Multiple sequence alignment - TraesCS6B01G269000

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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 TraesCS6B01G269000 chr6B 100.000 3719 0 0 1 3719 484102131 484098413 0.000000e+00 6868.0
1 TraesCS6B01G269000 chr6A 93.154 3082 154 27 43 3110 475999017 476002055 0.000000e+00 4470.0
2 TraesCS6B01G269000 chr6D 93.185 3052 152 25 75 3110 336365355 336368366 0.000000e+00 4433.0
3 TraesCS6B01G269000 chr2A 83.918 1455 230 4 1122 2574 653000214 653001666 0.000000e+00 1387.0
4 TraesCS6B01G269000 chr2D 83.838 1454 233 2 1122 2574 509229376 509230828 0.000000e+00 1382.0
5 TraesCS6B01G269000 chr2B 83.700 1454 235 2 1122 2574 598560814 598562266 0.000000e+00 1371.0
6 TraesCS6B01G269000 chr2B 100.000 31 0 0 13 43 178764972 178765002 1.440000e-04 58.4
7 TraesCS6B01G269000 chr5B 83.642 593 75 14 3135 3719 86046695 86046117 4.230000e-149 538.0
8 TraesCS6B01G269000 chr5B 73.727 491 97 27 1287 1761 495019895 495020369 2.970000e-36 163.0
9 TraesCS6B01G269000 chr1A 74.552 1340 267 60 1243 2539 339915563 339914255 5.510000e-143 518.0
10 TraesCS6B01G269000 chr1A 97.222 36 1 0 13 48 545994564 545994529 1.120000e-05 62.1
11 TraesCS6B01G269000 chr1D 73.891 1375 289 57 1243 2576 260588578 260589923 1.550000e-133 486.0
12 TraesCS6B01G269000 chr5A 73.828 512 104 26 1287 1783 523815683 523816179 3.820000e-40 176.0
13 TraesCS6B01G269000 chr5A 100.000 33 0 0 13 45 518246501 518246533 1.120000e-05 62.1
14 TraesCS6B01G269000 chr5D 74.134 491 95 27 1287 1761 412076982 412077456 1.370000e-39 174.0
15 TraesCS6B01G269000 chr7D 72.578 547 127 20 1958 2491 255058422 255057886 1.380000e-34 158.0
16 TraesCS6B01G269000 chr7D 79.592 147 26 4 1322 1466 255059082 255058938 6.570000e-18 102.0
17 TraesCS6B01G269000 chr7A 72.344 546 130 18 1958 2491 274662073 274661537 6.430000e-33 152.0
18 TraesCS6B01G269000 chr7A 81.308 107 17 3 255 359 29808325 29808220 2.380000e-12 84.2
19 TraesCS6B01G269000 chr7B 76.847 203 35 9 141 333 678734308 678734508 1.830000e-18 104.0
20 TraesCS6B01G269000 chr7B 95.000 40 1 1 13 52 444462649 444462611 1.120000e-05 62.1
21 TraesCS6B01G269000 chr4A 100.000 34 0 0 13 46 672245293 672245326 3.100000e-06 63.9
22 TraesCS6B01G269000 chr4A 100.000 31 0 0 13 43 559507972 559508002 1.440000e-04 58.4
23 TraesCS6B01G269000 chr3A 100.000 32 0 0 13 44 186745492 186745523 4.010000e-05 60.2
24 TraesCS6B01G269000 chr1B 100.000 31 0 0 13 43 12493449 12493419 1.440000e-04 58.4
25 TraesCS6B01G269000 chr1B 100.000 31 0 0 13 43 12563408 12563378 1.440000e-04 58.4


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 TraesCS6B01G269000 chr6B 484098413 484102131 3718 True 6868 6868 100.000 1 3719 1 chr6B.!!$R1 3718
1 TraesCS6B01G269000 chr6A 475999017 476002055 3038 False 4470 4470 93.154 43 3110 1 chr6A.!!$F1 3067
2 TraesCS6B01G269000 chr6D 336365355 336368366 3011 False 4433 4433 93.185 75 3110 1 chr6D.!!$F1 3035
3 TraesCS6B01G269000 chr2A 653000214 653001666 1452 False 1387 1387 83.918 1122 2574 1 chr2A.!!$F1 1452
4 TraesCS6B01G269000 chr2D 509229376 509230828 1452 False 1382 1382 83.838 1122 2574 1 chr2D.!!$F1 1452
5 TraesCS6B01G269000 chr2B 598560814 598562266 1452 False 1371 1371 83.700 1122 2574 1 chr2B.!!$F2 1452
6 TraesCS6B01G269000 chr5B 86046117 86046695 578 True 538 538 83.642 3135 3719 1 chr5B.!!$R1 584
7 TraesCS6B01G269000 chr1A 339914255 339915563 1308 True 518 518 74.552 1243 2539 1 chr1A.!!$R1 1296
