Multiple sequence alignment - TraesCS1D01G250300

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 TraesCS1D01G250300 chr1D 100.000 3634 0 0 1 3634 342847803 342851436 0.000000e+00 6711.0
1 TraesCS1D01G250300 chr1D 93.842 406 18 5 3038 3438 163709475 163709072 4.010000e-169 604.0
2 TraesCS1D01G250300 chr1B 94.586 2752 96 19 1 2711 459812578 459815317 0.000000e+00 4207.0
3 TraesCS1D01G250300 chr1A 94.246 2433 100 17 1 2415 442473358 442475768 0.000000e+00 3681.0
4 TraesCS1D01G250300 chr1A 89.934 457 22 11 2413 2845 442475952 442476408 5.270000e-158 568.0
5 TraesCS1D01G250300 chr1A 87.425 167 12 4 2861 3018 442476392 442476558 2.230000e-42 183.0
6 TraesCS1D01G250300 chr2D 96.947 393 7 4 3051 3438 193400976 193401368 0.000000e+00 654.0
7 TraesCS1D01G250300 chr2D 92.754 414 21 6 3030 3438 2671066 2671475 1.120000e-164 590.0
8 TraesCS1D01G250300 chr2D 97.902 143 3 0 3489 3631 193401368 193401510 7.790000e-62 248.0
9 TraesCS1D01G250300 chr2D 95.862 145 6 0 3490 3634 594478042 594477898 6.070000e-58 235.0
10 TraesCS1D01G250300 chr2D 94.521 146 7 1 3489 3634 471449528 471449384 1.310000e-54 224.0
11 TraesCS1D01G250300 chr2D 94.483 145 7 1 3490 3634 536487950 536487807 4.720000e-54 222.0
12 TraesCS1D01G250300 chr2D 100.000 50 0 0 3439 3488 17981652 17981701 3.860000e-15 93.5
13 TraesCS1D01G250300 chr7D 94.608 408 17 4 3035 3438 465908923 465909329 8.570000e-176 627.0
14 TraesCS1D01G250300 chr7D 95.105 143 7 0 3489 3631 465909329 465909471 3.650000e-55 226.0
15 TraesCS1D01G250300 chr6D 94.377 409 16 5 3036 3438 62136743 62137150 3.990000e-174 621.0
16 TraesCS1D01G250300 chr6D 93.705 413 20 4 3030 3438 387995050 387995460 6.670000e-172 614.0
17 TraesCS1D01G250300 chr5D 94.074 405 18 4 3038 3438 536698807 536699209 8.630000e-171 610.0
18 TraesCS1D01G250300 chr5D 100.000 50 0 0 3439 3488 79846750 79846701 3.860000e-15 93.5
19 TraesCS1D01G250300 chr5D 100.000 50 0 0 3439 3488 353394756 353394805 3.860000e-15 93.5
20 TraesCS1D01G250300 chr3D 93.350 406 21 4 3038 3438 441134678 441135082 2.420000e-166 595.0
21 TraesCS1D01G250300 chr3D 92.075 429 25 7 3018 3438 541302284 541301857 2.420000e-166 595.0
22 TraesCS1D01G250300 chr3D 95.105 143 6 1 3489 3631 441135082 441135223 1.310000e-54 224.0
23 TraesCS1D01G250300 chr3D 100.000 50 0 0 3439 3488 145421015 145421064 3.860000e-15 93.5
24 TraesCS1D01G250300 chr7A 95.205 146 6 1 3489 3634 467784651 467784507 2.820000e-56 230.0
25 TraesCS1D01G250300 chr5A 94.521 146 7 1 3489 3634 663924816 663924672 1.310000e-54 224.0
26 TraesCS1D01G250300 chr4A 94.521 146 7 1 3489 3634 640993201 640993057 1.310000e-54 224.0
27 TraesCS1D01G250300 chrUn 100.000 50 0 0 3439 3488 229499359 229499408 3.860000e-15 93.5
28 TraesCS1D01G250300 chrUn 100.000 50 0 0 3439 3488 233527627 233527578 3.860000e-15 93.5
29 TraesCS1D01G250300 chr4D 100.000 50 0 0 3439 3488 123686240 123686289 3.860000e-15 93.5
30 TraesCS1D01G250300 chr4B 100.000 50 0 0 3439 3488 23811607 23811558 3.860000e-15 93.5
31 TraesCS1D01G250300 chr4B 100.000 50 0 0 3439 3488 546985485 546985534 3.860000e-15 93.5


