Multiple sequence alignment - TraesCS2D01G079000

Loading Multiple Alignment...

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 TraesCS2D01G079000 chr2D 100.000 2457 0 0 1 2457 33877259 33879715 0.000000e+00 4538.0
1 TraesCS2D01G079000 chr2D 86.217 653 55 12 10 629 33730062 33729412 0.000000e+00 675.0
2 TraesCS2D01G079000 chr2D 89.496 476 35 12 1028 1496 24557098 24557565 2.720000e-164 588.0
3 TraesCS2D01G079000 chr2D 80.494 769 84 30 1651 2398 24557649 24558372 1.670000e-146 529.0
4 TraesCS2D01G079000 chr2D 86.797 409 46 5 614 1022 33729396 33728996 1.340000e-122 449.0
5 TraesCS2D01G079000 chr2D 96.154 52 1 1 1561 1612 461076413 461076363 1.570000e-12 84.2
6 TraesCS2D01G079000 chr2A 86.572 983 89 19 594 1570 36742416 36743361 0.000000e+00 1044.0
7 TraesCS2D01G079000 chr2A 90.162 803 66 8 777 1570 36673035 36672237 0.000000e+00 1033.0
8 TraesCS2D01G079000 chr2A 89.037 675 54 9 1624 2290 36743359 36744021 0.000000e+00 819.0
9 TraesCS2D01G079000 chr2A 88.483 547 52 7 1624 2168 36672239 36671702 0.000000e+00 651.0
10 TraesCS2D01G079000 chr2A 84.389 647 52 24 162 782 36689162 36688539 7.570000e-165 590.0
11 TraesCS2D01G079000 chr2A 84.236 628 60 22 952 1570 27345130 27344533 2.120000e-160 575.0
12 TraesCS2D01G079000 chr2A 85.493 517 46 13 1 504 36741732 36742232 1.690000e-141 512.0
13 TraesCS2D01G079000 chr2A 87.805 164 18 1 10 171 36690087 36689924 8.970000e-45 191.0
14 TraesCS2D01G079000 chr2A 89.510 143 14 1 2316 2457 36744082 36744224 1.940000e-41 180.0
15 TraesCS2D01G079000 chr2B 87.839 847 73 16 1624 2457 55913761 55914590 0.000000e+00 966.0
16 TraesCS2D01G079000 chr2B 91.143 700 49 8 876 1570 55913072 55913763 0.000000e+00 937.0
17 TraesCS2D01G079000 chr2B 91.234 616 43 8 960 1570 55923778 55924387 0.000000e+00 828.0
18 TraesCS2D01G079000 chr2B 84.615 702 60 15 10 668 55912376 55913072 0.000000e+00 654.0
19 TraesCS2D01G079000 chr2B 80.431 649 76 27 1651 2283 40279987 40279374 4.820000e-122 448.0
20 TraesCS2D01G079000 chr2B 83.365 523 46 13 246 743 22854802 22854296 1.730000e-121 446.0
21 TraesCS2D01G079000 chr2B 90.175 285 22 5 1827 2109 55924857 55925137 1.390000e-97 366.0
22 TraesCS2D01G079000 chr2B 90.830 229 20 1 744 972 55916528 55916755 3.070000e-79 305.0
23 TraesCS2D01G079000 chr2B 88.626 211 14 4 1624 1831 55924385 55924588 5.250000e-62 248.0
24 TraesCS2D01G079000 chr2B 86.463 229 24 3 514 742 55916267 55916488 6.790000e-61 244.0
25 TraesCS2D01G079000 chr2B 95.918 49 1 1 1564 1612 160906562 160906515 7.280000e-11 78.7
26 TraesCS2D01G079000 chr3B 83.748 523 44 13 246 743 170070077 170070583 8.010000e-125 457.0
27 TraesCS2D01G079000 chr3B 82.792 523 49 13 246 743 326530036 326529530 1.750000e-116 429.0
28 TraesCS2D01G079000 chr5D 83.925 479 62 9 971 1444 326369664 326370132 6.230000e-121 444.0
29 TraesCS2D01G079000 chr5D 93.443 61 4 0 1569 1629 487401537 487401477 9.360000e-15 91.6
30 TraesCS2D01G079000 chr5B 83.958 480 57 12 971 1444 378816066 378816531 2.240000e-120 442.0
31 TraesCS2D01G079000 chr5B 83.015 524 47 13 246 743 325636945 325636438 1.040000e-118 436.0
32 TraesCS2D01G079000 chr5B 82.016 506 75 11 964 1461 595659019 595659516 1.360000e-112 416.0
33 TraesCS2D01G079000 chr7D 96.721 61 1 1 1568 1627 101475460 101475400 1.550000e-17 100.0
