Multiple sequence alignment - TraesCS3B01G397500

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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 TraesCS3B01G397500 chr3B 100.000 3369 0 0 483 3851 627903915 627907283 0.000000e+00 6222
1 TraesCS3B01G397500 chr3B 100.000 273 0 0 1 273 627903433 627903705 4.440000e-139 505
2 TraesCS3B01G397500 chr3A 94.732 1082 43 5 841 1919 614756450 614757520 0.000000e+00 1670
3 TraesCS3B01G397500 chr3A 95.026 945 46 1 2082 3025 614758283 614759227 0.000000e+00 1483
4 TraesCS3B01G397500 chr3A 89.688 737 58 9 3126 3851 614759523 614760252 0.000000e+00 924
5 TraesCS3B01G397500 chr3A 98.023 354 6 1 483 836 315975756 315976108 7.070000e-172 614
6 TraesCS3B01G397500 chr3A 98.819 254 3 0 1 254 315974697 315974950 1.630000e-123 453
7 TraesCS3B01G397500 chr3A 100.000 221 0 0 53 273 315975220 315975440 3.580000e-110 409
8 TraesCS3B01G397500 chr3D 94.338 1095 48 7 832 1919 472399728 472400815 0.000000e+00 1666
9 TraesCS3B01G397500 chr3D 93.732 1037 47 10 2085 3111 472400833 472401861 0.000000e+00 1539
10 TraesCS3B01G397500 chr3D 89.262 745 53 13 3126 3851 472401961 472402697 0.000000e+00 907
11 TraesCS3B01G397500 chr5B 98.000 350 7 0 483 832 107835397 107835048 3.290000e-170 608
12 TraesCS3B01G397500 chr5B 98.256 344 5 1 487 830 21688575 21688233 5.500000e-168 601
13 TraesCS3B01G397500 chr5B 98.447 322 4 1 483 804 115655641 115655321 2.010000e-157 566
14 TraesCS3B01G397500 chr5B 99.138 232 2 0 1 232 115656059 115655828 5.950000e-113 418
15 TraesCS3B01G397500 chr5B 92.015 263 3 1 1 263 21689038 21688794 1.700000e-93 353
16 TraesCS3B01G397500 chr5B 94.675 169 6 2 1919 2087 92234873 92234708 3.820000e-65 259
17 TraesCS3B01G397500 chr5B 93.452 168 8 3 1920 2087 308557104 308556940 2.970000e-61 246
18 TraesCS3B01G397500 chr5A 98.276 348 5 1 483 830 21571133 21571479 3.290000e-170 608
19 TraesCS3B01G397500 chr5A 99.634 273 1 0 1 273 21570836 21571108 2.070000e-137 499
20 TraesCS3B01G397500 chr5A 94.048 168 7 2 1920 2087 29678150 29678314 6.390000e-63 252
21 TraesCS3B01G397500 chr1A 97.989 348 7 0 483 830 256980482 256980829 4.260000e-169 604
22 TraesCS3B01G397500 chr1A 96.569 204 7 0 1 204 508582188 508581985 4.770000e-89 339
23 TraesCS3B01G397500 chr1A 96.569 204 6 1 1 204 480553328 480553530 1.710000e-88 337
24 TraesCS3B01G397500 chr4B 97.959 343 7 0 488 830 78230162 78230504 2.560000e-166 595
25 TraesCS3B01G397500 chr4B 99.029 309 3 0 526 834 408966165 408965857 4.350000e-154 555
26 TraesCS3B01G397500 chr4B 93.452 168 7 1 1920 2087 159604385 159604548 2.970000e-61 246
27 TraesCS3B01G397500 chr2B 97.419 310 8 0 528 837 674385318 674385627 2.630000e-146 529
28 TraesCS3B01G397500 chr2B 100.000 221 0 0 53 273 674384974 674385194 3.580000e-110 409
29 TraesCS3B01G397500 chr2B 94.545 165 2 2 1923 2087 118465813 118465656 8.260000e-62 248
30 TraesCS3B01G397500 chr2B 93.491 169 8 3 1919 2087 743582875 743583040 8.260000e-62 248
31 TraesCS3B01G397500 chr4A 95.926 270 11 0 1 270 28590537 28590806 4.570000e-119 438
32 TraesCS3B01G397500 chr2A 90.370 270 8 2 1 270 769246681 769246932 4.770000e-89 339
33 TraesCS3B01G397500 chr2A 90.335 269 8 2 1 269 1233481 1233731 1.710000e-88 337
