Multiple sequence alignment - TraesCS7B01G146000

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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 TraesCS7B01G146000 chr7B 100.000 6273 0 0 3447 9719 189896322 189902594 0.000000e+00 11585.0
1 TraesCS7B01G146000 chr7B 100.000 3174 0 0 1 3174 189892876 189896049 0.000000e+00 5862.0
2 TraesCS7B01G146000 chr7B 96.253 774 26 3 1 774 604312423 604311653 0.000000e+00 1266.0
3 TraesCS7B01G146000 chr7B 77.623 934 199 10 3774 4702 586052011 586051083 8.530000e-155 558.0
4 TraesCS7B01G146000 chr7D 95.896 2388 51 11 801 3174 211643446 211641092 0.000000e+00 3823.0
5 TraesCS7B01G146000 chr7D 96.567 2243 51 10 5543 7760 211639504 211637263 0.000000e+00 3692.0
6 TraesCS7B01G146000 chr7D 96.301 1757 50 9 7892 9643 211636952 211635206 0.000000e+00 2870.0
7 TraesCS7B01G146000 chr7D 97.107 968 19 3 3764 4724 211640494 211639529 0.000000e+00 1624.0
8 TraesCS7B01G146000 chr7D 94.393 321 14 1 3447 3763 211641041 211640721 3.150000e-134 490.0
9 TraesCS7B01G146000 chr7D 95.364 151 6 1 7761 7910 211637117 211636967 1.260000e-58 239.0
10 TraesCS7B01G146000 chr7D 94.167 120 7 0 5425 5544 123678369 123678488 6.000000e-42 183.0
11 TraesCS7B01G146000 chr7D 97.500 40 1 0 7905 7944 40415896 40415935 1.750000e-07 69.4
12 TraesCS7B01G146000 chr7D 96.970 33 0 1 7501 7533 513097752 513097783 5.000000e-03 54.7
13 TraesCS7B01G146000 chr7A 97.017 2179 50 9 5545 7718 223529305 223527137 0.000000e+00 3650.0
14 TraesCS7B01G146000 chr7A 94.136 1603 31 11 1515 3112 223532899 223531355 0.000000e+00 2381.0
15 TraesCS7B01G146000 chr7A 97.107 968 19 3 3764 4724 223530300 223529335 0.000000e+00 1624.0
16 TraesCS7B01G146000 chr7A 96.229 716 15 1 801 1516 223533685 223532982 0.000000e+00 1162.0
17 TraesCS7B01G146000 chr7A 88.491 921 40 21 8830 9719 223525942 223525057 0.000000e+00 1053.0
18 TraesCS7B01G146000 chr7A 93.238 488 16 7 8357 8844 223526432 223525962 0.000000e+00 702.0
19 TraesCS7B01G146000 chr7A 96.241 399 13 1 7892 8288 223526833 223526435 0.000000e+00 652.0
20 TraesCS7B01G146000 chr7A 92.835 321 19 1 3447 3763 223530847 223530527 6.880000e-126 462.0
21 TraesCS7B01G146000 chr7A 92.053 151 4 4 7760 7910 223526988 223526846 1.280000e-48 206.0
22 TraesCS7B01G146000 chr1B 85.124 1647 225 12 5546 7177 570856020 570854379 0.000000e+00 1666.0
23 TraesCS7B01G146000 chr1B 81.741 1654 259 23 5544 7177 6854384 6852754 0.000000e+00 1341.0
24 TraesCS7B01G146000 chr1B 96.770 774 23 2 1 773 295768794 295769566 0.000000e+00 1290.0
25 TraesCS7B01G146000 chr1B 85.921 483 60 5 4772 5253 407289846 407289371 8.710000e-140 508.0
26 TraesCS7B01G146000 chr4B 83.202 1649 258 15 5545 7177 187360406 187362051 0.000000e+00 1493.0
27 TraesCS7B01G146000 chr4B 80.152 922 167 14 3783 4696 187359435 187360348 0.000000e+00 675.0
28 TraesCS7B01G146000 chr6A 84.840 1471 208 9 5721 7177 573847504 573846035 0.000000e+00 1467.0
29 TraesCS7B01G146000 chr6A 82.322 956 165 4 3771 4724 573848631 573847678 0.000000e+00 826.0
30 TraesCS7B01G146000 chr6B 82.888 1648 252 23 5546 7177 62115063 62116696 0.000000e+00 1454.0
31 TraesCS7B01G146000 chr6B 96.253 774 27 2 1 773 67945464 67946236 0.000000e+00 1267.0
32 TraesCS7B01G146000 chr6B 80.282 923 166 15 3783 4697 62114095 62115009 0.000000e+00 682.0
33 TraesCS7B01G146000 chr5B 96.762 772 23 2 1 772 237825647 237824878 0.000000e+00 1286.0
34 TraesCS7B01G146000 chr2B 96.406 779 27 1 1 779 316103311 316104088 0.000000e+00 1282.0
