Multiple sequence alignment - TraesCS6B01G278700

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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 TraesCS6B01G278700 chr6B 100.000 3537 0 0 1 3537 504075799 504072263 0.000000e+00 6532.0
1 TraesCS6B01G278700 chr6B 94.554 661 29 3 58 718 272474354 272473701 0.000000e+00 1014.0
2 TraesCS6B01G278700 chr6B 91.172 725 54 5 1 725 336242442 336243156 0.000000e+00 976.0
3 TraesCS6B01G278700 chr6D 93.103 1740 76 12 1374 3084 319244531 319246255 0.000000e+00 2508.0
4 TraesCS6B01G278700 chr6D 93.939 528 22 2 858 1376 319243971 319244497 0.000000e+00 789.0
5 TraesCS6B01G278700 chr6D 89.170 277 15 7 3096 3370 319246386 319246649 7.320000e-87 331.0
6 TraesCS6B01G278700 chr6A 90.553 1916 87 33 1375 3230 457072662 457074543 0.000000e+00 2449.0
7 TraesCS6B01G278700 chr6A 94.964 417 18 1 963 1376 457072211 457072627 0.000000e+00 651.0
8 TraesCS6B01G278700 chr6A 88.302 265 20 3 706 970 457071801 457072054 1.230000e-79 307.0
9 TraesCS6B01G278700 chr6A 92.857 70 3 1 3303 3370 457074713 457074782 2.250000e-17 100.0
10 TraesCS6B01G278700 chr2D 90.509 727 53 6 1 718 429025351 429026070 0.000000e+00 946.0
11 TraesCS6B01G278700 chr2D 93.529 170 9 1 3366 3533 95918746 95918915 5.860000e-63 252.0
12 TraesCS6B01G278700 chr2D 93.452 168 11 0 3366 3533 96085253 96085420 2.110000e-62 250.0
13 TraesCS6B01G278700 chr7D 91.908 173 14 0 3362 3534 577917842 577917670 3.530000e-60 243.0
14 TraesCS6B01G278700 chr7D 92.771 166 12 0 3368 3533 597300969 597300804 1.270000e-59 241.0
15 TraesCS6B01G278700 chr7D 92.771 166 11 1 3368 3533 376090489 376090653 4.560000e-59 239.0
16 TraesCS6B01G278700 chr5D 92.814 167 11 1 3368 3534 491437952 491438117 1.270000e-59 241.0
17 TraesCS6B01G278700 chr2A 92.727 165 12 0 3369 3533 124382014 124381850 4.560000e-59 239.0
18 TraesCS6B01G278700 chr4B 91.813 171 13 1 3364 3533 80990819 80990649 1.640000e-58 237.0
19 TraesCS6B01G278700 chr3D 91.279 172 14 1 3366 3537 250043995 250044165 2.120000e-57 233.0
20 TraesCS6B01G278700 chr1D 87.421 159 18 2 1219 1376 474877403 474877246 7.800000e-42 182.0
21 TraesCS6B01G278700 chr1D 87.755 147 16 2 1231 1376 474900588 474900443 1.690000e-38 171.0
22 TraesCS6B01G278700 chr1D 84.756 164 25 0 1213 1376 474823606 474823443 7.860000e-37 165.0
23 TraesCS6B01G278700 chr1D 84.615 156 22 2 1222 1376 474883657 474883503 1.700000e-33 154.0
24 TraesCS6B01G278700 chr1D 82.286 175 23 5 1209 1376 474904335 474904162 1.020000e-30 145.0
25 TraesCS6B01G278700 chr1A 87.421 159 18 2 1219 1376 570388640 570388483 7.800000e-42 182.0
26 TraesCS6B01G278700 chr1A 83.562 73 10 2 999 1070 99903710 99903781 2.280000e-07 67.6
27 TraesCS6B01G278700 chr1B 83.537 164 22 3 1217 1376 660101782 660101620 7.910000e-32 148.0
28 TraesCS6B01G278700 chr1B 86.301 73 8 2 999 1070 134435150 134435221 1.050000e-10 78.7
29 TraesCS6B01G278700 chr1B 84.615 78 7 4 3292 3367 26174782 26174856 4.900000e-09 73.1
30 TraesCS6B01G278700 chrUn 90.000 60 6 0 1009 1068 9922307 9922366 1.050000e-10 78.7


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 TraesCS6B01G278700 chr6B 504072263 504075799 3536 True 6532.000000 6532 100.000000 1 3537 1 chr6B.!!$R2 3536
1 TraesCS6B01G278700 chr6B 272473701 272474354 653 True 1014.000000 1014 94.554000 58 718 1 chr6B.!!$R1 660