34 TraesCS3B01G397500 chr7A 96.078 204 8 0 1 204 585306151 585305948 2.220000e-87 333
35 TraesCS3B01G397500 chr7A 94.083 169 7 3 1919 2087 108201755 108201920 1.780000e-63 254
36 TraesCS3B01G397500 chr7A 93.452 168 8 2 1920 2087 509467305 509467141 2.970000e-61 246
37 TraesCS3B01G397500 chr4D 92.090 177 9 3 1911 2087 50424241 50424412 1.070000e-60 244


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 TraesCS3B01G397500 chr3B 627903433 627907283 3850 False 3363.500000 6222 100.000000 1 3851 2 chr3B.!!$F1 3850
1 TraesCS3B01G397500 chr3A 614756450 614760252 3802 False 1359.000000 1670 93.148667 841 3851 3 chr3A.!!$F2 3010
2 TraesCS3B01G397500 chr3A 315974697 315976108 1411 False 492.000000 614 98.947333 1 836 3 chr3A.!!$F1 835
3 TraesCS3B01G397500 chr3D 472399728 472402697 2969 False 1370.666667 1666 92.444000 832 3851 3 chr3D.!!$F1 3019
4 TraesCS3B01G397500 chr5B 115655321 115656059 738 True 492.000000 566 98.792500 1 804 2 chr5B.!!$R5 803
5 TraesCS3B01G397500 chr5B 21688233 21689038 805 True 477.000000 601 95.135500 1 830 2 chr5B.!!$R4 829
6 TraesCS3B01G397500 chr5A 21570836 21571479 643 False 553.500000 608 98.955000 1 830 2 chr5A.!!$F2 829
7 TraesCS3B01G397500 chr2B 674384974 674385627 653 False 469.000000 529 98.709500 53 837 2 chr2B.!!$F2 784

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
876 1454 1.079405 CTTCGCCCGTTAAGGAGCA 60.079 57.895 2.57 0.0 45.00 4.26 F
882 1460 1.303091 CCCGTTAAGGAGCAAACCCG 61.303 60.000 0.00 0.0 45.00 5.28 F
2304 3496 0.037232 CTTTGTGGAGGTCGAGGGAC 60.037 60.000 0.00 0.0 42.66 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 2429 1.063174 GCATTGATCTCGTCCTTGTGC 59.937 52.381 0.0 0.0 0.00 4.57 R
2604 3796 1.732259 GTGGTTGGAGTTATGAGTGCG 59.268 52.381 0.0 0.0 0.00 5.34 R
3809 5221 1.272147 GCAAATCCTCTCCCAGGTTGT 60.272 52.381 0.0 0.0 43.95 3.32 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
737 1315 4.914177 TTACGGGTTTGAGGGTTTAGAT 57.086 40.909 0.00 0.00 0.00 1.98
876 1454 1.079405 CTTCGCCCGTTAAGGAGCA 60.079 57.895 2.57 0.00 45.00 4.26
882 1460 1.303091 CCCGTTAAGGAGCAAACCCG 61.303 60.000 0.00 0.00 45.00 5.28
1071 1649 2.442272 CCCCATCGTCCTCTCGGT 60.442 66.667 0.00 0.00 0.00 4.69
1122 1700 4.845580 CTCCGCTGCTCGCCCAAT 62.846 66.667 0.00 0.00 36.73 3.16
1248 1829 3.721706 AAGAAGGCGGGGCAGGAG 61.722 66.667 0.00 0.00 0.00 3.69
1485 2069 4.003788 CGGTGGGAGTTCGTGCCT 62.004 66.667 0.00 0.00 37.61 4.75
1778 2362 4.629523 GGTGGCGTTCCGGGACAA 62.630 66.667 14.76 0.00 34.14 3.18
1892 2476 1.527311 GTTGAAAGAGGTGAGTGCGTC 59.473 52.381 0.00 0.00 0.00 5.19
1912 2497 6.149633 GCGTCATCTTGTGGTAAAAGATTTT 58.850 36.000 0.00 0.00 41.39 1.82
1919 3036 8.696410 TCTTGTGGTAAAAGATTTTGTTTGAC 57.304 30.769 0.82 0.00 0.00 3.18
1921 3038 8.472683 TTGTGGTAAAAGATTTTGTTTGACAG 57.527 30.769 0.82 0.00 0.00 3.51
1942 3059 8.988064 GACAGTTTGTCTAATTCACATCTAGA 57.012 34.615 0.00 0.00 43.73 2.43
1944 3061 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
1971 3088 8.635765 TTTTTAAGGATGTCACATCTAAGCTT 57.364 30.769 17.46 13.56 0.00 3.74
1974 3091 3.776969 AGGATGTCACATCTAAGCTTCCA 59.223 43.478 17.46 0.00 0.00 3.53
1975 3092 3.873952 GGATGTCACATCTAAGCTTCCAC 59.126 47.826 17.46 0.00 0.00 4.02
1976 3093 4.507710 GATGTCACATCTAAGCTTCCACA 58.492 43.478 10.81 0.00 0.00 4.17