8 TraesCS6B01G269000 chr1D 260588578 260589923 1345 False 486 486 73.891 1243 2576 1 chr1D.!!$F1 1333

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
144 147 0.109689 ACGTGCGAAGTGAGTCTAGC 60.110 55.0 0.00 0.0 0.00 3.42 F
762 775 0.390472 CTCGCTCACCTTCCTTCCAC 60.390 60.0 0.00 0.0 0.00 4.02 F
1566 1582 0.178767 TGCATATGCGACCTCTGCTT 59.821 50.0 22.21 0.0 45.83 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1183 0.185175 AAACGGACCAGGCTTCCTTT 59.815 50.0 3.84 0.00 0.00 3.11 R
1824 1840 0.793617 AACCAAGGAGGAGGAGGAGA 59.206 55.0 0.00 0.00 41.22 3.71 R
3124 3161 0.029267 ATGAGGAGAGGCCATCCCTT 60.029 55.0 20.43 6.02 46.60 3.95 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 3.624900 GTCTATATAGACGTGCGTTGCA 58.375 45.455 23.60 0.00 42.72 4.08
34 35 2.553770 TGCGTTGCACGTACATGC 59.446 55.556 7.04 7.04 44.73 4.06
35 36 1.958715 TGCGTTGCACGTACATGCT 60.959 52.632 15.74 0.00 46.28 3.79
36 37 1.206578 GCGTTGCACGTACATGCTT 59.793 52.632 15.74 0.00 46.28 3.91
37 38 0.440758 GCGTTGCACGTACATGCTTA 59.559 50.000 15.74 0.21 46.28 3.09
38 39 1.785518 GCGTTGCACGTACATGCTTAC 60.786 52.381 15.74 11.77 46.28 2.34
39 40 1.724623 CGTTGCACGTACATGCTTACT 59.275 47.619 15.74 0.00 46.28 2.24
40 41 2.918600 CGTTGCACGTACATGCTTACTA 59.081 45.455 15.74 0.00 46.28 1.82
41 42 3.001070 CGTTGCACGTACATGCTTACTAG 60.001 47.826 15.74 0.00 46.28 2.57
106 107 4.137116 AGAAGCAGTACAACTTCACACA 57.863 40.909 22.48 0.00 43.84 3.72
107 108 3.871594 AGAAGCAGTACAACTTCACACAC 59.128 43.478 22.48 3.46 43.84 3.82
144 147 0.109689 ACGTGCGAAGTGAGTCTAGC 60.110 55.000 0.00 0.00 0.00 3.42
160 163 5.911752 AGTCTAGCTCAGATGGTTATGTTG 58.088 41.667 0.00 0.00 35.17 3.33
172 176 5.968528 TGGTTATGTTGTTATGGTGGAAC 57.031 39.130 0.00 0.00 0.00 3.62
191 195 5.069781 TGGAACCAACCCATCAAAGTTTAAG 59.930 40.000 0.00 0.00 0.00 1.85
226 230 5.912955 GGCGTTGGTGCTTGTATATTTATTC 59.087 40.000 0.00 0.00 34.52 1.75
231 235 7.801716 TGGTGCTTGTATATTTATTCCAGTC 57.198 36.000 0.00 0.00 0.00 3.51
232 236 7.342581 TGGTGCTTGTATATTTATTCCAGTCA 58.657 34.615 0.00 0.00 0.00 3.41
238 242 9.489084 CTTGTATATTTATTCCAGTCATTCCGA 57.511 33.333 0.00 0.00 0.00 4.55
253 257 3.507103 TTCCGACGATATTTGTTCCGA 57.493 42.857 0.00 0.00 0.00 4.55
255 259 2.124903 CCGACGATATTTGTTCCGAGG 58.875 52.381 0.00 0.00 0.00 4.63
260 264 2.364324 CGATATTTGTTCCGAGGGAGGA 59.636 50.000 0.00 0.00 38.79 3.71
272 276 2.491022 GGGAGGAGATGTCCCGTCG 61.491 68.421 5.02 0.00 44.54 5.12
298 302 2.695359 GGAGGCGTTTGTGATGACTTA 58.305 47.619 0.00 0.00 30.76 2.24
299 303 2.415512 GGAGGCGTTTGTGATGACTTAC 59.584 50.000 0.00 0.00 30.76 2.34
312 316 8.087982 TGTGATGACTTACTCAATCTCAAAAC 57.912 34.615 0.00 0.00 30.60 2.43
333 337 2.017782 GATGTGTCGGCTCAGTCTCTA 58.982 52.381 0.00 0.00 0.00 2.43
341 345 2.383855 GGCTCAGTCTCTAGGATGTGT 58.616 52.381 0.00 0.00 0.00 3.72
365 373 1.295792 AGGTGTTAAGTGTGCGTGTG 58.704 50.000 0.00 0.00 0.00 3.82
369 377 1.666700 TGTTAAGTGTGCGTGTGTTCC 59.333 47.619 0.00 0.00 0.00 3.62
374 382 1.748493 AGTGTGCGTGTGTTCCAAAAT 59.252 42.857 0.00 0.00 0.00 1.82
380 389 3.565902 TGCGTGTGTTCCAAAATGTGATA 59.434 39.130 0.00 0.00 0.00 2.15
428 437 8.693504 GCGTCTGCGTATGTATTATAGTAAAAA 58.306 33.333 0.00 0.00 40.81 1.94
482 493 9.846248 AGAAGTTTTAAGAATGAATTGGAATCG 57.154 29.630 0.00 0.00 0.00 3.34
486 497 9.203421 GTTTTAAGAATGAATTGGAATCGGTTT 57.797 29.630 0.00 0.00 0.00 3.27
487 498 9.771534 TTTTAAGAATGAATTGGAATCGGTTTT 57.228 25.926 0.00 0.00 0.00 2.43
488 499 9.771534 TTTAAGAATGAATTGGAATCGGTTTTT 57.228 25.926 0.00 0.00 0.00 1.94
