Multiple sequence alignment - TraesCS1B01G238000

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 TraesCS1B01G238000 chr1B 100.000 3365 0 0 1 3365 426070589 426073953 0.000000e+00 6215.0
1 TraesCS1B01G238000 chr1D 94.761 2348 82 12 353 2692 314572793 314575107 0.000000e+00 3616.0
2 TraesCS1B01G238000 chr1D 92.553 282 12 6 1 275 314572384 314572663 2.430000e-106 396.0
3 TraesCS1B01G238000 chr1D 81.784 269 19 12 3003 3263 314575583 314575829 7.360000e-47 198.0
4 TraesCS1B01G238000 chr1D 94.495 109 4 1 3259 3365 314575867 314575975 2.080000e-37 167.0
5 TraesCS1B01G238000 chr1D 92.188 64 0 4 276 338 314572688 314572747 5.980000e-13 86.1
6 TraesCS1B01G238000 chr1A 94.284 2152 102 13 546 2692 394851143 394853278 0.000000e+00 3273.0
7 TraesCS1B01G238000 chr1A 87.671 584 16 24 1 542 394850411 394850980 2.200000e-176 628.0
8 TraesCS1B01G238000 chr1A 89.600 250 17 7 2755 2997 394853317 394853564 3.260000e-80 309.0
9 TraesCS1B01G238000 chr1A 79.798 396 17 22 3003 3365 394853770 394854135 2.610000e-56 230.0
10 TraesCS1B01G238000 chr7B 84.395 801 119 2 1561 2355 604035526 604034726 0.000000e+00 782.0
11 TraesCS1B01G238000 chr7A 83.697 687 106 3 1687 2367 642254108 642253422 0.000000e+00 643.0
12 TraesCS1B01G238000 chr6D 88.923 325 33 3 1059 1382 12345144 12345466 6.770000e-107 398.0
13 TraesCS1B01G238000 chr6D 80.000 170 20 9 334 493 12344911 12345076 2.740000e-21 113.0
14 TraesCS1B01G238000 chr6D 93.548 62 3 1 2699 2759 293177508 293177569 1.290000e-14 91.6
15 TraesCS1B01G238000 chr6B 82.895 456 51 6 1480 1935 22711235 22711663 5.270000e-103 385.0
16 TraesCS1B01G238000 chr6B 88.235 323 32 4 1061 1382 22710861 22711178 6.810000e-102 381.0
17 TraesCS1B01G238000 chr6B 93.220 59 3 1 2699 2756 560706125 560706183 5.980000e-13 86.1
18 TraesCS1B01G238000 chr6B 93.220 59 3 1 2699 2756 560745576 560745634 5.980000e-13 86.1
19 TraesCS1B01G238000 chr7D 92.537 67 4 1 2699 2764 21264544 21264610 9.940000e-16 95.3
20 TraesCS1B01G238000 chr5D 95.000 60 3 0 2703 2762 525738250 525738309 9.940000e-16 95.3
21 TraesCS1B01G238000 chr5D 94.737 57 3 0 2703 2759 320627375 320627431 4.620000e-14 89.8
22 TraesCS1B01G238000 chr2D 87.654 81 8 1 313 391 80421848 80421928 3.570000e-15 93.5
23 TraesCS1B01G238000 chr3D 94.737 57 3 0 2703 2759 435678573 435678629 4.620000e-14 89.8
24 TraesCS1B01G238000 chr2B 94.737 57 2 1 2703 2758 248148870 248148814 1.660000e-13 87.9
25 TraesCS1B01G238000 chr2B 85.366 82 9 1 313 391 132095937 132096018 7.740000e-12 82.4
26 TraesCS1B01G238000 chr3B 90.625 64 5 1 2700 2762 236509985 236510048 2.150000e-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 TraesCS1B01G238000 chr1B 426070589 426073953 3364 False 6215.00 6215 100.00000 1 3365 1 chr1B.!!$F1 3364
1 TraesCS1B01G238000 chr1D 314572384 314575975 3591 False 892.62 3616 91.15620 1 3365 5 chr1D.!!$F1 3364
2 TraesCS1B01G238000 chr1A 394850411 394854135 3724 False 1110.00 3273 87.83825 1 3365 4 chr1A.!!$F1 3364
