Multiple sequence alignment - TraesCS4B01G164600

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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 TraesCS4B01G164600 chr4B 100.000 4012 0 0 1 4012 343638123 343642134 0.000000e+00 7409.0
1 TraesCS4B01G164600 chr4B 93.051 3166 124 18 1 3144 343785503 343788594 0.000000e+00 4540.0
2 TraesCS4B01G164600 chr4B 90.279 1687 132 14 2332 4010 288476720 288475058 0.000000e+00 2178.0
3 TraesCS4B01G164600 chr4B 95.158 950 45 1 3062 4010 343788485 343789434 0.000000e+00 1498.0
4 TraesCS4B01G164600 chr4B 91.616 978 76 3 3035 4010 200933663 200934636 0.000000e+00 1347.0
5 TraesCS4B01G164600 chr4B 92.506 894 62 5 3120 4009 368726016 368726908 0.000000e+00 1275.0
6 TraesCS4B01G164600 chr4B 85.651 676 67 17 662 1331 613126989 613127640 0.000000e+00 684.0
7 TraesCS4B01G164600 chr6B 90.796 1684 122 9 2330 4010 244462235 244460582 0.000000e+00 2220.0
8 TraesCS4B01G164600 chr6B 92.663 1254 72 11 2757 4010 238437118 238435885 0.000000e+00 1788.0
9 TraesCS4B01G164600 chr6B 86.935 620 64 13 656 1269 663065093 663065701 0.000000e+00 680.0
10 TraesCS4B01G164600 chr6B 90.020 501 30 9 1517 2001 4666696 4667192 7.320000e-177 630.0
11 TraesCS4B01G164600 chr6B 84.569 499 25 21 1 471 425110762 425111236 7.910000e-122 448.0
12 TraesCS4B01G164600 chr6B 88.482 191 21 1 1634 1823 692624818 692625008 3.120000e-56 230.0
13 TraesCS4B01G164600 chr5B 90.755 1179 83 12 1995 3171 291688954 291687800 0.000000e+00 1550.0
14 TraesCS4B01G164600 chr5B 92.331 978 69 4 3035 4010 291687879 291686906 0.000000e+00 1386.0
15 TraesCS4B01G164600 chr5B 90.491 978 73 6 3037 4010 345109429 345110390 0.000000e+00 1273.0
16 TraesCS4B01G164600 chr5B 92.651 694 47 4 656 1349 291690081 291689392 0.000000e+00 996.0
17 TraesCS4B01G164600 chr4D 87.454 1355 105 25 2017 3328 261239222 261237890 0.000000e+00 1500.0
18 TraesCS4B01G164600 chr4D 86.603 1254 93 38 656 1869 261240765 261239547 0.000000e+00 1315.0
19 TraesCS4B01G164600 chr4D 89.934 914 66 11 649 1539 125862577 125861667 0.000000e+00 1155.0
20 TraesCS4B01G164600 chr4D 89.847 916 63 14 649 1539 125871411 125872321 0.000000e+00 1149.0
21 TraesCS4B01G164600 chr4D 89.606 914 63 13 649 1539 125938165 125937261 0.000000e+00 1133.0
22 TraesCS4B01G164600 chr4D 84.350 984 110 13 2359 3328 225340776 225339823 0.000000e+00 924.0
23 TraesCS4B01G164600 chr6D 86.284 1378 117 36 1995 3328 297179049 297177700 0.000000e+00 1432.0
24 TraesCS4B01G164600 chr6D 87.995 783 59 19 656 1415 297180457 297179687 0.000000e+00 893.0
25 TraesCS4B01G164600 chr6D 96.581 117 4 0 1517 1633 297179672 297179556 1.140000e-45 195.0
26 TraesCS4B01G164600 chr6D 93.878 98 6 0 1854 1951 297179481 297179384 8.980000e-32 148.0
27 TraesCS4B01G164600 chr6D 95.588 68 3 0 446 513 46528966 46528899 4.240000e-20 110.0
28 TraesCS4B01G164600 chr7A 89.173 1136 83 14 1995 3129 583641342 583642438 0.000000e+00 1380.0
29 TraesCS4B01G164600 chr7A 99.394 165 1 0 1995 2159 644066277 644066113 2.340000e-77 300.0
30 TraesCS4B01G164600 chr5A 84.821 1423 135 48 2174 3537 345672215 345670815 0.000000e+00 1356.0
31 TraesCS4B01G164600 chr5A 84.786 1216 128 25 2141 3328 178868307 178867121 0.000000e+00 1168.0
32 TraesCS4B01G164600 chr3B 90.928 981 77 6 3035 4012 762524949 762523978 0.000000e+00 1308.0
33 TraesCS4B01G164600 chr3B 84.216 1039 125 14 2304 3327 318290925 318291939 0.000000e+00 974.0
34 TraesCS4B01G164600 chr3B 93.463 566 33 4 1 562 320751330 320750765 0.000000e+00 837.0
35 TraesCS4B01G164600 chr3B 86.441 59 3 1 1839 1897 217053971 217053918 4.330000e-05 60.2
36 TraesCS4B01G164600 chr7D 85.816 1262 103 34 656 1869 501730202 501731435 0.000000e+00 1269.0
