Multiple sequence alignment - TraesCS3A01G485900

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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 TraesCS3A01G485900 chr3A 100.000 4176 0 0 1 4176 714605600 714601425 0.000000e+00 7712.0
1 TraesCS3A01G485900 chr3A 89.363 1852 103 29 915 2692 714624167 714625998 0.000000e+00 2242.0
2 TraesCS3A01G485900 chr3A 93.436 716 46 1 1977 2692 714594258 714593544 0.000000e+00 1061.0
3 TraesCS3A01G485900 chr3A 88.757 676 67 5 2699 3366 714588968 714588294 0.000000e+00 819.0
4 TraesCS3A01G485900 chr3A 86.776 673 72 6 2699 3365 714646625 714647286 0.000000e+00 734.0
5 TraesCS3A01G485900 chr3A 75.302 579 111 30 8 571 421165665 421166226 8.970000e-62 248.0
6 TraesCS3A01G485900 chr3A 79.714 350 37 18 1623 1970 714594995 714594678 5.430000e-54 222.0
7 TraesCS3A01G485900 chr3A 79.612 206 33 9 285 487 472576680 472576481 5.630000e-29 139.0
8 TraesCS3A01G485900 chr3B 88.939 1103 93 15 1470 2550 773763001 773761906 0.000000e+00 1334.0
9 TraesCS3A01G485900 chr3B 86.102 1252 106 25 1468 2692 773746607 773745397 0.000000e+00 1286.0
10 TraesCS3A01G485900 chr3B 86.719 1024 107 17 2689 3692 773758384 773757370 0.000000e+00 1110.0
11 TraesCS3A01G485900 chr3B 92.857 574 41 0 1977 2550 773897347 773897920 0.000000e+00 833.0
12 TraesCS3A01G485900 chr3B 88.540 637 60 6 2699 3323 773901263 773901898 0.000000e+00 760.0
13 TraesCS3A01G485900 chr3B 88.431 631 63 8 2699 3323 773743714 773743088 0.000000e+00 752.0
14 TraesCS3A01G485900 chr3B 80.889 450 50 15 1509 1949 773883273 773883695 5.210000e-84 322.0
15 TraesCS3A01G485900 chr3B 77.108 581 92 33 12 569 410110595 410111157 8.780000e-77 298.0
16 TraesCS3A01G485900 chr3B 81.283 374 43 17 3810 4173 773878109 773878465 1.140000e-70 278.0
17 TraesCS3A01G485900 chr3B 84.138 290 41 5 1498 1785 37739716 37739430 4.110000e-70 276.0
18 TraesCS3A01G485900 chr3B 87.647 170 21 0 3131 3300 773877938 773878107 9.160000e-47 198.0
19 TraesCS3A01G485900 chr3B 90.714 140 10 3 4038 4176 773750172 773750035 2.560000e-42 183.0
20 TraesCS3A01G485900 chr3B 85.496 131 13 4 3867 3992 773751420 773751291 9.420000e-27 132.0
21 TraesCS3A01G485900 chr3B 94.737 57 3 0 2634 2690 773761877 773761821 5.750000e-14 89.8
22 TraesCS3A01G485900 chr3B 92.982 57 4 0 2634 2690 773897949 773898005 2.680000e-12 84.2
23 TraesCS3A01G485900 chr3D 95.906 806 28 3 3374 4176 579420527 579419724 0.000000e+00 1301.0
24 TraesCS3A01G485900 chr3D 90.929 904 51 10 1668 2550 579583600 579584493 0.000000e+00 1186.0
25 TraesCS3A01G485900 chr3D 91.805 842 43 8 1877 2692 579425743 579424902 0.000000e+00 1149.0
26 TraesCS3A01G485900 chr3D 95.938 640 24 2 2689 3328 579421160 579420523 0.000000e+00 1037.0
27 TraesCS3A01G485900 chr3D 87.994 683 70 9 2693 3366 579383693 579383014 0.000000e+00 797.0
28 TraesCS3A01G485900 chr3D 87.370 673 75 6 2699 3365 579588192 579588860 0.000000e+00 763.0
29 TraesCS3A01G485900 chr3D 79.424 729 72 37 1038 1714 579426698 579425996 1.070000e-120 444.0
30 TraesCS3A01G485900 chr3D 83.524 437 45 16 1468 1899 579398106 579397692 2.360000e-102 383.0
31 TraesCS3A01G485900 chr3D 80.000 320 48 14 22 330 600084642 600084328 5.430000e-54 222.0
