Multiple sequence alignment - TraesCS5B01G045500

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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 TraesCS5B01G045500 chr5B 100.000 2348 0 0 1 2348 50652744 50655091 0.000000e+00 4337.0
1 TraesCS5B01G045500 chr5B 94.521 657 20 8 1675 2323 49885810 49885162 0.000000e+00 1000.0
2 TraesCS5B01G045500 chr5B 90.785 662 26 8 1663 2323 50060436 50059809 0.000000e+00 852.0
3 TraesCS5B01G045500 chr5B 93.410 349 17 1 1 349 50060806 50060464 1.610000e-141 512.0
4 TraesCS5B01G045500 chr5B 92.550 349 20 4 1 349 49889005 49888663 1.620000e-136 496.0
5 TraesCS5B01G045500 chr5B 93.333 315 20 1 1008 1321 536589172 536588858 4.570000e-127 464.0
6 TraesCS5B01G045500 chr5B 92.638 326 15 2 1 323 49886541 49886222 5.910000e-126 460.0
7 TraesCS5B01G045500 chr5B 93.311 299 8 6 1662 1957 49888636 49888347 4.640000e-117 431.0
8 TraesCS5B01G045500 chr5B 85.063 395 40 11 922 1316 511469226 511468851 3.660000e-103 385.0
9 TraesCS5B01G045500 chr5B 91.597 238 19 1 1313 1549 511468817 511468580 6.260000e-86 327.0
10 TraesCS5B01G045500 chr5B 97.710 131 3 0 1947 2077 49887993 49887863 2.350000e-55 226.0
11 TraesCS5B01G045500 chr5B 95.575 113 5 0 1313 1425 146278664 146278552 5.150000e-42 182.0
12 TraesCS5B01G045500 chr5B 94.231 104 6 0 910 1013 536589386 536589283 2.420000e-35 159.0
13 TraesCS5B01G045500 chr5B 94.444 90 5 0 1582 1671 550925096 550925185 3.150000e-29 139.0
14 TraesCS5B01G045500 chr5B 95.349 86 4 0 186 271 49887852 49887767 1.130000e-28 137.0
15 TraesCS5B01G045500 chr5B 97.015 67 1 1 1748 1814 49887773 49887708 6.860000e-21 111.0
16 TraesCS5B01G045500 chr5B 97.297 37 1 0 2312 2348 49885146 49885110 1.950000e-06 63.9
17 TraesCS5B01G045500 chr5B 97.059 34 1 0 2312 2345 50059793 50059760 9.060000e-05 58.4
18 TraesCS5B01G045500 chr5D 95.626 663 17 6 1662 2320 48468214 48468868 0.000000e+00 1053.0
19 TraesCS5B01G045500 chr5D 95.413 436 9 2 1662 2097 47094035 47093611 0.000000e+00 684.0
20 TraesCS5B01G045500 chr5D 95.129 349 11 1 1 349 47094404 47094062 1.590000e-151 545.0
21 TraesCS5B01G045500 chr5D 93.808 323 12 2 1 321 48467858 48468174 1.630000e-131 479.0
22 TraesCS5B01G045500 chr5D 91.746 315 25 1 1008 1321 441022517 441022203 9.960000e-119 436.0
23 TraesCS5B01G045500 chr5D 95.283 212 8 1 2112 2323 47093213 47093004 3.740000e-88 335.0
24 TraesCS5B01G045500 chr5D 96.460 113 4 0 1313 1425 134796393 134796281 1.110000e-43 187.0
25 TraesCS5B01G045500 chr5D 97.115 104 3 0 910 1013 441022731 441022628 2.400000e-40 176.0
26 TraesCS5B01G045500 chr5D 94.505 91 4 1 1576 1665 86401039 86400949 3.150000e-29 139.0
27 TraesCS5B01G045500 chr5D 97.297 37 1 0 2312 2348 48468887 48468923 1.950000e-06 63.9
28 TraesCS5B01G045500 chr5A 95.030 664 27 4 1662 2323 37925749 37925090 0.000000e+00 1038.0
29 TraesCS5B01G045500 chr5A 95.166 662 19 3 1662 2323 38195522 38194874 0.000000e+00 1033.0
30 TraesCS5B01G045500 chr5A 92.550 349 20 1 1 349 38195892 38195550 1.620000e-136 496.0
31 TraesCS5B01G045500 chr5A 94.788 307 16 0 1008 1314 557129117 557128811 1.630000e-131 479.0
32 TraesCS5B01G045500 chr5A 89.136 359 14 9 1 347 37926484 37926139 7.760000e-115 424.0
33 TraesCS5B01G045500 chr5A 95.575 113 5 0 1313 1425 158967478 158967366 5.150000e-42 182.0
34 TraesCS5B01G045500 chr5A 96.154 104 4 0 910 1013 557129331 557129228 1.120000e-38 171.0