37 TraesCS4B01G164600 chr7D 91.383 940 57 12 2017 2955 501731759 501732675 0.000000e+00 1266.0
38 TraesCS4B01G164600 chr7D 91.793 463 25 7 112 564 152037831 152037372 2.030000e-177 632.0
39 TraesCS4B01G164600 chr7D 86.118 389 30 12 1171 1539 103531376 103531760 8.080000e-107 398.0
40 TraesCS4B01G164600 chr7D 92.453 53 4 0 1517 1569 501731130 501731182 4.300000e-10 76.8
41 TraesCS4B01G164600 chr7D 100.000 33 0 0 561 593 152037404 152037372 1.200000e-05 62.1
42 TraesCS4B01G164600 chr5D 86.484 1206 99 25 1995 3174 140960828 140959661 0.000000e+00 1266.0
43 TraesCS4B01G164600 chr5D 91.181 669 54 4 3347 4012 20270073 20269407 0.000000e+00 904.0
44 TraesCS4B01G164600 chr5D 89.831 708 45 9 656 1349 140962219 140961525 0.000000e+00 883.0
45 TraesCS4B01G164600 chr5D 93.274 565 35 2 1 562 16498934 16498370 0.000000e+00 830.0
46 TraesCS4B01G164600 chr5D 93.750 480 28 2 1 479 20275296 20274818 0.000000e+00 719.0
47 TraesCS4B01G164600 chr5D 87.324 568 50 8 2749 3315 20270736 20270190 7.320000e-177 630.0
48 TraesCS4B01G164600 chr5D 96.581 117 4 0 1517 1633 140961451 140961335 1.140000e-45 195.0
49 TraesCS4B01G164600 chr5D 92.857 98 7 0 1854 1951 140961260 140961163 4.180000e-30 143.0
50 TraesCS4B01G164600 chr5D 86.957 69 6 1 561 629 20274790 20274725 1.550000e-09 75.0
51 TraesCS4B01G164600 chr3D 87.992 1016 87 11 2315 3316 571760246 571759252 0.000000e+00 1168.0
52 TraesCS4B01G164600 chr3D 89.912 912 64 13 649 1537 57605533 57606439 0.000000e+00 1149.0
53 TraesCS4B01G164600 chr3D 91.467 668 49 5 3348 4012 571759138 571758476 0.000000e+00 911.0
54 TraesCS4B01G164600 chr3D 92.970 569 37 2 1 566 571777297 571776729 0.000000e+00 826.0
55 TraesCS4B01G164600 chr3D 92.845 573 33 4 1 565 420323487 420324059 0.000000e+00 824.0
56 TraesCS4B01G164600 chr3D 100.000 28 0 0 627 654 57605451 57605478 7.000000e-03 52.8
57 TraesCS4B01G164600 chr1D 93.333 750 48 2 1995 2743 428055843 428055095 0.000000e+00 1107.0
58 TraesCS4B01G164600 chr1D 94.821 560 25 3 1 557 417104248 417104806 0.000000e+00 870.0
59 TraesCS4B01G164600 chr1D 93.628 565 31 3 1 562 463803522 463802960 0.000000e+00 839.0
60 TraesCS4B01G164600 chr1D 96.774 31 1 0 561 591 463802990 463802960 7.000000e-03 52.8
61 TraesCS4B01G164600 chr6A 89.035 912 62 12 658 1537 529358783 529359688 0.000000e+00 1096.0
62 TraesCS4B01G164600 chr6A 83.307 1252 128 41 2332 3537 436391637 436392853 0.000000e+00 1079.0
63 TraesCS4B01G164600 chr6A 86.792 424 27 9 1134 1537 136654565 136654979 2.840000e-121 446.0
64 TraesCS4B01G164600 chr4A 87.199 914 68 11 649 1539 433611617 433610730 0.000000e+00 994.0
65 TraesCS4B01G164600 chr4A 99.394 165 1 0 1995 2159 429488620 429488784 2.340000e-77 300.0
66 TraesCS4B01G164600 chr7B 86.730 844 83 12 2330 3171 669509569 669510385 0.000000e+00 911.0
67 TraesCS4B01G164600 chr7B 84.658 906 98 17 2437 3328 452411561 452412439 0.000000e+00 865.0
68 TraesCS4B01G164600 chr7B 83.521 267 22 8 1634 1897 688413017 688413264 3.120000e-56 230.0
69 TraesCS4B01G164600 chr7B 88.785 107 9 1 1720 1823 632610834 632610940 1.170000e-25 128.0
70 TraesCS4B01G164600 chr2D 94.245 417 22 1 145 559 397121613 397122029 1.570000e-178 636.0
71 TraesCS4B01G164600 chr2D 93.878 147 9 0 1 147 397117498 397117644 5.220000e-54 222.0
72 TraesCS4B01G164600 chr1A 99.394 165 1 0 1995 2159 575419497 575419661 2.340000e-77 300.0
73 TraesCS4B01G164600 chr2B 88.083 193 20 1 1634 1823 786389682 786389874 4.030000e-55 226.0


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 TraesCS4B01G164600 chr4B 343638123 343642134 4011 False 7409.000000 7409 100.000000 1 4012 1 chr4B.!!$F2 4011
1 TraesCS4B01G164600 chr4B 343785503 343789434 3931 False 3019.000000 4540 94.104500 1 4010 2 chr4B.!!$F5 4009