34 TraesCS2D01G079000 chr7D 97.872 47 1 0 1566 1612 79628341 79628387 5.630000e-12 82.4
35 TraesCS2D01G079000 chr7D 92.593 54 4 0 1559 1612 443416023 443416076 7.280000e-11 78.7
36 TraesCS2D01G079000 chr4B 94.915 59 3 0 1569 1627 586994197 586994255 2.600000e-15 93.5
37 TraesCS2D01G079000 chr3D 91.803 61 2 2 1568 1626 213035676 213035735 5.630000e-12 82.4
38 TraesCS2D01G079000 chr4A 89.831 59 6 0 1568 1626 91750112 91750054 2.620000e-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 TraesCS2D01G079000 chr2D 33877259 33879715 2456 False 4538.000000 4538 100.000000 1 2457 1 chr2D.!!$F1 2456
1 TraesCS2D01G079000 chr2D 33728996 33730062 1066 True 562.000000 675 86.507000 10 1022 2 chr2D.!!$R2 1012
2 TraesCS2D01G079000 chr2D 24557098 24558372 1274 False 558.500000 588 84.995000 1028 2398 2 chr2D.!!$F2 1370
3 TraesCS2D01G079000 chr2A 36671702 36673035 1333 True 842.000000 1033 89.322500 777 2168 2 chr2A.!!$R2 1391
4 TraesCS2D01G079000 chr2A 36741732 36744224 2492 False 638.750000 1044 87.653000 1 2457 4 chr2A.!!$F1 2456
5 TraesCS2D01G079000 chr2A 27344533 27345130 597 True 575.000000 575 84.236000 952 1570 1 chr2A.!!$R1 618
6 TraesCS2D01G079000 chr2A 36688539 36690087 1548 True 390.500000 590 86.097000 10 782 2 chr2A.!!$R3 772
7 TraesCS2D01G079000 chr2B 55912376 55916755 4379 False 621.200000 966 88.178000 10 2457 5 chr2B.!!$F1 2447
8 TraesCS2D01G079000 chr2B 55923778 55925137 1359 False 480.666667 828 90.011667 960 2109 3 chr2B.!!$F2 1149
9 TraesCS2D01G079000 chr2B 40279374 40279987 613 True 448.000000 448 80.431000 1651 2283 1 chr2B.!!$R2 632
10 TraesCS2D01G079000 chr2B 22854296 22854802 506 True 446.000000 446 83.365000 246 743 1 chr2B.!!$R1 497
11 TraesCS2D01G079000 chr3B 170070077 170070583 506 False 457.000000 457 83.748000 246 743 1 chr3B.!!$F1 497
12 TraesCS2D01G079000 chr3B 326529530 326530036 506 True 429.000000 429 82.792000 246 743 1 chr3B.!!$R1 497
13 TraesCS2D01G079000 chr5B 325636438 325636945 507 True 436.000000 436 83.015000 246 743 1 chr5B.!!$R1 497

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
935 1844 0.03582 TTGTCGCCATCCCTAACCAC 60.036 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 3715 0.034616 CCTCTCATCCGCAATCCTCC 59.965 60.0 0.0 0.0 0.0 4.3 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
22 25 3.761311 TTTCTTTTGTTACAACGGCGT 57.239 38.095 6.77 6.77 0.00 5.68
28 31 1.301165 GTTACAACGGCGTCCTGGT 60.301 57.895 15.17 12.20 0.00 4.00
41 44 1.746615 CCTGGTGTGCTGGAATCCG 60.747 63.158 0.00 0.00 0.00 4.18
68 71 1.621301 CGACTGTTTCCTGAGCTGCG 61.621 60.000 0.00 0.00 0.00 5.18
81 84 1.661509 GCTGCGCTTGGTTCCAAAC 60.662 57.895 9.73 0.65 0.00 2.93
83 86 1.781025 CTGCGCTTGGTTCCAAACGA 61.781 55.000 24.94 12.66 37.61 3.85
86 89 1.472990 CGCTTGGTTCCAAACGAAAC 58.527 50.000 18.62 0.00 37.61 2.78
90 102 3.847105 GCTTGGTTCCAAACGAAACTACG 60.847 47.826 5.76 0.00 39.12 3.51
91 103 2.211806 TGGTTCCAAACGAAACTACGG 58.788 47.619 0.00 0.00 39.12 4.02
206 993 5.122239 TGCTACTGCATCACAAAGAACATAC 59.878 40.000 0.00 0.00 45.31 2.39
284 1081 4.079970 AGCTGCTATGCTTGCATCATTAT 58.920 39.130 11.64 0.00 40.93 1.28
386 1191 6.798427 ATCATCTTCCTGCAAGAACTAGTA 57.202 37.500 0.00 0.00 44.66 1.82