1977 3094 4.350368 TGTCACATCTAAGCTTCCACAA 57.650 40.909 0.00 0.00 0.00 3.33
1978 3095 4.065088 TGTCACATCTAAGCTTCCACAAC 58.935 43.478 0.00 0.00 0.00 3.32
1979 3096 4.202357 TGTCACATCTAAGCTTCCACAACT 60.202 41.667 0.00 0.00 0.00 3.16
1981 3098 6.109359 GTCACATCTAAGCTTCCACAACTAT 58.891 40.000 0.00 0.00 0.00 2.12
1982 3099 7.093509 TGTCACATCTAAGCTTCCACAACTATA 60.094 37.037 0.00 0.00 0.00 1.31
1983 3100 7.928706 GTCACATCTAAGCTTCCACAACTATAT 59.071 37.037 0.00 0.00 0.00 0.86
1985 3102 9.764363 CACATCTAAGCTTCCACAACTATATAA 57.236 33.333 0.00 0.00 0.00 0.98
1988 3105 8.833231 TCTAAGCTTCCACAACTATATAATGC 57.167 34.615 0.00 0.00 0.00 3.56
1989 3106 8.428852 TCTAAGCTTCCACAACTATATAATGCA 58.571 33.333 0.00 0.00 0.00 3.96
1992 3183 5.239306 GCTTCCACAACTATATAATGCAGCA 59.761 40.000 0.00 0.00 0.00 4.41
1994 3185 6.618287 TCCACAACTATATAATGCAGCAAC 57.382 37.500 0.00 0.00 0.00 4.17
1997 3188 6.914215 CCACAACTATATAATGCAGCAACAAG 59.086 38.462 0.00 0.00 0.00 3.16
1998 3189 7.201723 CCACAACTATATAATGCAGCAACAAGA 60.202 37.037 0.00 0.00 0.00 3.02
1999 3190 8.183536 CACAACTATATAATGCAGCAACAAGAA 58.816 33.333 0.00 0.00 0.00 2.52
2001 3192 9.013490 CAACTATATAATGCAGCAACAAGAAAC 57.987 33.333 0.00 0.00 0.00 2.78
2049 3240 8.474006 AAAAATAGACCACAAACAAAGTGAAC 57.526 30.769 0.00 0.00 39.30 3.18
2050 3241 6.767524 AATAGACCACAAACAAAGTGAACA 57.232 33.333 0.00 0.00 39.30 3.18
2051 3242 6.959639 ATAGACCACAAACAAAGTGAACAT 57.040 33.333 0.00 0.00 39.30 2.71
2052 3243 5.248870 AGACCACAAACAAAGTGAACATC 57.751 39.130 0.00 0.00 39.30 3.06
2056 3247 4.440525 CCACAAACAAAGTGAACATCAGCT 60.441 41.667 0.00 0.00 39.30 4.24
2057 3248 5.104374 CACAAACAAAGTGAACATCAGCTT 58.896 37.500 0.00 0.00 39.30 3.74
2058 3249 6.264832 CACAAACAAAGTGAACATCAGCTTA 58.735 36.000 0.00 0.00 39.30 3.09
2060 3251 8.075574 CACAAACAAAGTGAACATCAGCTTATA 58.924 33.333 0.00 0.00 39.30 0.98
2061 3252 8.796475 ACAAACAAAGTGAACATCAGCTTATAT 58.204 29.630 0.00 0.00 0.00 0.86
2062 3253 9.069078 CAAACAAAGTGAACATCAGCTTATATG 57.931 33.333 0.00 0.00 0.00 1.78
2064 3255 7.755591 ACAAAGTGAACATCAGCTTATATGTG 58.244 34.615 6.83 0.00 36.47 3.21
2065 3256 7.607607 ACAAAGTGAACATCAGCTTATATGTGA 59.392 33.333 6.83 0.00 36.47 3.58
2066 3257 7.545362 AAGTGAACATCAGCTTATATGTGAC 57.455 36.000 6.83 7.15 36.47 3.67
2067 3258 6.643388 AGTGAACATCAGCTTATATGTGACA 58.357 36.000 6.83 0.00 36.47 3.58
2068 3259 7.278135 AGTGAACATCAGCTTATATGTGACAT 58.722 34.615 2.65 2.65 36.47 3.06
2070 3261 9.045223 GTGAACATCAGCTTATATGTGACATAA 57.955 33.333 9.61 0.00 36.47 1.90
2071 3262 9.045223 TGAACATCAGCTTATATGTGACATAAC 57.955 33.333 9.61 0.34 36.47 1.89
2072 3263 9.265901 GAACATCAGCTTATATGTGACATAACT 57.734 33.333 9.61 2.62 36.47 2.24
2127 3319 8.554528 CCATATTTGTTATAAGCACAGAGTGAG 58.445 37.037 0.58 0.00 35.23 3.51
2141 3333 6.035866 GCACAGAGTGAGTTTCAGATCTAATG 59.964 42.308 0.00 0.00 35.23 1.90
2250 3442 2.892852 TGAGCTGTCCAAGAAATTTGGG 59.107 45.455 0.00 0.00 39.96 4.12
2298 3490 0.523072 CATTGCCTTTGTGGAGGTCG 59.477 55.000 0.00 0.00 39.11 4.79
2304 3496 0.037232 CTTTGTGGAGGTCGAGGGAC 60.037 60.000 0.00 0.00 42.66 4.46
2336 3528 5.874093 AGAGTTCATAAATAGGGCATGGAG 58.126 41.667 0.00 0.00 0.00 3.86
2404 3596 5.575957 TCCTCGATCACAAGTATTACGAAC 58.424 41.667 0.00 0.00 0.00 3.95