35 TraesCS5B01G045500 chr5A 97.297 37 1 0 2312 2348 37925074 37925038 1.950000e-06 63.9
36 TraesCS5B01G045500 chr5A 97.297 37 1 0 2312 2348 38194858 38194822 1.950000e-06 63.9
37 TraesCS5B01G045500 chr6A 90.534 412 21 11 346 743 52324582 52324175 1.600000e-146 529.0
38 TraesCS5B01G045500 chr6A 89.372 414 24 15 346 743 52329901 52329492 9.690000e-139 503.0
39 TraesCS5B01G045500 chr6A 96.629 267 9 0 1050 1316 16649662 16649396 5.950000e-121 444.0
40 TraesCS5B01G045500 chr6A 92.089 316 20 3 1003 1316 52329284 52328972 7.700000e-120 440.0
41 TraesCS5B01G045500 chr6A 91.401 314 26 1 1003 1316 52323967 52323655 1.670000e-116 429.0
42 TraesCS5B01G045500 chr6A 93.191 235 15 1 1313 1546 16649361 16649127 6.210000e-91 344.0
43 TraesCS5B01G045500 chr6A 92.766 235 16 1 1313 1546 52323621 52323387 2.890000e-89 339.0
44 TraesCS5B01G045500 chr6A 91.489 235 19 1 1313 1546 52328938 52328704 2.910000e-84 322.0
45 TraesCS5B01G045500 chr6A 91.935 62 4 1 956 1016 52324164 52324103 4.160000e-13 86.1
46 TraesCS5B01G045500 chr6A 91.935 62 4 1 956 1016 52329481 52329420 4.160000e-13 86.1
47 TraesCS5B01G045500 chr4D 86.939 490 33 4 349 808 503797477 503796989 2.670000e-144 521.0
48 TraesCS5B01G045500 chr4D 95.469 309 14 0 1008 1316 503796215 503795907 5.830000e-136 494.0
49 TraesCS5B01G045500 chr4D 91.960 199 7 2 1315 1504 503795871 503795673 1.070000e-68 270.0
50 TraesCS5B01G045500 chr4D 88.166 169 12 1 853 1013 503796494 503796326 6.620000e-46 195.0
51 TraesCS5B01G045500 chr4D 97.872 47 1 0 816 862 503796908 503796862 5.380000e-12 82.4
52 TraesCS5B01G045500 chr4D 100.000 34 0 0 1418 1451 503796917 503796884 1.950000e-06 63.9
53 TraesCS5B01G045500 chr3A 93.610 313 5 3 1748 2057 481660532 481660832 9.890000e-124 453.0
54 TraesCS5B01G045500 chr3A 94.853 272 12 2 2050 2320 481661036 481661306 7.760000e-115 424.0
55 TraesCS5B01G045500 chr3A 89.199 287 9 6 1 271 481660258 481660538 2.890000e-89 339.0
56 TraesCS5B01G045500 chr3A 90.291 103 6 4 1562 1663 465578442 465578541 5.270000e-27 132.0
57 TraesCS5B01G045500 chr3A 97.297 37 1 0 2312 2348 481661325 481661361 1.950000e-06 63.9
58 TraesCS5B01G045500 chr2B 92.509 267 20 0 1050 1316 526519327 526519593 1.320000e-102 383.0
59 TraesCS5B01G045500 chr2B 93.103 232 14 1 1313 1542 526519627 526519858 2.890000e-89 339.0
60 TraesCS5B01G045500 chr2B 80.859 256 44 5 388 640 65417783 65418036 1.840000e-46 196.0
61 TraesCS5B01G045500 chr2B 88.961 154 17 0 650 803 65418101 65418254 8.560000e-45 191.0
62 TraesCS5B01G045500 chr2B 97.674 86 2 0 1582 1667 280495793 280495708 5.230000e-32 148.0
63 TraesCS5B01G045500 chr2B 100.000 34 0 0 1418 1451 65418325 65418358 1.950000e-06 63.9
64 TraesCS5B01G045500 chr3D 93.789 161 9 1 349 508 557799491 557799331 8.380000e-60 241.0
65 TraesCS5B01G045500 chr7D 91.925 161 13 0 650 810 66979877 66979717 2.350000e-55 226.0
66 TraesCS5B01G045500 chr7D 93.617 94 5 1 1582 1674 424092348 424092255 3.150000e-29 139.0
67 TraesCS5B01G045500 chr7A 91.304 161 11 2 650 810 73730654 73730811 1.410000e-52 217.0
68 TraesCS5B01G045500 chr7A 86.458 192 20 6 346 534 676070552 676070364 3.060000e-49 206.0
69 TraesCS5B01G045500 chr6B 95.327 107 5 0 1437 1543 688752203 688752309 1.120000e-38 171.0
70 TraesCS5B01G045500 chr6B 87.500 144 18 0 667 810 468013235 468013092 1.440000e-37 167.0
