Multiple sequence alignment - TraesCS1B01G356700

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 TraesCS1B01G356700 chr1B 100.000 1992 0 0 1 1992 585681428 585679437 0.000000e+00 3679.0
1 TraesCS1B01G356700 chr1B 100.000 259 0 0 2361 2619 585679068 585678810 1.820000e-131 479.0
2 TraesCS1B01G356700 chr1D 88.894 1981 143 36 15 1962 433465207 433463271 0.000000e+00 2368.0
3 TraesCS1B01G356700 chr1D 86.466 266 28 7 2361 2619 433462914 433462650 4.270000e-73 285.0
4 TraesCS1B01G356700 chr1A 87.269 2003 148 52 21 1953 531987721 531985756 0.000000e+00 2187.0
5 TraesCS1B01G356700 chr3D 98.361 122 2 0 998 1119 384567788 384567667 5.680000e-52 215.0
6 TraesCS1B01G356700 chr3D 83.544 158 26 0 1228 1385 384567571 384567414 5.840000e-32 148.0
7 TraesCS1B01G356700 chr3B 98.361 122 2 0 998 1119 499806131 499806010 5.680000e-52 215.0
8 TraesCS1B01G356700 chr3B 83.117 154 26 0 1228 1381 499805913 499805760 9.770000e-30 141.0
9 TraesCS1B01G356700 chr3B 86.667 75 10 0 1539 1613 105367668 105367594 1.670000e-12 84.2
10 TraesCS1B01G356700 chr3A 97.541 122 3 0 998 1119 507120906 507120785 2.640000e-50 209.0
11 TraesCS1B01G356700 chr3A 83.544 158 26 0 1228 1385 507120697 507120540 5.840000e-32 148.0
12 TraesCS1B01G356700 chr2A 94.286 35 2 0 478 512 288123227 288123193 1.000000e-03 54.7


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 TraesCS1B01G356700 chr1B 585678810 585681428 2618 True 2079.0 3679 100.000 1 2619 2 chr1B.!!$R1 2618
1 TraesCS1B01G356700 chr1D 433462650 433465207 2557 True 1326.5 2368 87.680 15 2619 2 chr1D.!!$R1 2604
2 TraesCS1B01G356700 chr1A 531985756 531987721 1965 True 2187.0 2187 87.269 21 1953 1 chr1A.!!$R1 1932

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
966 1008 0.037232 CCCTCCTCACCTTGAACGTC 60.037 60.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2055 0.320771 GCCGCGACAATAGATGGGAT 60.321 55.0 8.23 0.0 0.0 3.85 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
47 50 3.706086 ACAAGTTTGCTTCCTCCACAATT 59.294 39.130 0.00 0.00 31.49 2.32
49 52 4.326504 AGTTTGCTTCCTCCACAATTTG 57.673 40.909 0.00 0.00 0.00 2.32
50 53 6.478020 CAAGTTTGCTTCCTCCACAATTTGG 61.478 44.000 0.78 1.49 38.76 3.28
51 54 8.575040 CAAGTTTGCTTCCTCCACAATTTGGA 62.575 42.308 0.78 8.48 41.90 3.53
70 73 3.282885 GGAGCTCAGGAATTAACCCTTG 58.717 50.000 17.19 0.00 0.00 3.61
88 91 5.174395 CCCTTGTTTTGAATTGTGTTCACA 58.826 37.500 1.23 1.23 0.00 3.58
105 108 5.166398 GTTCACACGTAAATAGTAGGTGCT 58.834 41.667 6.20 0.00 36.96 4.40
106 109 5.395682 TCACACGTAAATAGTAGGTGCTT 57.604 39.130 6.20 0.00 36.96 3.91
111 114 5.686397 CACGTAAATAGTAGGTGCTTCTAGC 59.314 44.000 0.00 0.00 42.82 3.42
115 118 5.692613 AATAGTAGGTGCTTCTAGCGTAG 57.307 43.478 0.00 0.00 46.26 3.51