2604 3796 0.883370 GTGTGGTTGGAACGGAGGAC 60.883 60.000 0.00 0.00 0.00 3.85
2861 4053 5.241403 TCTATGTGGTGATTGGTGAACTT 57.759 39.130 0.00 0.00 0.00 2.66
2876 4068 6.980593 TGGTGAACTTGTAAATCATTTCTGG 58.019 36.000 0.00 0.00 0.00 3.86
2897 4089 4.706476 TGGTGAAGGAGGCAGAAATTTATG 59.294 41.667 8.46 8.46 0.00 1.90
2900 4092 6.377146 GGTGAAGGAGGCAGAAATTTATGTTA 59.623 38.462 13.94 0.00 0.00 2.41
2906 4098 4.941263 AGGCAGAAATTTATGTTACGAGCA 59.059 37.500 13.94 0.00 0.00 4.26
2907 4099 5.028375 GGCAGAAATTTATGTTACGAGCAC 58.972 41.667 13.94 0.00 0.00 4.40
2915 4107 7.940178 ATTTATGTTACGAGCACGATTCATA 57.060 32.000 11.40 11.70 42.66 2.15
2935 4127 0.250209 AGTGGTGCAGCAGAAGTGAG 60.250 55.000 20.85 0.00 0.00 3.51
2938 4130 1.168407 GGTGCAGCAGAAGTGAGCAA 61.168 55.000 11.86 0.00 37.79 3.91
2944 4136 3.603532 CAGCAGAAGTGAGCAAGGATAA 58.396 45.455 0.00 0.00 0.00 1.75
2958 4150 8.902806 TGAGCAAGGATAATATTTTACCACAAG 58.097 33.333 0.00 0.00 0.00 3.16
2984 4176 3.322828 TGACAGGTACCTTTGTCTACCAC 59.677 47.826 26.13 8.11 43.15 4.16
2991 4183 6.729569 AGGTACCTTTGTCTACCACTTTATCT 59.270 38.462 9.21 0.00 35.71 1.98
3032 4234 6.443849 TCCAGTTTCTCCCATAACTTCAGTAT 59.556 38.462 0.00 0.00 32.50 2.12
3049 4251 4.083537 TCAGTATGAAAATGTGTTCGCCAC 60.084 41.667 0.00 0.00 45.97 5.01
3050 4252 4.072131 AGTATGAAAATGTGTTCGCCACT 58.928 39.130 6.61 0.00 44.81 4.00
3060 4262 1.939934 TGTTCGCCACTGAAAGACTTG 59.060 47.619 0.00 0.00 37.43 3.16
3067 4269 3.503748 GCCACTGAAAGACTTGTATTGCT 59.496 43.478 0.00 0.00 37.43 3.91
3071 4273 6.138761 CACTGAAAGACTTGTATTGCTTGAC 58.861 40.000 0.00 0.00 37.43 3.18
3075 4277 5.536554 AAGACTTGTATTGCTTGACGATG 57.463 39.130 0.00 0.00 0.00 3.84
3076 4278 4.820897 AGACTTGTATTGCTTGACGATGA 58.179 39.130 0.00 0.00 0.00 2.92
3077 4279 5.237815 AGACTTGTATTGCTTGACGATGAA 58.762 37.500 0.00 0.00 0.00 2.57
3078 4280 5.700832 AGACTTGTATTGCTTGACGATGAAA 59.299 36.000 0.00 0.00 0.00 2.69
3079 4281 6.204688 AGACTTGTATTGCTTGACGATGAAAA 59.795 34.615 0.00 0.00 0.00 2.29
3080 4282 6.913170 ACTTGTATTGCTTGACGATGAAAAT 58.087 32.000 0.00 0.00 0.00 1.82
3082 4284 7.326789 ACTTGTATTGCTTGACGATGAAAATTG 59.673 33.333 0.00 0.00 0.00 2.32
3091 4401 7.946237 GCTTGACGATGAAAATTGTTTATTGTG 59.054 33.333 0.00 0.00 0.00 3.33
3116 4426 9.391006 TGTATCAAAATACAAAGTGATACTCCC 57.609 33.333 18.39 0.00 46.81 4.30
3118 4428 8.738645 ATCAAAATACAAAGTGATACTCCCTC 57.261 34.615 0.00 0.00 0.00 4.30
3121 4431 6.875972 AATACAAAGTGATACTCCCTCTGT 57.124 37.500 0.00 0.00 0.00 3.41
3122 4432 7.973048 AATACAAAGTGATACTCCCTCTGTA 57.027 36.000 0.00 0.00 0.00 2.74
3123 4433 5.662674 ACAAAGTGATACTCCCTCTGTAC 57.337 43.478 0.00 0.00 0.00 2.90
3126 4520 4.864483 AGTGATACTCCCTCTGTACAGA 57.136 45.455 23.80 23.80 35.85 3.41
3133 4527 9.877222 TGATACTCCCTCTGTACAGAAATATAA 57.123 33.333 25.14 11.16 36.94 0.98
3137 4531 9.084533 ACTCCCTCTGTACAGAAATATAAGATC 57.915 37.037 25.14 0.00 36.94 2.75
3158 4552 5.738619 TCTTAATGCACAGAACTACCTGA 57.261 39.130 0.00 0.00 37.59 3.86
3223 4617 4.691860 TCATTTCAAGAGCAGCTAAAGC 57.308 40.909 0.00 0.00 42.49 3.51
3227 4621 5.458041 TTTCAAGAGCAGCTAAAGCAAAT 57.542 34.783 4.54 0.00 45.16 2.32
3229 4623 6.764308 TTCAAGAGCAGCTAAAGCAAATAT 57.236 33.333 4.54 0.00 45.16 1.28
3247 4641 9.537192 AGCAAATATTACATCAAATGAACATGG 57.463 29.630 0.00 0.00 0.00 3.66