71 TraesCS5B01G045500 chr6B 89.109 101 8 3 1448 1546 704099720 704099621 3.170000e-24 122.0
72 TraesCS5B01G045500 chr6B 97.778 45 1 0 816 860 468013019 468012975 6.960000e-11 78.7
73 TraesCS5B01G045500 chr4A 93.103 116 8 0 419 534 642898048 642897933 1.120000e-38 171.0
74 TraesCS5B01G045500 chr4A 93.548 93 4 2 1575 1667 212813153 212813243 1.130000e-28 137.0
75 TraesCS5B01G045500 chr1B 94.393 107 6 0 1437 1543 57810992 57810886 5.190000e-37 165.0
76 TraesCS5B01G045500 chr6D 95.556 90 4 0 1582 1671 2103645 2103734 6.760000e-31 145.0
77 TraesCS5B01G045500 chrUn 95.455 88 4 0 1582 1669 94636262 94636349 8.750000e-30 141.0
78 TraesCS5B01G045500 chr2D 86.842 114 12 3 1553 1666 625194556 625194446 8.810000e-25 124.0
79 TraesCS5B01G045500 chr4B 95.833 48 1 1 545 591 74853091 74853044 2.500000e-10 76.8


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 TraesCS5B01G045500 chr5B 50652744 50655091 2347 False 4337.000000 4337 100.000000 1 2348 1 chr5B.!!$F1 2347
1 TraesCS5B01G045500 chr5B 50059760 50060806 1046 True 474.133333 852 93.751333 1 2345 3 chr5B.!!$R3 2344
2 TraesCS5B01G045500 chr5B 49885110 49889005 3895 True 365.612500 1000 95.048875 1 2348 8 chr5B.!!$R2 2347
3 TraesCS5B01G045500 chr5B 511468580 511469226 646 True 356.000000 385 88.330000 922 1549 2 chr5B.!!$R4 627
4 TraesCS5B01G045500 chr5B 536588858 536589386 528 True 311.500000 464 93.782000 910 1321 2 chr5B.!!$R5 411
5 TraesCS5B01G045500 chr5D 48467858 48468923 1065 False 531.966667 1053 95.577000 1 2348 3 chr5D.!!$F1 2347
6 TraesCS5B01G045500 chr5D 47093004 47094404 1400 True 521.333333 684 95.275000 1 2323 3 chr5D.!!$R3 2322
7 TraesCS5B01G045500 chr5D 441022203 441022731 528 True 306.000000 436 94.430500 910 1321 2 chr5D.!!$R4 411
8 TraesCS5B01G045500 chr5A 38194822 38195892 1070 True 530.966667 1033 95.004333 1 2348 3 chr5A.!!$R3 2347
9 TraesCS5B01G045500 chr5A 37925038 37926484 1446 True 508.633333 1038 93.821000 1 2348 3 chr5A.!!$R2 2347
10 TraesCS5B01G045500 chr5A 557128811 557129331 520 True 325.000000 479 95.471000 910 1314 2 chr5A.!!$R4 404
11 TraesCS5B01G045500 chr6A 16649127 16649662 535 True 394.000000 444 94.910000 1050 1546 2 chr6A.!!$R1 496
12 TraesCS5B01G045500 chr6A 52323387 52324582 1195 True 345.775000 529 91.659000 346 1546 4 chr6A.!!$R2 1200
13 TraesCS5B01G045500 chr6A 52328704 52329901 1197 True 337.775000 503 91.221250 346 1546 4 chr6A.!!$R3 1200
14 TraesCS5B01G045500 chr4D 503795673 503797477 1804 True 271.050000 521 93.401000 349 1504 6 chr4D.!!$R1 1155
15 TraesCS5B01G045500 chr3A 481660258 481661361 1103 False 319.975000 453 93.739750 1 2348 4 chr3A.!!$F2 2347
16 TraesCS5B01G045500 chr2B 526519327 526519858 531 False 361.000000 383 92.806000 1050 1542 2 chr2B.!!$F2 492

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
413 822 0.241481 TTTGCGCCGGTGGTAAAATC 59.759 50.0 18.41 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 2764 0.824759 CCTCCAAAGTACTCCCTCCG 59.175 60.0 0.0 0.0 0.0 4.63 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
33 34 2.660715 TGCGCTTTTATGAAATTGTGCG 59.339 40.909 9.73 9.14 44.10 5.34
56 57 6.086371 GCGTTTCTAGCACTTTTCATGTAAAC 59.914 38.462 0.00 0.00 34.19 2.01
63 64 4.219033 CACTTTTCATGTAAACGGACTGC 58.781 43.478 0.00 0.00 0.00 4.40
74 75 2.761786 ACGGACTGCTATTACCCCTA 57.238 50.000 0.00 0.00 0.00 3.53
