Multiple sequence alignment - TraesCS1B01G314600

Loading Multiple Alignment...

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 TraesCS1B01G314600 chr1B 100.000 3770 0 0 1 3770 539483421 539479652 0.000000e+00 6962.0
1 TraesCS1B01G314600 chr1A 90.647 3122 137 57 1 3046 497499556 497496514 0.000000e+00 4004.0
2 TraesCS1B01G314600 chr1A 84.758 269 35 6 3076 3343 497493473 497493210 8.030000e-67 265.0
3 TraesCS1B01G314600 chr1D 94.175 2644 73 26 473 3068 401566340 401563730 0.000000e+00 3954.0
4 TraesCS1B01G314600 chr1D 85.625 320 33 9 3456 3770 401563206 401562895 1.310000e-84 324.0
5 TraesCS1B01G314600 chr1D 91.549 71 6 0 3321 3391 401563302 401563232 8.620000e-17 99.0
6 TraesCS1B01G314600 chr1D 86.250 80 6 4 3312 3389 252487518 252487442 8.680000e-12 82.4
7 TraesCS1B01G314600 chr3B 79.122 1504 278 29 1275 2758 584576720 584575233 0.000000e+00 1005.0
8 TraesCS1B01G314600 chr3B 74.740 289 46 18 32 309 18850859 18850587 1.850000e-18 104.0
9 TraesCS1B01G314600 chr3A 79.982 1109 216 6 1275 2380 587552826 587551721 0.000000e+00 813.0
10 TraesCS1B01G314600 chr3A 86.577 298 38 2 2462 2758 587551621 587551325 1.010000e-85 327.0
11 TraesCS1B01G314600 chr3D 79.892 1109 217 6 1275 2380 445738413 445737308 0.000000e+00 808.0
12 TraesCS1B01G314600 chr3D 87.248 298 36 2 2462 2758 445737198 445736902 4.660000e-89 339.0
13 TraesCS1B01G314600 chr2A 86.260 131 14 3 3166 3294 193449777 193449649 5.080000e-29 139.0
14 TraesCS1B01G314600 chr2A 85.271 129 17 2 3164 3291 216837909 216837782 8.500000e-27 132.0
15 TraesCS1B01G314600 chr2A 83.465 127 20 1 3168 3294 777098215 777098090 2.380000e-22 117.0
16 TraesCS1B01G314600 chr2B 73.604 394 80 18 1684 2059 382911132 382910745 3.060000e-26 130.0
17 TraesCS1B01G314600 chr2B 83.088 136 21 2 3158 3291 585195710 585195845 5.110000e-24 122.0
18 TraesCS1B01G314600 chr6D 85.714 119 14 2 3168 3286 1486632 1486517 5.110000e-24 122.0
19 TraesCS1B01G314600 chr6D 92.308 65 5 0 3306 3370 310527560 310527624 4.010000e-15 93.5
20 TraesCS1B01G314600 chr6D 87.342 79 7 2 3312 3387 416962255 416962333 1.870000e-13 87.9
21 TraesCS1B01G314600 chr6D 85.057 87 10 2 3304 3387 416014493 416014579 6.710000e-13 86.1
22 TraesCS1B01G314600 chr6D 85.057 87 10 2 3304 3387 416122044 416122130 6.710000e-13 86.1
23 TraesCS1B01G314600 chr5B 84.211 133 14 5 3168 3294 617080906 617080775 5.110000e-24 122.0
24 TraesCS1B01G314600 chr5B 88.312 77 5 3 3314 3390 673048510 673048438 5.190000e-14 89.8
25 TraesCS1B01G314600 chr5D 84.874 119 14 2 3167 3282 373781802 373781685 2.380000e-22 117.0
26 TraesCS1B01G314600 chr5D 88.732 71 5 2 3314 3384 511610351 511610284 2.410000e-12 84.2
27 TraesCS1B01G314600 chr7D 82.443 131 17 6 3168 3294 513211738 513211610 3.980000e-20 110.0
28 TraesCS1B01G314600 chr5A 87.356 87 7 4 3670 3754 454443578 454443662 3.100000e-16 97.1
29 TraesCS1B01G314600 chr2D 87.838 74 6 2 3320 3393 620639104 620639174 2.410000e-12 84.2


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 TraesCS1B01G314600 chr1B 539479652 539483421 3769 True 6962.0 6962 100.000000 1 3770 1 chr1B.!!$R1 3769
1 TraesCS1B01G314600 chr1A 497493210 497499556 6346 True 2134.5 4004 87.702500 1 3343 2 chr1A.!!$R1 3342
2 TraesCS1B01G314600 chr1D 401562895 401566340 3445 True 1459.0 3954 90.449667 473 3770 3 chr1D.!!$R2 3297
3 TraesCS1B01G314600 chr3B 584575233 584576720 1487 True 1005.0 1005 79.122000 1275 2758 1 chr3B.!!$R2 1483
