Multiple sequence alignment - TraesCS3B01G206000

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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 TraesCS3B01G206000 chr3B 100.000 4042 0 0 1 4042 240801219 240805260 0.000000e+00 7465.0
1 TraesCS3B01G206000 chr3B 71.759 1080 256 34 1137 2196 681006673 681007723 4.010000e-65 259.0
2 TraesCS3B01G206000 chr3B 97.802 91 2 0 3952 4042 335601750 335601840 1.500000e-34 158.0
3 TraesCS3B01G206000 chr3B 97.802 91 2 0 3952 4042 411018393 411018483 1.500000e-34 158.0
4 TraesCS3B01G206000 chr3B 95.745 94 4 0 3949 4042 601172470 601172563 7.000000e-33 152.0
5 TraesCS3B01G206000 chr3D 94.396 2891 107 8 87 2930 165584564 165587446 0.000000e+00 4390.0
6 TraesCS3B01G206000 chr3D 92.269 996 42 11 2928 3912 165587479 165588450 0.000000e+00 1380.0
7 TraesCS3B01G206000 chr3D 71.978 1092 263 30 1137 2211 516666974 516665909 8.550000e-72 281.0
8 TraesCS3B01G206000 chr3D 98.387 62 1 0 1 62 165584505 165584566 4.270000e-20 110.0
9 TraesCS3B01G206000 chr7D 89.551 1761 134 14 1198 2930 83163812 83162074 0.000000e+00 2187.0
10 TraesCS3B01G206000 chr7D 82.056 574 70 19 3368 3921 83100437 83099877 3.680000e-125 459.0
11 TraesCS3B01G206000 chr7D 83.133 415 38 9 2962 3376 83101056 83100674 2.310000e-92 350.0
12 TraesCS3B01G206000 chr7D 84.324 370 42 14 3567 3921 83347396 83347028 8.310000e-92 348.0
13 TraesCS3B01G206000 chr7D 80.711 197 30 4 3369 3565 83347754 83347566 3.260000e-31 147.0
14 TraesCS3B01G206000 chr3A 90.333 631 46 4 3306 3921 203413737 203414367 0.000000e+00 813.0
15 TraesCS3B01G206000 chr7A 81.469 572 74 21 3368 3921 85082829 85082272 1.330000e-119 440.0
16 TraesCS3B01G206000 chr7B 82.090 536 67 15 3404 3921 32476156 32475632 8.030000e-117 431.0
17 TraesCS3B01G206000 chr7B 89.706 68 7 0 3309 3376 32476481 32476414 2.000000e-13 87.9
18 TraesCS3B01G206000 chr6B 97.802 91 2 0 3952 4042 67590416 67590506 1.500000e-34 158.0
19 TraesCS3B01G206000 chr6B 97.802 91 2 0 3952 4042 522039413 522039503 1.500000e-34 158.0
20 TraesCS3B01G206000 chr5B 97.802 91 2 0 3952 4042 510944639 510944729 1.500000e-34 158.0
21 TraesCS3B01G206000 chr5B 96.739 92 3 0 3951 4042 121139848 121139939 1.950000e-33 154.0
22 TraesCS3B01G206000 chr4B 97.802 91 2 0 3952 4042 395959189 395959279 1.500000e-34 158.0
23 TraesCS3B01G206000 chrUn 96.703 91 3 0 3952 4042 56844799 56844889 7.000000e-33 152.0


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 TraesCS3B01G206000 chr3B 240801219 240805260 4041 False 7465.00 7465 100.000000 1 4042 1 chr3B.!!$F1 4041
1 TraesCS3B01G206000 chr3B 681006673 681007723 1050 False 259.00 259 71.759000 1137 2196 1 chr3B.!!$F5 1059
2 TraesCS3B01G206000 chr3D 165584505 165588450 3945 False 1960.00 4390 95.017333 1 3912 3 chr3D.!!$F1 3911
3 TraesCS3B01G206000 chr3D 516665909 516666974 1065 True 281.00 281 71.978000 1137 2211 1 chr3D.!!$R1 1074
4 TraesCS3B01G206000 chr7D 83162074 83163812 1738 True 2187.00 2187 89.551000 1198 2930 1 chr7D.!!$R1 1732
5 TraesCS3B01G206000 chr7D 83099877 83101056 1179 True 404.50 459 82.594500 2962 3921 2 chr7D.!!$R2 959
6 TraesCS3B01G206000 chr7D 83347028 83347754 726 True 247.50 348 82.517500 3369 3921 2 chr7D.!!$R3 552
7 TraesCS3B01G206000 chr3A 203413737 203414367 630 False 813.00 813 90.333000 3306 3921 1 chr3A.!!$F1 615
8 TraesCS3B01G206000 chr7A 85082272 85082829 557 True 440.00 440 81.469000 3368 3921 1 chr7A.!!$R1 553
9 TraesCS3B01G206000 chr7B 32475632 32476481 849 True 259.45 431 85.898000 3309 3921 2 chr7B.!!$R1 612

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