32 TraesCS3A01G485900 chr3D 80.913 241 23 11 1728 1968 579426009 579425792 7.180000e-38 169.0
33 TraesCS3A01G485900 chr3D 96.875 96 3 0 1977 2072 579397653 579397558 1.200000e-35 161.0
34 TraesCS3A01G485900 chr4A 78.966 561 50 26 1502 2035 714667343 714667862 1.870000e-83 320.0
35 TraesCS3A01G485900 chr4A 87.302 63 6 2 426 487 105969226 105969165 2.080000e-08 71.3
36 TraesCS3A01G485900 chr2B 86.207 290 35 5 1498 1785 120491243 120491529 4.050000e-80 309.0
37 TraesCS3A01G485900 chr2B 85.214 257 35 3 1531 1785 315136402 315136657 1.150000e-65 261.0
38 TraesCS3A01G485900 chr2B 74.426 653 89 45 236 837 24246043 24245418 4.230000e-50 209.0
39 TraesCS3A01G485900 chr2B 77.978 277 46 15 304 569 73970399 73970127 4.320000e-35 159.0
40 TraesCS3A01G485900 chr2A 76.531 588 100 31 12 576 8455045 8455617 1.900000e-73 287.0
41 TraesCS3A01G485900 chr1B 76.372 656 84 40 257 887 565329018 565329627 1.900000e-73 287.0
42 TraesCS3A01G485900 chr1B 84.828 290 39 5 1498 1785 670761408 670761694 1.900000e-73 287.0
43 TraesCS3A01G485900 chr4B 84.536 291 38 7 1498 1785 622342306 622342020 8.840000e-72 281.0
44 TraesCS3A01G485900 chr4D 78.252 469 73 26 380 837 325115771 325116221 1.480000e-69 274.0
45 TraesCS3A01G485900 chr4D 75.325 616 82 46 289 875 499573365 499572791 9.030000e-57 231.0
46 TraesCS3A01G485900 chr7B 74.966 735 103 55 149 837 199983215 199983914 3.200000e-66 263.0
47 TraesCS3A01G485900 chr5B 77.098 441 79 19 121 548 331887437 331887006 6.980000e-58 235.0
48 TraesCS3A01G485900 chr5B 76.136 352 68 16 229 572 244742429 244742772 2.000000e-38 171.0
49 TraesCS3A01G485900 chr5B 82.979 94 11 4 378 468 543822807 543822898 3.460000e-11 80.5
50 TraesCS3A01G485900 chr5D 79.795 292 40 18 183 465 80367711 80367992 1.180000e-45 195.0
51 TraesCS3A01G485900 chr5D 76.378 381 48 21 407 774 170322836 170322485 2.580000e-37 167.0
52 TraesCS3A01G485900 chr2D 74.866 374 69 23 210 572 399028574 399028215 3.360000e-31 147.0
53 TraesCS3A01G485900 chrUn 79.646 226 25 10 1502 1720 230759903 230760114 4.350000e-30 143.0
54 TraesCS3A01G485900 chr7A 84.354 147 21 2 12 158 493116108 493116252 4.350000e-30 143.0


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 TraesCS3A01G485900 chr3A 714601425 714605600 4175 True 7712.000000 7712 100.000000 1 4176 1 chr3A.!!$R3 4175
1 TraesCS3A01G485900 chr3A 714624167 714625998 1831 False 2242.000000 2242 89.363000 915 2692 1 chr3A.!!$F2 1777
2 TraesCS3A01G485900 chr3A 714588294 714588968 674 True 819.000000 819 88.757000 2699 3366 1 chr3A.!!$R2 667
3 TraesCS3A01G485900 chr3A 714646625 714647286 661 False 734.000000 734 86.776000 2699 3365 1 chr3A.!!$F3 666
4 TraesCS3A01G485900 chr3A 714593544 714594995 1451 True 641.500000 1061 86.575000 1623 2692 2 chr3A.!!$R4 1069
5 TraesCS3A01G485900 chr3A 421165665 421166226 561 False 248.000000 248 75.302000 8 571 1 chr3A.!!$F1 563
6 TraesCS3A01G485900 chr3B 773757370 773763001 5631 True 844.600000 1334 90.131667 1470 3692 3 chr3B.!!$R3 2222
7 TraesCS3A01G485900 chr3B 773743088 773751420 8332 True 588.250000 1286 87.685750 1468 4176 4 chr3B.!!$R2 2708
8 TraesCS3A01G485900 chr3B 773897347 773901898 4551 False 559.066667 833 91.459667 1977 3323 3 chr3B.!!$F4 1346