4 TraesCS1B01G314600 chr3A 587551325 587552826 1501 True 570.0 813 83.279500 1275 2758 2 chr3A.!!$R1 1483
5 TraesCS1B01G314600 chr3D 445736902 445738413 1511 True 573.5 808 83.570000 1275 2758 2 chr3D.!!$R1 1483

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
641 663 0.250510 GCAGCTATAAGTCCCTGCCC 60.251 60.000 0.0 0.0 43.58 5.36 F
1228 1263 1.194547 CCTCCAACAACAACATCGTCG 59.805 52.381 0.0 0.0 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2142 1.320344 TACCTGAGCTTGCCGTCGAT 61.320 55.0 0.00 0.00 0.0 3.59 R
2965 3079 0.038744 ACTAGCCCCCATATGCATGC 59.961 55.0 11.82 11.82 0.0 4.06 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
25 26 0.462047 GGTGTTCGGGCTACATGGAG 60.462 60.000 0.00 0.00 0.00 3.86
34 35 2.356741 GGGCTACATGGAGCACCTTTTA 60.357 50.000 30.68 0.00 44.76 1.52
35 36 3.555966 GGCTACATGGAGCACCTTTTAT 58.444 45.455 30.68 0.00 44.76 1.40
104 105 8.578308 AAAAATTACATTGACATATGGATGCG 57.422 30.769 7.80 0.00 36.43 4.73
113 114 4.339814 TGACATATGGATGCGTACTACACA 59.660 41.667 7.80 0.00 36.43 3.72
115 116 5.230182 ACATATGGATGCGTACTACACATG 58.770 41.667 7.80 0.00 36.43 3.21
116 117 3.819564 ATGGATGCGTACTACACATGT 57.180 42.857 0.00 0.00 0.00 3.21
117 118 2.887337 TGGATGCGTACTACACATGTG 58.113 47.619 24.25 24.25 0.00 3.21
118 119 1.593006 GGATGCGTACTACACATGTGC 59.407 52.381 25.68 10.36 0.00 4.57
119 120 2.267426 GATGCGTACTACACATGTGCA 58.733 47.619 25.68 15.89 35.10 4.57
120 121 2.156343 TGCGTACTACACATGTGCAA 57.844 45.000 25.68 13.12 0.00 4.08
121 122 2.484889 TGCGTACTACACATGTGCAAA 58.515 42.857 25.68 10.57 0.00 3.68
122 123 2.872858 TGCGTACTACACATGTGCAAAA 59.127 40.909 25.68 6.60 0.00 2.44
123 124 3.500299 TGCGTACTACACATGTGCAAAAT 59.500 39.130 25.68 8.44 0.00 1.82
124 125 4.023622 TGCGTACTACACATGTGCAAAATT 60.024 37.500 25.68 7.68 0.00 1.82
125 126 4.915085 GCGTACTACACATGTGCAAAATTT 59.085 37.500 25.68 6.93 0.00 1.82
126 127 5.059221 GCGTACTACACATGTGCAAAATTTC 59.941 40.000 25.68 7.99 0.00 2.17
127 128 6.139435 CGTACTACACATGTGCAAAATTTCA 58.861 36.000 25.68 0.00 0.00 2.69
128 129 6.801377 CGTACTACACATGTGCAAAATTTCAT 59.199 34.615 25.68 4.67 0.00 2.57
129 130 7.201257 CGTACTACACATGTGCAAAATTTCATG 60.201 37.037 25.68 13.31 0.00 3.07
130 131 6.747125 ACTACACATGTGCAAAATTTCATGA 58.253 32.000 25.68 0.00 0.00 3.07
184 185 6.812481 AAAAAGAGAGTGAAAATTCGTTGC 57.188 33.333 0.00 0.00 0.00 4.17
185 186 5.757850 AAAGAGAGTGAAAATTCGTTGCT 57.242 34.783 0.00 0.00 0.00 3.91
187 188 5.757850 AGAGAGTGAAAATTCGTTGCTTT 57.242 34.783 0.00 0.00 0.00 3.51
190 191 7.875971 AGAGAGTGAAAATTCGTTGCTTTTAT 58.124 30.769 0.00 0.00 0.00 1.40
208 210 7.064609 TGCTTTTATATAGTGAACAGAGCACAC 59.935 37.037 0.00 0.00 38.70 3.82
212 214 6.775594 ATATAGTGAACAGAGCACACACTA 57.224 37.500 0.00 0.00 44.32 2.74
218 220 4.202253 TGAACAGAGCACACACTATTCACT 60.202 41.667 0.00 0.00 0.00 3.41
219 221 3.657634 ACAGAGCACACACTATTCACTG 58.342 45.455 0.00 0.00 0.00 3.66
233 235 7.066887 ACACTATTCACTGTGTGTTCAAAATCA 59.933 33.333 7.79 0.00 44.52 2.57
234 236 8.077991 CACTATTCACTGTGTGTTCAAAATCAT 58.922 33.333 7.79 0.00 34.79 2.45
235 237 8.632679 ACTATTCACTGTGTGTTCAAAATCATT 58.367 29.630 7.79 0.00 34.79 2.57
275 281 2.742053 AGCTCGCGTGTCAATGTATTTT 59.258 40.909 5.77 0.00 0.00 1.82
299 311 6.519382 TGTCATAAAAATTTGCACACATGGA 58.481 32.000 0.00 0.00 0.00 3.41
304 316 8.597227 CATAAAAATTTGCACACATGGAGTATG 58.403 33.333 0.00 0.00 42.68 2.39
325 337 8.990203 AGTATGCATCTGTATGATATTCTGGAT 58.010 33.333 0.19 0.00 34.84 3.41