467 489 1.021390 GCACGAGTGGCATGCTACTT 61.021 55.000 33.61 18.99 37.88 2.24 F
1101 1148 0.171679 TGCATGCCGATTTGCTTCTG 59.828 50.000 16.68 0.00 39.60 3.02 F
1326 1373 1.147376 CAACCTTGACACGGGGACA 59.853 57.895 2.65 0.00 0.00 4.02 F
2095 2159 1.135689 GCTTTGTGCAATACCACCTCG 60.136 52.381 0.00 0.00 42.31 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1373 0.321653 GGAGCTTGACACGGACCAAT 60.322 55.000 0.0 0.0 0.00 3.16 R
2095 2159 2.488153 GTTCAGACCAATTGCCAGTACC 59.512 50.000 0.0 0.0 0.00 3.34 R
2504 2580 4.216902 CCACAAGAACAATCTCATCAAGCA 59.783 41.667 0.0 0.0 33.77 3.91 R
3940 4755 0.114560 TTATTTTTCCCACGCCCCCA 59.885 50.000 0.0 0.0 0.00 4.96 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
83 84 9.573133 CTTTCCAGATTTAATGTTATGTCAACC 57.427 33.333 0.00 0.00 0.00 3.77
84 85 7.315247 TCCAGATTTAATGTTATGTCAACCG 57.685 36.000 0.00 0.00 0.00 4.44
85 86 5.971202 CCAGATTTAATGTTATGTCAACCGC 59.029 40.000 0.00 0.00 0.00 5.68
86 87 6.183360 CCAGATTTAATGTTATGTCAACCGCT 60.183 38.462 0.00 0.00 0.00 5.52
87 88 7.250569 CAGATTTAATGTTATGTCAACCGCTT 58.749 34.615 0.00 0.00 0.00 4.68
88 89 8.394877 CAGATTTAATGTTATGTCAACCGCTTA 58.605 33.333 0.00 0.00 0.00 3.09
127 128 3.572255 TCACTTGGATTTTACCCTTGTGC 59.428 43.478 0.00 0.00 32.24 4.57
148 149 2.480419 CGATGAGGAGTGTTGTTTGACC 59.520 50.000 0.00 0.00 0.00 4.02
159 160 1.816074 TGTTTGACCCGATTAGCACC 58.184 50.000 0.00 0.00 0.00 5.01
194 195 5.277250 AGGGGAATGTTGGGTTTAATTAGG 58.723 41.667 0.00 0.00 0.00 2.69
274 275 1.367346 TGCACCCCTCTTTGGACATA 58.633 50.000 0.00 0.00 38.35 2.29
288 289 4.730949 TGGACATACCCTTTACTCTTCG 57.269 45.455 0.00 0.00 38.00 3.79
381 382 9.017509 ACATCATCAATGAAGATTTACACACTT 57.982 29.630 0.00 0.00 40.69 3.16
465 487 3.093278 GCACGAGTGGCATGCTAC 58.907 61.111 25.24 25.24 36.40 3.58
467 489 1.021390 GCACGAGTGGCATGCTACTT 61.021 55.000 33.61 18.99 37.88 2.24
479 501 1.579429 GCTACTTGCACAAACCCCG 59.421 57.895 0.00 0.00 42.31 5.73
484 506 3.723097 TTGCACAAACCCCGAGGCA 62.723 57.895 0.00 0.00 36.11 4.75
501 523 2.908351 AGGCAATTGCATCCTTTCCTTT 59.092 40.909 30.32 0.00 44.36 3.11
529 552 1.140312 ACCCCAAAGAGTGAGAGCAA 58.860 50.000 0.00 0.00 0.00 3.91
539 562 1.078214 TGAGAGCAATTGCCCTCCG 60.078 57.895 31.56 0.00 44.09 4.63
561 584 4.371231 CCCCTTCCCTCCCACCCT 62.371 72.222 0.00 0.00 0.00 4.34
592 615 4.537751 TCTCTCAGGACCGATCAAGTTAT 58.462 43.478 0.00 0.00 0.00 1.89
715 738 2.436173 ACATGGAAACCCTAGCTCTAGC 59.564 50.000 0.00 0.00 42.49 3.42
721 744 3.371285 GAAACCCTAGCTCTAGCGTTTTG 59.629 47.826 16.33 0.00 41.52 2.44
805 828 7.042797 ACATAATTTGGTTGGATGCATAGTC 57.957 36.000 0.00 0.00 0.00 2.59
807 830 5.999205 AATTTGGTTGGATGCATAGTCAA 57.001 34.783 0.00 2.19 0.00 3.18
928 951 8.937634 AATTTTATGTTGATTGCTTCTCCATC 57.062 30.769 0.00 0.00 0.00 3.51
933 956 2.621338 TGATTGCTTCTCCATCGTGAC 58.379 47.619 0.00 0.00 0.00 3.67
942 965 1.208052 CTCCATCGTGACAGGGTTCAT 59.792 52.381 0.00 0.00 0.00 2.57
951 974 4.613622 CGTGACAGGGTTCATGTGAATTTC 60.614 45.833 0.00 0.00 36.33 2.17
1032 1055 3.294493 GCTGCGTGCCCAAGGAAA 61.294 61.111 0.00 0.00 35.15 3.13
1066 1113 2.532843 TGGTGGTACCCTACAACTCTC 58.467 52.381 10.07 0.00 37.50 3.20
1071 1118 2.434702 GGTACCCTACAACTCTCCATGG 59.565 54.545 4.97 4.97 0.00 3.66
1101 1148 0.171679 TGCATGCCGATTTGCTTCTG 59.828 50.000 16.68 0.00 39.60 3.02
1110 1157 2.363683 GATTTGCTTCTGCTGGTAGCT 58.636 47.619 15.61 0.00 42.97 3.32
1115 1162 1.364626 CTTCTGCTGGTAGCTTGGCG 61.365 60.000 0.00 0.00 42.97 5.69
1216 1263 1.449601 GGTCGTGGCATCACCGATT 60.450 57.895 1.19 0.00 43.94 3.34