9 TraesCS3A01G485900 chr3B 410110595 410111157 562 False 298.000000 298 77.108000 12 569 1 chr3B.!!$F1 557
10 TraesCS3A01G485900 chr3B 773877938 773878465 527 False 238.000000 278 84.465000 3131 4173 2 chr3B.!!$F3 1042
11 TraesCS3A01G485900 chr3D 579583600 579588860 5260 False 974.500000 1186 89.149500 1668 3365 2 chr3D.!!$F1 1697
12 TraesCS3A01G485900 chr3D 579419724 579426698 6974 True 820.000000 1301 88.797200 1038 4176 5 chr3D.!!$R4 3138
13 TraesCS3A01G485900 chr3D 579383014 579383693 679 True 797.000000 797 87.994000 2693 3366 1 chr3D.!!$R1 673
14 TraesCS3A01G485900 chr3D 579397558 579398106 548 True 272.000000 383 90.199500 1468 2072 2 chr3D.!!$R3 604
15 TraesCS3A01G485900 chr4A 714667343 714667862 519 False 320.000000 320 78.966000 1502 2035 1 chr4A.!!$F1 533
16 TraesCS3A01G485900 chr2B 24245418 24246043 625 True 209.000000 209 74.426000 236 837 1 chr2B.!!$R1 601
17 TraesCS3A01G485900 chr2A 8455045 8455617 572 False 287.000000 287 76.531000 12 576 1 chr2A.!!$F1 564
18 TraesCS3A01G485900 chr1B 565329018 565329627 609 False 287.000000 287 76.372000 257 887 1 chr1B.!!$F1 630
19 TraesCS3A01G485900 chr4D 499572791 499573365 574 True 231.000000 231 75.325000 289 875 1 chr4D.!!$R1 586
20 TraesCS3A01G485900 chr7B 199983215 199983914 699 False 263.000000 263 74.966000 149 837 1 chr7B.!!$F1 688

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
876 1104 0.107654 GGTCCCCAGTTCGAATCCAG 60.108 60.0 0.00 0.0 0.00 3.86 F
1173 1421 0.174845 TCCGCAACTCCATACCTTCG 59.825 55.0 0.00 0.0 0.00 3.79 F
2252 6210 0.106708 ATGGCACTGGCTGTATACCG 59.893 55.0 3.97 0.0 40.87 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 6088 0.040067 CCACAGCGAACAAAGGAAGC 60.040 55.0 0.00 0.0 0.00 3.86 R
2524 6482 0.614697 TGAGATCCTCCGAGGCACAA 60.615 55.0 9.87 0.0 34.61 3.33 R
3624 12743 0.098200 CAGCCACAACATCAGCATCG 59.902 55.0 0.00 0.0 0.00 3.84 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
20 21 4.676951 CATGGTGTTGGGCCGGGT 62.677 66.667 2.18 0.00 0.00 5.28
35 37 4.204799 GGCCGGGTCATATAGTTTTTCTT 58.795 43.478 2.18 0.00 0.00 2.52
36 38 4.275196 GGCCGGGTCATATAGTTTTTCTTC 59.725 45.833 2.18 0.00 0.00 2.87
39 41 6.238402 GCCGGGTCATATAGTTTTTCTTCTTC 60.238 42.308 2.18 0.00 0.00 2.87
40 42 6.260271 CCGGGTCATATAGTTTTTCTTCTTCC 59.740 42.308 0.00 0.00 0.00 3.46
42 44 6.822170 GGGTCATATAGTTTTTCTTCTTCCGT 59.178 38.462 0.00 0.00 0.00 4.69
43 45 7.201617 GGGTCATATAGTTTTTCTTCTTCCGTG 60.202 40.741 0.00 0.00 0.00 4.94
44 46 7.333672 GGTCATATAGTTTTTCTTCTTCCGTGT 59.666 37.037 0.00 0.00 0.00 4.49
45 47 8.169268 GTCATATAGTTTTTCTTCTTCCGTGTG 58.831 37.037 0.00 0.00 0.00 3.82
62 64 4.446051 CCGTGTGTTTTAATCCGCAAAAAT 59.554 37.500 0.00 0.00 0.00 1.82
107 109 0.109226 CAACGACCTCCCTCTTCGAC 60.109 60.000 0.00 0.00 36.58 4.20
113 115 0.528470 CCTCCCTCTTCGACACAGAC 59.472 60.000 0.00 0.00 0.00 3.51
137 139 1.270412 TGTAACCACTACGCCAACCAG 60.270 52.381 0.00 0.00 32.65 4.00
158 160 5.123227 CAGCCGGATCTGGTTAATTAGAAA 58.877 41.667 21.88 0.00 0.00 2.52
159 161 5.588648 CAGCCGGATCTGGTTAATTAGAAAA 59.411 40.000 21.88 0.00 0.00 2.29
468 586 8.788409 ACTTTTCTCAATTTCGATGAACTTTC 57.212 30.769 0.00 0.00 0.00 2.62