603 615 1.990060 ACTGGCATGTCCCGTAGCT 60.990 57.895 0.00 0.00 29.85 3.32
762 775 0.390472 CTCGCTCACCTTCCTTCCAC 60.390 60.000 0.00 0.00 0.00 4.02
931 944 3.810896 GCAATCAACCGGGCGGAC 61.811 66.667 6.32 0.00 38.96 4.79
1017 1033 3.157252 ATGTCGCCCTGCTCCGAT 61.157 61.111 0.00 0.00 35.76 4.18
1092 1108 1.381851 CTCTTTGCTCCCCAAGGCT 59.618 57.895 0.00 0.00 34.34 4.58
1281 1297 1.598962 CCTCGCGATGCCCATGATT 60.599 57.895 10.36 0.00 0.00 2.57
1566 1582 0.178767 TGCATATGCGACCTCTGCTT 59.821 50.000 22.21 0.00 45.83 3.91
1627 1643 2.769095 GAGACCTACATTCTTGCCTCCT 59.231 50.000 0.00 0.00 0.00 3.69
1770 1786 2.179517 GTGCTCGTCTCCGTCCTG 59.820 66.667 0.00 0.00 35.01 3.86
1776 1792 2.052690 CGTCTCCGTCCTGGGACAT 61.053 63.158 18.33 0.00 44.77 3.06
1824 1840 3.146066 TGTGCTCGCCAATCTAAACTTT 58.854 40.909 0.00 0.00 0.00 2.66
1853 1869 4.403432 CCTCCTCCTTGGTTACGTATTGTA 59.597 45.833 0.00 0.00 37.07 2.41
2106 2134 4.070552 GGCTTCGGCGTCTCCACT 62.071 66.667 6.85 0.00 42.91 4.00
2118 2146 1.446792 CTCCACTCGCGTCAGCAAT 60.447 57.895 5.77 0.00 45.49 3.56
2451 2479 1.404391 CTCGCGTTCTGGTACCACTAT 59.596 52.381 11.60 0.00 0.00 2.12
2632 2660 1.902918 AGCGGCAAAGGCATTCACA 60.903 52.632 1.45 0.00 43.71 3.58
2713 2741 1.148310 CGAGCAACCAAACGATCAGT 58.852 50.000 0.00 0.00 0.00 3.41
2746 2774 3.125316 CGGCCTATTTACGATTTCGGAA 58.875 45.455 0.00 0.00 44.95 4.30
2797 2825 0.757188 GGAGAGGAATCGGAGGCTGA 60.757 60.000 0.00 0.00 0.00 4.26
2841 2869 4.164221 ACCCATTGGTAATCTGTACAGAGG 59.836 45.833 28.29 21.73 45.45 3.69
2858 2892 9.219603 TGTACAGAGGTTTTTAATCTTCTGATG 57.780 33.333 15.40 0.00 39.18 3.07
2933 2968 5.479716 TCTTTTCTTCGACAAAACAGACC 57.520 39.130 0.00 0.00 0.00 3.85
2934 2969 4.334481 TCTTTTCTTCGACAAAACAGACCC 59.666 41.667 0.00 0.00 0.00 4.46
3045 3082 7.485418 TGACGAACTACAATAAACAATGTGT 57.515 32.000 0.00 0.00 0.00 3.72
3110 3147 7.678947 ACTCCATAAGTTCAAATGAGACAAG 57.321 36.000 0.00 0.00 33.03 3.16
3111 3148 6.656693 ACTCCATAAGTTCAAATGAGACAAGG 59.343 38.462 0.00 0.00 33.03 3.61
3112 3149 6.778821 TCCATAAGTTCAAATGAGACAAGGA 58.221 36.000 0.00 0.00 0.00 3.36
3113 3150 6.881065 TCCATAAGTTCAAATGAGACAAGGAG 59.119 38.462 0.00 0.00 0.00 3.69
3114 3151 6.881065 CCATAAGTTCAAATGAGACAAGGAGA 59.119 38.462 0.00 0.00 0.00 3.71
3115 3152 7.391554 CCATAAGTTCAAATGAGACAAGGAGAA 59.608 37.037 0.00 0.00 0.00 2.87
3116 3153 6.625873 AAGTTCAAATGAGACAAGGAGAAC 57.374 37.500 0.00 0.00 35.58 3.01
3117 3154 5.934781 AGTTCAAATGAGACAAGGAGAACT 58.065 37.500 0.00 0.00 39.47 3.01
3118 3155 7.067496 AGTTCAAATGAGACAAGGAGAACTA 57.933 36.000 0.00 0.00 41.64 2.24
3119 3156 7.684529 AGTTCAAATGAGACAAGGAGAACTAT 58.315 34.615 0.00 0.00 41.64 2.12
3120 3157 7.605691 AGTTCAAATGAGACAAGGAGAACTATG 59.394 37.037 0.00 0.00 41.64 2.23
3121 3158 7.009179 TCAAATGAGACAAGGAGAACTATGT 57.991 36.000 0.00 0.00 0.00 2.29
3122 3159 6.875726 TCAAATGAGACAAGGAGAACTATGTG 59.124 38.462 0.00 0.00 0.00 3.21
3123 3160 6.611613 AATGAGACAAGGAGAACTATGTGA 57.388 37.500 0.00 0.00 0.00 3.58
3124 3161 6.611613 ATGAGACAAGGAGAACTATGTGAA 57.388 37.500 0.00 0.00 0.00 3.18
3125 3162 6.419484 TGAGACAAGGAGAACTATGTGAAA 57.581 37.500 0.00 0.00 0.00 2.69
3126 3163 6.459066 TGAGACAAGGAGAACTATGTGAAAG 58.541 40.000 0.00 0.00 0.00 2.62
3127 3164 5.799213 AGACAAGGAGAACTATGTGAAAGG 58.201 41.667 0.00 0.00 0.00 3.11
3128 3165 4.911390 ACAAGGAGAACTATGTGAAAGGG 58.089 43.478 0.00 0.00 0.00 3.95
3129 3166 4.597507 ACAAGGAGAACTATGTGAAAGGGA 59.402 41.667 0.00 0.00 0.00 4.20