136 139 6.074994 CGTAGCGCTAGTTATTCCTTGTTAAG 60.075 42.308 19.48 0.00 0.00 1.85
160 163 3.507233 TGGGATGAGATTTGTGAGTTTGC 59.493 43.478 0.00 0.00 0.00 3.68
181 192 6.429791 TGCGTTTGTATATAGCAATTGTGT 57.570 33.333 7.40 0.00 34.66 3.72
198 209 2.162408 TGTGTGCGTGTGTGAATTGAAA 59.838 40.909 0.00 0.00 0.00 2.69
220 231 5.743636 AACATGGCTTAAATCCACATTGT 57.256 34.783 0.00 0.00 36.26 2.71
239 250 9.559958 CACATTGTATTCTTATGGTTTTGTCTC 57.440 33.333 0.00 0.00 0.00 3.36
240 251 9.295825 ACATTGTATTCTTATGGTTTTGTCTCA 57.704 29.630 0.00 0.00 0.00 3.27
254 265 9.567776 TGGTTTTGTCTCATAATTCTTTCTACA 57.432 29.630 0.00 0.00 0.00 2.74
347 368 7.375053 TCAAAGTGTTTTTCTAACATATGGGC 58.625 34.615 7.80 0.00 32.23 5.36
348 369 5.560966 AGTGTTTTTCTAACATATGGGCG 57.439 39.130 7.80 0.00 32.23 6.13
350 371 5.475564 AGTGTTTTTCTAACATATGGGCGTT 59.524 36.000 7.80 0.00 32.23 4.84
352 373 7.175293 AGTGTTTTTCTAACATATGGGCGTTAA 59.825 33.333 7.80 0.00 32.23 2.01
353 374 7.483691 GTGTTTTTCTAACATATGGGCGTTAAG 59.516 37.037 7.80 0.00 32.23 1.85
362 383 1.310904 TGGGCGTTAAGTGTTTGGAC 58.689 50.000 0.00 0.00 0.00 4.02
363 384 1.134037 TGGGCGTTAAGTGTTTGGACT 60.134 47.619 0.00 0.00 0.00 3.85
376 397 5.704515 AGTGTTTGGACTCATGAAAGATCAG 59.295 40.000 0.00 0.00 39.39 2.90
394 415 2.555547 GCCAAACAACGGCTGAGCT 61.556 57.895 3.72 0.00 46.56 4.09
407 428 2.028567 GGCTGAGCTTAGACTTGACACT 60.029 50.000 10.16 0.00 0.00 3.55
409 430 3.553922 GCTGAGCTTAGACTTGACACTGT 60.554 47.826 10.16 0.00 0.00 3.55
415 436 4.570772 GCTTAGACTTGACACTGTTGTTCA 59.429 41.667 0.00 0.00 35.47 3.18
417 438 2.930040 AGACTTGACACTGTTGTTCACG 59.070 45.455 0.00 0.00 35.47 4.35
425 446 2.845967 CACTGTTGTTCACGTTTTGCTC 59.154 45.455 0.00 0.00 0.00 4.26
438 459 6.143758 TCACGTTTTGCTCAATTTATTTCAGC 59.856 34.615 0.00 0.00 0.00 4.26
439 460 5.982516 ACGTTTTGCTCAATTTATTTCAGCA 59.017 32.000 0.00 0.00 38.32 4.41
446 467 6.310956 TGCTCAATTTATTTCAGCATTTTCCG 59.689 34.615 0.00 0.00 35.17 4.30
447 468 6.531240 GCTCAATTTATTTCAGCATTTTCCGA 59.469 34.615 0.00 0.00 0.00 4.55
450 471 7.754924 TCAATTTATTTCAGCATTTTCCGAGAC 59.245 33.333 0.00 0.00 0.00 3.36
453 474 2.163818 TCAGCATTTTCCGAGACGTT 57.836 45.000 0.00 0.00 0.00 3.99
465 486 1.725292 CGAGACGTTCGTTCAGGAGAC 60.725 57.143 10.63 0.00 44.27 3.36
467 488 0.040603 GACGTTCGTTCAGGAGACGT 60.041 55.000 0.00 0.00 34.98 4.34
468 489 0.383231 ACGTTCGTTCAGGAGACGTT 59.617 50.000 0.00 0.00 0.00 3.99
469 490 1.050767 CGTTCGTTCAGGAGACGTTC 58.949 55.000 0.00 0.00 0.00 3.95
482 509 3.848917 GGAGACGTTCCATCGAATACGAG 60.849 52.174 15.56 0.00 46.01 4.18
512 539 8.138074 TCTATAATGACTTCGTCAATCTCAAGG 58.862 37.037 0.36 0.00 45.96 3.61
517 544 5.209818 ACTTCGTCAATCTCAAGGTGTTA 57.790 39.130 0.00 0.00 0.00 2.41
528 555 0.392998 AAGGTGTTATGCGGGCTCAG 60.393 55.000 0.00 0.00 0.00 3.35
