGGC 59.517 50.000 3.43 0.00 39.68 4.70
2729 11143 4.141846 ACTCACTCACTTGCAGAAAAGAGA 60.142 41.667 9.65 0.00 0.00 3.10
2732 11146 3.873361 TCACTCACTCACTTGCAGAAAAG 59.127 43.478 0.00 0.00 0.00 2.27
2733 11147 3.872696 TCACTCACTCACTTGCAGAAAA 58.127 40.909 0.00 0.00 0.00 2.29
2734 11148 3.541996 TCACTCACTCACTTGCAGAAA 57.458 42.857 0.00 0.00 0.00 2.52
2735 11149 3.541996 TTCACTCACTCACTTGCAGAA 57.458 42.857 0.00 0.00 0.00 3.02
2775 11606 4.273724 TGCTATTTACAACGACACAGCAAA 59.726 37.500 0.00 0.00 35.03 3.68
2777 11608 3.394719 TGCTATTTACAACGACACAGCA 58.605 40.909 0.00 0.00 35.55 4.41
2779 11610 3.994392 ACCTGCTATTTACAACGACACAG 59.006 43.478 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.