3 TraesCS1B01G238000 chr7B 604034726 604035526 800 True 782.00 782 84.39500 1561 2355 1 chr7B.!!$R1 794
4 TraesCS1B01G238000 chr7A 642253422 642254108 686 True 643.00 643 83.69700 1687 2367 1 chr7A.!!$R1 680
5 TraesCS1B01G238000 chr6D 12344911 12345466 555 False 255.50 398 84.46150 334 1382 2 chr6D.!!$F2 1048
6 TraesCS1B01G238000 chr6B 22710861 22711663 802 False 383.00 385 85.56500 1061 1935 2 chr6B.!!$F3 874

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
468 545 0.332632 AGCTTGGCTGCCATTAGGAA 59.667 50.0 24.03 5.13 37.57 3.36 F
1959 2231 0.111253 CAGAGGGCCCAGTTGAAACT 59.889 55.0 27.56 0.00 40.60 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2567 0.179018 AAGCCTTCTTCGCCTTGTGT 60.179 50.0 0.0 0.0 0.00 3.72 R
3087 3575 0.807496 CTAGCTCTTGGCACTTTGGC 59.193 55.0 0.0 0.0 44.79 4.52 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
112 116 8.169977 TGTTAAATCATTGAGTTTCTGCTTCT 57.830 30.769 4.51 0.00 0.00 2.85
113 117 8.077991 TGTTAAATCATTGAGTTTCTGCTTCTG 58.922 33.333 4.51 0.00 0.00 3.02
114 118 6.889301 AAATCATTGAGTTTCTGCTTCTGA 57.111 33.333 0.00 0.00 0.00 3.27
115 119 6.497785 AATCATTGAGTTTCTGCTTCTGAG 57.502 37.500 0.00 0.00 0.00 3.35
182 186 6.226787 GTCTATATGACTATGGCTGCAAAGT 58.773 40.000 0.50 0.87 42.21 2.66
254 260 4.096532 GCTTTGGTGCTTTCCCTTCTATAC 59.903 45.833 0.00 0.00 0.00 1.47
260 266 5.763698 GGTGCTTTCCCTTCTATACCAATAC 59.236 44.000 0.00 0.00 0.00 1.89
338 383 9.643693 ATTATCCAATACAGAAAACAAAGCTTG 57.356 29.630 0.00 0.00 0.00 4.01
343 388 3.848726 ACAGAAAACAAAGCTTGGTGTG 58.151 40.909 7.40 5.86 34.12 3.82
436 513 1.608542 GCCATGCCAATCAAGTTTGCA 60.609 47.619 0.00 0.00 0.00 4.08
437 514 2.070783 CCATGCCAATCAAGTTTGCAC 58.929 47.619 0.00 0.00 0.00 4.57
438 515 2.289195 CCATGCCAATCAAGTTTGCACT 60.289 45.455 0.00 0.00 33.11 4.40
439 516 2.512485 TGCCAATCAAGTTTGCACTG 57.488 45.000 0.00 0.00 31.60 3.66
440 517 1.142474 GCCAATCAAGTTTGCACTGC 58.858 50.000 0.00 0.00 31.60 4.40
441 518 1.538634 GCCAATCAAGTTTGCACTGCA 60.539 47.619 0.00 0.00 36.47 4.41
442 519 2.129607 CCAATCAAGTTTGCACTGCAC 58.870 47.619 2.26 0.00 38.71 4.57
443 520 2.223876 CCAATCAAGTTTGCACTGCACT 60.224 45.455 2.26 0.00 38.71 4.40
468 545 0.332632 AGCTTGGCTGCCATTAGGAA 59.667 50.000 24.03 5.13 37.57 3.36
497 574 9.442062 TTCCTCTACATCAGTATATTTGGGTAA 57.558 33.333 0.00 0.00 0.00 2.85
544 622 8.710551 TGATTGAATATTTGTCATTGTTGTTGC 58.289 29.630 0.00 0.00 0.00 4.17
552 789 7.872163 TTTGTCATTGTTGTTGCATAGAATC 57.128 32.000 0.00 0.00 0.00 2.52
568 805 6.017275 GCATAGAATCAATCTGCTTTAGCTGT 60.017 38.462 0.00 0.00 42.66 4.40
576 813 8.792830 TCAATCTGCTTTAGCTGTTAAATAGT 57.207 30.769 0.00 0.00 42.66 2.12
610 847 9.573166 TGGCTATATCTTTAAGCATAATGTTGT 57.427 29.630 0.00 0.00 38.01 3.32
625 862 7.626028 GCATAATGTTGTACATGTGACATGTGA 60.626 37.037 34.35 21.02 37.97 3.58
627 864 4.064388 TGTTGTACATGTGACATGTGAGG 58.936 43.478 34.35 9.64 33.76 3.86
