Multiple sequence alignment - TraesCS1B01G243500

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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 TraesCS1B01G243500 chr1B 100.000 2693 0 0 1 2693 432380365 432377673 0.000000e+00 4974.0
1 TraesCS1B01G243500 chr1B 79.872 313 45 7 256 555 367885383 367885076 2.100000e-51 213.0
2 TraesCS1B01G243500 chr1A 88.562 2483 142 65 253 2693 403631570 403633952 0.000000e+00 2881.0
3 TraesCS1B01G243500 chr1A 94.030 134 7 1 115 248 403631406 403631538 4.550000e-48 202.0
4 TraesCS1B01G243500 chr1D 93.795 1112 53 8 848 1958 319618133 319617037 0.000000e+00 1657.0
5 TraesCS1B01G243500 chr1D 90.133 375 25 3 2331 2693 319616011 319615637 6.750000e-131 477.0
6 TraesCS1B01G243500 chr1D 91.117 349 14 8 1961 2300 319616976 319616636 8.790000e-125 457.0
7 TraesCS1B01G243500 chr1D 83.838 495 54 14 251 740 319618611 319618138 5.290000e-122 448.0
8 TraesCS1B01G243500 chr1D 94.928 138 7 0 113 250 319618776 319618639 1.620000e-52 217.0
9 TraesCS1B01G243500 chr2A 81.744 1227 137 48 592 1746 2709326 2708115 0.000000e+00 944.0
10 TraesCS1B01G243500 chr2B 82.368 1174 121 45 592 1711 7684514 7683373 0.000000e+00 942.0
11 TraesCS1B01G243500 chr2B 95.327 107 5 0 1 107 66712600 66712706 1.280000e-38 171.0
12 TraesCS1B01G243500 chr2B 95.370 108 4 1 1 107 760254676 760254569 1.280000e-38 171.0
13 TraesCS1B01G243500 chr2B 94.393 107 6 0 1 107 690728950 690728844 5.960000e-37 165.0
14 TraesCS1B01G243500 chr2B 84.524 84 9 4 374 456 772147691 772147611 2.220000e-11 80.5
15 TraesCS1B01G243500 chr2D 81.927 1173 128 45 593 1695 3004302 3005460 0.000000e+00 915.0
16 TraesCS1B01G243500 chr2D 94.828 58 3 0 134 191 3004164 3004221 1.030000e-14 91.6
17 TraesCS1B01G243500 chr7D 92.056 214 11 4 2106 2318 470228025 470227817 2.030000e-76 296.0
18 TraesCS1B01G243500 chr7D 84.790 309 18 8 2413 2693 470227796 470227489 1.580000e-72 283.0
19 TraesCS1B01G243500 chr7D 97.143 35 1 0 2047 2081 470228058 470228024 2.900000e-05 60.2
20 TraesCS1B01G243500 chr4D 83.442 308 33 9 258 553 291531717 291532018 1.230000e-68 270.0
21 TraesCS1B01G243500 chr4D 82.857 315 34 13 257 553 357262900 357262588 5.720000e-67 265.0
22 TraesCS1B01G243500 chr3D 96.262 107 4 0 1 107 358192170 358192276 2.760000e-40 176.0
23 TraesCS1B01G243500 chr5A 95.327 107 5 0 1 107 437204491 437204385 1.280000e-38 171.0
24 TraesCS1B01G243500 chr5A 86.667 120 10 3 253 372 28226666 28226779 7.830000e-26 128.0
25 TraesCS1B01G243500 chr6A 94.393 107 6 0 1 107 453126815 453126921 5.960000e-37 165.0
26 TraesCS1B01G243500 chr5B 77.922 308 35 15 256 552 33559009 33558724 7.720000e-36 161.0
27 TraesCS1B01G243500 chr5B 93.458 107 7 0 1 107 55629717 55629611 2.780000e-35 159.0
28 TraesCS1B01G243500 chr4B 93.458 107 7 0 1 107 215916302 215916196 2.780000e-35 159.0
29 TraesCS1B01G243500 chr4B 93.519 108 6 1 1 107 344650170 344650277 2.780000e-35 159.0
30 TraesCS1B01G243500 chr6B 79.882 169 28 6 324 489 51578440 51578275 4.710000e-23 119.0
31 TraesCS1B01G243500 chr7B 76.596 235 41 9 257 489 111326324 111326102 1.690000e-22 117.0


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 TraesCS1B01G243500 chr1B 432377673 432380365 2692 True 4974.000000 4974 100.000000 1 2693 1 chr1B.!!$R2 2692