2 TraesCS6B01G278700 chr6B 336242442 336243156 714 False 976.000000 976 91.172000 1 725 1 chr6B.!!$F1 724
3 TraesCS6B01G278700 chr6D 319243971 319246649 2678 False 1209.333333 2508 92.070667 858 3370 3 chr6D.!!$F1 2512
4 TraesCS6B01G278700 chr6A 457071801 457074782 2981 False 876.750000 2449 91.669000 706 3370 4 chr6A.!!$F1 2664
5 TraesCS6B01G278700 chr2D 429025351 429026070 719 False 946.000000 946 90.509000 1 718 1 chr2D.!!$F3 717

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
612 622 0.255890 ACCGATTTGCACTATGGCCT 59.744 50.0 3.32 0.0 0.0 5.19 F
1723 1944 0.107214 CGCCCCTGAGCAATTCCTTA 60.107 55.0 0.00 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1989 0.244994 CACTCTCCACCGAAGTCCAG 59.755 60.0 0.0 0.0 0.0 3.86 R
3516 4055 0.325296 TGCTACTCCCTCCGTTCCAT 60.325 55.0 0.0 0.0 0.0 3.41 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
38 39 3.194542 ACTTCTCACTTCAGCTAGCGATT 59.805 43.478 9.55 0.00 0.00 3.34
81 82 3.429141 CTTCTGCCAGCGCCACAG 61.429 66.667 13.99 13.99 0.00 3.66
145 146 1.831652 CTGGAGAAGCCCAGTTCGGT 61.832 60.000 0.00 0.00 46.62 4.69
286 287 2.605607 CCCATGGGGTCACTGCTCA 61.606 63.158 24.53 0.00 38.25 4.26
329 339 1.730851 GGGATTCGGAGGGAATAGGT 58.269 55.000 0.00 0.00 45.33 3.08
464 474 2.560542 GGGAGAGATATGTGCGAGATGT 59.439 50.000 0.00 0.00 0.00 3.06
487 497 0.788391 GTGTTTTCCTGTACGAGCGG 59.212 55.000 0.00 0.00 0.00 5.52
491 501 0.974010 TTTCCTGTACGAGCGGGGAT 60.974 55.000 8.51 0.00 35.63 3.85
574 584 0.879090 GCTTCGGGAAAAACACGGAT 59.121 50.000 0.00 0.00 46.40 4.18
612 622 0.255890 ACCGATTTGCACTATGGCCT 59.744 50.000 3.32 0.00 0.00 5.19
617 627 4.154195 CCGATTTGCACTATGGCCTAATAC 59.846 45.833 3.32 0.00 0.00 1.89
651 661 2.564721 GCTTCCCGCAGCAAAACCT 61.565 57.895 0.00 0.00 39.83 3.50
747 757 3.375699 ACCACGGACCAGAATTCTCTAT 58.624 45.455 4.57 0.00 0.00 1.98
748 758 3.133003 ACCACGGACCAGAATTCTCTATG 59.867 47.826 4.57 0.00 0.00 2.23
754 764 5.302059 CGGACCAGAATTCTCTATGGTAAGA 59.698 44.000 15.07 0.00 45.92 2.10
759 769 6.463614 CCAGAATTCTCTATGGTAAGACAGGG 60.464 46.154 4.57 0.00 0.00 4.45
762 772 4.603094 TCTCTATGGTAAGACAGGGTGA 57.397 45.455 0.00 0.00 0.00 4.02
782 792 3.057104 TGACGTTCGACCACTGACATATT 60.057 43.478 0.00 0.00 0.00 1.28
783 793 3.250744 ACGTTCGACCACTGACATATTG 58.749 45.455 0.00 0.00 0.00 1.90
784 794 3.057104 ACGTTCGACCACTGACATATTGA 60.057 43.478 0.00 0.00 0.00 2.57
785 795 3.303495 CGTTCGACCACTGACATATTGAC 59.697 47.826 0.00 0.00 0.00 3.18
786 796 4.242475 GTTCGACCACTGACATATTGACA 58.758 43.478 0.00 0.00 0.00 3.58
787 797 4.736126 TCGACCACTGACATATTGACAT 57.264 40.909 0.00 0.00 0.00 3.06
788 798 5.845391 TCGACCACTGACATATTGACATA 57.155 39.130 0.00 0.00 0.00 2.29
789 799 6.405278 TCGACCACTGACATATTGACATAT 57.595 37.500 0.00 0.00 0.00 1.78
800 810 2.435372 TTGACATATGGGCCAGGTTC 57.565 50.000 13.78 6.32 0.00 3.62
812 822 2.036256 AGGTTCAGGCCCACATGC 59.964 61.111 0.00 0.00 0.00 4.06
831 841 1.002624 CAGTGGCCCAACGGTACAT 60.003 57.895 0.00 0.00 0.00 2.29
851 861 0.608582 ACCGTACGTCAGAGGAGCTT 60.609 55.000 15.21 0.00 0.00 3.74
970 982 2.279120 GGCTGTCGATCGCCTCAG 60.279 66.667 21.39 21.39 42.98 3.35
973 1149 2.362503 TGTCGATCGCCTCAGGGT 60.363 61.111 11.09 0.00 34.45 4.34