754 991 5.909610 GTGTCTCAGGAAAAGATTTGTTTCG 59.090 40.000 0.00 0.00 36.11 3.46
757 994 5.241506 TCTCAGGAAAAGATTTGTTTCGCAT 59.758 36.000 0.00 0.00 36.11 4.73
784 1021 3.428862 CGCCAACCCAGAAATTACCATTC 60.429 47.826 0.00 0.00 0.00 2.67
786 1023 3.130340 CCAACCCAGAAATTACCATTCGG 59.870 47.826 0.00 0.00 38.77 4.30
798 1035 7.575414 AATTACCATTCGGCATGTTGTTATA 57.425 32.000 0.00 0.00 34.57 0.98
888 1125 5.904362 GAAGTATTCATGTTTGCTTCCCT 57.096 39.130 13.40 0.00 46.62 4.20
889 1126 6.272822 GAAGTATTCATGTTTGCTTCCCTT 57.727 37.500 13.40 0.00 46.62 3.95
890 1127 6.670695 AAGTATTCATGTTTGCTTCCCTTT 57.329 33.333 0.00 0.00 0.00 3.11
912 1149 7.201609 CCTTTCCTTTCAACTTTTTAGTTTGCC 60.202 37.037 0.00 0.00 0.00 4.52
931 1168 7.888546 AGTTTGCCTTATGGTTTATTCTGTAGT 59.111 33.333 0.00 0.00 35.27 2.73
974 1211 9.649167 AAAAAGAAGGAATCTGCATAATCAAAG 57.351 29.630 0.00 0.00 38.79 2.77
1019 1256 6.265196 TCTTTGATGTTGCATGGTTACTTCTT 59.735 34.615 0.00 0.00 0.00 2.52
1031 1268 9.476202 GCATGGTTACTTCTTCAAACTATTTTT 57.524 29.630 0.00 0.00 0.00 1.94
1254 1495 3.592059 CCGGAAGATTGTAAAGGTTCGA 58.408 45.455 0.00 0.00 0.00 3.71
1428 1697 4.054671 CCTCTCAACTTGTTGAGTCAGAC 58.945 47.826 30.49 0.00 46.37 3.51
1873 2142 2.229784 CCTTCTTTCAACATGGGTGCTC 59.770 50.000 0.00 0.00 0.00 4.26
1875 2147 0.523072 CTTTCAACATGGGTGCTCCG 59.477 55.000 0.00 0.00 38.76 4.63
1959 2231 0.111253 CAGAGGGCCCAGTTGAAACT 59.889 55.000 27.56 0.00 40.60 2.66
1971 2243 3.744660 AGTTGAAACTGGCGAAGAGAAT 58.255 40.909 0.00 0.00 37.98 2.40
2295 2567 1.071987 CAAGGCTGCAGTGGAGACA 59.928 57.895 20.80 0.00 38.70 3.41
2370 2645 1.834458 CGTCCGACGTTTGAAACCCC 61.834 60.000 12.91 0.00 36.74 4.95
2478 2753 6.618287 AAAACATATCGTACCCATGTCATG 57.382 37.500 5.79 5.79 31.82 3.07
2499 2774 1.507141 GGTTTCTGGCGTGTCCTGTG 61.507 60.000 0.00 0.00 35.49 3.66
2658 2939 3.257393 GAGTCATCACCACATCACTGTC 58.743 50.000 0.00 0.00 31.62 3.51
2671 2952 5.122711 CACATCACTGTCTTATGCATGTTCA 59.877 40.000 10.16 2.72 31.62 3.18
2692 2973 1.320382 CGTCGCGTTTGCACATGTTC 61.320 55.000 5.77 0.00 42.97 3.18
2693 2974 0.316607 GTCGCGTTTGCACATGTTCA 60.317 50.000 5.77 0.00 42.97 3.18
2695 2976 0.976963 CGCGTTTGCACATGTTCATC 59.023 50.000 0.00 0.00 42.97 2.92
2696 2977 1.400113 CGCGTTTGCACATGTTCATCT 60.400 47.619 0.00 0.00 42.97 2.90
2697 2978 2.664916 GCGTTTGCACATGTTCATCTT 58.335 42.857 0.00 0.00 42.15 2.40
2698 2979 3.052036 GCGTTTGCACATGTTCATCTTT 58.948 40.909 0.00 0.00 42.15 2.52
2699 2980 3.121261 GCGTTTGCACATGTTCATCTTTG 60.121 43.478 0.00 0.00 42.15 2.77
2700 2981 4.043750 CGTTTGCACATGTTCATCTTTGT 58.956 39.130 0.00 0.00 0.00 2.83
2704 2985 5.008619 TGCACATGTTCATCTTTGTGTTT 57.991 34.783 0.00 0.00 0.00 2.83
2705 2986 4.804665 TGCACATGTTCATCTTTGTGTTTG 59.195 37.500 0.00 0.00 0.00 2.93
2706 2987 4.318263 GCACATGTTCATCTTTGTGTTTGC 60.318 41.667 0.00 0.00 0.00 3.68
2707 2988 4.804665 CACATGTTCATCTTTGTGTTTGCA 59.195 37.500 0.00 0.00 0.00 4.08