2 TraesCS4B01G164600 chr4B 288475058 288476720 1662 True 2178.000000 2178 90.279000 2332 4010 1 chr4B.!!$R1 1678
3 TraesCS4B01G164600 chr4B 200933663 200934636 973 False 1347.000000 1347 91.616000 3035 4010 1 chr4B.!!$F1 975
4 TraesCS4B01G164600 chr4B 368726016 368726908 892 False 1275.000000 1275 92.506000 3120 4009 1 chr4B.!!$F3 889
5 TraesCS4B01G164600 chr4B 613126989 613127640 651 False 684.000000 684 85.651000 662 1331 1 chr4B.!!$F4 669
6 TraesCS4B01G164600 chr6B 244460582 244462235 1653 True 2220.000000 2220 90.796000 2330 4010 1 chr6B.!!$R2 1680
7 TraesCS4B01G164600 chr6B 238435885 238437118 1233 True 1788.000000 1788 92.663000 2757 4010 1 chr6B.!!$R1 1253
8 TraesCS4B01G164600 chr6B 663065093 663065701 608 False 680.000000 680 86.935000 656 1269 1 chr6B.!!$F3 613
9 TraesCS4B01G164600 chr5B 291686906 291690081 3175 True 1310.666667 1550 91.912333 656 4010 3 chr5B.!!$R1 3354
10 TraesCS4B01G164600 chr5B 345109429 345110390 961 False 1273.000000 1273 90.491000 3037 4010 1 chr5B.!!$F1 973
11 TraesCS4B01G164600 chr4D 261237890 261240765 2875 True 1407.500000 1500 87.028500 656 3328 2 chr4D.!!$R4 2672
12 TraesCS4B01G164600 chr4D 125861667 125862577 910 True 1155.000000 1155 89.934000 649 1539 1 chr4D.!!$R1 890
13 TraesCS4B01G164600 chr4D 125871411 125872321 910 False 1149.000000 1149 89.847000 649 1539 1 chr4D.!!$F1 890
14 TraesCS4B01G164600 chr4D 125937261 125938165 904 True 1133.000000 1133 89.606000 649 1539 1 chr4D.!!$R2 890
15 TraesCS4B01G164600 chr4D 225339823 225340776 953 True 924.000000 924 84.350000 2359 3328 1 chr4D.!!$R3 969
16 TraesCS4B01G164600 chr6D 297177700 297180457 2757 True 667.000000 1432 91.184500 656 3328 4 chr6D.!!$R2 2672
17 TraesCS4B01G164600 chr7A 583641342 583642438 1096 False 1380.000000 1380 89.173000 1995 3129 1 chr7A.!!$F1 1134
18 TraesCS4B01G164600 chr5A 345670815 345672215 1400 True 1356.000000 1356 84.821000 2174 3537 1 chr5A.!!$R2 1363
19 TraesCS4B01G164600 chr5A 178867121 178868307 1186 True 1168.000000 1168 84.786000 2141 3328 1 chr5A.!!$R1 1187
20 TraesCS4B01G164600 chr3B 762523978 762524949 971 True 1308.000000 1308 90.928000 3035 4012 1 chr3B.!!$R3 977
21 TraesCS4B01G164600 chr3B 318290925 318291939 1014 False 974.000000 974 84.216000 2304 3327 1 chr3B.!!$F1 1023
22 TraesCS4B01G164600 chr3B 320750765 320751330 565 True 837.000000 837 93.463000 1 562 1 chr3B.!!$R2 561
23 TraesCS4B01G164600 chr7D 501730202 501732675 2473 False 870.600000 1269 89.884000 656 2955 3 chr7D.!!$F2 2299
24 TraesCS4B01G164600 chr5D 16498370 16498934 564 True 830.000000 830 93.274000 1 562 1 chr5D.!!$R1 561
25 TraesCS4B01G164600 chr5D 140959661 140962219 2558 True 621.750000 1266 91.438250 656 3174 4 chr5D.!!$R3 2518
26 TraesCS4B01G164600 chr5D 20269407 20275296 5889 True 582.000000 904 89.803000 1 4012 4 chr5D.!!$R2 4011
27 TraesCS4B01G164600 chr3D 571758476 571760246 1770 True 1039.500000 1168 89.729500 2315 4012 2 chr3D.!!$R2 1697
28 TraesCS4B01G164600 chr3D 571776729 571777297 568 True 826.000000 826 92.970000 1 566 1 chr3D.!!$R1 565
29 TraesCS4B01G164600 chr3D 420323487 420324059 572 False 824.000000 824 92.845000 1 565 1 chr3D.!!$F1 564
30 TraesCS4B01G164600 chr3D 57605451 57606439 988 False 600.900000 1149 94.956000 627 1537 2 chr3D.!!$F2 910
31 TraesCS4B01G164600 chr1D 428055095 428055843 748 True 1107.000000 1107 93.333000 1995 2743 1 chr1D.!!$R1 748
32 TraesCS4B01G164600 chr1D 417104248 417104806 558 False 870.000000 870 94.821000 1 557 1 chr1D.!!$F1 556
33 TraesCS4B01G164600 chr1D 463802960 463803522 562 True 445.900000 839 95.201000 1 591 2 chr1D.!!$R2 590
34 TraesCS4B01G164600 chr6A 529358783 529359688 905 False 1096.000000 1096 89.035000 658 1537 1 chr6A.!!$F3 879