1203 1388 2.378084 GCCGAAACGAACCGTCTCC 61.378 63.158 0.00 0.00 39.99 3.71
1271 1456 1.595382 GAGATCCCCGACAATGCCG 60.595 63.158 0.00 0.00 0.00 5.69
1450 1671 1.961180 ATCCTTCGCTCCCGTTCCTG 61.961 60.000 0.00 0.00 35.54 3.86
1525 1746 0.390860 GCAGATGCTGGGACTCGTAT 59.609 55.000 0.00 0.00 38.21 3.06
1669 1890 1.657804 ACGATCTCTTCCTGGGGTTT 58.342 50.000 0.00 0.00 0.00 3.27
1723 1944 0.107214 CGCCCCTGAGCAATTCCTTA 60.107 55.000 0.00 0.00 0.00 2.69
1768 1989 1.167155 TCTCATCGGAGACTAGGCGC 61.167 60.000 0.00 0.00 45.12 6.53
1777 1998 1.226717 GACTAGGCGCTGGACTTCG 60.227 63.158 7.64 0.00 30.49 3.79
1786 2007 1.536943 GCTGGACTTCGGTGGAGAGT 61.537 60.000 0.00 0.00 0.00 3.24
2032 2253 3.545703 ACTCTGTGTTTGGGTTCTTGAG 58.454 45.455 0.00 0.00 0.00 3.02
2110 2331 1.078143 GAGGCAGCCGGACAAAGAT 60.078 57.895 5.05 0.00 0.00 2.40
2148 2369 2.104622 TGCTTGCGATCCATCCAGATTA 59.895 45.455 0.00 0.00 0.00 1.75
2283 2504 5.799213 TGTTCCTTGTTTTGTGGAAATGTT 58.201 33.333 0.00 0.00 40.94 2.71
2306 2537 1.079127 GGGAGTCGCTGCTGCTTTA 60.079 57.895 14.03 0.00 36.97 1.85
2325 2556 5.392057 GCTTTAATGTACTTGGAGTGGAAGC 60.392 44.000 0.00 0.00 0.00 3.86
2357 2588 2.496899 CCAGTTGTTGGGTATGAGCT 57.503 50.000 0.00 0.00 43.75 4.09
2389 2620 3.153919 GTTTTGTGGACTGGCTTGGATA 58.846 45.455 0.00 0.00 0.00 2.59
2390 2621 3.737559 TTTGTGGACTGGCTTGGATAT 57.262 42.857 0.00 0.00 0.00 1.63
2391 2622 4.853468 TTTGTGGACTGGCTTGGATATA 57.147 40.909 0.00 0.00 0.00 0.86
2392 2623 5.387113 TTTGTGGACTGGCTTGGATATAT 57.613 39.130 0.00 0.00 0.00 0.86
2407 2638 7.652524 TTGGATATATATGTCTCAGGCTCTC 57.347 40.000 9.09 0.00 0.00 3.20
2434 2665 6.091441 GCTCCTATGTCTACTTCAGTTTGTTG 59.909 42.308 0.00 0.00 0.00 3.33
2487 2726 4.734398 TTTGTGGCTTTGAACATCACTT 57.266 36.364 0.00 0.00 0.00 3.16
2544 2796 2.290960 GGTCACTTTGTTAGCCCCTCAT 60.291 50.000 0.00 0.00 0.00 2.90
2563 2815 4.406456 TCATGTGGGCTAAATTTGACACT 58.594 39.130 0.00 0.00 0.00 3.55
2583 2835 8.801299 TGACACTTTATCTATCTGGATCTCATC 58.199 37.037 0.00 0.00 0.00 2.92
2659 2911 3.997021 AGTCGTGACATTTCTTCCACATC 59.003 43.478 2.44 0.00 0.00 3.06
2695 2947 9.390795 CATCACTCTCTTGTCTGTTTTATTTTG 57.609 33.333 0.00 0.00 0.00 2.44
2733 2985 8.915057 AATCTTTATCAGTGATCTGGTATTGG 57.085 34.615 9.42 0.00 41.59 3.16
2736 2988 1.138859 TCAGTGATCTGGTATTGGGCG 59.861 52.381 0.00 0.00 41.59 6.13
2748 3000 0.618458 ATTGGGCGCTGACCTTTCTA 59.382 50.000 7.64 0.00 0.00 2.10
2803 3060 4.277672 GGTGACAATCATTATGCAGCTGAT 59.722 41.667 20.43 10.74 0.00 2.90
2804 3061 5.471116 GGTGACAATCATTATGCAGCTGATA 59.529 40.000 20.43 9.70 0.00 2.15
2805 3062 6.348295 GGTGACAATCATTATGCAGCTGATAG 60.348 42.308 20.43 0.04 0.00 2.08
2806 3063 6.426025 GTGACAATCATTATGCAGCTGATAGA 59.574 38.462 20.43 6.05 0.00 1.98
2807 3064 6.649557 TGACAATCATTATGCAGCTGATAGAG 59.350 38.462 20.43 8.71 0.00 2.43
2846 3109 9.915629 TTCTCACTTTTCTTAGTAGAAGATGTC 57.084 33.333 0.00 0.00 41.25 3.06
2856 3120 5.568620 AGTAGAAGATGTCTTTGTTGGGT 57.431 39.130 0.00 0.00 37.84 4.51
2881 3145 8.993121 GTCAGAGAACAGAATAATTCAGTCAAA 58.007 33.333 0.00 0.00 0.00 2.69
2882 3146 9.730705 TCAGAGAACAGAATAATTCAGTCAAAT 57.269 29.630 0.00 0.00 0.00 2.32
2944 3208 9.506018 AATGATTATTTTCTTCTTGGGTTTTGG 57.494 29.630 0.00 0.00 0.00 3.28
2957 3221 4.877773 TGGGTTTTGGCAGATGGTATTAT 58.122 39.130 0.00 0.00 0.00 1.28