2709 2990 4.717233 TGTTCATCTTTGTGTTTGCACT 57.283 36.364 0.00 0.00 45.44 4.40
2710 2991 5.826601 TGTTCATCTTTGTGTTTGCACTA 57.173 34.783 0.00 0.00 45.44 2.74
2711 2992 6.201226 TGTTCATCTTTGTGTTTGCACTAA 57.799 33.333 0.00 0.00 45.44 2.24
2713 2994 6.696583 TGTTCATCTTTGTGTTTGCACTAATG 59.303 34.615 0.00 0.00 45.44 1.90
2714 2995 6.389830 TCATCTTTGTGTTTGCACTAATGT 57.610 33.333 0.00 0.00 45.44 2.71
2715 2996 7.503521 TCATCTTTGTGTTTGCACTAATGTA 57.496 32.000 0.00 0.00 45.44 2.29
2716 2997 7.584108 TCATCTTTGTGTTTGCACTAATGTAG 58.416 34.615 0.00 0.00 45.44 2.74
2717 2998 6.935741 TCTTTGTGTTTGCACTAATGTAGT 57.064 33.333 0.00 0.00 45.44 2.73
2745 3026 9.557338 TCAAAAACGTTTTTATATTATGGGACG 57.443 29.630 32.12 18.06 38.23 4.79
2746 3027 8.800031 CAAAAACGTTTTTATATTATGGGACGG 58.200 33.333 32.12 15.00 38.23 4.79
2747 3028 7.862512 AAACGTTTTTATATTATGGGACGGA 57.137 32.000 7.96 0.00 33.95 4.69
2748 3029 7.486802 AACGTTTTTATATTATGGGACGGAG 57.513 36.000 0.00 0.00 33.95 4.63
2749 3030 5.993441 ACGTTTTTATATTATGGGACGGAGG 59.007 40.000 0.00 0.00 33.95 4.30
2750 3031 5.410439 CGTTTTTATATTATGGGACGGAGGG 59.590 44.000 0.00 0.00 0.00 4.30
2751 3032 6.536447 GTTTTTATATTATGGGACGGAGGGA 58.464 40.000 0.00 0.00 0.00 4.20
2752 3033 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
2753 3034 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2762 3043 3.148412 GGACGGAGGGAGTAGAATAGAC 58.852 54.545 0.00 0.00 0.00 2.59
2799 3080 4.095483 GGATGGCTTGTCTGTATTGTGAAG 59.905 45.833 0.00 0.00 0.00 3.02
2803 3084 4.515191 GGCTTGTCTGTATTGTGAAGTCAA 59.485 41.667 0.00 0.00 0.00 3.18
2822 3103 5.254032 AGTCAATCTCTTGGGGAGGTTTTAT 59.746 40.000 0.00 0.00 42.22 1.40
2849 3130 0.473755 TGTCCACAACAGTGCCATCT 59.526 50.000 0.00 0.00 32.81 2.90
2853 3134 0.038892 CACAACAGTGCCATCTTGCC 60.039 55.000 0.00 0.00 0.00 4.52
2865 3146 3.181510 GCCATCTTGCCACTAGTTTTACG 60.182 47.826 0.00 0.00 0.00 3.18
2867 3148 4.142902 CCATCTTGCCACTAGTTTTACGTG 60.143 45.833 0.00 0.00 0.00 4.49
2970 3258 4.394300 GCATCTGCACACTCTTTATCAAGT 59.606 41.667 0.00 0.00 41.59 3.16
2998 3286 2.687935 TGAGCTTGTTTGAACTTGGGTC 59.312 45.455 0.00 0.00 0.00 4.46
3000 3288 3.365472 AGCTTGTTTGAACTTGGGTCTT 58.635 40.909 0.00 0.00 0.00 3.01
3001 3289 3.131046 AGCTTGTTTGAACTTGGGTCTTG 59.869 43.478 0.00 0.00 0.00 3.02
3056 3544 6.384178 AAAAAGAACGAAAGAAAAACACGG 57.616 33.333 0.00 0.00 0.00 4.94
3078 3566 3.190874 CATGGACGCTTTTCCTACTCTC 58.809 50.000 0.00 0.00 36.51 3.20
3082 3570 1.891150 ACGCTTTTCCTACTCTCGGAA 59.109 47.619 0.00 0.00 38.71 4.30
3083 3571 2.496470 ACGCTTTTCCTACTCTCGGAAT 59.504 45.455 0.00 0.00 40.05 3.01
3084 3572 3.117046 CGCTTTTCCTACTCTCGGAATC 58.883 50.000 0.00 0.00 40.05 2.52
3085 3573 3.459145 GCTTTTCCTACTCTCGGAATCC 58.541 50.000 0.00 0.00 40.05 3.01
3086 3574 3.133183 GCTTTTCCTACTCTCGGAATCCT 59.867 47.826 0.00 0.00 40.05 3.24
3087 3575 4.688021 CTTTTCCTACTCTCGGAATCCTG 58.312 47.826 0.00 0.00 40.05 3.86
3090 3578 1.403814 CTACTCTCGGAATCCTGCCA 58.596 55.000 0.00 0.00 0.00 4.92
