Multiple sequence alignment - TraesCS3B01G366300

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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 TraesCS3B01G366300 chr3B 100.000 4249 0 0 1 4249 578763794 578759546 0.000000e+00 7847.0
1 TraesCS3B01G366300 chr3B 83.153 1846 207 56 2116 3910 578613473 578611681 0.000000e+00 1591.0
2 TraesCS3B01G366300 chr3B 88.798 982 101 8 973 1953 578614496 578613523 0.000000e+00 1195.0
3 TraesCS3B01G366300 chr3B 79.970 1338 182 47 2851 4133 578603793 578602487 0.000000e+00 907.0
4 TraesCS3B01G366300 chr3B 91.071 560 47 1 1020 1579 578605191 578604635 0.000000e+00 754.0
5 TraesCS3B01G366300 chr3B 88.165 583 62 5 100 676 578811757 578811176 0.000000e+00 688.0
6 TraesCS3B01G366300 chr3B 87.193 570 66 4 113 676 578775115 578774547 4.020000e-180 641.0
7 TraesCS3B01G366300 chr3B 100.000 227 0 0 4536 4762 578759259 578759033 2.050000e-113 420.0
8 TraesCS3B01G366300 chr3B 81.262 523 70 18 1681 2181 578592290 578591774 9.600000e-107 398.0
9 TraesCS3B01G366300 chr3B 88.462 78 9 0 4017 4094 578587349 578587272 1.410000e-15 95.3
10 TraesCS3B01G366300 chr3B 84.536 97 9 5 5 98 578763697 578763790 1.830000e-14 91.6
11 TraesCS3B01G366300 chr3B 97.222 36 1 0 847 882 578593375 578593340 1.430000e-05 62.1
12 TraesCS3B01G366300 chr3D 93.188 4301 194 57 1 4249 441254346 441250093 0.000000e+00 6228.0
13 TraesCS3B01G366300 chr3D 90.702 570 50 2 1010 1578 441176075 441175508 0.000000e+00 756.0
14 TraesCS3B01G366300 chr3D 80.689 958 138 30 1740 2686 441184690 441183769 0.000000e+00 701.0
15 TraesCS3B01G366300 chr3D 87.789 606 64 9 979 1579 441185343 441184743 0.000000e+00 701.0
16 TraesCS3B01G366300 chr3D 88.336 583 59 6 100 676 441261808 441261229 0.000000e+00 691.0
17 TraesCS3B01G366300 chr3D 86.481 540 65 5 141 675 441423369 441422833 1.910000e-163 586.0
18 TraesCS3B01G366300 chr3D 87.500 264 33 0 1716 1979 441175482 441175219 5.990000e-79 305.0
19 TraesCS3B01G366300 chr3D 91.818 110 8 1 673 781 477910559 477910668 8.250000e-33 152.0
20 TraesCS3B01G366300 chr3D 100.000 32 0 0 67 98 441254311 441254342 5.150000e-05 60.2
21 TraesCS3B01G366300 chr3A 94.328 2098 75 22 2170 4249 581839411 581837340 0.000000e+00 3175.0
22 TraesCS3B01G366300 chr3A 95.012 1203 49 4 973 2170 581840884 581839688 0.000000e+00 1879.0
23 TraesCS3B01G366300 chr3A 95.858 676 16 8 1 676 581842100 581841437 0.000000e+00 1083.0
24 TraesCS3B01G366300 chr3A 81.387 1096 160 29 3042 4120 581603670 581602602 0.000000e+00 854.0
25 TraesCS3B01G366300 chr3A 83.746 849 116 16 2880 3724 582282595 582281765 0.000000e+00 784.0
26 TraesCS3B01G366300 chr3A 90.418 574 48 5 1010 1579 581605302 581604732 0.000000e+00 749.0
27 TraesCS3B01G366300 chr3A 88.644 590 59 7 993 1579 581615678 581615094 0.000000e+00 712.0
28 TraesCS3B01G366300 chr3A 79.290 1014 142 32 1681 2686 581615096 581614143 0.000000e+00 647.0
29 TraesCS3B01G366300 chr3A 88.675 468 49 4 212 676 581849627 581849161 6.920000e-158 568.0
30 TraesCS3B01G366300 chr3A 89.509 448 43 3 229 675 582285294 582284850 8.950000e-157 564.0
31 TraesCS3B01G366300 chr3A 81.143 525 67 22 1681 2181 581372373 581371857 4.470000e-105 392.0
32 TraesCS3B01G366300 chr3A 94.253 174 9 1 777 950 581841440 581841268 1.020000e-66 265.0
33 TraesCS3B01G366300 chr6B 87.335 1137 130 11 974 2105 696332450 696331323 0.000000e+00 1290.0
34 TraesCS3B01G366300 chr6B 84.568 1147 124 33 3035 4159 696330363 696329248 0.000000e+00 1088.0