1 TraesCS1B01G243500 chr1A 403631406 403633952 2546 False 1541.500000 2881 91.296000 115 2693 2 chr1A.!!$F1 2578
2 TraesCS1B01G243500 chr1D 319615637 319618776 3139 True 651.200000 1657 90.762200 113 2693 5 chr1D.!!$R1 2580
3 TraesCS1B01G243500 chr2A 2708115 2709326 1211 True 944.000000 944 81.744000 592 1746 1 chr2A.!!$R1 1154
4 TraesCS1B01G243500 chr2B 7683373 7684514 1141 True 942.000000 942 82.368000 592 1711 1 chr2B.!!$R1 1119
5 TraesCS1B01G243500 chr2D 3004164 3005460 1296 False 503.300000 915 88.377500 134 1695 2 chr2D.!!$F1 1561
6 TraesCS1B01G243500 chr7D 470227489 470228058 569 True 213.066667 296 91.329667 2047 2693 3 chr7D.!!$R1 646

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
51 52 0.108472 GTAGCCGACACCCTACAACC 60.108 60.0 0.0 0.0 35.24 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 2101 0.044855 AGTAGATGTTCCCAGGCCCT 59.955 55.0 0.0 0.0 0.0 5.19 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
25 26 4.760047 CCGGCTCCGTCACCCAAG 62.760 72.222 7.59 0.00 37.81 3.61
27 28 4.329545 GGCTCCGTCACCCAAGCA 62.330 66.667 0.00 0.00 36.47 3.91
28 29 2.281484 GCTCCGTCACCCAAGCAA 60.281 61.111 0.00 0.00 34.86 3.91
29 30 2.617274 GCTCCGTCACCCAAGCAAC 61.617 63.158 0.00 0.00 34.86 4.17
30 31 1.966451 CTCCGTCACCCAAGCAACC 60.966 63.158 0.00 0.00 0.00 3.77
31 32 2.983592 CCGTCACCCAAGCAACCC 60.984 66.667 0.00 0.00 0.00 4.11
32 33 3.353836 CGTCACCCAAGCAACCCG 61.354 66.667 0.00 0.00 0.00 5.28
33 34 2.203294 GTCACCCAAGCAACCCGT 60.203 61.111 0.00 0.00 0.00 5.28
34 35 1.071814 GTCACCCAAGCAACCCGTA 59.928 57.895 0.00 0.00 0.00 4.02
35 36 0.953960 GTCACCCAAGCAACCCGTAG 60.954 60.000 0.00 0.00 0.00 3.51
36 37 2.033602 ACCCAAGCAACCCGTAGC 59.966 61.111 0.00 0.00 0.00 3.58
37 38 2.750237 CCCAAGCAACCCGTAGCC 60.750 66.667 0.00 0.00 0.00 3.93
38 39 3.124921 CCAAGCAACCCGTAGCCG 61.125 66.667 0.00 0.00 0.00 5.52
39 40 2.047655 CAAGCAACCCGTAGCCGA 60.048 61.111 0.00 0.00 35.63 5.54
40 41 2.047560 AAGCAACCCGTAGCCGAC 60.048 61.111 0.00 0.00 35.63 4.79
41 42 2.874664 AAGCAACCCGTAGCCGACA 61.875 57.895 0.00 0.00 35.63 4.35
42 43 3.116531 GCAACCCGTAGCCGACAC 61.117 66.667 0.00 0.00 35.63 3.67
43 44 2.433664 CAACCCGTAGCCGACACC 60.434 66.667 0.00 0.00 35.63 4.16
44 45 3.698820 AACCCGTAGCCGACACCC 61.699 66.667 0.00 0.00 35.63 4.61
45 46 4.691359 ACCCGTAGCCGACACCCT 62.691 66.667 0.00 0.00 35.63 4.34
46 47 2.440796 CCCGTAGCCGACACCCTA 60.441 66.667 0.00 0.00 35.63 3.53
47 48 2.779033 CCCGTAGCCGACACCCTAC 61.779 68.421 0.00 0.00 35.63 3.18
48 49 2.048023 CCGTAGCCGACACCCTACA 61.048 63.158 0.00 0.00 34.92 2.74
49 50 1.597797 CCGTAGCCGACACCCTACAA 61.598 60.000 0.00 0.00 34.92 2.41
50 51 0.457337 CGTAGCCGACACCCTACAAC 60.457 60.000 0.00 0.00 34.92 3.32
51 52 0.108472 GTAGCCGACACCCTACAACC 60.108 60.000 0.00 0.00 35.24 3.77
52 53 0.542467 TAGCCGACACCCTACAACCA 60.542 55.000 0.00 0.00 0.00 3.67
53 54 1.071814 GCCGACACCCTACAACCAA 59.928 57.895 0.00 0.00 0.00 3.67
54 55 0.953960 GCCGACACCCTACAACCAAG 60.954 60.000 0.00 0.00 0.00 3.61
55 56 0.682852 CCGACACCCTACAACCAAGA 59.317 55.000 0.00 0.00 0.00 3.02
56 57 1.607251 CCGACACCCTACAACCAAGAC 60.607 57.143 0.00 0.00 0.00 3.01
57 58 1.607251 CGACACCCTACAACCAAGACC 60.607 57.143 0.00 0.00 0.00 3.85
58 59 0.395312 ACACCCTACAACCAAGACCG 59.605 55.000 0.00 0.00 0.00 4.79