3130 3167 5.251700 ACAAGGAGAACTATGTGAAAGGGAT 59.748 40.000 0.00 0.00 0.00 3.85
3131 3168 5.365021 AGGAGAACTATGTGAAAGGGATG 57.635 43.478 0.00 0.00 0.00 3.51
3132 3169 4.164988 AGGAGAACTATGTGAAAGGGATGG 59.835 45.833 0.00 0.00 0.00 3.51
3133 3170 3.879892 GAGAACTATGTGAAAGGGATGGC 59.120 47.826 0.00 0.00 0.00 4.40
3142 3179 0.253347 AAAGGGATGGCCTCTCCTCA 60.253 55.000 20.22 0.00 35.26 3.86
3143 3180 0.029267 AAGGGATGGCCTCTCCTCAT 60.029 55.000 20.22 7.96 35.26 2.90
3145 3182 2.065483 GGATGGCCTCTCCTCATCC 58.935 63.158 15.46 8.66 46.59 3.51
3146 3183 3.162394 GATGGCCTCTCCTCATCCT 57.838 57.895 3.32 0.00 33.23 3.24
3147 3184 0.975887 GATGGCCTCTCCTCATCCTC 59.024 60.000 3.32 0.00 33.23 3.71
3192 3231 3.411517 CCCCGCCACCTCCATTCT 61.412 66.667 0.00 0.00 0.00 2.40
3219 3258 3.075005 CGGTCGGACCATCCACCT 61.075 66.667 25.80 0.00 38.47 4.00
3224 3263 2.735772 CGGACCATCCACCTCCCTG 61.736 68.421 0.00 0.00 35.91 4.45
3228 3267 3.813724 CATCCACCTCCCTGCCCC 61.814 72.222 0.00 0.00 0.00 5.80
3236 3275 4.823732 TCCCTGCCCCTAGCCAGG 62.824 72.222 12.77 12.77 42.71 4.45
3242 3281 1.690985 GCCCCTAGCCAGGTTCTCT 60.691 63.158 0.00 0.00 40.79 3.10
3246 3285 0.461961 CCTAGCCAGGTTCTCTTCGG 59.538 60.000 0.00 0.00 37.15 4.30
3284 3326 1.134401 TGCCTTGATGATTCTCCGGTC 60.134 52.381 0.00 0.00 0.00 4.79
3285 3327 1.139853 GCCTTGATGATTCTCCGGTCT 59.860 52.381 0.00 0.00 0.00 3.85
3286 3328 2.831333 CCTTGATGATTCTCCGGTCTG 58.169 52.381 0.00 0.00 0.00 3.51
3288 3330 1.194218 TGATGATTCTCCGGTCTGCA 58.806 50.000 0.00 0.00 0.00 4.41
3289 3331 1.134699 TGATGATTCTCCGGTCTGCAC 60.135 52.381 0.00 0.00 0.00 4.57
3328 3370 3.474806 CGTCTGGAACGCCATGAC 58.525 61.111 0.00 0.00 45.76 3.06
3339 3381 0.170339 CGCCATGACACTCGACTACA 59.830 55.000 0.00 0.00 0.00 2.74
3345 3387 2.578786 TGACACTCGACTACAAGGACA 58.421 47.619 0.00 0.00 0.00 4.02
3347 3389 3.382227 TGACACTCGACTACAAGGACAAA 59.618 43.478 0.00 0.00 0.00 2.83
3356 3398 0.823356 ACAAGGACAAATGCTGGCGT 60.823 50.000 0.00 0.00 31.39 5.68
3357 3399 1.164411 CAAGGACAAATGCTGGCGTA 58.836 50.000 0.00 0.00 31.39 4.42
3360 3402 0.447801 GGACAAATGCTGGCGTACTG 59.552 55.000 0.00 0.00 31.39 2.74
3364 3406 0.036164 AAATGCTGGCGTACTGTCCA 59.964 50.000 0.00 0.00 0.00 4.02
3365 3407 0.253044 AATGCTGGCGTACTGTCCAT 59.747 50.000 0.00 0.00 0.00 3.41
3383 3425 2.223572 CCATCAGCCAATTACGCCTTTC 60.224 50.000 0.00 0.00 0.00 2.62
3384 3426 2.489938 TCAGCCAATTACGCCTTTCT 57.510 45.000 0.00 0.00 0.00 2.52
3394 3436 1.871080 ACGCCTTTCTGTCACAAGAG 58.129 50.000 0.00 0.00 0.00 2.85
3398 3440 2.549778 GCCTTTCTGTCACAAGAGCTCT 60.550 50.000 11.45 11.45 0.00 4.09
3418 3460 3.330405 TCTGGAACCCATCTCAATGTCAA 59.670 43.478 0.00 0.00 30.82 3.18
3431 3473 2.743664 CAATGTCAAGGTCGAATCTGCA 59.256 45.455 0.00 0.00 0.00 4.41
3444 3486 0.534427 ATCTGCATGCCTGGACATCG 60.534 55.000 16.68 0.00 0.00 3.84
3455 3497 0.390340 TGGACATCGACTGCTTGCTC 60.390 55.000 0.00 0.00 0.00 4.26
3470 3512 1.300542 GCTCCTCGCATGCTACCTC 60.301 63.158 17.13 0.00 38.92 3.85
3488 3530 3.419858 CAGGGATGCCTTGGAGGT 58.580 61.111 1.40 0.00 37.80 3.85
3490 3532 2.190578 GGGATGCCTTGGAGGTCG 59.809 66.667 0.00 0.00 37.80 4.79
3523 3565 0.193069 ATGCCCCTCCAGCTATCTCT 59.807 55.000 0.00 0.00 0.00 3.10
3524 3566 0.030705 TGCCCCTCCAGCTATCTCTT 60.031 55.000 0.00 0.00 0.00 2.85
3536 3578 3.769844 AGCTATCTCTTTCCACCTTTCGA 59.230 43.478 0.00 0.00 0.00 3.71
3539 3581 5.235401 GCTATCTCTTTCCACCTTTCGAATC 59.765 44.000 0.00 0.00 0.00 2.52
3550 3592 4.273480 CACCTTTCGAATCACTGTGTCTTT 59.727 41.667 7.79 0.75 0.00 2.52