35 TraesCS7B01G146000 chr2B 96.521 776 23 2 1 773 296026387 296027161 0.000000e+00 1280.0
36 TraesCS7B01G146000 chr2B 96.378 773 23 2 1 773 220466583 220467350 0.000000e+00 1267.0
37 TraesCS7B01G146000 chr2B 75.891 842 135 35 4712 5536 499568400 499569190 1.540000e-97 368.0
38 TraesCS7B01G146000 chr4A 96.248 773 27 2 1 773 151959312 151958542 0.000000e+00 1266.0
39 TraesCS7B01G146000 chr4A 95.791 784 31 2 1 783 744303196 744302414 0.000000e+00 1264.0
40 TraesCS7B01G146000 chr5D 94.708 737 30 6 4809 5545 478167771 478168498 0.000000e+00 1136.0
41 TraesCS7B01G146000 chr5D 81.208 447 78 6 5546 5987 3974308 3974753 1.200000e-93 355.0
42 TraesCS7B01G146000 chr5D 94.828 116 6 0 5432 5547 464126245 464126130 2.160000e-41 182.0
43 TraesCS7B01G146000 chr5D 90.741 108 7 2 4712 4817 478167632 478167738 3.660000e-29 141.0
44 TraesCS7B01G146000 chr5D 90.625 96 8 1 4802 4896 478167700 478167795 1.020000e-24 126.0
45 TraesCS7B01G146000 chr2D 94.437 737 34 3 4809 5545 329404162 329403433 0.000000e+00 1127.0
46 TraesCS7B01G146000 chr2D 79.091 1650 309 26 5546 7175 634830263 634828630 0.000000e+00 1103.0
47 TraesCS7B01G146000 chr2D 79.834 481 95 2 3771 4250 523312959 523312480 5.590000e-92 350.0
48 TraesCS7B01G146000 chr2D 90.909 187 14 2 4712 4896 329404323 329404138 2.100000e-61 248.0
49 TraesCS7B01G146000 chr2A 92.229 489 34 3 4712 5197 140641936 140641449 0.000000e+00 689.0
50 TraesCS7B01G146000 chr2A 97.917 48 1 0 5200 5247 140634374 140634327 6.260000e-12 84.2
51 TraesCS7B01G146000 chr2A 91.489 47 4 0 7899 7945 750176182 750176228 2.270000e-06 65.8
52 TraesCS7B01G146000 chr3D 82.103 799 137 5 3771 4567 43674402 43673608 0.000000e+00 678.0
53 TraesCS7B01G146000 chr3D 88.472 373 38 2 5546 5913 43673473 43673101 6.930000e-121 446.0
54 TraesCS7B01G146000 chr3D 95.000 40 2 0 4802 4841 40695678 40695639 8.150000e-06 63.9
55 TraesCS7B01G146000 chr5A 77.519 943 202 10 3765 4702 473243149 473244086 8.530000e-155 558.0
56 TraesCS7B01G146000 chr5A 77.671 936 195 13 3774 4702 685967380 685966452 8.530000e-155 558.0
57 TraesCS7B01G146000 chr3B 79.656 639 106 12 5543 6176 235889504 235890123 1.160000e-118 438.0
58 TraesCS7B01G146000 chr6D 96.970 33 1 0 7496 7528 464120142 464120174 1.000000e-03 56.5


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 TraesCS7B01G146000 chr7B 189892876 189902594 9718 False 8723.500000 11585 100.000000 1 9719 2 chr7B.!!$F1 9718
1 TraesCS7B01G146000 chr7B 604311653 604312423 770 True 1266.000000 1266 96.253000 1 774 1 chr7B.!!$R2 773
2 TraesCS7B01G146000 chr7B 586051083 586052011 928 True 558.000000 558 77.623000 3774 4702 1 chr7B.!!$R1 928
3 TraesCS7B01G146000 chr7D 211635206 211643446 8240 True 2123.000000 3823 95.938000 801 9643 6 chr7D.!!$R1 8842
4 TraesCS7B01G146000 chr7A 223525057 223533685 8628 True 1321.333333 3650 94.149667 801 9719 9 chr7A.!!$R1 8918
5 TraesCS7B01G146000 chr1B 570854379 570856020 1641 True 1666.000000 1666 85.124000 5546 7177 1 chr1B.!!$R3 1631
6 TraesCS7B01G146000 chr1B 6852754 6854384 1630 True 1341.000000 1341 81.741000 5544 7177 1 chr1B.!!$R1 1633
7 TraesCS7B01G146000 chr1B 295768794 295769566 772 False 1290.000000 1290 96.770000 1 773 1 chr1B.!!$F1 772
8 TraesCS7B01G146000 chr4B 187359435 187362051 2616 False 1084.000000 1493 81.677000 3783 7177 2 chr4B.!!$F1 3394
9 TraesCS7B01G146000 chr6A 573846035 573848631 2596 True 1146.500000 1467 83.581000 3771 7177 2 chr6A.!!$R1 3406