1326 1373 1.147376 CAACCTTGACACGGGGACA 59.853 57.895 2.65 0.00 0.00 4.02
1416 1469 1.208844 TCCAGAGGGACGAGGACTCT 61.209 60.000 0.00 0.00 42.00 3.24
2095 2159 1.135689 GCTTTGTGCAATACCACCTCG 60.136 52.381 0.00 0.00 42.31 4.63
2227 2303 9.685005 CTTGGTACGTAATTTCTTTTTATCTCG 57.315 33.333 0.00 0.00 0.00 4.04
2289 2365 5.810587 TCGTATCATCTTGTTTAGAAGCCAC 59.189 40.000 0.00 0.00 36.22 5.01
2432 2508 7.235399 ACAGTTTTCTCACAATTAATCCCCATT 59.765 33.333 0.00 0.00 0.00 3.16
2504 2580 6.058183 GTCATAATCACCCAATTCAGTAGCT 58.942 40.000 0.00 0.00 0.00 3.32
2508 2584 2.040278 TCACCCAATTCAGTAGCTGCTT 59.960 45.455 7.79 0.00 0.00 3.91
2509 2585 2.163010 CACCCAATTCAGTAGCTGCTTG 59.837 50.000 7.79 0.29 0.00 4.01
2598 2682 3.004734 GGATGCCCGGTTTCTTCATATTG 59.995 47.826 0.00 0.00 0.00 1.90
2755 2841 3.574284 TGGAACATGTGCTATTGTTGC 57.426 42.857 3.21 9.54 42.44 4.17
2758 2844 3.305950 GGAACATGTGCTATTGTTGCCAA 60.306 43.478 3.21 0.00 37.98 4.52
2814 2900 3.708451 ACTTGTGTGGGGGATAAATTCC 58.292 45.455 0.00 0.00 44.62 3.01
2826 2912 7.129660 TGGGGGATAAATTCCTGTAACTTATCA 59.870 37.037 0.00 0.00 44.75 2.15
2874 2971 0.512952 CTTCGACCAGAACAAAGCGG 59.487 55.000 0.00 0.00 34.66 5.52
2995 3127 9.764363 TTTGGTATAGATTGTATGATGTCTCAC 57.236 33.333 0.00 0.00 33.22 3.51
3017 3149 5.301805 CACCTGACACCTCCTTTTGTATTTT 59.698 40.000 0.00 0.00 0.00 1.82
3177 3310 1.234615 AACAACTCATTCCCGCGGTG 61.235 55.000 26.12 16.51 0.00 4.94
3184 3317 3.515316 ATTCCCGCGGTGCCTATCG 62.515 63.158 26.12 5.84 0.00 2.92
3324 3457 9.059260 TGATCATGAAGTGTATTATTGGACATG 57.941 33.333 0.00 0.00 35.46 3.21
3502 4125 1.005037 TCTAGTGGCAGCAACACCG 60.005 57.895 1.78 0.00 39.63 4.94
3513 4136 1.444119 GCAACACCGCAAGACAAGGA 61.444 55.000 0.00 0.00 43.02 3.36
3514 4137 0.588252 CAACACCGCAAGACAAGGAG 59.412 55.000 0.00 0.00 43.02 3.69
3532 4155 8.834004 ACAAGGAGGTACTATTCACTATGTTA 57.166 34.615 0.00 0.00 41.55 2.41
3632 4430 2.052782 AAAACAGTCAGGAACGCCTT 57.947 45.000 0.00 0.00 43.90 4.35
3652 4450 6.949352 CCTTACTTCAGGCATAATGACAAT 57.051 37.500 0.00 0.00 0.00 2.71
3676 4474 9.684448 AATAGTAATACTCATTGACGATCACAG 57.316 33.333 0.00 0.00 0.00 3.66
3683 4481 0.669318 TTGACGATCACAGCCGGAAC 60.669 55.000 5.05 0.00 0.00 3.62
3768 4577 5.757850 ACAACTCCACAAGATCTTTGAAC 57.242 39.130 4.86 0.00 0.00 3.18
3802 4612 3.858247 AGGAATAGACTTACGGCAACAC 58.142 45.455 0.00 0.00 0.00 3.32
3805 4615 4.270325 GGAATAGACTTACGGCAACACATC 59.730 45.833 0.00 0.00 0.00 3.06
3825 4635 7.281774 ACACATCACAAGATAGCTCAAATAAGG 59.718 37.037 0.00 0.00 31.88 2.69
3869 4679 4.903054 TCTCAAGCTCAACATTCATGTCT 58.097 39.130 0.00 0.00 40.80 3.41
3878 4692 9.890629 AGCTCAACATTCATGTCTAGTATTAAA 57.109 29.630 0.00 0.00 40.80 1.52
3921 4736 1.133025 CCCAAAATGCACTTCGCTAGG 59.867 52.381 0.00 0.00 43.06 3.02
3922 4737 1.812571 CCAAAATGCACTTCGCTAGGT 59.187 47.619 0.00 0.00 43.06 3.08
3923 4738 2.414559 CCAAAATGCACTTCGCTAGGTG 60.415 50.000 0.00 0.00 43.06 4.00
3924 4739 2.185004 AAATGCACTTCGCTAGGTGT 57.815 45.000 2.45 0.00 43.06 4.16
3925 4740 1.442769 AATGCACTTCGCTAGGTGTG 58.557 50.000 2.45 0.00 43.06 3.82
3926 4741 0.321671 ATGCACTTCGCTAGGTGTGT 59.678 50.000 2.45 0.00 43.06 3.72
3927 4742 0.599991 TGCACTTCGCTAGGTGTGTG 60.600 55.000 2.45 0.00 43.06 3.82
3928 4743 0.600255 GCACTTCGCTAGGTGTGTGT 60.600 55.000 2.45 0.00 37.77 3.72
3929 4744 1.139989 CACTTCGCTAGGTGTGTGTG 58.860 55.000 0.00 0.00 0.00 3.82
3930 4745 0.750850 ACTTCGCTAGGTGTGTGTGT 59.249 50.000 0.00 0.00 0.00 3.72
3931 4746 1.139989 CTTCGCTAGGTGTGTGTGTG 58.860 55.000 0.00 0.00 0.00 3.82
3932 4747 0.462375 TTCGCTAGGTGTGTGTGTGT 59.538 50.000 0.00 0.00 0.00 3.72