3091 3579 1.757118 CTACTCTCGGAATCCTGCCAA 59.243 52.381 0.00 0.00 0.00 4.52
3092 3580 0.984230 ACTCTCGGAATCCTGCCAAA 59.016 50.000 0.00 0.00 0.00 3.28
3093 3581 1.065854 ACTCTCGGAATCCTGCCAAAG 60.066 52.381 0.00 0.00 0.00 2.77
3104 3592 1.152694 TGCCAAAGTGCCAAGAGCT 60.153 52.632 0.00 0.00 44.23 4.09
3106 3594 0.807496 GCCAAAGTGCCAAGAGCTAG 59.193 55.000 0.00 0.00 44.23 3.42
3132 3623 7.489757 GCAAAACATTCTCTAGTGGAGTAGTAG 59.510 40.741 3.16 0.00 42.40 2.57
3133 3624 6.702716 AACATTCTCTAGTGGAGTAGTAGC 57.297 41.667 3.16 0.00 42.40 3.58
3135 3626 5.591067 ACATTCTCTAGTGGAGTAGTAGCAC 59.409 44.000 3.16 0.00 42.40 4.40
3137 3628 6.556974 TTCTCTAGTGGAGTAGTAGCACTA 57.443 41.667 3.16 0.00 42.40 2.74
3138 3629 6.164417 TCTCTAGTGGAGTAGTAGCACTAG 57.836 45.833 3.62 3.62 43.80 2.57
3139 3630 5.662208 TCTCTAGTGGAGTAGTAGCACTAGT 59.338 44.000 7.44 0.00 43.27 2.57
3140 3631 6.156602 TCTCTAGTGGAGTAGTAGCACTAGTT 59.843 42.308 7.44 0.00 43.27 2.24
3141 3632 7.344093 TCTCTAGTGGAGTAGTAGCACTAGTTA 59.656 40.741 7.44 0.00 43.27 2.24
3142 3633 8.032045 TCTAGTGGAGTAGTAGCACTAGTTAT 57.968 38.462 7.44 0.00 43.27 1.89
3143 3634 6.945938 AGTGGAGTAGTAGCACTAGTTATG 57.054 41.667 0.00 0.00 34.66 1.90
3144 3635 5.299782 AGTGGAGTAGTAGCACTAGTTATGC 59.700 44.000 0.00 0.00 43.74 3.14
3145 3636 5.067413 GTGGAGTAGTAGCACTAGTTATGCA 59.933 44.000 6.59 0.00 45.92 3.96
3146 3637 5.655090 TGGAGTAGTAGCACTAGTTATGCAA 59.345 40.000 6.59 0.00 45.92 4.08
3147 3638 6.183360 TGGAGTAGTAGCACTAGTTATGCAAG 60.183 42.308 6.59 0.00 45.92 4.01
3148 3639 6.150396 AGTAGTAGCACTAGTTATGCAAGG 57.850 41.667 6.59 0.00 45.92 3.61
3149 3640 5.892119 AGTAGTAGCACTAGTTATGCAAGGA 59.108 40.000 6.59 0.00 45.92 3.36
3179 3670 5.070180 AGTCATGACTGGACATCCTATCAAG 59.930 44.000 27.37 5.31 40.75 3.02
3203 3694 6.482973 AGCAATGTTTTTCGTTTTGGAATCAT 59.517 30.769 0.00 0.00 0.00 2.45
3207 3698 6.266323 TGTTTTTCGTTTTGGAATCATTCGA 58.734 32.000 0.00 0.00 0.00 3.71
3209 3700 5.682943 TTTCGTTTTGGAATCATTCGACT 57.317 34.783 0.00 0.00 0.00 4.18
3210 3701 4.921470 TCGTTTTGGAATCATTCGACTC 57.079 40.909 0.00 0.00 0.00 3.36
3211 3702 3.366724 TCGTTTTGGAATCATTCGACTCG 59.633 43.478 0.00 0.00 0.00 4.18
3212 3703 3.122948 CGTTTTGGAATCATTCGACTCGT 59.877 43.478 0.00 0.00 0.00 4.18
3214 3705 5.548250 GTTTTGGAATCATTCGACTCGTAC 58.452 41.667 0.00 0.00 0.00 3.67
3215 3706 3.431922 TGGAATCATTCGACTCGTACC 57.568 47.619 0.00 0.00 0.00 3.34
3216 3707 2.223409 TGGAATCATTCGACTCGTACCG 60.223 50.000 0.00 0.00 0.00 4.02
3263 3764 2.412112 CTCCGCGTACCTAGGCAC 59.588 66.667 9.30 5.13 36.94 5.01
3302 3845 4.337060 CGAGTGCGACGTGGACCA 62.337 66.667 0.11 0.00 40.31 4.02
3313 3856 3.512680 GACGTGGACCAGACTTATCTTG 58.487 50.000 0.00 0.00 30.42 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.844884 AGTTCCTTTGGAGCTTGTATACC 58.155 43.478 0.00 0.00 40.30 2.73
182 186 9.684448 TGAATGTTTTATTCGCAGATAACAAAA 57.316 25.926 0.00 0.00 35.04 2.44