326 338 9.610705 GTATGCATCTGTATGATATTCTGGATT 57.389 33.333 0.19 0.00 34.84 3.01
327 339 8.734218 ATGCATCTGTATGATATTCTGGATTC 57.266 34.615 0.00 0.00 34.84 2.52
328 340 7.108194 TGCATCTGTATGATATTCTGGATTCC 58.892 38.462 0.00 0.00 34.84 3.01
335 347 9.056005 TGTATGATATTCTGGATTCCTTTTTCG 57.944 33.333 3.95 0.00 0.00 3.46
336 348 9.057089 GTATGATATTCTGGATTCCTTTTTCGT 57.943 33.333 3.95 0.00 0.00 3.85
337 349 7.553881 TGATATTCTGGATTCCTTTTTCGTC 57.446 36.000 3.95 0.00 0.00 4.20
338 350 7.109501 TGATATTCTGGATTCCTTTTTCGTCA 58.890 34.615 3.95 0.00 0.00 4.35
339 351 7.609918 TGATATTCTGGATTCCTTTTTCGTCAA 59.390 33.333 3.95 0.00 0.00 3.18
340 352 6.648879 ATTCTGGATTCCTTTTTCGTCAAA 57.351 33.333 3.95 0.00 0.00 2.69
341 353 6.648879 TTCTGGATTCCTTTTTCGTCAAAT 57.351 33.333 3.95 0.00 0.00 2.32
342 354 6.648879 TCTGGATTCCTTTTTCGTCAAATT 57.351 33.333 3.95 0.00 0.00 1.82
431 445 2.897780 GCATTTCTGCGCCAAAACA 58.102 47.368 4.18 0.00 38.92 2.83
518 538 3.649277 CTGGGGAGACGCTGGAACG 62.649 68.421 0.00 0.00 45.02 3.95
603 625 4.394712 CCTCGGCACCGCTCCTTT 62.395 66.667 3.66 0.00 39.59 3.11
632 654 3.406361 CGCGGCGGCAGCTATAAG 61.406 66.667 22.01 3.16 44.37 1.73
641 663 0.250510 GCAGCTATAAGTCCCTGCCC 60.251 60.000 0.00 0.00 43.58 5.36
760 787 2.053244 CTTCCATGGCCTCCTCATAGT 58.947 52.381 6.96 0.00 0.00 2.12
825 856 4.386951 TACGCACGCACCCAGCAT 62.387 61.111 0.00 0.00 46.13 3.79
826 857 3.007973 TACGCACGCACCCAGCATA 62.008 57.895 0.00 0.00 46.13 3.14
827 858 3.864686 CGCACGCACCCAGCATAC 61.865 66.667 0.00 0.00 46.13 2.39
828 859 2.745884 GCACGCACCCAGCATACA 60.746 61.111 0.00 0.00 46.13 2.29
829 860 2.114670 GCACGCACCCAGCATACAT 61.115 57.895 0.00 0.00 46.13 2.29
830 861 1.723273 CACGCACCCAGCATACATG 59.277 57.895 0.00 0.00 46.13 3.21
877 912 3.976375 CGTCGTCGGATGCATGCG 61.976 66.667 31.81 31.81 43.28 4.73
954 989 1.405463 TGATATATAGCGCTCGCCAGG 59.595 52.381 16.34 0.00 43.17 4.45
994 1029 3.002583 TGCTGCCACCGATCCTGA 61.003 61.111 0.00 0.00 0.00 3.86
996 1031 1.596477 GCTGCCACCGATCCTGATC 60.596 63.158 0.00 0.00 34.56 2.92
1003 1038 2.549563 CCACCGATCCTGATCTTGATGG 60.550 54.545 5.66 1.89 35.72 3.51
1228 1263 1.194547 CCTCCAACAACAACATCGTCG 59.805 52.381 0.00 0.00 0.00 5.12
1671 1706 2.357760 GCCGCCAAGACGTACCAA 60.358 61.111 0.00 0.00 0.00 3.67
1881 1916 1.687612 CTCCACCAGGTTCATGGCT 59.312 57.895 3.32 0.00 44.80 4.75
2772 2851 1.686110 CTACCTCCCCGCCTGAAGT 60.686 63.158 0.00 0.00 0.00 3.01
2778 2857 2.370445 CCCCGCCTGAAGTCCTGAT 61.370 63.158 0.00 0.00 0.00 2.90
2782 2861 0.250234 CGCCTGAAGTCCTGATCCAA 59.750 55.000 0.00 0.00 0.00 3.53
2783 2862 1.743996 GCCTGAAGTCCTGATCCAAC 58.256 55.000 0.00 0.00 0.00 3.77
2853 2950 2.380064 AGGCCATGAGTTTGTTTCCA 57.620 45.000 5.01 0.00 0.00 3.53
2917 3028 8.265165 TGTGTAATTGTGTTACTGTTGTTGTA 57.735 30.769 0.00 0.00 0.00 2.41
2918 3029 8.727910 TGTGTAATTGTGTTACTGTTGTTGTAA 58.272 29.630 0.00 0.00 0.00 2.41
2964 3078 8.871629 TTTTTGCTCTGGTGGAATATAACTAA 57.128 30.769 0.00 0.00 0.00 2.24
2965 3079 8.506168 TTTTGCTCTGGTGGAATATAACTAAG 57.494 34.615 0.00 0.00 0.00 2.18
2966 3080 5.611374 TGCTCTGGTGGAATATAACTAAGC 58.389 41.667 0.00 0.00 0.00 3.09
2967 3081 5.130311 TGCTCTGGTGGAATATAACTAAGCA 59.870 40.000 0.00 0.00 32.91 3.91
2968 3082 6.183361 TGCTCTGGTGGAATATAACTAAGCAT 60.183 38.462 0.00 0.00 30.58 3.79
2969 3083 6.148480 GCTCTGGTGGAATATAACTAAGCATG 59.852 42.308 0.00 0.00 0.00 4.06
2970 3084 5.997746 TCTGGTGGAATATAACTAAGCATGC 59.002 40.000 10.51 10.51 0.00 4.06