2958 3222 6.019656 TGGGTTTTGGCAGATGGTATTATA 57.980 37.500 0.00 0.00 0.00 0.98
2959 3223 6.619464 TGGGTTTTGGCAGATGGTATTATAT 58.381 36.000 0.00 0.00 0.00 0.86
2960 3224 7.760607 TGGGTTTTGGCAGATGGTATTATATA 58.239 34.615 0.00 0.00 0.00 0.86
3034 3313 6.203530 CACTGTAACTTCAAGATCTCAGCAAA 59.796 38.462 0.00 0.00 0.00 3.68
3041 3320 7.814642 ACTTCAAGATCTCAGCAAATTAACTG 58.185 34.615 0.00 2.00 35.15 3.16
3084 3363 2.223947 TGCATATGTAGCACCGGTACTG 60.224 50.000 18.04 1.30 37.41 2.74
3089 3368 1.271379 TGTAGCACCGGTACTGTCTTG 59.729 52.381 18.04 0.00 37.41 3.02
3127 3525 2.028112 CACCTTTACTACCTGCAGCTCA 60.028 50.000 8.66 0.00 0.00 4.26
3144 3542 2.749076 GCTCAAGTATGCATTGGACACA 59.251 45.455 3.54 0.00 0.00 3.72
3151 3549 8.530311 TCAAGTATGCATTGGACACATTAAAAT 58.470 29.630 3.54 0.00 0.00 1.82
3239 3776 7.596995 CGGCCTACAAATTTATTTTCAGTTGAA 59.403 33.333 0.00 0.00 0.00 2.69
3256 3793 5.347635 CAGTTGAACATTTCATCCATGCAAG 59.652 40.000 0.00 0.00 39.84 4.01
3269 3806 4.630111 TCCATGCAAGGATGAAACAAAAC 58.370 39.130 6.57 0.00 31.23 2.43
3278 3815 4.058124 GGATGAAACAAAACCAGCCTTTC 58.942 43.478 0.00 0.00 33.88 2.62
3287 3824 1.382914 ACCAGCCTTTCCATTACCCT 58.617 50.000 0.00 0.00 0.00 4.34
3288 3825 1.285078 ACCAGCCTTTCCATTACCCTC 59.715 52.381 0.00 0.00 0.00 4.30
3289 3826 1.284785 CCAGCCTTTCCATTACCCTCA 59.715 52.381 0.00 0.00 0.00 3.86
3290 3827 2.648059 CAGCCTTTCCATTACCCTCAG 58.352 52.381 0.00 0.00 0.00 3.35
3291 3828 1.064389 AGCCTTTCCATTACCCTCAGC 60.064 52.381 0.00 0.00 0.00 4.26
3292 3829 2.024306 GCCTTTCCATTACCCTCAGCC 61.024 57.143 0.00 0.00 0.00 4.85
3296 3833 1.500474 TCCATTACCCTCAGCCTCAG 58.500 55.000 0.00 0.00 0.00 3.35
3306 3843 3.432890 CCCTCAGCCTCAGGTTTATTCTC 60.433 52.174 0.00 0.00 0.00 2.87
3322 3859 7.362142 GGTTTATTCTCTTCCTTGAGCGAAATT 60.362 37.037 0.00 0.00 34.29 1.82
3378 3917 5.428253 TCATCCAAAGAAATACTCCTTCCG 58.572 41.667 0.00 0.00 0.00 4.30
3379 3918 4.903045 TCCAAAGAAATACTCCTTCCGT 57.097 40.909 0.00 0.00 0.00 4.69
3380 3919 5.237236 TCCAAAGAAATACTCCTTCCGTT 57.763 39.130 0.00 0.00 0.00 4.44
3381 3920 5.243207 TCCAAAGAAATACTCCTTCCGTTC 58.757 41.667 0.00 0.00 0.00 3.95
3382 3921 4.395231 CCAAAGAAATACTCCTTCCGTTCC 59.605 45.833 0.00 0.00 0.00 3.62
3383 3922 5.246307 CAAAGAAATACTCCTTCCGTTCCT 58.754 41.667 0.00 0.00 0.00 3.36
3384 3923 6.403878 CAAAGAAATACTCCTTCCGTTCCTA 58.596 40.000 0.00 0.00 0.00 2.94
3385 3924 6.616237 AAGAAATACTCCTTCCGTTCCTAA 57.384 37.500 0.00 0.00 0.00 2.69
3386 3925 6.616237 AGAAATACTCCTTCCGTTCCTAAA 57.384 37.500 0.00 0.00 0.00 1.85
3387 3926 7.196637 AGAAATACTCCTTCCGTTCCTAAAT 57.803 36.000 0.00 0.00 0.00 1.40
3388 3927 8.315220 AGAAATACTCCTTCCGTTCCTAAATA 57.685 34.615 0.00 0.00 0.00 1.40
3389 3928 8.935741 AGAAATACTCCTTCCGTTCCTAAATAT 58.064 33.333 0.00 0.00 0.00 1.28
3390 3929 9.557061 GAAATACTCCTTCCGTTCCTAAATATT 57.443 33.333 0.00 0.00 0.00 1.28
3391 3930 9.916360 AAATACTCCTTCCGTTCCTAAATATTT 57.084 29.630 5.89 5.89 0.00 1.40
3392 3931 8.904099 ATACTCCTTCCGTTCCTAAATATTTG 57.096 34.615 11.05 1.40 0.00 2.32
3393 3932 6.718294 ACTCCTTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
3394 3933 6.822170 ACTCCTTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
3395 3934 6.954232 TCCTTCCGTTCCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