260 266 5.337554 TGGACATTAAAGTGACGTAGATCG 58.662 41.667 0.00 0.00 46.00 3.69
343 388 8.986477 AAATGGCAAACTTATGTGAATAGAAC 57.014 30.769 0.00 0.00 0.00 3.01
440 517 4.709840 AGCCAAGCTGCAGTAGTG 57.290 55.556 16.64 10.68 37.57 2.74
468 545 9.799106 CCCAAATATACTGATGTAGAGGAAAAT 57.201 33.333 0.00 0.00 31.51 1.82
544 622 7.493743 ACAGCTAAAGCAGATTGATTCTATG 57.506 36.000 4.54 0.00 45.16 2.23
552 789 9.922305 GTACTATTTAACAGCTAAAGCAGATTG 57.078 33.333 4.54 0.00 45.16 2.67
610 847 2.903135 TGTCCCTCACATGTCACATGTA 59.097 45.455 23.13 10.77 0.00 2.29
614 851 0.035317 GCTGTCCCTCACATGTCACA 59.965 55.000 0.00 0.00 33.23 3.58
615 852 1.016130 CGCTGTCCCTCACATGTCAC 61.016 60.000 0.00 0.00 33.23 3.67
625 862 2.526873 ACAACTCCCGCTGTCCCT 60.527 61.111 0.00 0.00 0.00 4.20
627 864 1.374758 CAGACAACTCCCGCTGTCC 60.375 63.158 0.00 0.00 42.45 4.02
654 891 2.513897 GCCATGCGTCCCCAGTAC 60.514 66.667 0.00 0.00 0.00 2.73
735 972 4.909696 TGCGAAACAAATCTTTTCCTGA 57.090 36.364 0.00 0.00 30.44 3.86
784 1021 3.065019 GTTGCCTATAACAACATGCCG 57.935 47.619 11.56 0.00 45.35 5.69
798 1035 6.418057 TTGTGAAGGAAAATTATGTTGCCT 57.582 33.333 0.00 0.00 0.00 4.75
808 1045 9.750125 GACTAAACAAGATTTGTGAAGGAAAAT 57.250 29.630 0.00 0.00 44.59 1.82
866 1103 5.904362 AGGGAAGCAAACATGAATACTTC 57.096 39.130 0.00 7.19 34.23 3.01
886 1123 7.201609 GGCAAACTAAAAAGTTGAAAGGAAAGG 60.202 37.037 0.00 0.00 31.64 3.11
887 1124 7.549134 AGGCAAACTAAAAAGTTGAAAGGAAAG 59.451 33.333 0.00 0.00 31.64 2.62
888 1125 7.390823 AGGCAAACTAAAAAGTTGAAAGGAAA 58.609 30.769 0.00 0.00 31.64 3.13
889 1126 6.941857 AGGCAAACTAAAAAGTTGAAAGGAA 58.058 32.000 0.00 0.00 31.64 3.36
890 1127 6.538945 AGGCAAACTAAAAAGTTGAAAGGA 57.461 33.333 0.00 0.00 31.64 3.36
912 1149 8.458843 CAACCCAACTACAGAATAAACCATAAG 58.541 37.037 0.00 0.00 0.00 1.73
931 1168 4.162320 TCTTTTTGTATTGCACCAACCCAA 59.838 37.500 0.00 0.00 0.00 4.12
987 1224 5.128171 ACCATGCAACATCAAAGATTAGCAT 59.872 36.000 0.00 0.00 41.64 3.79
997 1234 5.534278 TGAAGAAGTAACCATGCAACATCAA 59.466 36.000 0.00 0.00 0.00 2.57
1031 1268 7.229306 ACATCAACAAACTGAAGAGAGCATAAA 59.771 33.333 0.00 0.00 0.00 1.40
1072 1313 3.614870 GCCATCCTTACAAGTTTTGGCTG 60.615 47.826 14.79 0.00 38.91 4.85
1254 1495 2.435586 GCTGATGGCTGCTGACGT 60.436 61.111 0.00 0.00 38.06 4.34
1391 1660 2.180276 GAGAGGGTGCTTCAGTTAGGA 58.820 52.381 0.00 0.00 0.00 2.94
1428 1697 0.798776 CTGTAACTTCTGCCTTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
1873 2142 0.804989 GCAGAACTCCCATTGTTCGG 59.195 55.000 0.00 0.00 45.84 4.30
1875 2147 1.177401 GGGCAGAACTCCCATTGTTC 58.823 55.000 0.00 0.00 43.37 3.18
1959 2231 1.406069 GCCTTCTCATTCTCTTCGCCA 60.406 52.381 0.00 0.00 0.00 5.69
1971 2243 2.568956 AGCAGTGAATACAGCCTTCTCA 59.431 45.455 0.00 0.00 39.88 3.27
2106 2378 1.449778 GAGCCGGTAGTTGCCCTTC 60.450 63.158 1.90 0.00 0.00 3.46
2295 2567 0.179018 AAGCCTTCTTCGCCTTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