469 587 7.862873 ACTTTTCTCAATTTCGATGAACTTTCC 59.137 33.333 0.00 0.00 0.00 3.13
728 954 7.247929 ACCGTTACAGAAAAAGAGAAGAAAG 57.752 36.000 0.00 0.00 0.00 2.62
729 955 6.260271 ACCGTTACAGAAAAAGAGAAGAAAGG 59.740 38.462 0.00 0.00 0.00 3.11
730 956 6.482308 CCGTTACAGAAAAAGAGAAGAAAGGA 59.518 38.462 0.00 0.00 0.00 3.36
756 984 0.463620 TGGTTTGCAAAGCTTCCCAC 59.536 50.000 33.85 13.07 37.31 4.61
822 1050 1.329256 AGTTAGTGAGCACAGGTCGT 58.671 50.000 3.19 0.00 32.15 4.34
826 1054 1.007734 GTGAGCACAGGTCGTTCGA 60.008 57.895 0.00 0.00 32.15 3.71
830 1058 2.740714 GCACAGGTCGTTCGATGGC 61.741 63.158 0.00 0.00 0.00 4.40
831 1059 1.374125 CACAGGTCGTTCGATGGCA 60.374 57.895 0.00 0.00 0.00 4.92
837 1065 0.577269 GTCGTTCGATGGCATAGTGC 59.423 55.000 0.00 0.00 44.08 4.40
849 1077 2.554142 GCATAGTGCACTGCTATGTGA 58.446 47.619 29.57 6.90 44.48 3.58
850 1078 2.938451 GCATAGTGCACTGCTATGTGAA 59.062 45.455 29.57 6.09 44.48 3.18
852 1080 2.105006 AGTGCACTGCTATGTGAAGG 57.895 50.000 20.97 0.00 40.12 3.46
853 1081 1.089920 GTGCACTGCTATGTGAAGGG 58.910 55.000 10.32 0.00 40.12 3.95
856 1084 2.304470 TGCACTGCTATGTGAAGGGTAA 59.696 45.455 1.98 0.00 40.12 2.85
857 1085 2.939103 GCACTGCTATGTGAAGGGTAAG 59.061 50.000 8.75 0.00 40.12 2.34
858 1086 3.535561 CACTGCTATGTGAAGGGTAAGG 58.464 50.000 0.00 0.00 40.12 2.69
861 1089 2.504175 TGCTATGTGAAGGGTAAGGTCC 59.496 50.000 0.00 0.00 0.00 4.46
869 1097 1.600638 GGGTAAGGTCCCCAGTTCG 59.399 63.158 0.00 0.00 42.15 3.95
872 1100 1.558294 GGTAAGGTCCCCAGTTCGAAT 59.442 52.381 0.00 0.00 0.00 3.34
873 1101 2.419713 GGTAAGGTCCCCAGTTCGAATC 60.420 54.545 0.00 0.00 0.00 2.52
874 1102 0.618981 AAGGTCCCCAGTTCGAATCC 59.381 55.000 0.00 0.00 0.00 3.01
875 1103 0.546747 AGGTCCCCAGTTCGAATCCA 60.547 55.000 0.00 0.00 0.00 3.41
876 1104 0.107654 GGTCCCCAGTTCGAATCCAG 60.108 60.000 0.00 0.00 0.00 3.86
877 1105 0.744771 GTCCCCAGTTCGAATCCAGC 60.745 60.000 0.00 0.00 0.00 4.85
878 1106 0.909610 TCCCCAGTTCGAATCCAGCT 60.910 55.000 0.00 0.00 0.00 4.24
879 1107 0.462759 CCCCAGTTCGAATCCAGCTC 60.463 60.000 0.00 0.00 0.00 4.09
880 1108 0.462759 CCCAGTTCGAATCCAGCTCC 60.463 60.000 0.00 0.00 0.00 4.70
881 1109 0.462759 CCAGTTCGAATCCAGCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
882 1110 0.462759 CAGTTCGAATCCAGCTCCCC 60.463 60.000 0.00 0.00 0.00 4.81
883 1111 1.153147 GTTCGAATCCAGCTCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
902 1130 2.490165 CGCTCCCGGACTTCTTCTA 58.510 57.895 0.73 0.00 0.00 2.10
905 1133 2.353406 CGCTCCCGGACTTCTTCTAAAA 60.353 50.000 0.73 0.00 0.00 1.52
906 1134 3.671716 GCTCCCGGACTTCTTCTAAAAA 58.328 45.455 0.73 0.00 0.00 1.94
951 1179 1.152546 ACCTGGGCCAAACCTGAAC 60.153 57.895 8.04 0.00 39.10 3.18
973 1201 2.982026 GGCTTCCTCCTTGCCAATT 58.018 52.632 0.00 0.00 45.46 2.32
974 1202 0.820226 GGCTTCCTCCTTGCCAATTC 59.180 55.000 0.00 0.00 45.46 2.17
975 1203 1.549203 GCTTCCTCCTTGCCAATTCA 58.451 50.000 0.00 0.00 0.00 2.57
985 1213 2.079170 TGCCAATTCAACTGGTCCAA 57.921 45.000 0.00 0.00 36.24 3.53
998 1226 1.603739 GTCCAAAGACTGGCCCACC 60.604 63.158 0.00 0.00 45.98 4.61
1004 1232 4.408821 GACTGGCCCACCGATGCA 62.409 66.667 0.00 0.00 39.70 3.96
1161 1409 3.723348 GGCACCGTCTTCCGCAAC 61.723 66.667 0.00 0.00 34.38 4.17