3551 3593 4.273480 ACCTTTCGAATCACTGTGTCTTTG 59.727 41.667 7.79 7.13 0.00 2.77
3552 3594 3.878086 TTCGAATCACTGTGTCTTTGC 57.122 42.857 7.79 0.00 0.00 3.68
3553 3595 2.143122 TCGAATCACTGTGTCTTTGCC 58.857 47.619 7.79 0.00 0.00 4.52
3556 3598 1.237285 ATCACTGTGTCTTTGCCCGC 61.237 55.000 7.79 0.00 0.00 6.13
3561 3603 2.594303 TGTCTTTGCCCGCTGGTG 60.594 61.111 0.00 0.00 0.00 4.17
3562 3604 3.365265 GTCTTTGCCCGCTGGTGG 61.365 66.667 0.00 0.00 0.00 4.61
3592 3634 1.667154 CCTCGGCGAGGTTGAGATCA 61.667 60.000 40.56 1.78 44.25 2.92
3603 3645 0.755079 TTGAGATCATCTCCCCGCAG 59.245 55.000 12.37 0.00 42.73 5.18
3613 3655 2.111878 CCCCGCAGATCCACATCC 59.888 66.667 0.00 0.00 0.00 3.51
3615 3657 2.446848 CCCGCAGATCCACATCCCT 61.447 63.158 0.00 0.00 0.00 4.20
3620 3662 2.681976 CGCAGATCCACATCCCTTTCTT 60.682 50.000 0.00 0.00 0.00 2.52
3630 3672 0.178861 TCCCTTTCTTCCCCTGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
3631 3673 0.701147 CCCTTTCTTCCCCTGCTCTT 59.299 55.000 0.00 0.00 0.00 2.85
3634 3676 1.002544 CTTTCTTCCCCTGCTCTTCGT 59.997 52.381 0.00 0.00 0.00 3.85
3636 3678 1.219393 CTTCCCCTGCTCTTCGTCC 59.781 63.158 0.00 0.00 0.00 4.79
3638 3680 4.821589 CCCCTGCTCTTCGTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
3657 3699 2.437895 GCCGCCAGGGTAGGTTTC 60.438 66.667 0.00 0.00 38.44 2.78
3683 3725 1.897225 ATCTCGCACTGCCTTCTGCT 61.897 55.000 0.00 0.00 42.00 4.24
3685 3727 1.633852 CTCGCACTGCCTTCTGCTTC 61.634 60.000 0.00 0.00 42.00 3.86
3690 3732 1.073722 CTGCCTTCTGCTTCCACCA 59.926 57.895 0.00 0.00 42.00 4.17
3697 3739 1.067295 TCTGCTTCCACCACCTCAAT 58.933 50.000 0.00 0.00 0.00 2.57
3701 3743 1.171308 CTTCCACCACCTCAATGCAG 58.829 55.000 0.00 0.00 0.00 4.41
3703 3745 2.345760 CCACCACCTCAATGCAGCC 61.346 63.158 0.00 0.00 0.00 4.85
3707 3749 1.318158 CCACCTCAATGCAGCCTTCC 61.318 60.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.624900 TGCAACGCACGTCTATATAGAC 58.375 45.455 26.64 26.64 40.56 2.59
5 6 3.974871 TGCAACGCACGTCTATATAGA 57.025 42.857 8.44 8.44 31.71 1.98
23 24 6.032094 TCTTTACTAGTAAGCATGTACGTGC 58.968 40.000 28.92 28.92 45.38 5.34
24 25 7.913821 TGATCTTTACTAGTAAGCATGTACGTG 59.086 37.037 14.73 10.89 0.00 4.49
25 26 7.993101 TGATCTTTACTAGTAAGCATGTACGT 58.007 34.615 14.73 0.00 0.00 3.57
26 27 8.851960 TTGATCTTTACTAGTAAGCATGTACG 57.148 34.615 14.73 0.00 0.00 3.67
29 30 9.155975 CTGTTTGATCTTTACTAGTAAGCATGT 57.844 33.333 14.73 2.41 0.00 3.21
30 31 9.155975 ACTGTTTGATCTTTACTAGTAAGCATG 57.844 33.333 14.73 7.74 0.00 4.06
32 33 9.635520 GTACTGTTTGATCTTTACTAGTAAGCA 57.364 33.333 14.73 9.61 0.00 3.91
33 34 9.857957 AGTACTGTTTGATCTTTACTAGTAAGC 57.142 33.333 14.73 7.45 0.00 3.09
67 68 4.083110 GCTTCTATATTACCACCGCGTAGA 60.083 45.833 4.92 0.00 0.00 2.59
106 107 0.608130 TGTGCTGAACCGCTGATAGT 59.392 50.000 0.00 0.00 0.00 2.12
107 108 1.002366 GTGTGCTGAACCGCTGATAG 58.998 55.000 0.00 0.00 0.00 2.08
144 147 6.038603 CCACCATAACAACATAACCATCTGAG 59.961 42.308 0.00 0.00 0.00 3.35
172 176 6.405278 AAGACTTAAACTTTGATGGGTTGG 57.595 37.500 0.00 0.00 0.00 3.77
175 179 7.746703 AGTCTAAGACTTAAACTTTGATGGGT 58.253 34.615 0.00 0.00 40.28 4.51
191 195 1.798813 CACCAACGCCAAGTCTAAGAC 59.201 52.381 0.00 0.00 0.00 3.01
204 208 7.022055 TGGAATAAATATACAAGCACCAACG 57.978 36.000 0.00 0.00 0.00 4.10
226 230 4.119862 ACAAATATCGTCGGAATGACTGG 58.880 43.478 0.00 0.00 45.87 4.00
231 235 3.799963 TCGGAACAAATATCGTCGGAATG 59.200 43.478 0.00 0.00 0.00 2.67