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 TraesCS1D01G250300 chr1D 342847803 342851436 3633 False 6711.000000 6711 100.0000 1 3634 1 chr1D.!!$F1 3633
1 TraesCS1D01G250300 chr1B 459812578 459815317 2739 False 4207.000000 4207 94.5860 1 2711 1 chr1B.!!$F1 2710
2 TraesCS1D01G250300 chr1A 442473358 442476558 3200 False 1477.333333 3681 90.5350 1 3018 3 chr1A.!!$F1 3017
3 TraesCS1D01G250300 chr2D 193400976 193401510 534 False 451.000000 654 97.4245 3051 3631 2 chr2D.!!$F3 580
4 TraesCS1D01G250300 chr7D 465908923 465909471 548 False 426.500000 627 94.8565 3035 3631 2 chr7D.!!$F1 596
5 TraesCS1D01G250300 chr3D 441134678 441135223 545 False 409.500000 595 94.2275 3038 3631 2 chr3D.!!$F2 593

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
144 145 1.002544 CACTGACACTTCCCTTCCTCC 59.997 57.143 0.00 0.0 0.00 4.30 F
459 466 2.654877 GCCATTTGCTGCTGCTGT 59.345 55.556 17.00 0.0 40.48 4.40 F
1544 1551 0.035317 GTACCCCGGTCCGTTTCTTT 59.965 55.000 11.06 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1529 0.036105 GAAACGGACCGGGGTACATT 60.036 55.0 20.0 0.0 0.0 2.71 R
1923 1946 0.248990 AAACACATGCACGCACCAAG 60.249 50.0 0.0 0.0 0.0 3.61 R
3001 3264 0.032813 TTACCTACTCCCTCCACCCG 60.033 60.0 0.0 0.0 0.0 5.28 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
51 52 5.765677 CGTCCATATGGTCTCTCTTTCTCTA 59.234 44.000 21.28 0.00 36.34 2.43
144 145 1.002544 CACTGACACTTCCCTTCCTCC 59.997 57.143 0.00 0.00 0.00 4.30
341 342 5.465390 TCATCAGGTAAAACAAGTGAAGTCG 59.535 40.000 0.00 0.00 0.00 4.18
459 466 2.654877 GCCATTTGCTGCTGCTGT 59.345 55.556 17.00 0.00 40.48 4.40
543 550 8.905702 CAGCTTGTACTTGTAAATGAAAATGAC 58.094 33.333 0.00 0.00 0.00 3.06
682 689 5.827797 TGTACTTTGCTCTTTTTGTCCTGAT 59.172 36.000 0.00 0.00 0.00 2.90
685 692 4.853924 TTGCTCTTTTTGTCCTGATTCC 57.146 40.909 0.00 0.00 0.00 3.01
689 696 4.520492 GCTCTTTTTGTCCTGATTCCTCAA 59.480 41.667 0.00 0.00 0.00 3.02
691 698 6.461509 GCTCTTTTTGTCCTGATTCCTCAAAA 60.462 38.462 0.00 0.00 36.60 2.44
692 699 7.416964 TCTTTTTGTCCTGATTCCTCAAAAA 57.583 32.000 11.60 11.60 41.97 1.94
1102 1109 6.327154 TGTGATCACTGAATTTCGTACGTAT 58.673 36.000 25.55 7.45 0.00 3.06
1227 1234 7.004555 TGCTACTTCTCCTTCACTCAAATAA 57.995 36.000 0.00 0.00 0.00 1.40
1313 1320 8.517062 AAAGACCTTCAGAAATTCCATATGAG 57.483 34.615 3.65 0.00 0.00 2.90
1423 1430 3.829601 CTCTCTTCTGTACTTGACCCTGT 59.170 47.826 0.00 0.00 0.00 4.00
1464 1471 6.470235 GCAGTGCATATTTACATGTTCTGTTC 59.530 38.462 11.09 0.00 39.39 3.18
1520 1527 6.057321 TGTTAAAATCGTAGGGGAGAATGT 57.943 37.500 0.00 0.00 0.00 2.71
1522 1529 4.837093 AAAATCGTAGGGGAGAATGTGA 57.163 40.909 0.00 0.00 0.00 3.58
1544 1551 0.035317 GTACCCCGGTCCGTTTCTTT 59.965 55.000 11.06 0.00 0.00 2.52
1556 1563 5.180492 GGTCCGTTTCTTTGTCATTGTATCA 59.820 40.000 0.00 0.00 0.00 2.15
1613 1620 0.539438 TCAACAGCCACCCCAATGTC 60.539 55.000 0.00 0.00 0.00 3.06
1708 1715 3.634504 AGCTGTATGATTTGGATTGGCA 58.365 40.909 0.00 0.00 0.00 4.92
1829 1837 3.435327 TGCTGTTGCTATTAAACCGACAG 59.565 43.478 12.77 12.77 41.67 3.51