35 TraesCS4B01G164600 chr6A 436391637 436392853 1216 False 1079.000000 1079 83.307000 2332 3537 1 chr6A.!!$F2 1205
36 TraesCS4B01G164600 chr4A 433610730 433611617 887 True 994.000000 994 87.199000 649 1539 1 chr4A.!!$R1 890
37 TraesCS4B01G164600 chr7B 669509569 669510385 816 False 911.000000 911 86.730000 2330 3171 1 chr7B.!!$F3 841
38 TraesCS4B01G164600 chr7B 452411561 452412439 878 False 865.000000 865 84.658000 2437 3328 1 chr7B.!!$F1 891
39 TraesCS4B01G164600 chr2D 397117498 397122029 4531 False 429.000000 636 94.061500 1 559 2 chr2D.!!$F1 558

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
905 5000 0.696501 TCCCCCTGAGCTACCAAAAC 59.303 55.0 0.0 0.0 0.0 2.43 F
2515 9783 0.899720 CCACTACTTAACCCTCGGCA 59.100 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2705 9997 0.809385 TCGTAGCGGAAGACAAGGAG 59.191 55.0 0.00 0.0 0.0 3.69 R
3940 11768 0.671472 CACAAGACAGAGGCATGCGA 60.671 55.0 12.44 0.0 0.0 5.10 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
212 4184 6.837471 TGATGGTTGATCATGATGTTTCAA 57.163 33.333 14.30 9.17 36.06 2.69
325 4297 8.846211 CCATTTTCTTAGTTTTGGTCAGAACTA 58.154 33.333 9.21 9.21 37.08 2.24
351 4323 4.083110 GGTTGTGATGATCCTGAAGTTGTG 60.083 45.833 0.00 0.00 0.00 3.33
378 4350 8.291191 TGCAAAATGATGTTGTAATGATCCTA 57.709 30.769 0.00 0.00 0.00 2.94
585 4567 4.080687 TGGTGCAAAATGATGATGTCTGA 58.919 39.130 0.00 0.00 0.00 3.27
586 4568 4.523558 TGGTGCAAAATGATGATGTCTGAA 59.476 37.500 0.00 0.00 0.00 3.02
587 4569 5.186215 TGGTGCAAAATGATGATGTCTGAAT 59.814 36.000 0.00 0.00 0.00 2.57
588 4570 6.377712 TGGTGCAAAATGATGATGTCTGAATA 59.622 34.615 0.00 0.00 0.00 1.75
589 4571 7.068962 TGGTGCAAAATGATGATGTCTGAATAT 59.931 33.333 0.00 0.00 0.00 1.28
590 4572 7.924412 GGTGCAAAATGATGATGTCTGAATATT 59.076 33.333 0.00 0.00 0.00 1.28
591 4573 9.309516 GTGCAAAATGATGATGTCTGAATATTT 57.690 29.630 0.00 0.00 0.00 1.40
592 4574 9.878667 TGCAAAATGATGATGTCTGAATATTTT 57.121 25.926 0.00 0.00 0.00 1.82
596 4578 9.811995 AAATGATGATGTCTGAATATTTTGGTG 57.188 29.630 0.00 0.00 0.00 4.17
597 4579 6.798482 TGATGATGTCTGAATATTTTGGTGC 58.202 36.000 0.00 0.00 0.00 5.01
598 4580 6.377712 TGATGATGTCTGAATATTTTGGTGCA 59.622 34.615 0.00 0.00 0.00 4.57
599 4581 6.587206 TGATGTCTGAATATTTTGGTGCAA 57.413 33.333 0.00 0.00 0.00 4.08
600 4582 6.990798 TGATGTCTGAATATTTTGGTGCAAA 58.009 32.000 0.00 0.00 0.00 3.68
601 4583 7.440198 TGATGTCTGAATATTTTGGTGCAAAA 58.560 30.769 0.00 0.00 45.41 2.44
612 4594 3.872511 TGGTGCAAAATGATGATGTCC 57.127 42.857 0.00 0.00 0.00 4.02
613 4595 3.433343 TGGTGCAAAATGATGATGTCCT 58.567 40.909 0.00 0.00 0.00 3.85
654 4636 5.818136 TTCAGAGTTGTTTTGGTCAGAAG 57.182 39.130 0.00 0.00 0.00 2.85
905 5000 0.696501 TCCCCCTGAGCTACCAAAAC 59.303 55.000 0.00 0.00 0.00 2.43
1069 5186 1.190643 CCACTCCTCCTCTCCACTTC 58.809 60.000 0.00 0.00 0.00 3.01
1172 5395 2.363795 CTCCCTGGCGACCCACTA 60.364 66.667 0.00 0.00 35.79 2.74
1194 5429 1.287191 CATCGACGGAGATGGCGAT 59.713 57.895 12.70 0.00 43.07 4.58
1285 5593 1.135689 GCACATGCTGTTTAGGGTTCG 60.136 52.381 0.00 0.00 38.21 3.95
1309 5630 1.001597 GTAGCCGAAGTAGATCCACGG 60.002 57.143 0.00 0.00 45.26 4.94
1471 6028 8.409358 AGTTGTTCAGTTTTAAGCCAATATCT 57.591 30.769 0.00 0.00 0.00 1.98
1557 6153 5.843673 TTGCTATCTTGAGTCAGTCTAGG 57.156 43.478 0.00 0.00 0.00 3.02
1558 6154 4.211125 TGCTATCTTGAGTCAGTCTAGGG 58.789 47.826 0.00 0.00 0.00 3.53
1559 6155 4.211920 GCTATCTTGAGTCAGTCTAGGGT 58.788 47.826 0.00 0.00 0.00 4.34
1560 6156 4.647399 GCTATCTTGAGTCAGTCTAGGGTT 59.353 45.833 0.00 0.00 0.00 4.11
1561 6157 5.451242 GCTATCTTGAGTCAGTCTAGGGTTG 60.451 48.000 0.00 0.00 0.00 3.77
1562 6158 2.563179 TCTTGAGTCAGTCTAGGGTTGC 59.437 50.000 0.00 0.00 0.00 4.17
1563 6159 2.310779 TGAGTCAGTCTAGGGTTGCT 57.689 50.000 0.00 0.00 0.00 3.91