75 76 3.036452 ACGGACTGCTATTACCCCTAA 57.964 47.619 0.00 0.00 0.00 2.69
76 77 2.697229 ACGGACTGCTATTACCCCTAAC 59.303 50.000 0.00 0.00 0.00 2.34
77 78 2.696707 CGGACTGCTATTACCCCTAACA 59.303 50.000 0.00 0.00 0.00 2.41
78 79 3.323979 CGGACTGCTATTACCCCTAACAT 59.676 47.826 0.00 0.00 0.00 2.71
79 80 4.525487 CGGACTGCTATTACCCCTAACATA 59.475 45.833 0.00 0.00 0.00 2.29
131 132 6.166279 TGAAGACTGTTGTTCCAGATGATAC 58.834 40.000 0.00 0.00 36.30 2.24
315 337 4.916983 TTTTGCTGCTTTAGTGTGTCAT 57.083 36.364 0.00 0.00 0.00 3.06
323 345 4.037803 TGCTTTAGTGTGTCATTTGCACAT 59.962 37.500 9.77 0.00 46.66 3.21
412 821 0.674534 TTTTGCGCCGGTGGTAAAAT 59.325 45.000 18.41 0.00 0.00 1.82
413 822 0.241481 TTTGCGCCGGTGGTAAAATC 59.759 50.000 18.41 0.00 0.00 2.17
439 848 2.916703 GCCATGCACCCAACACCA 60.917 61.111 0.00 0.00 0.00 4.17
442 851 1.831726 CATGCACCCAACACCACCA 60.832 57.895 0.00 0.00 0.00 4.17
475 884 1.302271 GAGGAAAGTTTCGGCCGGT 60.302 57.895 27.83 4.67 0.00 5.28
888 1777 3.634072 CGCGCAGGTGCATAGCTC 61.634 66.667 8.75 0.00 42.21 4.09
889 1778 2.512286 GCGCAGGTGCATAGCTCA 60.512 61.111 0.30 0.00 42.21 4.26
938 1835 1.811266 GTCGCACATCGGCATGACT 60.811 57.895 0.00 0.00 43.43 3.41
1001 1898 2.134287 CCTCCCGTCGTCCATGGAT 61.134 63.158 19.62 0.00 31.73 3.41
1398 2500 3.369366 CCTCTTGCTCCTCTTCTTCTTCC 60.369 52.174 0.00 0.00 0.00 3.46
1543 2654 1.225704 GATGCTTGGGGGTGGAGAG 59.774 63.158 0.00 0.00 0.00 3.20
1545 2656 4.432741 GCTTGGGGGTGGAGAGGC 62.433 72.222 0.00 0.00 0.00 4.70
1547 2658 4.608514 TTGGGGGTGGAGAGGCCA 62.609 66.667 5.01 0.00 46.96 5.36
1554 2665 3.691342 TGGAGAGGCCAACGACGG 61.691 66.667 5.01 0.00 45.87 4.79
1562 2673 2.579201 CCAACGACGGCTGGAGAT 59.421 61.111 11.70 0.00 34.35 2.75
1563 2674 1.811266 CCAACGACGGCTGGAGATG 60.811 63.158 11.70 0.00 34.35 2.90
1564 2675 2.125512 AACGACGGCTGGAGATGC 60.126 61.111 0.00 0.00 0.00 3.91
1565 2676 2.650116 AACGACGGCTGGAGATGCT 61.650 57.895 0.00 0.00 0.00 3.79
1566 2677 2.279120 CGACGGCTGGAGATGCTC 60.279 66.667 0.00 0.00 0.00 4.26
1567 2678 2.780094 CGACGGCTGGAGATGCTCT 61.780 63.158 0.00 0.00 0.00 4.09
1568 2679 1.519719 GACGGCTGGAGATGCTCTT 59.480 57.895 0.00 0.00 0.00 2.85
1569 2680 0.747255 GACGGCTGGAGATGCTCTTA 59.253 55.000 0.00 0.00 0.00 2.10
1581 2693 4.450053 AGATGCTCTTATTCAGTGCTTCC 58.550 43.478 7.70 0.00 42.82 3.46
1582 2694 2.991250 TGCTCTTATTCAGTGCTTCCC 58.009 47.619 0.00 0.00 41.79 3.97
1583 2695 2.293170 GCTCTTATTCAGTGCTTCCCC 58.707 52.381 0.00 0.00 38.72 4.81
1584 2696 2.092699 GCTCTTATTCAGTGCTTCCCCT 60.093 50.000 0.00 0.00 38.72 4.79
1585 2697 3.802866 CTCTTATTCAGTGCTTCCCCTC 58.197 50.000 0.00 0.00 0.00 4.30
1586 2698 2.505819 TCTTATTCAGTGCTTCCCCTCC 59.494 50.000 0.00 0.00 0.00 4.30
1588 2700 1.201429 ATTCAGTGCTTCCCCTCCGT 61.201 55.000 0.00 0.00 0.00 4.69
1590 2702 1.073199 CAGTGCTTCCCCTCCGTTT 59.927 57.895 0.00 0.00 0.00 3.60
1592 2704 1.072505 GTGCTTCCCCTCCGTTTCA 59.927 57.895 0.00 0.00 0.00 2.69
1593 2705 0.536460 GTGCTTCCCCTCCGTTTCAA 60.536 55.000 0.00 0.00 0.00 2.69
1594 2706 0.183971 TGCTTCCCCTCCGTTTCAAA 59.816 50.000 0.00 0.00 0.00 2.69
1595 2707 1.324383 GCTTCCCCTCCGTTTCAAAA 58.676 50.000 0.00 0.00 0.00 2.44
1596 2708 1.000607 GCTTCCCCTCCGTTTCAAAAC 60.001 52.381 0.00 0.00 35.59 2.43
1597 2709 2.303175 CTTCCCCTCCGTTTCAAAACA 58.697 47.619 6.45 0.00 38.81 2.83
1598 2710 1.975660 TCCCCTCCGTTTCAAAACAG 58.024 50.000 6.45 0.00 38.81 3.16