1834 1842 5.178623 TGTTGCTATTAAACCGACAGAGTTG 59.821 40.000 0.00 0.00 0.00 3.16
1850 1858 7.096023 CGACAGAGTTGAGGTGCAAATATATAC 60.096 40.741 0.00 0.00 38.44 1.47
2057 2080 2.029844 GCTCGTCTCTGTGTTGGCC 61.030 63.158 0.00 0.00 0.00 5.36
2060 2083 0.396435 TCGTCTCTGTGTTGGCCAAT 59.604 50.000 23.66 0.00 0.00 3.16
2129 2152 3.572642 TGTTCACTCACAAGAGGAGGTA 58.427 45.455 0.00 0.00 46.44 3.08
2153 2178 3.014623 TCTTGCATGCAATCTTCTCAGG 58.985 45.455 31.96 17.36 35.20 3.86
2183 2223 5.106396 CCATCTTGTTGCCTAGAGTGAAAAG 60.106 44.000 0.00 0.00 0.00 2.27
2385 2429 1.736032 GCGACGACAATGTAAGCTCCT 60.736 52.381 0.00 0.00 0.00 3.69
2397 2441 1.356124 AAGCTCCTCGGCCATATCAT 58.644 50.000 2.24 0.00 0.00 2.45
2401 2445 2.544694 GCTCCTCGGCCATATCATATCG 60.545 54.545 2.24 0.00 0.00 2.92
2407 2451 5.438761 TCGGCCATATCATATCGTATCAG 57.561 43.478 2.24 0.00 0.00 2.90
2438 2668 0.837272 CATCGGGGTAAGTGGGTGAT 59.163 55.000 0.00 0.00 0.00 3.06
2664 2915 0.031994 CTGTTTTTGTTCCGGCAGGG 59.968 55.000 2.05 0.00 38.33 4.45
2677 2928 1.901464 GCAGGGCCTTCCGTTTTCA 60.901 57.895 1.32 0.00 41.52 2.69
2728 2982 4.016444 TGGAAGTTGTTCAGCTGTTTTCT 58.984 39.130 14.67 4.65 33.93 2.52
2730 2984 5.037385 GGAAGTTGTTCAGCTGTTTTCTTC 58.963 41.667 14.67 18.91 33.93 2.87
2734 2988 2.872245 TGTTCAGCTGTTTTCTTCCTCG 59.128 45.455 14.67 0.00 0.00 4.63
2755 3009 4.113354 CGAAGGTAGGTGTAGCATTCTTC 58.887 47.826 0.00 0.00 0.00 2.87
2760 3014 2.983229 AGGTGTAGCATTCTTCTGCAG 58.017 47.619 7.63 7.63 44.77 4.41
2761 3015 2.012673 GGTGTAGCATTCTTCTGCAGG 58.987 52.381 15.13 0.00 44.77 4.85
2763 3017 1.020437 GTAGCATTCTTCTGCAGGGC 58.980 55.000 15.13 8.40 44.77 5.19
2784 3038 5.961396 GCAGGAAGCAAATATCATGAGAT 57.039 39.130 0.09 0.00 44.79 2.75
2803 3057 8.581263 CATGAGATTGAATAAGTTTGCTTTTCG 58.419 33.333 0.00 0.00 36.22 3.46
2844 3098 9.952188 GCCCAGATAATAAAGTATTCAAAAGTC 57.048 33.333 0.00 0.00 0.00 3.01
2871 3125 5.786264 TTTTTGCGGGGTAAAGTATTCAA 57.214 34.783 0.00 0.00 0.00 2.69
2872 3126 5.786264 TTTTGCGGGGTAAAGTATTCAAA 57.214 34.783 0.00 0.00 0.00 2.69
2873 3127 5.786264 TTTGCGGGGTAAAGTATTCAAAA 57.214 34.783 0.00 0.00 0.00 2.44
2874 3128 5.379732 TTGCGGGGTAAAGTATTCAAAAG 57.620 39.130 0.00 0.00 0.00 2.27
2875 3129 4.400120 TGCGGGGTAAAGTATTCAAAAGT 58.600 39.130 0.00 0.00 0.00 2.66
2938 3196 5.824243 AAAACGACTTGTACAGATTCTCG 57.176 39.130 0.00 2.33 0.00 4.04
2961 3219 8.929260 TCGTCTACAGGTAAATATTATCTCCA 57.071 34.615 0.00 0.00 0.00 3.86
2966 3224 7.272144 ACAGGTAAATATTATCTCCATCCCC 57.728 40.000 0.00 0.00 0.00 4.81
2967 3225 7.031917 ACAGGTAAATATTATCTCCATCCCCT 58.968 38.462 0.00 0.00 0.00 4.79
2968 3226 7.521115 ACAGGTAAATATTATCTCCATCCCCTT 59.479 37.037 0.00 0.00 0.00 3.95
3009 3272 1.865865 CGGATGTAATTCGGGTGGAG 58.134 55.000 0.00 0.00 43.11 3.86
3011 3274 1.202770 GGATGTAATTCGGGTGGAGGG 60.203 57.143 0.00 0.00 0.00 4.30
3018 3281 1.807771 TTCGGGTGGAGGGAGTAGGT 61.808 60.000 0.00 0.00 0.00 3.08
3019 3282 0.920763 TCGGGTGGAGGGAGTAGGTA 60.921 60.000 0.00 0.00 0.00 3.08