35 TraesCS3B01G366300 chr6B 86.213 573 47 18 2494 3046 696330944 696330384 4.100000e-165 592.0
36 TraesCS3B01G366300 chr6B 85.409 562 66 9 141 687 696333298 696332738 1.920000e-158 569.0
37 TraesCS3B01G366300 chr6B 85.135 370 48 5 1900 2266 696331324 696330959 5.820000e-99 372.0
38 TraesCS3B01G366300 chrUn 83.297 910 131 19 2910 3814 108217856 108216963 0.000000e+00 819.0
39 TraesCS3B01G366300 chr4B 84.834 811 115 8 2897 3705 666056745 666057549 0.000000e+00 809.0
40 TraesCS3B01G366300 chr6A 85.639 759 103 5 2855 3612 4679567 4678814 0.000000e+00 793.0
41 TraesCS3B01G366300 chr6A 90.517 116 11 0 666 781 101842735 101842620 2.290000e-33 154.0
42 TraesCS3B01G366300 chr2D 92.920 113 7 1 670 781 192181589 192181477 3.810000e-36 163.0
43 TraesCS3B01G366300 chr7B 92.105 114 7 2 673 784 357651484 357651597 4.930000e-35 159.0
44 TraesCS3B01G366300 chr7B 92.593 108 5 3 673 778 213457572 213457678 8.250000e-33 152.0
45 TraesCS3B01G366300 chr2A 92.727 110 7 1 670 778 205917597 205917706 1.770000e-34 158.0
46 TraesCS3B01G366300 chr7A 93.269 104 6 1 673 775 252178398 252178501 8.250000e-33 152.0
47 TraesCS3B01G366300 chr4D 86.719 128 11 6 658 782 259497245 259497369 2.310000e-28 137.0


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 TraesCS3B01G366300 chr3B 578759033 578763794 4761 True 4133.50 7847 100.00000 1 4762 2 chr3B.!!$R7 4761
1 TraesCS3B01G366300 chr3B 578611681 578614496 2815 True 1393.00 1591 85.97550 973 3910 2 chr3B.!!$R6 2937
2 TraesCS3B01G366300 chr3B 578602487 578605191 2704 True 830.50 907 85.52050 1020 4133 2 chr3B.!!$R5 3113
3 TraesCS3B01G366300 chr3B 578811176 578811757 581 True 688.00 688 88.16500 100 676 1 chr3B.!!$R3 576
4 TraesCS3B01G366300 chr3B 578774547 578775115 568 True 641.00 641 87.19300 113 676 1 chr3B.!!$R2 563
5 TraesCS3B01G366300 chr3B 578591774 578593375 1601 True 230.05 398 89.24200 847 2181 2 chr3B.!!$R4 1334
6 TraesCS3B01G366300 chr3D 441250093 441254346 4253 True 6228.00 6228 93.18800 1 4249 1 chr3D.!!$R1 4248
7 TraesCS3B01G366300 chr3D 441183769 441185343 1574 True 701.00 701 84.23900 979 2686 2 chr3D.!!$R5 1707
8 TraesCS3B01G366300 chr3D 441261229 441261808 579 True 691.00 691 88.33600 100 676 1 chr3D.!!$R2 576
9 TraesCS3B01G366300 chr3D 441422833 441423369 536 True 586.00 586 86.48100 141 675 1 chr3D.!!$R3 534
10 TraesCS3B01G366300 chr3D 441175219 441176075 856 True 530.50 756 89.10100 1010 1979 2 chr3D.!!$R4 969
11 TraesCS3B01G366300 chr3A 581837340 581842100 4760 True 1600.50 3175 94.86275 1 4249 4 chr3A.!!$R5 4248
12 TraesCS3B01G366300 chr3A 581602602 581605302 2700 True 801.50 854 85.90250 1010 4120 2 chr3A.!!$R3 3110
13 TraesCS3B01G366300 chr3A 581614143 581615678 1535 True 679.50 712 83.96700 993 2686 2 chr3A.!!$R4 1693
14 TraesCS3B01G366300 chr3A 582281765 582285294 3529 True 674.00 784 86.62750 229 3724 2 chr3A.!!$R6 3495
15 TraesCS3B01G366300 chr3A 581371857 581372373 516 True 392.00 392 81.14300 1681 2181 1 chr3A.!!$R1 500
16 TraesCS3B01G366300 chr6B 696329248 696333298 4050 True 782.20 1290 85.73200 141 4159 5 chr6B.!!$R1 4018
17 TraesCS3B01G366300 chrUn 108216963 108217856 893 True 819.00 819 83.29700 2910 3814 1 chrUn.!!$R1 904
18 TraesCS3B01G366300 chr4B 666056745 666057549 804 False 809.00 809 84.83400 2897 3705 1 chr4B.!!$F1 808
19 TraesCS3B01G366300 chr6A 4678814 4679567 753 True 793.00 793 85.63900 2855 3612 1 chr6A.!!$R1 757