10 TraesCS7B01G146000 chr6B 67945464 67946236 772 False 1267.000000 1267 96.253000 1 773 1 chr6B.!!$F1 772
11 TraesCS7B01G146000 chr6B 62114095 62116696 2601 False 1068.000000 1454 81.585000 3783 7177 2 chr6B.!!$F2 3394
12 TraesCS7B01G146000 chr5B 237824878 237825647 769 True 1286.000000 1286 96.762000 1 772 1 chr5B.!!$R1 771
13 TraesCS7B01G146000 chr2B 316103311 316104088 777 False 1282.000000 1282 96.406000 1 779 1 chr2B.!!$F3 778
14 TraesCS7B01G146000 chr2B 296026387 296027161 774 False 1280.000000 1280 96.521000 1 773 1 chr2B.!!$F2 772
15 TraesCS7B01G146000 chr2B 220466583 220467350 767 False 1267.000000 1267 96.378000 1 773 1 chr2B.!!$F1 772
16 TraesCS7B01G146000 chr2B 499568400 499569190 790 False 368.000000 368 75.891000 4712 5536 1 chr2B.!!$F4 824
17 TraesCS7B01G146000 chr4A 151958542 151959312 770 True 1266.000000 1266 96.248000 1 773 1 chr4A.!!$R1 772
18 TraesCS7B01G146000 chr4A 744302414 744303196 782 True 1264.000000 1264 95.791000 1 783 1 chr4A.!!$R2 782
19 TraesCS7B01G146000 chr5D 478167632 478168498 866 False 467.666667 1136 92.024667 4712 5545 3 chr5D.!!$F2 833
20 TraesCS7B01G146000 chr2D 634828630 634830263 1633 True 1103.000000 1103 79.091000 5546 7175 1 chr2D.!!$R2 1629
21 TraesCS7B01G146000 chr2D 329403433 329404323 890 True 687.500000 1127 92.673000 4712 5545 2 chr2D.!!$R3 833
22 TraesCS7B01G146000 chr3D 43673101 43674402 1301 True 562.000000 678 85.287500 3771 5913 2 chr3D.!!$R2 2142
23 TraesCS7B01G146000 chr5A 473243149 473244086 937 False 558.000000 558 77.519000 3765 4702 1 chr5A.!!$F1 937
24 TraesCS7B01G146000 chr5A 685966452 685967380 928 True 558.000000 558 77.671000 3774 4702 1 chr5A.!!$R1 928
25 TraesCS7B01G146000 chr3B 235889504 235890123 619 False 438.000000 438 79.656000 5543 6176 1 chr3B.!!$F1 633

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
963 971 1.226831 GAGCGCTCGGAGGAAGAAG 60.227 63.158 23.61 0.0 0.00 2.85 F
1064 1072 0.451783 GCATTCGCCGGATTTTCAGT 59.548 50.000 5.05 0.0 0.00 3.41 F
2782 2882 1.226717 GTCACCAAAAACGCGCCAA 60.227 52.632 5.73 0.0 0.00 4.52 F
4299 5040 0.037046 CCTGCATTTGCCCTGTTTCC 60.037 55.000 0.00 0.0 41.18 3.13 F
4434 5175 0.035630 ACATGCTCCAGCTGAGGTTC 60.036 55.000 17.39 0.0 41.73 3.62 F
5374 6189 0.167689 GCAGGAGCAAGAAAGAAGCG 59.832 55.000 0.00 0.0 41.58 4.68 F
5923 6749 1.029408 TGTGCTGACAAAACCTGCGT 61.029 50.000 0.00 0.0 0.00 5.24 F
7131 7971 1.209504 CCCCTCGTGCATTTCTCCTTA 59.790 52.381 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 2867 1.657822 AAAATTGGCGCGTTTTTGGT 58.342 40.000 8.43 0.00 0.00 3.67 R
2918 3020 2.601763 CCGCCGCACTTACTTTAGTTAG 59.398 50.000 0.00 0.00 0.00 2.34 R
4434 5175 0.463833 GGTTAAGGATGTGCGGAGGG 60.464 60.000 0.00 0.00 0.00 4.30 R
5699 6520 0.037975 CAAAGGGGCAGACATGTTGC 60.038 55.000 18.79 18.79 40.80 4.17 R
6391 7225 3.610040 ATCCACAACACTATTCAGCGA 57.390 42.857 0.00 0.00 0.00 4.93 R
7010 7848 0.179121 CGTGGCGTATAAGCTGGTCA 60.179 55.000 10.52 0.00 37.29 4.02 R
7707 8556 0.038310 TCGGCACAGGAGAGAGAGAA 59.962 55.000 0.00 0.00 0.00 2.87 R
8862 9945 0.035317 TGGACAGTCCAGTGCACATC 59.965 55.000 19.21 6.07 42.67 3.06 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
382 386 3.063485 GCACGTAAAATTGCCATGGTTT 58.937 40.909 14.67 8.41 32.21 3.27
593 601 5.047847 AGTTTTGAAGATTTCGTCGAGACA 58.952 37.500 4.02 0.00 29.51 3.41
615 623 7.827236 AGACAGATTTAATGGTGAAAACGGATA 59.173 33.333 0.00 0.00 0.00 2.59