3020 3283 0.032813 CGGGTGGAGGGAGTAGGTAA 60.033 60.000 0.00 0.00 0.00 2.85
3021 3284 1.412649 CGGGTGGAGGGAGTAGGTAAT 60.413 57.143 0.00 0.00 0.00 1.89
3022 3285 2.158415 CGGGTGGAGGGAGTAGGTAATA 60.158 54.545 0.00 0.00 0.00 0.98
3023 3286 3.508426 GGGTGGAGGGAGTAGGTAATAG 58.492 54.545 0.00 0.00 0.00 1.73
3024 3287 3.116823 GGGTGGAGGGAGTAGGTAATAGT 60.117 52.174 0.00 0.00 0.00 2.12
3025 3288 4.554683 GGTGGAGGGAGTAGGTAATAGTT 58.445 47.826 0.00 0.00 0.00 2.24
3026 3289 4.344390 GGTGGAGGGAGTAGGTAATAGTTG 59.656 50.000 0.00 0.00 0.00 3.16
3027 3290 4.961099 GTGGAGGGAGTAGGTAATAGTTGT 59.039 45.833 0.00 0.00 0.00 3.32
3028 3291 5.068855 GTGGAGGGAGTAGGTAATAGTTGTC 59.931 48.000 0.00 0.00 0.00 3.18
3029 3292 5.043582 TGGAGGGAGTAGGTAATAGTTGTCT 60.044 44.000 0.00 0.00 0.00 3.41
3030 3293 5.898397 GGAGGGAGTAGGTAATAGTTGTCTT 59.102 44.000 0.00 0.00 0.00 3.01
3031 3294 7.065504 GGAGGGAGTAGGTAATAGTTGTCTTA 58.934 42.308 0.00 0.00 0.00 2.10
3032 3295 7.231115 GGAGGGAGTAGGTAATAGTTGTCTTAG 59.769 44.444 0.00 0.00 0.00 2.18
3033 3296 7.880623 AGGGAGTAGGTAATAGTTGTCTTAGA 58.119 38.462 0.00 0.00 0.00 2.10
3367 3634 1.280998 AGTGTACATGGCAACTACCCC 59.719 52.381 0.00 0.00 37.61 4.95
3429 3700 2.355197 CCGAACATGTCAGTTGCCATA 58.645 47.619 0.00 0.00 0.00 2.74
3431 3702 3.378112 CCGAACATGTCAGTTGCCATATT 59.622 43.478 0.00 0.00 0.00 1.28
3434 3705 5.286797 CGAACATGTCAGTTGCCATATTTTG 59.713 40.000 0.00 0.00 0.00 2.44
3435 3706 4.497300 ACATGTCAGTTGCCATATTTTGC 58.503 39.130 0.00 0.00 0.00 3.68
3436 3707 4.021280 ACATGTCAGTTGCCATATTTTGCA 60.021 37.500 0.00 0.00 35.27 4.08
3438 3709 3.573538 TGTCAGTTGCCATATTTTGCAGT 59.426 39.130 0.00 0.00 38.95 4.40
3439 3710 4.168760 GTCAGTTGCCATATTTTGCAGTC 58.831 43.478 0.00 0.00 38.95 3.51
3440 3711 3.119884 TCAGTTGCCATATTTTGCAGTCG 60.120 43.478 0.00 0.00 38.95 4.18
3441 3712 3.081061 AGTTGCCATATTTTGCAGTCGA 58.919 40.909 0.00 0.00 38.95 4.20
3442 3713 3.505680 AGTTGCCATATTTTGCAGTCGAA 59.494 39.130 0.00 0.00 38.95 3.71
3443 3714 4.022416 AGTTGCCATATTTTGCAGTCGAAA 60.022 37.500 0.00 0.00 38.95 3.46
3444 3715 4.717233 TGCCATATTTTGCAGTCGAAAT 57.283 36.364 0.00 0.18 39.15 2.17
3445 3716 4.422840 TGCCATATTTTGCAGTCGAAATG 58.577 39.130 4.66 0.00 37.02 2.32
3446 3717 3.243643 GCCATATTTTGCAGTCGAAATGC 59.756 43.478 15.17 15.17 44.11 3.56
3447 3718 3.798337 CCATATTTTGCAGTCGAAATGCC 59.202 43.478 18.29 4.50 43.18 4.40
3448 3719 4.440525 CCATATTTTGCAGTCGAAATGCCT 60.441 41.667 18.29 6.16 43.18 4.75
3449 3720 2.704725 TTTTGCAGTCGAAATGCCTC 57.295 45.000 18.29 0.00 43.18 4.70
3450 3721 0.881118 TTTGCAGTCGAAATGCCTCC 59.119 50.000 18.29 0.00 43.18 4.30
3451 3722 0.036732 TTGCAGTCGAAATGCCTCCT 59.963 50.000 18.29 0.00 43.18 3.69
3452 3723 0.391661 TGCAGTCGAAATGCCTCCTC 60.392 55.000 18.29 0.00 43.18 3.71
3453 3724 1.092345 GCAGTCGAAATGCCTCCTCC 61.092 60.000 11.82 0.00 37.73 4.30
3454 3725 0.539051 CAGTCGAAATGCCTCCTCCT 59.461 55.000 0.00 0.00 0.00 3.69
3455 3726 0.827368 AGTCGAAATGCCTCCTCCTC 59.173 55.000 0.00 0.00 0.00 3.71
3456 3727 0.537188 GTCGAAATGCCTCCTCCTCA 59.463 55.000 0.00 0.00 0.00 3.86