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
269 284 0.804989 GCGGACTGAAAGGTGGATTG 59.195 55.000 0.00 0.0 39.30 2.67 F
624 645 3.888323 TGCTTGACTTAAGGTTTGCATGA 59.112 39.130 7.53 0.0 36.87 3.07 F
2310 3515 1.398390 CTATTCTGGCTTTGACACGGC 59.602 52.381 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1755 1.827969 ACGGAGCTGCTCTCTTATGTT 59.172 47.619 27.09 2.51 41.60 2.71 R
2434 3672 3.067833 GTTGCCTCACTTCTTAGTCCAC 58.932 50.000 0.00 0.00 30.26 4.02 R
3817 5230 0.178992 TGCAGTTAAGCAAGCCACCT 60.179 50.000 0.00 0.00 42.46 4.00 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
71 72 7.436933 TCAGTCACATATCTTACTGGCTAATG 58.563 38.462 0.00 0.00 39.80 1.90
73 74 8.360390 CAGTCACATATCTTACTGGCTAATGTA 58.640 37.037 0.00 0.00 36.53 2.29
74 75 8.924303 AGTCACATATCTTACTGGCTAATGTAA 58.076 33.333 0.00 0.00 0.00 2.41
77 78 9.494271 CACATATCTTACTGGCTAATGTAATGT 57.506 33.333 0.00 0.00 0.00 2.71
78 79 9.494271 ACATATCTTACTGGCTAATGTAATGTG 57.506 33.333 0.00 0.00 0.00 3.21
79 80 6.867662 ATCTTACTGGCTAATGTAATGTGC 57.132 37.500 0.00 0.00 0.00 4.57
80 81 5.989477 TCTTACTGGCTAATGTAATGTGCT 58.011 37.500 0.00 0.00 0.00 4.40
81 82 6.414732 TCTTACTGGCTAATGTAATGTGCTT 58.585 36.000 0.00 0.00 0.00 3.91
82 83 6.538742 TCTTACTGGCTAATGTAATGTGCTTC 59.461 38.462 0.00 0.00 0.00 3.86
83 84 4.588899 ACTGGCTAATGTAATGTGCTTCA 58.411 39.130 0.00 0.00 0.00 3.02
85 86 5.476599 ACTGGCTAATGTAATGTGCTTCAAA 59.523 36.000 0.00 0.00 0.00 2.69
86 87 5.953183 TGGCTAATGTAATGTGCTTCAAAG 58.047 37.500 0.00 0.00 0.00 2.77
87 88 5.105797 TGGCTAATGTAATGTGCTTCAAAGG 60.106 40.000 0.00 0.00 0.00 3.11
88 89 5.105756 GGCTAATGTAATGTGCTTCAAAGGT 60.106 40.000 0.00 0.00 0.00 3.50
89 90 6.389906 GCTAATGTAATGTGCTTCAAAGGTT 58.610 36.000 0.00 0.00 0.00 3.50
90 91 7.362574 GGCTAATGTAATGTGCTTCAAAGGTTA 60.363 37.037 0.00 0.00 0.00 2.85
91 92 8.026607 GCTAATGTAATGTGCTTCAAAGGTTAA 58.973 33.333 0.00 0.00 0.00 2.01
92 93 9.906660 CTAATGTAATGTGCTTCAAAGGTTAAA 57.093 29.630 0.00 0.00 0.00 1.52
94 95 9.606631 AATGTAATGTGCTTCAAAGGTTAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
95 96 9.777297 ATGTAATGTGCTTCAAAGGTTAAAAAT 57.223 25.926 0.00 0.00 0.00 1.82
269 284 0.804989 GCGGACTGAAAGGTGGATTG 59.195 55.000 0.00 0.00 39.30 2.67
371 389 8.233868 TGTTATTATTTTGACATCCTTGTGACG 58.766 33.333 0.00 0.00 35.79 4.35
375 393 5.412526 TTTTGACATCCTTGTGACGTAAC 57.587 39.130 0.00 0.00 35.79 2.50
594 615 7.170658 CCGGATTCTATTCTTCAAAGATCTCAC 59.829 40.741 0.00 0.00 34.49 3.51
624 645 3.888323 TGCTTGACTTAAGGTTTGCATGA 59.112 39.130 7.53 0.00 36.87 3.07
731 765 9.486497 AGAATGTATCTAGCACAGAAATACATG 57.514 33.333 10.20 0.00 38.01 3.21
777 811 5.531753 AGTAATATGGATCGGAGGGAGTA 57.468 43.478 0.00 0.00 0.00 2.59
959 1054 7.172703 GCCACAGTTTAGTTAGTGTCATACTTT 59.827 37.037 0.00 0.00 40.89 2.66
1232 1755 3.363627 TCATCAATGCAATAGGTGGCAA 58.636 40.909 0.00 0.00 44.20 4.52
1249 1772 2.354199 GGCAAACATAAGAGAGCAGCTC 59.646 50.000 15.25 15.25 44.29 4.09
1403 1926 8.451908 AGCTGAAACTCATAACTAACAACTTT 57.548 30.769 0.00 0.00 0.00 2.66
1561 2085 1.909700 ACCAACTAGGCCACAACATG 58.090 50.000 5.01 0.00 43.14 3.21
1580 2104 8.967218 ACAACATGACATTCTTCAATAAAAACG 58.033 29.630 0.00 0.00 0.00 3.60
1866 2392 4.702131 GGATATTGCCAGAACAAGAAGTGT 59.298 41.667 0.00 0.00 44.64 3.55
2053 2824 8.809066 TCTACAGAGGCATTTGTACTTTAACTA 58.191 33.333 0.00 0.00 0.00 2.24
2054 2825 7.907214 ACAGAGGCATTTGTACTTTAACTAG 57.093 36.000 0.00 0.00 0.00 2.57