232 236 4.049186 CTCGGAACAAATATCGTCGGAAT 58.951 43.478 0.00 0.00 0.00 3.01
238 242 2.102588 CCTCCCTCGGAACAAATATCGT 59.897 50.000 0.00 0.00 0.00 3.73
243 247 1.952621 TCTCCTCCCTCGGAACAAAT 58.047 50.000 0.00 0.00 31.44 2.32
253 257 1.075896 GACGGGACATCTCCTCCCT 60.076 63.158 2.05 0.00 45.00 4.20
255 259 1.453379 TCGACGGGACATCTCCTCC 60.453 63.158 0.00 0.00 36.68 4.30
286 290 8.559536 GTTTTGAGATTGAGTAAGTCATCACAA 58.440 33.333 0.00 0.00 34.17 3.33
298 302 4.150627 CGACACATCGTTTTGAGATTGAGT 59.849 41.667 0.00 0.00 43.66 3.41
299 303 4.632023 CGACACATCGTTTTGAGATTGAG 58.368 43.478 0.00 0.00 43.66 3.02
321 325 2.383855 ACACATCCTAGAGACTGAGCC 58.616 52.381 0.00 0.00 0.00 4.70
322 326 3.445450 TGAACACATCCTAGAGACTGAGC 59.555 47.826 0.00 0.00 0.00 4.26
327 331 5.361285 ACACCTATGAACACATCCTAGAGAC 59.639 44.000 0.00 0.00 30.24 3.36
333 337 6.173339 CACTTAACACCTATGAACACATCCT 58.827 40.000 0.00 0.00 0.00 3.24
341 345 3.743911 CACGCACACTTAACACCTATGAA 59.256 43.478 0.00 0.00 0.00 2.57
365 373 7.398834 GCATATGCTTATCACATTTTGGAAC 57.601 36.000 20.64 0.00 38.21 3.62
395 404 2.666026 ACATACGCAGACGCTCATATG 58.334 47.619 0.00 0.00 45.53 1.78
396 405 4.703645 ATACATACGCAGACGCTCATAT 57.296 40.909 0.00 0.00 45.53 1.78
428 437 2.418197 CCCCGACGTGTGATGAACTATT 60.418 50.000 0.00 0.00 0.00 1.73
430 439 0.528924 CCCCGACGTGTGATGAACTA 59.471 55.000 0.00 0.00 0.00 2.24
486 497 7.042335 TGCAATTTCGGTTCCTTTAAGAAAAA 58.958 30.769 0.00 0.00 34.97 1.94
487 498 6.574350 TGCAATTTCGGTTCCTTTAAGAAAA 58.426 32.000 0.00 0.00 34.97 2.29
488 499 6.150396 TGCAATTTCGGTTCCTTTAAGAAA 57.850 33.333 0.00 0.00 35.64 2.52
489 500 5.776173 TGCAATTTCGGTTCCTTTAAGAA 57.224 34.783 0.00 0.00 0.00 2.52
490 501 5.391523 CGATGCAATTTCGGTTCCTTTAAGA 60.392 40.000 0.17 0.00 33.05 2.10
491 502 4.793216 CGATGCAATTTCGGTTCCTTTAAG 59.207 41.667 0.17 0.00 33.05 1.85
492 503 4.216687 ACGATGCAATTTCGGTTCCTTTAA 59.783 37.500 12.42 0.00 40.83 1.52
493 504 3.754323 ACGATGCAATTTCGGTTCCTTTA 59.246 39.130 12.42 0.00 40.83 1.85
603 615 4.379652 GAATTTTCAGCTTTGCCTTTCCA 58.620 39.130 0.00 0.00 0.00 3.53
687 699 0.731417 CAAGCGGGATTGCTCTCTTG 59.269 55.000 0.00 0.00 46.60 3.02
931 944 2.829458 GAGAGGGACGTCTCGGGG 60.829 72.222 16.46 0.00 38.71 5.73
975 991 0.108804 CCGCGAAACAGAGGAGCTAA 60.109 55.000 8.23 0.00 32.51 3.09
1006 1022 2.202932 CGTGGAATCGGAGCAGGG 60.203 66.667 0.00 0.00 0.00 4.45
1075 1091 1.075482 CAGCCTTGGGGAGCAAAGA 59.925 57.895 0.00 0.00 33.58 2.52
1092 1108 2.927856 ATGGGCACGACCACCTCA 60.928 61.111 0.00 0.00 44.72 3.86
1160 1176 1.026718 CCAGGCTTCCTTTACCGCTG 61.027 60.000 0.00 0.00 0.00 5.18
1167 1183 0.185175 AAACGGACCAGGCTTCCTTT 59.815 50.000 3.84 0.00 0.00 3.11
1241 1257 4.603946 GTATGGACCGCGCCTCCC 62.604 72.222 16.10 7.81 0.00 4.30
1566 1582 3.952508 TCCTGGCCGCAGAGCAAA 61.953 61.111 0.00 0.00 0.00 3.68
1605 1621 2.501723 GGAGGCAAGAATGTAGGTCTCA 59.498 50.000 0.00 0.00 0.00 3.27
1770 1786 2.196776 CCCCTGATGCCATGTCCC 59.803 66.667 0.00 0.00 0.00 4.46
1800 1816 2.939103 GTTTAGATTGGCGAGCACAGAT 59.061 45.455 0.00 0.00 0.00 2.90
1824 1840 0.793617 AACCAAGGAGGAGGAGGAGA 59.206 55.000 0.00 0.00 41.22 3.71
1853 1869 1.893808 CGCTTGTGCACTCCCTTGT 60.894 57.895 19.41 0.00 39.64 3.16
1962 1990 0.896940 TCTCGTACCACCACCACTCC 60.897 60.000 0.00 0.00 0.00 3.85
2106 2134 1.344226 CGAGTTCATTGCTGACGCGA 61.344 55.000 15.93 0.00 39.65 5.87
2169 2197 2.184322 GCGAACCCGAGCATGAGA 59.816 61.111 0.00 0.00 38.22 3.27
2451 2479 2.528818 CCACAGGCCCTGGAAGTCA 61.529 63.158 16.70 0.00 35.51 3.41