59 60 0.682852 CACCCTACAACCAAGACCGA 59.317 55.000 0.00 0.00 0.00 4.69
60 61 1.071071 CACCCTACAACCAAGACCGAA 59.929 52.381 0.00 0.00 0.00 4.30
61 62 1.770061 ACCCTACAACCAAGACCGAAA 59.230 47.619 0.00 0.00 0.00 3.46
62 63 2.148768 CCCTACAACCAAGACCGAAAC 58.851 52.381 0.00 0.00 0.00 2.78
63 64 2.148768 CCTACAACCAAGACCGAAACC 58.851 52.381 0.00 0.00 0.00 3.27
64 65 1.796459 CTACAACCAAGACCGAAACCG 59.204 52.381 0.00 0.00 0.00 4.44
65 66 1.281656 CAACCAAGACCGAAACCGC 59.718 57.895 0.00 0.00 0.00 5.68
66 67 1.895231 AACCAAGACCGAAACCGCC 60.895 57.895 0.00 0.00 0.00 6.13
67 68 3.419759 CCAAGACCGAAACCGCCG 61.420 66.667 0.00 0.00 0.00 6.46
68 69 4.084888 CAAGACCGAAACCGCCGC 62.085 66.667 0.00 0.00 0.00 6.53
69 70 4.309950 AAGACCGAAACCGCCGCT 62.310 61.111 0.00 0.00 0.00 5.52
70 71 4.736896 AGACCGAAACCGCCGCTC 62.737 66.667 0.00 0.00 0.00 5.03
92 93 4.570663 GTCCACGCCGATCCCGAG 62.571 72.222 7.35 0.04 38.22 4.63
145 146 9.658475 CAGTTTCTCACATACACGAAAATTAAA 57.342 29.630 0.00 0.00 0.00 1.52
151 152 9.658475 CTCACATACACGAAAATTAAACTTGAA 57.342 29.630 0.00 0.00 0.00 2.69
254 283 5.856156 TCTCGGGTGAACAGTAAAATTGTA 58.144 37.500 0.00 0.00 0.00 2.41
276 305 9.645059 TTGTACAAACATTGACAAAAATTCTCA 57.355 25.926 5.64 0.00 34.97 3.27
315 344 7.250445 TCATCACGAAATAACATTCATGGAG 57.750 36.000 0.00 0.00 0.00 3.86
316 345 7.047271 TCATCACGAAATAACATTCATGGAGA 58.953 34.615 0.00 0.00 0.00 3.71
319 348 7.047271 TCACGAAATAACATTCATGGAGATCA 58.953 34.615 0.00 0.00 0.00 2.92
386 416 5.662211 ACATTTTGAAGTGCTGATTTTGC 57.338 34.783 0.00 0.00 0.00 3.68
419 453 8.041323 ACCACGACTTCTATAAATGTCATTTCT 58.959 33.333 14.07 7.65 33.82 2.52
465 499 5.477510 AGAACTTTTGTCAATGTTTGCACA 58.522 33.333 0.00 0.00 37.31 4.57
466 500 5.348451 AGAACTTTTGTCAATGTTTGCACAC 59.652 36.000 0.00 0.00 35.03 3.82
468 502 4.993584 ACTTTTGTCAATGTTTGCACACAA 59.006 33.333 10.18 0.00 35.03 3.33
476 510 7.074502 GTCAATGTTTGCACACAAAAAGAAAA 58.925 30.769 10.18 0.00 46.94 2.29
519 562 8.970553 CGTTTTGTTTTTGAATTTTACTGTTCG 58.029 29.630 0.00 0.00 0.00 3.95
520 563 9.256715 GTTTTGTTTTTGAATTTTACTGTTCGG 57.743 29.630 0.00 0.00 0.00 4.30
522 565 6.334202 TGTTTTTGAATTTTACTGTTCGGCT 58.666 32.000 0.00 0.00 0.00 5.52
523 566 6.474102 TGTTTTTGAATTTTACTGTTCGGCTC 59.526 34.615 0.00 0.00 0.00 4.70
524 567 5.759506 TTTGAATTTTACTGTTCGGCTCA 57.240 34.783 0.00 0.00 0.00 4.26
525 568 5.356882 TTGAATTTTACTGTTCGGCTCAG 57.643 39.130 0.00 0.00 38.68 3.35
526 569 4.637276 TGAATTTTACTGTTCGGCTCAGA 58.363 39.130 8.78 0.00 36.81 3.27
527 570 5.245531 TGAATTTTACTGTTCGGCTCAGAT 58.754 37.500 8.78 0.00 36.81 2.90
528 571 5.122239 TGAATTTTACTGTTCGGCTCAGATG 59.878 40.000 8.78 0.00 36.81 2.90
529 572 3.953712 TTTACTGTTCGGCTCAGATGA 57.046 42.857 8.78 0.00 36.81 2.92
530 573 3.510388 TTACTGTTCGGCTCAGATGAG 57.490 47.619 5.45 5.45 44.75 2.90
538 581 2.027314 CTCAGATGAGCTCGCGGG 59.973 66.667 6.13 2.60 35.13 6.13
539 582 4.212913 TCAGATGAGCTCGCGGGC 62.213 66.667 26.87 26.87 0.00 6.13
540 583 4.519437 CAGATGAGCTCGCGGGCA 62.519 66.667 35.41 14.87 34.17 5.36
541 584 4.218578 AGATGAGCTCGCGGGCAG 62.219 66.667 35.41 11.87 34.17 4.85
542 585 4.212913 GATGAGCTCGCGGGCAGA 62.213 66.667 35.41 19.85 34.17 4.26
543 586 3.723235 GATGAGCTCGCGGGCAGAA 62.723 63.158 35.41 18.66 34.17 3.02