2971 3085 5.689835 TGGTGGAATATAACTAAGCATGCA 58.310 37.500 21.98 0.00 0.00 3.96
2972 3086 6.306199 TGGTGGAATATAACTAAGCATGCAT 58.694 36.000 21.98 11.22 0.00 3.96
2987 3101 3.813957 GCATGCATATGGGGGCTAGTTAA 60.814 47.826 14.21 0.00 34.79 2.01
3006 3120 5.593095 AGTTAACCCCTCTCAAAAGAACAAC 59.407 40.000 0.88 0.00 0.00 3.32
3010 3124 2.221055 CCCTCTCAAAAGAACAACGACG 59.779 50.000 0.00 0.00 0.00 5.12
3026 3143 4.361451 ACGACGGAAGAAACGTATACAT 57.639 40.909 3.32 0.00 45.68 2.29
3027 3144 4.100529 ACGACGGAAGAAACGTATACATG 58.899 43.478 3.32 0.00 45.68 3.21
3117 6301 5.009410 CCTCTCAAATCATTGTAATGGGAGC 59.991 44.000 4.89 0.00 37.79 4.70
3128 6400 8.375506 TCATTGTAATGGGAGCTACTATAAAGG 58.624 37.037 0.00 0.00 37.03 3.11
3214 6486 2.660236 GACACTTCGTTATGTCACGGTC 59.340 50.000 9.70 0.00 43.89 4.79
3218 6490 3.374988 ACTTCGTTATGTCACGGTCGATA 59.625 43.478 0.00 0.00 40.74 2.92
3249 6521 6.892485 TCTTTTGATCTAGCATGGAGATTCA 58.108 36.000 0.00 0.00 33.71 2.57
3266 6538 8.751242 TGGAGATTCATGCAGAAAAATTCATTA 58.249 29.630 0.00 0.00 40.22 1.90
3338 6642 1.895798 TGGCTAGGTCTCAGTTGACTG 59.104 52.381 4.77 4.77 45.08 3.51
3401 6705 2.711978 AAAGAAATACTCCCTCCGCC 57.288 50.000 0.00 0.00 0.00 6.13
3402 6706 1.880941 AAGAAATACTCCCTCCGCCT 58.119 50.000 0.00 0.00 0.00 5.52
3403 6707 1.415200 AGAAATACTCCCTCCGCCTC 58.585 55.000 0.00 0.00 0.00 4.70
3404 6708 1.120530 GAAATACTCCCTCCGCCTCA 58.879 55.000 0.00 0.00 0.00 3.86
3405 6709 1.694696 GAAATACTCCCTCCGCCTCAT 59.305 52.381 0.00 0.00 0.00 2.90
3406 6710 2.696526 AATACTCCCTCCGCCTCATA 57.303 50.000 0.00 0.00 0.00 2.15
3408 6712 2.696526 TACTCCCTCCGCCTCATAAT 57.303 50.000 0.00 0.00 0.00 1.28
3409 6713 1.051812 ACTCCCTCCGCCTCATAATG 58.948 55.000 0.00 0.00 0.00 1.90
3410 6714 1.051812 CTCCCTCCGCCTCATAATGT 58.948 55.000 0.00 0.00 0.00 2.71
3411 6715 2.248248 CTCCCTCCGCCTCATAATGTA 58.752 52.381 0.00 0.00 0.00 2.29
3412 6716 2.632996 CTCCCTCCGCCTCATAATGTAA 59.367 50.000 0.00 0.00 0.00 2.41
3413 6717 2.632996 TCCCTCCGCCTCATAATGTAAG 59.367 50.000 0.00 0.00 0.00 2.34
3414 6718 2.632996 CCCTCCGCCTCATAATGTAAGA 59.367 50.000 0.00 0.00 0.00 2.10
3415 6719 3.555168 CCCTCCGCCTCATAATGTAAGAC 60.555 52.174 0.00 0.00 0.00 3.01
3416 6720 3.322254 CCTCCGCCTCATAATGTAAGACT 59.678 47.826 0.00 0.00 0.00 3.24
3417 6721 4.202264 CCTCCGCCTCATAATGTAAGACTT 60.202 45.833 0.00 0.00 0.00 3.01
3418 6722 5.353394 TCCGCCTCATAATGTAAGACTTT 57.647 39.130 0.00 0.00 0.00 2.66
3419 6723 5.741011 TCCGCCTCATAATGTAAGACTTTT 58.259 37.500 0.00 0.00 0.00 2.27
3420 6724 6.177610 TCCGCCTCATAATGTAAGACTTTTT 58.822 36.000 0.00 0.00 0.00 1.94
3441 6745 6.854496 TTTTTACACTAGTTGCACGAATCT 57.146 33.333 0.00 0.00 0.00 2.40
3442 6746 6.854496 TTTTACACTAGTTGCACGAATCTT 57.146 33.333 0.00 0.00 0.00 2.40
3443 6747 6.462073 TTTACACTAGTTGCACGAATCTTC 57.538 37.500 0.00 0.00 0.00 2.87
3444 6748 3.990092 ACACTAGTTGCACGAATCTTCA 58.010 40.909 0.00 0.00 0.00 3.02
3445 6749 4.569943 ACACTAGTTGCACGAATCTTCAT 58.430 39.130 0.00 0.00 0.00 2.57
3446 6750 5.720202 ACACTAGTTGCACGAATCTTCATA 58.280 37.500 0.00 0.00 0.00 2.15
3447 6751 5.577164 ACACTAGTTGCACGAATCTTCATAC 59.423 40.000 0.00 0.00 0.00 2.39
3448 6752 5.576774 CACTAGTTGCACGAATCTTCATACA 59.423 40.000 0.00 0.00 0.00 2.29
3449 6753 6.256539 CACTAGTTGCACGAATCTTCATACAT 59.743 38.462 0.00 0.00 0.00 2.29
3450 6754 5.475273 AGTTGCACGAATCTTCATACATG 57.525 39.130 0.00 0.00 0.00 3.21
3451 6755 5.178061 AGTTGCACGAATCTTCATACATGA 58.822 37.500 0.00 0.00 34.44 3.07
3452 6756 5.819379 AGTTGCACGAATCTTCATACATGAT 59.181 36.000 0.00 0.00 36.56 2.45