1564 6160 1.895798 TGAGTCAGTCTAGGGTTGCTG 59.104 52.381 0.00 0.00 0.00 4.41
1565 6161 1.896465 GAGTCAGTCTAGGGTTGCTGT 59.104 52.381 0.00 0.00 0.00 4.40
1566 6162 2.300437 GAGTCAGTCTAGGGTTGCTGTT 59.700 50.000 0.00 0.00 0.00 3.16
1567 6163 2.300437 AGTCAGTCTAGGGTTGCTGTTC 59.700 50.000 0.00 0.00 0.00 3.18
1568 6164 1.623811 TCAGTCTAGGGTTGCTGTTCC 59.376 52.381 0.00 0.00 0.00 3.62
1569 6165 1.347707 CAGTCTAGGGTTGCTGTTCCA 59.652 52.381 0.00 0.00 0.00 3.53
1570 6166 2.026822 CAGTCTAGGGTTGCTGTTCCAT 60.027 50.000 0.00 0.00 0.00 3.41
1571 6167 2.026822 AGTCTAGGGTTGCTGTTCCATG 60.027 50.000 0.00 0.00 0.00 3.66
1572 6168 1.985159 TCTAGGGTTGCTGTTCCATGT 59.015 47.619 0.00 0.00 0.00 3.21
1573 6169 2.375174 TCTAGGGTTGCTGTTCCATGTT 59.625 45.455 0.00 0.00 0.00 2.71
1574 6170 2.086610 AGGGTTGCTGTTCCATGTTT 57.913 45.000 0.00 0.00 0.00 2.83
1575 6171 3.237268 AGGGTTGCTGTTCCATGTTTA 57.763 42.857 0.00 0.00 0.00 2.01
1576 6172 2.890945 AGGGTTGCTGTTCCATGTTTAC 59.109 45.455 0.00 0.00 0.00 2.01
1577 6173 2.625790 GGGTTGCTGTTCCATGTTTACA 59.374 45.455 0.00 0.00 0.00 2.41
1578 6174 3.068873 GGGTTGCTGTTCCATGTTTACAA 59.931 43.478 0.00 0.00 0.00 2.41
1579 6175 4.048504 GGTTGCTGTTCCATGTTTACAAC 58.951 43.478 0.00 0.00 36.34 3.32
1580 6176 4.440802 GGTTGCTGTTCCATGTTTACAACA 60.441 41.667 12.54 0.00 46.94 3.33
1581 6177 4.991153 TGCTGTTCCATGTTTACAACAA 57.009 36.364 0.00 0.00 45.86 2.83
1582 6178 5.528043 TGCTGTTCCATGTTTACAACAAT 57.472 34.783 0.00 0.00 45.86 2.71
1583 6179 5.911752 TGCTGTTCCATGTTTACAACAATT 58.088 33.333 0.00 0.00 45.86 2.32
1584 6180 7.043961 TGCTGTTCCATGTTTACAACAATTA 57.956 32.000 0.00 0.00 45.86 1.40
1585 6181 7.492524 TGCTGTTCCATGTTTACAACAATTAA 58.507 30.769 0.00 0.00 45.86 1.40
1749 6409 5.580297 GCTTAGCTGCAGAATCCAGTATATC 59.420 44.000 20.43 0.00 32.93 1.63
1858 6518 8.638873 TGTAAACTCTTCATCTTCAAGTCACTA 58.361 33.333 0.00 0.00 0.00 2.74
2291 9543 4.679654 CACTTTTTCCATCGTAAACTTGGC 59.320 41.667 0.00 0.00 0.00 4.52
2408 9663 6.871044 TTTGAGTTCTTCGAGATCGTAATG 57.129 37.500 1.70 0.00 40.80 1.90
2513 9781 4.806640 TTAACCACTACTTAACCCTCGG 57.193 45.455 0.00 0.00 0.00 4.63
2514 9782 0.900421 ACCACTACTTAACCCTCGGC 59.100 55.000 0.00 0.00 0.00 5.54
2515 9783 0.899720 CCACTACTTAACCCTCGGCA 59.100 55.000 0.00 0.00 0.00 5.69
2828 10120 2.689983 CTCTCTGCCTCTCTTCTTCCTC 59.310 54.545 0.00 0.00 0.00 3.71
2829 10121 1.756538 CTCTGCCTCTCTTCTTCCTCC 59.243 57.143 0.00 0.00 0.00 4.30
2830 10122 1.360852 TCTGCCTCTCTTCTTCCTCCT 59.639 52.381 0.00 0.00 0.00 3.69
2831 10123 1.481772 CTGCCTCTCTTCTTCCTCCTG 59.518 57.143 0.00 0.00 0.00 3.86
2832 10124 0.177836 GCCTCTCTTCTTCCTCCTGC 59.822 60.000 0.00 0.00 0.00 4.85
2833 10125 0.829990 CCTCTCTTCTTCCTCCTGCC 59.170 60.000 0.00 0.00 0.00 4.85
2834 10126 1.566211 CTCTCTTCTTCCTCCTGCCA 58.434 55.000 0.00 0.00 0.00 4.92
2835 10127 1.481772 CTCTCTTCTTCCTCCTGCCAG 59.518 57.143 0.00 0.00 0.00 4.85
2836 10128 1.203237 TCTCTTCTTCCTCCTGCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
2837 10129 2.043115 TCTCTTCTTCCTCCTGCCAGTA 59.957 50.000 0.00 0.00 0.00 2.74
2838 10130 2.834549 CTCTTCTTCCTCCTGCCAGTAA 59.165 50.000 0.00 0.00 0.00 2.24
2839 10131 2.834549 TCTTCTTCCTCCTGCCAGTAAG 59.165 50.000 0.00 0.00 0.00 2.34
2840 10132 0.905357 TCTTCCTCCTGCCAGTAAGC 59.095 55.000 0.00 0.00 0.00 3.09
2841 10133 0.908198 CTTCCTCCTGCCAGTAAGCT 59.092 55.000 0.00 0.00 0.00 3.74
2842 10134 0.905357 TTCCTCCTGCCAGTAAGCTC 59.095 55.000 0.00 0.00 0.00 4.09
2843 10135 0.041833 TCCTCCTGCCAGTAAGCTCT 59.958 55.000 0.00 0.00 0.00 4.09
2844 10136 0.463620 CCTCCTGCCAGTAAGCTCTC 59.536 60.000 0.00 0.00 0.00 3.20
2845 10137 1.484038 CTCCTGCCAGTAAGCTCTCT 58.516 55.000 0.00 0.00 0.00 3.10
