Multiple sequence alignment - TraesCS4A01G131500

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 TraesCS4A01G131500 chr4A 100.000 6874 0 0 1 6874 175851558 175858431 0.000000e+00 12694.0
1 TraesCS4A01G131500 chr4A 83.784 74 9 3 5179 5251 625488056 625488127 4.450000e-07 67.6
2 TraesCS4A01G131500 chr4D 94.058 6227 219 59 705 6874 303523289 303517157 0.000000e+00 9310.0
3 TraesCS4A01G131500 chr4D 93.285 685 26 6 5 681 303523955 303523283 0.000000e+00 992.0
4 TraesCS4A01G131500 chr4B 93.045 3379 99 44 3553 6874 377940257 377936958 0.000000e+00 4813.0
5 TraesCS4A01G131500 chr4B 92.567 2341 118 25 1216 3529 377942725 377940414 0.000000e+00 3308.0
6 TraesCS4A01G131500 chr4B 92.274 1152 45 10 79 1214 377943889 377942766 0.000000e+00 1594.0
7 TraesCS4A01G131500 chr4B 92.982 57 4 0 1 57 377944310 377944254 4.420000e-12 84.2
8 TraesCS4A01G131500 chr3A 83.212 137 23 0 5178 5314 587408089 587408225 7.240000e-25 126.0
9 TraesCS4A01G131500 chr5D 83.784 74 9 3 5179 5251 543609489 543609418 4.450000e-07 67.6
10 TraesCS4A01G131500 chr5B 88.889 54 6 0 5212 5265 685566344 685566291 4.450000e-07 67.6
11 TraesCS4A01G131500 chr1D 80.000 90 14 4 4927 5014 48885950 48886037 5.760000e-06 63.9
12 TraesCS4A01G131500 chr1A 81.013 79 11 4 4938 5014 48785635 48785711 7.450000e-05 60.2


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 TraesCS4A01G131500 chr4A 175851558 175858431 6873 False 12694.0 12694 100.0000 1 6874 1 chr4A.!!$F1 6873
1 TraesCS4A01G131500 chr4D 303517157 303523955 6798 True 5151.0 9310 93.6715 5 6874 2 chr4D.!!$R1 6869
2 TraesCS4A01G131500 chr4B 377936958 377944310 7352 True 2449.8 4813 92.7170 1 6874 4 chr4B.!!$R1 6873

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
504 848 0.393808 GCCTTGAATCGCACCCCTAA 60.394 55.0 0.00 0.0 0.00 2.69 F
1183 1544 0.247736 CAGGACAGTGAGTACCCTGC 59.752 60.0 0.00 0.0 35.99 4.85 F
1467 1871 0.438830 GTAAGTGTCGGCAAAGCTCG 59.561 55.0 0.00 0.0 0.00 5.03 F
2170 2593 0.179137 CGCCGACAATCAGCTGACTA 60.179 55.0 20.97 0.0 0.00 2.59 F
2464 2889 0.649475 CATCTTTCTCCTGCTTCGCG 59.351 55.0 0.00 0.0 0.00 5.87 F
3488 3926 0.698238 ACCAAGATAGCAGTGGCCAA 59.302 50.0 7.24 0.0 42.56 4.52 F
3908 4487 0.610687 AGGTGAAGCTCTTCCCTTCG 59.389 55.0 7.12 0.0 41.16 3.79 F
5043 5675 0.824109 TGTCTGATAGCGACAAGGGG 59.176 55.0 3.73 0.0 38.36 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1819 0.385029 TGTTGTTGCTGCATGTCACC 59.615 50.000 1.84 0.00 0.00 4.02 R
2170 2593 1.063492 TGATGAGATTGGCAATGGGCT 60.063 47.619 19.07 8.61 44.01 5.19 R
3457 3895 0.179134 ATCTTGGTACTCACGCGAGC 60.179 55.000 15.93 0.00 43.66 5.03 R
3479 3917 0.243636 GAAACCGGAATTGGCCACTG 59.756 55.000 9.46 0.00 0.00 3.66 R
3650 4229 0.318441 CCGAGAAGCACTTCACCAGA 59.682 55.000 12.65 0.00 41.84 3.86 R
5078 5710 0.102120 CCTGAGCCGATCACTGAGTC 59.898 60.000 0.00 0.00 33.22 3.36 R
5083 5715 0.179062 GAATGCCTGAGCCGATCACT 60.179 55.000 0.00 0.00 38.69 3.41 R
6040 6685 1.069296 TGCAACAAATGTAGTGCGCTC 60.069 47.619 9.73 4.74 35.23 5.03 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
33 34 0.824759 AAGGCAGCCTAGTCGGTAAG 59.175 55.000 16.56 0.00 31.13 2.34
40 41 1.682323 GCCTAGTCGGTAAGAAGAGGG 59.318 57.143 0.00 0.00 34.90 4.30
42 43 1.334243 CTAGTCGGTAAGAAGAGGGCG 59.666 57.143 0.00 0.00 0.00 6.13
120 464 6.978080 CAGTGTTTACAAATTAGCCACTTGTT 59.022 34.615 0.00 0.00 35.09 2.83
196 540 6.822676 AGATCAAGCTCAGTTTATCTTCCTTG 59.177 38.462 0.00 0.00 0.00 3.61
208 552 7.229506 AGTTTATCTTCCTTGTTTTGTGAGGAG 59.770 37.037 0.00 0.00 40.46 3.69