3457 3728 1.066143 GTCGAAATGCCTCCTCCTCAA 60.066 52.381 0.00 0.00 0.00 3.02
3458 3729 1.628340 TCGAAATGCCTCCTCCTCAAA 59.372 47.619 0.00 0.00 0.00 2.69
3459 3730 2.039746 TCGAAATGCCTCCTCCTCAAAA 59.960 45.455 0.00 0.00 0.00 2.44
3460 3731 2.162408 CGAAATGCCTCCTCCTCAAAAC 59.838 50.000 0.00 0.00 0.00 2.43
3461 3732 2.222227 AATGCCTCCTCCTCAAAACC 57.778 50.000 0.00 0.00 0.00 3.27
3462 3733 1.376649 ATGCCTCCTCCTCAAAACCT 58.623 50.000 0.00 0.00 0.00 3.50
3463 3734 1.149101 TGCCTCCTCCTCAAAACCTT 58.851 50.000 0.00 0.00 0.00 3.50
3464 3735 2.344592 TGCCTCCTCCTCAAAACCTTA 58.655 47.619 0.00 0.00 0.00 2.69
3465 3736 2.714250 TGCCTCCTCCTCAAAACCTTAA 59.286 45.455 0.00 0.00 0.00 1.85
3466 3737 3.244911 TGCCTCCTCCTCAAAACCTTAAG 60.245 47.826 0.00 0.00 0.00 1.85
3467 3738 3.874193 GCCTCCTCCTCAAAACCTTAAGG 60.874 52.174 20.42 20.42 42.17 2.69
3468 3739 3.587506 CCTCCTCCTCAAAACCTTAAGGA 59.412 47.826 28.52 3.98 38.94 3.36
3471 3742 4.293662 CTCCTCAAAACCTTAAGGAGCT 57.706 45.455 28.52 8.98 46.10 4.09
3472 3743 4.006319 CTCCTCAAAACCTTAAGGAGCTG 58.994 47.826 28.52 18.97 46.10 4.24
3473 3744 2.489722 CCTCAAAACCTTAAGGAGCTGC 59.510 50.000 28.52 0.00 38.94 5.25
3474 3745 2.151202 TCAAAACCTTAAGGAGCTGCG 58.849 47.619 28.52 10.67 38.94 5.18
3475 3746 1.880027 CAAAACCTTAAGGAGCTGCGT 59.120 47.619 28.52 0.00 38.94 5.24
3476 3747 2.271944 AAACCTTAAGGAGCTGCGTT 57.728 45.000 28.52 6.98 38.94 4.84
3477 3748 1.809684 AACCTTAAGGAGCTGCGTTC 58.190 50.000 28.52 0.00 38.94 3.95
3478 3749 0.389948 ACCTTAAGGAGCTGCGTTCG 60.390 55.000 28.52 0.00 38.94 3.95
3479 3750 1.696832 CCTTAAGGAGCTGCGTTCGC 61.697 60.000 17.21 10.34 37.39 4.70
3480 3751 0.737715 CTTAAGGAGCTGCGTTCGCT 60.738 55.000 17.63 0.00 41.15 4.93
3481 3752 0.320421 TTAAGGAGCTGCGTTCGCTT 60.320 50.000 17.63 5.69 37.96 4.68
3482 3753 0.736325 TAAGGAGCTGCGTTCGCTTC 60.736 55.000 17.63 12.00 37.96 3.86
3483 3754 2.715532 AAGGAGCTGCGTTCGCTTCA 62.716 55.000 17.63 0.00 37.96 3.02
3484 3755 2.317609 GGAGCTGCGTTCGCTTCAA 61.318 57.895 17.63 0.00 37.96 2.69
3485 3756 1.131420 GAGCTGCGTTCGCTTCAAG 59.869 57.895 17.63 8.10 37.96 3.02
3486 3757 2.174349 GCTGCGTTCGCTTCAAGG 59.826 61.111 17.63 3.48 0.00 3.61
3487 3758 2.863153 CTGCGTTCGCTTCAAGGG 59.137 61.111 17.63 0.00 0.00 3.95
3540 3811 1.938625 GCAGATGGCAACTCTCTCTC 58.061 55.000 0.00 0.00 43.97 3.20
3548 3819 3.904339 TGGCAACTCTCTCTCTTTTACCT 59.096 43.478 0.00 0.00 37.61 3.08
3631 3903 2.963101 GGTGGCAACTCCTAAGGTTTTT 59.037 45.455 0.00 0.00 46.90 1.94
3632 3904 4.146564 GGTGGCAACTCCTAAGGTTTTTA 58.853 43.478 0.00 0.00 46.90 1.52
3633 3905 4.585581 GGTGGCAACTCCTAAGGTTTTTAA 59.414 41.667 0.00 0.00 46.90 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.635817 AACTGGGACTGCCAGTGTGT 61.636 55.000 21.95 4.85 46.24 3.72
144 145 1.127582 CCAGAGAGAAAAGAAAGCGCG 59.872 52.381 0.00 0.00 0.00 6.86
341 342 3.852536 CGAGAACCTCATCAACGAAGTAC 59.147 47.826 0.00 0.00 45.00 2.73
459 466 0.531657 AGCAGCAGCAACAACAACAA 59.468 45.000 3.17 0.00 45.49 2.83
543 550 0.798776 CAACAACCTAAGCAGGAGCG 59.201 55.000 0.00 0.00 45.91 5.03