2194 3248 5.699097 TTTGGTTAAGAACTTGGGAATCG 57.301 39.130 0.00 0.00 0.00 3.34
2310 3515 1.398390 CTATTCTGGCTTTGACACGGC 59.602 52.381 0.00 0.00 0.00 5.68
2374 3599 5.154222 GTGTAGTTTGATTGCCTAAACTGC 58.846 41.667 11.40 10.60 44.36 4.40
2391 3616 2.286872 CTGCTATTGCTGCTGCTAGTT 58.713 47.619 17.00 0.00 40.48 2.24
3101 4490 3.945921 CAGGACTGGAGTATCTACACGAA 59.054 47.826 0.00 0.00 33.73 3.85
3122 4511 4.999469 ATCATGCACCCCATCAATAGTA 57.001 40.909 0.00 0.00 29.71 1.82
3362 4757 0.537371 CCGGCCAATCCCCAGTATTC 60.537 60.000 2.24 0.00 0.00 1.75
3586 4981 2.354188 GTTGCCGGCGGTTTCAAC 60.354 61.111 28.82 26.44 33.16 3.18
3661 5056 2.719376 TGCCAAAGCAGTTCCAGTC 58.281 52.632 0.00 0.00 46.52 3.51
3814 5227 6.375455 ACATCTTGCTTAGATAAAGTTGGGTG 59.625 38.462 2.25 0.00 41.78 4.61
3816 5229 3.352648 TGCTTAGATAAAGTTGGGTGGC 58.647 45.455 0.00 0.00 37.53 5.01
3817 5230 3.245087 TGCTTAGATAAAGTTGGGTGGCA 60.245 43.478 0.00 0.00 37.53 4.92
3818 5231 3.378427 GCTTAGATAAAGTTGGGTGGCAG 59.622 47.826 0.00 0.00 37.53 4.85
3819 5232 2.514458 AGATAAAGTTGGGTGGCAGG 57.486 50.000 0.00 0.00 0.00 4.85
3820 5233 1.710809 AGATAAAGTTGGGTGGCAGGT 59.289 47.619 0.00 0.00 0.00 4.00
3821 5234 1.818674 GATAAAGTTGGGTGGCAGGTG 59.181 52.381 0.00 0.00 0.00 4.00
3822 5235 0.178975 TAAAGTTGGGTGGCAGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
3823 5236 4.603535 AGTTGGGTGGCAGGTGGC 62.604 66.667 0.00 0.00 43.74 5.01
3924 5340 7.230913 TGCTTGTTTATAGCTACTACTCCCTAG 59.769 40.741 0.00 0.00 39.38 3.02
3959 5375 5.779922 CATGAAGCATCCTATTCCATTTGG 58.220 41.667 0.00 0.00 0.00 3.28
3991 5407 6.297080 TGGTCCATTAATTGGTACTCGTAA 57.703 37.500 0.00 0.00 46.52 3.18
4058 5497 4.582240 GCCTTTTATTCCCCAATCTCTCTG 59.418 45.833 0.00 0.00 0.00 3.35
4060 5499 5.340360 CCTTTTATTCCCCAATCTCTCTGGT 60.340 44.000 0.00 0.00 31.45 4.00
4081 5520 4.096984 GGTAAGGCTGTGGATTCAAATCAG 59.903 45.833 5.19 0.00 37.15 2.90
4151 5613 2.031314 CACAGAATCATAAGCCACAGCG 59.969 50.000 0.00 0.00 46.67 5.18
4167 5629 0.321653 AGCGACGAAAGGGCAGAAAT 60.322 50.000 0.00 0.00 37.16 2.17
4177 5639 0.033781 GGGCAGAAATGCAAAGCACA 59.966 50.000 2.29 0.00 43.04 4.57
4552 6014 2.844839 ATGGCCTCTAGTCGCCCC 60.845 66.667 16.83 1.79 45.07 5.80
4553 6015 3.696518 ATGGCCTCTAGTCGCCCCA 62.697 63.158 16.83 6.60 45.07 4.96
4554 6016 3.851128 GGCCTCTAGTCGCCCCAC 61.851 72.222 10.64 0.00 39.39 4.61
4555 6017 2.760385 GCCTCTAGTCGCCCCACT 60.760 66.667 0.00 0.00 0.00 4.00
4556 6018 2.787567 GCCTCTAGTCGCCCCACTC 61.788 68.421 0.00 0.00 0.00 3.51
4557 6019 2.482333 CCTCTAGTCGCCCCACTCG 61.482 68.421 0.00 0.00 0.00 4.18
4558 6020 3.127352 CTCTAGTCGCCCCACTCGC 62.127 68.421 0.00 0.00 0.00 5.03
4559 6021 4.208686 CTAGTCGCCCCACTCGCC 62.209 72.222 0.00 0.00 0.00 5.54
4579 6041 4.735132 CCGCGGGCAGTTTCTCGA 62.735 66.667 20.10 0.00 0.00 4.04
4580 6042 3.181967 CGCGGGCAGTTTCTCGAG 61.182 66.667 5.93 5.93 0.00 4.04
4581 6043 2.048127 GCGGGCAGTTTCTCGAGT 60.048 61.111 13.13 0.00 0.00 4.18
4582 6044 2.095252 GCGGGCAGTTTCTCGAGTC 61.095 63.158 13.13 4.73 0.00 3.36
4583 6045 1.801913 CGGGCAGTTTCTCGAGTCG 60.802 63.158 13.13 6.09 0.00 4.18
4584 6046 1.446272 GGGCAGTTTCTCGAGTCGG 60.446 63.158 13.54 3.60 0.00 4.79
4585 6047 2.095252 GGCAGTTTCTCGAGTCGGC 61.095 63.158 13.54 14.99 0.00 5.54
4586 6048 2.437343 GCAGTTTCTCGAGTCGGCG 61.437 63.158 13.54 0.00 0.00 6.46
4587 6049 1.801913 CAGTTTCTCGAGTCGGCGG 60.802 63.158 13.54 3.82 0.00 6.13