261 605 0.586319 CGGCTTCGCTTTCACTTCAA 59.414 50.000 0.00 0.00 0.00 2.69
285 629 4.805719 TGTCGATCACAGATTAACATCAGC 59.194 41.667 0.00 0.00 0.00 4.26
377 721 9.851686 TTGTCAGCATAGTCCAAAATATAATCT 57.148 29.630 0.00 0.00 0.00 2.40
445 789 6.122277 GTGATAAAGAAGGTCAATCATGGGA 58.878 40.000 0.00 0.00 0.00 4.37
504 848 0.393808 GCCTTGAATCGCACCCCTAA 60.394 55.000 0.00 0.00 0.00 2.69
505 849 1.750682 GCCTTGAATCGCACCCCTAAT 60.751 52.381 0.00 0.00 0.00 1.73
506 850 2.222027 CCTTGAATCGCACCCCTAATC 58.778 52.381 0.00 0.00 0.00 1.75
531 875 7.333423 TCATCATCACTAAACTCCTTTAAACCG 59.667 37.037 0.00 0.00 0.00 4.44
534 878 5.310451 TCACTAAACTCCTTTAAACCGCAT 58.690 37.500 0.00 0.00 0.00 4.73
535 879 5.180492 TCACTAAACTCCTTTAAACCGCATG 59.820 40.000 0.00 0.00 0.00 4.06
536 880 5.180492 CACTAAACTCCTTTAAACCGCATGA 59.820 40.000 0.00 0.00 0.00 3.07
537 881 5.766174 ACTAAACTCCTTTAAACCGCATGAA 59.234 36.000 0.00 0.00 0.00 2.57
538 882 5.722021 AAACTCCTTTAAACCGCATGAAT 57.278 34.783 0.00 0.00 0.00 2.57
554 898 6.128849 CCGCATGAATAAAAACAGACTTTTGG 60.129 38.462 0.00 0.00 31.15 3.28
562 906 1.602311 ACAGACTTTTGGAGCAGCAG 58.398 50.000 0.00 0.00 0.00 4.24
696 1048 4.103103 GCCCTTTTGACCGCTCGC 62.103 66.667 0.00 0.00 0.00 5.03
866 1225 4.037923 CCTGTATCTTTCTCTCCAGAGCTC 59.962 50.000 5.27 5.27 41.80 4.09
1034 1395 1.618640 GCTCACTTCTTGCGTCCGTC 61.619 60.000 0.00 0.00 0.00 4.79
1035 1396 1.006571 TCACTTCTTGCGTCCGTCC 60.007 57.895 0.00 0.00 0.00 4.79
1036 1397 2.049433 ACTTCTTGCGTCCGTCCG 60.049 61.111 0.00 0.00 0.00 4.79
1037 1398 2.049433 CTTCTTGCGTCCGTCCGT 60.049 61.111 0.00 0.00 0.00 4.69
1038 1399 2.355363 TTCTTGCGTCCGTCCGTG 60.355 61.111 0.00 0.00 0.00 4.94
1073 1434 1.077212 CATGGAGGAAGCTGGTGGG 60.077 63.158 0.00 0.00 0.00 4.61
1103 1464 2.664081 GGGTCTGAGAGGGGTGCTG 61.664 68.421 0.00 0.00 0.00 4.41
1183 1544 0.247736 CAGGACAGTGAGTACCCTGC 59.752 60.000 0.00 0.00 35.99 4.85
1211 1572 6.072112 TCCATTCTTGCTTAGTTTCACAAC 57.928 37.500 0.00 0.00 0.00 3.32
1292 1694 4.561606 CCAAGTAGTATAACTCACGTGTGC 59.438 45.833 16.51 0.00 0.00 4.57
1300 1702 5.892160 ATAACTCACGTGTGCTAACTCTA 57.108 39.130 16.51 0.00 0.00 2.43
1301 1703 3.555917 ACTCACGTGTGCTAACTCTAC 57.444 47.619 16.51 0.00 0.00 2.59
1302 1704 3.147629 ACTCACGTGTGCTAACTCTACT 58.852 45.455 16.51 0.00 0.00 2.57
1303 1705 4.321718 ACTCACGTGTGCTAACTCTACTA 58.678 43.478 16.51 0.00 0.00 1.82
1304 1706 4.153835 ACTCACGTGTGCTAACTCTACTAC 59.846 45.833 16.51 0.00 0.00 2.73
1306 1708 3.439476 CACGTGTGCTAACTCTACTACCT 59.561 47.826 7.58 0.00 0.00 3.08
1338 1742 2.448705 GCTTCTGTTCTCCGAGCGC 61.449 63.158 0.00 0.00 0.00 5.92
1370 1774 4.717629 CAGAACTCGCCGCCGACA 62.718 66.667 0.00 0.00 38.82 4.35
1412 1816 1.748879 CGGTGTTTCGCCATGGGAT 60.749 57.895 15.13 0.00 32.88 3.85
1467 1871 0.438830 GTAAGTGTCGGCAAAGCTCG 59.561 55.000 0.00 0.00 0.00 5.03
1486 1891 4.209452 TCGACAAGAATTTCACTGCAAC 57.791 40.909 0.00 0.00 0.00 4.17
1487 1892 3.876914 TCGACAAGAATTTCACTGCAACT 59.123 39.130 0.00 0.00 0.00 3.16
1503 1908 1.455383 AACTTCCGCCAAAGTGCCAG 61.455 55.000 0.00 0.00 39.40 4.85
1828 2236 4.877251 ACCTTGTAAGTTTCTAAACGTGCA 59.123 37.500 7.87 7.87 43.51 4.57
1881 2291 6.591834 GTCACTATGCTCATGTCTTGTACTTT 59.408 38.462 0.00 0.00 0.00 2.66
1889 2299 0.941542 GTCTTGTACTTTGTGCCGCA 59.058 50.000 0.00 0.00 0.00 5.69
1924 2334 4.641777 GCAGGTTGCAGCTTTCAC 57.358 55.556 0.00 0.00 44.26 3.18
1992 2415 2.027192 TGTAAGAGATTCACTGGTGCCC 60.027 50.000 0.00 0.00 0.00 5.36