3396 3935 7.399634 TCCTTCCGTTCCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
3397 3936 7.886446 TCCTTCCGTTCCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
3398 3937 8.182227 CCTTCCGTTCCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
3399 3938 8.857694 TTCCGTTCCTAAATATTTGTCTTTCT 57.142 30.769 11.05 0.00 0.00 2.52
3400 3939 9.947433 TTCCGTTCCTAAATATTTGTCTTTCTA 57.053 29.630 11.05 0.00 0.00 2.10
3401 3940 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
3438 3977 8.668510 AGTAACTACATATGGAGCAAAATGAG 57.331 34.615 15.30 0.00 0.00 2.90
3439 3978 8.267894 AGTAACTACATATGGAGCAAAATGAGT 58.732 33.333 15.30 0.00 0.00 3.41
3440 3979 6.932356 ACTACATATGGAGCAAAATGAGTG 57.068 37.500 15.30 0.00 0.00 3.51
3441 3980 6.653020 ACTACATATGGAGCAAAATGAGTGA 58.347 36.000 15.30 0.00 0.00 3.41
3442 3981 7.112122 ACTACATATGGAGCAAAATGAGTGAA 58.888 34.615 15.30 0.00 0.00 3.18
3443 3982 7.776969 ACTACATATGGAGCAAAATGAGTGAAT 59.223 33.333 15.30 0.00 0.00 2.57
3444 3983 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
3445 3984 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
3446 3985 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
3447 3986 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
3448 3987 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
3449 3988 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
3463 4002 8.976353 AGTGAATCTACACTCTCAAATATGTCT 58.024 33.333 0.00 0.00 46.36 3.41
3493 4032 8.716646 ACATTCGTATGTGATAGTCAATTTGA 57.283 30.769 6.89 0.00 43.29 2.69
3494 4033 9.161629 ACATTCGTATGTGATAGTCAATTTGAA 57.838 29.630 6.89 0.00 43.29 2.69
3495 4034 9.986833 CATTCGTATGTGATAGTCAATTTGAAA 57.013 29.630 0.00 0.00 0.00 2.69
3498 4037 9.599866 TCGTATGTGATAGTCAATTTGAAATCT 57.400 29.630 17.38 8.22 0.00 2.40
3527 4066 7.568199 AAAGACAAATATTATGGAACGGAGG 57.432 36.000 0.00 0.00 0.00 4.30
3528 4067 5.621193 AGACAAATATTATGGAACGGAGGG 58.379 41.667 0.00 0.00 0.00 4.30
3529 4068 5.368523 AGACAAATATTATGGAACGGAGGGA 59.631 40.000 0.00 0.00 0.00 4.20
3530 4069 5.621193 ACAAATATTATGGAACGGAGGGAG 58.379 41.667 0.00 0.00 0.00 4.30
3531 4070 5.132144 ACAAATATTATGGAACGGAGGGAGT 59.868 40.000 0.00 0.00 0.00 3.85
3532 4071 6.328148 ACAAATATTATGGAACGGAGGGAGTA 59.672 38.462 0.00 0.00 0.00 2.59
3533 4072 6.607004 AATATTATGGAACGGAGGGAGTAG 57.393 41.667 0.00 0.00 0.00 2.57
3534 4073 1.700955 TATGGAACGGAGGGAGTAGC 58.299 55.000 0.00 0.00 0.00 3.58
3535 4074 0.325296 ATGGAACGGAGGGAGTAGCA 60.325 55.000 0.00 0.00 0.00 3.49
3536 4075 0.543410 TGGAACGGAGGGAGTAGCAA 60.543 55.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.140052 TCAGCTCCAGAACGGTTTTCA 59.860 47.619 0.00 0.00 35.57 2.69
81 82 3.849020 GCTTCTTAGCTCCCAATTGGGC 61.849 54.545 35.18 25.03 45.73 5.36
86 87 1.409381 GCAGGCTTCTTAGCTCCCAAT 60.409 52.381 0.00 0.00 46.90 3.16
145 146 1.235112 GGGCCTACTACCCCAGCTA 59.765 63.158 0.84 0.00 42.01 3.32
329 339 0.261991 ACAGATCCGGCCTTCCTAGA 59.738 55.000 0.00 0.00 0.00 2.43
423 433 2.422127 CCTCTCTCGTTCTCTTCCTCAC 59.578 54.545 0.00 0.00 0.00 3.51
464 474 3.064207 GCTCGTACAGGAAAACACATCA 58.936 45.455 0.00 0.00 0.00 3.07
487 497 4.202131 ACGTTTCGATCCTTCTCTTATCCC 60.202 45.833 0.00 0.00 0.00 3.85
491 501 6.453092 AGAAAACGTTTCGATCCTTCTCTTA 58.547 36.000 15.01 0.00 0.00 2.10