3248 4642 8.277713 GCAAATATTACATCAAATGAACATGGC 58.722 33.333 0.00 0.00 0.00 4.40
3249 4643 9.537192 CAAATATTACATCAAATGAACATGGCT 57.463 29.630 0.00 0.00 0.00 4.75
3255 4649 9.941325 TTACATCAAATGAACATGGCTATTTTT 57.059 25.926 0.00 0.00 0.00 1.94
3300 4710 5.238583 ACAACTTGGTCTGTAGCTGATAAC 58.761 41.667 0.00 0.00 0.00 1.89
3303 4713 6.210287 ACTTGGTCTGTAGCTGATAACTAC 57.790 41.667 0.00 0.00 40.37 2.73
3323 4733 8.752005 AACTACTGCATATACACAAATCCATT 57.248 30.769 0.00 0.00 0.00 3.16
3437 4848 1.947456 ACGGAAGTTTTCTGTCTTGCC 59.053 47.619 0.00 0.00 45.92 4.52
3445 4856 4.762251 AGTTTTCTGTCTTGCCAATCCTAC 59.238 41.667 0.00 0.00 0.00 3.18
3487 4899 5.587043 TCCTCTGAACTACTCGAAATCTCTC 59.413 44.000 0.00 0.00 0.00 3.20
3496 4908 3.445805 ACTCGAAATCTCTCTGTCTTCCC 59.554 47.826 0.00 0.00 0.00 3.97
3503 4915 3.036819 TCTCTCTGTCTTCCCATCCATG 58.963 50.000 0.00 0.00 0.00 3.66
3519 4931 5.240183 CCATCCATGGCTACACTTGAATAAG 59.760 44.000 6.96 0.00 41.75 1.73
3533 4945 8.603181 ACACTTGAATAAGCAATTTGTTGAAAC 58.397 29.630 0.00 0.00 37.43 2.78
3538 4950 7.279536 TGAATAAGCAATTTGTTGAAACTGCAA 59.720 29.630 4.07 0.00 34.35 4.08
3554 4966 2.353889 CTGCAATTCTCGGAGGACAATG 59.646 50.000 4.96 0.00 0.00 2.82
3571 4983 5.512232 GGACAATGAGTGAACCTCTCTTTCT 60.512 44.000 0.00 0.00 41.11 2.52
3598 5010 6.041637 ACCTCCATATGCAAGAACGAGTATTA 59.958 38.462 0.00 0.00 0.00 0.98
3606 5018 8.662781 ATGCAAGAACGAGTATTACATACATT 57.337 30.769 0.00 0.00 38.21 2.71
3607 5019 7.905126 TGCAAGAACGAGTATTACATACATTG 58.095 34.615 0.00 0.00 38.21 2.82
3608 5020 7.547722 TGCAAGAACGAGTATTACATACATTGT 59.452 33.333 0.00 0.00 42.62 2.71
3609 5021 8.388103 GCAAGAACGAGTATTACATACATTGTT 58.612 33.333 0.00 0.00 39.87 2.83
3635 5047 7.114754 AGTCATGAAAATGATCTGTGGTATGT 58.885 34.615 0.00 0.00 32.61 2.29
3646 5058 3.141398 CTGTGGTATGTTTGCTGTCAGT 58.859 45.455 0.93 0.00 0.00 3.41
3682 5094 7.015226 TGCACTATTTGGTTTATCTCAATCG 57.985 36.000 0.00 0.00 0.00 3.34
3710 5122 8.310382 CCTAAGAGATGTCTACCTATTTCCATG 58.690 40.741 0.00 0.00 30.45 3.66
3716 5128 5.730550 TGTCTACCTATTTCCATGTCACAC 58.269 41.667 0.00 0.00 0.00 3.82
3769 5181 1.208293 CAGTCCCCACCTCTTTAGAGC 59.792 57.143 1.09 0.00 40.75 4.09
3838 5250 6.550854 CCTGGGAGAGGATTTGCATAAAAATA 59.449 38.462 0.00 0.00 46.33 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.363147 GTGGACCTCGGAGCTCCT 60.363 66.667 29.73 11.86 0.00 3.69
737 1315 3.648339 AAAACGCCGTAGACTAGAACA 57.352 42.857 0.00 0.00 0.00 3.18
876 1454 1.270252 ACCGTTAACATCGTCGGGTTT 60.270 47.619 6.39 0.00 46.06 3.27
882 1460 2.178474 TAGCGACCGTTAACATCGTC 57.822 50.000 22.93 17.13 38.13 4.20
1071 1649 3.622263 AGGCTGGGGTGTAGGGGA 61.622 66.667 0.00 0.00 0.00 4.81
1133 1711 1.559965 GGGTTTAGGAGGTTCCGGCT 61.560 60.000 0.00 0.00 42.75 5.52
1203 1784 2.881352 CTCGTCGCCTTCGCCTTC 60.881 66.667 0.00 0.00 35.26 3.46
1291 1872 2.434359 CTTCTTGGTCCGACGGGC 60.434 66.667 15.25 13.14 0.00 6.13
1845 2429 1.063174 GCATTGATCTCGTCCTTGTGC 59.937 52.381 0.00 0.00 0.00 4.57
1892 2476 9.311916 TCAAACAAAATCTTTTACCACAAGATG 57.688 29.630 0.00 0.00 39.61 2.90
1946 3063 8.635765 AAGCTTAGATGTGACATCCTTAAAAA 57.364 30.769 21.05 6.46 0.00 1.94
1947 3064 7.336931 GGAAGCTTAGATGTGACATCCTTAAAA 59.663 37.037 21.05 8.00 0.00 1.52