2003 2426 0.839277 CTGGTGCCCCACAGATGATA 59.161 55.000 0.00 0.00 35.17 2.15
2004 2427 0.546122 TGGTGCCCCACAGATGATAC 59.454 55.000 0.00 0.00 35.17 2.24
2045 2468 6.169094 TGTGATTCAGTTTTTGCAGGAAAAA 58.831 32.000 8.40 8.40 40.52 1.94
2169 2592 1.446792 CGCCGACAATCAGCTGACT 60.447 57.895 20.97 4.71 0.00 3.41
2170 2593 0.179137 CGCCGACAATCAGCTGACTA 60.179 55.000 20.97 0.00 0.00 2.59
2287 2712 5.065731 GGGTATTGTCATTTCTGAAGCAGAG 59.934 44.000 0.00 0.00 41.75 3.35
2302 2727 2.902486 AGCAGAGATGAGAAGTGGAACA 59.098 45.455 0.00 0.00 41.43 3.18
2421 2846 4.213564 ACTGATTCATCTGTGAGTTCCC 57.786 45.455 0.00 0.00 37.54 3.97
2435 2860 2.660064 TTCCCGAAGCCCTCTCTGC 61.660 63.158 0.00 0.00 0.00 4.26
2464 2889 0.649475 CATCTTTCTCCTGCTTCGCG 59.351 55.000 0.00 0.00 0.00 5.87
2469 2894 0.737367 TTCTCCTGCTTCGCGACATG 60.737 55.000 9.15 1.46 0.00 3.21
2608 3033 2.151202 GACGAAACTCTGCCCAATTCA 58.849 47.619 0.00 0.00 0.00 2.57
2626 3051 7.496591 CCCAATTCATCTTATTTTGTTGGATGG 59.503 37.037 0.00 0.00 37.61 3.51
2627 3052 8.042515 CCAATTCATCTTATTTTGTTGGATGGT 58.957 33.333 0.00 0.00 37.61 3.55
2666 3091 9.739276 AATCTTCTATATGTTTGTTTGGACAGA 57.261 29.630 0.00 0.00 37.04 3.41
2693 3118 2.289756 GGATAGAAATTCCCTCTCCGGC 60.290 54.545 0.00 0.00 0.00 6.13
2702 3127 3.003173 CTCTCCGGCCCAGTTCCA 61.003 66.667 0.00 0.00 0.00 3.53
2754 3179 3.786576 CGAGCTGTAAGTTGTCTACGATG 59.213 47.826 0.00 0.00 35.30 3.84
2810 3235 6.382869 AGCCATTGTAAGCACATTATCTTC 57.617 37.500 0.00 0.00 33.76 2.87
2919 3344 3.747193 CACTAAGCAATTTACACCGCAG 58.253 45.455 0.00 0.00 0.00 5.18
2963 3388 1.457346 GAACCACCAGGCTTGATCTG 58.543 55.000 0.00 0.00 39.06 2.90
3116 3542 7.864108 TTGCAACTTCACAGTATATATGCTT 57.136 32.000 0.00 0.00 34.23 3.91
3135 3561 3.314635 GCTTGGATGGCTAAATCTGACAG 59.685 47.826 0.00 0.00 0.00 3.51
3159 3585 1.001181 CTTGTGATGCCAAACCAAGGG 59.999 52.381 0.00 0.00 31.19 3.95
3256 3682 1.539776 CGCGCAAAAACCTTGTCTGC 61.540 55.000 8.75 0.00 0.00 4.26
3258 3684 1.869342 GCGCAAAAACCTTGTCTGCAT 60.869 47.619 0.30 0.00 33.19 3.96
3332 3770 0.998145 AAGGCCTCTTTGCAGGATCT 59.002 50.000 5.23 0.00 35.20 2.75
3475 3913 1.211969 GCTCGCGTGAGTACCAAGA 59.788 57.895 25.72 0.00 44.48 3.02
3479 3917 1.065102 TCGCGTGAGTACCAAGATAGC 59.935 52.381 5.77 0.00 0.00 2.97
3484 3922 3.735208 CGTGAGTACCAAGATAGCAGTGG 60.735 52.174 0.00 0.00 38.46 4.00
3488 3926 0.698238 ACCAAGATAGCAGTGGCCAA 59.302 50.000 7.24 0.00 42.56 4.52
3504 3942 1.904287 CCAATTCCGGTTTCCAGACA 58.096 50.000 0.00 0.00 0.00 3.41
3617 4196 2.464189 GCGTACTGCAACGTGACG 59.536 61.111 12.18 2.24 44.64 4.35
3908 4487 0.610687 AGGTGAAGCTCTTCCCTTCG 59.389 55.000 7.12 0.00 41.16 3.79
3914 4493 4.162690 CTCTTCCCTTCGGGCGGG 62.163 72.222 0.00 0.00 43.94 6.13
4040 4619 2.606587 CCCCTTCCCAGGTCACCAG 61.607 68.421 0.00 0.00 38.79 4.00
4053 4632 2.063266 GTCACCAGCGAACAACGATAA 58.937 47.619 0.00 0.00 45.77 1.75
4056 4635 3.861113 TCACCAGCGAACAACGATAATAC 59.139 43.478 0.00 0.00 45.77 1.89
4057 4636 3.000925 CACCAGCGAACAACGATAATACC 59.999 47.826 0.00 0.00 45.77 2.73
4058 4637 3.118884 ACCAGCGAACAACGATAATACCT 60.119 43.478 0.00 0.00 45.77 3.08
4059 4638 3.869246 CCAGCGAACAACGATAATACCTT 59.131 43.478 0.00 0.00 45.77 3.50
4134 4730 1.304381 ACCATGTGGGATGTGTGGC 60.304 57.895 3.77 0.00 41.15 5.01
4242 4838 4.477975 GAGCTGCCGTCTACGCGT 62.478 66.667 19.17 19.17 38.18 6.01
4283 4879 1.003233 GAAGGCCACGGAAGAGCTT 60.003 57.895 5.01 0.00 34.99 3.74
4324 4920 7.582352 ACGCCTTCTCTTAAAATAAACTTGTC 58.418 34.615 0.00 0.00 0.00 3.18