548 575 5.076182 TCAGGATCTCAGAGGTGCTAATAG 58.924 45.833 4.05 0.00 0.00 1.73
551 578 5.074377 AGGATCTCAGAGGTGCTAATAGAGA 59.926 44.000 2.13 0.00 35.42 3.10
552 579 5.183140 GGATCTCAGAGGTGCTAATAGAGAC 59.817 48.000 0.00 0.00 33.96 3.36
553 580 5.117406 TCTCAGAGGTGCTAATAGAGACA 57.883 43.478 0.00 0.00 0.00 3.41
554 581 5.510430 TCTCAGAGGTGCTAATAGAGACAA 58.490 41.667 0.00 0.00 0.00 3.18
555 582 6.132658 TCTCAGAGGTGCTAATAGAGACAAT 58.867 40.000 0.00 0.00 0.00 2.71
556 583 6.040278 TCTCAGAGGTGCTAATAGAGACAATG 59.960 42.308 0.00 0.00 0.00 2.82
557 584 5.893824 TCAGAGGTGCTAATAGAGACAATGA 59.106 40.000 0.00 0.00 0.00 2.57
559 586 5.896678 AGAGGTGCTAATAGAGACAATGAGT 59.103 40.000 0.00 0.00 0.00 3.41
564 591 6.035435 GTGCTAATAGAGACAATGAGTGTGTG 59.965 42.308 0.00 0.00 41.96 3.82
566 593 4.815533 ATAGAGACAATGAGTGTGTGCT 57.184 40.909 0.00 0.00 41.96 4.40
569 596 1.605710 AGACAATGAGTGTGTGCTTGC 59.394 47.619 0.00 0.00 41.96 4.01
570 597 1.334556 GACAATGAGTGTGTGCTTGCA 59.665 47.619 0.00 0.00 41.96 4.08
588 615 0.736636 CATGCGTGCATTCATGGAGT 59.263 50.000 18.09 0.00 37.13 3.85
589 616 0.736636 ATGCGTGCATTCATGGAGTG 59.263 50.000 0.51 0.00 33.01 3.51
590 617 0.321475 TGCGTGCATTCATGGAGTGA 60.321 50.000 0.00 0.00 34.25 3.41
591 618 0.376152 GCGTGCATTCATGGAGTGAG 59.624 55.000 0.00 0.00 38.29 3.51
592 619 1.730501 CGTGCATTCATGGAGTGAGT 58.269 50.000 0.00 0.00 38.29 3.41
594 621 2.430465 GTGCATTCATGGAGTGAGTGT 58.570 47.619 0.00 0.00 44.07 3.55
595 622 3.599343 GTGCATTCATGGAGTGAGTGTA 58.401 45.455 0.00 0.00 44.07 2.90
596 623 4.194640 GTGCATTCATGGAGTGAGTGTAT 58.805 43.478 0.00 0.00 44.07 2.29
597 624 4.272018 GTGCATTCATGGAGTGAGTGTATC 59.728 45.833 0.00 0.00 44.07 2.24
598 625 4.162888 TGCATTCATGGAGTGAGTGTATCT 59.837 41.667 0.00 0.00 44.07 1.98
599 626 4.510711 GCATTCATGGAGTGAGTGTATCTG 59.489 45.833 0.00 0.00 44.07 2.90
600 627 5.683249 GCATTCATGGAGTGAGTGTATCTGA 60.683 44.000 0.00 0.00 44.07 3.27
601 628 6.343703 CATTCATGGAGTGAGTGTATCTGAA 58.656 40.000 0.00 0.00 39.12 3.02
624 652 3.844577 TCCACGTTCGGAAAAACAAAA 57.155 38.095 0.00 0.00 29.93 2.44
632 660 0.579630 GGAAAAACAAAAAGCGGCCG 59.420 50.000 24.05 24.05 0.00 6.13
651 679 2.241722 CGGCGTCAAATTTGCAACTAG 58.758 47.619 13.54 2.40 0.00 2.57
656 684 3.058293 CGTCAAATTTGCAACTAGGCTCA 60.058 43.478 13.54 0.00 34.04 4.26
661 689 0.771127 TTGCAACTAGGCTCAACCCT 59.229 50.000 0.00 0.00 40.58 4.34
675 703 2.081462 CAACCCTGGTTTACATCGTCC 58.919 52.381 0.00 0.00 36.00 4.79
723 751 3.223589 AGCAAAACCGGTGCCCAC 61.224 61.111 8.52 0.00 43.27 4.61
779 817 1.827789 AGGTCCGCAAGCAAAGCAA 60.828 52.632 0.00 0.00 0.00 3.91
909 947 1.746615 CCCAATCCACGCACCAGAG 60.747 63.158 0.00 0.00 0.00 3.35
944 982 1.002011 GCCACTCCCCCAGAGAAAC 60.002 63.158 0.00 0.00 46.50 2.78