389 1194 5.392767 TCTTCCTGCAAGAACTAGTACTG 57.607 43.478 5.39 0.00 38.26 2.74
395 1200 2.354203 GCAAGAACTAGTACTGCTGCCT 60.354 50.000 5.39 0.00 0.00 4.75
441 1247 4.932200 CCTGGAAACTTGATGTAGAGACAC 59.068 45.833 0.00 0.00 38.76 3.67
488 1296 8.709646 ACTCTGTATTTTCGTGTGAAATAAGAC 58.290 33.333 0.00 0.00 43.32 3.01
497 1305 6.330278 TCGTGTGAAATAAGACATACTCAGG 58.670 40.000 0.00 0.00 0.00 3.86
513 1343 8.424918 ACATACTCAGGATTCTATTTTCGATGT 58.575 33.333 0.00 0.00 0.00 3.06
531 1361 1.239347 GTTGGAGCTTTCCTGTGGTC 58.761 55.000 0.00 0.00 0.00 4.02
537 1367 0.398318 GCTTTCCTGTGGTCTGGAGT 59.602 55.000 0.00 0.00 41.46 3.85
554 1384 2.027837 GGAGTTTGCCATGGAAGCATTT 60.028 45.455 18.40 0.00 40.59 2.32
555 1385 2.997986 GAGTTTGCCATGGAAGCATTTG 59.002 45.455 18.40 0.00 40.59 2.32
558 1388 4.040217 AGTTTGCCATGGAAGCATTTGTAA 59.960 37.500 18.40 0.00 40.59 2.41
644 1550 4.184629 GCATTCTAGGGTGTCTTGTGTAG 58.815 47.826 0.00 0.00 0.00 2.74
646 1552 2.176889 TCTAGGGTGTCTTGTGTAGGC 58.823 52.381 0.00 0.00 0.00 3.93
672 1580 7.707774 TTTTACCTCAAAATTACTTTGCTGC 57.292 32.000 0.00 0.00 43.60 5.25
678 1586 6.583806 CCTCAAAATTACTTTGCTGCTGTTAG 59.416 38.462 0.00 0.00 43.60 2.34
679 1587 7.270757 TCAAAATTACTTTGCTGCTGTTAGA 57.729 32.000 0.00 0.00 43.60 2.10
683 1591 6.884280 ATTACTTTGCTGCTGTTAGAGTTT 57.116 33.333 0.00 0.00 0.00 2.66
690 1598 5.419542 TGCTGCTGTTAGAGTTTACTATGG 58.580 41.667 0.00 0.00 0.00 2.74
732 1641 8.753133 ACAGATCTGATCACAATACTTGAGTTA 58.247 33.333 29.27 0.00 0.00 2.24
738 1647 9.994432 CTGATCACAATACTTGAGTTAATTTCC 57.006 33.333 0.00 0.00 0.00 3.13
739 1648 8.956426 TGATCACAATACTTGAGTTAATTTCCC 58.044 33.333 0.00 0.00 0.00 3.97
742 1651 9.444600 TCACAATACTTGAGTTAATTTCCCTAC 57.555 33.333 0.00 0.00 0.00 3.18
743 1652 9.449719 CACAATACTTGAGTTAATTTCCCTACT 57.550 33.333 0.00 0.00 0.00 2.57
744 1653 9.449719 ACAATACTTGAGTTAATTTCCCTACTG 57.550 33.333 0.00 0.00 0.00 2.74
756 1665 5.693769 TTTCCCTACTGCTACTTGCTATT 57.306 39.130 0.00 0.00 43.37 1.73
757 1666 6.801718 TTTCCCTACTGCTACTTGCTATTA 57.198 37.500 0.00 0.00 43.37 0.98
763 1672 8.560374 CCCTACTGCTACTTGCTATTATTTTTC 58.440 37.037 0.00 0.00 43.37 2.29
806 1715 4.755629 GGCCGGCTTTAATTTGGTTTTTAA 59.244 37.500 28.56 0.00 0.00 1.52
844 1753 9.566432 GATAATCCAGTGAAGTCTAAATCCATT 57.434 33.333 0.00 0.00 0.00 3.16
921 1830 1.767289 AGAGTAGTTGCACGTTGTCG 58.233 50.000 0.00 0.00 43.34 4.35
931 1840 0.390603 CACGTTGTCGCCATCCCTAA 60.391 55.000 0.00 0.00 41.18 2.69
935 1844 0.035820 TTGTCGCCATCCCTAACCAC 60.036 55.000 0.00 0.00 0.00 4.16
939 1848 0.748005 CGCCATCCCTAACCACCTTG 60.748 60.000 0.00 0.00 0.00 3.61
975 1884 3.689161 TGGATTTTTACATCGTCCAGCTG 59.311 43.478 6.78 6.78 34.23 4.24
976 1885 3.487544 GGATTTTTACATCGTCCAGCTGC 60.488 47.826 8.66 0.00 0.00 5.25
985 1894 0.244994 CGTCCAGCTGCAAGTCTACT 59.755 55.000 8.66 0.00 35.30 2.57
986 1895 1.734047 CGTCCAGCTGCAAGTCTACTC 60.734 57.143 8.66 0.00 35.30 2.59
997 1906 5.230942 TGCAAGTCTACTCAAAGAAGCTAC 58.769 41.667 0.00 0.00 0.00 3.58
1014 1923 2.883026 CTACCTATGAGGACTCCTGGG 58.117 57.143 0.93 5.66 37.67 4.45
1033 1942 5.376625 CTGGGCATGCTAAGAAGGTAATTA 58.623 41.667 18.92 0.00 0.00 1.40
1106 2018 1.678970 GACTGGTGTCATTGGCCCC 60.679 63.158 0.00 0.00 42.48 5.80