775 783 1.807742 TGGGCGTTAACATTTCCGAAG 59.192 47.619 6.39 0.00 0.00 3.79
778 786 3.058085 GGGCGTTAACATTTCCGAAGAAA 60.058 43.478 6.39 0.00 45.78 2.52
832 840 5.478332 AGAAAAGGATTTAGCAAACAGAGGG 59.522 40.000 0.00 0.00 37.28 4.30
923 931 2.285834 CCGATATCGTTGCAGTTTCAGC 60.286 50.000 22.81 0.00 37.74 4.26
963 971 1.226831 GAGCGCTCGGAGGAAGAAG 60.227 63.158 23.61 0.00 0.00 2.85
964 972 2.888051 GCGCTCGGAGGAAGAAGC 60.888 66.667 7.20 0.00 0.00 3.86
965 973 2.202810 CGCTCGGAGGAAGAAGCC 60.203 66.667 7.20 0.00 0.00 4.35
966 974 2.202810 GCTCGGAGGAAGAAGCCG 60.203 66.667 7.20 0.00 46.08 5.52
1064 1072 0.451783 GCATTCGCCGGATTTTCAGT 59.548 50.000 5.05 0.00 0.00 3.41
1709 1807 1.453562 TGCAAGGACTTGTGCAGCA 60.454 52.632 13.08 0.00 45.52 4.41
1832 1931 9.563898 TTTGATCTGAATGAATTTTCTTCATCG 57.436 29.630 1.27 0.00 38.11 3.84
1833 1932 8.496707 TGATCTGAATGAATTTTCTTCATCGA 57.503 30.769 1.27 0.00 38.11 3.59
1834 1933 9.117183 TGATCTGAATGAATTTTCTTCATCGAT 57.883 29.630 0.00 0.00 38.11 3.59
2203 2302 9.893305 ACTGCATATTTGTGAAGTTTTAACTAC 57.107 29.630 0.00 0.00 38.57 2.73
2308 2407 4.430441 ACTCCCTCTGGTTCTATCAAAGT 58.570 43.478 0.00 0.00 0.00 2.66
2680 2780 7.223777 CCATTTTAAGAGCAGCTCTAGTAGAAC 59.776 40.741 25.66 0.00 40.28 3.01
2699 2799 1.750930 CGGCATATCCACAGCCTCT 59.249 57.895 0.00 0.00 46.14 3.69
2712 2812 2.158726 ACAGCCTCTAAAACCGGTTTGA 60.159 45.455 32.23 24.39 32.36 2.69
2782 2882 1.226717 GTCACCAAAAACGCGCCAA 60.227 52.632 5.73 0.00 0.00 4.52
2819 2921 1.533625 TTTGGGCAAGATCAACCTCG 58.466 50.000 0.00 0.00 0.00 4.63
2832 2934 8.562892 CAAGATCAACCTCGAGCAATTATAAAT 58.437 33.333 6.99 0.00 0.00 1.40
2918 3020 9.869844 CACTGCAGCTTAATACATATAGAAAAC 57.130 33.333 15.27 0.00 0.00 2.43
3091 3194 1.318158 CCAAATGCAGTGCTCCCTCC 61.318 60.000 17.60 0.00 0.00 4.30
3104 3207 0.765903 TCCCTCCTGGCATCCATCTC 60.766 60.000 0.00 0.00 30.82 2.75
3149 3644 3.744719 CACCCGCTTCCTCGTCGA 61.745 66.667 0.00 0.00 0.00 4.20
3165 3660 1.213013 CGAACACGACCTCCTCCTG 59.787 63.158 0.00 0.00 0.00 3.86
3168 3663 1.122019 AACACGACCTCCTCCTGCTT 61.122 55.000 0.00 0.00 0.00 3.91
3169 3664 1.079543 CACGACCTCCTCCTGCTTG 60.080 63.158 0.00 0.00 0.00 4.01
3170 3665 1.228894 ACGACCTCCTCCTGCTTGA 60.229 57.895 0.00 0.00 0.00 3.02
3173 3668 0.179936 GACCTCCTCCTGCTTGATGG 59.820 60.000 0.00 0.00 0.00 3.51
3494 3989 2.690778 GCCTTGTGCGATGTCCCAC 61.691 63.158 0.00 0.00 0.00 4.61
3554 4049 2.637589 GCCGGCCTTTTATAGCGC 59.362 61.111 18.11 0.00 0.00 5.92
3684 4179 3.560278 CGGCCGCGACATTGGTAC 61.560 66.667 14.67 0.00 0.00 3.34
3685 4180 3.560278 GGCCGCGACATTGGTACG 61.560 66.667 8.23 0.00 0.00 3.67
3719 4218 3.124066 AGGGGAAGAGGAAGGGAAATAC 58.876 50.000 0.00 0.00 0.00 1.89
3824 4549 0.320771 AGGACAAGACGCCACACATC 60.321 55.000 0.00 0.00 0.00 3.06
3826 4551 0.320771 GACAAGACGCCACACATCCT 60.321 55.000 0.00 0.00 0.00 3.24
3981 4706 4.238514 CCTAGCTGAGTGACTGTGTTTAC 58.761 47.826 0.00 0.00 0.00 2.01
4032 4764 1.610363 AGCGCATCCGAGAATCTCTA 58.390 50.000 11.47 0.00 36.29 2.43
4299 5040 0.037046 CCTGCATTTGCCCTGTTTCC 60.037 55.000 0.00 0.00 41.18 3.13
4434 5175 0.035630 ACATGCTCCAGCTGAGGTTC 60.036 55.000 17.39 0.00 41.73 3.62
4539 5280 4.157656 GGTTTCTACATGCATGCCTTTGTA 59.842 41.667 26.53 17.85 0.00 2.41
4621 5362 5.762279 ACTTTGTTTCTAAGGGGAAGTGAA 58.238 37.500 0.00 0.00 0.00 3.18
4629 5370 1.729586 AGGGGAAGTGAACACAGCTA 58.270 50.000 7.68 0.00 0.00 3.32