945 983 1.296715 CCACTCCCCCAGAGAAACG 59.703 63.158 0.00 0.00 46.50 3.60
946 984 1.376037 CACTCCCCCAGAGAAACGC 60.376 63.158 0.00 0.00 46.50 4.84
947 985 2.269241 CTCCCCCAGAGAAACGCC 59.731 66.667 0.00 0.00 46.50 5.68
959 1001 2.125766 GAAACGCCCCTCCTCACCTT 62.126 60.000 0.00 0.00 0.00 3.50
966 1008 0.037232 CCCTCCTCACCTTGAACGTC 60.037 60.000 0.00 0.00 0.00 4.34
968 1010 0.679505 CTCCTCACCTTGAACGTCCA 59.320 55.000 0.00 0.00 0.00 4.02
969 1011 1.070134 CTCCTCACCTTGAACGTCCAA 59.930 52.381 0.00 0.00 0.00 3.53
980 1022 1.166531 AACGTCCAAGGAAGCAGCAC 61.167 55.000 1.81 0.00 0.00 4.40
983 1025 0.819259 GTCCAAGGAAGCAGCACACA 60.819 55.000 0.00 0.00 0.00 3.72
984 1026 0.106769 TCCAAGGAAGCAGCACACAA 60.107 50.000 0.00 0.00 0.00 3.33
986 1028 1.027357 CAAGGAAGCAGCACACAAGT 58.973 50.000 0.00 0.00 0.00 3.16
987 1029 1.002033 CAAGGAAGCAGCACACAAGTC 60.002 52.381 0.00 0.00 0.00 3.01
988 1030 0.536006 AGGAAGCAGCACACAAGTCC 60.536 55.000 0.00 0.00 0.00 3.85
993 1035 3.872603 AGCACACAAGTCCGGCCA 61.873 61.111 2.24 0.00 0.00 5.36
1014 1056 0.036952 CCAAGATGTCGTGGCAGACT 60.037 55.000 14.98 4.59 41.47 3.24
1171 1217 6.324561 TCAGATTTCCTGTATGATCTCTCG 57.675 41.667 0.00 0.00 43.38 4.04
1173 1219 6.998673 TCAGATTTCCTGTATGATCTCTCGTA 59.001 38.462 0.00 0.00 43.38 3.43
1175 1221 7.174080 CAGATTTCCTGTATGATCTCTCGTAGA 59.826 40.741 0.00 0.00 38.10 2.59
1177 1223 7.825331 TTTCCTGTATGATCTCTCGTAGATT 57.175 36.000 4.85 0.00 45.35 2.40
1178 1224 7.441890 TTCCTGTATGATCTCTCGTAGATTC 57.558 40.000 4.85 1.03 45.35 2.52
1179 1225 5.639931 TCCTGTATGATCTCTCGTAGATTCG 59.360 44.000 4.85 0.00 45.35 3.34
1184 1234 6.627395 ATGATCTCTCGTAGATTCGTTTCT 57.373 37.500 4.85 0.00 45.35 2.52
1189 1239 4.921547 TCTCGTAGATTCGTTTCTCCATG 58.078 43.478 0.00 0.00 33.89 3.66
1226 1276 2.039084 TGGTTTTGGTTTTTGTGTGGCT 59.961 40.909 0.00 0.00 0.00 4.75
1394 1452 1.867166 CATGCATGCATCTCTCGAGT 58.133 50.000 30.07 4.31 33.90 4.18
1395 1453 2.210961 CATGCATGCATCTCTCGAGTT 58.789 47.619 30.07 3.48 33.90 3.01
1398 1456 2.674852 TGCATGCATCTCTCGAGTTTTC 59.325 45.455 18.46 0.26 0.00 2.29
1400 1458 4.115516 GCATGCATCTCTCGAGTTTTCTA 58.884 43.478 14.21 0.00 0.00 2.10
1439 1513 9.865321 ATGTTCTTGAAAAATTGATTGATCGAT 57.135 25.926 0.00 0.00 32.29 3.59
1440 1514 9.345517 TGTTCTTGAAAAATTGATTGATCGATC 57.654 29.630 18.72 18.72 30.63 3.69
1456 1530 1.576356 GATCCCTGTGCTTCGTCATC 58.424 55.000 0.00 0.00 0.00 2.92
1468 1542 1.355971 TCGTCATCTTACTTTGCGGC 58.644 50.000 0.00 0.00 0.00 6.53
1653 1727 0.526739 TAACGGCGTCCACGATGATG 60.527 55.000 15.17 0.00 43.02 3.07
1654 1728 2.104132 CGGCGTCCACGATGATGA 59.896 61.111 2.58 0.00 43.02 2.92
1655 1729 1.300156 CGGCGTCCACGATGATGAT 60.300 57.895 2.58 0.00 43.02 2.45
1656 1730 1.278172 CGGCGTCCACGATGATGATC 61.278 60.000 2.58 0.00 43.02 2.92