1332 2255 8.267894 ACTGGTATACTTAATCTGCTTCATGTT 58.732 33.333 2.25 0.00 0.00 2.71
1333 2256 8.662781 TGGTATACTTAATCTGCTTCATGTTC 57.337 34.615 2.25 0.00 0.00 3.18
1393 2318 1.666189 GACATAAAGGGTCTGAAGCGC 59.334 52.381 0.00 0.00 32.54 5.92
1570 2502 4.037208 TGCGGTATTGAGTTAGCTAGGTAC 59.963 45.833 0.00 0.00 0.00 3.34
1571 2503 4.277921 GCGGTATTGAGTTAGCTAGGTACT 59.722 45.833 0.00 2.69 46.37 2.73
1572 2504 5.562501 GCGGTATTGAGTTAGCTAGGTACTC 60.563 48.000 14.59 14.59 41.75 2.59
1573 2505 5.048852 CGGTATTGAGTTAGCTAGGTACTCC 60.049 48.000 17.48 5.52 41.75 3.85
1574 2506 5.243507 GGTATTGAGTTAGCTAGGTACTCCC 59.756 48.000 17.48 10.02 41.75 4.30
1576 2508 4.167652 TGAGTTAGCTAGGTACTCCCTC 57.832 50.000 17.48 14.51 44.81 4.30
1577 2509 3.117587 TGAGTTAGCTAGGTACTCCCTCC 60.118 52.174 17.48 0.00 44.81 4.30
1578 2510 2.158638 AGTTAGCTAGGTACTCCCTCCG 60.159 54.545 0.00 0.00 44.81 4.63
1579 2511 1.516110 TAGCTAGGTACTCCCTCCGT 58.484 55.000 0.00 0.00 44.81 4.69
1580 2512 0.183252 AGCTAGGTACTCCCTCCGTC 59.817 60.000 0.00 0.00 44.81 4.79
1581 2513 0.822944 GCTAGGTACTCCCTCCGTCC 60.823 65.000 0.00 0.00 44.81 4.79
1582 2514 0.534652 CTAGGTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 44.81 4.79
1583 2515 0.982852 TAGGTACTCCCTCCGTCCGA 60.983 60.000 0.00 0.00 44.81 4.55
1584 2516 1.152798 GGTACTCCCTCCGTCCGAT 60.153 63.158 0.00 0.00 0.00 4.18
1585 2517 0.109342 GGTACTCCCTCCGTCCGATA 59.891 60.000 0.00 0.00 0.00 2.92
1586 2518 1.477558 GGTACTCCCTCCGTCCGATAA 60.478 57.143 0.00 0.00 0.00 1.75
1587 2519 2.512705 GTACTCCCTCCGTCCGATAAT 58.487 52.381 0.00 0.00 0.00 1.28
1588 2520 2.965671 ACTCCCTCCGTCCGATAATA 57.034 50.000 0.00 0.00 0.00 0.98
1589 2521 3.453059 ACTCCCTCCGTCCGATAATAT 57.547 47.619 0.00 0.00 0.00 1.28
1590 2522 4.581309 ACTCCCTCCGTCCGATAATATA 57.419 45.455 0.00 0.00 0.00 0.86
1591 2523 4.927049 ACTCCCTCCGTCCGATAATATAA 58.073 43.478 0.00 0.00 0.00 0.98
1592 2524 4.948621 ACTCCCTCCGTCCGATAATATAAG 59.051 45.833 0.00 0.00 0.00 1.73
1593 2525 5.183530 TCCCTCCGTCCGATAATATAAGA 57.816 43.478 0.00 0.00 0.00 2.10
1594 2526 5.191426 TCCCTCCGTCCGATAATATAAGAG 58.809 45.833 0.00 0.00 0.00 2.85
1595 2527 4.202030 CCCTCCGTCCGATAATATAAGAGC 60.202 50.000 0.00 0.00 0.00 4.09
1596 2528 4.496010 CCTCCGTCCGATAATATAAGAGCG 60.496 50.000 0.00 0.00 0.00 5.03
1597 2529 4.005650 TCCGTCCGATAATATAAGAGCGT 58.994 43.478 0.00 0.00 0.00 5.07
1598 2530 4.456911 TCCGTCCGATAATATAAGAGCGTT 59.543 41.667 0.00 0.00 0.00 4.84
1599 2531 5.048504 TCCGTCCGATAATATAAGAGCGTTT 60.049 40.000 0.00 0.00 0.00 3.60
1600 2532 5.632347 CCGTCCGATAATATAAGAGCGTTTT 59.368 40.000 0.00 0.00 0.00 2.43
1601 2533 6.145048 CCGTCCGATAATATAAGAGCGTTTTT 59.855 38.462 0.00 0.00 0.00 1.94
1602 2534 7.001922 CGTCCGATAATATAAGAGCGTTTTTG 58.998 38.462 0.00 0.00 0.00 2.44
1603 2535 7.096353 CGTCCGATAATATAAGAGCGTTTTTGA 60.096 37.037 0.00 0.00 0.00 2.69
1604 2536 8.002665 GTCCGATAATATAAGAGCGTTTTTGAC 58.997 37.037 0.00 0.00 0.00 3.18
1605 2537 7.707464 TCCGATAATATAAGAGCGTTTTTGACA 59.293 33.333 0.00 0.00 0.00 3.58
1606 2538 7.792508 CCGATAATATAAGAGCGTTTTTGACAC 59.207 37.037 0.00 0.00 0.00 3.67
1607 2539 8.540492 CGATAATATAAGAGCGTTTTTGACACT 58.460 33.333 0.00 0.00 0.00 3.55
1610 2542 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