638 645 2.739913 CACTAAGAAAATCGCGGGTGAA 59.260 45.455 6.13 0.00 0.00 3.18
694 701 4.794278 ACAACAACCGGAAAGAGTTTTT 57.206 36.364 9.46 0.00 0.00 1.94
695 702 5.677852 GCTTACAACAACCGGAAAGAGTTTT 60.678 40.000 9.46 0.94 0.00 2.43
696 703 4.201980 GCTTACAACAACCGGAAAGAGTTT 60.202 41.667 9.46 0.00 0.00 2.66
708 715 4.728608 CGAACACTTTCTGCTTACAACAAC 59.271 41.667 0.00 0.00 0.00 3.32
796 803 3.658725 AGGGACTACTAGTGCAATGGAT 58.341 45.455 3.97 0.00 38.40 3.41
797 804 3.116096 AGGGACTACTAGTGCAATGGA 57.884 47.619 3.97 0.00 38.40 3.41
798 805 3.914426 AAGGGACTACTAGTGCAATGG 57.086 47.619 5.39 0.00 38.49 3.16
814 821 9.657419 AATGTTTATTTCTAGCAAATGAAAGGG 57.343 29.630 9.20 0.00 35.93 3.95
1102 1109 7.772166 AGATGAGTACACGATCTGAAAATACA 58.228 34.615 0.00 0.00 0.00 2.29
1398 1405 2.416162 GGTCAAGTACAGAAGAGAGGCG 60.416 54.545 0.00 0.00 0.00 5.52
1459 1466 7.065085 TCAGAAAGAGTCAAAAACAGAGAACAG 59.935 37.037 0.00 0.00 0.00 3.16
1464 1471 6.484643 TGGATCAGAAAGAGTCAAAAACAGAG 59.515 38.462 0.00 0.00 0.00 3.35
1520 1527 1.193462 AACGGACCGGGGTACATTCA 61.193 55.000 20.00 0.00 0.00 2.57
1522 1529 0.036105 GAAACGGACCGGGGTACATT 60.036 55.000 20.00 0.00 0.00 2.71
1544 1551 7.393841 TGATCTTTGCATTGATACAATGACA 57.606 32.000 22.93 17.55 34.14 3.58
1556 1563 1.822990 CCACTGCCTGATCTTTGCATT 59.177 47.619 5.13 0.00 33.97 3.56
1613 1620 5.638783 GAGAAGATTTCACCATTTGAGCTG 58.361 41.667 0.00 0.00 34.94 4.24
1708 1715 3.205395 TTTTTGCTGCGCTGGTGT 58.795 50.000 16.47 0.00 0.00 4.16
1850 1858 8.539770 AATACTTCTGTTCGGCAATCTATATG 57.460 34.615 0.00 0.00 0.00 1.78
1910 1933 2.159627 CGCACCAAGTCATAAACTCCAC 59.840 50.000 0.00 0.00 37.17 4.02
1911 1934 2.224426 ACGCACCAAGTCATAAACTCCA 60.224 45.455 0.00 0.00 37.17 3.86
1923 1946 0.248990 AAACACATGCACGCACCAAG 60.249 50.000 0.00 0.00 0.00 3.61
2129 2152 4.077108 TGAGAAGATTGCATGCAAGAGTT 58.923 39.130 34.15 26.06 39.47 3.01
2135 2158 2.362736 GACCTGAGAAGATTGCATGCA 58.637 47.619 18.46 18.46 0.00 3.96
2153 2178 2.134789 AGGCAACAAGATGGATGGAC 57.865 50.000 0.00 0.00 41.41 4.02
2199 2239 1.324435 CTGCACACCACATAATCGACG 59.676 52.381 0.00 0.00 0.00 5.12
2385 2429 5.130350 TCTGATACGATATGATATGGCCGA 58.870 41.667 0.00 0.00 0.00 5.54
2397 2441 8.725148 CGATGGATGATATGATCTGATACGATA 58.275 37.037 2.06 0.00 0.00 2.92
2401 2445 6.453943 CCCGATGGATGATATGATCTGATAC 58.546 44.000 2.06 0.00 0.00 2.24
2407 2451 5.129485 ACTTACCCCGATGGATGATATGATC 59.871 44.000 0.00 0.00 38.00 2.92
2526 2756 1.374125 TGTGGATCTTGACGTGCCG 60.374 57.895 0.00 0.00 0.00 5.69
2664 2915 4.871513 AGAAAGAAATGAAAACGGAAGGC 58.128 39.130 0.00 0.00 0.00 4.35
2670 2921 5.687285 CAGTCCCAAGAAAGAAATGAAAACG 59.313 40.000 0.00 0.00 0.00 3.60
2677 2928 3.565307 TGTGCAGTCCCAAGAAAGAAAT 58.435 40.909 0.00 0.00 0.00 2.17
2728 2982 2.097825 GCTACACCTACCTTCGAGGAA 58.902 52.381 7.76 0.00 37.67 3.36
2730 2984 1.471119 TGCTACACCTACCTTCGAGG 58.529 55.000 0.03 0.03 42.49 4.63
2734 2988 5.112686 CAGAAGAATGCTACACCTACCTTC 58.887 45.833 0.00 0.00 0.00 3.46
2760 3014 3.225104 TCATGATATTTGCTTCCTGCCC 58.775 45.455 0.00 0.00 42.00 5.36