1599 2711 1.491332 TCCCCTCCGTTTCAAAACAGA 59.509 47.619 6.45 0.00 38.81 3.41
1600 2712 2.107552 TCCCCTCCGTTTCAAAACAGAT 59.892 45.455 6.45 0.00 38.81 2.90
1601 2713 2.228822 CCCCTCCGTTTCAAAACAGATG 59.771 50.000 6.45 0.00 38.81 2.90
1602 2714 3.146066 CCCTCCGTTTCAAAACAGATGA 58.854 45.455 6.45 0.00 38.81 2.92
1603 2715 3.058224 CCCTCCGTTTCAAAACAGATGAC 60.058 47.826 6.45 0.00 38.81 3.06
1604 2716 3.058224 CCTCCGTTTCAAAACAGATGACC 60.058 47.826 6.45 0.00 38.81 4.02
1605 2717 2.882137 TCCGTTTCAAAACAGATGACCC 59.118 45.455 6.45 0.00 38.81 4.46
1606 2718 2.621055 CCGTTTCAAAACAGATGACCCA 59.379 45.455 6.45 0.00 38.81 4.51
1607 2719 3.067461 CCGTTTCAAAACAGATGACCCAA 59.933 43.478 6.45 0.00 38.81 4.12
1608 2720 4.041723 CGTTTCAAAACAGATGACCCAAC 58.958 43.478 6.45 0.00 38.81 3.77
1609 2721 4.202010 CGTTTCAAAACAGATGACCCAACT 60.202 41.667 6.45 0.00 38.81 3.16
1610 2722 5.660460 GTTTCAAAACAGATGACCCAACTT 58.340 37.500 0.81 0.00 38.74 2.66
1611 2723 5.930837 TTCAAAACAGATGACCCAACTTT 57.069 34.783 0.00 0.00 0.00 2.66
1612 2724 5.261209 TCAAAACAGATGACCCAACTTTG 57.739 39.130 0.00 0.00 0.00 2.77
1613 2725 4.709397 TCAAAACAGATGACCCAACTTTGT 59.291 37.500 0.00 0.00 0.00 2.83
1614 2726 5.888724 TCAAAACAGATGACCCAACTTTGTA 59.111 36.000 0.00 0.00 0.00 2.41
1615 2727 5.767816 AAACAGATGACCCAACTTTGTAC 57.232 39.130 0.00 0.00 0.00 2.90
1616 2728 4.706842 ACAGATGACCCAACTTTGTACT 57.293 40.909 0.00 0.00 0.00 2.73
1617 2729 5.818678 ACAGATGACCCAACTTTGTACTA 57.181 39.130 0.00 0.00 0.00 1.82
1618 2730 6.182507 ACAGATGACCCAACTTTGTACTAA 57.817 37.500 0.00 0.00 0.00 2.24
1619 2731 6.597562 ACAGATGACCCAACTTTGTACTAAA 58.402 36.000 0.00 0.00 0.00 1.85
1620 2732 6.710744 ACAGATGACCCAACTTTGTACTAAAG 59.289 38.462 13.08 13.08 0.00 1.85
1621 2733 6.710744 CAGATGACCCAACTTTGTACTAAAGT 59.289 38.462 14.04 14.04 41.82 2.66
1623 2735 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
1624 2736 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
1625 2737 6.993902 TGACCCAACTTTGTACTAAAGTTAGG 59.006 38.462 26.64 26.64 46.95 2.69
1626 2738 7.140522 ACCCAACTTTGTACTAAAGTTAGGA 57.859 36.000 30.53 0.00 45.56 2.94
1627 2739 6.994496 ACCCAACTTTGTACTAAAGTTAGGAC 59.006 38.462 30.53 6.50 45.56 3.85
1636 2748 7.430992 GTACTAAAGTTAGGACAAAGTTGGG 57.569 40.000 8.33 0.00 42.86 4.12
1637 2749 6.009908 ACTAAAGTTAGGACAAAGTTGGGT 57.990 37.500 3.26 0.00 35.08 4.51
1638 2750 6.060136 ACTAAAGTTAGGACAAAGTTGGGTC 58.940 40.000 3.26 0.43 35.08 4.46
1639 2751 4.513406 AAGTTAGGACAAAGTTGGGTCA 57.487 40.909 9.41 0.00 35.74 4.02
1640 2752 4.724279 AGTTAGGACAAAGTTGGGTCAT 57.276 40.909 9.41 5.58 35.74 3.06
1641 2753 4.652822 AGTTAGGACAAAGTTGGGTCATC 58.347 43.478 9.41 0.00 35.74 2.92
1642 2754 4.351111 AGTTAGGACAAAGTTGGGTCATCT 59.649 41.667 9.41 2.63 35.74 2.90
1643 2755 5.546499 AGTTAGGACAAAGTTGGGTCATCTA 59.454 40.000 9.41 1.89 35.74 1.98
1644 2756 6.215636 AGTTAGGACAAAGTTGGGTCATCTAT 59.784 38.462 9.41 0.00 35.74 1.98
1645 2757 5.520748 AGGACAAAGTTGGGTCATCTATT 57.479 39.130 9.41 0.00 35.74 1.73
1646 2758 5.892348 AGGACAAAGTTGGGTCATCTATTT 58.108 37.500 9.41 0.00 35.74 1.40
1647 2759 6.314917 AGGACAAAGTTGGGTCATCTATTTT 58.685 36.000 9.41 0.00 35.74 1.82
1648 2760 6.209391 AGGACAAAGTTGGGTCATCTATTTTG 59.791 38.462 9.41 0.00 35.74 2.44