4588 6050 3.179939 GTTTCTCGAGTCGGCGGC 61.180 66.667 13.54 1.71 0.00 6.53
4589 6051 4.771356 TTTCTCGAGTCGGCGGCG 62.771 66.667 27.15 27.15 0.00 6.46
4615 6077 2.045242 CAGCTGCACTGGCTCCAT 60.045 61.111 0.00 0.00 43.19 3.41
4616 6078 2.045242 AGCTGCACTGGCTCCATG 60.045 61.111 1.02 0.00 41.91 3.66
4617 6079 2.360852 GCTGCACTGGCTCCATGT 60.361 61.111 0.00 0.00 41.91 3.21
4618 6080 1.078214 GCTGCACTGGCTCCATGTA 60.078 57.895 0.00 0.00 41.91 2.29
4619 6081 1.372087 GCTGCACTGGCTCCATGTAC 61.372 60.000 0.00 0.00 41.91 2.90
4620 6082 0.745845 CTGCACTGGCTCCATGTACC 60.746 60.000 0.00 0.00 41.91 3.34
4621 6083 1.299648 GCACTGGCTCCATGTACCA 59.700 57.895 0.00 0.00 36.96 3.25
4622 6084 1.026718 GCACTGGCTCCATGTACCAC 61.027 60.000 0.00 0.00 36.96 4.16
4623 6085 0.740868 CACTGGCTCCATGTACCACG 60.741 60.000 0.00 0.00 0.00 4.94
4624 6086 0.902984 ACTGGCTCCATGTACCACGA 60.903 55.000 0.00 0.00 0.00 4.35
4625 6087 0.460284 CTGGCTCCATGTACCACGAC 60.460 60.000 0.00 0.00 0.00 4.34
4626 6088 0.902984 TGGCTCCATGTACCACGACT 60.903 55.000 0.00 0.00 0.00 4.18
4627 6089 0.460284 GGCTCCATGTACCACGACTG 60.460 60.000 0.00 0.00 0.00 3.51
4628 6090 0.246635 GCTCCATGTACCACGACTGT 59.753 55.000 0.00 0.00 0.00 3.55
4629 6091 1.475280 GCTCCATGTACCACGACTGTA 59.525 52.381 0.00 0.00 0.00 2.74
4630 6092 2.479730 GCTCCATGTACCACGACTGTAG 60.480 54.545 0.00 0.00 0.00 2.74
4631 6093 2.753452 CTCCATGTACCACGACTGTAGT 59.247 50.000 0.00 0.00 0.00 2.73
4632 6094 2.490509 TCCATGTACCACGACTGTAGTG 59.509 50.000 13.26 13.26 39.19 2.74
4643 6105 3.056458 TGTAGTGGACAGGCGGTG 58.944 61.111 0.00 0.00 32.86 4.94
4644 6106 2.264794 GTAGTGGACAGGCGGTGG 59.735 66.667 0.00 0.00 0.00 4.61
4645 6107 3.702048 TAGTGGACAGGCGGTGGC 61.702 66.667 0.00 0.00 38.90 5.01
4658 6120 2.609610 GTGGCCTGGTGGGGAGTA 60.610 66.667 3.32 0.00 35.12 2.59
4659 6121 2.285368 TGGCCTGGTGGGGAGTAG 60.285 66.667 3.32 0.00 35.12 2.57
4660 6122 3.090532 GGCCTGGTGGGGAGTAGG 61.091 72.222 0.00 0.00 35.12 3.18
4661 6123 2.040606 GCCTGGTGGGGAGTAGGA 59.959 66.667 0.00 0.00 35.12 2.94
4662 6124 1.384643 GCCTGGTGGGGAGTAGGAT 60.385 63.158 0.00 0.00 35.12 3.24
4663 6125 1.411651 GCCTGGTGGGGAGTAGGATC 61.412 65.000 0.00 0.00 35.12 3.36
4664 6126 0.266152 CCTGGTGGGGAGTAGGATCT 59.734 60.000 0.00 0.00 31.91 2.75
4665 6127 1.418334 CTGGTGGGGAGTAGGATCTG 58.582 60.000 0.00 0.00 0.00 2.90
4666 6128 1.015609 TGGTGGGGAGTAGGATCTGA 58.984 55.000 0.00 0.00 0.00 3.27
4667 6129 1.343075 TGGTGGGGAGTAGGATCTGAC 60.343 57.143 0.00 0.00 0.00 3.51
4668 6130 1.033574 GTGGGGAGTAGGATCTGACG 58.966 60.000 0.00 0.00 0.00 4.35
4669 6131 0.106167 TGGGGAGTAGGATCTGACGG 60.106 60.000 0.00 0.00 0.00 4.79
4670 6132 0.828343 GGGGAGTAGGATCTGACGGG 60.828 65.000 0.00 0.00 0.00 5.28
4671 6133 0.828343 GGGAGTAGGATCTGACGGGG 60.828 65.000 0.00 0.00 0.00 5.73
4672 6134 1.465200 GGAGTAGGATCTGACGGGGC 61.465 65.000 0.00 0.00 0.00 5.80
4673 6135 0.755698 GAGTAGGATCTGACGGGGCA 60.756 60.000 0.00 0.00 0.00 5.36
4674 6136 0.757188 AGTAGGATCTGACGGGGCAG 60.757 60.000 0.00 0.00 37.24 4.85
4675 6137 1.457643 TAGGATCTGACGGGGCAGG 60.458 63.158 0.93 0.00 36.55 4.85
4676 6138 1.944896 TAGGATCTGACGGGGCAGGA 61.945 60.000 0.93 0.00 36.55 3.86
4677 6139 2.501610 GATCTGACGGGGCAGGAC 59.498 66.667 0.93 0.00 36.55 3.85
4678 6140 3.083997 ATCTGACGGGGCAGGACC 61.084 66.667 0.93 0.00 36.55 4.46
4679 6141 3.924013 ATCTGACGGGGCAGGACCA 62.924 63.158 0.93 0.00 42.05 4.02
4680 6142 4.394712 CTGACGGGGCAGGACCAC 62.395 72.222 0.00 0.00 42.05 4.16