1165 1413 2.342279 CCGTCTTCCGCAACTCCA 59.658 61.111 0.00 0.00 34.38 3.86
1170 1418 1.207329 GTCTTCCGCAACTCCATACCT 59.793 52.381 0.00 0.00 0.00 3.08
1173 1421 0.174845 TCCGCAACTCCATACCTTCG 59.825 55.000 0.00 0.00 0.00 3.79
1491 4838 4.082408 CAGGATTCAGTACACGTCTGGTTA 60.082 45.833 3.21 0.00 34.15 2.85
1493 4840 5.041940 GGATTCAGTACACGTCTGGTTATC 58.958 45.833 3.21 4.66 34.15 1.75
1503 4850 5.184479 ACACGTCTGGTTATCTAACTGCTAA 59.816 40.000 0.00 0.00 36.47 3.09
1505 4852 6.757010 CACGTCTGGTTATCTAACTGCTAAAT 59.243 38.462 0.00 0.00 36.47 1.40
1510 4865 7.070696 TCTGGTTATCTAACTGCTAAATGCCTA 59.929 37.037 0.52 0.00 35.38 3.93
1514 4869 6.927294 ATCTAACTGCTAAATGCCTACAAC 57.073 37.500 0.00 0.00 42.00 3.32
1539 4894 6.127479 CCAGAGCTATATGTATCCCTGTTCTC 60.127 46.154 0.00 0.00 0.00 2.87
1540 4895 5.650266 AGAGCTATATGTATCCCTGTTCTCG 59.350 44.000 0.00 0.00 0.00 4.04
1543 4898 5.183331 GCTATATGTATCCCTGTTCTCGACA 59.817 44.000 0.00 0.00 36.65 4.35
1575 4930 4.710324 TCAAGTCAACAGTTTATCCCGTT 58.290 39.130 0.00 0.00 0.00 4.44
1584 4946 6.737254 ACAGTTTATCCCGTTTGTTAGATG 57.263 37.500 0.00 0.00 0.00 2.90
1652 5019 1.226916 CGCTGATCTGCTTCTCGCT 60.227 57.895 20.58 0.00 40.11 4.93
1657 5024 1.410153 TGATCTGCTTCTCGCTATGCA 59.590 47.619 0.00 0.00 40.11 3.96
1659 5026 1.933005 CTGCTTCTCGCTATGCAGC 59.067 57.895 10.32 0.00 44.72 5.25
1743 5123 6.859112 TTAACTACAGAATCTGAAGCCTCT 57.141 37.500 18.20 0.00 35.18 3.69
1838 5219 5.728351 TGGATCGTTAAATGTCGATTTCC 57.272 39.130 0.00 0.97 44.90 3.13
2108 6066 2.507324 GCCGACCTTCTCACGCTC 60.507 66.667 0.00 0.00 0.00 5.03
2130 6088 2.355837 CCCGACATACATCGCCGG 60.356 66.667 0.00 0.00 40.87 6.13
2247 6205 0.911053 TGATGATGGCACTGGCTGTA 59.089 50.000 3.97 0.00 40.87 2.74
2252 6210 0.106708 ATGGCACTGGCTGTATACCG 59.893 55.000 3.97 0.00 40.87 4.02
2265 6223 1.547372 GTATACCGTGTGTCCTGTGGT 59.453 52.381 0.00 0.00 36.72 4.16
2524 6482 1.002544 GCCACTACCTTCTGCTTGAGT 59.997 52.381 0.00 0.00 0.00 3.41
2550 6508 2.554124 CCTCGGAGGATCTCATGCTCTA 60.554 54.545 19.57 0.00 45.78 2.43
2712 11782 4.872664 AGTAGGATTACTATCTTGCGTGC 58.127 43.478 0.00 0.00 38.35 5.34
2736 11806 8.136800 TGCAGTTATTCATTAAAGGCATACATG 58.863 33.333 0.00 0.00 30.47 3.21
3168 12254 1.014044 CGAGACCACCCATGTCAACG 61.014 60.000 0.00 0.00 35.15 4.10
3224 12310 2.513897 AACGCCTGATAAGCCGCC 60.514 61.111 0.00 0.00 0.00 6.13
3235 12321 3.311322 TGATAAGCCGCCGTATTTTTCTG 59.689 43.478 0.00 0.00 0.00 3.02
3310 12398 5.421693 ACGGAGACTCTTACAGTAGTAGAGA 59.578 44.000 14.03 0.00 34.41 3.10
3312 12400 6.183360 CGGAGACTCTTACAGTAGTAGAGAGA 60.183 46.154 14.03 0.00 38.03 3.10
3347 12439 3.723348 GAGTTTCGCCCGTGCACC 61.723 66.667 12.15 0.00 37.32 5.01
3370 12462 4.202010 CGTTTCTCAGTTGTCCCAACAATT 60.202 41.667 9.53 0.00 46.58 2.32
3385 12477 8.040727 GTCCCAACAATTTGCTAAAGGATTTAT 58.959 33.333 0.00 0.00 40.24 1.40
3457 12549 8.646900 TGGTATGCCTTAAAGAAATTCTTGTTT 58.353 29.630 9.21 0.00 34.51 2.83
3458 12550 9.489084 GGTATGCCTTAAAGAAATTCTTGTTTT 57.511 29.630 9.21 0.00 36.71 2.43
3537 12654 3.646491 TTCTATGTCGTGACGAGTACG 57.354 47.619 8.41 0.00 45.75 3.67
3624 12743 5.532779 AGAAGAAAGGTTGGATGTGTTTCTC 59.467 40.000 0.00 0.00 36.64 2.87