1649 2761 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1650 2762 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1651 2763 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1652 2764 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1653 2765 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1654 2766 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1655 2767 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1656 2768 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1657 2769 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1658 2770 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1659 2771 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1660 2772 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1661 2773 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1668 2780 1.066358 GGAACGGAGGGAGTACTTTGG 60.066 57.143 0.00 0.00 0.00 3.28
1710 2822 5.284582 AGTGAAGAGGATAAGTGGGAGATT 58.715 41.667 0.00 0.00 0.00 2.40
1816 2930 6.988622 AGTATATATACACGTGGCTCTCTC 57.011 41.667 21.57 4.07 35.74 3.20
1817 2931 6.713276 AGTATATATACACGTGGCTCTCTCT 58.287 40.000 21.57 6.32 35.74 3.10
1818 2932 6.819649 AGTATATATACACGTGGCTCTCTCTC 59.180 42.308 21.57 3.42 35.74 3.20
1819 2933 2.428544 ATACACGTGGCTCTCTCTCT 57.571 50.000 21.57 0.00 0.00 3.10
1820 2934 2.201921 TACACGTGGCTCTCTCTCTT 57.798 50.000 21.57 0.00 0.00 2.85
1821 2935 1.333177 ACACGTGGCTCTCTCTCTTT 58.667 50.000 21.57 0.00 0.00 2.52
2226 6762 4.388485 CATCATACAAATGGGATGGACGA 58.612 43.478 0.00 0.00 34.84 4.20
2269 6810 3.634910 ACCACACTGACCCAACATTTTAC 59.365 43.478 0.00 0.00 0.00 2.01
2278 6819 7.118496 TGACCCAACATTTTACTGATTTGTT 57.882 32.000 0.00 0.00 0.00 2.83
2310 6854 4.429505 TCTCTGAAGATGGAGAGGGAAAA 58.570 43.478 0.00 0.00 37.02 2.29
2315 6886 3.643199 AGATGGAGAGGGAAAAGAAGC 57.357 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.577427 CCGTTTACATGAAAAGTGCTAGAAAC 59.423 38.462 0.00 0.00 0.00 2.78
56 57 2.696707 TGTTAGGGGTAATAGCAGTCCG 59.303 50.000 0.00 0.00 0.00 4.79
74 75 8.966868 CCCACTATTTCAACCTATGTTTATGTT 58.033 33.333 0.00 0.00 30.42 2.71
75 76 8.333235 TCCCACTATTTCAACCTATGTTTATGT 58.667 33.333 0.00 0.00 30.42 2.29
76 77 8.746052 TCCCACTATTTCAACCTATGTTTATG 57.254 34.615 0.00 0.00 30.42 1.90
77 78 9.574516 GATCCCACTATTTCAACCTATGTTTAT 57.425 33.333 0.00 0.00 30.42 1.40
78 79 8.778059 AGATCCCACTATTTCAACCTATGTTTA 58.222 33.333 0.00 0.00 30.42 2.01
79 80 7.643123 AGATCCCACTATTTCAACCTATGTTT 58.357 34.615 0.00 0.00 30.42 2.83
315 337 1.963855 CGGACCGGTGATGTGCAAA 60.964 57.895 14.63 0.00 0.00 3.68
323 345 3.618750 GGGAACACGGACCGGTGA 61.619 66.667 14.63 0.00 40.38 4.02
405 814 1.101635 GGCTGGGGCGAGATTTTACC 61.102 60.000 0.00 0.00 39.81 2.85
439 848 1.472480 CTCAAATCCGGCGAAAATGGT 59.528 47.619 9.30 0.00 0.00 3.55
442 851 2.122783 TCCTCAAATCCGGCGAAAAT 57.877 45.000 9.30 0.00 0.00 1.82
475 884 0.776810 TTGGGTTTCTCATGGGAGCA 59.223 50.000 0.00 0.00 41.13 4.26
518 927 0.110373 CGTGAAAAGGTAGCGTTGGC 60.110 55.000 0.00 0.00 40.37 4.52
521 930 0.584876 GCACGTGAAAAGGTAGCGTT 59.415 50.000 22.23 0.00 33.28 4.84
522 931 0.531090 TGCACGTGAAAAGGTAGCGT 60.531 50.000 22.23 0.00 36.13 5.07
810 1249 3.007920 AGGAGGTCCAGGCTGCAG 61.008 66.667 10.11 10.11 38.89 4.41
811 1250 3.005539 GAGGAGGTCCAGGCTGCA 61.006 66.667 9.56 0.00 38.89 4.41
812 1251 3.791586 GGAGGAGGTCCAGGCTGC 61.792 72.222 9.56 0.00 46.10 5.25