574 584 0.396435 TGAAGCGAGCTTTTCCCAGA 59.604 50.000 11.92 0.00 36.26 3.86
612 622 5.839621 AGCTAAATTCTCGAAGCGGTATTA 58.160 37.500 0.00 0.00 39.94 0.98
617 627 2.285488 GGAAGCTAAATTCTCGAAGCGG 59.715 50.000 0.00 0.00 39.94 5.52
747 757 1.342174 GAACGTCACCCTGTCTTACCA 59.658 52.381 0.00 0.00 0.00 3.25
748 758 1.668047 CGAACGTCACCCTGTCTTACC 60.668 57.143 0.00 0.00 0.00 2.85
754 764 2.129146 TGGTCGAACGTCACCCTGT 61.129 57.895 0.00 0.00 0.00 4.00
759 769 0.248743 TGTCAGTGGTCGAACGTCAC 60.249 55.000 0.00 12.25 0.00 3.67
762 772 3.057104 TCAATATGTCAGTGGTCGAACGT 60.057 43.478 0.00 0.00 0.00 3.99
782 792 1.212688 CTGAACCTGGCCCATATGTCA 59.787 52.381 0.00 0.00 0.00 3.58
783 793 1.477558 CCTGAACCTGGCCCATATGTC 60.478 57.143 0.00 0.00 0.00 3.06
784 794 0.552848 CCTGAACCTGGCCCATATGT 59.447 55.000 0.00 0.00 0.00 2.29
785 795 0.825010 GCCTGAACCTGGCCCATATG 60.825 60.000 0.00 0.00 41.62 1.78
786 796 1.538666 GCCTGAACCTGGCCCATAT 59.461 57.895 0.00 0.00 41.62 1.78
787 797 3.006677 GCCTGAACCTGGCCCATA 58.993 61.111 0.00 0.00 41.62 2.74
812 822 2.359478 GTACCGTTGGGCCACTGG 60.359 66.667 19.17 19.17 36.48 4.00
831 841 0.251354 AGCTCCTCTGACGTACGGTA 59.749 55.000 21.06 6.89 0.00 4.02
835 845 2.159352 GGAAGAAGCTCCTCTGACGTAC 60.159 54.545 0.00 0.00 32.21 3.67
906 918 1.621814 TGACTAGGGTTTGGGAAGACG 59.378 52.381 0.00 0.00 0.00 4.18
907 919 2.612221 CGTGACTAGGGTTTGGGAAGAC 60.612 54.545 0.00 0.00 0.00 3.01
970 982 2.416260 GCTCGTGGATCGGTACCC 59.584 66.667 6.25 0.00 40.32 3.69
973 1149 2.125326 CAGGGCTCGTGGATCGGTA 61.125 63.158 0.00 0.00 40.32 4.02
982 1158 1.109920 ATCGCATACTCAGGGCTCGT 61.110 55.000 0.00 0.00 0.00 4.18
1080 1265 2.066999 GGAATGGGGAGAGGCGTCT 61.067 63.158 9.04 9.04 34.86 4.18
1108 1293 3.009115 TGCTTCGGGGAAGGGGAG 61.009 66.667 7.42 0.00 39.76 4.30
1203 1388 2.964740 TCTTCTTCATCTGCAACGGAG 58.035 47.619 0.00 0.00 0.00 4.63
1271 1456 1.297745 GCGACAGGATCTCGACGAC 60.298 63.158 7.00 0.00 32.65 4.34
1432 1653 2.283676 AGGAACGGGAGCGAAGGA 60.284 61.111 0.00 0.00 0.00 3.36
1525 1746 3.495434 TTCTTCTTGTTCCGCCCTTTA 57.505 42.857 0.00 0.00 0.00 1.85
1768 1989 0.244994 CACTCTCCACCGAAGTCCAG 59.755 60.000 0.00 0.00 0.00 3.86
1777 1998 1.484444 AAGGCCACTCACTCTCCACC 61.484 60.000 5.01 0.00 0.00 4.61
1786 2007 1.134037 ACGGTTTTGTAAGGCCACTCA 60.134 47.619 5.01 0.00 0.00 3.41
2032 2253 4.816925 GTCCACTTTCCACTAGCATAATCC 59.183 45.833 0.00 0.00 0.00 3.01
2148 2369 5.562635 TGTCGGTGAGGTAAACCAAATTAT 58.437 37.500 1.26 0.00 37.57 1.28
2160 2381 1.760613 TCTTCTTGTTGTCGGTGAGGT 59.239 47.619 0.00 0.00 0.00 3.85
2306 2537 3.412386 GTGCTTCCACTCCAAGTACATT 58.588 45.455 0.00 0.00 36.70 2.71
2325 2556 5.280945 CCAACAACTGGTATTTGTGAAGTG 58.719 41.667 0.00 0.00 40.78 3.16
2357 2588 5.124776 CCAGTCCACAAAACAAGACACTTAA 59.875 40.000 0.00 0.00 0.00 1.85
2389 2620 4.676109 AGCTGAGAGCCTGAGACATATAT 58.324 43.478 0.00 0.00 43.77 0.86
2390 2621 4.078537 GAGCTGAGAGCCTGAGACATATA 58.921 47.826 0.00 0.00 43.77 0.86
2391 2622 2.892852 GAGCTGAGAGCCTGAGACATAT 59.107 50.000 0.00 0.00 43.77 1.78
2392 2623 2.305928 GAGCTGAGAGCCTGAGACATA 58.694 52.381 0.00 0.00 43.77 2.29
2407 2638 5.590530 AACTGAAGTAGACATAGGAGCTG 57.409 43.478 0.00 0.00 0.00 4.24
2544 2796 6.719370 AGATAAAGTGTCAAATTTAGCCCACA 59.281 34.615 0.00 0.00 29.65 4.17