1657 1731 0.249447 GGCGTCCACGATGATGATCA 60.249 55.000 2.58 0.00 43.02 2.92
1717 1791 4.340950 ACGGAAATATATGTGGGCCTTTTG 59.659 41.667 4.53 0.00 0.00 2.44
1749 1823 2.664185 CGGCTCTGGCATCCATCG 60.664 66.667 0.00 0.00 40.87 3.84
1768 1842 0.737219 GCTCATGATGACCAGTTGCC 59.263 55.000 0.00 0.00 0.00 4.52
1779 1853 2.956333 GACCAGTTGCCCTAACAAGTTT 59.044 45.455 0.00 0.00 41.88 2.66
1867 1947 8.092521 TGAATTGTGTTGACAACAAATTTTGT 57.907 26.923 22.16 8.97 44.90 2.83
1962 2052 5.179182 TGCAATCGCATATATAGGTTGTGTG 59.821 40.000 12.27 0.00 45.36 3.82
1963 2053 5.621422 CAATCGCATATATAGGTTGTGTGC 58.379 41.667 0.00 0.00 0.00 4.57
1964 2054 4.329462 TCGCATATATAGGTTGTGTGCA 57.671 40.909 0.00 0.00 0.00 4.57
1965 2055 4.698575 TCGCATATATAGGTTGTGTGCAA 58.301 39.130 0.00 0.00 0.00 4.08
1966 2056 5.304778 TCGCATATATAGGTTGTGTGCAAT 58.695 37.500 0.00 0.00 36.92 3.56
1967 2057 5.408299 TCGCATATATAGGTTGTGTGCAATC 59.592 40.000 0.00 0.00 36.92 2.67
1968 2058 5.390885 CGCATATATAGGTTGTGTGCAATCC 60.391 44.000 0.00 0.00 36.40 3.01
1969 2059 5.106157 GCATATATAGGTTGTGTGCAATCCC 60.106 44.000 0.00 0.00 36.40 3.85
1970 2060 2.897271 ATAGGTTGTGTGCAATCCCA 57.103 45.000 0.00 0.00 36.40 4.37
1971 2061 2.897271 TAGGTTGTGTGCAATCCCAT 57.103 45.000 0.00 0.00 36.40 4.00
1972 2062 1.549203 AGGTTGTGTGCAATCCCATC 58.451 50.000 0.00 0.00 36.40 3.51
1973 2063 1.076024 AGGTTGTGTGCAATCCCATCT 59.924 47.619 0.00 0.00 36.40 2.90
1974 2064 2.308570 AGGTTGTGTGCAATCCCATCTA 59.691 45.455 0.00 0.00 36.40 1.98
1975 2065 3.053395 AGGTTGTGTGCAATCCCATCTAT 60.053 43.478 0.00 0.00 36.40 1.98
1976 2066 3.701040 GGTTGTGTGCAATCCCATCTATT 59.299 43.478 0.00 0.00 36.92 1.73
1977 2067 4.440525 GGTTGTGTGCAATCCCATCTATTG 60.441 45.833 0.00 0.00 36.92 1.90
1978 2068 3.966979 TGTGTGCAATCCCATCTATTGT 58.033 40.909 0.00 0.00 36.82 2.71
1979 2069 3.947196 TGTGTGCAATCCCATCTATTGTC 59.053 43.478 0.00 0.00 36.82 3.18
1980 2070 3.002656 GTGTGCAATCCCATCTATTGTCG 59.997 47.826 0.00 0.00 36.82 4.35
1981 2071 2.031682 GTGCAATCCCATCTATTGTCGC 60.032 50.000 0.00 0.00 36.82 5.19
1982 2072 1.195448 GCAATCCCATCTATTGTCGCG 59.805 52.381 0.00 0.00 36.82 5.87
1983 2073 1.800586 CAATCCCATCTATTGTCGCGG 59.199 52.381 6.13 0.00 31.13 6.46
1984 2074 0.320771 ATCCCATCTATTGTCGCGGC 60.321 55.000 2.29 2.29 0.00 6.53
1985 2075 2.310233 CCCATCTATTGTCGCGGCG 61.310 63.158 17.70 17.70 0.00 6.46
1986 2076 2.546321 CATCTATTGTCGCGGCGC 59.454 61.111 24.21 24.21 0.00 6.53
1987 2077 2.661866 ATCTATTGTCGCGGCGCC 60.662 61.111 27.87 19.07 0.00 6.53
1988 2078 4.884257 TCTATTGTCGCGGCGCCC 62.884 66.667 27.87 17.69 0.00 6.13
2392 2482 5.897377 ACATAGTTGCTTACAATTGGGTC 57.103 39.130 10.83 0.00 38.27 4.46
2396 2486 5.453567 AGTTGCTTACAATTGGGTCTTTC 57.546 39.130 10.83 0.00 38.27 2.62