1948 3065 6.823689 GGAAGCTTAGATGTGACATCCTTAAA 59.176 38.462 21.05 10.18 0.00 1.52
1949 3066 6.070251 TGGAAGCTTAGATGTGACATCCTTAA 60.070 38.462 21.05 13.11 0.00 1.85
1950 3067 5.425217 TGGAAGCTTAGATGTGACATCCTTA 59.575 40.000 21.05 6.22 0.00 2.69
1953 3070 3.873952 GTGGAAGCTTAGATGTGACATCC 59.126 47.826 21.05 6.31 0.00 3.51
1954 3071 4.507710 TGTGGAAGCTTAGATGTGACATC 58.492 43.478 17.46 17.46 0.00 3.06
1957 3074 4.319177 AGTTGTGGAAGCTTAGATGTGAC 58.681 43.478 0.00 0.00 0.00 3.67
1958 3075 4.623932 AGTTGTGGAAGCTTAGATGTGA 57.376 40.909 0.00 0.00 0.00 3.58
1959 3076 9.764363 TTATATAGTTGTGGAAGCTTAGATGTG 57.236 33.333 0.00 0.00 0.00 3.21
1962 3079 9.442047 GCATTATATAGTTGTGGAAGCTTAGAT 57.558 33.333 0.00 0.00 0.00 1.98
1963 3080 8.428852 TGCATTATATAGTTGTGGAAGCTTAGA 58.571 33.333 0.00 0.00 0.00 2.10
1964 3081 8.607441 TGCATTATATAGTTGTGGAAGCTTAG 57.393 34.615 0.00 0.00 0.00 2.18
1965 3082 7.173218 GCTGCATTATATAGTTGTGGAAGCTTA 59.827 37.037 0.00 0.00 0.00 3.09
1966 3083 6.016777 GCTGCATTATATAGTTGTGGAAGCTT 60.017 38.462 0.00 0.00 0.00 3.74
1967 3084 5.471456 GCTGCATTATATAGTTGTGGAAGCT 59.529 40.000 0.00 0.00 0.00 3.74
1969 3086 6.866010 TGCTGCATTATATAGTTGTGGAAG 57.134 37.500 0.00 0.00 0.00 3.46
1971 3088 6.118852 TGTTGCTGCATTATATAGTTGTGGA 58.881 36.000 1.84 0.00 0.00 4.02
1974 3091 7.864108 TCTTGTTGCTGCATTATATAGTTGT 57.136 32.000 1.84 0.00 0.00 3.32
1975 3092 9.013490 GTTTCTTGTTGCTGCATTATATAGTTG 57.987 33.333 1.84 0.00 0.00 3.16
1976 3093 8.739039 TGTTTCTTGTTGCTGCATTATATAGTT 58.261 29.630 1.84 0.00 0.00 2.24
1977 3094 8.279970 TGTTTCTTGTTGCTGCATTATATAGT 57.720 30.769 1.84 0.00 0.00 2.12
1978 3095 9.571810 TTTGTTTCTTGTTGCTGCATTATATAG 57.428 29.630 1.84 0.00 0.00 1.31
1979 3096 9.920133 TTTTGTTTCTTGTTGCTGCATTATATA 57.080 25.926 1.84 0.00 0.00 0.86
1981 3098 8.654230 TTTTTGTTTCTTGTTGCTGCATTATA 57.346 26.923 1.84 0.00 0.00 0.98
1982 3099 7.551035 TTTTTGTTTCTTGTTGCTGCATTAT 57.449 28.000 1.84 0.00 0.00 1.28
1983 3100 6.974932 TTTTTGTTTCTTGTTGCTGCATTA 57.025 29.167 1.84 0.00 0.00 1.90
2024 3215 8.091449 TGTTCACTTTGTTTGTGGTCTATTTTT 58.909 29.630 0.00 0.00 36.21 1.94
2025 3216 7.607250 TGTTCACTTTGTTTGTGGTCTATTTT 58.393 30.769 0.00 0.00 36.21 1.82
2026 3217 7.164230 TGTTCACTTTGTTTGTGGTCTATTT 57.836 32.000 0.00 0.00 36.21 1.40
2027 3218 6.767524 TGTTCACTTTGTTTGTGGTCTATT 57.232 33.333 0.00 0.00 36.21 1.73
2028 3219 6.545666 TGATGTTCACTTTGTTTGTGGTCTAT 59.454 34.615 0.00 0.00 36.21 1.98
2030 3221 4.704540 TGATGTTCACTTTGTTTGTGGTCT 59.295 37.500 0.00 0.00 36.21 3.85
2031 3222 4.992688 TGATGTTCACTTTGTTTGTGGTC 58.007 39.130 0.00 0.00 36.21 4.02
2032 3223 4.677779 GCTGATGTTCACTTTGTTTGTGGT 60.678 41.667 0.00 0.00 36.21 4.16
2033 3224 3.798337 GCTGATGTTCACTTTGTTTGTGG 59.202 43.478 0.00 0.00 36.21 4.17
2034 3225 4.675510 AGCTGATGTTCACTTTGTTTGTG 58.324 39.130 0.00 0.00 36.82 3.33
2035 3226 4.989279 AGCTGATGTTCACTTTGTTTGT 57.011 36.364 0.00 0.00 0.00 2.83
2036 3227 9.069078 CATATAAGCTGATGTTCACTTTGTTTG 57.931 33.333 0.00 0.00 0.00 2.93
2038 3229 8.239314 CACATATAAGCTGATGTTCACTTTGTT 58.761 33.333 6.46 0.00 34.01 2.83
2039 3230 7.607607 TCACATATAAGCTGATGTTCACTTTGT 59.392 33.333 6.46 0.00 34.01 2.83
2040 3231 7.907045 GTCACATATAAGCTGATGTTCACTTTG 59.093 37.037 6.46 0.00 34.01 2.77