2846 10138 2.660572 CTCCTGCCAGTAAGCTCTCTA 58.339 52.381 0.00 0.00 0.00 2.43
2847 10139 2.360801 CTCCTGCCAGTAAGCTCTCTAC 59.639 54.545 0.00 0.00 0.00 2.59
2848 10140 1.410882 CCTGCCAGTAAGCTCTCTACC 59.589 57.143 0.00 0.00 0.00 3.18
2849 10141 2.103373 CTGCCAGTAAGCTCTCTACCA 58.897 52.381 0.00 0.00 0.00 3.25
2850 10142 2.100584 CTGCCAGTAAGCTCTCTACCAG 59.899 54.545 0.00 0.00 0.00 4.00
2851 10143 1.202475 GCCAGTAAGCTCTCTACCAGC 60.202 57.143 0.00 0.00 37.12 4.85
2852 10144 2.103373 CCAGTAAGCTCTCTACCAGCA 58.897 52.381 0.00 0.00 39.56 4.41
2853 10145 2.697751 CCAGTAAGCTCTCTACCAGCAT 59.302 50.000 0.00 0.00 39.56 3.79
2854 10146 3.492309 CCAGTAAGCTCTCTACCAGCATG 60.492 52.174 0.00 0.00 39.56 4.06
2855 10147 3.382865 CAGTAAGCTCTCTACCAGCATGA 59.617 47.826 0.00 0.00 39.69 3.07
2856 10148 4.039004 CAGTAAGCTCTCTACCAGCATGAT 59.961 45.833 0.00 0.00 39.69 2.45
2940 10300 3.285215 GCAGCAGCGGGGATGATG 61.285 66.667 0.00 0.00 38.42 3.07
2941 10301 2.507452 CAGCAGCGGGGATGATGA 59.493 61.111 0.00 0.00 37.55 2.92
2942 10302 1.597302 CAGCAGCGGGGATGATGAG 60.597 63.158 0.00 0.00 37.55 2.90
2943 10303 2.281345 GCAGCGGGGATGATGAGG 60.281 66.667 0.00 0.00 0.00 3.86
2944 10304 2.811514 GCAGCGGGGATGATGAGGA 61.812 63.158 0.00 0.00 0.00 3.71
2945 10305 1.370437 CAGCGGGGATGATGAGGAG 59.630 63.158 0.00 0.00 0.00 3.69
2946 10306 2.031768 GCGGGGATGATGAGGAGC 59.968 66.667 0.00 0.00 0.00 4.70
2947 10307 2.811514 GCGGGGATGATGAGGAGCA 61.812 63.158 0.00 0.00 0.00 4.26
2948 10308 1.370437 CGGGGATGATGAGGAGCAG 59.630 63.158 0.00 0.00 0.00 4.24
2949 10309 1.117749 CGGGGATGATGAGGAGCAGA 61.118 60.000 0.00 0.00 0.00 4.26
2950 10310 0.686224 GGGGATGATGAGGAGCAGAG 59.314 60.000 0.00 0.00 0.00 3.35
2951 10311 1.422531 GGGATGATGAGGAGCAGAGT 58.577 55.000 0.00 0.00 0.00 3.24
2952 10312 1.070445 GGGATGATGAGGAGCAGAGTG 59.930 57.143 0.00 0.00 0.00 3.51
2953 10313 1.070445 GGATGATGAGGAGCAGAGTGG 59.930 57.143 0.00 0.00 0.00 4.00
2954 10314 1.070445 GATGATGAGGAGCAGAGTGGG 59.930 57.143 0.00 0.00 0.00 4.61
2955 10315 0.041684 TGATGAGGAGCAGAGTGGGA 59.958 55.000 0.00 0.00 0.00 4.37
2956 10316 1.198713 GATGAGGAGCAGAGTGGGAA 58.801 55.000 0.00 0.00 0.00 3.97
2957 10317 1.556911 GATGAGGAGCAGAGTGGGAAA 59.443 52.381 0.00 0.00 0.00 3.13
2958 10318 0.979665 TGAGGAGCAGAGTGGGAAAG 59.020 55.000 0.00 0.00 0.00 2.62
2959 10319 1.270907 GAGGAGCAGAGTGGGAAAGA 58.729 55.000 0.00 0.00 0.00 2.52
2960 10320 1.625818 GAGGAGCAGAGTGGGAAAGAA 59.374 52.381 0.00 0.00 0.00 2.52
3015 10459 1.681538 GGATGACGAGGAGTAGAGCA 58.318 55.000 0.00 0.00 0.00 4.26
3018 10462 0.618981 TGACGAGGAGTAGAGCAGGA 59.381 55.000 0.00 0.00 0.00 3.86
3101 10671 2.028484 GTGGTGGCTGACGACGAA 59.972 61.111 0.00 0.00 0.00 3.85
3129 10753 3.233980 TGGTGCCTGACGCTGACT 61.234 61.111 0.00 0.00 38.78 3.41
3213 10915 2.552155 GGCGATAGGACCATGCCAATTA 60.552 50.000 10.39 0.00 45.06 1.40
3671 11487 1.820519 GATTTGCATGACTCAAGCCCA 59.179 47.619 0.00 0.00 0.00 5.36
3932 11760 9.950680 CGTTGAATAGTTTTTGATAATATGCCT 57.049 29.630 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 4.582869 TCAGTCTCATGCATTTTGCTACT 58.417 39.130 0.00 0.00 45.31 2.57
212 4184 7.451255 TGATCACCAAAACTACATGATTTTCCT 59.549 33.333 0.00 0.00 30.23 3.36
325 4297 4.927049 ACTTCAGGATCATCACAACCAAT 58.073 39.130 0.00 0.00 0.00 3.16
351 4323 7.924412 AGGATCATTACAACATCATTTTGCATC 59.076 33.333 0.00 0.00 0.00 3.91
388 4361 9.390795 CTGAAAACAACATCTCAATTCAGTTAG 57.609 33.333 0.00 0.00 38.17 2.34
589 4571 4.996122 GGACATCATCATTTTGCACCAAAA 59.004 37.500 5.69 5.69 45.41 2.44
590 4572 4.283978 AGGACATCATCATTTTGCACCAAA 59.716 37.500 0.00 0.00 0.00 3.28
591 4573 3.833650 AGGACATCATCATTTTGCACCAA 59.166 39.130 0.00 0.00 0.00 3.67
592 4574 3.433343 AGGACATCATCATTTTGCACCA 58.567 40.909 0.00 0.00 0.00 4.17