4753 5494 0.250467 AACTGCTCCATCGCAACACT 60.250 50.000 0.00 0.00 39.80 3.55
4817 5621 1.754380 TATATTGCAGCTCCGGCGGT 61.754 55.000 27.32 3.11 44.37 5.68
4877 5681 1.006102 CAGCTTCAACGACTCCGGT 60.006 57.895 0.00 0.00 40.78 5.28
4927 5731 2.390599 CGTTGCATAGCAGCACCGT 61.391 57.895 6.64 0.00 44.00 4.83
5069 5874 0.179113 CCGCTGCACCAACAAAAAGT 60.179 50.000 0.00 0.00 0.00 2.66
5122 5928 2.261671 CTTCACACGGGTAGCGCT 59.738 61.111 17.26 17.26 0.00 5.92
5124 5930 2.486636 CTTCACACGGGTAGCGCTGA 62.487 60.000 22.90 3.47 0.00 4.26
5257 6064 1.346395 TCACAGGAGCGCCTAAGAAAA 59.654 47.619 9.34 0.00 44.80 2.29
5258 6065 1.734465 CACAGGAGCGCCTAAGAAAAG 59.266 52.381 9.34 0.00 44.80 2.27
5295 6104 3.773119 TGTGTAAGGTATTGGAGAGGACC 59.227 47.826 0.00 0.00 0.00 4.46
5334 6143 2.727123 TGCTTTGAGGTTGAGGAACA 57.273 45.000 0.00 0.00 33.27 3.18
5353 6162 1.289244 ACATCCATGGAGGGGTTCCC 61.289 60.000 28.76 0.00 46.19 3.97
5374 6189 0.167689 GCAGGAGCAAGAAAGAAGCG 59.832 55.000 0.00 0.00 41.58 4.68
5420 6241 3.938963 GGAAAGAATGAATGGTCTGCGTA 59.061 43.478 0.00 0.00 0.00 4.42
5452 6273 3.181489 GGAGATAAGGAAAGCGAACGAGA 60.181 47.826 0.00 0.00 0.00 4.04
5760 6581 2.287584 TCCTCTTGGAATCCATGGGTT 58.712 47.619 10.92 10.92 39.87 4.11
5923 6749 1.029408 TGTGCTGACAAAACCTGCGT 61.029 50.000 0.00 0.00 0.00 5.24
6022 6853 1.986882 AAGCCCAGACCTCAGTTTTG 58.013 50.000 0.00 0.00 0.00 2.44
6391 7225 2.080654 TAGCCCTTGCCTTGTGTTTT 57.919 45.000 0.00 0.00 38.69 2.43
6594 7428 6.043012 CCCTTTAATGATCCTCTCATCTCAGT 59.957 42.308 0.00 0.00 44.03 3.41
6912 7750 5.798132 TGAGTTAGCTCATATGCCAATAGG 58.202 41.667 5.01 0.00 45.94 2.57
6994 7832 3.175133 AGGATTACCTTGCGCCTTG 57.825 52.632 4.18 0.00 45.36 3.61
7010 7848 2.890945 GCCTTGTTGTGATTACCTTGGT 59.109 45.455 0.00 0.00 0.00 3.67
7035 7873 3.120792 CAGCTTATACGCCACGTTACAT 58.879 45.455 0.00 0.00 41.54 2.29
7131 7971 1.209504 CCCCTCGTGCATTTCTCCTTA 59.790 52.381 0.00 0.00 0.00 2.69
7143 7987 7.012421 GTGCATTTCTCCTTAAATATCCGAAGT 59.988 37.037 0.00 0.00 0.00 3.01
7212 8056 1.709578 TCTCCTGCTACCCTGCATAG 58.290 55.000 0.00 0.00 42.48 2.23
7248 8092 4.101448 GTCCCCTCGCATGCCAGT 62.101 66.667 13.15 0.00 0.00 4.00
7318 8162 6.152831 ACAACCTAGCTTCAAACTTGAAACTT 59.847 34.615 12.06 2.12 45.61 2.66
7398 8242 3.767673 GGCCTATAGTCCGAATGGTATGA 59.232 47.826 0.00 0.00 36.30 2.15
7602 8451 1.480789 GTTTTGGGGTGAGGTGTTGT 58.519 50.000 0.00 0.00 0.00 3.32
7630 8479 8.950210 CATACTGGTTTTGATAGTGTTTCTGAT 58.050 33.333 0.00 0.00 0.00 2.90
7705 8554 2.808919 TCCATCTTCTTCCTCGTGTCT 58.191 47.619 0.00 0.00 0.00 3.41
7706 8555 2.755655 TCCATCTTCTTCCTCGTGTCTC 59.244 50.000 0.00 0.00 0.00 3.36
7707 8556 2.757868 CCATCTTCTTCCTCGTGTCTCT 59.242 50.000 0.00 0.00 0.00 3.10
7728 8593 1.110442 CTCTCTCTCCTGTGCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
7756 8621 1.813102 AATCTCCTCCATCTCCACCC 58.187 55.000 0.00 0.00 0.00 4.61
7802 8813 0.522626 TGCACGTACGTAGCAAGCTA 59.477 50.000 29.88 15.23 34.97 3.32
8153 9200 7.597369 GTGTCCTTTTCTTGTTGTTAACACTTT 59.403 33.333 8.07 0.00 41.97 2.66
8256 9303 3.555966 CACCCCTTGAAGTTCTTTCTGT 58.444 45.455 4.17 0.00 36.71 3.41
8271 9318 3.777106 TTCTGTATCAGCCATCCCATC 57.223 47.619 0.00 0.00 0.00 3.51
8330 9377 1.073763 TGGCCCGAATATCCTCATTGG 59.926 52.381 0.00 0.00 37.10 3.16
8332 9379 1.545428 GCCCGAATATCCTCATTGGCA 60.545 52.381 0.00 0.00 37.58 4.92
8433 9480 3.989705 TGCTTATCGTCGACATGTTTG 57.010 42.857 17.16 0.00 0.00 2.93