544 587 3.729965 ATGAGCTCGCGGGCAGAAG 62.730 63.158 35.41 10.15 34.17 2.85
545 588 4.135153 GAGCTCGCGGGCAGAAGA 62.135 66.667 35.41 0.00 34.17 2.87
546 589 3.438017 GAGCTCGCGGGCAGAAGAT 62.438 63.158 35.41 11.66 34.17 2.40
547 590 3.267860 GCTCGCGGGCAGAAGATG 61.268 66.667 29.34 0.00 0.00 2.90
548 591 2.496341 CTCGCGGGCAGAAGATGA 59.504 61.111 6.13 0.00 0.00 2.92
549 592 1.880340 CTCGCGGGCAGAAGATGAC 60.880 63.158 6.13 0.00 35.46 3.06
567 610 3.476552 TGACTTTTGCCTCTTACCACAG 58.523 45.455 0.00 0.00 0.00 3.66
695 748 3.103738 GCACAGCTCGAAATATGCTTTG 58.896 45.455 5.62 5.62 37.50 2.77
704 757 4.332543 TCGAAATATGCTTTGCTGTGGTAG 59.667 41.667 0.00 0.00 0.00 3.18
721 774 2.224548 GGTAGTATAAAGCAGGCCCCAG 60.225 54.545 0.00 0.00 0.00 4.45
734 824 1.598701 GCCCCAGTCACATTGCCTTC 61.599 60.000 0.00 0.00 0.00 3.46
740 830 1.377202 TCACATTGCCTTCGCTCCC 60.377 57.895 0.00 0.00 35.36 4.30
742 832 1.675641 ACATTGCCTTCGCTCCCAC 60.676 57.895 0.00 0.00 35.36 4.61
755 845 0.882927 CTCCCACTTTTCAACGGCGA 60.883 55.000 16.62 0.00 0.00 5.54
770 873 1.432270 GGCGAAAATGGAGCCGAGAG 61.432 60.000 0.00 0.00 41.53 3.20
808 911 1.665442 GCCCGCATCCACTGTTTTT 59.335 52.632 0.00 0.00 0.00 1.94
810 917 0.243636 CCCGCATCCACTGTTTTTCC 59.756 55.000 0.00 0.00 0.00 3.13
814 921 3.452474 CGCATCCACTGTTTTTCCAAAA 58.548 40.909 0.00 0.00 0.00 2.44
815 922 3.490526 CGCATCCACTGTTTTTCCAAAAG 59.509 43.478 0.00 0.00 0.00 2.27
816 923 3.248363 GCATCCACTGTTTTTCCAAAAGC 59.752 43.478 0.00 0.00 0.00 3.51
817 924 4.696455 CATCCACTGTTTTTCCAAAAGCT 58.304 39.130 1.11 0.00 31.44 3.74
818 925 4.817318 TCCACTGTTTTTCCAAAAGCTT 57.183 36.364 0.00 0.00 31.44 3.74
911 1034 1.324383 TCCCTTTTGCTTTCCCGTTC 58.676 50.000 0.00 0.00 0.00 3.95
919 1044 1.370064 CTTTCCCGTTCGGACACCT 59.630 57.895 13.08 0.00 41.83 4.00
1116 1312 0.106868 CCAAGATCATCCTGCAGCCA 60.107 55.000 8.66 0.00 0.00 4.75
1207 1403 4.227134 CCGGCCTGGTGATCCTCG 62.227 72.222 0.00 0.00 34.23 4.63
1346 1542 0.251165 AACATCTCCAACCCCAACCG 60.251 55.000 0.00 0.00 0.00 4.44
1392 1588 1.444553 CGCCGTCGAGCTCTTCTTT 60.445 57.895 12.85 0.00 38.10 2.52
1463 1659 0.321122 GGGCAGTTCACAGTCCTCAG 60.321 60.000 0.00 0.00 0.00 3.35
1550 1764 4.630644 TGAAGAGCAACAAGATCCTCTT 57.369 40.909 8.78 8.78 44.74 2.85
1697 1911 2.031245 GCACAACATCAACGTGATTGGA 60.031 45.455 0.00 0.00 34.28 3.53
1720 1941 6.238703 GGAATCTGGATGCTCTTTTCATCTTC 60.239 42.308 3.44 0.43 40.02 2.87
1725 1946 6.684686 TGGATGCTCTTTTCATCTTCTTTTG 58.315 36.000 3.44 0.00 40.02 2.44
1729 1950 5.750067 TGCTCTTTTCATCTTCTTTTGTTGC 59.250 36.000 0.00 0.00 0.00 4.17
1740 1963 9.377383 CATCTTCTTTTGTTGCATCAAATTTTC 57.623 29.630 20.54 0.00 37.20 2.29
1741 1964 8.489990 TCTTCTTTTGTTGCATCAAATTTTCA 57.510 26.923 20.54 7.39 37.20 2.69
1833 2057 8.131100 ACCATTCACAGCAATCTAAAATTATCG 58.869 33.333 0.00 0.00 0.00 2.92
1835 2059 5.737353 TCACAGCAATCTAAAATTATCGCG 58.263 37.500 0.00 0.00 0.00 5.87
1873 2098 8.833231 TTATGTCTGAAAACCAAACAAACAAA 57.167 26.923 0.00 0.00 0.00 2.83
1874 2099 6.532365 TGTCTGAAAACCAAACAAACAAAC 57.468 33.333 0.00 0.00 0.00 2.93
1875 2100 6.049149 TGTCTGAAAACCAAACAAACAAACA 58.951 32.000 0.00 0.00 0.00 2.83
1876 2101 6.538742 TGTCTGAAAACCAAACAAACAAACAA 59.461 30.769 0.00 0.00 0.00 2.83
1885 2110 0.106521 CAAACAAACAAGGGCCTGGG 59.893 55.000 13.78 8.47 0.00 4.45