2583 2835 9.630098 ACAAGTTGCATATTAAAGACAATTGAG 57.370 29.630 13.59 0.00 0.00 3.02
2654 2906 3.542648 AGTGATGATGCTTCCAGATGTG 58.457 45.455 0.00 0.00 0.00 3.21
2659 2911 3.823281 AGAGAGTGATGATGCTTCCAG 57.177 47.619 0.00 0.00 0.00 3.86
2666 2918 6.798315 AAAACAGACAAGAGAGTGATGATG 57.202 37.500 0.00 0.00 0.00 3.07
2667 2919 9.512588 AAATAAAACAGACAAGAGAGTGATGAT 57.487 29.630 0.00 0.00 0.00 2.45
2668 2920 8.908786 AAATAAAACAGACAAGAGAGTGATGA 57.091 30.769 0.00 0.00 0.00 2.92
2724 2976 1.819632 GGTCAGCGCCCAATACCAG 60.820 63.158 2.29 0.00 0.00 4.00
2727 2979 0.733150 GAAAGGTCAGCGCCCAATAC 59.267 55.000 2.29 0.00 0.00 1.89
2733 2985 4.093556 GCATAATATAGAAAGGTCAGCGCC 59.906 45.833 2.29 0.00 0.00 6.53
2736 2988 9.311916 CTCTATGCATAATATAGAAAGGTCAGC 57.688 37.037 8.00 0.00 36.87 4.26
2803 3060 8.540507 AAGTGAGAAATAACCATCTAGCTCTA 57.459 34.615 0.00 0.00 0.00 2.43
2804 3061 7.430760 AAGTGAGAAATAACCATCTAGCTCT 57.569 36.000 0.00 0.00 0.00 4.09
2805 3062 8.499403 AAAAGTGAGAAATAACCATCTAGCTC 57.501 34.615 0.00 0.00 0.00 4.09
2806 3063 8.325046 AGAAAAGTGAGAAATAACCATCTAGCT 58.675 33.333 0.00 0.00 0.00 3.32
2807 3064 8.499403 AGAAAAGTGAGAAATAACCATCTAGC 57.501 34.615 0.00 0.00 0.00 3.42
2846 3109 3.808728 TCTGTTCTCTGACCCAACAAAG 58.191 45.455 0.00 0.00 29.78 2.77
2856 3120 9.730705 ATTTGACTGAATTATTCTGTTCTCTGA 57.269 29.630 16.45 3.97 41.16 3.27
2881 3145 2.575279 AGAAGGTTCCTCAGACATGCAT 59.425 45.455 0.00 0.00 0.00 3.96
2882 3146 1.980765 AGAAGGTTCCTCAGACATGCA 59.019 47.619 0.00 0.00 0.00 3.96
2957 3221 8.954729 TGGACAAGAAGATTCCCCAATTATATA 58.045 33.333 0.00 0.00 0.00 0.86
2958 3222 7.825709 TGGACAAGAAGATTCCCCAATTATAT 58.174 34.615 0.00 0.00 0.00 0.86
2959 3223 7.219601 TGGACAAGAAGATTCCCCAATTATA 57.780 36.000 0.00 0.00 0.00 0.98
2960 3224 6.091076 TGGACAAGAAGATTCCCCAATTAT 57.909 37.500 0.00 0.00 0.00 1.28
3034 3313 8.380742 TCCTAATCCAAGAAGAGACAGTTAAT 57.619 34.615 0.00 0.00 0.00 1.40
3041 3320 5.115480 CAGCTTCCTAATCCAAGAAGAGAC 58.885 45.833 3.28 0.00 39.50 3.36
3102 3500 3.326747 CTGCAGGTAGTAAAGGTGTGTC 58.673 50.000 5.57 0.00 0.00 3.67
3151 3549 8.911918 TCAGGTTACAGCTTCTGTTAAAATAA 57.088 30.769 4.70 0.00 42.59 1.40
3211 3609 5.047660 ACTGAAAATAAATTTGTAGGCCGCA 60.048 36.000 0.00 0.00 0.00 5.69
3256 3793 3.751479 AAGGCTGGTTTTGTTTCATCC 57.249 42.857 0.00 0.00 0.00 3.51
3269 3806 1.284785 TGAGGGTAATGGAAAGGCTGG 59.715 52.381 0.00 0.00 0.00 4.85
3278 3815 0.471617 CCTGAGGCTGAGGGTAATGG 59.528 60.000 12.76 0.00 0.00 3.16
3287 3824 4.080863 GGAAGAGAATAAACCTGAGGCTGA 60.081 45.833 0.00 0.00 0.00 4.26
3288 3825 4.080638 AGGAAGAGAATAAACCTGAGGCTG 60.081 45.833 0.00 0.00 0.00 4.85
3289 3826 4.107820 AGGAAGAGAATAAACCTGAGGCT 58.892 43.478 0.00 0.00 0.00 4.58
3290 3827 4.495690 AGGAAGAGAATAAACCTGAGGC 57.504 45.455 0.00 0.00 0.00 4.70
3291 3828 6.054860 TCAAGGAAGAGAATAAACCTGAGG 57.945 41.667 0.00 0.00 0.00 3.86
3292 3829 5.584251 GCTCAAGGAAGAGAATAAACCTGAG 59.416 44.000 0.00 0.00 37.87 3.35
3296 3833 4.504858 TCGCTCAAGGAAGAGAATAAACC 58.495 43.478 0.00 0.00 37.87 3.27
3306 3843 5.362556 TTCTCAAATTTCGCTCAAGGAAG 57.637 39.130 0.00 0.00 0.00 3.46
3322 3859 9.995003 AAGCCACATTGTAATTTAATTTCTCAA 57.005 25.926 0.00 1.16 0.00 3.02
3370 3909 7.048512 AGACAAATATTTAGGAACGGAAGGAG 58.951 38.462 0.00 0.00 0.00 3.69