3453 6757 5.912360 TGCACGAATCTTCATACATGATC 57.088 39.130 0.00 0.00 36.56 2.92
3454 6758 5.604565 TGCACGAATCTTCATACATGATCT 58.395 37.500 0.00 0.00 36.56 2.75
3479 6783 9.227490 CTCACGAATATATAATCGATTGAGACC 57.773 37.037 23.53 3.36 41.17 3.85
3480 6784 7.908601 TCACGAATATATAATCGATTGAGACCG 59.091 37.037 23.50 15.53 41.43 4.79
3492 6796 4.945645 AGACCGGACCAAGTCTCA 57.054 55.556 9.46 0.00 39.08 3.27
3498 6802 0.109689 CGGACCAAGTCTCAGTCGAC 60.110 60.000 7.70 7.70 32.47 4.20
3500 6804 2.434428 GGACCAAGTCTCAGTCGACTA 58.566 52.381 19.57 0.00 43.14 2.59
3516 6820 6.533723 CAGTCGACTAATATTTAGCAACACCA 59.466 38.462 19.57 0.00 0.00 4.17
3518 6822 7.604927 AGTCGACTAATATTTAGCAACACCAAA 59.395 33.333 18.46 0.00 0.00 3.28
3614 6921 8.633075 TGTCAAGATTTGTGATGTTTTCTTTC 57.367 30.769 0.00 0.00 0.00 2.62
3616 6923 7.922811 GTCAAGATTTGTGATGTTTTCTTTCCT 59.077 33.333 0.00 0.00 0.00 3.36
3617 6924 9.130661 TCAAGATTTGTGATGTTTTCTTTCCTA 57.869 29.630 0.00 0.00 0.00 2.94
3627 6934 7.860373 TGATGTTTTCTTTCCTATGTTGTTTCG 59.140 33.333 0.00 0.00 0.00 3.46
3631 6938 9.673454 GTTTTCTTTCCTATGTTGTTTCGTTAT 57.327 29.630 0.00 0.00 0.00 1.89
3682 6990 9.830975 ATTATACATTAATTTTTGACTTGCCCC 57.169 29.630 0.00 0.00 0.00 5.80
3754 7062 5.043189 CCTGTTTGGGTAAGTCGATTTTC 57.957 43.478 0.00 0.00 0.00 2.29
3763 7071 4.820173 GGTAAGTCGATTTTCCTATTGGGG 59.180 45.833 8.77 0.00 35.33 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.220749 GTGCTCCATGTAGCCCGAA 59.779 57.895 7.92 0.00 42.05 4.30
99 100 2.267426 TGCACATGTGTAGTACGCATC 58.733 47.619 26.01 14.51 45.28 3.91
103 104 6.139435 TGAAATTTTGCACATGTGTAGTACG 58.861 36.000 26.01 0.00 0.00 3.67
104 105 7.807433 TCATGAAATTTTGCACATGTGTAGTAC 59.193 33.333 26.01 10.29 40.32 2.73
113 114 9.491675 TGTATTTTCTCATGAAATTTTGCACAT 57.508 25.926 0.00 0.00 41.24 3.21
163 164 5.757850 AGCAACGAATTTTCACTCTCTTT 57.242 34.783 0.00 0.00 0.00 2.52
175 176 9.988350 CTGTTCACTATATAAAAGCAACGAATT 57.012 29.630 0.00 0.00 0.00 2.17
176 177 9.378551 TCTGTTCACTATATAAAAGCAACGAAT 57.621 29.630 0.00 0.00 0.00 3.34
178 179 7.010183 GCTCTGTTCACTATATAAAAGCAACGA 59.990 37.037 0.00 0.00 0.00 3.85
179 180 7.119997 GCTCTGTTCACTATATAAAAGCAACG 58.880 38.462 0.00 0.00 0.00 4.10
183 184 7.064609 TGTGTGCTCTGTTCACTATATAAAAGC 59.935 37.037 0.00 0.00 35.58 3.51
184 185 8.383619 GTGTGTGCTCTGTTCACTATATAAAAG 58.616 37.037 0.00 0.00 35.58 2.27
185 186 8.094548 AGTGTGTGCTCTGTTCACTATATAAAA 58.905 33.333 0.00 0.00 37.55 1.52
187 188 7.170393 AGTGTGTGCTCTGTTCACTATATAA 57.830 36.000 0.00 0.00 37.55 0.98
190 191 6.775594 ATAGTGTGTGCTCTGTTCACTATA 57.224 37.500 12.41 0.00 44.83 1.31
196 198 4.151335 CAGTGAATAGTGTGTGCTCTGTTC 59.849 45.833 0.00 0.00 37.08 3.18
199 201 3.657634 ACAGTGAATAGTGTGTGCTCTG 58.342 45.455 0.00 0.00 38.99 3.35
208 210 7.416817 TGATTTTGAACACACAGTGAATAGTG 58.583 34.615 7.81 2.79 41.40 2.74
212 214 8.632679 ACTAATGATTTTGAACACACAGTGAAT 58.367 29.630 7.81 0.00 36.96 2.57
218 220 8.465999 AGACAAACTAATGATTTTGAACACACA 58.534 29.630 0.05 0.00 36.41 3.72
219 221 8.856490 AGACAAACTAATGATTTTGAACACAC 57.144 30.769 0.05 0.00 36.41 3.82
253 255 1.560923 ATACATTGACACGCGAGCTC 58.439 50.000 15.93 2.73 0.00 4.09
275 281 6.519382 TCCATGTGTGCAAATTTTTATGACA 58.481 32.000 0.00 0.00 0.00 3.58
291 297 3.920231 ACAGATGCATACTCCATGTGT 57.080 42.857 0.00 0.00 40.88 3.72
292 298 5.544650 TCATACAGATGCATACTCCATGTG 58.455 41.667 0.00 0.00 39.20 3.21