2044 2329 6.983906 ATTTCCATCACAACTCCTTTTCTT 57.016 33.333 0.00 0.00 0.00 2.52
2045 2330 5.772825 TTCCATCACAACTCCTTTTCTTG 57.227 39.130 0.00 0.00 0.00 3.02
2175 2461 5.203528 ACCCCTCCAAGATCACATTTATTG 58.796 41.667 0.00 0.00 0.00 1.90
2318 3199 2.018355 TACCTTGCACCCTGTAGTGA 57.982 50.000 0.00 0.00 40.34 3.41
2319 3200 0.396811 ACCTTGCACCCTGTAGTGAC 59.603 55.000 0.00 0.00 40.34 3.67
2320 3201 0.321653 CCTTGCACCCTGTAGTGACC 60.322 60.000 0.00 0.00 40.34 4.02
2321 3202 0.396435 CTTGCACCCTGTAGTGACCA 59.604 55.000 0.00 0.00 40.34 4.02
2322 3203 0.840617 TTGCACCCTGTAGTGACCAA 59.159 50.000 0.00 0.00 40.34 3.67
2324 3205 1.423541 TGCACCCTGTAGTGACCAAAT 59.576 47.619 0.00 0.00 40.34 2.32
2325 3206 2.640332 TGCACCCTGTAGTGACCAAATA 59.360 45.455 0.00 0.00 40.34 1.40
2326 3207 3.270877 GCACCCTGTAGTGACCAAATAG 58.729 50.000 0.00 0.00 40.34 1.73
2421 3313 5.163478 GGCATCCTGAGTGATTTTGCTATTT 60.163 40.000 0.00 0.00 0.00 1.40
2455 3347 7.566760 TTTCATCTTTCTGTTAGCACTTTGA 57.433 32.000 0.00 0.00 0.00 2.69
2465 3357 4.333649 TGTTAGCACTTTGATATCAGCAGC 59.666 41.667 14.87 13.01 0.00 5.25
2466 3358 2.995283 AGCACTTTGATATCAGCAGCA 58.005 42.857 14.87 0.00 0.00 4.41
2468 3360 3.128242 AGCACTTTGATATCAGCAGCAAC 59.872 43.478 14.87 5.77 0.00 4.17
2470 3362 4.730035 GCACTTTGATATCAGCAGCAACTC 60.730 45.833 5.39 0.00 0.00 3.01
2473 3365 5.353678 ACTTTGATATCAGCAGCAACTCTTC 59.646 40.000 5.39 0.00 0.00 2.87
2481 3388 1.130749 GCAGCAACTCTTCATCAGCAG 59.869 52.381 0.00 0.00 0.00 4.24
2490 3397 4.070716 CTCTTCATCAGCAGGTTTGTTCT 58.929 43.478 0.00 0.00 0.00 3.01
2504 3411 7.201530 GCAGGTTTGTTCTCACAGTATATGTAC 60.202 40.741 0.00 0.00 41.41 2.90
2520 3427 2.235016 TGTACTGGGTGTGATTTTGCC 58.765 47.619 0.00 0.00 0.00 4.52
2633 3559 0.606401 GTATGCATCGTGGATGGGGG 60.606 60.000 0.19 0.00 40.10 5.40
2653 3579 2.436417 GGCTAGCACTTGATTTGTGGA 58.564 47.619 18.24 0.00 36.08 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.760047 CTTGGGTGACGGAGCCGG 62.760 72.222 14.07 0.00 46.29 6.13
10 11 3.842925 TTGCTTGGGTGACGGAGCC 62.843 63.158 0.00 0.00 43.26 4.70
11 12 2.281484 TTGCTTGGGTGACGGAGC 60.281 61.111 0.00 0.00 38.83 4.70
12 13 1.966451 GGTTGCTTGGGTGACGGAG 60.966 63.158 0.00 0.00 0.00 4.63
13 14 2.112297 GGTTGCTTGGGTGACGGA 59.888 61.111 0.00 0.00 0.00 4.69
14 15 2.983592 GGGTTGCTTGGGTGACGG 60.984 66.667 0.00 0.00 0.00 4.79
15 16 2.718747 TACGGGTTGCTTGGGTGACG 62.719 60.000 0.00 0.00 0.00 4.35
16 17 0.953960 CTACGGGTTGCTTGGGTGAC 60.954 60.000 0.00 0.00 0.00 3.67
17 18 1.373435 CTACGGGTTGCTTGGGTGA 59.627 57.895 0.00 0.00 0.00 4.02
18 19 2.332654 GCTACGGGTTGCTTGGGTG 61.333 63.158 0.00 0.00 0.00 4.61
19 20 2.033602 GCTACGGGTTGCTTGGGT 59.966 61.111 0.00 0.00 0.00 4.51
20 21 2.750237 GGCTACGGGTTGCTTGGG 60.750 66.667 5.32 0.00 0.00 4.12
21 22 3.124921 CGGCTACGGGTTGCTTGG 61.125 66.667 5.32 0.00 36.18 3.61
22 23 2.047655 TCGGCTACGGGTTGCTTG 60.048 61.111 5.32 0.00 41.39 4.01
23 24 2.047560 GTCGGCTACGGGTTGCTT 60.048 61.111 5.32 0.00 41.39 3.91
24 25 3.307906 TGTCGGCTACGGGTTGCT 61.308 61.111 5.32 0.00 41.39 3.91
25 26 3.116531 GTGTCGGCTACGGGTTGC 61.117 66.667 0.00 0.00 41.39 4.17
26 27 2.433664 GGTGTCGGCTACGGGTTG 60.434 66.667 0.00 0.00 41.39 3.77
27 28 2.786512 TAGGGTGTCGGCTACGGGTT 62.787 60.000 0.00 0.00 41.39 4.11