4687 6149 3.782443 GGCAGGACCACCCCGTAG 61.782 72.222 0.00 0.00 38.86 3.51
4688 6150 4.468689 GCAGGACCACCCCGTAGC 62.469 72.222 0.00 0.00 36.73 3.58
4689 6151 4.143333 CAGGACCACCCCGTAGCG 62.143 72.222 0.00 0.00 36.73 4.26
4690 6152 4.691359 AGGACCACCCCGTAGCGT 62.691 66.667 0.00 0.00 36.73 5.07
4691 6153 4.139234 GGACCACCCCGTAGCGTC 62.139 72.222 0.00 0.00 0.00 5.19
4692 6154 3.066814 GACCACCCCGTAGCGTCT 61.067 66.667 0.00 0.00 0.00 4.18
4693 6155 3.352338 GACCACCCCGTAGCGTCTG 62.352 68.421 0.00 0.00 0.00 3.51
4694 6156 4.814294 CCACCCCGTAGCGTCTGC 62.814 72.222 0.00 0.00 43.24 4.26
4704 6166 3.870606 GCGTCTGCGAGCCTAAAA 58.129 55.556 0.00 0.00 41.33 1.52
4705 6167 2.159181 GCGTCTGCGAGCCTAAAAA 58.841 52.632 0.00 0.00 41.33 1.94
4706 6168 0.727398 GCGTCTGCGAGCCTAAAAAT 59.273 50.000 0.00 0.00 41.33 1.82
4707 6169 1.267582 GCGTCTGCGAGCCTAAAAATC 60.268 52.381 0.00 0.00 41.33 2.17
4708 6170 2.271800 CGTCTGCGAGCCTAAAAATCT 58.728 47.619 0.00 0.00 41.33 2.40
4709 6171 2.673368 CGTCTGCGAGCCTAAAAATCTT 59.327 45.455 0.00 0.00 41.33 2.40
4710 6172 3.125316 CGTCTGCGAGCCTAAAAATCTTT 59.875 43.478 0.00 0.00 41.33 2.52
4711 6173 4.653004 GTCTGCGAGCCTAAAAATCTTTC 58.347 43.478 0.00 0.00 0.00 2.62
4712 6174 4.154195 GTCTGCGAGCCTAAAAATCTTTCA 59.846 41.667 0.00 0.00 0.00 2.69
4713 6175 4.759693 TCTGCGAGCCTAAAAATCTTTCAA 59.240 37.500 0.00 0.00 0.00 2.69
4714 6176 5.240623 TCTGCGAGCCTAAAAATCTTTCAAA 59.759 36.000 0.00 0.00 0.00 2.69
4715 6177 6.024552 TGCGAGCCTAAAAATCTTTCAAAT 57.975 33.333 0.00 0.00 0.00 2.32
4716 6178 6.454795 TGCGAGCCTAAAAATCTTTCAAATT 58.545 32.000 0.00 0.00 0.00 1.82
4717 6179 6.928492 TGCGAGCCTAAAAATCTTTCAAATTT 59.072 30.769 0.00 0.00 0.00 1.82
4718 6180 8.085296 TGCGAGCCTAAAAATCTTTCAAATTTA 58.915 29.630 0.00 0.00 0.00 1.40
4719 6181 8.921670 GCGAGCCTAAAAATCTTTCAAATTTAA 58.078 29.630 0.00 0.00 0.00 1.52
4722 6184 9.974980 AGCCTAAAAATCTTTCAAATTTAACGA 57.025 25.926 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 9.777297 ACATATTTTTAACCTTTGAAGCACATT 57.223 25.926 0.00 0.00 0.00 2.71
269 284 6.889301 ACCATGTTCATGAATGATATGACC 57.111 37.500 12.12 0.00 35.51 4.02
624 645 5.705609 ACAAAAGGAATTACGCAACAGAT 57.294 34.783 0.00 0.00 0.00 2.90
731 765 5.289595 TGTCGCTCAAATGGATGTATCTAC 58.710 41.667 0.00 0.00 0.00 2.59
927 1021 2.568623 AACTAAACTGTGGCCAGAGG 57.431 50.000 31.49 17.18 41.50 3.69
1008 1524 5.066593 CCTTCTAATCTAGGGGCACAATTC 58.933 45.833 0.00 0.00 0.00 2.17
1190 1711 9.071276 TGATGAAAGGGAAATTTAGAGCATATC 57.929 33.333 0.00 0.00 0.00 1.63
1232 1755 1.827969 ACGGAGCTGCTCTCTTATGTT 59.172 47.619 27.09 2.51 41.60 2.71
1249 1772 7.799914 GTGTTTAACATGAAAGTTTAGGTACGG 59.200 37.037 0.00 0.00 33.07 4.02
1403 1926 4.883585 CCTCCTTTTCCGATGATTGATTGA 59.116 41.667 0.00 0.00 0.00 2.57
1866 2392 6.545508 CATGAAATCATAAACGAGTGCAAGA 58.454 36.000 0.00 0.00 34.26 3.02
2075 2850 9.463443 CTTTTTAGATTGAACAGGTTTAGGTTG 57.537 33.333 0.00 0.00 0.00 3.77
2310 3515 4.572985 TTTGAAAATCCTGACTGCAGTG 57.427 40.909 27.27 11.00 40.63 3.66
2374 3599 6.703607 ACTGTATTAACTAGCAGCAGCAATAG 59.296 38.462 3.17 0.00 45.49 1.73
2391 3616 4.781087 AGGCCTACCAACTCAACTGTATTA 59.219 41.667 1.29 0.00 39.06 0.98
2434 3672 3.067833 GTTGCCTCACTTCTTAGTCCAC 58.932 50.000 0.00 0.00 30.26 4.02
2789 4100 7.153985 ACAGATGATGGTTAAAACACAAATGG 58.846 34.615 0.00 0.00 0.00 3.16
3101 4490 3.889859 ACTATTGATGGGGTGCATGAT 57.110 42.857 0.00 0.00 0.00 2.45