2385 2660 3.430556 TCCGACACATACACATCAAAACG 59.569 43.478 0.00 0.00 0.00 3.60
2478 2753 1.227853 AGGACACGCCAGAAACCAC 60.228 57.895 0.00 0.00 40.02 4.16
2499 2774 2.358737 CACCGTTCCAGACCAGCC 60.359 66.667 0.00 0.00 0.00 4.85
2658 2939 2.657427 CGCGACGATGAACATGCATAAG 60.657 50.000 0.00 0.00 0.00 1.73
2671 2952 1.132436 CATGTGCAAACGCGACGAT 59.868 52.632 15.93 0.00 0.00 3.73
2721 3002 8.738106 TCCGTCCCATAATATAAAAACGTTTTT 58.262 29.630 33.94 33.94 42.51 1.94
2722 3003 8.278729 TCCGTCCCATAATATAAAAACGTTTT 57.721 30.769 20.26 20.26 0.00 2.43
2723 3004 7.012610 CCTCCGTCCCATAATATAAAAACGTTT 59.987 37.037 7.96 7.96 0.00 3.60
2724 3005 6.484308 CCTCCGTCCCATAATATAAAAACGTT 59.516 38.462 0.00 0.00 0.00 3.99
2727 3008 6.536447 TCCCTCCGTCCCATAATATAAAAAC 58.464 40.000 0.00 0.00 0.00 2.43
2729 3010 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
2730 3011 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
2731 3012 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2732 3013 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2733 3014 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2734 3015 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
2735 3016 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2736 3017 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2737 3018 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2738 3019 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
2739 3020 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2740 3021 2.107901 TCTATTCTACTCCCTCCGTCCC 59.892 54.545 0.00 0.00 0.00 4.46
2741 3022 3.148412 GTCTATTCTACTCCCTCCGTCC 58.852 54.545 0.00 0.00 0.00 4.79
2742 3023 2.807392 CGTCTATTCTACTCCCTCCGTC 59.193 54.545 0.00 0.00 0.00 4.79
2743 3024 2.486907 CCGTCTATTCTACTCCCTCCGT 60.487 54.545 0.00 0.00 0.00 4.69
2744 3025 2.152830 CCGTCTATTCTACTCCCTCCG 58.847 57.143 0.00 0.00 0.00 4.63
2745 3026 3.148412 GTCCGTCTATTCTACTCCCTCC 58.852 54.545 0.00 0.00 0.00 4.30
2746 3027 4.089408 AGTCCGTCTATTCTACTCCCTC 57.911 50.000 0.00 0.00 0.00 4.30
2747 3028 5.562635 CATAGTCCGTCTATTCTACTCCCT 58.437 45.833 0.00 0.00 37.26 4.20
2748 3029 4.156373 GCATAGTCCGTCTATTCTACTCCC 59.844 50.000 0.00 0.00 37.26 4.30
2749 3030 4.156373 GGCATAGTCCGTCTATTCTACTCC 59.844 50.000 0.00 0.00 37.26 3.85
2750 3031 4.142859 CGGCATAGTCCGTCTATTCTACTC 60.143 50.000 0.00 0.00 44.18 2.59
2751 3032 3.752222 CGGCATAGTCCGTCTATTCTACT 59.248 47.826 0.00 0.00 44.18 2.57
2752 3033 4.080969 CGGCATAGTCCGTCTATTCTAC 57.919 50.000 0.00 0.00 44.18 2.59
2774 3055 3.758023 CACAATACAGACAAGCCATCCAA 59.242 43.478 0.00 0.00 0.00 3.53
2799 3080 3.441500 AAACCTCCCCAAGAGATTGAC 57.558 47.619 0.00 0.00 46.50 3.18
2803 3084 6.347061 AATGATAAAACCTCCCCAAGAGAT 57.653 37.500 0.00 0.00 46.50 2.75
2822 3103 3.563808 GCACTGTTGTGGACACTAAATGA 59.436 43.478 3.91 0.00 43.97 2.57
2853 3134 4.365723 AGTGTGTCCACGTAAAACTAGTG 58.634 43.478 0.00 0.00 46.56 2.74
2865 3146 2.622064 AGAACCTGAAGTGTGTCCAC 57.378 50.000 0.00 0.00 42.17 4.02