4325 4921 7.227910 ACGCCTTCTCTTAAAATAAACTTGTCA 59.772 33.333 0.00 0.00 0.00 3.58
4326 4922 7.746475 CGCCTTCTCTTAAAATAAACTTGTCAG 59.254 37.037 0.00 0.00 0.00 3.51
4327 4923 8.784043 GCCTTCTCTTAAAATAAACTTGTCAGA 58.216 33.333 0.00 0.00 0.00 3.27
4382 4978 3.886549 ACGAGTACGAGTGAAGTGAAAG 58.113 45.455 0.00 0.00 42.66 2.62
4503 5099 2.668550 AACAACTTCGCGGAGGCC 60.669 61.111 20.69 0.00 35.02 5.19
4762 5358 1.918800 AGCCTCACCGGTAAGCCTT 60.919 57.895 6.87 0.00 34.25 4.35
4763 5359 1.449778 GCCTCACCGGTAAGCCTTC 60.450 63.158 6.87 0.00 34.25 3.46
4772 5372 1.476477 GGTAAGCCTTCCTCTCGTCT 58.524 55.000 0.00 0.00 0.00 4.18
4773 5373 1.826096 GGTAAGCCTTCCTCTCGTCTT 59.174 52.381 0.00 0.00 0.00 3.01
4783 5383 1.395608 CCTCTCGTCTTGTCTCGTCTC 59.604 57.143 0.00 0.00 0.00 3.36
4813 5445 5.520288 CCATATCAAGTCAAGTACAAGTCCG 59.480 44.000 0.00 0.00 0.00 4.79
5031 5663 4.384647 GGCCTCTCCAAATTAGTGTCTGAT 60.385 45.833 0.00 0.00 34.01 2.90
5043 5675 0.824109 TGTCTGATAGCGACAAGGGG 59.176 55.000 3.73 0.00 38.36 4.79
5078 5710 2.767505 AGTCAAAGGAACGCTGGTAAG 58.232 47.619 0.00 0.00 0.00 2.34
5083 5715 1.629043 AGGAACGCTGGTAAGACTCA 58.371 50.000 0.00 0.00 0.00 3.41
5084 5716 1.546476 AGGAACGCTGGTAAGACTCAG 59.454 52.381 0.00 0.00 0.00 3.35
5087 5719 1.617322 ACGCTGGTAAGACTCAGTGA 58.383 50.000 9.49 0.00 42.26 3.41
5088 5720 2.171840 ACGCTGGTAAGACTCAGTGAT 58.828 47.619 9.49 0.00 42.26 3.06
5089 5721 2.164624 ACGCTGGTAAGACTCAGTGATC 59.835 50.000 9.49 0.00 42.26 2.92
5096 5728 1.102154 AGACTCAGTGATCGGCTCAG 58.898 55.000 0.00 0.00 33.51 3.35
5101 5733 0.463295 CAGTGATCGGCTCAGGCATT 60.463 55.000 0.00 0.00 40.87 3.56
5130 5762 1.955778 CAGTTGCACATGTTCCTTCCA 59.044 47.619 0.00 0.00 0.00 3.53
5131 5763 2.030540 CAGTTGCACATGTTCCTTCCAG 60.031 50.000 0.00 0.00 0.00 3.86
5132 5764 2.158623 AGTTGCACATGTTCCTTCCAGA 60.159 45.455 0.00 0.00 0.00 3.86
5133 5765 2.189594 TGCACATGTTCCTTCCAGAG 57.810 50.000 0.00 0.00 0.00 3.35
5134 5766 1.421268 TGCACATGTTCCTTCCAGAGT 59.579 47.619 0.00 0.00 0.00 3.24
5135 5767 2.158623 TGCACATGTTCCTTCCAGAGTT 60.159 45.455 0.00 0.00 0.00 3.01
5136 5768 2.485814 GCACATGTTCCTTCCAGAGTTC 59.514 50.000 0.00 0.00 0.00 3.01
5137 5769 3.077359 CACATGTTCCTTCCAGAGTTCC 58.923 50.000 0.00 0.00 0.00 3.62
5158 5790 2.945008 CAGTGAATGTGACTTGGTGTGT 59.055 45.455 0.00 0.00 0.00 3.72
5162 5794 5.047377 AGTGAATGTGACTTGGTGTGTTTTT 60.047 36.000 0.00 0.00 0.00 1.94
5217 5849 2.770164 ACTACATGTCCCAGCAACTC 57.230 50.000 0.00 0.00 0.00 3.01
5220 5852 0.250901 ACATGTCCCAGCAACTCACC 60.251 55.000 0.00 0.00 0.00 4.02
5247 5879 1.500844 CGACGTCTACAGCTTCGGT 59.499 57.895 14.70 0.00 0.00 4.69
5289 5921 4.838152 GCCAGGCAGCCGATCGAA 62.838 66.667 18.66 0.00 0.00 3.71
5601 6233 1.005867 TCGCCACCCTTACAACGAC 60.006 57.895 0.00 0.00 0.00 4.34
5614 6246 0.321653 CAACGACCCTCTCCCAAAGG 60.322 60.000 0.00 0.00 0.00 3.11
5664 6299 2.095161 CGACTACAGCGGAGGATATTCC 60.095 54.545 0.00 0.00 36.58 3.01
5708 6343 1.907255 GTAGCTGGTTTCTGGTAGGGT 59.093 52.381 0.00 0.00 0.00 4.34
5723 6358 1.223487 GGGTTTCTATGCTGGCCGA 59.777 57.895 0.00 0.00 0.00 5.54
5839 6484 8.365399 TCTTATTAGAGTGATTTTGTATGGCG 57.635 34.615 0.00 0.00 0.00 5.69
5840 6485 8.201464 TCTTATTAGAGTGATTTTGTATGGCGA 58.799 33.333 0.00 0.00 0.00 5.54
5841 6486 8.902540 TTATTAGAGTGATTTTGTATGGCGAT 57.097 30.769 0.00 0.00 0.00 4.58
5842 6487 7.807977 ATTAGAGTGATTTTGTATGGCGATT 57.192 32.000 0.00 0.00 0.00 3.34
5843 6488 5.490139 AGAGTGATTTTGTATGGCGATTG 57.510 39.130 0.00 0.00 0.00 2.67