299 311 8.371571 TCCAGAATATCATACAGATGCATACT 57.628 34.615 0.00 0.00 37.57 2.12
304 316 7.337167 AGGAATCCAGAATATCATACAGATGC 58.663 38.462 0.61 0.00 37.57 3.91
309 321 9.056005 CGAAAAAGGAATCCAGAATATCATACA 57.944 33.333 0.61 0.00 0.00 2.29
379 391 3.619979 CGAGCTACATGGAGGTCCTTTTT 60.620 47.826 27.43 0.00 40.20 1.94
380 392 2.093447 CGAGCTACATGGAGGTCCTTTT 60.093 50.000 27.43 0.00 40.20 2.27
381 393 1.482593 CGAGCTACATGGAGGTCCTTT 59.517 52.381 27.43 0.00 40.20 3.11
385 397 0.031449 GCTCGAGCTACATGGAGGTC 59.969 60.000 29.88 24.63 39.98 3.85
387 399 0.249238 GTGCTCGAGCTACATGGAGG 60.249 60.000 35.27 0.00 42.66 4.30
388 400 0.457443 TGTGCTCGAGCTACATGGAG 59.543 55.000 35.27 0.00 42.66 3.86
389 401 0.894835 TTGTGCTCGAGCTACATGGA 59.105 50.000 35.27 19.73 42.66 3.41
399 413 2.622942 AGAAATGCCTTTTTGTGCTCGA 59.377 40.909 0.00 0.00 0.00 4.04
431 445 4.825634 CCTTAGATCATGCCATGTTGACAT 59.174 41.667 4.31 0.00 36.96 3.06
445 459 0.179702 CTGCAGCCAGCCTTAGATCA 59.820 55.000 0.00 0.00 44.83 2.92
501 521 3.691342 CGTTCCAGCGTCTCCCCA 61.691 66.667 0.00 0.00 0.00 4.96
518 538 2.482142 CGCTCTGTCCCTGTTTAGATCC 60.482 54.545 0.00 0.00 0.00 3.36
551 571 1.233019 GCATGCAGTGTGTCTGTCTT 58.767 50.000 14.21 0.00 45.23 3.01
586 608 4.394712 AAAGGAGCGGTGCCGAGG 62.395 66.667 15.45 0.00 42.83 4.63
824 855 5.303333 TGCCTTTGATGAATGATGCATGTAT 59.697 36.000 2.46 0.00 0.00 2.29
825 856 4.645588 TGCCTTTGATGAATGATGCATGTA 59.354 37.500 2.46 0.00 0.00 2.29
826 857 3.449377 TGCCTTTGATGAATGATGCATGT 59.551 39.130 2.46 0.00 0.00 3.21
827 858 4.053469 TGCCTTTGATGAATGATGCATG 57.947 40.909 2.46 0.00 0.00 4.06
828 859 4.631131 CATGCCTTTGATGAATGATGCAT 58.369 39.130 0.00 0.00 38.63 3.96
829 860 3.739830 GCATGCCTTTGATGAATGATGCA 60.740 43.478 6.36 0.00 35.97 3.96
830 861 2.800544 GCATGCCTTTGATGAATGATGC 59.199 45.455 6.36 0.00 0.00 3.91
841 872 2.164219 ACGATTTGTAGGCATGCCTTTG 59.836 45.455 42.49 28.76 45.70 2.77
842 873 2.423538 GACGATTTGTAGGCATGCCTTT 59.576 45.455 42.49 23.74 45.70 3.11
843 874 2.017049 GACGATTTGTAGGCATGCCTT 58.983 47.619 42.49 25.81 45.70 4.35
877 912 4.875544 TCGAATGAATTGATCGGAAACC 57.124 40.909 4.80 0.00 37.20 3.27
920 955 7.414651 GCGCTATATATCAAGTTCTGCTCTCTA 60.415 40.741 0.00 0.00 0.00 2.43
976 1011 2.321263 ATCAGGATCGGTGGCAGCAG 62.321 60.000 17.80 9.63 0.00 4.24
977 1012 2.315781 GATCAGGATCGGTGGCAGCA 62.316 60.000 17.80 4.41 0.00 4.41
978 1013 1.596477 GATCAGGATCGGTGGCAGC 60.596 63.158 6.62 6.62 0.00 5.25
991 1026 1.203928 GTCGTCGCCATCAAGATCAG 58.796 55.000 0.00 0.00 0.00 2.90
994 1029 0.385751 ATCGTCGTCGCCATCAAGAT 59.614 50.000 0.00 0.00 36.96 2.40
996 1031 0.525455 TCATCGTCGTCGCCATCAAG 60.525 55.000 0.00 0.00 36.96 3.02
1003 1038 1.013323 GCATTGTCATCGTCGTCGC 60.013 57.895 0.00 0.00 36.96 5.19
1350 1385 0.323629 GCTGCCAGTGGTAGGTGTAA 59.676 55.000 26.35 0.00 35.94 2.41
1630 1665 2.750237 GGTGAACATGGGCGGGTC 60.750 66.667 0.00 0.00 0.00 4.46
1671 1706 1.738099 GACGTTGCAGATGCGGAGT 60.738 57.895 0.00 0.00 45.83 3.85
2107 2142 1.320344 TACCTGAGCTTGCCGTCGAT 61.320 55.000 0.00 0.00 0.00 3.59
2488 2567 4.194720 CGTCTTCCTCTCCGCCGG 62.195 72.222 0.00 0.00 0.00 6.13
2772 2851 8.501904 TCAATGGATTAATTAGTTGGATCAGGA 58.498 33.333 0.00 0.00 0.00 3.86
2867 2964 5.168569 CACACAAGAATGGAGTACGTACAT 58.831 41.667 26.55 12.32 0.00 2.29
2917 3028 5.567138 AAGAAAATCGATCGCCAAGAATT 57.433 34.783 11.09 0.53 0.00 2.17
2918 3029 5.567138 AAAGAAAATCGATCGCCAAGAAT 57.433 34.783 11.09 0.00 0.00 2.40
2947 3061 5.764686 TGCATGCTTAGTTATATTCCACCAG 59.235 40.000 20.33 0.00 0.00 4.00