3371 3910 6.954232 AGACAAATATTTAGGAACGGAAGGA 58.046 36.000 0.00 0.00 0.00 3.36
3372 3911 7.625828 AAGACAAATATTTAGGAACGGAAGG 57.374 36.000 0.00 0.00 0.00 3.46
3373 3912 8.947115 AGAAAGACAAATATTTAGGAACGGAAG 58.053 33.333 0.00 0.00 0.00 3.46
3374 3913 8.857694 AGAAAGACAAATATTTAGGAACGGAA 57.142 30.769 0.00 0.00 0.00 4.30
3375 3914 9.947433 TTAGAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
3412 3951 9.113838 CTCATTTTGCTCCATATGTAGTTACTT 57.886 33.333 1.24 0.00 0.00 2.24
3413 3952 8.267894 ACTCATTTTGCTCCATATGTAGTTACT 58.732 33.333 1.24 0.00 0.00 2.24
3414 3953 8.338259 CACTCATTTTGCTCCATATGTAGTTAC 58.662 37.037 1.24 0.00 0.00 2.50
3415 3954 8.264347 TCACTCATTTTGCTCCATATGTAGTTA 58.736 33.333 1.24 0.00 0.00 2.24
3416 3955 7.112122 TCACTCATTTTGCTCCATATGTAGTT 58.888 34.615 1.24 0.00 0.00 2.24
3417 3956 6.653020 TCACTCATTTTGCTCCATATGTAGT 58.347 36.000 1.24 0.00 0.00 2.73
3418 3957 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
3419 3958 7.994911 AGATTCACTCATTTTGCTCCATATGTA 59.005 33.333 1.24 0.00 0.00 2.29
3420 3959 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
3421 3960 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
3422 3961 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
3423 3962 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
3424 3963 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
3425 3964 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
3426 3965 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3427 3966 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3467 4006 9.810545 TCAAATTGACTATCACATACGAATGTA 57.189 29.630 0.00 0.00 44.70 2.29
3469 4008 9.986833 TTTCAAATTGACTATCACATACGAATG 57.013 29.630 0.00 0.00 39.17 2.67
3472 4011 9.599866 AGATTTCAAATTGACTATCACATACGA 57.400 29.630 15.34 0.00 0.00 3.43
3501 4040 8.466798 CCTCCGTTCCATAATATTTGTCTTTTT 58.533 33.333 0.00 0.00 0.00 1.94
3502 4041 7.068226 CCCTCCGTTCCATAATATTTGTCTTTT 59.932 37.037 0.00 0.00 0.00 2.27
3503 4042 6.546034 CCCTCCGTTCCATAATATTTGTCTTT 59.454 38.462 0.00 0.00 0.00 2.52
3504 4043 6.062095 CCCTCCGTTCCATAATATTTGTCTT 58.938 40.000 0.00 0.00 0.00 3.01
3505 4044 5.368523 TCCCTCCGTTCCATAATATTTGTCT 59.631 40.000 0.00 0.00 0.00 3.41
3506 4045 5.617252 TCCCTCCGTTCCATAATATTTGTC 58.383 41.667 0.00 0.00 0.00 3.18
3507 4046 5.132144 ACTCCCTCCGTTCCATAATATTTGT 59.868 40.000 0.00 0.00 0.00 2.83
3508 4047 5.621193 ACTCCCTCCGTTCCATAATATTTG 58.379 41.667 0.00 0.00 0.00 2.32
3509 4048 5.906772 ACTCCCTCCGTTCCATAATATTT 57.093 39.130 0.00 0.00 0.00 1.40
3510 4049 5.046520 GCTACTCCCTCCGTTCCATAATATT 60.047 44.000 0.00 0.00 0.00 1.28
3511 4050 4.466726 GCTACTCCCTCCGTTCCATAATAT 59.533 45.833 0.00 0.00 0.00 1.28
3512 4051 3.830755 GCTACTCCCTCCGTTCCATAATA 59.169 47.826 0.00 0.00 0.00 0.98
3513 4052 2.633481 GCTACTCCCTCCGTTCCATAAT 59.367 50.000 0.00 0.00 0.00 1.28
3514 4053 2.037144 GCTACTCCCTCCGTTCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
3515 4054 1.063492 TGCTACTCCCTCCGTTCCATA 60.063 52.381 0.00 0.00 0.00 2.74
3516 4055 0.325296 TGCTACTCCCTCCGTTCCAT 60.325 55.000 0.00 0.00 0.00 3.41
3517 4056 0.543410 TTGCTACTCCCTCCGTTCCA 60.543 55.000 0.00 0.00 0.00 3.53
3518 4057 2.283824 TTGCTACTCCCTCCGTTCC 58.716 57.895 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.