2397 2487 4.023193 AGTTGCTTACAATTGGGTCTTTCG 60.023 41.667 10.83 0.00 38.27 3.46
2425 2515 3.799366 TGAGACGGAACTTTGCACTTTA 58.201 40.909 0.00 0.00 0.00 1.85
2462 2552 6.296026 ACTTGCTACCACTAGATTTTTCACA 58.704 36.000 0.00 0.00 0.00 3.58
2476 2566 8.406172 AGATTTTTCACACACACATTTTGTAC 57.594 30.769 0.00 0.00 35.67 2.90
2494 2593 1.432514 ACTCATGTTGCTGCACTACG 58.567 50.000 0.00 0.00 0.00 3.51
2495 2594 1.270305 ACTCATGTTGCTGCACTACGT 60.270 47.619 0.00 0.00 0.00 3.57
2496 2595 2.029380 ACTCATGTTGCTGCACTACGTA 60.029 45.455 0.00 0.00 0.00 3.57
2497 2596 2.333926 TCATGTTGCTGCACTACGTAC 58.666 47.619 0.00 0.00 0.00 3.67
2525 2624 0.036483 TGCTGTATGTCGTGCCACAT 60.036 50.000 0.00 0.00 40.28 3.21
2529 2628 3.242413 GCTGTATGTCGTGCCACATTAAG 60.242 47.826 0.00 0.20 38.07 1.85
2531 2630 4.570930 TGTATGTCGTGCCACATTAAGAA 58.429 39.130 0.00 0.00 38.07 2.52
2556 2656 5.994416 ACATATTACCAGTGGGGAAATCT 57.006 39.130 15.21 0.60 41.48 2.40
2559 2659 3.899052 TTACCAGTGGGGAAATCTACG 57.101 47.619 15.21 0.00 41.15 3.51
2574 2674 9.884465 GGGAAATCTACGAGAATAATTCAATTG 57.116 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.552034 GTGGAGTAATTAAGCATGACTATTGAC 58.448 37.037 0.00 0.00 0.00 3.18
1 2 8.264347 TGTGGAGTAATTAAGCATGACTATTGA 58.736 33.333 0.00 0.00 0.00 2.57
2 3 8.437360 TGTGGAGTAATTAAGCATGACTATTG 57.563 34.615 0.00 0.00 0.00 1.90
3 4 9.113838 CTTGTGGAGTAATTAAGCATGACTATT 57.886 33.333 0.00 0.00 0.00 1.73
4 5 8.267894 ACTTGTGGAGTAATTAAGCATGACTAT 58.732 33.333 0.00 0.00 36.65 2.12
5 6 7.620880 ACTTGTGGAGTAATTAAGCATGACTA 58.379 34.615 0.00 0.00 36.65 2.59
6 7 6.476378 ACTTGTGGAGTAATTAAGCATGACT 58.524 36.000 0.00 0.00 36.65 3.41
7 8 6.743575 ACTTGTGGAGTAATTAAGCATGAC 57.256 37.500 0.00 0.00 36.65 3.06
8 9 7.592938 CAAACTTGTGGAGTAATTAAGCATGA 58.407 34.615 0.00 0.00 37.72 3.07
9 10 6.308766 GCAAACTTGTGGAGTAATTAAGCATG 59.691 38.462 0.00 0.00 37.72 4.06
10 11 6.209391 AGCAAACTTGTGGAGTAATTAAGCAT 59.791 34.615 0.00 0.00 37.72 3.79
11 12 5.534654 AGCAAACTTGTGGAGTAATTAAGCA 59.465 36.000 0.00 0.00 37.72 3.91
12 13 6.013842 AGCAAACTTGTGGAGTAATTAAGC 57.986 37.500 0.00 0.00 37.72 3.09
13 14 7.040409 AGGAAGCAAACTTGTGGAGTAATTAAG 60.040 37.037 0.00 0.00 37.72 1.85
19 20 3.496160 GGAGGAAGCAAACTTGTGGAGTA 60.496 47.826 0.00 0.00 37.72 2.59
47 50 2.919602 AGGGTTAATTCCTGAGCTCCAA 59.080 45.455 12.15 1.54 32.53 3.53
49 52 3.282885 CAAGGGTTAATTCCTGAGCTCC 58.717 50.000 12.15 0.00 34.34 4.70
50 53 3.956744 ACAAGGGTTAATTCCTGAGCTC 58.043 45.455 6.82 6.82 34.34 4.09
51 54 4.388577 AACAAGGGTTAATTCCTGAGCT 57.611 40.909 0.00 0.00 34.87 4.09
52 55 5.010617 TCAAAACAAGGGTTAATTCCTGAGC 59.989 40.000 1.72 0.00 35.82 4.26
70 73 6.856494 TTACGTGTGAACACAATTCAAAAC 57.144 33.333 13.63 0.00 46.75 2.43
88 91 5.505324 CGCTAGAAGCACCTACTATTTACGT 60.505 44.000 0.00 0.00 42.58 3.57
