Multiple sequence alignment - TraesCS3A01G392400

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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 TraesCS3A01G392400 chr3A 100.000 3560 0 0 1 3560 640362343 640365902 0.000000e+00 6575.0
1 TraesCS3A01G392400 chr3A 90.165 1576 142 8 1037 2605 640391385 640392954 0.000000e+00 2039.0
2 TraesCS3A01G392400 chr3A 89.797 1480 135 12 1138 2609 640497840 640499311 0.000000e+00 1882.0
3 TraesCS3A01G392400 chr3D 95.197 2644 77 13 862 3482 501062450 501059834 0.000000e+00 4133.0
4 TraesCS3A01G392400 chr3D 91.082 1581 123 12 1037 2608 501032258 501030687 0.000000e+00 2122.0
5 TraesCS3A01G392400 chr3D 91.552 580 49 0 247 826 41275027 41275606 0.000000e+00 800.0
6 TraesCS3A01G392400 chr3D 91.267 584 50 1 246 829 41368752 41369334 0.000000e+00 795.0
7 TraesCS3A01G392400 chr3D 92.527 281 20 1 1404 1684 549642850 549642571 5.540000e-108 401.0
8 TraesCS3A01G392400 chr3D 95.161 248 7 3 1 246 501062687 501062443 1.550000e-103 387.0
9 TraesCS3A01G392400 chr3D 87.975 316 26 6 1330 1633 501046513 501046828 2.610000e-96 363.0
10 TraesCS3A01G392400 chr3D 90.863 197 16 2 1515 1711 54395460 54395266 2.730000e-66 263.0
11 TraesCS3A01G392400 chr3D 100.000 60 0 0 3478 3537 523716067 523716126 1.040000e-20 111.0
12 TraesCS3A01G392400 chr3D 100.000 33 0 0 832 864 41275637 41275669 1.070000e-05 62.1
13 TraesCS3A01G392400 chr3D 100.000 31 0 0 1681 1711 549642586 549642556 1.380000e-04 58.4
14 TraesCS3A01G392400 chr3B 96.992 1729 43 4 881 2609 662528073 662526354 0.000000e+00 2896.0
15 TraesCS3A01G392400 chr3B 89.816 1689 129 23 889 2561 662479935 662478274 0.000000e+00 2126.0
16 TraesCS3A01G392400 chr3B 93.528 309 17 3 1403 1711 461747723 461748028 1.160000e-124 457.0
17 TraesCS3A01G392400 chr3B 89.459 351 32 4 3136 3482 662525484 662525135 4.220000e-119 438.0
18 TraesCS3A01G392400 chr3B 94.000 250 8 5 1 246 662528339 662528093 4.340000e-99 372.0
19 TraesCS3A01G392400 chr3B 79.515 371 43 14 2608 2957 662526319 662525961 2.140000e-57 233.0
20 TraesCS3A01G392400 chr3B 88.636 44 5 0 3080 3123 627198988 627199031 2.000000e-03 54.7
21 TraesCS3A01G392400 chr5B 91.126 586 51 1 245 829 529722950 529722365 0.000000e+00 793.0
22 TraesCS3A01G392400 chr4D 91.126 586 50 1 246 829 491554204 491554789 0.000000e+00 793.0
23 TraesCS3A01G392400 chr4D 98.333 60 1 0 3478 3537 450906190 450906131 4.860000e-19 106.0
24 TraesCS3A01G392400 chr2D 90.909 583 53 0 247 829 585030990 585031572 0.000000e+00 784.0
25 TraesCS3A01G392400 chr2D 90.738 583 54 0 247 829 618825352 618825934 0.000000e+00 778.0
26 TraesCS3A01G392400 chr2D 100.000 60 0 0 3478 3537 200932580 200932639 1.040000e-20 111.0
27 TraesCS3A01G392400 chr2D 100.000 30 0 0 3094 3123 58842507 58842478 4.960000e-04 56.5
28 TraesCS3A01G392400 chr6B 90.646 588 51 1 246 829 333707355 333706768 0.000000e+00 778.0
29 TraesCS3A01G392400 chr6B 89.130 138 14 1 677 814 572181951 572181815 1.700000e-38 171.0
30 TraesCS3A01G392400 chr7D 90.355 591 54 3 240 829 242800049 242800637 0.000000e+00 773.0