2960 3074 1.548582 GCCCCCATATGCATGCTTAGT 60.549 52.381 20.33 5.03 0.00 2.24
2961 3075 1.180029 GCCCCCATATGCATGCTTAG 58.820 55.000 20.33 10.38 0.00 2.18
2962 3076 0.779358 AGCCCCCATATGCATGCTTA 59.221 50.000 20.33 17.39 0.00 3.09
2963 3077 0.779358 TAGCCCCCATATGCATGCTT 59.221 50.000 20.33 15.55 0.00 3.91
2964 3078 0.330604 CTAGCCCCCATATGCATGCT 59.669 55.000 20.33 10.80 0.00 3.79
2965 3079 0.038744 ACTAGCCCCCATATGCATGC 59.961 55.000 11.82 11.82 0.00 4.06
2966 3080 2.592102 AACTAGCCCCCATATGCATG 57.408 50.000 10.16 0.00 0.00 4.06
2967 3081 3.245264 GGTTAACTAGCCCCCATATGCAT 60.245 47.826 3.79 3.79 0.00 3.96
2968 3082 2.107552 GGTTAACTAGCCCCCATATGCA 59.892 50.000 5.42 0.00 0.00 3.96
2969 3083 2.554564 GGGTTAACTAGCCCCCATATGC 60.555 54.545 5.42 0.00 40.52 3.14
2970 3084 3.434940 GGGTTAACTAGCCCCCATATG 57.565 52.381 5.42 0.00 40.52 1.78
2987 3101 2.171870 TCGTTGTTCTTTTGAGAGGGGT 59.828 45.455 0.00 0.00 0.00 4.95
3006 3120 4.100529 ACATGTATACGTTTCTTCCGTCG 58.899 43.478 0.00 0.00 39.60 5.12
3010 3124 6.730960 TTCCAACATGTATACGTTTCTTCC 57.269 37.500 0.00 0.00 0.00 3.46
3026 3143 6.571537 GCCGATCCTTAATTTTCTTTCCAACA 60.572 38.462 0.00 0.00 0.00 3.33
3027 3144 5.805486 GCCGATCCTTAATTTTCTTTCCAAC 59.195 40.000 0.00 0.00 0.00 3.77
3065 3182 4.771114 ATGTGGAGATTATTCGTTCCCA 57.229 40.909 0.00 0.00 0.00 4.37
3066 3183 7.011482 GCATATATGTGGAGATTATTCGTTCCC 59.989 40.741 14.14 0.00 0.00 3.97
3067 3184 7.011482 GGCATATATGTGGAGATTATTCGTTCC 59.989 40.741 14.14 0.00 0.00 3.62
3068 3185 7.011482 GGGCATATATGTGGAGATTATTCGTTC 59.989 40.741 14.14 0.00 0.00 3.95
3070 3187 6.156949 AGGGCATATATGTGGAGATTATTCGT 59.843 38.462 14.14 0.00 0.00 3.85
3071 3188 6.586344 AGGGCATATATGTGGAGATTATTCG 58.414 40.000 14.14 0.00 0.00 3.34
3072 3189 7.800092 AGAGGGCATATATGTGGAGATTATTC 58.200 38.462 14.14 0.00 0.00 1.75
3073 3190 7.404104 TGAGAGGGCATATATGTGGAGATTATT 59.596 37.037 14.14 0.00 0.00 1.40
3074 3191 6.905215 TGAGAGGGCATATATGTGGAGATTAT 59.095 38.462 14.14 0.00 0.00 1.28
3128 6400 7.916914 ACAGGTAGTTAAATGATGTGGTAAC 57.083 36.000 0.00 0.00 0.00 2.50
3162 6434 8.451908 ACTGAGACTTAGCAAAACTGTAAAAT 57.548 30.769 0.00 0.00 0.00 1.82
3195 6467 1.647213 CGACCGTGACATAACGAAGTG 59.353 52.381 0.00 0.00 45.00 3.16
3209 6481 8.794553 AGATCAAAAGAATATAGTATCGACCGT 58.205 33.333 0.00 0.00 0.00 4.83
3218 6490 9.941325 CTCCATGCTAGATCAAAAGAATATAGT 57.059 33.333 0.00 0.00 0.00 2.12
3305 6609 7.023120 TGAGACCTAGCCATACCCTAATTTAT 58.977 38.462 0.00 0.00 0.00 1.40
3307 6611 5.224441 TGAGACCTAGCCATACCCTAATTT 58.776 41.667 0.00 0.00 0.00 1.82
3308 6612 4.827789 TGAGACCTAGCCATACCCTAATT 58.172 43.478 0.00 0.00 0.00 1.40
3313 6617 2.089600 ACTGAGACCTAGCCATACCC 57.910 55.000 0.00 0.00 0.00 3.69
3315 6619 3.702045 AGTCAACTGAGACCTAGCCATAC 59.298 47.826 0.00 0.00 39.34 2.39
3317 6621 2.499289 CAGTCAACTGAGACCTAGCCAT 59.501 50.000 4.05 0.00 46.59 4.40
3319 6623 2.663826 CAGTCAACTGAGACCTAGCC 57.336 55.000 4.05 0.00 46.59 3.93
3382 6686 2.170817 GAGGCGGAGGGAGTATTTCTTT 59.829 50.000 0.00 0.00 0.00 2.52
3384 6688 1.343075 TGAGGCGGAGGGAGTATTTCT 60.343 52.381 0.00 0.00 0.00 2.52
3391 6695 1.051812 ACATTATGAGGCGGAGGGAG 58.948 55.000 0.00 0.00 0.00 4.30
3392 6696 2.391926 TACATTATGAGGCGGAGGGA 57.608 50.000 0.00 0.00 0.00 4.20
3393 6697 2.632996 TCTTACATTATGAGGCGGAGGG 59.367 50.000 0.00 0.00 0.00 4.30
3394 6698 3.322254 AGTCTTACATTATGAGGCGGAGG 59.678 47.826 0.00 0.00 0.00 4.30