2867 3148 3.945285 TCAAAAGAACCTGAAGTGTGTCC 59.055 43.478 0.00 0.00 0.00 4.02
2940 3228 2.125952 TGTGCAGATGCTCGACCG 60.126 61.111 6.35 0.00 42.66 4.79
2970 3258 2.203337 AAACAAGCTCAGCCCGCA 60.203 55.556 0.00 0.00 0.00 5.69
2998 3286 7.240674 TGCAAACGTACTAGCAATAAATCAAG 58.759 34.615 0.00 0.00 33.48 3.02
3000 3288 6.370442 ACTGCAAACGTACTAGCAATAAATCA 59.630 34.615 0.00 0.00 36.44 2.57
3001 3289 6.772078 ACTGCAAACGTACTAGCAATAAATC 58.228 36.000 0.00 0.00 36.44 2.17
3041 3529 2.050691 CCATGCCGTGTTTTTCTTTCG 58.949 47.619 0.00 0.00 0.00 3.46
3042 3530 3.049912 GTCCATGCCGTGTTTTTCTTTC 58.950 45.455 0.00 0.00 0.00 2.62
3046 3534 1.001745 GCGTCCATGCCGTGTTTTTC 61.002 55.000 5.15 0.00 0.00 2.29
3056 3544 1.666189 GAGTAGGAAAAGCGTCCATGC 59.334 52.381 6.86 0.00 40.48 4.06
3078 3566 1.508088 GCACTTTGGCAGGATTCCG 59.492 57.895 0.00 0.00 0.00 4.30
3087 3575 0.807496 CTAGCTCTTGGCACTTTGGC 59.193 55.000 0.00 0.00 44.79 4.52
3090 3578 2.276732 TTGCTAGCTCTTGGCACTTT 57.723 45.000 17.23 0.00 44.79 2.66
3091 3579 2.276732 TTTGCTAGCTCTTGGCACTT 57.723 45.000 17.23 0.00 44.79 3.16
3092 3580 1.882623 GTTTTGCTAGCTCTTGGCACT 59.117 47.619 17.23 0.00 44.79 4.40
3093 3581 1.608590 TGTTTTGCTAGCTCTTGGCAC 59.391 47.619 17.23 3.84 44.79 5.01
3104 3592 6.360370 ACTCCACTAGAGAATGTTTTGCTA 57.640 37.500 0.00 0.00 46.50 3.49
3106 3594 6.166982 ACTACTCCACTAGAGAATGTTTTGC 58.833 40.000 0.00 0.00 46.50 3.68
3143 3634 2.490903 AGTCATGACTTGCAATCCTTGC 59.509 45.455 22.89 4.93 44.00 4.01
3144 3635 3.119602 CCAGTCATGACTTGCAATCCTTG 60.120 47.826 25.84 11.06 40.20 3.61
3145 3636 3.087031 CCAGTCATGACTTGCAATCCTT 58.913 45.455 25.84 0.00 40.20 3.36
3146 3637 2.306805 TCCAGTCATGACTTGCAATCCT 59.693 45.455 25.84 0.00 40.20 3.24
3147 3638 2.421424 GTCCAGTCATGACTTGCAATCC 59.579 50.000 25.84 6.20 40.20 3.01
3148 3639 3.076621 TGTCCAGTCATGACTTGCAATC 58.923 45.455 25.84 12.89 40.20 2.67
3149 3640 3.144657 TGTCCAGTCATGACTTGCAAT 57.855 42.857 25.84 0.93 40.20 3.56
3179 3670 6.042144 TGATTCCAAAACGAAAAACATTGC 57.958 33.333 0.00 0.00 0.00 3.56
3211 3702 1.205820 GGTGAAAACTGCGCGGTAC 59.794 57.895 24.63 16.82 0.00 3.34
3212 3703 0.947180 GAGGTGAAAACTGCGCGGTA 60.947 55.000 24.63 3.33 0.00 4.02
3214 3705 2.556287 GAGGTGAAAACTGCGCGG 59.444 61.111 16.39 16.39 0.00 6.46
3215 3706 2.170985 CGAGGTGAAAACTGCGCG 59.829 61.111 0.00 0.00 0.00 6.86
3216 3707 2.127232 GCGAGGTGAAAACTGCGC 60.127 61.111 0.00 0.00 37.60 6.09
3245 3746 2.831742 TGCCTAGGTACGCGGAGG 60.832 66.667 12.47 9.90 0.00 4.30
3246 3747 2.412112 GTGCCTAGGTACGCGGAG 59.588 66.667 14.67 0.00 0.00 4.63
3247 3748 3.142838 GGTGCCTAGGTACGCGGA 61.143 66.667 21.95 0.00 0.00 5.54
3302 3845 6.684538 ACATACTCCTACCCAAGATAAGTCT 58.315 40.000 0.00 0.00 35.82 3.24
3313 3856 6.148315 GTGTTTGTTGTTACATACTCCTACCC 59.852 42.308 0.00 0.00 37.20 3.69


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

AutoCloner maintained by Alex Coulton.