31 TraesCS3A01G392400 chr7D 100.000 60 0 0 3478 3537 307120600 307120541 1.040000e-20 111.0
32 TraesCS3A01G392400 chr7D 96.970 33 1 0 3091 3123 611766130 611766162 4.960000e-04 56.5
33 TraesCS3A01G392400 chr6A 90.476 588 52 1 243 826 379712645 379713232 0.000000e+00 773.0
34 TraesCS3A01G392400 chr6A 100.000 58 0 0 3478 3535 64687903 64687960 1.350000e-19 108.0
35 TraesCS3A01G392400 chr6A 96.970 33 1 0 3091 3123 509559410 509559442 4.960000e-04 56.5
36 TraesCS3A01G392400 chr5D 93.515 293 18 1 1419 1711 47629229 47629520 5.460000e-118 435.0
37 TraesCS3A01G392400 chr5D 91.964 112 8 1 703 814 482617585 482617695 4.760000e-34 156.0
38 TraesCS3A01G392400 chr5D 97.059 34 1 0 3090 3123 547799011 547799044 1.380000e-04 58.4
39 TraesCS3A01G392400 chr5D 96.970 33 1 0 3091 3123 547518573 547518605 4.960000e-04 56.5
40 TraesCS3A01G392400 chr1D 92.208 308 23 1 1404 1711 489787947 489788253 5.460000e-118 435.0
41 TraesCS3A01G392400 chr1D 100.000 60 0 0 3478 3537 185788930 185788871 1.040000e-20 111.0
42 TraesCS3A01G392400 chr4B 89.855 138 13 1 677 814 26330221 26330085 3.650000e-40 176.0
43 TraesCS3A01G392400 chr4B 90.698 43 3 1 3081 3123 42939396 42939355 4.960000e-04 56.5
44 TraesCS3A01G392400 chr4B 100.000 30 0 0 3094 3123 119340232 119340203 4.960000e-04 56.5
45 TraesCS3A01G392400 chr4B 100.000 30 0 0 3094 3123 579402825 579402796 4.960000e-04 56.5
46 TraesCS3A01G392400 chr1A 90.370 135 12 1 677 811 394291914 394291781 3.650000e-40 176.0
47 TraesCS3A01G392400 chr1A 98.333 60 1 0 3478 3537 94735019 94734960 4.860000e-19 106.0
48 TraesCS3A01G392400 chr6D 89.922 129 12 1 677 805 425729122 425728995 7.910000e-37 165.0
49 TraesCS3A01G392400 chr6D 98.333 60 1 0 3478 3537 102373001 102372942 4.860000e-19 106.0
50 TraesCS3A01G392400 chr6D 98.333 60 1 0 3478 3537 317938392 317938451 4.860000e-19 106.0
51 TraesCS3A01G392400 chr6D 95.000 60 3 0 3478 3537 153926204 153926263 1.050000e-15 95.3
52 TraesCS3A01G392400 chr2B 88.406 138 15 1 677 814 98582616 98582480 7.910000e-37 165.0
53 TraesCS3A01G392400 chr2B 86.957 138 17 1 677 814 152507177 152507041 1.710000e-33 154.0
54 TraesCS3A01G392400 chr4A 87.770 139 15 2 676 814 485409936 485409800 1.020000e-35 161.0
55 TraesCS3A01G392400 chr4A 100.000 59 0 0 3478 3536 275493042 275493100 3.760000e-20 110.0
56 TraesCS3A01G392400 chrUn 100.000 60 0 0 3478 3537 86468362 86468421 1.040000e-20 111.0
57 TraesCS3A01G392400 chrUn 100.000 60 0 0 3478 3537 189420191 189420250 1.040000e-20 111.0
58 TraesCS3A01G392400 chrUn 100.000 60 0 0 3478 3537 206772163 206772104 1.040000e-20 111.0
59 TraesCS3A01G392400 chr7A 100.000 60 0 0 3478 3537 60252728 60252669 1.040000e-20 111.0
60 TraesCS3A01G392400 chr7A 100.000 60 0 0 3478 3537 120867986 120868045 1.040000e-20 111.0


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 TraesCS3A01G392400 chr3A 640362343 640365902 3559 False 6575.00 6575 100.0000 1 3560 1 chr3A.!!$F1 3559
1 TraesCS3A01G392400 chr3A 640391385 640392954 1569 False 2039.00 2039 90.1650 1037 2605 1 chr3A.!!$F2 1568