28 29 3.286694 TAGGGTGTCGGCTACGGGT 62.287 63.158 0.00 0.00 41.39 5.28
29 30 2.440796 TAGGGTGTCGGCTACGGG 60.441 66.667 0.00 0.00 41.39 5.28
30 31 1.597797 TTGTAGGGTGTCGGCTACGG 61.598 60.000 0.00 0.00 41.39 4.02
31 32 0.457337 GTTGTAGGGTGTCGGCTACG 60.457 60.000 0.00 0.00 42.74 3.51
32 33 0.108472 GGTTGTAGGGTGTCGGCTAC 60.108 60.000 0.00 0.00 0.00 3.58
33 34 0.542467 TGGTTGTAGGGTGTCGGCTA 60.542 55.000 0.00 0.00 0.00 3.93
34 35 1.412453 TTGGTTGTAGGGTGTCGGCT 61.412 55.000 0.00 0.00 0.00 5.52
35 36 0.953960 CTTGGTTGTAGGGTGTCGGC 60.954 60.000 0.00 0.00 0.00 5.54
36 37 0.682852 TCTTGGTTGTAGGGTGTCGG 59.317 55.000 0.00 0.00 0.00 4.79
37 38 1.607251 GGTCTTGGTTGTAGGGTGTCG 60.607 57.143 0.00 0.00 0.00 4.35
38 39 1.607251 CGGTCTTGGTTGTAGGGTGTC 60.607 57.143 0.00 0.00 0.00 3.67
39 40 0.395312 CGGTCTTGGTTGTAGGGTGT 59.605 55.000 0.00 0.00 0.00 4.16
40 41 0.682852 TCGGTCTTGGTTGTAGGGTG 59.317 55.000 0.00 0.00 0.00 4.61
41 42 1.426751 TTCGGTCTTGGTTGTAGGGT 58.573 50.000 0.00 0.00 0.00 4.34
42 43 2.148768 GTTTCGGTCTTGGTTGTAGGG 58.851 52.381 0.00 0.00 0.00 3.53
43 44 2.148768 GGTTTCGGTCTTGGTTGTAGG 58.851 52.381 0.00 0.00 0.00 3.18
44 45 1.796459 CGGTTTCGGTCTTGGTTGTAG 59.204 52.381 0.00 0.00 0.00 2.74
45 46 1.868469 CGGTTTCGGTCTTGGTTGTA 58.132 50.000 0.00 0.00 0.00 2.41
46 47 1.441732 GCGGTTTCGGTCTTGGTTGT 61.442 55.000 0.00 0.00 36.79 3.32
47 48 1.281656 GCGGTTTCGGTCTTGGTTG 59.718 57.895 0.00 0.00 36.79 3.77
48 49 1.895231 GGCGGTTTCGGTCTTGGTT 60.895 57.895 0.00 0.00 36.79 3.67
49 50 2.281276 GGCGGTTTCGGTCTTGGT 60.281 61.111 0.00 0.00 36.79 3.67
50 51 3.419759 CGGCGGTTTCGGTCTTGG 61.420 66.667 0.00 0.00 36.79 3.61
51 52 4.084888 GCGGCGGTTTCGGTCTTG 62.085 66.667 9.78 0.00 36.79 3.02
52 53 4.309950 AGCGGCGGTTTCGGTCTT 62.310 61.111 5.44 0.00 36.79 3.01
75 76 4.570663 CTCGGGATCGGCGTGGAC 62.571 72.222 6.85 0.00 36.95 4.02
101 102 3.969642 GAAAATGTGCGCGGCCTGG 62.970 63.158 8.83 0.00 0.00 4.45
102 103 2.504681 GAAAATGTGCGCGGCCTG 60.505 61.111 8.83 0.00 0.00 4.85
103 104 2.981560 CTGAAAATGTGCGCGGCCT 61.982 57.895 8.83 0.00 0.00 5.19
104 105 2.504681 CTGAAAATGTGCGCGGCC 60.505 61.111 8.83 0.00 0.00 6.13
105 106 0.939106 AAACTGAAAATGTGCGCGGC 60.939 50.000 8.83 0.00 0.00 6.53
106 107 1.052287 GAAACTGAAAATGTGCGCGG 58.948 50.000 8.83 0.00 0.00 6.46
107 108 1.971962 GAGAAACTGAAAATGTGCGCG 59.028 47.619 0.00 0.00 0.00 6.86
108 109 2.721090 GTGAGAAACTGAAAATGTGCGC 59.279 45.455 0.00 0.00 0.00 6.09
109 110 3.951306 TGTGAGAAACTGAAAATGTGCG 58.049 40.909 0.00 0.00 0.00 5.34
110 111 6.360681 GTGTATGTGAGAAACTGAAAATGTGC 59.639 38.462 0.00 0.00 0.00 4.57
111 112 6.574832 CGTGTATGTGAGAAACTGAAAATGTG 59.425 38.462 0.00 0.00 0.00 3.21
145 146 5.922544 GCAATCTTGTGCATAAAGTTCAAGT 59.077 36.000 9.86 0.00 44.29 3.16
254 283 7.201548 GCACTGAGAATTTTTGTCAATGTTTGT 60.202 33.333 0.00 0.00 33.38 2.83
270 299 6.395426 TGAAATTTTGTGAGCACTGAGAAT 57.605 33.333 1.99 0.00 0.00 2.40
276 305 4.275689 TCGTGATGAAATTTTGTGAGCACT 59.724 37.500 1.99 0.00 0.00 4.40
329 359 4.111916 CACTTTTGGAGCGTCAATTTTGT 58.888 39.130 0.00 0.00 0.00 2.83
339 369 6.820470 TTCAAAAATAACACTTTTGGAGCG 57.180 33.333 7.87 0.00 41.84 5.03
419 453 3.493877 CGGTGCTTGCAAAATTTCATCAA 59.506 39.130 0.00 0.00 0.00 2.57