3248 4643 1.078710 AGGGTCGAGGTAGCCAAGT 59.921 57.895 0.00 0.00 39.59 3.16
3362 4757 2.854522 GACGGTTTGAGGGTCCATG 58.145 57.895 0.00 0.00 0.00 3.66
3442 4837 1.055040 ATACTGATCCAGCAGCCTCC 58.945 55.000 0.00 0.00 39.51 4.30
3661 5056 4.259970 CGTTGCTTACTCCTGAAATCATCG 60.260 45.833 0.00 0.00 0.00 3.84
3814 5227 0.895559 AGTTAAGCAAGCCACCTGCC 60.896 55.000 0.00 0.00 42.71 4.85
3816 5229 0.242017 GCAGTTAAGCAAGCCACCTG 59.758 55.000 0.00 0.00 0.00 4.00
3817 5230 0.178992 TGCAGTTAAGCAAGCCACCT 60.179 50.000 0.00 0.00 42.46 4.00
3818 5231 2.340427 TGCAGTTAAGCAAGCCACC 58.660 52.632 0.00 0.00 42.46 4.61
3909 5325 3.673543 AACTGCTAGGGAGTAGTAGCT 57.326 47.619 0.00 0.00 46.74 3.32
3910 5326 4.159879 TGAAAACTGCTAGGGAGTAGTAGC 59.840 45.833 0.00 0.00 46.74 3.58
3911 5327 5.916661 TGAAAACTGCTAGGGAGTAGTAG 57.083 43.478 0.00 0.00 46.74 2.57
3924 5340 2.746269 TGCTTCATGCTTGAAAACTGC 58.254 42.857 15.12 14.46 41.22 4.40
3959 5375 4.981794 CAATTAATGGACCAACGAGTTCC 58.018 43.478 0.00 0.00 0.00 3.62
4058 5497 4.016444 TGATTTGAATCCACAGCCTTACC 58.984 43.478 1.56 0.00 34.50 2.85
4060 5499 5.178096 TCTGATTTGAATCCACAGCCTTA 57.822 39.130 1.56 0.00 34.50 2.69
4081 5520 8.119226 CAGAGGATTTGATCGAAACAAGTATTC 58.881 37.037 0.00 7.13 0.00 1.75
4151 5613 3.702478 GCATTTCTGCCCTTTCGTC 57.298 52.632 0.00 0.00 42.88 4.20
4167 5629 2.794103 AGGTATGTCATGTGCTTTGCA 58.206 42.857 0.00 0.00 35.60 4.08
4177 5639 2.621998 CGACGAGGGTTAGGTATGTCAT 59.378 50.000 0.00 0.00 0.00 3.06
4538 6000 2.760385 AGTGGGGCGACTAGAGGC 60.760 66.667 0.00 2.08 0.00 4.70
4539 6001 2.482333 CGAGTGGGGCGACTAGAGG 61.482 68.421 0.00 0.00 0.00 3.69
4540 6002 3.111939 CGAGTGGGGCGACTAGAG 58.888 66.667 0.00 0.00 0.00 2.43
4541 6003 3.138798 GCGAGTGGGGCGACTAGA 61.139 66.667 0.00 0.00 0.00 2.43
4542 6004 4.208686 GGCGAGTGGGGCGACTAG 62.209 72.222 0.00 0.00 33.04 2.57
4562 6024 4.735132 TCGAGAAACTGCCCGCGG 62.735 66.667 21.04 21.04 0.00 6.46
4563 6025 3.181967 CTCGAGAAACTGCCCGCG 61.182 66.667 6.58 0.00 0.00 6.46
4564 6026 2.048127 ACTCGAGAAACTGCCCGC 60.048 61.111 21.68 0.00 0.00 6.13
4565 6027 1.801913 CGACTCGAGAAACTGCCCG 60.802 63.158 21.68 5.31 0.00 6.13
4566 6028 1.446272 CCGACTCGAGAAACTGCCC 60.446 63.158 21.68 0.00 0.00 5.36
4567 6029 2.095252 GCCGACTCGAGAAACTGCC 61.095 63.158 21.68 0.00 0.00 4.85
4568 6030 2.437343 CGCCGACTCGAGAAACTGC 61.437 63.158 21.68 15.48 0.00 4.40
4569 6031 1.801913 CCGCCGACTCGAGAAACTG 60.802 63.158 21.68 5.61 0.00 3.16
4570 6032 2.567049 CCGCCGACTCGAGAAACT 59.433 61.111 21.68 0.00 0.00 2.66
4571 6033 3.179939 GCCGCCGACTCGAGAAAC 61.180 66.667 21.68 9.04 0.00 2.78
4572 6034 4.771356 CGCCGCCGACTCGAGAAA 62.771 66.667 21.68 0.00 36.29 2.52
4598 6060 2.045242 ATGGAGCCAGTGCAGCTG 60.045 61.111 10.11 10.11 41.75 4.24
4599 6061 1.556373 TACATGGAGCCAGTGCAGCT 61.556 55.000 0.00 0.00 45.23 4.24
4600 6062 1.078214 TACATGGAGCCAGTGCAGC 60.078 57.895 0.00 0.00 41.13 5.25
4601 6063 0.745845 GGTACATGGAGCCAGTGCAG 60.746 60.000 0.00 0.00 41.13 4.41
4602 6064 1.299648 GGTACATGGAGCCAGTGCA 59.700 57.895 0.00 0.00 41.13 4.57
4603 6065 1.026718 GTGGTACATGGAGCCAGTGC 61.027 60.000 4.29 0.00 44.52 4.40
4604 6066 0.740868 CGTGGTACATGGAGCCAGTG 60.741 60.000 4.29 0.00 44.52 3.66
4605 6067 1.596934 CGTGGTACATGGAGCCAGT 59.403 57.895 4.29 0.00 44.52 4.00
4606 6068 4.521075 CGTGGTACATGGAGCCAG 57.479 61.111 4.29 0.00 44.52 4.85
4626 6088 2.579657 CCACCGCCTGTCCACTACA 61.580 63.158 0.00 0.00 36.42 2.74