1611 2543 4.795970 AAGAGCGTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
1612 2544 3.131396 AGAGCGTTTTTGACACTAGTGG 58.869 45.455 26.12 9.07 34.19 4.00
1613 2545 2.218603 AGCGTTTTTGACACTAGTGGG 58.781 47.619 26.12 3.08 34.19 4.61
1614 2546 2.158871 AGCGTTTTTGACACTAGTGGGA 60.159 45.455 26.12 9.75 34.19 4.37
1615 2547 2.032290 GCGTTTTTGACACTAGTGGGAC 60.032 50.000 26.12 16.63 34.19 4.46
1616 2548 2.220133 CGTTTTTGACACTAGTGGGACG 59.780 50.000 26.12 19.56 34.19 4.79
1617 2549 2.536761 TTTTGACACTAGTGGGACGG 57.463 50.000 26.12 0.74 34.19 4.79
1618 2550 1.707106 TTTGACACTAGTGGGACGGA 58.293 50.000 26.12 5.00 34.19 4.69
1619 2551 1.254026 TTGACACTAGTGGGACGGAG 58.746 55.000 26.12 0.00 34.19 4.63
1620 2552 0.611062 TGACACTAGTGGGACGGAGG 60.611 60.000 26.12 0.00 34.19 4.30
1621 2553 1.305046 ACACTAGTGGGACGGAGGG 60.305 63.158 26.12 0.00 34.19 4.30
1622 2554 1.000019 CACTAGTGGGACGGAGGGA 60.000 63.158 15.49 0.00 0.00 4.20
1623 2555 1.038130 CACTAGTGGGACGGAGGGAG 61.038 65.000 15.49 0.00 0.00 4.30
1624 2556 1.306970 CTAGTGGGACGGAGGGAGT 59.693 63.158 0.00 0.00 0.00 3.85
1625 2557 0.549950 CTAGTGGGACGGAGGGAGTA 59.450 60.000 0.00 0.00 0.00 2.59
1633 2565 1.473278 GACGGAGGGAGTAGTTCTGTG 59.527 57.143 0.00 0.00 30.90 3.66
1684 2625 3.614176 CGATGCTATATGTCATGGTTCGG 59.386 47.826 0.00 0.00 0.00 4.30
1685 2626 4.569943 GATGCTATATGTCATGGTTCGGT 58.430 43.478 0.00 0.00 0.00 4.69
1686 2627 4.415881 TGCTATATGTCATGGTTCGGTT 57.584 40.909 0.00 0.00 0.00 4.44
1687 2628 4.377021 TGCTATATGTCATGGTTCGGTTC 58.623 43.478 0.00 0.00 0.00 3.62
1688 2629 4.141824 TGCTATATGTCATGGTTCGGTTCA 60.142 41.667 0.00 0.00 0.00 3.18
1691 2632 2.849294 TGTCATGGTTCGGTTCATGA 57.151 45.000 10.02 10.02 44.95 3.07
1701 2642 1.134401 TCGGTTCATGATCTTGGCCTC 60.134 52.381 3.32 0.00 0.00 4.70
1702 2643 1.134280 CGGTTCATGATCTTGGCCTCT 60.134 52.381 3.32 0.00 0.00 3.69
1721 2680 5.545588 CCTCTGTCACCATAATAGTCCATG 58.454 45.833 0.00 0.00 0.00 3.66
1737 2696 3.319122 GTCCATGTTCTTTGGCTTCAGTT 59.681 43.478 0.00 0.00 34.06 3.16
1815 2774 4.391216 GGAGTTGATGTGACAAGTCAGATG 59.609 45.833 16.34 0.00 46.10 2.90
1840 3073 9.701098 TGATAACGTTTTGTATCAGTCTAAACT 57.299 29.630 5.91 0.00 35.60 2.66
1921 3162 9.549078 TTAGATTTGTGTTGTATACTGTGTTCA 57.451 29.630 4.17 0.00 0.00 3.18
1973 3219 7.144722 TCCAATTCTGTAACAGTTTATGCAG 57.855 36.000 0.00 0.00 32.61 4.41
2017 3265 1.305465 ATTCCATTGCTGCCTGCCA 60.305 52.632 0.00 0.00 42.00 4.92
2054 3302 8.364129 TCTGTTTCAACATTTTATTTTCAGCC 57.636 30.769 0.00 0.00 38.41 4.85
2187 3439 9.956797 TTAACATCGTACGTAAAATTTAAGCTC 57.043 29.630 16.05 0.00 0.00 4.09
2304 3559 3.744238 ATGGGTTTGGTAGTTTTGCAC 57.256 42.857 0.00 0.00 0.00 4.57
2308 3563 3.368531 GGGTTTGGTAGTTTTGCACACAA 60.369 43.478 0.00 0.00 0.00 3.33
2309 3564 4.246458 GGTTTGGTAGTTTTGCACACAAA 58.754 39.130 0.00 0.00 43.97 2.83
2367 3657 4.201891 GCTGTTTGCACCATCTTATCTCAG 60.202 45.833 0.00 0.00 42.31 3.35
2376 3666 6.629128 CACCATCTTATCTCAGTATAGCAGG 58.371 44.000 0.00 0.00 0.00 4.85
2399 3689 2.158534 ACTGCCTATCAACCAACAACCA 60.159 45.455 0.00 0.00 0.00 3.67
2405 3695 5.047660 GCCTATCAACCAACAACCATTGTAA 60.048 40.000 0.00 0.00 44.59 2.41
2408 3698 7.598493 CCTATCAACCAACAACCATTGTAAAAG 59.402 37.037 0.00 0.00 44.59 2.27