499 533 6.474102 TGAGCCGAACAGTAAAATTCAAAAAC 59.526 34.615 0.00 0.00 0.00 2.43
522 565 4.212913 GCCCGCGAGCTCATCTGA 62.213 66.667 15.40 0.00 0.00 3.27
523 566 4.519437 TGCCCGCGAGCTCATCTG 62.519 66.667 15.33 0.00 0.00 2.90
524 567 4.218578 CTGCCCGCGAGCTCATCT 62.219 66.667 15.33 0.00 0.00 2.90
525 568 3.723235 TTCTGCCCGCGAGCTCATC 62.723 63.158 15.33 3.61 0.00 2.92
526 569 3.729965 CTTCTGCCCGCGAGCTCAT 62.730 63.158 15.33 0.00 0.00 2.90
527 570 4.441695 CTTCTGCCCGCGAGCTCA 62.442 66.667 15.33 0.00 0.00 4.26
528 571 3.438017 ATCTTCTGCCCGCGAGCTC 62.438 63.158 15.33 2.73 0.00 4.09
529 572 3.465403 ATCTTCTGCCCGCGAGCT 61.465 61.111 15.33 0.00 0.00 4.09
530 573 3.267860 CATCTTCTGCCCGCGAGC 61.268 66.667 8.23 6.70 0.00 5.03
531 574 1.880340 GTCATCTTCTGCCCGCGAG 60.880 63.158 8.23 0.00 0.00 5.03
532 575 1.888436 AAGTCATCTTCTGCCCGCGA 61.888 55.000 8.23 0.00 0.00 5.87
533 576 1.021390 AAAGTCATCTTCTGCCCGCG 61.021 55.000 0.00 0.00 32.90 6.46
534 577 1.135575 CAAAAGTCATCTTCTGCCCGC 60.136 52.381 0.00 0.00 32.90 6.13
535 578 1.135575 GCAAAAGTCATCTTCTGCCCG 60.136 52.381 0.00 0.00 40.53 6.13
536 579 2.643933 GCAAAAGTCATCTTCTGCCC 57.356 50.000 0.00 0.00 40.53 5.36
538 581 3.080319 AGAGGCAAAAGTCATCTTCTGC 58.920 45.455 0.00 0.00 44.22 4.26
539 582 5.123027 GGTAAGAGGCAAAAGTCATCTTCTG 59.877 44.000 0.00 0.00 32.69 3.02
540 583 5.221925 TGGTAAGAGGCAAAAGTCATCTTCT 60.222 40.000 0.00 0.00 32.69 2.85
541 584 5.003804 TGGTAAGAGGCAAAAGTCATCTTC 58.996 41.667 0.00 0.00 32.69 2.87
542 585 4.762251 GTGGTAAGAGGCAAAAGTCATCTT 59.238 41.667 0.00 0.00 34.71 2.40
543 586 4.202461 TGTGGTAAGAGGCAAAAGTCATCT 60.202 41.667 0.00 0.00 0.00 2.90
544 587 4.072131 TGTGGTAAGAGGCAAAAGTCATC 58.928 43.478 0.00 0.00 0.00 2.92
545 588 4.074970 CTGTGGTAAGAGGCAAAAGTCAT 58.925 43.478 0.00 0.00 0.00 3.06
546 589 3.135712 TCTGTGGTAAGAGGCAAAAGTCA 59.864 43.478 0.00 0.00 0.00 3.41
547 590 3.498777 GTCTGTGGTAAGAGGCAAAAGTC 59.501 47.826 0.00 0.00 0.00 3.01
548 591 3.118038 TGTCTGTGGTAAGAGGCAAAAGT 60.118 43.478 0.00 0.00 26.35 2.66
549 592 3.476552 TGTCTGTGGTAAGAGGCAAAAG 58.523 45.455 0.00 0.00 26.35 2.27
567 610 3.133721 ACTCCATCTTGAGGCATACTGTC 59.866 47.826 0.00 0.00 36.66 3.51
695 748 2.872858 GCCTGCTTTATACTACCACAGC 59.127 50.000 0.00 0.00 0.00 4.40
704 757 1.211949 TGACTGGGGCCTGCTTTATAC 59.788 52.381 0.84 0.00 0.00 1.47
721 774 1.648467 GGGAGCGAAGGCAATGTGAC 61.648 60.000 0.00 0.00 43.41 3.67
734 824 1.574428 CCGTTGAAAAGTGGGAGCG 59.426 57.895 0.00 0.00 0.00 5.03
770 873 2.306255 CTGGCCTGCCATTCATTGCC 62.306 60.000 11.98 0.00 46.15 4.52
771 874 1.143183 CTGGCCTGCCATTCATTGC 59.857 57.895 11.98 0.00 46.15 3.56
772 875 1.820581 CCTGGCCTGCCATTCATTG 59.179 57.895 11.98 0.00 46.15 2.82
773 876 2.062177 GCCTGGCCTGCCATTCATT 61.062 57.895 11.98 0.00 46.15 2.57
774 877 2.443390 GCCTGGCCTGCCATTCAT 60.443 61.111 11.98 0.00 46.15 2.57
788 891 2.713531 AAAACAGTGGATGCGGGCCT 62.714 55.000 0.84 0.00 0.00 5.19
803 906 7.834068 AAGAAGAAGAAGCTTTTGGAAAAAC 57.166 32.000 0.00 0.00 0.00 2.43
808 911 6.406961 GGGAAAAAGAAGAAGAAGCTTTTGGA 60.407 38.462 0.00 0.00 39.99 3.53
810 917 6.577103 AGGGAAAAAGAAGAAGAAGCTTTTG 58.423 36.000 0.00 0.00 39.99 2.44
814 921 4.830046 GGAAGGGAAAAAGAAGAAGAAGCT 59.170 41.667 0.00 0.00 0.00 3.74
815 922 4.021894 GGGAAGGGAAAAAGAAGAAGAAGC 60.022 45.833 0.00 0.00 0.00 3.86