5844 6489 4.336433 AGAGTGATTTTGTATGGCGATTGG 59.664 41.667 0.00 0.00 0.00 3.16
5845 6490 3.115554 GTGATTTTGTATGGCGATTGGC 58.884 45.455 0.00 0.00 42.51 4.52
5846 6491 2.223456 TGATTTTGTATGGCGATTGGCG 60.223 45.455 1.48 0.00 44.92 5.69
5912 6557 2.094234 GCCACCAAACAAACAGTTCTGT 60.094 45.455 0.00 0.00 40.26 3.41
5923 6568 9.826574 AAACAAACAGTTCTGTATGAGTACTTA 57.173 29.630 5.87 0.00 40.26 2.24
5924 6569 9.998106 AACAAACAGTTCTGTATGAGTACTTAT 57.002 29.630 5.39 5.39 34.74 1.73
5928 6573 8.235359 ACAGTTCTGTATGAGTACTTATACCC 57.765 38.462 26.37 15.64 30.21 3.69
5929 6574 8.060075 ACAGTTCTGTATGAGTACTTATACCCT 58.940 37.037 26.37 17.06 30.21 4.34
5930 6575 9.570468 CAGTTCTGTATGAGTACTTATACCCTA 57.430 37.037 26.37 14.11 30.21 3.53
5931 6576 9.571816 AGTTCTGTATGAGTACTTATACCCTAC 57.428 37.037 26.37 21.04 32.87 3.18
5932 6577 9.571816 GTTCTGTATGAGTACTTATACCCTACT 57.428 37.037 26.37 0.00 32.87 2.57
6028 6673 4.291540 TGCTTCTTGTTTCATCACACAC 57.708 40.909 0.00 0.00 0.00 3.82
6029 6674 3.693578 TGCTTCTTGTTTCATCACACACA 59.306 39.130 0.00 0.00 0.00 3.72
6040 6685 8.013947 TGTTTCATCACACACAAAAATGTTTTG 58.986 29.630 11.02 11.02 35.64 2.44
6161 6807 2.754552 TGCCATGTTTCATTGCTAGTCC 59.245 45.455 7.19 0.00 0.00 3.85
6195 6841 6.261826 GTCAGGAATTTGGATCAGATTACCAG 59.738 42.308 0.00 0.00 35.08 4.00
6247 6893 0.249489 AGGCACACTGACTCGACAAC 60.249 55.000 0.00 0.00 18.29 3.32
6320 6967 0.803380 CTGCAAAAGCTAATGCCGCC 60.803 55.000 18.00 0.00 41.87 6.13
6663 7310 4.778579 AGCAGATGAACATTATCAGTGCT 58.221 39.130 9.80 9.80 43.46 4.40
6720 7367 0.868406 GCAGGTACACAGTGTGAAGC 59.132 55.000 29.58 19.03 36.96 3.86
6774 7421 2.228582 TGCCATTGTTCCAGACGAAATG 59.771 45.455 0.00 0.00 30.39 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.329913 CAATACATATTTTAGAAGGCAATACGC 57.670 33.333 0.00 0.00 41.28 4.42
132 476 3.531538 TCTTTCTTGCGTTCAGTTGAGT 58.468 40.909 0.00 0.00 0.00 3.41
196 540 5.464168 CATGGTTGAATCTCCTCACAAAAC 58.536 41.667 0.00 0.00 0.00 2.43
208 552 1.180029 AGGCAGTGCATGGTTGAATC 58.820 50.000 18.61 0.00 0.00 2.52
261 605 5.464722 GCTGATGTTAATCTGTGATCGACAT 59.535 40.000 0.00 7.82 34.96 3.06
285 629 4.066490 AGAGATAATAGGACCGTGTCTCG 58.934 47.826 11.34 0.00 36.60 4.04
445 789 8.622572 ATTTGGTGGGGATTAAACTAATGATT 57.377 30.769 0.00 0.00 0.00 2.57
504 848 9.178758 GGTTTAAAGGAGTTTAGTGATGATGAT 57.821 33.333 0.00 0.00 29.71 2.45
505 849 7.333423 CGGTTTAAAGGAGTTTAGTGATGATGA 59.667 37.037 0.00 0.00 29.71 2.92
506 850 7.464358 CGGTTTAAAGGAGTTTAGTGATGATG 58.536 38.462 0.00 0.00 29.71 3.07
531 875 7.359514 GCTCCAAAAGTCTGTTTTTATTCATGC 60.360 37.037 0.00 0.00 0.00 4.06
534 878 7.106439 TGCTCCAAAAGTCTGTTTTTATTCA 57.894 32.000 0.00 0.00 0.00 2.57
535 879 6.144563 GCTGCTCCAAAAGTCTGTTTTTATTC 59.855 38.462 0.00 0.00 0.00 1.75
536 880 5.985530 GCTGCTCCAAAAGTCTGTTTTTATT 59.014 36.000 0.00 0.00 0.00 1.40
537 881 5.068987 TGCTGCTCCAAAAGTCTGTTTTTAT 59.931 36.000 0.00 0.00 0.00 1.40
538 882 4.400884 TGCTGCTCCAAAAGTCTGTTTTTA 59.599 37.500 0.00 0.00 0.00 1.52
554 898 1.095807 TCATGCTCATGCTGCTGCTC 61.096 55.000 17.00 2.00 38.65 4.26
562 906 3.488721 GGTCTTTCATGTCATGCTCATGC 60.489 47.826 19.02 9.55 41.40 4.06
708 1060 3.807538 TACGTCTCGCTGTCCGCC 61.808 66.667 0.00 0.00 36.73 6.13
775 1127 1.376553 GCCTCAAGCTCCCACTGTC 60.377 63.158 0.00 0.00 38.99 3.51
776 1128 2.753029 GCCTCAAGCTCCCACTGT 59.247 61.111 0.00 0.00 38.99 3.55
866 1225 4.573900 AGCTAAAATGATAGGATCCTGCG 58.426 43.478 25.28 3.85 0.00 5.18
1008 1369 1.424493 GCAAGAAGTGAGCCGATCGG 61.424 60.000 30.03 30.03 38.57 4.18