3933 4748 0.249280 TCGCTAGGTGTGTGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
3934 4749 1.221466 CGCTAGGTGTGTGTGTGTGG 61.221 60.000 0.00 0.00 0.00 4.17
3935 4750 0.884704 GCTAGGTGTGTGTGTGTGGG 60.885 60.000 0.00 0.00 0.00 4.61
3936 4751 0.468226 CTAGGTGTGTGTGTGTGGGT 59.532 55.000 0.00 0.00 0.00 4.51
3937 4752 0.179234 TAGGTGTGTGTGTGTGGGTG 59.821 55.000 0.00 0.00 0.00 4.61
3938 4753 1.377987 GGTGTGTGTGTGTGGGTGT 60.378 57.895 0.00 0.00 0.00 4.16
3939 4754 1.653094 GGTGTGTGTGTGTGGGTGTG 61.653 60.000 0.00 0.00 0.00 3.82
3940 4755 0.958382 GTGTGTGTGTGTGGGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
3941 4756 0.957888 TGTGTGTGTGTGGGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
3942 4757 1.377856 TGTGTGTGTGGGTGTGTGG 60.378 57.895 0.00 0.00 0.00 4.17
3943 4758 2.118404 GTGTGTGTGGGTGTGTGGG 61.118 63.158 0.00 0.00 0.00 4.61
3944 4759 2.518349 GTGTGTGGGTGTGTGGGG 60.518 66.667 0.00 0.00 0.00 4.96
3945 4760 3.814906 TGTGTGGGTGTGTGGGGG 61.815 66.667 0.00 0.00 0.00 5.40
3954 4769 4.589675 GTGTGGGGGCGTGGGAAA 62.590 66.667 0.00 0.00 0.00 3.13
3955 4770 3.822035 TGTGGGGGCGTGGGAAAA 61.822 61.111 0.00 0.00 0.00 2.29
3956 4771 2.522193 GTGGGGGCGTGGGAAAAA 60.522 61.111 0.00 0.00 0.00 1.94
3957 4772 1.911269 GTGGGGGCGTGGGAAAAAT 60.911 57.895 0.00 0.00 0.00 1.82
3958 4773 0.612453 GTGGGGGCGTGGGAAAAATA 60.612 55.000 0.00 0.00 0.00 1.40
3959 4774 0.114560 TGGGGGCGTGGGAAAAATAA 59.885 50.000 0.00 0.00 0.00 1.40
3960 4775 1.273324 TGGGGGCGTGGGAAAAATAAT 60.273 47.619 0.00 0.00 0.00 1.28
3961 4776 1.834896 GGGGGCGTGGGAAAAATAATT 59.165 47.619 0.00 0.00 0.00 1.40
3962 4777 2.237643 GGGGGCGTGGGAAAAATAATTT 59.762 45.455 0.00 0.00 0.00 1.82
3963 4778 3.451540 GGGGGCGTGGGAAAAATAATTTA 59.548 43.478 0.00 0.00 0.00 1.40
3964 4779 4.442332 GGGGGCGTGGGAAAAATAATTTAG 60.442 45.833 0.00 0.00 0.00 1.85
3965 4780 4.403113 GGGGCGTGGGAAAAATAATTTAGA 59.597 41.667 0.00 0.00 0.00 2.10
3966 4781 5.451381 GGGGCGTGGGAAAAATAATTTAGAG 60.451 44.000 0.00 0.00 0.00 2.43
3967 4782 5.451381 GGGCGTGGGAAAAATAATTTAGAGG 60.451 44.000 0.00 0.00 0.00 3.69
3968 4783 5.041287 GCGTGGGAAAAATAATTTAGAGGC 58.959 41.667 0.00 0.00 0.00 4.70
3969 4784 5.393678 GCGTGGGAAAAATAATTTAGAGGCA 60.394 40.000 0.00 0.00 0.00 4.75
3970 4785 6.033966 CGTGGGAAAAATAATTTAGAGGCAC 58.966 40.000 0.00 0.00 0.00 5.01
3971 4786 6.338146 GTGGGAAAAATAATTTAGAGGCACC 58.662 40.000 0.00 0.00 0.00 5.01
3972 4787 6.154534 GTGGGAAAAATAATTTAGAGGCACCT 59.845 38.462 0.00 0.00 0.00 4.00
3973 4788 7.340999 GTGGGAAAAATAATTTAGAGGCACCTA 59.659 37.037 0.00 0.00 0.00 3.08
3974 4789 7.559897 TGGGAAAAATAATTTAGAGGCACCTAG 59.440 37.037 0.00 0.00 0.00 3.02
3975 4790 7.560262 GGGAAAAATAATTTAGAGGCACCTAGT 59.440 37.037 0.00 0.00 0.00 2.57
3976 4791 8.967918 GGAAAAATAATTTAGAGGCACCTAGTT 58.032 33.333 0.00 0.00 0.00 2.24
3978 4793 9.755122 AAAAATAATTTAGAGGCACCTAGTTCT 57.245 29.630 0.00 0.00 0.00 3.01
3979 4794 9.755122 AAAATAATTTAGAGGCACCTAGTTCTT 57.245 29.630 0.00 0.00 0.00 2.52
3980 4795 8.966069 AATAATTTAGAGGCACCTAGTTCTTC 57.034 34.615 0.00 0.00 0.00 2.87
3981 4796 6.628644 AATTTAGAGGCACCTAGTTCTTCT 57.371 37.500 0.00 0.00 0.00 2.85
3982 4797 7.735326 AATTTAGAGGCACCTAGTTCTTCTA 57.265 36.000 0.00 0.00 0.00 2.10
3983 4798 7.735326 ATTTAGAGGCACCTAGTTCTTCTAA 57.265 36.000 0.00 0.00 0.00 2.10
3984 4799 7.549147 TTTAGAGGCACCTAGTTCTTCTAAA 57.451 36.000 7.32 7.32 0.00 1.85
3985 4800 7.549147 TTAGAGGCACCTAGTTCTTCTAAAA 57.451 36.000 0.00 0.00 0.00 1.52
3986 4801 6.628644 AGAGGCACCTAGTTCTTCTAAAAT 57.371 37.500 0.00 0.00 0.00 1.82