816 923 5.389520 AGGGAAGGGAAAAAGAAGAAGAAG 58.610 41.667 0.00 0.00 0.00 2.85
817 924 5.134509 AGAGGGAAGGGAAAAAGAAGAAGAA 59.865 40.000 0.00 0.00 0.00 2.52
818 925 4.665483 AGAGGGAAGGGAAAAAGAAGAAGA 59.335 41.667 0.00 0.00 0.00 2.87
911 1034 0.736325 CCAAGCGAGTAAGGTGTCCG 60.736 60.000 0.00 0.00 0.00 4.79
919 1044 2.353803 GGAGAAGAAGCCAAGCGAGTAA 60.354 50.000 0.00 0.00 0.00 2.24
969 1108 2.400399 CAGCAGCAACCAATCACAAAG 58.600 47.619 0.00 0.00 0.00 2.77
1260 1456 1.185618 TGTAGACGCTGTTGAGGGCT 61.186 55.000 0.00 0.00 35.53 5.19
1346 1542 1.812214 GATCACGACGCCGATCTTGC 61.812 60.000 16.58 0.00 39.50 4.01
1550 1764 1.203300 TGAAGGTCCCTCTGATGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
1697 1911 6.424883 AGAAGATGAAAAGAGCATCCAGATT 58.575 36.000 0.00 0.00 42.36 2.40
1720 1941 7.695820 TCCTTGAAAATTTGATGCAACAAAAG 58.304 30.769 23.57 15.39 41.88 2.27
1725 1946 6.790285 ACATCCTTGAAAATTTGATGCAAC 57.210 33.333 12.83 0.00 37.02 4.17
1729 1950 9.459640 CTGCTATACATCCTTGAAAATTTGATG 57.540 33.333 11.79 11.79 38.94 3.07
1740 1963 6.273825 AGTTTCGTACTGCTATACATCCTTG 58.726 40.000 0.00 0.00 35.19 3.61
1741 1964 6.466885 AGTTTCGTACTGCTATACATCCTT 57.533 37.500 0.00 0.00 35.19 3.36
1833 2057 1.933853 ACATAAACAGAGGAATCGCGC 59.066 47.619 0.00 0.00 0.00 6.86
1835 2059 4.433615 TCAGACATAAACAGAGGAATCGC 58.566 43.478 0.00 0.00 0.00 4.58
1873 2098 1.142688 AGATGTTCCCAGGCCCTTGT 61.143 55.000 0.00 0.00 0.00 3.16
1874 2099 0.918983 TAGATGTTCCCAGGCCCTTG 59.081 55.000 0.00 0.00 0.00 3.61
1875 2100 0.919710 GTAGATGTTCCCAGGCCCTT 59.080 55.000 0.00 0.00 0.00 3.95
1876 2101 0.044855 AGTAGATGTTCCCAGGCCCT 59.955 55.000 0.00 0.00 0.00 5.19
1885 2110 9.490379 CCTAAATATGGTAACCAGTAGATGTTC 57.510 37.037 0.00 0.00 36.75 3.18
2142 2428 3.747852 TCTTGGAGGGGTCCTTATGAAT 58.252 45.455 0.00 0.00 31.76 2.57
2143 2429 3.214694 TCTTGGAGGGGTCCTTATGAA 57.785 47.619 0.00 0.00 31.76 2.57
2144 2430 2.961536 TCTTGGAGGGGTCCTTATGA 57.038 50.000 0.00 0.00 31.76 2.15
2266 2561 3.005155 AGCTTGAGATTGTTTGTTGAGGC 59.995 43.478 0.00 0.00 0.00 4.70
2318 3199 7.477945 AGTGTGCTAACTACTACTATTTGGT 57.522 36.000 0.00 0.00 0.00 3.67
2346 3238 7.526142 AGCTGTTTCTTCGATCCTATGTATA 57.474 36.000 0.00 0.00 0.00 1.47
2455 3347 5.032327 TGATGAAGAGTTGCTGCTGATAT 57.968 39.130 0.00 0.00 0.00 1.63
2465 3357 3.567164 ACAAACCTGCTGATGAAGAGTTG 59.433 43.478 0.00 0.00 0.00 3.16
2466 3358 3.825328 ACAAACCTGCTGATGAAGAGTT 58.175 40.909 0.00 0.00 0.00 3.01
2468 3360 4.070716 AGAACAAACCTGCTGATGAAGAG 58.929 43.478 0.00 0.00 0.00 2.85
2470 3362 3.817084 TGAGAACAAACCTGCTGATGAAG 59.183 43.478 0.00 0.00 0.00 3.02
2473 3365 2.880268 TGTGAGAACAAACCTGCTGATG 59.120 45.455 0.00 0.00 0.00 3.07
2504 3411 2.671914 CGAATGGCAAAATCACACCCAG 60.672 50.000 0.00 0.00 0.00 4.45
2508 3415 2.723124 ACCGAATGGCAAAATCACAC 57.277 45.000 0.00 0.00 39.70 3.82
2520 3427 7.596248 ACAGAATGATGAAAGAAAAACCGAATG 59.404 33.333 0.00 0.00 39.69 2.67
2633 3559 2.436417 TCCACAAATCAAGTGCTAGCC 58.564 47.619 13.29 3.49 35.69 3.93
2644 3570 6.630444 ATCAAGCTGATACATCCACAAATC 57.370 37.500 0.00 0.00 34.88 2.17
2653 3579 5.067954 TGCAAGCATATCAAGCTGATACAT 58.932 37.500 7.69 0.00 41.62 2.29


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

AutoCloner maintained by Alex Coulton.