2041 3232 7.607607 TGTCACATATAAGCTGATGTTCACTTT 59.392 33.333 6.46 0.00 34.01 2.66
2043 3234 6.643388 TGTCACATATAAGCTGATGTTCACT 58.357 36.000 6.46 0.00 34.01 3.41
2044 3235 6.908870 TGTCACATATAAGCTGATGTTCAC 57.091 37.500 6.46 7.22 34.01 3.18
2046 3237 9.265901 AGTTATGTCACATATAAGCTGATGTTC 57.734 33.333 0.00 4.81 34.01 3.18
2066 3257 8.759641 GCAGTTTCTAGATGTGACATAGTTATG 58.240 37.037 0.00 0.00 39.55 1.90
2067 3258 8.478066 TGCAGTTTCTAGATGTGACATAGTTAT 58.522 33.333 0.00 0.00 0.00 1.89
2068 3259 7.836842 TGCAGTTTCTAGATGTGACATAGTTA 58.163 34.615 0.00 0.00 0.00 2.24
2070 3261 6.286240 TGCAGTTTCTAGATGTGACATAGT 57.714 37.500 0.00 0.00 0.00 2.12
2071 3262 7.783090 AATGCAGTTTCTAGATGTGACATAG 57.217 36.000 0.00 0.00 0.00 2.23
2076 3267 9.929180 GGTATATAATGCAGTTTCTAGATGTGA 57.071 33.333 0.00 0.00 0.00 3.58
2077 3268 9.710900 TGGTATATAATGCAGTTTCTAGATGTG 57.289 33.333 0.00 0.00 0.00 3.21
2123 3315 7.840342 ATCACACATTAGATCTGAAACTCAC 57.160 36.000 5.18 0.00 0.00 3.51
2127 3319 9.443283 GCAATTATCACACATTAGATCTGAAAC 57.557 33.333 5.18 0.00 0.00 2.78
2141 3333 1.818060 TGGCCTGTGCAATTATCACAC 59.182 47.619 3.32 1.98 39.29 3.82
2210 3402 3.141398 TCAATGGTTCTGAAGAGTGTGC 58.859 45.455 0.00 0.00 0.00 4.57
2298 3490 3.243771 TGAACTCTTTTGTCTCGTCCCTC 60.244 47.826 0.00 0.00 0.00 4.30
2304 3496 7.466050 GCCCTATTTATGAACTCTTTTGTCTCG 60.466 40.741 0.00 0.00 0.00 4.04
2336 3528 3.450457 CACCTCTATGATATCAGCCTCCC 59.550 52.174 11.78 0.00 0.00 4.30
2404 3596 2.588877 CGGGGTGGCTCGCTTATG 60.589 66.667 3.62 0.00 0.00 1.90
2604 3796 1.732259 GTGGTTGGAGTTATGAGTGCG 59.268 52.381 0.00 0.00 0.00 5.34
2861 4053 5.945784 CCTCCTTCACCAGAAATGATTTACA 59.054 40.000 0.00 0.00 32.35 2.41
2876 4068 5.904362 ACATAAATTTCTGCCTCCTTCAC 57.096 39.130 3.63 0.00 0.00 3.18
2897 4089 4.026804 CCACTTATGAATCGTGCTCGTAAC 60.027 45.833 8.17 1.84 38.33 2.50
2900 4092 2.094182 ACCACTTATGAATCGTGCTCGT 60.094 45.455 8.17 0.00 38.33 4.18
2906 4098 2.009774 GCTGCACCACTTATGAATCGT 58.990 47.619 0.00 0.00 0.00 3.73
2907 4099 2.009051 TGCTGCACCACTTATGAATCG 58.991 47.619 0.00 0.00 0.00 3.34
2915 4107 0.181114 TCACTTCTGCTGCACCACTT 59.819 50.000 0.00 0.00 0.00 3.16
2935 4127 8.903820 ACTCTTGTGGTAAAATATTATCCTTGC 58.096 33.333 0.00 0.00 0.00 4.01
2944 4136 7.231467 ACCTGTCAACTCTTGTGGTAAAATAT 58.769 34.615 0.00 0.00 31.94 1.28
2958 4150 4.338379 AGACAAAGGTACCTGTCAACTC 57.662 45.455 27.21 13.05 42.17 3.01
3011 4203 8.561738 TTTCATACTGAAGTTATGGGAGAAAC 57.438 34.615 0.00 0.00 37.70 2.78
3017 4209 8.055279 ACACATTTTCATACTGAAGTTATGGG 57.945 34.615 0.00 8.29 37.70 4.00
3018 4210 9.559958 GAACACATTTTCATACTGAAGTTATGG 57.440 33.333 0.00 0.00 37.70 2.74
3042 4244 2.325583 ACAAGTCTTTCAGTGGCGAA 57.674 45.000 0.00 0.00 0.00 4.70
3043 4245 3.678056 ATACAAGTCTTTCAGTGGCGA 57.322 42.857 0.00 0.00 0.00 5.54
3046 4248 5.239306 TCAAGCAATACAAGTCTTTCAGTGG 59.761 40.000 0.00 0.00 0.00 4.00
3049 4251 5.177511 TCGTCAAGCAATACAAGTCTTTCAG 59.822 40.000 0.00 0.00 0.00 3.02
3050 4252 5.053811 TCGTCAAGCAATACAAGTCTTTCA 58.946 37.500 0.00 0.00 0.00 2.69
3060 4262 7.566858 AACAATTTTCATCGTCAAGCAATAC 57.433 32.000 0.00 0.00 0.00 1.89
3067 4269 8.864069 ACACAATAAACAATTTTCATCGTCAA 57.136 26.923 0.00 0.00 0.00 3.18
3113 4423 9.661954 AAGATCTTATATTTCTGTACAGAGGGA 57.338 33.333 23.97 15.11 38.88 4.20