2761 3015 4.139786 TCTCATGATATTTGCTTCCTGCC 58.860 43.478 0.00 0.00 42.00 4.85
2763 3017 7.506328 TCAATCTCATGATATTTGCTTCCTG 57.494 36.000 3.69 0.00 31.70 3.86
2784 3038 7.535940 CGTTATCCGAAAAGCAAACTTATTCAA 59.464 33.333 0.00 0.00 39.56 2.69
2803 3057 1.068741 CTGGGCACTACTCCGTTATCC 59.931 57.143 0.00 0.00 0.00 2.59
2849 3103 5.786264 TTGAATACTTTACCCCGCAAAAA 57.214 34.783 0.00 0.00 0.00 1.94
2850 3104 5.786264 TTTGAATACTTTACCCCGCAAAA 57.214 34.783 0.00 0.00 0.00 2.44
2851 3105 5.302313 ACTTTTGAATACTTTACCCCGCAAA 59.698 36.000 0.00 0.00 0.00 3.68
2852 3106 4.828387 ACTTTTGAATACTTTACCCCGCAA 59.172 37.500 0.00 0.00 0.00 4.85
2853 3107 4.400120 ACTTTTGAATACTTTACCCCGCA 58.600 39.130 0.00 0.00 0.00 5.69
2854 3108 4.456566 TGACTTTTGAATACTTTACCCCGC 59.543 41.667 0.00 0.00 0.00 6.13
2855 3109 6.563222 TTGACTTTTGAATACTTTACCCCG 57.437 37.500 0.00 0.00 0.00 5.73
2856 3110 8.418662 AGTTTTGACTTTTGAATACTTTACCCC 58.581 33.333 0.00 0.00 0.00 4.95
2871 3125 9.533253 CCTGAAACAATCAATAGTTTTGACTTT 57.467 29.630 0.00 0.00 38.01 2.66
2872 3126 8.912988 TCCTGAAACAATCAATAGTTTTGACTT 58.087 29.630 0.00 0.00 38.01 3.01
2873 3127 8.463930 TCCTGAAACAATCAATAGTTTTGACT 57.536 30.769 0.00 0.00 38.01 3.41
2874 3128 9.696917 ATTCCTGAAACAATCAATAGTTTTGAC 57.303 29.630 0.00 0.00 38.01 3.18
2875 3129 9.695526 CATTCCTGAAACAATCAATAGTTTTGA 57.304 29.630 0.00 0.00 38.01 2.69
2920 3178 4.343811 AGACGAGAATCTGTACAAGTCG 57.656 45.455 0.00 3.96 33.15 4.18
2927 3185 7.876936 ATTTACCTGTAGACGAGAATCTGTA 57.123 36.000 0.00 0.00 0.00 2.74
2956 3214 9.332713 ACAAATTTTAATAAAAGGGGATGGAGA 57.667 29.630 4.43 0.00 33.22 3.71
2976 3234 9.193133 CGAATTACATCCGTATCTAGACAAATT 57.807 33.333 0.00 0.00 0.00 1.82
3001 3264 0.032813 TTACCTACTCCCTCCACCCG 60.033 60.000 0.00 0.00 0.00 5.28
3009 3272 8.709272 ATCTAAGACAACTATTACCTACTCCC 57.291 38.462 0.00 0.00 0.00 4.30
3021 3284 9.754382 AGTGTTTTCGTAAATCTAAGACAACTA 57.246 29.630 0.00 0.00 31.44 2.24
3022 3285 8.658499 AGTGTTTTCGTAAATCTAAGACAACT 57.342 30.769 0.00 0.00 31.44 3.16
3025 3288 8.693504 CGTTAGTGTTTTCGTAAATCTAAGACA 58.306 33.333 11.91 0.00 30.70 3.41
3026 3289 7.681650 GCGTTAGTGTTTTCGTAAATCTAAGAC 59.318 37.037 11.91 6.90 30.70 3.01
3027 3290 7.148755 GGCGTTAGTGTTTTCGTAAATCTAAGA 60.149 37.037 11.91 0.00 30.70 2.10
3028 3291 6.952083 GGCGTTAGTGTTTTCGTAAATCTAAG 59.048 38.462 11.91 9.18 30.70 2.18
3029 3292 6.128580 GGGCGTTAGTGTTTTCGTAAATCTAA 60.129 38.462 9.31 9.31 0.00 2.10
3030 3293 5.348451 GGGCGTTAGTGTTTTCGTAAATCTA 59.652 40.000 0.00 0.00 0.00 1.98
3031 3294 4.152938 GGGCGTTAGTGTTTTCGTAAATCT 59.847 41.667 0.00 0.00 0.00 2.40
3032 3295 4.083908 TGGGCGTTAGTGTTTTCGTAAATC 60.084 41.667 0.00 0.00 0.00 2.17
3033 3296 3.814283 TGGGCGTTAGTGTTTTCGTAAAT 59.186 39.130 0.00 0.00 0.00 1.40
3037 3300 0.939419 GTGGGCGTTAGTGTTTTCGT 59.061 50.000 0.00 0.00 0.00 3.85
3139 3402 0.968901 CACCAGCCCAGTCCTACGTA 60.969 60.000 0.00 0.00 0.00 3.57
3429 3700 2.094545 GGAGGCATTTCGACTGCAAAAT 60.095 45.455 18.05 0.00 41.83 1.82
3431 3702 0.881118 GGAGGCATTTCGACTGCAAA 59.119 50.000 18.05 0.00 41.83 3.68