3642 12761 0.036105 TCGATGCTGATGTTGTGGCT 60.036 50.000 0.00 0.00 0.00 4.75
3686 12805 2.826128 ACTCTTGCTGACGGTATTCTGA 59.174 45.455 0.00 0.00 0.00 3.27
3695 12814 4.607955 TGACGGTATTCTGAAGCTAATCG 58.392 43.478 0.00 0.00 0.00 3.34
3727 12846 5.605534 ACTAGTGCTGTTATCCATGACATC 58.394 41.667 0.00 0.00 0.00 3.06
3739 12858 3.684305 TCCATGACATCAAGTTGTTAGCG 59.316 43.478 2.11 0.00 0.00 4.26
3785 12904 9.903682 CCTTTATTATTCATGTAATTGAGCCTG 57.096 33.333 0.00 0.00 0.00 4.85
4003 13128 9.160496 GATTAACCAATCTTATATCTCAGGCAG 57.840 37.037 0.00 0.00 38.03 4.85
4047 13189 4.393371 GTCTTGAATCCTGGCACTAAGTTC 59.607 45.833 0.00 0.00 0.00 3.01
4048 13190 3.350219 TGAATCCTGGCACTAAGTTCC 57.650 47.619 0.00 0.00 0.00 3.62
4078 13221 7.667043 TTAACATAACACTAACTGGCTTCAG 57.333 36.000 0.00 0.00 43.84 3.02
4128 13271 7.925483 CCAAGGATAATTCAAAGTGAAACACAA 59.075 33.333 4.75 0.00 40.12 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.600173 CCGGCCCAACACCATGTT 60.600 61.111 0.00 0.00 42.08 2.71
2 3 4.676951 CCCGGCCCAACACCATGT 62.677 66.667 0.00 0.00 0.00 3.21
3 4 4.676951 ACCCGGCCCAACACCATG 62.677 66.667 0.00 0.00 0.00 3.66
6 7 2.279037 ATATGACCCGGCCCAACACC 62.279 60.000 0.00 0.00 0.00 4.16
10 11 1.513858 AACTATATGACCCGGCCCAA 58.486 50.000 0.00 0.00 0.00 4.12
20 21 7.876068 ACACACGGAAGAAGAAAAACTATATGA 59.124 33.333 0.00 0.00 0.00 2.15
35 37 2.481185 GCGGATTAAAACACACGGAAGA 59.519 45.455 0.00 0.00 0.00 2.87
36 38 2.224549 TGCGGATTAAAACACACGGAAG 59.775 45.455 0.00 0.00 0.00 3.46
39 41 2.690173 TTGCGGATTAAAACACACGG 57.310 45.000 0.00 0.00 0.00 4.94
40 42 5.568747 ATTTTTGCGGATTAAAACACACG 57.431 34.783 0.00 0.00 0.00 4.49
78 80 1.463444 GGAGGTCGTTGGTTTGAATCG 59.537 52.381 0.00 0.00 0.00 3.34
119 121 0.320946 GCTGGTTGGCGTAGTGGTTA 60.321 55.000 0.00 0.00 0.00 2.85
137 139 6.635030 ATTTTCTAATTAACCAGATCCGGC 57.365 37.500 0.00 0.00 0.00 6.13
434 549 8.786937 TCGAAATTGAGAAAAGTTCATCAAAG 57.213 30.769 2.60 0.00 33.66 2.77
436 551 8.567104 TCATCGAAATTGAGAAAAGTTCATCAA 58.433 29.630 0.00 0.00 34.10 2.57
449 564 8.256611 TCTAAGGAAAGTTCATCGAAATTGAG 57.743 34.615 0.00 0.00 30.27 3.02
454 572 7.094631 TCGAATCTAAGGAAAGTTCATCGAAA 58.905 34.615 0.00 0.00 33.29 3.46
455 573 6.627243 TCGAATCTAAGGAAAGTTCATCGAA 58.373 36.000 0.00 0.00 33.29 3.71
700 925 8.047413 TCTTCTCTTTTTCTGTAACGGTTTTT 57.953 30.769 0.00 0.00 0.00 1.94
737 963 0.463620 GTGGGAAGCTTTGCAAACCA 59.536 50.000 8.05 11.00 0.00 3.67
738 964 0.463620 TGTGGGAAGCTTTGCAAACC 59.536 50.000 8.05 7.90 0.00 3.27
743 970 2.644992 CGGTGTGGGAAGCTTTGC 59.355 61.111 0.00 0.00 0.00 3.68
744 971 3.354678 CCGGTGTGGGAAGCTTTG 58.645 61.111 0.00 0.00 0.00 2.77
822 1050 1.655484 CAGTGCACTATGCCATCGAA 58.345 50.000 21.20 0.00 44.23 3.71
826 1054 2.501261 CATAGCAGTGCACTATGCCAT 58.499 47.619 21.20 12.52 44.23 4.40
831 1059 3.432749 CCCTTCACATAGCAGTGCACTAT 60.433 47.826 21.20 13.92 39.35 2.12
837 1065 3.055094 ACCTTACCCTTCACATAGCAGTG 60.055 47.826 0.00 0.00 40.85 3.66
838 1066 3.182152 ACCTTACCCTTCACATAGCAGT 58.818 45.455 0.00 0.00 0.00 4.40
842 1070 3.840124 GGGACCTTACCCTTCACATAG 57.160 52.381 0.00 0.00 45.90 2.23
858 1086 0.744771 GCTGGATTCGAACTGGGGAC 60.745 60.000 0.00 0.00 0.00 4.46