3987 4802 6.410540 AGAGGCACCTAGTTCTTCTAAAATG 58.589 40.000 0.00 0.00 0.00 2.32
3988 4803 6.213600 AGAGGCACCTAGTTCTTCTAAAATGA 59.786 38.462 0.00 0.00 0.00 2.57
3989 4804 6.779860 AGGCACCTAGTTCTTCTAAAATGAA 58.220 36.000 0.00 0.00 0.00 2.57
3990 4805 6.881602 AGGCACCTAGTTCTTCTAAAATGAAG 59.118 38.462 0.00 0.00 43.36 3.02
4015 4830 9.481340 AGAAAAAGAAAAATGATAGGACTTTGC 57.519 29.630 0.00 0.00 0.00 3.68
4016 4831 9.260002 GAAAAAGAAAAATGATAGGACTTTGCA 57.740 29.630 0.00 0.00 0.00 4.08
4017 4832 9.783081 AAAAAGAAAAATGATAGGACTTTGCAT 57.217 25.926 0.00 0.00 0.00 3.96
4018 4833 8.767478 AAAGAAAAATGATAGGACTTTGCATG 57.233 30.769 0.00 0.00 0.00 4.06
4019 4834 6.335777 AGAAAAATGATAGGACTTTGCATGC 58.664 36.000 11.82 11.82 0.00 4.06
4020 4835 5.927281 AAAATGATAGGACTTTGCATGCT 57.073 34.783 20.33 0.00 0.00 3.79
4021 4836 5.927281 AAATGATAGGACTTTGCATGCTT 57.073 34.783 20.33 0.00 0.00 3.91
4022 4837 5.511234 AATGATAGGACTTTGCATGCTTC 57.489 39.130 20.33 9.66 0.00 3.86
4023 4838 4.226427 TGATAGGACTTTGCATGCTTCT 57.774 40.909 20.33 4.88 0.00 2.85
4024 4839 5.357742 TGATAGGACTTTGCATGCTTCTA 57.642 39.130 20.33 7.20 0.00 2.10
4025 4840 5.363101 TGATAGGACTTTGCATGCTTCTAG 58.637 41.667 20.33 12.47 0.00 2.43
4026 4841 3.710209 AGGACTTTGCATGCTTCTAGT 57.290 42.857 20.33 15.47 0.00 2.57
4027 4842 3.341823 AGGACTTTGCATGCTTCTAGTG 58.658 45.455 20.33 4.74 0.00 2.74
4028 4843 3.008375 AGGACTTTGCATGCTTCTAGTGA 59.992 43.478 20.33 0.00 0.00 3.41
4029 4844 3.753272 GGACTTTGCATGCTTCTAGTGAA 59.247 43.478 20.33 0.00 0.00 3.18
4030 4845 4.378874 GGACTTTGCATGCTTCTAGTGAAC 60.379 45.833 20.33 5.28 0.00 3.18
4031 4846 3.503748 ACTTTGCATGCTTCTAGTGAACC 59.496 43.478 20.33 0.00 0.00 3.62
4032 4847 3.423539 TTGCATGCTTCTAGTGAACCT 57.576 42.857 20.33 0.00 0.00 3.50
4033 4848 2.703416 TGCATGCTTCTAGTGAACCTG 58.297 47.619 20.33 0.00 0.00 4.00
4034 4849 1.399791 GCATGCTTCTAGTGAACCTGC 59.600 52.381 11.37 0.00 0.00 4.85
4035 4850 2.938756 GCATGCTTCTAGTGAACCTGCT 60.939 50.000 11.37 0.00 30.65 4.24
4036 4851 2.462456 TGCTTCTAGTGAACCTGCTG 57.538 50.000 0.00 0.00 0.00 4.41
4037 4852 1.694150 TGCTTCTAGTGAACCTGCTGT 59.306 47.619 0.00 0.00 0.00 4.40
4038 4853 2.897326 TGCTTCTAGTGAACCTGCTGTA 59.103 45.455 0.00 0.00 0.00 2.74
4039 4854 3.056536 TGCTTCTAGTGAACCTGCTGTAG 60.057 47.826 0.00 0.00 0.00 2.74
4040 4855 3.193691 GCTTCTAGTGAACCTGCTGTAGA 59.806 47.826 0.00 0.00 0.00 2.59
4041 4856 4.739195 CTTCTAGTGAACCTGCTGTAGAC 58.261 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 6.785191 AGCGGTTGACATAACATTAAATCTG 58.215 36.000 0.00 0.00 0.00 2.90
63 64 7.391148 AAGCGGTTGACATAACATTAAATCT 57.609 32.000 0.00 0.00 0.00 2.40
64 65 9.382244 GATAAGCGGTTGACATAACATTAAATC 57.618 33.333 10.73 0.00 0.00 2.17
65 66 8.349983 GGATAAGCGGTTGACATAACATTAAAT 58.650 33.333 10.73 0.00 0.00 1.40
66 67 7.337184 TGGATAAGCGGTTGACATAACATTAAA 59.663 33.333 10.73 0.00 0.00 1.52
67 68 6.824196 TGGATAAGCGGTTGACATAACATTAA 59.176 34.615 10.73 0.00 0.00 1.40
68 69 6.350103 TGGATAAGCGGTTGACATAACATTA 58.650 36.000 10.73 0.00 0.00 1.90
69 70 5.189928 TGGATAAGCGGTTGACATAACATT 58.810 37.500 10.73 0.00 0.00 2.71
70 71 4.776349 TGGATAAGCGGTTGACATAACAT 58.224 39.130 10.73 0.00 0.00 2.71
71 72 4.209307 TGGATAAGCGGTTGACATAACA 57.791 40.909 10.73 0.00 0.00 2.41
72 73 5.751243 AATGGATAAGCGGTTGACATAAC 57.249 39.130 10.73 0.00 0.00 1.89
73 74 5.067153 CCAAATGGATAAGCGGTTGACATAA 59.933 40.000 10.73 0.00 37.39 1.90
74 75 4.578516 CCAAATGGATAAGCGGTTGACATA 59.421 41.667 10.73 0.00 37.39 2.29
75 76 3.381272 CCAAATGGATAAGCGGTTGACAT 59.619 43.478 10.73 8.58 37.39 3.06
76 77 2.752354 CCAAATGGATAAGCGGTTGACA 59.248 45.455 10.73 6.51 37.39 3.58