2 TraesCS3A01G392400 chr3A 640497840 640499311 1471 False 1882.00 1882 89.7970 1138 2609 1 chr3A.!!$F3 1471
3 TraesCS3A01G392400 chr3D 501059834 501062687 2853 True 2260.00 4133 95.1790 1 3482 2 chr3D.!!$R3 3481
4 TraesCS3A01G392400 chr3D 501030687 501032258 1571 True 2122.00 2122 91.0820 1037 2608 1 chr3D.!!$R2 1571
5 TraesCS3A01G392400 chr3D 41368752 41369334 582 False 795.00 795 91.2670 246 829 1 chr3D.!!$F1 583
6 TraesCS3A01G392400 chr3D 41275027 41275669 642 False 431.05 800 95.7760 247 864 2 chr3D.!!$F4 617
7 TraesCS3A01G392400 chr3B 662478274 662479935 1661 True 2126.00 2126 89.8160 889 2561 1 chr3B.!!$R1 1672
8 TraesCS3A01G392400 chr3B 662525135 662528339 3204 True 984.75 2896 89.9915 1 3482 4 chr3B.!!$R2 3481
9 TraesCS3A01G392400 chr5B 529722365 529722950 585 True 793.00 793 91.1260 245 829 1 chr5B.!!$R1 584
10 TraesCS3A01G392400 chr4D 491554204 491554789 585 False 793.00 793 91.1260 246 829 1 chr4D.!!$F1 583
11 TraesCS3A01G392400 chr2D 585030990 585031572 582 False 784.00 784 90.9090 247 829 1 chr2D.!!$F2 582
12 TraesCS3A01G392400 chr2D 618825352 618825934 582 False 778.00 778 90.7380 247 829 1 chr2D.!!$F3 582
13 TraesCS3A01G392400 chr6B 333706768 333707355 587 True 778.00 778 90.6460 246 829 1 chr6B.!!$R1 583
14 TraesCS3A01G392400 chr7D 242800049 242800637 588 False 773.00 773 90.3550 240 829 1 chr7D.!!$F1 589
15 TraesCS3A01G392400 chr6A 379712645 379713232 587 False 773.00 773 90.4760 243 826 1 chr6A.!!$F2 583

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
290 297 0.315886 TCGCGAGCTAAACAAGTGGA 59.684 50.0 3.71 0.0 0.0 4.02 F
1059 1091 0.179156 GGCAATCACACCAAGATGCG 60.179 55.0 0.00 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2135 4.299547 AGCACCGAGTTGAGCGCA 62.300 61.111 11.47 0.0 0.00 6.09 R
2659 2734 1.226660 CCATTTGCCCGATGAACGC 60.227 57.895 0.00 0.0 41.07 4.84 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
138 145 2.993899 ACCTCGCAGAAATAAGAACACG 59.006 45.455 0.00 0.00 34.09 4.49
179 186 6.114187 AGACCTGATTGAGTTGTATGACAA 57.886 37.500 0.00 0.00 35.42 3.18
220 227 1.469940 CGGAACAGACGAGATCCCTTG 60.470 57.143 0.00 0.00 0.00 3.61
234 241 8.701895 ACGAGATCCCTTGTTAATCAACTAATA 58.298 33.333 0.00 0.00 33.22 0.98
235 242 9.542462 CGAGATCCCTTGTTAATCAACTAATAA 57.458 33.333 0.00 0.00 35.56 1.40
290 297 0.315886 TCGCGAGCTAAACAAGTGGA 59.684 50.000 3.71 0.00 0.00 4.02
414 421 4.324669 CGAGTACTCGTGTAACTCGTTAGA 59.675 45.833 32.24 0.00 46.99 2.10
428 435 4.164294 CTCGTTAGACTCGGTACAAAAGG 58.836 47.826 0.00 0.00 0.00 3.11
432 439 3.382048 AGACTCGGTACAAAAGGTCAC 57.618 47.619 0.00 0.00 0.00 3.67
452 459 1.002134 CAAGCACCCTTCGTCCCAT 60.002 57.895 0.00 0.00 0.00 4.00
478 485 3.743911 CACAACACAACGCCTAGATGTTA 59.256 43.478 0.00 0.00 33.30 2.41
547 554 8.458052 GTTGATCATTGTGGTCATGTACAATTA 58.542 33.333 17.05 12.68 43.00 1.40
561 568 9.241919 TCATGTACAATTATTTCTGGTCAATGT 57.758 29.630 0.00 0.00 0.00 2.71
625 636 7.900782 AAGTTAAACTCGTACATGCTTACAT 57.099 32.000 0.00 0.00 36.79 2.29
637 648 7.325821 CGTACATGCTTACATTTGTTTGTGAAT 59.674 33.333 0.00 0.00 32.87 2.57