1044 1405 4.450122 CTCCATGCACGCACGCAC 62.450 66.667 0.00 0.00 46.56 5.34
1047 1408 2.741985 TTCCTCCATGCACGCACG 60.742 61.111 0.00 0.00 0.00 5.34
1048 1409 3.044059 GCTTCCTCCATGCACGCAC 62.044 63.158 0.00 0.00 0.00 5.34
1049 1410 2.747460 GCTTCCTCCATGCACGCA 60.747 61.111 0.00 0.00 0.00 5.24
1073 1434 1.448540 CAGACCCATCCTCGCACAC 60.449 63.158 0.00 0.00 0.00 3.82
1103 1464 4.774503 AGCAAGGCCAGAGCGAGC 62.775 66.667 5.01 0.00 41.24 5.03
1183 1544 5.649395 TGAAACTAAGCAAGAATGGATGAGG 59.351 40.000 0.00 0.00 0.00 3.86
1211 1572 8.078596 TGTCTCATCATCGATGAATTGTACTAG 58.921 37.037 30.41 17.36 46.51 2.57
1292 1694 6.074195 CGATCGACTCAAGGTAGTAGAGTTAG 60.074 46.154 10.26 0.00 42.29 2.34
1300 1702 1.402259 CTGCGATCGACTCAAGGTAGT 59.598 52.381 21.57 0.00 0.00 2.73
1301 1703 1.862008 GCTGCGATCGACTCAAGGTAG 60.862 57.143 21.57 3.23 0.00 3.18
1302 1704 0.100682 GCTGCGATCGACTCAAGGTA 59.899 55.000 21.57 0.00 0.00 3.08
1303 1705 1.153745 GCTGCGATCGACTCAAGGT 60.154 57.895 21.57 0.00 0.00 3.50
1304 1706 0.459237 AAGCTGCGATCGACTCAAGG 60.459 55.000 21.57 0.00 0.00 3.61
1306 1708 0.528017 AGAAGCTGCGATCGACTCAA 59.472 50.000 21.57 0.00 0.00 3.02
1338 1742 4.125703 GAGTTCTGCCACTGATCCATTAG 58.874 47.826 0.00 0.00 0.00 1.73
1370 1774 2.053244 GGATCATCAGACTGTCCCCAT 58.947 52.381 3.76 0.00 0.00 4.00
1412 1816 1.902918 GTTGCTGCATGTCACCCCA 60.903 57.895 1.84 0.00 0.00 4.96
1415 1819 0.385029 TGTTGTTGCTGCATGTCACC 59.615 50.000 1.84 0.00 0.00 4.02
1467 1871 4.978580 GGAAGTTGCAGTGAAATTCTTGTC 59.021 41.667 0.00 0.00 31.97 3.18
1828 2236 0.464916 ACCGAAAACAAGAAGGCCGT 60.465 50.000 0.00 0.00 0.00 5.68
1881 2291 1.659233 CTTCAAACCATGCGGCACA 59.341 52.632 4.03 0.00 34.57 4.57
1889 2299 3.094572 CTGCCAGAATCCTTCAAACCAT 58.905 45.455 0.00 0.00 0.00 3.55
1924 2334 1.442526 GCTCATCAGGGATGTTGCCG 61.443 60.000 6.15 0.00 40.55 5.69
1987 2397 1.959042 CAGTATCATCTGTGGGGCAC 58.041 55.000 0.00 0.00 34.56 5.01
1992 2415 4.397103 ACAAATGTGCAGTATCATCTGTGG 59.603 41.667 0.00 0.00 37.70 4.17
2169 2592 2.175284 TGATGAGATTGGCAATGGGCTA 59.825 45.455 19.07 0.00 44.01 3.93
2170 2593 1.063492 TGATGAGATTGGCAATGGGCT 60.063 47.619 19.07 8.61 44.01 5.19
2264 2689 5.877012 TCTCTGCTTCAGAAATGACAATACC 59.123 40.000 0.00 0.00 40.18 2.73
2265 2690 6.974932 TCTCTGCTTCAGAAATGACAATAC 57.025 37.500 0.00 0.00 40.18 1.89
2266 2691 7.333323 TCATCTCTGCTTCAGAAATGACAATA 58.667 34.615 8.33 0.00 41.30 1.90
2267 2692 6.178324 TCATCTCTGCTTCAGAAATGACAAT 58.822 36.000 8.33 0.00 41.30 2.71
2268 2693 5.554070 TCATCTCTGCTTCAGAAATGACAA 58.446 37.500 8.33 0.00 41.30 3.18
2269 2694 5.046807 TCTCATCTCTGCTTCAGAAATGACA 60.047 40.000 8.33 0.00 41.30 3.58
2270 2695 5.417811 TCTCATCTCTGCTTCAGAAATGAC 58.582 41.667 8.33 0.00 41.30 3.06
2287 2712 7.870445 GGTTAGAGATATGTTCCACTTCTCATC 59.130 40.741 0.00 0.00 36.20 2.92
2302 2727 6.606395 ACCAGAAACAGTACGGTTAGAGATAT 59.394 38.462 11.89 0.00 0.00 1.63
2421 2846 1.543802 CTATAGGCAGAGAGGGCTTCG 59.456 57.143 0.00 0.00 44.09 3.79
2435 2860 7.243604 AGCAGGAGAAAGATGAATCTATAGG 57.756 40.000 0.00 0.00 35.76 2.57
2483 2908 1.959042 AGCCTGCACCGAATATCTTG 58.041 50.000 0.00 0.00 0.00 3.02
2608 3033 5.127682 GGCAGACCATCCAACAAAATAAGAT 59.872 40.000 0.00 0.00 35.26 2.40
2626 3051 9.531942 CATATAGAAGATTCATATCTGGCAGAC 57.468 37.037 21.37 5.04 40.26 3.51
2627 3052 9.264653 ACATATAGAAGATTCATATCTGGCAGA 57.735 33.333 21.19 21.19 40.26 4.26
2666 3091 2.104963 GAGGGAATTTCTATCCAGCCGT 59.895 50.000 0.00 0.00 38.80 5.68