77 78 3.013921 TCCAAATGGATAAGCGGTTGAC 58.986 45.455 10.73 3.64 39.78 3.18
78 79 3.358111 TCCAAATGGATAAGCGGTTGA 57.642 42.857 10.73 0.00 39.78 3.18
86 87 7.829725 CAAGTGATTCTTGTCCAAATGGATAA 58.170 34.615 5.27 8.37 45.89 1.75
87 88 7.395190 CAAGTGATTCTTGTCCAAATGGATA 57.605 36.000 5.27 0.00 45.89 2.59
88 89 6.276832 CAAGTGATTCTTGTCCAAATGGAT 57.723 37.500 5.27 0.00 45.89 3.41
127 128 2.480419 GGTCAAACAACACTCCTCATCG 59.520 50.000 0.00 0.00 0.00 3.84
148 149 2.422597 TCAAACACTGGTGCTAATCGG 58.577 47.619 0.17 0.00 0.00 4.18
159 160 5.336690 CCAACATTCCCCTAATCAAACACTG 60.337 44.000 0.00 0.00 0.00 3.66
194 195 6.826668 AGCCTTAAAATGTATTAATTGGGGC 58.173 36.000 0.00 0.00 34.80 5.80
229 230 7.047891 AGAACCAACATCGATTGCTAATTAGA 58.952 34.615 16.85 0.00 0.00 2.10
230 231 7.251704 AGAACCAACATCGATTGCTAATTAG 57.748 36.000 8.20 8.20 0.00 1.73
240 241 1.812571 GGTGCAAGAACCAACATCGAT 59.187 47.619 0.00 0.00 40.22 3.59
242 243 0.240945 GGGTGCAAGAACCAACATCG 59.759 55.000 0.00 0.00 42.47 3.84
274 275 3.305881 CGGAAGTTCGAAGAGTAAAGGGT 60.306 47.826 0.00 0.00 38.43 4.34
288 289 4.062991 TCAAAGAGTAAAGGCGGAAGTTC 58.937 43.478 0.00 0.00 0.00 3.01
465 487 2.919494 GCCTCGGGGTTTGTGCAAG 61.919 63.158 1.62 0.00 34.45 4.01
467 489 2.992817 ATTGCCTCGGGGTTTGTGCA 62.993 55.000 1.62 0.00 34.45 4.57
479 501 2.105766 AGGAAAGGATGCAATTGCCTC 58.894 47.619 26.94 24.81 41.18 4.70
484 506 4.263025 GGGTTGAAAGGAAAGGATGCAATT 60.263 41.667 0.00 0.00 0.00 2.32
501 523 2.203422 CTTTGGGGTGCGGGTTGA 60.203 61.111 0.00 0.00 0.00 3.18
539 562 2.770475 GGGAGGGAAGGGGAGAGC 60.770 72.222 0.00 0.00 0.00 4.09
561 584 1.283613 GGTCCTGAGAGAGGTCTGAGA 59.716 57.143 0.00 0.00 43.37 3.27
610 633 8.903059 ATACCTCTGGGAATATAAAGGAGTAG 57.097 38.462 0.00 0.00 36.25 2.57
694 717 2.436173 GCTAGAGCTAGGGTTTCCATGT 59.564 50.000 6.66 0.00 38.21 3.21
757 780 9.220906 TGTTTCCTACCCATTATACTACTCATT 57.779 33.333 0.00 0.00 0.00 2.57
776 799 5.248020 TGCATCCAACCAAATTATGTTTCCT 59.752 36.000 0.00 0.00 0.00 3.36
790 813 5.329035 ACAAATTGACTATGCATCCAACC 57.671 39.130 0.19 0.00 0.00 3.77
791 814 6.095440 ACCTACAAATTGACTATGCATCCAAC 59.905 38.462 0.19 0.00 0.00 3.77
805 828 6.015010 TCCACATAACCCAAACCTACAAATTG 60.015 38.462 0.00 0.00 0.00 2.32
807 830 5.646215 TCCACATAACCCAAACCTACAAAT 58.354 37.500 0.00 0.00 0.00 2.32
928 951 1.877637 TTCACATGAACCCTGTCACG 58.122 50.000 0.00 0.00 0.00 4.35
933 956 5.648178 TCATGAAATTCACATGAACCCTG 57.352 39.130 19.15 0.00 46.94 4.45
942 965 8.565896 AAGTACTAATGCTCATGAAATTCACA 57.434 30.769 0.00 0.00 0.00 3.58
951 974 6.199154 CGGTTCACTAAGTACTAATGCTCATG 59.801 42.308 0.00 0.00 0.00 3.07
958 981 7.436118 TGTTGTTCGGTTCACTAAGTACTAAT 58.564 34.615 0.00 0.00 0.00 1.73
960 983 6.389830 TGTTGTTCGGTTCACTAAGTACTA 57.610 37.500 0.00 0.00 0.00 1.82
1066 1113 2.475466 GCAGTGATGACGCCCATGG 61.475 63.158 4.14 4.14 35.17 3.66
1071 1118 2.406401 GCATGCAGTGATGACGCC 59.594 61.111 14.21 0.00 0.00 5.68
1110 1157 2.045045 CCATCCAGAAGGCGCCAA 60.045 61.111 31.54 6.66 33.74 4.52
1115 1162 1.003580 TCAAGTCACCATCCAGAAGGC 59.996 52.381 0.00 0.00 33.74 4.35
1181 1228 2.760159 CCGCGTGGGCAAATAGTGG 61.760 63.158 7.26 0.00 39.92 4.00
1326 1373 0.321653 GGAGCTTGACACGGACCAAT 60.322 55.000 0.00 0.00 0.00 3.16
1416 1469 0.620556 GGTTGAGGAGGAGAATGGCA 59.379 55.000 0.00 0.00 0.00 4.92
2095 2159 2.488153 GTTCAGACCAATTGCCAGTACC 59.512 50.000 0.00 0.00 0.00 3.34
2289 2365 7.251704 AGGACAAAATGAGAACATATTAGCG 57.748 36.000 0.00 0.00 35.50 4.26
2329 2405 4.686091 CGCTTCCGCTTCAGAATATATCAA 59.314 41.667 0.00 0.00 0.00 2.57