4627 6089 2.264794 CCACCGCCTGTCCACTAC 59.735 66.667 0.00 0.00 0.00 2.73
4628 6090 3.702048 GCCACCGCCTGTCCACTA 61.702 66.667 0.00 0.00 0.00 2.74
4641 6103 2.609610 TACTCCCCACCAGGCCAC 60.610 66.667 5.01 0.00 0.00 5.01
4642 6104 2.285368 CTACTCCCCACCAGGCCA 60.285 66.667 5.01 0.00 0.00 5.36
4643 6105 2.916553 ATCCTACTCCCCACCAGGCC 62.917 65.000 0.00 0.00 0.00 5.19
4644 6106 1.384643 ATCCTACTCCCCACCAGGC 60.385 63.158 0.00 0.00 0.00 4.85
4645 6107 0.266152 AGATCCTACTCCCCACCAGG 59.734 60.000 0.00 0.00 0.00 4.45
4646 6108 1.062886 TCAGATCCTACTCCCCACCAG 60.063 57.143 0.00 0.00 0.00 4.00
4647 6109 1.015609 TCAGATCCTACTCCCCACCA 58.984 55.000 0.00 0.00 0.00 4.17
4648 6110 1.415200 GTCAGATCCTACTCCCCACC 58.585 60.000 0.00 0.00 0.00 4.61
4649 6111 1.033574 CGTCAGATCCTACTCCCCAC 58.966 60.000 0.00 0.00 0.00 4.61
4650 6112 0.106167 CCGTCAGATCCTACTCCCCA 60.106 60.000 0.00 0.00 0.00 4.96
4651 6113 0.828343 CCCGTCAGATCCTACTCCCC 60.828 65.000 0.00 0.00 0.00 4.81
4652 6114 0.828343 CCCCGTCAGATCCTACTCCC 60.828 65.000 0.00 0.00 0.00 4.30
4653 6115 1.465200 GCCCCGTCAGATCCTACTCC 61.465 65.000 0.00 0.00 0.00 3.85
4654 6116 0.755698 TGCCCCGTCAGATCCTACTC 60.756 60.000 0.00 0.00 0.00 2.59
4655 6117 0.757188 CTGCCCCGTCAGATCCTACT 60.757 60.000 0.00 0.00 36.19 2.57
4656 6118 1.742768 CTGCCCCGTCAGATCCTAC 59.257 63.158 0.00 0.00 36.19 3.18
4657 6119 1.457643 CCTGCCCCGTCAGATCCTA 60.458 63.158 0.00 0.00 36.19 2.94
4658 6120 2.765807 CCTGCCCCGTCAGATCCT 60.766 66.667 0.00 0.00 36.19 3.24
4659 6121 2.764128 TCCTGCCCCGTCAGATCC 60.764 66.667 0.00 0.00 36.19 3.36
4660 6122 2.501610 GTCCTGCCCCGTCAGATC 59.498 66.667 0.00 0.00 36.19 2.75
4661 6123 3.083997 GGTCCTGCCCCGTCAGAT 61.084 66.667 0.00 0.00 36.19 2.90
4662 6124 4.631740 TGGTCCTGCCCCGTCAGA 62.632 66.667 0.00 0.00 36.19 3.27
4663 6125 4.394712 GTGGTCCTGCCCCGTCAG 62.395 72.222 0.00 0.00 36.04 3.51
4670 6132 3.782443 CTACGGGGTGGTCCTGCC 61.782 72.222 0.00 0.00 46.01 4.85
4671 6133 4.468689 GCTACGGGGTGGTCCTGC 62.469 72.222 0.00 0.00 46.01 4.85
4673 6135 4.691359 ACGCTACGGGGTGGTCCT 62.691 66.667 0.00 0.00 37.24 3.85
4674 6136 4.139234 GACGCTACGGGGTGGTCC 62.139 72.222 0.00 0.00 38.76 4.46
4675 6137 3.066814 AGACGCTACGGGGTGGTC 61.067 66.667 0.00 0.00 38.76 4.02
4676 6138 3.379445 CAGACGCTACGGGGTGGT 61.379 66.667 0.00 0.00 38.76 4.16
4677 6139 4.814294 GCAGACGCTACGGGGTGG 62.814 72.222 0.00 0.00 38.76 4.61
4680 6142 4.554363 CTCGCAGACGCTACGGGG 62.554 72.222 0.00 0.00 39.84 5.73
4683 6145 2.319011 TTAGGCTCGCAGACGCTACG 62.319 60.000 0.00 0.00 39.84 3.51
4684 6146 0.179145 TTTAGGCTCGCAGACGCTAC 60.179 55.000 0.00 0.00 39.84 3.58
4685 6147 0.528924 TTTTAGGCTCGCAGACGCTA 59.471 50.000 0.00 0.00 39.84 4.26
4686 6148 0.320421 TTTTTAGGCTCGCAGACGCT 60.320 50.000 0.00 0.00 39.84 5.07
4687 6149 0.727398 ATTTTTAGGCTCGCAGACGC 59.273 50.000 0.00 0.00 39.84 5.19
4688 6150 2.271800 AGATTTTTAGGCTCGCAGACG 58.728 47.619 0.00 0.00 42.01 4.18
4689 6151 4.154195 TGAAAGATTTTTAGGCTCGCAGAC 59.846 41.667 0.00 0.00 0.00 3.51
4690 6152 4.323417 TGAAAGATTTTTAGGCTCGCAGA 58.677 39.130 0.00 0.00 0.00 4.26
4691 6153 4.685169 TGAAAGATTTTTAGGCTCGCAG 57.315 40.909 0.00 0.00 0.00 5.18
4692 6154 5.446143 TTTGAAAGATTTTTAGGCTCGCA 57.554 34.783 0.00 0.00 0.00 5.10
4693 6155 6.951256 AATTTGAAAGATTTTTAGGCTCGC 57.049 33.333 0.00 0.00 0.00 5.03
4696 6158 9.974980 TCGTTAAATTTGAAAGATTTTTAGGCT 57.025 25.926 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.