2702 3127 2.354805 GGTGAGGTTATTCAGGTTCGCT 60.355 50.000 0.00 0.00 0.00 4.93
2810 3235 7.263100 TGGCTAAGTTGCTGAAACATATATG 57.737 36.000 11.29 11.29 41.61 1.78
2919 3344 6.250104 CGAACAAATTAGCAGCAGAAATCTTC 59.750 38.462 0.00 0.00 0.00 2.87
2963 3388 9.494271 TGCAATTAGACCAGATGAATTACTATC 57.506 33.333 0.00 0.00 0.00 2.08
3116 3542 3.264193 ACACTGTCAGATTTAGCCATCCA 59.736 43.478 6.91 0.00 0.00 3.41
3135 3561 1.680735 TGGTTTGGCATCACAAGACAC 59.319 47.619 0.00 0.00 0.00 3.67
3159 3585 4.657436 AGAGTCTTCCGGATTGTATGAC 57.343 45.455 4.15 7.48 0.00 3.06
3332 3770 3.641986 GAACGCGTTGCCGTCCAA 61.642 61.111 31.89 0.00 41.16 3.53
3457 3895 0.179134 ATCTTGGTACTCACGCGAGC 60.179 55.000 15.93 0.00 43.66 5.03
3475 3913 0.466189 CCGGAATTGGCCACTGCTAT 60.466 55.000 3.88 0.00 37.74 2.97
3479 3917 0.243636 GAAACCGGAATTGGCCACTG 59.756 55.000 9.46 0.00 0.00 3.66
3484 3922 0.526211 GTCTGGAAACCGGAATTGGC 59.474 55.000 9.46 0.00 41.00 4.52
3488 3926 1.271379 CCACTGTCTGGAAACCGGAAT 60.271 52.381 9.46 0.00 43.95 3.01
3517 3955 4.636206 GGCAGGAGTTTGTAAGTAAGATGG 59.364 45.833 0.00 0.00 0.00 3.51
3650 4229 0.318441 CCGAGAAGCACTTCACCAGA 59.682 55.000 12.65 0.00 41.84 3.86
3914 4493 2.038837 GGTGCGGTTGAAGTAGGGC 61.039 63.158 0.00 0.00 0.00 5.19
4040 4619 6.036408 AGGTAAAAGGTATTATCGTTGTTCGC 59.964 38.462 0.00 0.00 39.67 4.70
4053 4632 5.830991 TGAGCAAACAACAGGTAAAAGGTAT 59.169 36.000 0.00 0.00 0.00 2.73
4056 4635 4.647424 TGAGCAAACAACAGGTAAAAGG 57.353 40.909 0.00 0.00 0.00 3.11
4057 4636 5.949233 GTTGAGCAAACAACAGGTAAAAG 57.051 39.130 13.66 0.00 46.19 2.27
4089 4681 1.131693 TCACTCAGCCACATACGTACG 59.868 52.381 15.01 15.01 0.00 3.67
4134 4730 2.464459 GCCCGTTCCGATCTGCAAG 61.464 63.158 0.00 0.00 0.00 4.01
4324 4920 6.636044 GTGAAGAAAATGCTTTCAGTTCTCTG 59.364 38.462 1.77 0.00 42.99 3.35
4325 4921 6.238869 GGTGAAGAAAATGCTTTCAGTTCTCT 60.239 38.462 1.77 0.00 42.99 3.10
4326 4922 5.917447 GGTGAAGAAAATGCTTTCAGTTCTC 59.083 40.000 1.77 0.00 42.99 2.87
4327 4923 5.506317 CGGTGAAGAAAATGCTTTCAGTTCT 60.506 40.000 1.77 0.00 42.99 3.01
4330 4926 3.004734 CCGGTGAAGAAAATGCTTTCAGT 59.995 43.478 0.00 0.00 42.99 3.41
4331 4927 3.568538 CCGGTGAAGAAAATGCTTTCAG 58.431 45.455 0.00 0.00 42.99 3.02
4359 4955 1.802960 TCACTTCACTCGTACTCGTCC 59.197 52.381 0.00 0.00 38.33 4.79
4361 4957 3.314635 ACTTTCACTTCACTCGTACTCGT 59.685 43.478 0.00 0.00 38.33 4.18
4362 4958 3.664486 CACTTTCACTTCACTCGTACTCG 59.336 47.826 0.00 0.00 38.55 4.18
4363 4959 3.982058 CCACTTTCACTTCACTCGTACTC 59.018 47.826 0.00 0.00 0.00 2.59
4364 4960 3.383825 ACCACTTTCACTTCACTCGTACT 59.616 43.478 0.00 0.00 0.00 2.73
4365 4961 3.489785 CACCACTTTCACTTCACTCGTAC 59.510 47.826 0.00 0.00 0.00 3.67
4366 4962 3.491964 CCACCACTTTCACTTCACTCGTA 60.492 47.826 0.00 0.00 0.00 3.43
4503 5099 2.125673 CCGTACCCCAGCTCGTTG 60.126 66.667 0.00 0.00 0.00 4.10
4762 5358 1.002201 AGACGAGACAAGACGAGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
4763 5359 1.395608 GAGACGAGACAAGACGAGAGG 59.604 57.143 0.00 0.00 0.00 3.69
4772 5372 5.529800 TGATATGGTTATCGAGACGAGACAA 59.470 40.000 0.00 0.00 39.91 3.18
4773 5373 5.061179 TGATATGGTTATCGAGACGAGACA 58.939 41.667 0.00 0.00 39.91 3.41
4783 5383 8.642908 TTGTACTTGACTTGATATGGTTATCG 57.357 34.615 0.00 0.00 37.61 2.92
5031 5663 3.291101 GACGTGCCCCTTGTCGCTA 62.291 63.158 0.00 0.00 0.00 4.26
5043 5675 2.591715 ACTTGGGTGCTGACGTGC 60.592 61.111 0.00 0.00 0.00 5.34
5078 5710 0.102120 CCTGAGCCGATCACTGAGTC 59.898 60.000 0.00 0.00 33.22 3.36
5083 5715 0.179062 GAATGCCTGAGCCGATCACT 60.179 55.000 0.00 0.00 38.69 3.41