593 4575 5.581126 TTAGGACATCATCATTTTGCACC 57.419 39.130 0.00 0.00 0.00 5.01
594 4576 6.567050 ACATTAGGACATCATCATTTTGCAC 58.433 36.000 0.00 0.00 0.00 4.57
595 4577 6.778834 ACATTAGGACATCATCATTTTGCA 57.221 33.333 0.00 0.00 0.00 4.08
596 4578 7.037438 ACAACATTAGGACATCATCATTTTGC 58.963 34.615 0.00 0.00 0.00 3.68
597 4579 8.991243 AACAACATTAGGACATCATCATTTTG 57.009 30.769 0.00 0.00 0.00 2.44
599 4581 9.426837 CAAAACAACATTAGGACATCATCATTT 57.573 29.630 0.00 0.00 0.00 2.32
600 4582 8.036575 CCAAAACAACATTAGGACATCATCATT 58.963 33.333 0.00 0.00 0.00 2.57
601 4583 7.178983 ACCAAAACAACATTAGGACATCATCAT 59.821 33.333 0.00 0.00 0.00 2.45
602 4584 6.493115 ACCAAAACAACATTAGGACATCATCA 59.507 34.615 0.00 0.00 0.00 3.07
603 4585 6.924111 ACCAAAACAACATTAGGACATCATC 58.076 36.000 0.00 0.00 0.00 2.92
604 4586 6.916360 ACCAAAACAACATTAGGACATCAT 57.084 33.333 0.00 0.00 0.00 2.45
605 4587 7.001674 ACTACCAAAACAACATTAGGACATCA 58.998 34.615 0.00 0.00 0.00 3.07
606 4588 7.448748 ACTACCAAAACAACATTAGGACATC 57.551 36.000 0.00 0.00 0.00 3.06
607 4589 7.833285 AACTACCAAAACAACATTAGGACAT 57.167 32.000 0.00 0.00 0.00 3.06
608 4590 7.648039 AAACTACCAAAACAACATTAGGACA 57.352 32.000 0.00 0.00 0.00 4.02
609 4591 8.192110 TGAAAACTACCAAAACAACATTAGGAC 58.808 33.333 0.00 0.00 0.00 3.85
610 4592 8.294954 TGAAAACTACCAAAACAACATTAGGA 57.705 30.769 0.00 0.00 0.00 2.94
611 4593 8.410141 TCTGAAAACTACCAAAACAACATTAGG 58.590 33.333 0.00 0.00 0.00 2.69
612 4594 9.450807 CTCTGAAAACTACCAAAACAACATTAG 57.549 33.333 0.00 0.00 0.00 1.73
613 4595 8.962679 ACTCTGAAAACTACCAAAACAACATTA 58.037 29.630 0.00 0.00 0.00 1.90
673 4744 3.621805 TTCAAGTCCCCGCTCGCA 61.622 61.111 0.00 0.00 0.00 5.10
698 4769 0.109458 ACTATGAAACGAGCGCACGA 60.109 50.000 33.02 11.64 37.03 4.35
1034 5130 1.837051 TGGGTCCACTTCTCAGCGT 60.837 57.895 0.00 0.00 0.00 5.07
1069 5186 3.151022 GGAGAGGAGGAGCGGGTG 61.151 72.222 0.00 0.00 0.00 4.61
1121 5344 1.694169 GGAGGAGAAGGGGATGCCA 60.694 63.158 5.30 0.00 0.00 4.92
1275 5583 2.496871 TCGGCTACAATCGAACCCTAAA 59.503 45.455 0.00 0.00 32.11 1.85
1285 5593 4.299978 GTGGATCTACTTCGGCTACAATC 58.700 47.826 1.27 0.00 0.00 2.67
1326 5647 4.742201 CGTGGACGCAGAGGGTGG 62.742 72.222 0.00 0.00 0.00 4.61
1368 5719 0.107361 GAACGTAATGGACCTGGGGG 60.107 60.000 0.00 0.00 38.88 5.40
1369 5720 0.107361 GGAACGTAATGGACCTGGGG 60.107 60.000 0.00 0.00 0.00 4.96
1370 5721 0.107361 GGGAACGTAATGGACCTGGG 60.107 60.000 0.00 0.00 0.00 4.45
1471 6028 2.351641 GCATTCAGAACACCGCATGAAA 60.352 45.455 0.00 0.00 35.47 2.69
1578 6174 2.819608 ACGGAGCAGCAACATTAATTGT 59.180 40.909 0.00 0.00 41.53 2.71
1579 6175 3.173599 CACGGAGCAGCAACATTAATTG 58.826 45.455 0.00 0.00 0.00 2.32
1580 6176 2.164219 CCACGGAGCAGCAACATTAATT 59.836 45.455 0.00 0.00 0.00 1.40
1581 6177 1.745087 CCACGGAGCAGCAACATTAAT 59.255 47.619 0.00 0.00 0.00 1.40
1582 6178 1.164411 CCACGGAGCAGCAACATTAA 58.836 50.000 0.00 0.00 0.00 1.40
1583 6179 0.036164 ACCACGGAGCAGCAACATTA 59.964 50.000 0.00 0.00 0.00 1.90
1584 6180 1.228245 ACCACGGAGCAGCAACATT 60.228 52.632 0.00 0.00 0.00 2.71
1585 6181 1.968017 CACCACGGAGCAGCAACAT 60.968 57.895 0.00 0.00 0.00 2.71
1716 6376 3.338249 TCTGCAGCTAAGCTTAAGGTTG 58.662 45.455 26.20 17.55 36.40 3.77
1718 6378 3.703001 TTCTGCAGCTAAGCTTAAGGT 57.297 42.857 9.47 0.12 36.40 3.50
1749 6409 3.533606 ACAGAGCCAGCATTACTACAG 57.466 47.619 0.00 0.00 0.00 2.74
1834 6494 9.477484 GTTAGTGACTTGAAGATGAAGAGTTTA 57.523 33.333 0.00 0.00 0.00 2.01
1858 6518 7.976826 TGACTTAGTTACGACAAAACATTGTT 58.023 30.769 0.00 0.00 34.90 2.83
1887 6547 2.159254 GCCTGAAGTGAAAAGTGCACAA 60.159 45.455 21.04 0.00 38.70 3.33
1968 6640 3.255642 GCCAAAGGTCAAAACTGAGCATA 59.744 43.478 7.04 0.00 38.64 3.14