2432 2508 9.161572 AGTAGATCAAGGACACTATAGAGTAGA 57.838 37.037 6.78 2.25 33.32 2.59
2504 2580 4.216902 CCACAAGAACAATCTCATCAAGCA 59.783 41.667 0.00 0.00 33.77 3.91
2508 2584 6.114187 AGTACCACAAGAACAATCTCATCA 57.886 37.500 0.00 0.00 33.77 3.07
2509 2585 8.723942 ATAAGTACCACAAGAACAATCTCATC 57.276 34.615 0.00 0.00 33.77 2.92
2558 2634 5.362430 GGCATCCTAATTCAATGGTTACCAA 59.638 40.000 8.63 0.00 36.95 3.67
2598 2682 5.577164 ACACGAATACTTAGTTGCATGAGAC 59.423 40.000 0.00 0.00 0.00 3.36
2814 2900 8.668510 ATGGTTTCTAGCATGATAAGTTACAG 57.331 34.615 0.00 0.00 40.79 2.74
2826 2912 9.547753 CTAACAATACTACATGGTTTCTAGCAT 57.452 33.333 0.00 0.00 42.99 3.79
2874 2971 4.973396 TGTTTCATCGAGCACAATCATTC 58.027 39.130 0.00 0.00 0.00 2.67
2956 3088 8.892723 CAATCTATACCAAAGTTATCAAGCACA 58.107 33.333 0.00 0.00 0.00 4.57
2957 3089 8.893727 ACAATCTATACCAAAGTTATCAAGCAC 58.106 33.333 0.00 0.00 0.00 4.40
2995 3127 6.405278 AAAAATACAAAAGGAGGTGTCAGG 57.595 37.500 0.00 0.00 0.00 3.86
3177 3310 6.663944 ATTTGTCTCAAAGTAACGATAGGC 57.336 37.500 0.00 0.00 43.77 3.93
3307 3440 5.725551 TTCCCCATGTCCAATAATACACT 57.274 39.130 0.00 0.00 0.00 3.55
3502 4125 4.870991 GTGAATAGTACCTCCTTGTCTTGC 59.129 45.833 0.00 0.00 0.00 4.01
3513 4136 8.150945 CCAGCAATAACATAGTGAATAGTACCT 58.849 37.037 0.00 0.00 0.00 3.08
3514 4137 8.148351 TCCAGCAATAACATAGTGAATAGTACC 58.852 37.037 0.00 0.00 0.00 3.34
3532 4155 2.163454 TGGAACCTGGTCCAGCAAT 58.837 52.632 13.99 1.06 42.97 3.56
3652 4450 7.139392 GCTGTGATCGTCAATGAGTATTACTA 58.861 38.462 0.00 0.00 0.00 1.82
3676 4474 1.162698 GTTCCCTGTAAAGTTCCGGC 58.837 55.000 0.00 0.00 0.00 6.13
3683 4481 6.110411 TCTAAGAAGGTGTTCCCTGTAAAG 57.890 41.667 0.00 0.00 45.47 1.85
3702 4501 1.294138 CGGGCGGTGGAGTTTCTAA 59.706 57.895 0.00 0.00 0.00 2.10
3703 4502 1.909781 ACGGGCGGTGGAGTTTCTA 60.910 57.895 0.00 0.00 0.00 2.10
3768 4577 4.214545 AGTCTATTCCTCTCGATTGCTACG 59.785 45.833 0.00 0.00 0.00 3.51
3802 4612 6.261603 TGCCTTATTTGAGCTATCTTGTGATG 59.738 38.462 0.00 0.00 34.32 3.07
3805 4615 6.441093 TTGCCTTATTTGAGCTATCTTGTG 57.559 37.500 0.00 0.00 0.00 3.33
3825 4635 4.994220 TCATTGTTTTGCATGTCATTGC 57.006 36.364 0.00 0.00 43.07 3.56
3869 4679 9.796180 TGTAAAGTTCCAGCCTTTTTAATACTA 57.204 29.630 0.00 0.00 34.20 1.82
3878 4692 5.047306 GGCTTATTGTAAAGTTCCAGCCTTT 60.047 40.000 0.00 0.00 42.05 3.11
3921 4736 0.958382 ACACACCCACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
3922 4737 0.957888 CACACACCCACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
3923 4738 1.653094 CCACACACCCACACACACAC 61.653 60.000 0.00 0.00 0.00 3.82
3924 4739 1.377856 CCACACACCCACACACACA 60.378 57.895 0.00 0.00 0.00 3.72
3925 4740 2.118404 CCCACACACCCACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
3926 4741 2.273776 CCCACACACCCACACACA 59.726 61.111 0.00 0.00 0.00 3.72
3927 4742 2.518349 CCCCACACACCCACACAC 60.518 66.667 0.00 0.00 0.00 3.82
3928 4743 3.814906 CCCCCACACACCCACACA 61.815 66.667 0.00 0.00 0.00 3.72
3937 4752 4.589675 TTTCCCACGCCCCCACAC 62.590 66.667 0.00 0.00 0.00 3.82
3938 4753 2.664835 ATTTTTCCCACGCCCCCACA 62.665 55.000 0.00 0.00 0.00 4.17
3939 4754 0.612453 TATTTTTCCCACGCCCCCAC 60.612 55.000 0.00 0.00 0.00 4.61
3940 4755 0.114560 TTATTTTTCCCACGCCCCCA 59.885 50.000 0.00 0.00 0.00 4.96
3941 4756 1.491668 ATTATTTTTCCCACGCCCCC 58.508 50.000 0.00 0.00 0.00 5.40
3942 4757 3.620427 AAATTATTTTTCCCACGCCCC 57.380 42.857 0.00 0.00 0.00 5.80
3943 4758 5.451381 CCTCTAAATTATTTTTCCCACGCCC 60.451 44.000 0.00 0.00 0.00 6.13
3944 4759 5.588240 CCTCTAAATTATTTTTCCCACGCC 58.412 41.667 0.00 0.00 0.00 5.68