3434 3705 1.092345 GGAGGAGGCATTTCGACTGC 61.092 60.000 10.05 10.05 42.79 4.40
3435 3706 0.539051 AGGAGGAGGCATTTCGACTG 59.461 55.000 0.00 0.00 26.49 3.51
3436 3707 0.827368 GAGGAGGAGGCATTTCGACT 59.173 55.000 0.00 0.00 32.98 4.18
3438 3709 1.275666 TTGAGGAGGAGGCATTTCGA 58.724 50.000 0.00 0.00 0.00 3.71
3439 3710 2.113860 TTTGAGGAGGAGGCATTTCG 57.886 50.000 0.00 0.00 0.00 3.46
3440 3711 2.493675 GGTTTTGAGGAGGAGGCATTTC 59.506 50.000 0.00 0.00 0.00 2.17
3441 3712 2.110721 AGGTTTTGAGGAGGAGGCATTT 59.889 45.455 0.00 0.00 0.00 2.32
3442 3713 1.713078 AGGTTTTGAGGAGGAGGCATT 59.287 47.619 0.00 0.00 0.00 3.56
3443 3714 1.376649 AGGTTTTGAGGAGGAGGCAT 58.623 50.000 0.00 0.00 0.00 4.40
3444 3715 1.149101 AAGGTTTTGAGGAGGAGGCA 58.851 50.000 0.00 0.00 0.00 4.75
3445 3716 3.348119 CTTAAGGTTTTGAGGAGGAGGC 58.652 50.000 0.00 0.00 0.00 4.70
3446 3717 3.587506 TCCTTAAGGTTTTGAGGAGGAGG 59.412 47.826 21.04 0.00 42.37 4.30
3447 3718 4.910458 TCCTTAAGGTTTTGAGGAGGAG 57.090 45.455 21.04 0.00 42.37 3.69
3451 3722 3.810743 GCAGCTCCTTAAGGTTTTGAGGA 60.811 47.826 21.04 0.00 44.32 3.71
3452 3723 2.489722 GCAGCTCCTTAAGGTTTTGAGG 59.510 50.000 21.04 7.06 40.51 3.86
3453 3724 2.160417 CGCAGCTCCTTAAGGTTTTGAG 59.840 50.000 21.04 11.63 31.91 3.02
3454 3725 2.151202 CGCAGCTCCTTAAGGTTTTGA 58.849 47.619 21.04 0.34 31.91 2.69
3455 3726 1.880027 ACGCAGCTCCTTAAGGTTTTG 59.120 47.619 21.04 16.72 31.91 2.44
3456 3727 2.271944 ACGCAGCTCCTTAAGGTTTT 57.728 45.000 21.04 5.12 31.91 2.43
3457 3728 2.152016 GAACGCAGCTCCTTAAGGTTT 58.848 47.619 21.04 5.47 31.91 3.27
3458 3729 1.809684 GAACGCAGCTCCTTAAGGTT 58.190 50.000 21.04 6.20 31.91 3.50
3459 3730 0.389948 CGAACGCAGCTCCTTAAGGT 60.390 55.000 21.04 0.00 35.64 3.50
3460 3731 1.696832 GCGAACGCAGCTCCTTAAGG 61.697 60.000 15.98 15.98 41.49 2.69
3461 3732 0.737715 AGCGAACGCAGCTCCTTAAG 60.738 55.000 20.66 0.00 41.83 1.85
3462 3733 0.320421 AAGCGAACGCAGCTCCTTAA 60.320 50.000 20.66 0.00 45.31 1.85
3463 3734 0.736325 GAAGCGAACGCAGCTCCTTA 60.736 55.000 20.66 0.00 45.31 2.69
3464 3735 2.029844 GAAGCGAACGCAGCTCCTT 61.030 57.895 20.66 5.48 45.31 3.36
3465 3736 2.433318 GAAGCGAACGCAGCTCCT 60.433 61.111 20.66 0.00 45.31 3.69
3466 3737 2.233007 CTTGAAGCGAACGCAGCTCC 62.233 60.000 20.66 5.83 45.31 4.70
3467 3738 1.131420 CTTGAAGCGAACGCAGCTC 59.869 57.895 20.66 13.66 45.31 4.09
3469 3740 2.174349 CCTTGAAGCGAACGCAGC 59.826 61.111 20.66 12.15 44.88 5.25
3470 3741 2.680913 CCCCTTGAAGCGAACGCAG 61.681 63.158 20.66 9.25 44.88 5.18
3471 3742 2.668212 CCCCTTGAAGCGAACGCA 60.668 61.111 20.66 0.00 44.88 5.24
3472 3743 3.431725 CCCCCTTGAAGCGAACGC 61.432 66.667 11.31 11.31 42.33 4.84
3486 3757 2.359478 CAGTTGCCGTGTACCCCC 60.359 66.667 0.00 0.00 0.00 5.40
3487 3758 3.053896 GCAGTTGCCGTGTACCCC 61.054 66.667 0.00 0.00 34.31 4.95
3540 3811 7.064490 AGCAAAAACAACATGTTCAGGTAAAAG 59.936 33.333 8.48 0.00 40.14 2.27
3548 3819 6.804677 AGACATAGCAAAAACAACATGTTCA 58.195 32.000 8.48 0.00 40.14 3.18


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

AutoCloner maintained by Alex Coulton.