861 1089 0.462759 GGAGCTGGATTCGAACTGGG 60.463 60.000 0.00 0.00 0.00 4.45
863 1091 0.462759 GGGGAGCTGGATTCGAACTG 60.463 60.000 0.00 0.00 0.00 3.16
864 1092 1.627297 GGGGGAGCTGGATTCGAACT 61.627 60.000 0.00 0.00 0.00 3.01
865 1093 1.153147 GGGGGAGCTGGATTCGAAC 60.153 63.158 0.00 0.00 0.00 3.95
882 1110 3.372554 GAAGAAGTCCGGGAGCGGG 62.373 68.421 0.00 0.00 0.00 6.13
883 1111 1.035932 TAGAAGAAGTCCGGGAGCGG 61.036 60.000 0.00 0.00 0.00 5.52
884 1112 0.815734 TTAGAAGAAGTCCGGGAGCG 59.184 55.000 0.00 0.00 0.00 5.03
885 1113 3.329929 TTTTAGAAGAAGTCCGGGAGC 57.670 47.619 0.00 0.00 0.00 4.70
905 1133 0.325272 GGAGGACGGAGCTCCTTTTT 59.675 55.000 29.73 13.12 37.97 1.94
906 1134 1.554583 GGGAGGACGGAGCTCCTTTT 61.555 60.000 29.73 14.34 37.97 2.27
907 1135 1.990614 GGGAGGACGGAGCTCCTTT 60.991 63.158 29.73 17.02 37.97 3.11
908 1136 2.364448 GGGAGGACGGAGCTCCTT 60.364 66.667 29.73 22.03 37.97 3.36
909 1137 2.463497 AAAGGGAGGACGGAGCTCCT 62.463 60.000 29.73 17.05 39.92 3.69
910 1138 1.962321 GAAAGGGAGGACGGAGCTCC 61.962 65.000 23.79 23.79 36.29 4.70
911 1139 1.518302 GAAAGGGAGGACGGAGCTC 59.482 63.158 4.71 4.71 0.00 4.09
912 1140 1.990614 GGAAAGGGAGGACGGAGCT 60.991 63.158 0.00 0.00 0.00 4.09
913 1141 2.585153 GGAAAGGGAGGACGGAGC 59.415 66.667 0.00 0.00 0.00 4.70
919 1147 1.541368 CAGGTGGGGAAAGGGAGGA 60.541 63.158 0.00 0.00 0.00 3.71
921 1149 3.090765 CCAGGTGGGGAAAGGGAG 58.909 66.667 0.00 0.00 0.00 4.30
951 1179 1.680314 GGCAAGGAGGAAGCCCAAG 60.680 63.158 0.00 0.00 42.58 3.61
985 1213 2.671070 CATCGGTGGGCCAGTCTT 59.329 61.111 6.40 0.00 34.09 3.01
1026 1254 0.107752 GGAGCAGAAGCCAGAAGAGG 60.108 60.000 0.00 0.00 43.56 3.69
1028 1256 0.837691 TGGGAGCAGAAGCCAGAAGA 60.838 55.000 0.00 0.00 43.56 2.87
1029 1257 0.392729 CTGGGAGCAGAAGCCAGAAG 60.393 60.000 0.00 0.00 43.56 2.85
1066 1307 2.180159 TTGGCGGTAGGGTTCAGAGC 62.180 60.000 0.00 0.00 0.00 4.09
1170 1418 2.283529 GGAGGAGTGAGCACCCGAA 61.284 63.158 0.00 0.00 0.00 4.30
1237 1489 0.469070 CTGAGCCCTGAGGATTGAGG 59.531 60.000 0.00 0.00 33.47 3.86
1238 1490 0.469070 CCTGAGCCCTGAGGATTGAG 59.531 60.000 0.00 0.00 35.91 3.02
1239 1491 1.630126 GCCTGAGCCCTGAGGATTGA 61.630 60.000 0.00 0.00 35.91 2.57
1503 4850 5.072329 ACATATAGCTCTGGTTGTAGGCATT 59.928 40.000 0.00 0.00 0.00 3.56
1505 4852 3.967326 ACATATAGCTCTGGTTGTAGGCA 59.033 43.478 0.00 0.00 0.00 4.75
1510 4865 5.247110 CAGGGATACATATAGCTCTGGTTGT 59.753 44.000 0.00 0.00 40.96 3.32
1539 4894 5.163963 TGTTGACTTGAATTCATCGATGTCG 60.164 40.000 24.09 6.58 41.45 4.35
1540 4895 6.128445 ACTGTTGACTTGAATTCATCGATGTC 60.128 38.462 24.09 15.23 0.00 3.06
1543 4898 6.808008 AACTGTTGACTTGAATTCATCGAT 57.192 33.333 9.40 0.00 0.00 3.59
1575 4930 6.530120 ACCACACACTGATAACATCTAACAA 58.470 36.000 0.00 0.00 0.00 2.83
1584 4946 4.819630 TCAAGGAAACCACACACTGATAAC 59.180 41.667 0.00 0.00 0.00 1.89
1652 5019 4.830765 GTCCGTGGCCGCTGCATA 62.831 66.667 15.69 0.00 40.13 3.14
1657 5024 4.379243 CTTCAGTCCGTGGCCGCT 62.379 66.667 15.69 0.00 0.00 5.52
1658 5025 4.373116 TCTTCAGTCCGTGGCCGC 62.373 66.667 6.11 6.11 0.00 6.53
1659 5026 2.432628 GTCTTCAGTCCGTGGCCG 60.433 66.667 0.00 0.00 0.00 6.13
1660 5027 1.374758 CTGTCTTCAGTCCGTGGCC 60.375 63.158 0.00 0.00 36.97 5.36