2410 3700 4.066646 ACCAACAACCATTGTAAAAGGC 57.933 40.909 0.00 0.00 44.59 4.35
2416 3707 3.866883 ACCATTGTAAAAGGCGATTGG 57.133 42.857 0.00 0.00 38.51 3.16
2421 3712 3.935818 TGTAAAAGGCGATTGGGGATA 57.064 42.857 0.00 0.00 0.00 2.59
2424 3715 0.478507 AAAGGCGATTGGGGATAGGG 59.521 55.000 0.00 0.00 0.00 3.53
2443 3734 0.034616 GGAGGATTGCGGATGAGAGG 59.965 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.600485 AGGACGCCGTTGTAACAAAAG 59.400 47.619 0.00 0.00 0.00 2.27
13 16 3.857038 ACACCAGGACGCCGTTGT 61.857 61.111 0.00 0.00 0.00 3.32
22 25 1.685224 GGATTCCAGCACACCAGGA 59.315 57.895 0.00 0.00 0.00 3.86
28 31 0.948623 CGTGAACGGATTCCAGCACA 60.949 55.000 15.55 3.62 33.49 4.57
41 44 1.521423 CAGGAAACAGTCGTCGTGAAC 59.479 52.381 0.00 0.00 32.63 3.18
50 53 2.157421 CGCAGCTCAGGAAACAGTC 58.843 57.895 0.00 0.00 0.00 3.51
68 71 2.863401 AGTTTCGTTTGGAACCAAGC 57.137 45.000 9.76 9.76 37.24 4.01
81 84 3.844577 TCTCTTTCTCCCGTAGTTTCG 57.155 47.619 0.00 0.00 0.00 3.46
83 86 5.286267 TGTTTCTCTTTCTCCCGTAGTTT 57.714 39.130 0.00 0.00 0.00 2.66
86 89 5.073311 TCATGTTTCTCTTTCTCCCGTAG 57.927 43.478 0.00 0.00 0.00 3.51
90 102 5.555966 AGTTCTCATGTTTCTCTTTCTCCC 58.444 41.667 0.00 0.00 0.00 4.30
91 103 7.875554 AGTAAGTTCTCATGTTTCTCTTTCTCC 59.124 37.037 0.00 0.00 0.00 3.71
206 993 9.817365 CTGTTGAGTAATTTTCAGTTGTGATAG 57.183 33.333 0.00 0.00 30.85 2.08
386 1191 3.243535 GCTGTTCTTTTTAAGGCAGCAGT 60.244 43.478 20.74 0.00 46.68 4.40
389 1194 2.319472 CGCTGTTCTTTTTAAGGCAGC 58.681 47.619 18.10 18.10 45.41 5.25
395 1200 3.112580 GCAGTTGCGCTGTTCTTTTTAA 58.887 40.909 9.73 0.00 46.64 1.52
441 1247 5.531634 AGTAAAACAGTGCAAACATGATGG 58.468 37.500 0.00 0.00 0.00 3.51
488 1296 8.824159 ACATCGAAAATAGAATCCTGAGTATG 57.176 34.615 0.00 0.00 0.00 2.39
492 1300 6.763135 TCCAACATCGAAAATAGAATCCTGAG 59.237 38.462 0.00 0.00 0.00 3.35
497 1305 6.610741 AGCTCCAACATCGAAAATAGAATC 57.389 37.500 0.00 0.00 0.00 2.52
513 1343 1.140312 AGACCACAGGAAAGCTCCAA 58.860 50.000 0.00 0.00 45.24 3.53
531 1361 0.529378 GCTTCCATGGCAAACTCCAG 59.471 55.000 6.96 0.00 39.89 3.86
537 1367 4.202295 TGTTACAAATGCTTCCATGGCAAA 60.202 37.500 6.96 0.00 43.14 3.68
568 1398 9.167311 GAAGTGAAGATGAATGTTAGGTTGTAT 57.833 33.333 0.00 0.00 0.00 2.29
570 1400 7.227156 AGAAGTGAAGATGAATGTTAGGTTGT 58.773 34.615 0.00 0.00 0.00 3.32
574 1404 7.413877 GCTGAAGAAGTGAAGATGAATGTTAGG 60.414 40.741 0.00 0.00 0.00 2.69
727 1636 6.037281 GCAAGTAGCAGTAGGGAAATTAACTC 59.963 42.308 0.00 0.00 44.79 3.01
757 1666 9.305555 CCTGGATTAGACATATGGATGAAAAAT 57.694 33.333 7.80 0.00 36.48 1.82
763 1672 4.521146 GCCCTGGATTAGACATATGGATG 58.479 47.826 7.80 0.00 39.16 3.51
772 1681 1.984288 AAGCCGGCCCTGGATTAGAC 61.984 60.000 26.15 0.00 35.46 2.59
897 1806 5.638783 GACAACGTGCAACTACTCTATAGT 58.361 41.667 0.00 0.00 39.91 2.12
903 1812 0.161024 GCGACAACGTGCAACTACTC 59.839 55.000 0.00 0.00 41.98 2.59
921 1830 0.623723 TCAAGGTGGTTAGGGATGGC 59.376 55.000 0.00 0.00 0.00 4.40
975 1884 4.627900 GGTAGCTTCTTTGAGTAGACTTGC 59.372 45.833 0.00 0.00 0.00 4.01
976 1885 6.031751 AGGTAGCTTCTTTGAGTAGACTTG 57.968 41.667 0.00 0.00 0.00 3.16
985 1894 5.273208 AGTCCTCATAGGTAGCTTCTTTGA 58.727 41.667 0.00 0.66 36.53 2.69