775 791 4.608951 GAGTTATACGAGTCGAGCCAATT 58.391 43.478 21.50 4.27 0.00 2.32
844 860 2.507324 GAGTTGGCTCGACTCGGC 60.507 66.667 0.00 1.17 35.52 5.54
847 863 4.116328 TTGGCTCGACTCGGCTCG 62.116 66.667 10.47 0.00 34.83 5.03
849 865 3.812019 GGCTCGACTCGGCTCGAA 61.812 66.667 10.47 0.00 42.00 3.71
850 866 2.409651 GCTCGACTCGGCTCGAAT 59.590 61.111 0.00 0.00 42.00 3.34
851 867 1.226717 GCTCGACTCGGCTCGAATT 60.227 57.895 0.00 0.00 42.00 2.17
852 868 1.203600 GCTCGACTCGGCTCGAATTC 61.204 60.000 0.00 0.00 42.00 2.17
853 869 0.592754 CTCGACTCGGCTCGAATTCC 60.593 60.000 0.00 0.00 42.00 3.01
854 870 1.138883 CGACTCGGCTCGAATTCCA 59.861 57.895 0.00 0.00 34.74 3.53
855 871 0.867753 CGACTCGGCTCGAATTCCAG 60.868 60.000 0.00 0.00 34.74 3.86
856 872 1.148759 GACTCGGCTCGAATTCCAGC 61.149 60.000 15.86 15.86 34.74 4.85
884 908 1.820581 GTCGTATGCCACCCAGCTA 59.179 57.895 0.00 0.00 0.00 3.32
965 997 8.624776 GCCTTGCAACAAGATCTAATTAACTAT 58.375 33.333 8.87 0.00 0.00 2.12
994 1026 0.601046 AGTGCATCAGACACCACACG 60.601 55.000 0.00 0.00 38.87 4.49
1059 1091 0.179156 GGCAATCACACCAAGATGCG 60.179 55.000 0.00 0.00 0.00 4.73
1305 1337 0.538057 CCTGCAAGCAGAAGGTGGAA 60.538 55.000 22.76 0.00 46.30 3.53
2100 2135 4.070552 GTGAAGGAGAGCCGCGGT 62.071 66.667 28.70 13.92 39.96 5.68
2617 2692 2.687935 GGAACACTTTCACTTCTGGCAA 59.312 45.455 0.00 0.00 32.80 4.52
2635 2710 3.411351 GTGCCGCAGTGTACGTGG 61.411 66.667 0.00 0.00 37.08 4.94
2837 2933 1.404315 CCTGGACTACTTCTTCGCCAC 60.404 57.143 0.00 0.00 0.00 5.01
2841 2937 0.388649 ACTACTTCTTCGCCACGCTG 60.389 55.000 0.00 0.00 0.00 5.18
3054 3523 5.496133 AGTATATCGTTACACTTGTCGCT 57.504 39.130 0.00 0.00 0.00 4.93
3071 3540 6.249478 TGTCGCTGAACAAAATTTAAAACG 57.751 33.333 0.00 0.00 0.00 3.60
3072 3541 5.800941 TGTCGCTGAACAAAATTTAAAACGT 59.199 32.000 0.00 0.00 0.00 3.99
3073 3542 6.965500 TGTCGCTGAACAAAATTTAAAACGTA 59.035 30.769 0.00 0.00 0.00 3.57
3074 3543 7.164498 TGTCGCTGAACAAAATTTAAAACGTAG 59.836 33.333 0.00 0.00 0.00 3.51
3118 3587 9.595823 TTCCTTCCGTAAAGAAATATAAGAGTG 57.404 33.333 0.00 0.00 37.12 3.51
3119 3588 8.755977 TCCTTCCGTAAAGAAATATAAGAGTGT 58.244 33.333 0.00 0.00 37.12 3.55
3120 3589 9.379791 CCTTCCGTAAAGAAATATAAGAGTGTT 57.620 33.333 0.00 0.00 37.12 3.32
3134 3603 9.813446 ATATAAGAGTGTTTACTTTTACGGAGG 57.187 33.333 0.00 0.00 36.62 4.30
3137 3606 6.585416 AGAGTGTTTACTTTTACGGAGGAAA 58.415 36.000 0.00 0.00 37.25 3.13
3169 3638 9.016438 TGTTTTGTTAGTTAAACTGAAGACCTT 57.984 29.630 0.00 0.00 38.99 3.50
3176 3645 1.308998 AACTGAAGACCTTTGTGCCG 58.691 50.000 0.00 0.00 0.00 5.69
3217 3686 7.344612 TCAAGAGGGAGTAACTCATGCTATTTA 59.655 37.037 0.00 0.00 37.43 1.40
3234 3706 9.923143 ATGCTATTTATGTAACGCAATAGAGTA 57.077 29.630 0.00 0.00 32.92 2.59
3248 3720 6.693545 CGCAATAGAGTAAGAGTAGGAAACAG 59.306 42.308 0.00 0.00 0.00 3.16
3255 3727 1.079503 GAGTAGGAAACAGCGCCTTG 58.920 55.000 2.29 0.00 35.73 3.61
3264 3736 2.740055 AGCGCCTTGTCTTGCTCG 60.740 61.111 2.29 0.00 30.37 5.03
3467 3939 5.591099 ACAAAACTGAGCACAATCGAAAAT 58.409 33.333 0.00 0.00 0.00 1.82