90 93 5.829829 ACGCTAGAAGCACCTACTATTTAC 58.170 41.667 0.00 0.00 42.58 2.01
111 114 3.703420 ACAAGGAATAACTAGCGCTACG 58.297 45.455 14.45 12.31 0.00 3.51
115 118 6.292919 CCATCTTAACAAGGAATAACTAGCGC 60.293 42.308 0.00 0.00 0.00 5.92
127 130 6.604795 ACAAATCTCATCCCATCTTAACAAGG 59.395 38.462 0.00 0.00 0.00 3.61
136 139 5.678107 GCAAACTCACAAATCTCATCCCATC 60.678 44.000 0.00 0.00 0.00 3.51
160 163 5.392297 CGCACACAATTGCTATATACAAACG 59.608 40.000 5.05 0.00 40.62 3.60
181 192 3.494045 TGTTTTCAATTCACACACGCA 57.506 38.095 0.00 0.00 0.00 5.24
187 198 7.387397 GGATTTAAGCCATGTTTTCAATTCACA 59.613 33.333 0.00 0.00 0.00 3.58
198 209 5.743636 ACAATGTGGATTTAAGCCATGTT 57.256 34.783 4.90 0.75 37.81 2.71
338 359 3.442273 CCAAACACTTAACGCCCATATGT 59.558 43.478 1.24 0.00 0.00 2.29
339 360 3.692101 TCCAAACACTTAACGCCCATATG 59.308 43.478 0.00 0.00 0.00 1.78
340 361 3.692593 GTCCAAACACTTAACGCCCATAT 59.307 43.478 0.00 0.00 0.00 1.78
341 362 3.075884 GTCCAAACACTTAACGCCCATA 58.924 45.455 0.00 0.00 0.00 2.74
342 363 1.883926 GTCCAAACACTTAACGCCCAT 59.116 47.619 0.00 0.00 0.00 4.00
343 364 1.134037 AGTCCAAACACTTAACGCCCA 60.134 47.619 0.00 0.00 0.00 5.36
344 365 1.534163 GAGTCCAAACACTTAACGCCC 59.466 52.381 0.00 0.00 0.00 6.13
346 367 3.496884 TCATGAGTCCAAACACTTAACGC 59.503 43.478 0.00 0.00 0.00 4.84
347 368 5.666969 TTCATGAGTCCAAACACTTAACG 57.333 39.130 0.00 0.00 0.00 3.18
348 369 7.259290 TCTTTCATGAGTCCAAACACTTAAC 57.741 36.000 0.00 0.00 0.00 2.01
350 371 7.223584 TGATCTTTCATGAGTCCAAACACTTA 58.776 34.615 0.00 0.00 0.00 2.24
352 373 5.624159 TGATCTTTCATGAGTCCAAACACT 58.376 37.500 0.00 0.00 0.00 3.55
353 374 5.618640 GCTGATCTTTCATGAGTCCAAACAC 60.619 44.000 0.00 0.00 0.00 3.32
362 383 5.159209 GTTGTTTGGCTGATCTTTCATGAG 58.841 41.667 0.00 0.00 0.00 2.90
363 384 4.320421 CGTTGTTTGGCTGATCTTTCATGA 60.320 41.667 0.00 0.00 0.00 3.07
392 413 4.570772 TGAACAACAGTGTCAAGTCTAAGC 59.429 41.667 0.00 0.00 36.80 3.09
394 415 4.565166 CGTGAACAACAGTGTCAAGTCTAA 59.435 41.667 0.00 0.00 36.80 2.10
407 428 3.560902 TTGAGCAAAACGTGAACAACA 57.439 38.095 0.00 0.00 0.00 3.33
409 430 7.763172 AATAAATTGAGCAAAACGTGAACAA 57.237 28.000 0.00 0.00 0.00 2.83
415 436 5.982516 TGCTGAAATAAATTGAGCAAAACGT 59.017 32.000 0.00 0.00 34.81 3.99
417 438 9.667989 AAAATGCTGAAATAAATTGAGCAAAAC 57.332 25.926 6.43 0.00 38.66 2.43
425 446 7.253420 CGTCTCGGAAAATGCTGAAATAAATTG 60.253 37.037 0.00 0.00 0.00 2.32
446 467 1.725292 CGTCTCCTGAACGAACGTCTC 60.725 57.143 0.00 2.16 0.00 3.36
447 468 0.237761 CGTCTCCTGAACGAACGTCT 59.762 55.000 0.00 0.00 0.00 4.18
450 471 1.050767 GAACGTCTCCTGAACGAACG 58.949 55.000 2.33 0.00 0.00 3.95
453 474 1.201647 GATGGAACGTCTCCTGAACGA 59.798 52.381 14.95 0.00 45.64 3.85
461 482 3.289911 CTCGTATTCGATGGAACGTCTC 58.710 50.000 0.00 0.00 45.21 3.36