986 1895 5.452636 GGAGTCCTCATAGGTAGCTTCTTTG 60.453 48.000 0.41 0.00 36.53 2.77
997 1906 0.399091 TGCCCAGGAGTCCTCATAGG 60.399 60.000 9.36 7.56 36.46 2.57
1014 1923 7.013274 TCCATTGTAATTACCTTCTTAGCATGC 59.987 37.037 10.51 10.51 0.00 4.06
1033 1942 5.659440 ACAAAAGTCAGTTGTTCCATTGT 57.341 34.783 0.00 0.00 35.70 2.71
1048 1957 7.502226 TCAGGATAACAACTGATGAACAAAAGT 59.498 33.333 0.00 0.00 38.71 2.66
1106 2018 8.723942 ATTAGAGCAGGAAGTATAGTTGTTTG 57.276 34.615 0.00 0.00 0.00 2.93
1307 2230 8.668510 AACATGAAGCAGATTAAGTATACCAG 57.331 34.615 0.00 0.00 0.00 4.00
1498 2424 9.537192 AACAAGCATTAATGATATTGATGTTGG 57.463 29.630 23.85 9.33 30.91 3.77
1546 2478 3.068307 ACCTAGCTAACTCAATACCGCAG 59.932 47.826 0.00 0.00 0.00 5.18
1570 2502 5.191426 TCTTATATTATCGGACGGAGGGAG 58.809 45.833 0.00 0.00 0.00 4.30
1571 2503 5.183530 TCTTATATTATCGGACGGAGGGA 57.816 43.478 0.00 0.00 0.00 4.20
1572 2504 4.202030 GCTCTTATATTATCGGACGGAGGG 60.202 50.000 0.00 0.00 0.00 4.30
1573 2505 4.496010 CGCTCTTATATTATCGGACGGAGG 60.496 50.000 0.00 0.00 0.00 4.30
1574 2506 4.094590 ACGCTCTTATATTATCGGACGGAG 59.905 45.833 0.00 0.00 0.00 4.63
1575 2507 4.005650 ACGCTCTTATATTATCGGACGGA 58.994 43.478 0.00 0.00 0.00 4.69
1576 2508 4.352600 ACGCTCTTATATTATCGGACGG 57.647 45.455 0.00 0.00 0.00 4.79
1577 2509 6.686130 AAAACGCTCTTATATTATCGGACG 57.314 37.500 0.00 0.00 0.00 4.79
1578 2510 8.002665 GTCAAAAACGCTCTTATATTATCGGAC 58.997 37.037 0.00 0.00 0.00 4.79
1579 2511 7.707464 TGTCAAAAACGCTCTTATATTATCGGA 59.293 33.333 0.00 0.00 0.00 4.55
1580 2512 7.792508 GTGTCAAAAACGCTCTTATATTATCGG 59.207 37.037 0.00 0.00 35.42 4.18
1581 2513 8.540492 AGTGTCAAAAACGCTCTTATATTATCG 58.460 33.333 0.00 0.00 45.69 2.92
1584 2516 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
1585 2517 8.656849 CACTAGTGTCAAAAACGCTCTTATATT 58.343 33.333 15.06 0.00 45.69 1.28
1586 2518 7.277981 CCACTAGTGTCAAAAACGCTCTTATAT 59.722 37.037 21.18 0.00 45.69 0.86
1587 2519 6.588756 CCACTAGTGTCAAAAACGCTCTTATA 59.411 38.462 21.18 0.00 45.69 0.98
1588 2520 5.408604 CCACTAGTGTCAAAAACGCTCTTAT 59.591 40.000 21.18 0.00 45.69 1.73
1589 2521 4.748102 CCACTAGTGTCAAAAACGCTCTTA 59.252 41.667 21.18 0.00 45.69 2.10
1590 2522 3.560068 CCACTAGTGTCAAAAACGCTCTT 59.440 43.478 21.18 0.00 45.69 2.85
1591 2523 3.131396 CCACTAGTGTCAAAAACGCTCT 58.869 45.455 21.18 0.00 45.69 4.09
1592 2524 2.223377 CCCACTAGTGTCAAAAACGCTC 59.777 50.000 21.18 0.00 45.69 5.03
1594 2526 2.032290 GTCCCACTAGTGTCAAAAACGC 60.032 50.000 21.18 0.00 38.74 4.84
1595 2527 2.220133 CGTCCCACTAGTGTCAAAAACG 59.780 50.000 21.18 15.49 0.00 3.60
1596 2528 2.546789 CCGTCCCACTAGTGTCAAAAAC 59.453 50.000 21.18 8.75 0.00 2.43
1597 2529 2.435069 TCCGTCCCACTAGTGTCAAAAA 59.565 45.455 21.18 0.50 0.00 1.94
1598 2530 2.036733 CTCCGTCCCACTAGTGTCAAAA 59.963 50.000 21.18 2.07 0.00 2.44
1599 2531 1.616865 CTCCGTCCCACTAGTGTCAAA 59.383 52.381 21.18 1.21 0.00 2.69
1600 2532 1.254026 CTCCGTCCCACTAGTGTCAA 58.746 55.000 21.18 3.70 0.00 3.18
1601 2533 0.611062 CCTCCGTCCCACTAGTGTCA 60.611 60.000 21.18 4.55 0.00 3.58
1602 2534 1.321074 CCCTCCGTCCCACTAGTGTC 61.321 65.000 21.18 10.30 0.00 3.67
1603 2535 1.305046 CCCTCCGTCCCACTAGTGT 60.305 63.158 21.18 0.00 0.00 3.55
1604 2536 1.000019 TCCCTCCGTCCCACTAGTG 60.000 63.158 16.34 16.34 0.00 2.74