8644 9691 1.811679 GCGAGGCAGCTGAACTACC 60.812 63.158 20.43 8.73 30.93 3.18
8755 9802 4.810790 AGAATCAATCGACGAAACTCTGT 58.189 39.130 0.00 0.00 0.00 3.41
8845 9928 4.651778 TGATCCGGATGTTCTCTTTTTGT 58.348 39.130 24.82 0.00 0.00 2.83
8862 9945 6.313411 TCTTTTTGTTTGCATTCTCAACCAAG 59.687 34.615 0.00 0.00 31.63 3.61
8908 9991 8.650143 AGACCAATTGGATGTATACACTTTTT 57.350 30.769 31.22 1.85 38.94 1.94
8953 10038 3.117701 TGACAAGAAACAAGATGGGGTCA 60.118 43.478 0.00 0.00 0.00 4.02
8986 10071 0.174617 GGACACTGAGCTGCCTACTC 59.825 60.000 0.00 0.00 34.62 2.59
9008 10093 1.626321 TCCTGAACCATCAAGGCGTTA 59.374 47.619 0.00 0.00 43.14 3.18
9049 10134 7.379529 CAGATGCTTTATCACTTTGTTTTCGTT 59.620 33.333 0.00 0.00 38.31 3.85
9064 10149 2.888513 TCGTTAGATATACGGCGAGC 57.111 50.000 16.62 0.00 39.38 5.03
9124 10209 2.115427 TCAGATCACGGGCCAAATAGA 58.885 47.619 4.39 0.00 0.00 1.98
9403 10488 3.818773 TCCGAAAATCAAGAACTCCAACC 59.181 43.478 0.00 0.00 0.00 3.77
9448 10533 6.077838 GGTCTAAGCAAAACGTTGACATAAG 58.922 40.000 0.00 0.00 36.83 1.73
9497 10582 6.677552 TGATTATGTTTACATTGGATCCCCA 58.322 36.000 9.90 0.00 41.64 4.96
9518 10603 1.410882 TGCATGATGGCACCAATGATG 59.589 47.619 0.00 4.19 39.25 3.07
9520 10605 1.410882 CATGATGGCACCAATGATGCA 59.589 47.619 0.50 0.00 45.27 3.96
9548 10633 1.469703 CCAATCTTGCACTGCGAATGA 59.530 47.619 0.00 0.00 0.00 2.57
9597 10683 5.435291 AGAATCTCAGGCTGTCATTAAAGG 58.565 41.667 15.27 0.00 0.00 3.11
9634 10720 2.542595 CGCTTCAACAAGAAACCGTACT 59.457 45.455 0.00 0.00 35.40 2.73
9637 10742 4.508861 GCTTCAACAAGAAACCGTACTACA 59.491 41.667 0.00 0.00 35.40 2.74
9641 10746 1.990563 CAAGAAACCGTACTACAGGCG 59.009 52.381 0.00 0.00 0.00 5.52
9671 10776 4.988598 CGCGTGTTGCCCCAGTCT 62.989 66.667 0.00 0.00 42.08 3.24
9672 10777 3.357079 GCGTGTTGCCCCAGTCTG 61.357 66.667 0.00 0.00 37.76 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
306 310 9.466497 TCATGGCAAGTCTAATTTCTTAATTCT 57.534 29.630 0.00 0.00 35.61 2.40
318 322 6.245408 AGTTTATGGTTCATGGCAAGTCTAA 58.755 36.000 0.00 0.00 0.00 2.10
507 512 4.072131 AGAAGTTGCCACGATGTTTACAT 58.928 39.130 0.00 0.00 39.70 2.29
552 560 9.952030 TTCAAAACTAGACCACATGTTGATATA 57.048 29.630 3.55 0.00 0.00 0.86
564 572 5.404366 CGACGAAATCTTCAAAACTAGACCA 59.596 40.000 0.00 0.00 0.00 4.02
782 790 7.778185 TTTCTAACTAGCTAGTCTTCACCTT 57.222 36.000 26.21 10.90 34.99 3.50
783 791 7.778185 TTTTCTAACTAGCTAGTCTTCACCT 57.222 36.000 26.21 11.63 34.99 4.00
784 792 8.305317 TCTTTTTCTAACTAGCTAGTCTTCACC 58.695 37.037 26.21 0.00 34.99 4.02
785 793 9.694137 TTCTTTTTCTAACTAGCTAGTCTTCAC 57.306 33.333 26.21 0.00 34.99 3.18
789 797 9.713713 CCTTTTCTTTTTCTAACTAGCTAGTCT 57.286 33.333 26.21 17.68 34.99 3.24
790 798 9.708092 TCCTTTTCTTTTTCTAACTAGCTAGTC 57.292 33.333 26.21 0.00 34.99 2.59
814 822 5.230182 CAAAACCCTCTGTTTGCTAAATCC 58.770 41.667 0.00 0.00 46.39 3.01
832 840 4.864704 TGGTCCTAGGAATTTGCAAAAC 57.135 40.909 17.19 12.93 0.00 2.43
923 931 2.260088 TTTCCCGGGATAAGGTGCGG 62.260 60.000 27.48 0.00 0.00 5.69
986 994 2.447047 ACCTCCATTTTTGTCTCCCTGT 59.553 45.455 0.00 0.00 0.00 4.00
1709 1807 0.106819 GATGGAGGCCAACTGCTGAT 60.107 55.000 5.01 0.00 36.95 2.90
1839 1938 9.868389 CGAATATCGATGAAGAAAATTCATTCA 57.132 29.630 8.54 9.09 43.74 2.57
1840 1939 8.835160 GCGAATATCGATGAAGAAAATTCATTC 58.165 33.333 8.54 3.83 43.74 2.67
1841 1940 8.344831 TGCGAATATCGATGAAGAAAATTCATT 58.655 29.630 8.54 0.00 43.74 2.57
1842 1941 7.864686 TGCGAATATCGATGAAGAAAATTCAT 58.135 30.769 8.54 2.86 43.74 2.57