5084 5716 0.462581 TGAATGCCTGAGCCGATCAC 60.463 55.000 0.00 0.00 38.69 3.06
5087 5719 0.250640 GGATGAATGCCTGAGCCGAT 60.251 55.000 0.00 0.00 38.69 4.18
5088 5720 1.146930 GGATGAATGCCTGAGCCGA 59.853 57.895 0.00 0.00 38.69 5.54
5089 5721 1.895707 GGGATGAATGCCTGAGCCG 60.896 63.158 0.00 0.00 38.69 5.52
5096 5728 0.458669 CAACTGCAGGGATGAATGCC 59.541 55.000 19.93 0.00 41.85 4.40
5130 5762 4.384056 CAAGTCACATTCACTGGAACTCT 58.616 43.478 0.00 0.00 35.46 3.24
5131 5763 3.499918 CCAAGTCACATTCACTGGAACTC 59.500 47.826 0.00 0.00 35.46 3.01
5132 5764 3.117888 ACCAAGTCACATTCACTGGAACT 60.118 43.478 0.00 0.00 35.46 3.01
5133 5765 3.003689 CACCAAGTCACATTCACTGGAAC 59.996 47.826 0.00 0.00 35.46 3.62
5134 5766 3.213506 CACCAAGTCACATTCACTGGAA 58.786 45.455 0.00 0.00 37.45 3.53
5135 5767 2.172505 ACACCAAGTCACATTCACTGGA 59.827 45.455 0.00 0.00 0.00 3.86
5136 5768 2.291465 CACACCAAGTCACATTCACTGG 59.709 50.000 0.00 0.00 0.00 4.00
5137 5769 2.945008 ACACACCAAGTCACATTCACTG 59.055 45.455 0.00 0.00 0.00 3.66
5162 5794 1.600636 CCCTGCAGGCGAAGAACAA 60.601 57.895 28.39 0.00 0.00 2.83
5170 5802 1.524621 CCAGATAACCCTGCAGGCG 60.525 63.158 28.39 21.83 40.58 5.52
5217 5849 1.512310 GACGTCGCTCTTCTCGGTG 60.512 63.158 0.00 0.00 0.00 4.94
5220 5852 0.720027 TGTAGACGTCGCTCTTCTCG 59.280 55.000 10.46 0.00 0.00 4.04
5247 5879 1.079612 CAGCTCGAGCATGACCACA 60.080 57.895 36.87 0.00 45.16 4.17
5289 5921 2.236395 CCTGACGATGTACTTCCCCTTT 59.764 50.000 3.35 0.00 0.00 3.11
5562 6194 1.415374 GAGCGCTTTTAGTGACGTCA 58.585 50.000 15.76 15.76 0.00 4.35
5614 6246 2.233431 AGTCTGTGCTCATGTCCTTCTC 59.767 50.000 0.00 0.00 0.00 2.87
5664 6299 2.143925 GGTTCGACCTTTGACTGGAAG 58.856 52.381 0.00 0.00 35.83 3.46
5708 6343 0.326595 TGGTTCGGCCAGCATAGAAA 59.673 50.000 2.24 0.00 43.61 2.52
5723 6358 3.181429 TGCTGAGGAGGAAGAAAATGGTT 60.181 43.478 0.00 0.00 0.00 3.67
5839 6484 5.452302 CGTTTTGATTAGAACATCGCCAATC 59.548 40.000 0.00 0.00 0.00 2.67
5840 6485 5.106317 ACGTTTTGATTAGAACATCGCCAAT 60.106 36.000 0.00 0.00 0.00 3.16
5841 6486 4.214545 ACGTTTTGATTAGAACATCGCCAA 59.785 37.500 0.00 0.00 0.00 4.52
5842 6487 3.749088 ACGTTTTGATTAGAACATCGCCA 59.251 39.130 0.00 0.00 0.00 5.69
5843 6488 4.336532 ACGTTTTGATTAGAACATCGCC 57.663 40.909 0.00 0.00 0.00 5.54
5844 6489 5.144359 ACAACGTTTTGATTAGAACATCGC 58.856 37.500 0.00 0.00 36.48 4.58
5845 6490 8.007716 AGTAACAACGTTTTGATTAGAACATCG 58.992 33.333 0.00 0.00 36.48 3.84
5846 6491 9.659830 AAGTAACAACGTTTTGATTAGAACATC 57.340 29.630 0.00 0.00 36.48 3.06
5960 6605 5.636123 TGGCAAAAGTTAGGACCAATCTAA 58.364 37.500 0.00 0.00 0.00 2.10
5966 6611 2.808933 CGTCTGGCAAAAGTTAGGACCA 60.809 50.000 0.00 0.00 0.00 4.02
6028 6673 4.502282 TGTAGTGCGCTCAAAACATTTTTG 59.498 37.500 9.73 5.22 0.00 2.44
6029 6674 4.677584 TGTAGTGCGCTCAAAACATTTTT 58.322 34.783 9.73 0.00 0.00 1.94
6040 6685 1.069296 TGCAACAAATGTAGTGCGCTC 60.069 47.619 9.73 4.74 35.23 5.03
6142 6788 5.587388 ATTGGACTAGCAATGAAACATGG 57.413 39.130 0.00 0.00 0.00 3.66
6161 6807 8.229253 TGATCCAAATTCCTGACATAGAATTG 57.771 34.615 12.08 8.05 40.84 2.32
6195 6841 1.790818 ATCGGGGGAGAACTTAGGAC 58.209 55.000 0.00 0.00 0.00 3.85
6456 7103 5.411361 CCTTCTGTAACGGAATTGATTCACA 59.589 40.000 6.11 1.45 38.53 3.58
6720 7367 3.313249 TGCCATTGTTATGCTCGATCTTG 59.687 43.478 0.00 0.00 0.00 3.02
6774 7421 3.345508 AACTATGGAAAGGGGACGAAC 57.654 47.619 0.00 0.00 0.00 3.95
6778 7425 3.353557 GTGGAAACTATGGAAAGGGGAC 58.646 50.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.