3479 3951 6.530181 GCACAATCGAAAATTAGGGGTAAAAG 59.470 38.462 0.00 0.00 0.00 2.27
3482 3954 3.127376 TCGAAAATTAGGGGTAAAAGCGC 59.873 43.478 0.00 0.00 0.00 5.92
3483 3955 3.431856 GAAAATTAGGGGTAAAAGCGCG 58.568 45.455 0.00 0.00 33.51 6.86
3484 3956 0.736636 AATTAGGGGTAAAAGCGCGC 59.263 50.000 26.66 26.66 33.51 6.86
3485 3957 0.393267 ATTAGGGGTAAAAGCGCGCA 60.393 50.000 35.10 9.85 33.51 6.09
3486 3958 0.393267 TTAGGGGTAAAAGCGCGCAT 60.393 50.000 35.10 20.88 33.51 4.73
3487 3959 0.393267 TAGGGGTAAAAGCGCGCATT 60.393 50.000 35.10 26.27 33.51 3.56
3488 3960 1.226575 GGGGTAAAAGCGCGCATTC 60.227 57.895 35.10 16.40 0.00 2.67
3489 3961 1.582680 GGGTAAAAGCGCGCATTCG 60.583 57.895 35.10 0.00 39.07 3.34
3500 3972 3.313750 GCATTCGCGCTACCAGAG 58.686 61.111 5.56 0.00 0.00 3.35
3501 3973 1.226974 GCATTCGCGCTACCAGAGA 60.227 57.895 5.56 0.00 0.00 3.10
3502 3974 1.211818 GCATTCGCGCTACCAGAGAG 61.212 60.000 5.56 0.00 0.00 3.20
3503 3975 1.066587 ATTCGCGCTACCAGAGAGC 59.933 57.895 5.56 0.00 46.68 4.09
3509 3981 3.488048 GCTACCAGAGAGCGCATAG 57.512 57.895 11.47 0.53 0.00 2.23
3510 3982 0.955178 GCTACCAGAGAGCGCATAGA 59.045 55.000 11.47 0.00 0.00 1.98
3511 3983 1.068610 GCTACCAGAGAGCGCATAGAG 60.069 57.143 11.47 0.00 0.00 2.43
3512 3984 1.539388 CTACCAGAGAGCGCATAGAGG 59.461 57.143 11.47 8.53 0.00 3.69
3513 3985 1.112315 ACCAGAGAGCGCATAGAGGG 61.112 60.000 11.47 6.31 0.00 4.30
3514 3986 1.112315 CCAGAGAGCGCATAGAGGGT 61.112 60.000 11.47 0.00 0.00 4.34
3515 3987 0.749649 CAGAGAGCGCATAGAGGGTT 59.250 55.000 11.47 0.00 0.00 4.11
3516 3988 1.137872 CAGAGAGCGCATAGAGGGTTT 59.862 52.381 11.47 0.00 0.00 3.27
3517 3989 1.137872 AGAGAGCGCATAGAGGGTTTG 59.862 52.381 11.47 0.00 0.00 2.93
3518 3990 0.179000 AGAGCGCATAGAGGGTTTGG 59.821 55.000 11.47 0.00 0.00 3.28
3519 3991 0.178068 GAGCGCATAGAGGGTTTGGA 59.822 55.000 11.47 0.00 0.00 3.53
3520 3992 0.179000 AGCGCATAGAGGGTTTGGAG 59.821 55.000 11.47 0.00 0.00 3.86
3521 3993 0.815615 GCGCATAGAGGGTTTGGAGG 60.816 60.000 0.30 0.00 0.00 4.30
3522 3994 0.830648 CGCATAGAGGGTTTGGAGGA 59.169 55.000 0.00 0.00 0.00 3.71
3523 3995 1.202580 CGCATAGAGGGTTTGGAGGAG 60.203 57.143 0.00 0.00 0.00 3.69
3524 3996 2.119495 GCATAGAGGGTTTGGAGGAGA 58.881 52.381 0.00 0.00 0.00 3.71
3525 3997 2.103941 GCATAGAGGGTTTGGAGGAGAG 59.896 54.545 0.00 0.00 0.00 3.20
3526 3998 2.552093 TAGAGGGTTTGGAGGAGAGG 57.448 55.000 0.00 0.00 0.00 3.69
3527 3999 0.912006 AGAGGGTTTGGAGGAGAGGC 60.912 60.000 0.00 0.00 0.00 4.70
3528 4000 1.151810 AGGGTTTGGAGGAGAGGCA 60.152 57.895 0.00 0.00 0.00 4.75
3529 4001 1.204113 AGGGTTTGGAGGAGAGGCAG 61.204 60.000 0.00 0.00 0.00 4.85
3530 4002 1.301293 GGTTTGGAGGAGAGGCAGG 59.699 63.158 0.00 0.00 0.00 4.85
3531 4003 1.201429 GGTTTGGAGGAGAGGCAGGA 61.201 60.000 0.00 0.00 0.00 3.86
3532 4004 0.693049 GTTTGGAGGAGAGGCAGGAA 59.307 55.000 0.00 0.00 0.00 3.36
3533 4005 0.987294 TTTGGAGGAGAGGCAGGAAG 59.013 55.000 0.00 0.00 0.00 3.46
3534 4006 1.557269 TTGGAGGAGAGGCAGGAAGC 61.557 60.000 0.00 0.00 44.65 3.86
3543 4015 4.233408 GCAGGAAGCGCAAAACTG 57.767 55.556 11.47 13.38 0.00 3.16