3133 4527 6.155221 TCAGGTAGTTCTGTGCATTAAGATCT 59.845 38.462 0.00 1.45 36.25 2.75
3134 4528 6.341316 TCAGGTAGTTCTGTGCATTAAGATC 58.659 40.000 0.00 0.00 36.25 2.75
3136 4530 5.738619 TCAGGTAGTTCTGTGCATTAAGA 57.261 39.130 0.00 0.00 36.25 2.10
3137 4531 6.801539 TTTCAGGTAGTTCTGTGCATTAAG 57.198 37.500 0.00 0.00 36.25 1.85
3198 4592 3.505464 AGCTGCTCTTGAAATGATTGC 57.495 42.857 0.00 0.00 0.00 3.56
3211 4605 7.642669 TGATGTAATATTTGCTTTAGCTGCTC 58.357 34.615 4.91 0.00 42.66 4.26
3223 4617 9.537192 AGCCATGTTCATTTGATGTAATATTTG 57.463 29.630 0.00 0.00 0.00 2.32
3229 4623 9.941325 AAAAATAGCCATGTTCATTTGATGTAA 57.059 25.926 0.00 0.00 0.00 2.41
3254 4648 7.946207 TGTAAGTGGCAAGTGATGAATAAAAA 58.054 30.769 0.00 0.00 0.00 1.94
3255 4649 7.517614 TGTAAGTGGCAAGTGATGAATAAAA 57.482 32.000 0.00 0.00 0.00 1.52
3273 4683 4.344102 TCAGCTACAGACCAAGTTGTAAGT 59.656 41.667 1.45 0.00 30.06 2.24
3274 4684 4.883083 TCAGCTACAGACCAAGTTGTAAG 58.117 43.478 1.45 0.00 30.06 2.34
3300 4710 8.501580 CAGAATGGATTTGTGTATATGCAGTAG 58.498 37.037 0.00 0.00 0.00 2.57
3303 4713 7.500720 TCAGAATGGATTTGTGTATATGCAG 57.499 36.000 0.00 0.00 36.16 4.41
3369 4780 8.798859 ACTATGAATGTACAATCTTTGCTCTT 57.201 30.769 12.06 0.00 0.00 2.85
3417 4828 1.947456 GGCAAGACAGAAAACTTCCGT 59.053 47.619 0.00 0.00 0.00 4.69
3425 4836 3.561313 GGGTAGGATTGGCAAGACAGAAA 60.561 47.826 5.96 0.00 0.00 2.52
3437 4848 4.819105 TGTACAACAGAGGGTAGGATTG 57.181 45.455 0.00 0.00 0.00 2.67
3445 4856 4.651503 AGAGGACATATGTACAACAGAGGG 59.348 45.833 20.30 0.00 0.00 4.30
3496 4908 5.278169 GCTTATTCAAGTGTAGCCATGGATG 60.278 44.000 18.40 0.00 34.00 3.51
3503 4915 6.389906 ACAAATTGCTTATTCAAGTGTAGCC 58.610 36.000 0.00 0.00 34.00 3.93
3533 4945 2.099141 TTGTCCTCCGAGAATTGCAG 57.901 50.000 0.00 0.00 0.00 4.41
3538 4950 3.099905 TCACTCATTGTCCTCCGAGAAT 58.900 45.455 0.00 0.00 32.39 2.40
3554 4966 3.576550 AGGTGAGAAAGAGAGGTTCACTC 59.423 47.826 3.35 0.00 46.98 3.51
3571 4983 2.499693 TCGTTCTTGCATATGGAGGTGA 59.500 45.455 4.56 0.33 0.00 4.02
3606 5018 6.942005 ACCACAGATCATTTTCATGACTAACA 59.058 34.615 0.00 0.00 42.46 2.41
3607 5019 7.383102 ACCACAGATCATTTTCATGACTAAC 57.617 36.000 0.00 0.00 42.46 2.34
3608 5020 9.112725 CATACCACAGATCATTTTCATGACTAA 57.887 33.333 0.00 0.00 42.46 2.24
3609 5021 8.267183 ACATACCACAGATCATTTTCATGACTA 58.733 33.333 0.00 0.00 42.46 2.59
3614 5026 7.037438 GCAAACATACCACAGATCATTTTCAT 58.963 34.615 0.00 0.00 0.00 2.57
3615 5027 6.209192 AGCAAACATACCACAGATCATTTTCA 59.791 34.615 0.00 0.00 0.00 2.69
3622 5034 4.002982 TGACAGCAAACATACCACAGATC 58.997 43.478 0.00 0.00 0.00 2.75
3635 5047 5.546621 ACTCCTAGTAAACTGACAGCAAA 57.453 39.130 1.25 0.00 0.00 3.68
3682 5094 7.506261 TGGAAATAGGTAGACATCTCTTAGGAC 59.494 40.741 0.00 0.00 0.00 3.85
3710 5122 1.871772 GCTGCATGTGAGGTGTGAC 59.128 57.895 0.00 0.00 0.00 3.67
3716 5128 2.789917 GCTTCGCTGCATGTGAGG 59.210 61.111 0.00 0.00 36.46 3.86
3769 5181 3.535561 AGGATTTAGCGACATGGACTTG 58.464 45.455 0.00 0.00 0.00 3.16
3809 5221 1.272147 GCAAATCCTCTCCCAGGTTGT 60.272 52.381 0.00 0.00 43.95 3.32
3812 5224 1.302907 ATGCAAATCCTCTCCCAGGT 58.697 50.000 0.00 0.00 43.95 4.00


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

AutoCloner maintained by Alex Coulton.