2632 2660 4.194720 GGCCGCGACTCTCACGAT 62.195 66.667 8.23 0.00 0.00 3.73
2713 2741 1.043116 ATAGGCCGTAGCTGTCAGCA 61.043 55.000 26.23 9.96 45.56 4.41
2797 2825 6.153680 TGGGTAACAAAAATTGTCACTCTGTT 59.846 34.615 0.00 0.00 44.59 3.16
2841 2869 8.665685 ACACCGATACATCAGAAGATTAAAAAC 58.334 33.333 0.00 0.00 30.20 2.43
2858 2892 7.923888 TCACTTCTGTAATACTACACCGATAC 58.076 38.462 0.00 0.00 34.28 2.24
2933 2968 2.945668 GCTGCTAAAGTAATGTGAGGGG 59.054 50.000 0.00 0.00 0.00 4.79
2934 2969 3.609853 TGCTGCTAAAGTAATGTGAGGG 58.390 45.455 0.00 0.00 0.00 4.30
3034 3071 9.790389 AATTAAAGTTGAACGACACATTGTTTA 57.210 25.926 0.00 0.00 32.12 2.01
3045 3082 9.767684 CACTATGCATTAATTAAAGTTGAACGA 57.232 29.630 3.54 0.00 0.00 3.85
3110 3147 4.455606 CCATCCCTTTCACATAGTTCTCC 58.544 47.826 0.00 0.00 0.00 3.71
3111 3148 3.879892 GCCATCCCTTTCACATAGTTCTC 59.120 47.826 0.00 0.00 0.00 2.87
3112 3149 3.372025 GGCCATCCCTTTCACATAGTTCT 60.372 47.826 0.00 0.00 0.00 3.01
3113 3150 2.952310 GGCCATCCCTTTCACATAGTTC 59.048 50.000 0.00 0.00 0.00 3.01
3114 3151 2.582636 AGGCCATCCCTTTCACATAGTT 59.417 45.455 5.01 0.00 43.06 2.24
3115 3152 2.173569 GAGGCCATCCCTTTCACATAGT 59.826 50.000 5.01 0.00 46.60 2.12
3116 3153 2.441001 AGAGGCCATCCCTTTCACATAG 59.559 50.000 5.01 0.00 46.60 2.23
3117 3154 2.439507 GAGAGGCCATCCCTTTCACATA 59.560 50.000 5.01 0.00 46.60 2.29
3118 3155 1.213926 GAGAGGCCATCCCTTTCACAT 59.786 52.381 5.01 0.00 46.60 3.21
3119 3156 0.620556 GAGAGGCCATCCCTTTCACA 59.379 55.000 5.01 0.00 46.60 3.58
3120 3157 0.106967 GGAGAGGCCATCCCTTTCAC 60.107 60.000 14.70 0.00 46.60 3.18
3121 3158 0.253347 AGGAGAGGCCATCCCTTTCA 60.253 55.000 20.43 0.00 46.60 2.69
3122 3159 0.472044 GAGGAGAGGCCATCCCTTTC 59.528 60.000 20.43 10.27 46.60 2.62
3123 3160 0.253347 TGAGGAGAGGCCATCCCTTT 60.253 55.000 20.43 5.35 46.60 3.11
3124 3161 0.029267 ATGAGGAGAGGCCATCCCTT 60.029 55.000 20.43 6.02 46.60 3.95
3126 3163 1.487850 GGATGAGGAGAGGCCATCCC 61.488 65.000 20.43 13.59 46.53 3.85
3127 3164 2.065483 GGATGAGGAGAGGCCATCC 58.935 63.158 17.28 17.28 46.34 3.51
3128 3165 0.975887 GAGGATGAGGAGAGGCCATC 59.024 60.000 5.01 1.65 40.02 3.51
3129 3166 0.473501 GGAGGATGAGGAGAGGCCAT 60.474 60.000 5.01 0.00 40.02 4.40
3130 3167 1.074926 GGAGGATGAGGAGAGGCCA 60.075 63.158 5.01 0.00 40.02 5.36
3131 3168 1.841103 GGGAGGATGAGGAGAGGCC 60.841 68.421 0.00 0.00 0.00 5.19
3132 3169 1.841103 GGGGAGGATGAGGAGAGGC 60.841 68.421 0.00 0.00 0.00 4.70
3133 3170 1.152139 GGGGGAGGATGAGGAGAGG 60.152 68.421 0.00 0.00 0.00 3.69
3142 3179 2.416923 GGAGGAGGAGGGGGAGGAT 61.417 68.421 0.00 0.00 0.00 3.24
3143 3180 3.036959 GGAGGAGGAGGGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
3145 3182 3.039526 AGGGAGGAGGAGGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
3146 3183 3.036959 GAGGGAGGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
3147 3184 4.548513 CGAGGGAGGAGGAGGGGG 62.549 77.778 0.00 0.00 0.00 5.40
3180 3219 2.190578 GCCGGAGAATGGAGGTGG 59.809 66.667 5.05 0.00 0.00 4.61
3182 3221 3.470888 CGGCCGGAGAATGGAGGT 61.471 66.667 20.10 0.00 0.00 3.85
3203 3242 2.732619 GGAGGTGGATGGTCCGACC 61.733 68.421 10.96 10.96 40.17 4.79
3204 3243 2.732619 GGGAGGTGGATGGTCCGAC 61.733 68.421 0.00 0.00 40.17 4.79
3205 3244 2.365105 GGGAGGTGGATGGTCCGA 60.365 66.667 0.00 0.00 40.17 4.55
3206 3245 2.365635 AGGGAGGTGGATGGTCCG 60.366 66.667 0.00 0.00 40.17 4.79
3207 3246 3.049080 GCAGGGAGGTGGATGGTCC 62.049 68.421 0.00 0.00 36.96 4.46
3208 3247 2.592308 GCAGGGAGGTGGATGGTC 59.408 66.667 0.00 0.00 0.00 4.02