1605 2537 1.306970 CTCCCTCCGTCCCACTAGT 59.693 63.158 0.00 0.00 0.00 2.57
1606 2538 0.549950 TACTCCCTCCGTCCCACTAG 59.450 60.000 0.00 0.00 0.00 2.57
1607 2539 0.549950 CTACTCCCTCCGTCCCACTA 59.450 60.000 0.00 0.00 0.00 2.74
1608 2540 1.306970 CTACTCCCTCCGTCCCACT 59.693 63.158 0.00 0.00 0.00 4.00
1609 2541 0.614134 AACTACTCCCTCCGTCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
1610 2542 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
1611 2543 0.033306 AGAACTACTCCCTCCGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
1612 2544 1.104630 CAGAACTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
1613 2545 1.473278 CACAGAACTACTCCCTCCGTC 59.527 57.143 0.00 0.00 0.00 4.79
1614 2546 1.203025 ACACAGAACTACTCCCTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
1615 2547 1.473278 GACACAGAACTACTCCCTCCG 59.527 57.143 0.00 0.00 0.00 4.63
1616 2548 2.526432 TGACACAGAACTACTCCCTCC 58.474 52.381 0.00 0.00 0.00 4.30
1617 2549 4.810191 ATTGACACAGAACTACTCCCTC 57.190 45.455 0.00 0.00 0.00 4.30
1618 2550 5.568620 AAATTGACACAGAACTACTCCCT 57.431 39.130 0.00 0.00 0.00 4.20
1619 2551 6.635030 AAAAATTGACACAGAACTACTCCC 57.365 37.500 0.00 0.00 0.00 4.30
1620 2552 8.603242 TCTAAAAATTGACACAGAACTACTCC 57.397 34.615 0.00 0.00 0.00 3.85
1655 2596 5.290400 CCATGACATATAGCATCGTAAGCTG 59.710 44.000 0.00 0.00 43.33 4.24
1664 2605 4.623932 ACCGAACCATGACATATAGCAT 57.376 40.909 0.00 0.00 0.00 3.79
1684 2625 2.941720 GACAGAGGCCAAGATCATGAAC 59.058 50.000 5.01 0.00 0.00 3.18
1685 2626 2.573009 TGACAGAGGCCAAGATCATGAA 59.427 45.455 5.01 0.00 0.00 2.57
1686 2627 2.093288 GTGACAGAGGCCAAGATCATGA 60.093 50.000 5.01 0.00 0.00 3.07
1687 2628 2.286872 GTGACAGAGGCCAAGATCATG 58.713 52.381 5.01 0.00 0.00 3.07
1688 2629 1.211457 GGTGACAGAGGCCAAGATCAT 59.789 52.381 5.01 0.00 0.00 2.45
1691 2632 2.777536 TGGTGACAGAGGCCAAGAT 58.222 52.632 5.01 0.00 35.01 2.40
1721 2680 6.803154 AGTACATAACTGAAGCCAAAGAAC 57.197 37.500 0.00 0.00 36.93 3.01
1737 2696 8.913487 TCGATGATAAAGACCTACAGTACATA 57.087 34.615 0.00 0.00 0.00 2.29
1783 2742 3.807622 GTCACATCAACTCCGAAACAAGA 59.192 43.478 0.00 0.00 0.00 3.02
1921 3162 5.527214 TCGATGATTTATCTCGGCAAATGTT 59.473 36.000 9.85 0.00 33.44 2.71
1973 3219 2.037772 ACTGAGTGGGATGTTGACTGAC 59.962 50.000 0.00 0.00 0.00 3.51
2017 3265 7.781548 ATGTTGAAACAGAGTTAACGTTAGT 57.218 32.000 8.23 0.00 43.04 2.24
2054 3302 3.258228 GGCTTCTTCTTCTTCTTCCTCG 58.742 50.000 0.00 0.00 0.00 4.63
2187 3439 5.047235 AGTGACTTTAAGGTAGCCAGTACAG 60.047 44.000 0.00 0.00 32.62 2.74
2347 3637 7.095439 GCTATACTGAGATAAGATGGTGCAAAC 60.095 40.741 0.00 0.00 0.00 2.93
2376 3666 1.533625 TGTTGGTTGATAGGCAGTGC 58.466 50.000 6.55 6.55 0.00 4.40
2399 3689 3.094484 TCCCCAATCGCCTTTTACAAT 57.906 42.857 0.00 0.00 0.00 2.71
2405 3695 0.478507 CCCTATCCCCAATCGCCTTT 59.521 55.000 0.00 0.00 0.00 3.11
2408 3698 1.842381 CTCCCCTATCCCCAATCGCC 61.842 65.000 0.00 0.00 0.00 5.54
2410 3700 0.178903 TCCTCCCCTATCCCCAATCG 60.179 60.000 0.00 0.00 0.00 3.34
2416 3707 1.679898 CGCAATCCTCCCCTATCCC 59.320 63.158 0.00 0.00 0.00 3.85
2421 3712 1.384502 TCATCCGCAATCCTCCCCT 60.385 57.895 0.00 0.00 0.00 4.79
2424 3715 0.034616 CCTCTCATCCGCAATCCTCC 59.965 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.