3544 4016 1.654220 GCAGGAAGCGCAAAACTGA 59.346 52.632 20.49 0.00 0.00 3.41
3545 4017 0.242017 GCAGGAAGCGCAAAACTGAT 59.758 50.000 20.49 0.00 0.00 2.90
3546 4018 1.973138 CAGGAAGCGCAAAACTGATG 58.027 50.000 11.47 0.00 0.00 3.07
3547 4019 0.883833 AGGAAGCGCAAAACTGATGG 59.116 50.000 11.47 0.00 0.00 3.51
3548 4020 0.109132 GGAAGCGCAAAACTGATGGG 60.109 55.000 11.47 0.00 0.00 4.00
3549 4021 0.881118 GAAGCGCAAAACTGATGGGA 59.119 50.000 11.47 0.00 32.93 4.37
3550 4022 1.269448 GAAGCGCAAAACTGATGGGAA 59.731 47.619 11.47 0.00 32.93 3.97
3551 4023 0.598065 AGCGCAAAACTGATGGGAAC 59.402 50.000 11.47 0.00 32.93 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 186 9.836076 GTTCCGCTAATAAACTAAAAATGTCTT 57.164 29.630 0.00 0.00 0.00 3.01
241 248 3.948735 TTTTTCCAGCCCTAGACGG 57.051 52.632 0.00 0.00 0.00 4.79
284 291 1.215647 GCCGAGTCACGATCCACTT 59.784 57.895 0.00 0.00 45.77 3.16
288 295 1.989966 TTCGAGCCGAGTCACGATCC 61.990 60.000 0.00 0.00 45.77 3.36
290 297 0.029567 GATTCGAGCCGAGTCACGAT 59.970 55.000 12.77 0.00 45.77 3.73
324 331 4.202245 AGCTTGGCTCGACTTGTTATTA 57.798 40.909 0.00 0.00 30.62 0.98
331 338 6.430000 TCTTAAATTAAAGCTTGGCTCGACTT 59.570 34.615 0.00 0.00 38.25 3.01
414 421 2.538512 GGTGACCTTTTGTACCGAGT 57.461 50.000 0.00 0.00 0.00 4.18
428 435 1.966451 CGAAGGGTGCTTGGGTGAC 60.966 63.158 0.00 0.00 0.00 3.67
432 439 2.359975 GGACGAAGGGTGCTTGGG 60.360 66.667 0.00 0.00 33.58 4.12
478 485 9.054922 CATGACCAAACAATTGTAATTTCCTTT 57.945 29.630 12.39 0.00 34.60 3.11
547 554 7.363181 CCATGTACATGAACATTGACCAGAAAT 60.363 37.037 32.72 0.00 41.20 2.17
551 558 4.701651 ACCATGTACATGAACATTGACCAG 59.298 41.667 32.72 15.83 41.20 4.00
561 568 6.353404 TCAAGTCAGTACCATGTACATGAA 57.647 37.500 32.72 19.33 41.20 2.57
775 791 7.009815 CGTTACTATAACGAGCTTGAATCCAAA 59.990 37.037 14.37 0.00 45.64 3.28
829 845 2.507324 GAGCCGAGTCGAGCCAAC 60.507 66.667 15.64 6.85 0.00 3.77
830 846 4.116328 CGAGCCGAGTCGAGCCAA 62.116 66.667 15.64 0.00 42.85 4.52
836 852 0.867753 CTGGAATTCGAGCCGAGTCG 60.868 60.000 5.29 5.29 41.51 4.18
837 853 1.148759 GCTGGAATTCGAGCCGAGTC 61.149 60.000 26.80 3.39 41.09 3.36
838 854 1.153549 GCTGGAATTCGAGCCGAGT 60.154 57.895 26.80 0.00 41.09 4.18
839 855 3.711348 GCTGGAATTCGAGCCGAG 58.289 61.111 26.80 0.63 41.09 4.63
843 859 1.876156 CATTAGGGCTGGAATTCGAGC 59.124 52.381 28.50 28.50 45.32 5.03
844 860 1.876156 GCATTAGGGCTGGAATTCGAG 59.124 52.381 12.73 12.73 0.00 4.04
847 863 0.954452 CGGCATTAGGGCTGGAATTC 59.046 55.000 0.00 0.00 40.61 2.17
848 864 0.258774 ACGGCATTAGGGCTGGAATT 59.741 50.000 0.00 0.00 44.55 2.17
849 865 0.179018 GACGGCATTAGGGCTGGAAT 60.179 55.000 0.00 0.00 44.55 3.01
850 866 1.223487 GACGGCATTAGGGCTGGAA 59.777 57.895 0.00 0.00 44.55 3.53
851 867 2.908015 GACGGCATTAGGGCTGGA 59.092 61.111 0.00 0.00 44.55 3.86
852 868 2.023414 TACGACGGCATTAGGGCTGG 62.023 60.000 0.00 0.00 44.55 4.85
853 869 0.033504 ATACGACGGCATTAGGGCTG 59.966 55.000 0.00 0.00 45.74 4.85
854 870 0.033504 CATACGACGGCATTAGGGCT 59.966 55.000 0.00 0.00 40.61 5.19
855 871 1.566018 GCATACGACGGCATTAGGGC 61.566 60.000 0.00 0.00 39.06 5.19