3395 6699 4.592485 AGTCTTACATTATGAGGCGGAG 57.408 45.455 0.00 0.00 0.00 4.63
3396 6700 5.353394 AAAGTCTTACATTATGAGGCGGA 57.647 39.130 0.00 0.00 0.00 5.54
3397 6701 6.436843 AAAAAGTCTTACATTATGAGGCGG 57.563 37.500 0.00 0.00 0.00 6.13
3418 6722 6.854496 AGATTCGTGCAACTAGTGTAAAAA 57.146 33.333 0.00 0.00 31.75 1.94
3419 6723 6.480651 TGAAGATTCGTGCAACTAGTGTAAAA 59.519 34.615 0.00 0.00 31.75 1.52
3420 6724 5.986741 TGAAGATTCGTGCAACTAGTGTAAA 59.013 36.000 0.00 0.00 31.75 2.01
3421 6725 5.534407 TGAAGATTCGTGCAACTAGTGTAA 58.466 37.500 0.00 0.00 31.75 2.41
3422 6726 5.128992 TGAAGATTCGTGCAACTAGTGTA 57.871 39.130 0.00 0.00 31.75 2.90
3423 6727 3.990092 TGAAGATTCGTGCAACTAGTGT 58.010 40.909 0.00 0.00 31.75 3.55
3424 6728 5.576774 TGTATGAAGATTCGTGCAACTAGTG 59.423 40.000 0.00 0.00 36.17 2.74
3425 6729 5.720202 TGTATGAAGATTCGTGCAACTAGT 58.280 37.500 3.46 0.00 36.17 2.57
3426 6730 6.476706 TCATGTATGAAGATTCGTGCAACTAG 59.523 38.462 9.19 0.00 41.09 2.57
3427 6731 6.337356 TCATGTATGAAGATTCGTGCAACTA 58.663 36.000 9.19 0.00 41.09 2.24
3428 6732 5.178061 TCATGTATGAAGATTCGTGCAACT 58.822 37.500 9.19 0.00 41.09 3.16
3429 6733 5.469373 TCATGTATGAAGATTCGTGCAAC 57.531 39.130 9.19 0.00 41.09 4.17
3430 6734 6.051074 AGATCATGTATGAAGATTCGTGCAA 58.949 36.000 9.19 0.00 41.09 4.08
3431 6735 5.604565 AGATCATGTATGAAGATTCGTGCA 58.395 37.500 7.82 7.82 41.77 4.57
3432 6736 5.693555 TGAGATCATGTATGAAGATTCGTGC 59.306 40.000 0.00 0.00 40.69 5.34
3433 6737 6.129247 CGTGAGATCATGTATGAAGATTCGTG 60.129 42.308 0.00 0.00 40.69 4.35
3434 6738 5.917447 CGTGAGATCATGTATGAAGATTCGT 59.083 40.000 0.00 0.00 40.69 3.85
3435 6739 6.145535 TCGTGAGATCATGTATGAAGATTCG 58.854 40.000 0.00 3.10 40.69 3.34
3436 6740 7.936950 TTCGTGAGATCATGTATGAAGATTC 57.063 36.000 0.00 0.00 40.69 2.52
3452 6756 9.989869 GTCTCAATCGATTATATATTCGTGAGA 57.010 33.333 26.53 26.53 41.33 3.27
3453 6757 9.227490 GGTCTCAATCGATTATATATTCGTGAG 57.773 37.037 24.43 24.43 38.66 3.51
3454 6758 7.908601 CGGTCTCAATCGATTATATATTCGTGA 59.091 37.037 20.55 17.26 36.74 4.35
3466 6770 1.191535 TGGTCCGGTCTCAATCGATT 58.808 50.000 4.39 4.39 0.00 3.34
3470 6774 1.550976 AGACTTGGTCCGGTCTCAATC 59.449 52.381 0.00 5.28 38.25 2.67
3479 6783 0.109689 GTCGACTGAGACTTGGTCCG 60.110 60.000 8.70 0.00 38.09 4.79
3480 6784 3.796667 GTCGACTGAGACTTGGTCC 57.203 57.895 8.70 0.00 38.09 4.46
3492 6796 6.636705 TGGTGTTGCTAAATATTAGTCGACT 58.363 36.000 23.66 23.66 0.00 4.18
3534 6838 7.778382 ACCTAAATTTAAAATATCAGGCGACCT 59.222 33.333 0.00 0.00 0.00 3.85
3535 6839 7.937649 ACCTAAATTTAAAATATCAGGCGACC 58.062 34.615 0.00 0.00 0.00 4.79
3603 6910 7.712797 ACGAAACAACATAGGAAAGAAAACAT 58.287 30.769 0.00 0.00 0.00 2.71
3604 6911 7.090953 ACGAAACAACATAGGAAAGAAAACA 57.909 32.000 0.00 0.00 0.00 2.83
3614 6921 8.932791 AGTGTAAGAATAACGAAACAACATAGG 58.067 33.333 0.00 0.00 0.00 2.57
3656 6964 9.830975 GGGGCAAGTCAAAAATTAATGTATAAT 57.169 29.630 0.00 0.00 0.00 1.28
3657 6965 9.041354 AGGGGCAAGTCAAAAATTAATGTATAA 57.959 29.630 0.00 0.00 0.00 0.98
3658 6966 8.474025 CAGGGGCAAGTCAAAAATTAATGTATA 58.526 33.333 0.00 0.00 0.00 1.47
3659 6967 7.038373 ACAGGGGCAAGTCAAAAATTAATGTAT 60.038 33.333 0.00 0.00 0.00 2.29
3660 6968 6.268847 ACAGGGGCAAGTCAAAAATTAATGTA 59.731 34.615 0.00 0.00 0.00 2.29
3667 6975 3.433456 CCAAACAGGGGCAAGTCAAAAAT 60.433 43.478 0.00 0.00 0.00 1.82
3707 7015 4.386954 GCAAGTCAAAAATTCAGCCTAAGC 59.613 41.667 0.00 0.00 40.32 3.09


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

AutoCloner maintained by Alex Coulton.