3209 3248 3.017581 GGCAGGGAGGTGGATGGT 61.018 66.667 0.00 0.00 0.00 3.55
3210 3249 3.813724 GGGCAGGGAGGTGGATGG 61.814 72.222 0.00 0.00 0.00 3.51
3211 3250 2.914734 TAGGGGCAGGGAGGTGGATG 62.915 65.000 0.00 0.00 0.00 3.51
3228 3267 0.179097 GCCGAAGAGAACCTGGCTAG 60.179 60.000 0.00 0.00 42.44 3.42
3236 3275 1.087501 GGATTGGTGCCGAAGAGAAC 58.912 55.000 0.00 0.00 0.00 3.01
3242 3281 1.299648 CTCAGGGATTGGTGCCGAA 59.700 57.895 0.00 0.00 41.45 4.30
3246 3285 0.393537 CAGTCCTCAGGGATTGGTGC 60.394 60.000 0.00 0.00 43.11 5.01
3268 3310 1.554617 TGCAGACCGGAGAATCATCAA 59.445 47.619 9.46 0.00 36.25 2.57
3293 3335 3.508840 CCAAGGGCGGCGCTAAAG 61.509 66.667 32.30 18.49 0.00 1.85
3318 3360 0.885879 TAGTCGAGTGTCATGGCGTT 59.114 50.000 2.10 0.00 0.00 4.84
3327 3369 4.307432 CATTTGTCCTTGTAGTCGAGTGT 58.693 43.478 2.10 0.00 0.00 3.55
3328 3370 3.123621 GCATTTGTCCTTGTAGTCGAGTG 59.876 47.826 2.10 0.00 0.00 3.51
3339 3381 1.165270 GTACGCCAGCATTTGTCCTT 58.835 50.000 0.00 0.00 0.00 3.36
3345 3387 0.036164 TGGACAGTACGCCAGCATTT 59.964 50.000 1.68 0.00 0.00 2.32
3347 3389 0.179073 GATGGACAGTACGCCAGCAT 60.179 55.000 13.41 0.00 40.20 3.79
3360 3402 0.663153 GGCGTAATTGGCTGATGGAC 59.337 55.000 3.74 0.00 0.00 4.02
3364 3406 2.684881 CAGAAAGGCGTAATTGGCTGAT 59.315 45.455 3.74 0.00 45.07 2.90
3365 3407 2.083774 CAGAAAGGCGTAATTGGCTGA 58.916 47.619 3.74 0.00 45.07 4.26
3383 3425 2.411904 GTTCCAGAGCTCTTGTGACAG 58.588 52.381 15.27 0.08 0.00 3.51
3384 3426 1.070758 GGTTCCAGAGCTCTTGTGACA 59.929 52.381 15.27 0.00 0.00 3.58
3394 3436 2.295885 CATTGAGATGGGTTCCAGAGC 58.704 52.381 0.00 0.00 36.75 4.09
3398 3440 3.561960 CCTTGACATTGAGATGGGTTCCA 60.562 47.826 0.00 0.00 37.60 3.53
3418 3460 0.463295 CAGGCATGCAGATTCGACCT 60.463 55.000 21.36 0.21 0.00 3.85
3431 3473 1.153289 GCAGTCGATGTCCAGGCAT 60.153 57.895 0.00 0.00 0.00 4.40
3455 3497 1.068753 CTGGAGGTAGCATGCGAGG 59.931 63.158 13.01 0.00 0.00 4.63
3470 3512 2.276309 GACCTCCAAGGCATCCCTGG 62.276 65.000 0.00 0.00 41.90 4.45
3485 3527 2.631160 TGAACATGTCAAACCGACCT 57.369 45.000 0.00 0.00 44.71 3.85
3488 3530 1.539388 GGCATGAACATGTCAAACCGA 59.461 47.619 13.45 0.00 42.66 4.69
3490 3532 1.066929 GGGGCATGAACATGTCAAACC 60.067 52.381 18.72 8.95 44.79 3.27
3523 3565 3.563808 CACAGTGATTCGAAAGGTGGAAA 59.436 43.478 0.00 0.00 0.00 3.13
3524 3566 3.138304 CACAGTGATTCGAAAGGTGGAA 58.862 45.455 0.00 0.00 0.00 3.53
3536 3578 1.238439 CGGGCAAAGACACAGTGATT 58.762 50.000 7.81 0.00 0.00 2.57
3539 3581 1.893808 AGCGGGCAAAGACACAGTG 60.894 57.895 0.00 0.00 0.00 3.66
3576 3618 0.387202 AGATGATCTCAACCTCGCCG 59.613 55.000 0.00 0.00 0.00 6.46
3584 3626 0.755079 CTGCGGGGAGATGATCTCAA 59.245 55.000 22.67 3.41 45.12 3.02
3592 3634 0.765903 ATGTGGATCTGCGGGGAGAT 60.766 55.000 2.08 2.08 35.27 2.75
3603 3645 2.423517 GGGGAAGAAAGGGATGTGGATC 60.424 54.545 0.00 0.00 0.00 3.36
3613 3655 1.677217 CGAAGAGCAGGGGAAGAAAGG 60.677 57.143 0.00 0.00 0.00 3.11
3615 3657 1.002087 GACGAAGAGCAGGGGAAGAAA 59.998 52.381 0.00 0.00 0.00 2.52
3620 3662 3.068691 CGGACGAAGAGCAGGGGA 61.069 66.667 0.00 0.00 0.00 4.81
3642 3684 2.818274 GCGAAACCTACCCTGGCG 60.818 66.667 0.00 0.00 0.00 5.69
3683 3725 0.895100 GCTGCATTGAGGTGGTGGAA 60.895 55.000 0.00 0.00 0.00 3.53
3685 3727 2.345760 GGCTGCATTGAGGTGGTGG 61.346 63.158 0.50 0.00 0.00 4.61
3690 3732 1.000396 GGGAAGGCTGCATTGAGGT 60.000 57.895 3.50 0.00 0.00 3.85
3697 3739 4.284550 GGTGGTGGGAAGGCTGCA 62.285 66.667 0.50 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.