1843 1942 7.245419 TGCGAATATCGATGAAGAAAATTCA 57.755 32.000 8.54 0.00 43.74 2.57
1844 1943 6.301842 GCTGCGAATATCGATGAAGAAAATTC 59.698 38.462 8.54 6.47 43.74 2.17
1845 1944 6.138761 GCTGCGAATATCGATGAAGAAAATT 58.861 36.000 8.54 0.00 43.74 1.82
1846 1945 5.334414 GGCTGCGAATATCGATGAAGAAAAT 60.334 40.000 8.54 0.00 43.74 1.82
2203 2302 5.404946 CCATCCTAATGCAAAGAAACACAG 58.595 41.667 0.00 0.00 0.00 3.66
2308 2407 2.064434 TGCAGATGTCCAAAACACCA 57.936 45.000 0.00 0.00 41.75 4.17
2699 2799 2.966516 AGGGCATTTCAAACCGGTTTTA 59.033 40.909 29.74 19.89 0.00 1.52
2767 2867 1.657822 AAAATTGGCGCGTTTTTGGT 58.342 40.000 8.43 0.00 0.00 3.67
2918 3020 2.601763 CCGCCGCACTTACTTTAGTTAG 59.398 50.000 0.00 0.00 0.00 2.34
3073 3176 0.323178 AGGAGGGAGCACTGCATTTG 60.323 55.000 3.30 0.00 0.00 2.32
3149 3644 1.122019 AAGCAGGAGGAGGTCGTGTT 61.122 55.000 0.00 0.00 42.16 3.32
3494 3989 2.074948 CCCCTCCACATCTCCCCTG 61.075 68.421 0.00 0.00 0.00 4.45
3514 4009 2.692741 CCCCTCCCCTTCTCCACC 60.693 72.222 0.00 0.00 0.00 4.61
3572 4067 3.814268 CATTTCCCCACGCCTGCG 61.814 66.667 10.40 10.40 46.03 5.18
3671 4166 3.560278 GCCCGTACCAATGTCGCG 61.560 66.667 0.00 0.00 0.00 5.87
3684 4179 4.521062 CCCTCTCTTCTGCGCCCG 62.521 72.222 4.18 0.00 0.00 6.13
3685 4180 4.168291 CCCCTCTCTTCTGCGCCC 62.168 72.222 4.18 0.00 0.00 6.13
3732 4231 5.528870 ACAACCCTCAATCGACAAATTTTC 58.471 37.500 0.00 0.00 0.00 2.29
3824 4549 1.273327 GCCTGTGGGTTTCAATGAAGG 59.727 52.381 0.00 0.00 34.45 3.46
3826 4551 2.079170 TGCCTGTGGGTTTCAATGAA 57.921 45.000 0.00 0.00 34.45 2.57
3981 4706 2.599973 GCTTTGGCAATGCTTTATGTCG 59.400 45.455 25.60 0.00 38.54 4.35
4032 4764 1.078426 GCTGGTGCGGGTAATCTGT 60.078 57.895 0.00 0.00 0.00 3.41
4299 5040 1.314534 TTGGCGATGGTGGCATGAAG 61.315 55.000 0.00 0.00 44.53 3.02
4434 5175 0.463833 GGTTAAGGATGTGCGGAGGG 60.464 60.000 0.00 0.00 0.00 4.30
4473 5214 1.792118 CGATGAGGATGGCGGACGTA 61.792 60.000 0.00 0.00 0.00 3.57
4539 5280 1.531423 CCTGTGCATGAAGCTTCAGT 58.469 50.000 31.14 17.89 45.94 3.41
4621 5362 2.657237 GACTGGCCGTAGCTGTGT 59.343 61.111 0.00 0.00 39.73 3.72
4629 5370 2.280592 GTGGTTTCGACTGGCCGT 60.281 61.111 0.00 0.00 0.00 5.68
4817 5621 1.003476 TCGGAGCTGCAATGAAGCA 60.003 52.632 16.64 0.00 43.37 3.91
4821 5625 2.125552 CCGTCGGAGCTGCAATGA 60.126 61.111 4.91 0.00 0.00 2.57
4850 5654 2.045045 TTGAAGCTGCGATGGGGG 60.045 61.111 0.00 0.00 0.00 5.40
4877 5681 1.665916 GAGCTGCAGTTGAGCGTCA 60.666 57.895 16.64 0.00 41.61 4.35
5100 5905 0.320421 GCTACCCGTGTGAAGCTCAA 60.320 55.000 0.00 0.00 32.18 3.02
5122 5928 3.337889 GCTGCGCAACACTCGTCA 61.338 61.111 13.05 0.00 0.00 4.35
5334 6143 2.321720 GGAACCCCTCCATGGATGT 58.678 57.895 16.63 10.32 44.67 3.06
5353 6162 1.199558 GCTTCTTTCTTGCTCCTGCTG 59.800 52.381 0.00 0.00 40.48 4.41
5354 6163 1.532523 GCTTCTTTCTTGCTCCTGCT 58.467 50.000 0.00 0.00 40.48 4.24
5355 6164 0.167689 CGCTTCTTTCTTGCTCCTGC 59.832 55.000 0.00 0.00 40.20 4.85
5356 6165 0.801251 CCGCTTCTTTCTTGCTCCTG 59.199 55.000 0.00 0.00 0.00 3.86
5357 6166 0.322008 CCCGCTTCTTTCTTGCTCCT 60.322 55.000 0.00 0.00 0.00 3.69
5358 6167 1.308783 CCCCGCTTCTTTCTTGCTCC 61.309 60.000 0.00 0.00 0.00 4.70
5359 6168 1.308783 CCCCCGCTTCTTTCTTGCTC 61.309 60.000 0.00 0.00 0.00 4.26
5699 6520 0.037975 CAAAGGGGCAGACATGTTGC 60.038 55.000 18.79 18.79 40.80 4.17
5923 6749 9.983024 TTATTCAAAACCCATCTTCCTTATGTA 57.017 29.630 0.00 0.00 0.00 2.29
6022 6853 6.753744 GCTGGGAAATATTGATGAAGACAAAC 59.246 38.462 0.00 0.00 0.00 2.93