2281 9533 3.314357 AGTTGGAACGAAGCCAAGTTTAC 59.686 43.478 8.26 0.00 44.54 2.01
2291 9543 3.926616 ACTGGACATAGTTGGAACGAAG 58.073 45.455 0.00 0.00 0.00 3.79
2594 9885 4.227134 CCATAGCCTGCGACGCCT 62.227 66.667 18.69 9.87 0.00 5.52
2705 9997 0.809385 TCGTAGCGGAAGACAAGGAG 59.191 55.000 0.00 0.00 0.00 3.69
2828 10120 1.410882 GGTAGAGAGCTTACTGGCAGG 59.589 57.143 20.34 1.78 34.17 4.85
2829 10121 2.100584 CTGGTAGAGAGCTTACTGGCAG 59.899 54.545 14.16 14.16 34.17 4.85
2830 10122 2.103373 CTGGTAGAGAGCTTACTGGCA 58.897 52.381 0.00 0.00 34.17 4.92
2831 10123 1.202475 GCTGGTAGAGAGCTTACTGGC 60.202 57.143 0.00 0.00 33.37 4.85
2832 10124 2.103373 TGCTGGTAGAGAGCTTACTGG 58.897 52.381 0.00 0.00 37.35 4.00
2833 10125 3.382865 TCATGCTGGTAGAGAGCTTACTG 59.617 47.826 0.00 0.00 37.35 2.74
2834 10126 3.636679 TCATGCTGGTAGAGAGCTTACT 58.363 45.455 0.00 0.00 37.35 2.24
2835 10127 4.305769 CATCATGCTGGTAGAGAGCTTAC 58.694 47.826 0.00 0.00 37.35 2.34
2836 10128 3.244009 GCATCATGCTGGTAGAGAGCTTA 60.244 47.826 1.02 0.00 40.96 3.09
2837 10129 2.485124 GCATCATGCTGGTAGAGAGCTT 60.485 50.000 1.02 0.00 40.96 3.74
2838 10130 1.070445 GCATCATGCTGGTAGAGAGCT 59.930 52.381 1.02 0.00 40.96 4.09
2839 10131 1.510776 GCATCATGCTGGTAGAGAGC 58.489 55.000 1.02 0.00 40.96 4.09
2850 10142 2.492012 CTGGTAGAGGAAGCATCATGC 58.508 52.381 0.00 0.00 45.46 4.06
2851 10143 2.158856 TGCTGGTAGAGGAAGCATCATG 60.159 50.000 0.00 0.00 41.83 3.07
2852 10144 2.121948 TGCTGGTAGAGGAAGCATCAT 58.878 47.619 0.00 0.00 41.83 2.45
2853 10145 1.571955 TGCTGGTAGAGGAAGCATCA 58.428 50.000 0.00 0.00 41.83 3.07
2856 10148 0.898326 TCGTGCTGGTAGAGGAAGCA 60.898 55.000 0.00 0.00 44.36 3.91
2940 10300 1.270907 TCTTTCCCACTCTGCTCCTC 58.729 55.000 0.00 0.00 0.00 3.71
2941 10301 1.627834 CTTCTTTCCCACTCTGCTCCT 59.372 52.381 0.00 0.00 0.00 3.69
2942 10302 1.625818 TCTTCTTTCCCACTCTGCTCC 59.374 52.381 0.00 0.00 0.00 4.70
2943 10303 2.354604 CCTCTTCTTTCCCACTCTGCTC 60.355 54.545 0.00 0.00 0.00 4.26
2944 10304 1.627834 CCTCTTCTTTCCCACTCTGCT 59.372 52.381 0.00 0.00 0.00 4.24
2945 10305 1.625818 TCCTCTTCTTTCCCACTCTGC 59.374 52.381 0.00 0.00 0.00 4.26
2946 10306 2.354604 GCTCCTCTTCTTTCCCACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
2947 10307 1.905894 GCTCCTCTTCTTTCCCACTCT 59.094 52.381 0.00 0.00 0.00 3.24
2948 10308 1.625818 TGCTCCTCTTCTTTCCCACTC 59.374 52.381 0.00 0.00 0.00 3.51
2949 10309 1.627834 CTGCTCCTCTTCTTTCCCACT 59.372 52.381 0.00 0.00 0.00 4.00
2950 10310 1.625818 TCTGCTCCTCTTCTTTCCCAC 59.374 52.381 0.00 0.00 0.00 4.61
2951 10311 1.905215 CTCTGCTCCTCTTCTTTCCCA 59.095 52.381 0.00 0.00 0.00 4.37
2952 10312 1.406751 GCTCTGCTCCTCTTCTTTCCC 60.407 57.143 0.00 0.00 0.00 3.97
2953 10313 1.277557 TGCTCTGCTCCTCTTCTTTCC 59.722 52.381 0.00 0.00 0.00 3.13
2954 10314 2.620242 CTGCTCTGCTCCTCTTCTTTC 58.380 52.381 0.00 0.00 0.00 2.62
2955 10315 1.278699 CCTGCTCTGCTCCTCTTCTTT 59.721 52.381 0.00 0.00 0.00 2.52
2956 10316 0.903942 CCTGCTCTGCTCCTCTTCTT 59.096 55.000 0.00 0.00 0.00 2.52
2957 10317 0.977108 CCCTGCTCTGCTCCTCTTCT 60.977 60.000 0.00 0.00 0.00 2.85
2958 10318 0.975040 TCCCTGCTCTGCTCCTCTTC 60.975 60.000 0.00 0.00 0.00 2.87
2959 10319 0.326427 ATCCCTGCTCTGCTCCTCTT 60.326 55.000 0.00 0.00 0.00 2.85
2960 10320 1.049855 CATCCCTGCTCTGCTCCTCT 61.050 60.000 0.00 0.00 0.00 3.69
3101 10671 2.742372 GGCACCACAATCGCGAGT 60.742 61.111 16.66 9.86 0.00 4.18
3129 10753 2.173758 TTAGGCACCACCATCGCGAA 62.174 55.000 15.24 0.00 43.14 4.70
3213 10915 3.223435 CACGGATGTACTCCTCTACCAT 58.777 50.000 8.96 0.00 42.47 3.55
3932 11760 3.081061 ACAGAGGCATGCGACAAATTTA 58.919 40.909 12.44 0.00 0.00 1.40
3940 11768 0.671472 CACAAGACAGAGGCATGCGA 60.671 55.000 12.44 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.