1661 5028 1.374758 CCTGTCTTCAGTCCGTGGC 60.375 63.158 0.00 0.00 39.82 5.01
1662 5029 1.293498 CCCTGTCTTCAGTCCGTGG 59.707 63.158 0.00 0.00 39.82 4.94
1663 5030 1.293498 CCCCTGTCTTCAGTCCGTG 59.707 63.158 0.00 0.00 39.82 4.94
1664 5031 2.584391 GCCCCTGTCTTCAGTCCGT 61.584 63.158 0.00 0.00 39.82 4.69
1665 5032 2.266055 GCCCCTGTCTTCAGTCCG 59.734 66.667 0.00 0.00 39.82 4.79
1666 5033 1.003233 GTGCCCCTGTCTTCAGTCC 60.003 63.158 0.00 0.00 39.82 3.85
1838 5219 5.762825 ATTGCACAGCTATGGTAGAATTG 57.237 39.130 0.00 0.00 0.00 2.32
2130 6088 0.040067 CCACAGCGAACAAAGGAAGC 60.040 55.000 0.00 0.00 0.00 3.86
2247 6205 1.053424 AACCACAGGACACACGGTAT 58.947 50.000 0.00 0.00 0.00 2.73
2252 6210 1.021968 GGTTCAACCACAGGACACAC 58.978 55.000 0.01 0.00 38.42 3.82
2265 6223 1.129917 TTCAGGTACCGGTGGTTCAA 58.870 50.000 19.93 1.27 37.09 2.69
2275 6233 3.568007 TGAACTGTTTGCATTCAGGTACC 59.432 43.478 18.40 2.73 36.17 3.34
2524 6482 0.614697 TGAGATCCTCCGAGGCACAA 60.615 55.000 9.87 0.00 34.61 3.33
2550 6508 6.126409 ACACCGTACAATTTGGGATCATTAT 58.874 36.000 0.78 0.00 0.00 1.28
2662 6620 6.169419 TGAAGTAAATCAAATGCAGTCGAG 57.831 37.500 0.00 0.00 0.00 4.04
2712 11782 8.632679 ACCATGTATGCCTTTAATGAATAACTG 58.367 33.333 0.00 0.00 0.00 3.16
2736 11806 4.909880 GCATGTTTCGAGTTGAGTTTAACC 59.090 41.667 0.00 0.00 0.00 2.85
2960 12032 2.807622 GGCATTCCGGACATTGCC 59.192 61.111 27.39 27.39 46.94 4.52
3142 12228 3.458163 GGGTGGTCTCGCATCCGA 61.458 66.667 0.00 0.00 42.01 4.55
3168 12254 6.293698 TCTACTCTCCAAGGTTGTTAAAACC 58.706 40.000 0.00 0.00 40.58 3.27
3224 12310 7.625828 ACCTTATTTCTCCCAGAAAAATACG 57.374 36.000 2.90 0.00 46.08 3.06
3235 12321 5.990668 TCTCTTTGCTACCTTATTTCTCCC 58.009 41.667 0.00 0.00 0.00 4.30
3310 12398 1.893801 CACTTTGAGACCCTACCGTCT 59.106 52.381 0.00 0.00 45.86 4.18
3312 12400 2.005370 TCACTTTGAGACCCTACCGT 57.995 50.000 0.00 0.00 0.00 4.83
3370 12462 4.644685 GGTGGCAGATAAATCCTTTAGCAA 59.355 41.667 0.00 0.00 34.13 3.91
3457 12549 6.557568 ACCCCAGAGGAAAATACAAATACAA 58.442 36.000 0.00 0.00 39.89 2.41
3458 12550 6.147437 ACCCCAGAGGAAAATACAAATACA 57.853 37.500 0.00 0.00 39.89 2.29
3624 12743 0.098200 CAGCCACAACATCAGCATCG 59.902 55.000 0.00 0.00 0.00 3.84
3642 12761 4.431416 ACCGGATAAAACATATCAGGCA 57.569 40.909 9.46 0.00 41.13 4.75
3686 12805 2.305009 AGTAGCCGTACCGATTAGCTT 58.695 47.619 0.00 0.00 35.03 3.74
3695 12814 1.101331 ACAGCACTAGTAGCCGTACC 58.899 55.000 11.98 0.00 0.00 3.34
3727 12846 5.092781 ACAAACTTCAACGCTAACAACTTG 58.907 37.500 0.00 0.00 0.00 3.16
3739 12858 7.652300 AAAGGAAACTCAAACAAACTTCAAC 57.348 32.000 0.00 0.00 42.68 3.18
3820 12939 9.787435 AAAATATGAAATAATGGCATCATGCTT 57.213 25.926 10.11 0.00 36.42 3.91
3995 13120 3.822735 TCCAATCAACTTTTCTGCCTGAG 59.177 43.478 0.00 0.00 0.00 3.35
4003 13128 4.689071 ACCGGTTTTCCAATCAACTTTTC 58.311 39.130 0.00 0.00 40.70 2.29
4047 13189 7.968405 GCCAGTTAGTGTTATGTTAATGAAAGG 59.032 37.037 0.00 0.00 0.00 3.11
4048 13190 8.730680 AGCCAGTTAGTGTTATGTTAATGAAAG 58.269 33.333 0.00 0.00 0.00 2.62
4078 13221 8.713271 TGGTACAAACTTTGTTTTGAATTCAAC 58.287 29.630 20.35 11.52 42.22 3.18


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

AutoCloner maintained by Alex Coulton.