874 1763 3.403277 CGTGAGCTATGCACCTGC 58.597 61.111 0.00 0.00 42.50 4.85
1301 2363 2.753029 GAGGGGCAGCAGTCTTGT 59.247 61.111 0.00 0.00 0.00 3.16
1478 2589 2.663188 GCATAGCGAGGAAGCGGG 60.663 66.667 0.00 0.00 43.00 6.13
1545 2656 1.811266 CATCTCCAGCCGTCGTTGG 60.811 63.158 6.67 6.67 41.58 3.77
1547 2658 2.125512 GCATCTCCAGCCGTCGTT 60.126 61.111 0.00 0.00 0.00 3.85
1549 2660 2.279120 GAGCATCTCCAGCCGTCG 60.279 66.667 0.00 0.00 0.00 5.12
1560 2671 3.563390 GGGAAGCACTGAATAAGAGCATC 59.437 47.826 0.00 0.00 44.23 3.91
1561 2672 3.549794 GGGAAGCACTGAATAAGAGCAT 58.450 45.455 0.00 0.00 44.23 3.79
1562 2673 2.356125 GGGGAAGCACTGAATAAGAGCA 60.356 50.000 0.00 0.00 44.23 4.26
1563 2674 2.092699 AGGGGAAGCACTGAATAAGAGC 60.093 50.000 0.00 0.00 42.32 4.09
1564 2675 3.432890 GGAGGGGAAGCACTGAATAAGAG 60.433 52.174 0.00 0.00 0.00 2.85
1565 2676 2.505819 GGAGGGGAAGCACTGAATAAGA 59.494 50.000 0.00 0.00 0.00 2.10
1566 2677 2.743183 CGGAGGGGAAGCACTGAATAAG 60.743 54.545 0.00 0.00 0.00 1.73
1567 2678 1.209504 CGGAGGGGAAGCACTGAATAA 59.790 52.381 0.00 0.00 0.00 1.40
1568 2679 0.830648 CGGAGGGGAAGCACTGAATA 59.169 55.000 0.00 0.00 0.00 1.75
1569 2680 1.201429 ACGGAGGGGAAGCACTGAAT 61.201 55.000 0.00 0.00 0.00 2.57
1585 2697 2.621055 TGGGTCATCTGTTTTGAAACGG 59.379 45.455 8.75 8.75 44.68 4.44
1586 2698 3.980646 TGGGTCATCTGTTTTGAAACG 57.019 42.857 2.53 0.00 41.74 3.60
1588 2700 5.930837 AAGTTGGGTCATCTGTTTTGAAA 57.069 34.783 0.00 0.00 0.00 2.69
1590 2702 4.709397 ACAAAGTTGGGTCATCTGTTTTGA 59.291 37.500 0.00 0.00 0.00 2.69
1592 2704 5.891551 AGTACAAAGTTGGGTCATCTGTTTT 59.108 36.000 0.00 0.00 0.00 2.43
1593 2705 5.445964 AGTACAAAGTTGGGTCATCTGTTT 58.554 37.500 0.00 0.00 0.00 2.83
1594 2706 5.048846 AGTACAAAGTTGGGTCATCTGTT 57.951 39.130 0.00 0.00 0.00 3.16
1595 2707 4.706842 AGTACAAAGTTGGGTCATCTGT 57.293 40.909 0.00 0.00 0.00 3.41
1596 2708 6.710744 ACTTTAGTACAAAGTTGGGTCATCTG 59.289 38.462 14.04 0.00 37.18 2.90
1597 2709 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
1598 2710 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
1599 2711 8.617290 CTAACTTTAGTACAAAGTTGGGTCAT 57.383 34.615 27.85 14.43 46.41 3.06
1604 2716 8.441312 TTGTCCTAACTTTAGTACAAAGTTGG 57.559 34.615 27.85 25.87 46.41 3.77
1609 2721 8.895737 CCAACTTTGTCCTAACTTTAGTACAAA 58.104 33.333 15.20 15.20 43.04 2.83
1610 2722 7.499895 CCCAACTTTGTCCTAACTTTAGTACAA 59.500 37.037 3.70 3.70 37.67 2.41
1611 2723 6.993902 CCCAACTTTGTCCTAACTTTAGTACA 59.006 38.462 0.00 0.00 29.26 2.90
1612 2724 6.994496 ACCCAACTTTGTCCTAACTTTAGTAC 59.006 38.462 0.00 0.00 0.00 2.73
1613 2725 7.140522 ACCCAACTTTGTCCTAACTTTAGTA 57.859 36.000 0.00 0.00 0.00 1.82
1614 2726 6.009908 ACCCAACTTTGTCCTAACTTTAGT 57.990 37.500 0.00 0.00 0.00 2.24
1615 2727 6.059484 TGACCCAACTTTGTCCTAACTTTAG 58.941 40.000 0.00 0.00 0.00 1.85
1616 2728 6.003859 TGACCCAACTTTGTCCTAACTTTA 57.996 37.500 0.00 0.00 0.00 1.85
1617 2729 4.862371 TGACCCAACTTTGTCCTAACTTT 58.138 39.130 0.00 0.00 0.00 2.66
1618 2730 4.513406 TGACCCAACTTTGTCCTAACTT 57.487 40.909 0.00 0.00 0.00 2.66
1619 2731 4.351111 AGATGACCCAACTTTGTCCTAACT 59.649 41.667 0.00 0.00 0.00 2.24
1620 2732 4.652822 AGATGACCCAACTTTGTCCTAAC 58.347 43.478 0.00 0.00 0.00 2.34
1621 2733 4.993705 AGATGACCCAACTTTGTCCTAA 57.006 40.909 0.00 0.00 0.00 2.69
1622 2734 6.636454 AATAGATGACCCAACTTTGTCCTA 57.364 37.500 0.00 0.00 0.00 2.94