856 872 0.949105 GGCATACGACGGCATTAGGG 60.949 60.000 0.00 0.00 0.00 3.53
857 873 0.249699 TGGCATACGACGGCATTAGG 60.250 55.000 0.00 0.00 33.43 2.69
858 874 0.859232 GTGGCATACGACGGCATTAG 59.141 55.000 0.00 0.00 41.40 1.73
859 875 0.531090 GGTGGCATACGACGGCATTA 60.531 55.000 0.00 0.00 41.40 1.90
860 876 1.817941 GGTGGCATACGACGGCATT 60.818 57.895 0.00 0.00 41.40 3.56
884 908 9.760926 TCAATCTCAACCACTATATATAGAGCT 57.239 33.333 23.70 3.32 34.50 4.09
965 997 2.500098 GTCTGATGCACTGGGGTTAGTA 59.500 50.000 0.00 0.00 0.00 1.82
966 998 1.279271 GTCTGATGCACTGGGGTTAGT 59.721 52.381 0.00 0.00 0.00 2.24
967 999 1.278985 TGTCTGATGCACTGGGGTTAG 59.721 52.381 0.00 0.00 0.00 2.34
968 1000 1.003118 GTGTCTGATGCACTGGGGTTA 59.997 52.381 0.00 0.00 34.30 2.85
969 1001 0.250901 GTGTCTGATGCACTGGGGTT 60.251 55.000 0.00 0.00 34.30 4.11
994 1026 1.413008 GGCAACATCGGCATTTTCGC 61.413 55.000 0.00 0.00 0.00 4.70
1059 1091 2.695359 TGGTTAGTGCAAATCGAGGAC 58.305 47.619 0.00 0.00 0.00 3.85
2100 2135 4.299547 AGCACCGAGTTGAGCGCA 62.300 61.111 11.47 0.00 0.00 6.09
2617 2692 2.355837 CACGTACACTGCGGCACT 60.356 61.111 0.00 0.00 0.00 4.40
2659 2734 1.226660 CCATTTGCCCGATGAACGC 60.227 57.895 0.00 0.00 41.07 4.84
2870 2966 2.267351 TTGTGCCACCATGCGAAGG 61.267 57.895 0.00 0.00 0.00 3.46
3046 3515 6.833880 CGTTTTAAATTTTGTTCAGCGACAAG 59.166 34.615 0.00 0.00 40.33 3.16
3092 3561 9.595823 CACTCTTATATTTCTTTACGGAAGGAA 57.404 33.333 0.00 0.00 37.26 3.36
3094 3563 8.943909 ACACTCTTATATTTCTTTACGGAAGG 57.056 34.615 1.66 0.00 35.98 3.46
3128 3597 9.457436 ACTAACAAAACATAATATTTCCTCCGT 57.543 29.630 0.00 0.00 0.00 4.69
3169 3638 1.173043 GGAATGTTCATCCGGCACAA 58.827 50.000 0.00 0.00 0.00 3.33
3176 3645 3.944015 CCTCTTGACAGGAATGTTCATCC 59.056 47.826 0.00 0.00 35.20 3.51
3217 3686 7.501559 TCCTACTCTTACTCTATTGCGTTACAT 59.498 37.037 0.00 0.00 0.00 2.29
3234 3706 0.977395 AGGCGCTGTTTCCTACTCTT 59.023 50.000 7.64 0.00 0.00 2.85
3248 3720 1.841663 TTTCGAGCAAGACAAGGCGC 61.842 55.000 0.00 0.00 34.54 6.53
3264 3736 4.801516 GGAGTAGAGTTGCTTCGAGATTTC 59.198 45.833 0.00 0.00 0.00 2.17
3355 3827 1.745087 ACTATGATTGCGCCAAGTTGG 59.255 47.619 18.17 18.17 41.55 3.77
3467 3939 0.393267 ATGCGCGCTTTTACCCCTAA 60.393 50.000 33.29 7.30 0.00 2.69
3483 3955 1.211818 CTCTCTGGTAGCGCGAATGC 61.212 60.000 12.10 0.00 37.91 3.56
3484 3956 1.211818 GCTCTCTGGTAGCGCGAATG 61.212 60.000 12.10 0.00 0.00 2.67
3485 3957 1.066587 GCTCTCTGGTAGCGCGAAT 59.933 57.895 12.10 0.00 0.00 3.34
3486 3958 2.490217 GCTCTCTGGTAGCGCGAA 59.510 61.111 12.10 0.00 0.00 4.70
3491 3963 0.955178 TCTATGCGCTCTCTGGTAGC 59.045 55.000 9.73 0.00 36.60 3.58
3492 3964 1.539388 CCTCTATGCGCTCTCTGGTAG 59.461 57.143 9.73 0.09 0.00 3.18
3493 3965 1.610363 CCTCTATGCGCTCTCTGGTA 58.390 55.000 9.73 0.00 0.00 3.25
3494 3966 1.112315 CCCTCTATGCGCTCTCTGGT 61.112 60.000 9.73 0.00 0.00 4.00
3495 3967 1.112315 ACCCTCTATGCGCTCTCTGG 61.112 60.000 9.73 5.63 0.00 3.86
3496 3968 0.749649 AACCCTCTATGCGCTCTCTG 59.250 55.000 9.73 0.00 0.00 3.35
3497 3969 1.137872 CAAACCCTCTATGCGCTCTCT 59.862 52.381 9.73 0.00 0.00 3.10