6239 7072 3.933861 AAGAGAGTGTGTGGAAAAGGT 57.066 42.857 0.00 0.00 0.00 3.50
6391 7225 3.610040 ATCCACAACACTATTCAGCGA 57.390 42.857 0.00 0.00 0.00 4.93
6594 7428 4.458989 GGTTCTCAGCCATGTTACATGAAA 59.541 41.667 25.02 7.61 0.00 2.69
6993 7831 3.117851 TGGTCACCAAGGTAATCACAACA 60.118 43.478 0.00 0.00 0.00 3.33
6994 7832 3.482436 TGGTCACCAAGGTAATCACAAC 58.518 45.455 0.00 0.00 0.00 3.32
7010 7848 0.179121 CGTGGCGTATAAGCTGGTCA 60.179 55.000 10.52 0.00 37.29 4.02
7035 7873 3.039011 GGACCTGAGACCAATAAGCCTA 58.961 50.000 0.00 0.00 0.00 3.93
7131 7971 8.142551 GTCATACAAGAGGTACTTCGGATATTT 58.857 37.037 0.00 0.00 41.55 1.40
7143 7987 3.773119 GGAACCAGGTCATACAAGAGGTA 59.227 47.826 0.00 0.00 36.16 3.08
7212 8056 4.319177 GGACCATAATACTCAGGTGATGC 58.681 47.826 0.00 0.00 33.77 3.91
7248 8092 3.118956 GGTCAACAATGTTTGGACCAACA 60.119 43.478 22.89 9.04 31.88 3.33
7318 8162 0.321210 TTTTCAGGAGAATGGCGCGA 60.321 50.000 12.10 0.00 32.89 5.87
7383 8227 7.546250 AATAGAGATTCATACCATTCGGACT 57.454 36.000 0.00 0.00 35.59 3.85
7602 8451 9.214957 CAGAAACACTATCAAAACCAGTATGTA 57.785 33.333 0.00 0.00 0.00 2.29
7630 8479 0.611618 GTTCATGTGTGCCCCATCCA 60.612 55.000 0.00 0.00 0.00 3.41
7705 8554 1.846007 GGCACAGGAGAGAGAGAAGA 58.154 55.000 0.00 0.00 0.00 2.87
7706 8555 0.455410 CGGCACAGGAGAGAGAGAAG 59.545 60.000 0.00 0.00 0.00 2.85
7707 8556 0.038310 TCGGCACAGGAGAGAGAGAA 59.962 55.000 0.00 0.00 0.00 2.87
7728 8593 1.254975 TGGAGGAGATTTCGGCGACA 61.255 55.000 10.16 2.52 0.00 4.35
7802 8813 2.833582 ATCGATCAGGCGACCCGT 60.834 61.111 0.00 0.00 43.79 5.28
8153 9200 7.012799 TGCGCAATTATGAATAATTAGGTGTCA 59.987 33.333 8.16 4.82 40.07 3.58
8256 9303 0.686789 CGGTGATGGGATGGCTGATA 59.313 55.000 0.00 0.00 0.00 2.15
8332 9379 9.726232 GATTTGCATTCACGCATATATCAATAT 57.274 29.630 0.00 0.00 42.62 1.28
8420 9467 1.194547 CCTGAACCAAACATGTCGACG 59.805 52.381 11.62 0.00 0.00 5.12
8433 9480 6.429385 CAGGCTTATATGAGAAATCCTGAACC 59.571 42.308 11.28 0.00 41.62 3.62
8644 9691 0.674895 GGTTGGTACTGGAGCTGCTG 60.675 60.000 7.01 10.59 0.00 4.41
8755 9802 5.048083 ACTCTGTGTTTCAGTTTGAAAGCAA 60.048 36.000 4.59 0.00 45.83 3.91
8845 9928 4.796946 GCACATCTTGGTTGAGAATGCAAA 60.797 41.667 0.00 0.00 39.64 3.68
8862 9945 0.035317 TGGACAGTCCAGTGCACATC 59.965 55.000 19.21 6.07 42.67 3.06
8908 9991 2.429610 GTCTAATTACCTCCTGACCGCA 59.570 50.000 0.00 0.00 0.00 5.69
8968 10053 0.179150 CGAGTAGGCAGCTCAGTGTC 60.179 60.000 8.61 0.00 33.45 3.67
8986 10071 1.361668 CGCCTTGATGGTTCAGGACG 61.362 60.000 0.00 0.00 38.35 4.79
9049 10134 2.511659 ACCTTGCTCGCCGTATATCTA 58.488 47.619 0.00 0.00 0.00 1.98
9064 10149 5.733373 GCAGTAAAGTTCTTCACCAACCTTG 60.733 44.000 0.00 0.00 0.00 3.61
9403 10488 3.379240 CCTCGCACTGTAATCATCTCTG 58.621 50.000 0.00 0.00 0.00 3.35
9497 10582 1.783071 TCATTGGTGCCATCATGCAT 58.217 45.000 0.00 0.00 44.30 3.96
9518 10603 0.174162 GCAAGATTGGTCATGGGTGC 59.826 55.000 0.00 0.00 0.00 5.01
9520 10605 1.076024 AGTGCAAGATTGGTCATGGGT 59.924 47.619 0.00 0.00 0.00 4.51
9597 10683 1.742880 GCGAAACGGGTTCCCTACC 60.743 63.158 6.31 0.00 46.99 3.18
9609 10695 2.781646 CGGTTTCTTGTTGAAGCGAAAC 59.218 45.455 0.00 0.00 42.57 2.78
9634 10720 1.180029 GGTAGGTTCAGTCGCCTGTA 58.820 55.000 0.00 0.00 39.82 2.74
9637 10742 2.348888 CGGGTAGGTTCAGTCGCCT 61.349 63.158 0.00 0.00 38.81 5.52
9641 10746 1.445582 CACGCGGGTAGGTTCAGTC 60.446 63.158 12.47 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.