1623 2735 5.520748 AATAGATGACCCAACTTTGTCCT 57.479 39.130 0.00 0.00 0.00 3.85
1624 2736 6.389906 CAAAATAGATGACCCAACTTTGTCC 58.610 40.000 0.00 0.00 0.00 4.02
1625 2737 6.208599 TCCAAAATAGATGACCCAACTTTGTC 59.791 38.462 0.00 0.00 0.00 3.18
1626 2738 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1627 2739 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1628 2740 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1629 2741 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1630 2742 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1631 2743 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1632 2744 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1633 2745 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1634 2746 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1635 2747 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1636 2748 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1637 2749 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1638 2750 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1639 2751 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1640 2752 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1641 2753 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1642 2754 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1643 2755 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1644 2756 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1645 2757 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1646 2758 2.019807 AAGTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
1647 2759 1.621814 CAAAGTACTCCCTCCGTTCCA 59.378 52.381 0.00 0.00 0.00 3.53
1648 2760 1.066358 CCAAAGTACTCCCTCCGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
1649 2761 1.897802 TCCAAAGTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 0.00 3.95
1650 2762 1.900486 CTCCAAAGTACTCCCTCCGTT 59.100 52.381 0.00 0.00 0.00 4.44
1651 2763 1.558233 CTCCAAAGTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
1652 2764 0.824759 CCTCCAAAGTACTCCCTCCG 59.175 60.000 0.00 0.00 0.00 4.63
1653 2765 1.832366 GTCCTCCAAAGTACTCCCTCC 59.168 57.143 0.00 0.00 0.00 4.30
1654 2766 2.498078 CTGTCCTCCAAAGTACTCCCTC 59.502 54.545 0.00 0.00 0.00 4.30
1655 2767 2.541466 CTGTCCTCCAAAGTACTCCCT 58.459 52.381 0.00 0.00 0.00 4.20
1656 2768 1.555533 CCTGTCCTCCAAAGTACTCCC 59.444 57.143 0.00 0.00 0.00 4.30
1657 2769 2.537143 TCCTGTCCTCCAAAGTACTCC 58.463 52.381 0.00 0.00 0.00 3.85
1658 2770 3.323979 TGTTCCTGTCCTCCAAAGTACTC 59.676 47.826 0.00 0.00 0.00 2.59
1659 2771 3.314693 TGTTCCTGTCCTCCAAAGTACT 58.685 45.455 0.00 0.00 0.00 2.73
1660 2772 3.071167 ACTGTTCCTGTCCTCCAAAGTAC 59.929 47.826 0.00 0.00 0.00 2.73
1661 2773 3.071023 CACTGTTCCTGTCCTCCAAAGTA 59.929 47.826 0.00 0.00 0.00 2.24
1668 2780 1.550976 CTACCCACTGTTCCTGTCCTC 59.449 57.143 0.00 0.00 0.00 3.71
1742 2854 7.439157 TTTGACAAGGATGAGTACTTCAATG 57.561 36.000 0.00 0.00 39.77 2.82
1791 2903 7.666388 AGAGAGAGCCACGTGTATATATACTTT 59.334 37.037 20.80 5.35 34.41 2.66
2278 6819 3.307269 CCATCTTCAGAGAAAGCTGTGGA 60.307 47.826 0.00 0.00 36.16 4.02
2310 6854 5.369699 TGACCTAGGCCTTTATTATGCTTCT 59.630 40.000 12.58 0.00 0.00 2.85
2315 6886 5.308237 AGTCCTGACCTAGGCCTTTATTATG 59.692 44.000 12.58 0.00 46.87 1.90


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

AutoCloner maintained by Alex Coulton.