3498 3970 1.576356 CAAACCCTCTATGCGCTCTC 58.424 55.000 9.73 0.00 0.00 3.20
3499 3971 0.179000 CCAAACCCTCTATGCGCTCT 59.821 55.000 9.73 0.00 0.00 4.09
3500 3972 0.178068 TCCAAACCCTCTATGCGCTC 59.822 55.000 9.73 0.00 0.00 5.03
3501 3973 0.179000 CTCCAAACCCTCTATGCGCT 59.821 55.000 9.73 0.00 0.00 5.92
3502 3974 0.815615 CCTCCAAACCCTCTATGCGC 60.816 60.000 0.00 0.00 0.00 6.09
3503 3975 0.830648 TCCTCCAAACCCTCTATGCG 59.169 55.000 0.00 0.00 0.00 4.73
3504 3976 2.103941 CTCTCCTCCAAACCCTCTATGC 59.896 54.545 0.00 0.00 0.00 3.14
3505 3977 2.703007 CCTCTCCTCCAAACCCTCTATG 59.297 54.545 0.00 0.00 0.00 2.23
3506 3978 2.961977 GCCTCTCCTCCAAACCCTCTAT 60.962 54.545 0.00 0.00 0.00 1.98
3507 3979 1.622725 GCCTCTCCTCCAAACCCTCTA 60.623 57.143 0.00 0.00 0.00 2.43
3508 3980 0.912006 GCCTCTCCTCCAAACCCTCT 60.912 60.000 0.00 0.00 0.00 3.69
3509 3981 1.201429 TGCCTCTCCTCCAAACCCTC 61.201 60.000 0.00 0.00 0.00 4.30
3510 3982 1.151810 TGCCTCTCCTCCAAACCCT 60.152 57.895 0.00 0.00 0.00 4.34
3511 3983 1.301293 CTGCCTCTCCTCCAAACCC 59.699 63.158 0.00 0.00 0.00 4.11
3512 3984 1.201429 TCCTGCCTCTCCTCCAAACC 61.201 60.000 0.00 0.00 0.00 3.27
3513 3985 0.693049 TTCCTGCCTCTCCTCCAAAC 59.307 55.000 0.00 0.00 0.00 2.93
3514 3986 0.987294 CTTCCTGCCTCTCCTCCAAA 59.013 55.000 0.00 0.00 0.00 3.28
3515 3987 1.557269 GCTTCCTGCCTCTCCTCCAA 61.557 60.000 0.00 0.00 35.15 3.53
3516 3988 1.992277 GCTTCCTGCCTCTCCTCCA 60.992 63.158 0.00 0.00 35.15 3.86
3517 3989 2.907236 GCTTCCTGCCTCTCCTCC 59.093 66.667 0.00 0.00 35.15 4.30
3518 3990 2.498726 CGCTTCCTGCCTCTCCTC 59.501 66.667 0.00 0.00 38.78 3.71
3519 3991 3.780173 GCGCTTCCTGCCTCTCCT 61.780 66.667 0.00 0.00 38.78 3.69
3520 3992 3.612247 TTGCGCTTCCTGCCTCTCC 62.612 63.158 9.73 0.00 38.78 3.71
3521 3993 1.237285 TTTTGCGCTTCCTGCCTCTC 61.237 55.000 9.73 0.00 38.78 3.20
3522 3994 1.228245 TTTTGCGCTTCCTGCCTCT 60.228 52.632 9.73 0.00 38.78 3.69
3523 3995 1.081175 GTTTTGCGCTTCCTGCCTC 60.081 57.895 9.73 0.00 38.78 4.70
3524 3996 1.529244 AGTTTTGCGCTTCCTGCCT 60.529 52.632 9.73 0.00 38.78 4.75
3525 3997 1.372128 CAGTTTTGCGCTTCCTGCC 60.372 57.895 9.73 0.00 38.78 4.85
3526 3998 0.242017 ATCAGTTTTGCGCTTCCTGC 59.758 50.000 9.73 0.00 38.57 4.85
3527 3999 1.401931 CCATCAGTTTTGCGCTTCCTG 60.402 52.381 9.73 9.65 0.00 3.86
3528 4000 0.883833 CCATCAGTTTTGCGCTTCCT 59.116 50.000 9.73 0.00 0.00 3.36
3529 4001 0.109132 CCCATCAGTTTTGCGCTTCC 60.109 55.000 9.73 0.00 0.00 3.46
3530 4002 0.881118 TCCCATCAGTTTTGCGCTTC 59.119 50.000 9.73 0.00 0.00 3.86
3531 4003 1.000274 GTTCCCATCAGTTTTGCGCTT 60.000 47.619 9.73 0.00 0.00 4.68
3532 4004 0.598065 GTTCCCATCAGTTTTGCGCT 59.402 50.000 9.73 0.00 0.00 5.92
3533 4005 0.388520 GGTTCCCATCAGTTTTGCGC 60.389 55.000 0.00 0.00 0.00 6.09
3534 4006 0.958091 TGGTTCCCATCAGTTTTGCG 59.042 50.000 0.00 0.00 0.00 4.85
3535 4007 2.365293 AGTTGGTTCCCATCAGTTTTGC 59.635 45.455 0.00 0.00 31.53 3.68
3536 4008 5.782893 TTAGTTGGTTCCCATCAGTTTTG 57.217 39.130 0.00 0.00 31.53 2.44


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

AutoCloner maintained by Alex Coulton.