3945 4760 5.041287 GCCTCTAAATTATTTTTCCCACGC 58.959 41.667 0.00 0.00 0.00 5.34
3946 4761 6.033966 GTGCCTCTAAATTATTTTTCCCACG 58.966 40.000 0.00 0.00 0.00 4.94
3947 4762 6.154534 AGGTGCCTCTAAATTATTTTTCCCAC 59.845 38.462 0.00 0.00 0.00 4.61
3948 4763 6.260663 AGGTGCCTCTAAATTATTTTTCCCA 58.739 36.000 0.00 0.00 0.00 4.37
3949 4764 6.791867 AGGTGCCTCTAAATTATTTTTCCC 57.208 37.500 0.00 0.00 0.00 3.97
3950 4765 8.521170 ACTAGGTGCCTCTAAATTATTTTTCC 57.479 34.615 0.00 0.00 0.00 3.13
3952 4767 9.755122 AGAACTAGGTGCCTCTAAATTATTTTT 57.245 29.630 0.00 0.00 0.00 1.94
3953 4768 9.755122 AAGAACTAGGTGCCTCTAAATTATTTT 57.245 29.630 0.00 0.00 0.00 1.82
3954 4769 9.397280 GAAGAACTAGGTGCCTCTAAATTATTT 57.603 33.333 0.00 0.00 0.00 1.40
3955 4770 8.773216 AGAAGAACTAGGTGCCTCTAAATTATT 58.227 33.333 0.00 0.00 0.00 1.40
3956 4771 8.325477 AGAAGAACTAGGTGCCTCTAAATTAT 57.675 34.615 0.00 0.00 0.00 1.28
3957 4772 7.735326 AGAAGAACTAGGTGCCTCTAAATTA 57.265 36.000 0.00 0.00 0.00 1.40
3958 4773 6.628644 AGAAGAACTAGGTGCCTCTAAATT 57.371 37.500 0.00 0.00 0.00 1.82
3959 4774 7.735326 TTAGAAGAACTAGGTGCCTCTAAAT 57.265 36.000 0.00 0.00 32.30 1.40
3960 4775 7.549147 TTTAGAAGAACTAGGTGCCTCTAAA 57.451 36.000 9.79 9.79 32.30 1.85
3961 4776 7.549147 TTTTAGAAGAACTAGGTGCCTCTAA 57.451 36.000 0.00 0.00 32.30 2.10
3962 4777 7.399191 TCATTTTAGAAGAACTAGGTGCCTCTA 59.601 37.037 0.00 0.00 32.30 2.43
3963 4778 6.213600 TCATTTTAGAAGAACTAGGTGCCTCT 59.786 38.462 0.00 0.00 32.30 3.69
3964 4779 6.407202 TCATTTTAGAAGAACTAGGTGCCTC 58.593 40.000 0.00 0.00 32.30 4.70
3965 4780 6.374417 TCATTTTAGAAGAACTAGGTGCCT 57.626 37.500 0.00 0.00 32.30 4.75
3966 4781 7.078011 CTTCATTTTAGAAGAACTAGGTGCC 57.922 40.000 0.00 0.00 46.18 5.01
3989 4804 9.481340 GCAAAGTCCTATCATTTTTCTTTTTCT 57.519 29.630 0.00 0.00 0.00 2.52
3990 4805 9.260002 TGCAAAGTCCTATCATTTTTCTTTTTC 57.740 29.630 0.00 0.00 0.00 2.29
3991 4806 9.783081 ATGCAAAGTCCTATCATTTTTCTTTTT 57.217 25.926 0.00 0.00 0.00 1.94
3992 4807 9.211485 CATGCAAAGTCCTATCATTTTTCTTTT 57.789 29.630 0.00 0.00 0.00 2.27
3993 4808 7.332678 GCATGCAAAGTCCTATCATTTTTCTTT 59.667 33.333 14.21 0.00 0.00 2.52
3994 4809 6.815142 GCATGCAAAGTCCTATCATTTTTCTT 59.185 34.615 14.21 0.00 0.00 2.52
3995 4810 6.154021 AGCATGCAAAGTCCTATCATTTTTCT 59.846 34.615 21.98 0.00 0.00 2.52
3996 4811 6.335777 AGCATGCAAAGTCCTATCATTTTTC 58.664 36.000 21.98 0.00 0.00 2.29
3997 4812 6.290294 AGCATGCAAAGTCCTATCATTTTT 57.710 33.333 21.98 0.00 0.00 1.94
3998 4813 5.927281 AGCATGCAAAGTCCTATCATTTT 57.073 34.783 21.98 0.00 0.00 1.82
3999 4814 5.655532 AGAAGCATGCAAAGTCCTATCATTT 59.344 36.000 21.98 0.00 0.00 2.32
4000 4815 5.198965 AGAAGCATGCAAAGTCCTATCATT 58.801 37.500 21.98 0.00 0.00 2.57
4001 4816 4.789807 AGAAGCATGCAAAGTCCTATCAT 58.210 39.130 21.98 0.00 0.00 2.45
4002 4817 4.226427 AGAAGCATGCAAAGTCCTATCA 57.774 40.909 21.98 0.00 0.00 2.15
4003 4818 5.236047 CACTAGAAGCATGCAAAGTCCTATC 59.764 44.000 21.98 3.73 0.00 2.08
4004 4819 5.104776 TCACTAGAAGCATGCAAAGTCCTAT 60.105 40.000 21.98 0.00 0.00 2.57
4005 4820 4.222810 TCACTAGAAGCATGCAAAGTCCTA 59.777 41.667 21.98 9.89 0.00 2.94
4006 4821 3.008375 TCACTAGAAGCATGCAAAGTCCT 59.992 43.478 21.98 9.27 0.00 3.85
4007 4822 3.338249 TCACTAGAAGCATGCAAAGTCC 58.662 45.455 21.98 1.77 0.00 3.85
4008 4823 4.716943 GTTCACTAGAAGCATGCAAAGTC 58.283 43.478 21.98 11.24 33.63 3.01
4009 4824 4.756084 GTTCACTAGAAGCATGCAAAGT 57.244 40.909 21.98 13.78 33.63 2.66
4019 4834 4.739195 GTCTACAGCAGGTTCACTAGAAG 58.261 47.826 0.00 0.00 33.63 2.85
4020 4835 4.785511 GTCTACAGCAGGTTCACTAGAA 57.214 45.455 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.