462 483 2.033049 CCTCGTATTCGATGGAACGTCT 59.967 50.000 0.00 0.00 45.21 4.18
465 486 1.129326 GCCTCGTATTCGATGGAACG 58.871 55.000 12.16 0.00 45.21 3.95
467 488 2.628178 AGATGCCTCGTATTCGATGGAA 59.372 45.455 12.16 0.00 45.21 3.53
468 489 2.239400 AGATGCCTCGTATTCGATGGA 58.761 47.619 12.16 4.48 45.21 3.41
469 490 2.732412 AGATGCCTCGTATTCGATGG 57.268 50.000 0.00 0.82 45.21 3.51
471 492 7.067615 AGTCATTATAGATGCCTCGTATTCGAT 59.932 37.037 0.00 0.00 45.21 3.59
476 503 6.151312 ACGAAGTCATTATAGATGCCTCGTAT 59.849 38.462 0.00 0.00 29.74 3.06
512 539 0.179045 ATCCTGAGCCCGCATAACAC 60.179 55.000 0.00 0.00 0.00 3.32
517 544 1.756408 CTGAGATCCTGAGCCCGCAT 61.756 60.000 0.00 0.00 0.00 4.73
528 555 5.183140 GTCTCTATTAGCACCTCTGAGATCC 59.817 48.000 6.17 0.00 32.76 3.36
548 575 2.350197 GCAAGCACACACTCATTGTCTC 60.350 50.000 0.00 0.00 35.67 3.36
551 578 1.391577 TGCAAGCACACACTCATTGT 58.608 45.000 0.00 0.00 39.97 2.71
552 579 2.324860 CATGCAAGCACACACTCATTG 58.675 47.619 0.00 0.00 0.00 2.82
553 580 1.336517 GCATGCAAGCACACACTCATT 60.337 47.619 14.21 0.00 0.00 2.57
554 581 0.242825 GCATGCAAGCACACACTCAT 59.757 50.000 14.21 0.00 0.00 2.90
555 582 1.655885 GCATGCAAGCACACACTCA 59.344 52.632 14.21 0.00 0.00 3.41
556 583 1.441515 CGCATGCAAGCACACACTC 60.442 57.895 19.57 0.00 0.00 3.51
557 584 2.188829 ACGCATGCAAGCACACACT 61.189 52.632 19.57 0.00 0.00 3.55
559 586 2.332159 CACGCATGCAAGCACACA 59.668 55.556 19.57 0.00 0.00 3.72
569 596 0.736636 ACTCCATGAATGCACGCATG 59.263 50.000 18.83 18.83 41.11 4.06
570 597 0.736636 CACTCCATGAATGCACGCAT 59.263 50.000 0.00 0.00 38.46 4.73
588 615 3.509967 ACGTGGATGTTCAGATACACTCA 59.490 43.478 0.00 0.00 35.30 3.41
589 616 4.111375 ACGTGGATGTTCAGATACACTC 57.889 45.455 0.00 0.00 35.30 3.51
590 617 4.495422 GAACGTGGATGTTCAGATACACT 58.505 43.478 6.82 0.00 45.92 3.55
591 618 3.303495 CGAACGTGGATGTTCAGATACAC 59.697 47.826 11.35 0.00 46.77 2.90
592 619 3.507786 CGAACGTGGATGTTCAGATACA 58.492 45.455 11.35 0.00 46.77 2.29
594 621 2.756207 TCCGAACGTGGATGTTCAGATA 59.244 45.455 11.35 0.00 46.77 1.98
595 622 1.548719 TCCGAACGTGGATGTTCAGAT 59.451 47.619 11.35 0.00 46.77 2.90
596 623 0.963225 TCCGAACGTGGATGTTCAGA 59.037 50.000 11.35 3.61 46.77 3.27
597 624 1.790755 TTCCGAACGTGGATGTTCAG 58.209 50.000 11.35 1.44 46.77 3.02
598 625 2.242047 TTTCCGAACGTGGATGTTCA 57.758 45.000 11.35 0.00 46.77 3.18
599 626 3.242804 TGTTTTTCCGAACGTGGATGTTC 60.243 43.478 0.00 2.16 43.76 3.18
600 627 2.683867 TGTTTTTCCGAACGTGGATGTT 59.316 40.909 0.00 0.00 38.00 2.71
601 628 2.290464 TGTTTTTCCGAACGTGGATGT 58.710 42.857 0.00 0.00 38.00 3.06
632 660 2.595386 CCTAGTTGCAAATTTGACGCC 58.405 47.619 22.31 4.54 0.00 5.68
651 679 2.092323 GATGTAAACCAGGGTTGAGCC 58.908 52.381 4.14 0.00 38.47 4.70
656 684 1.003928 GGGACGATGTAAACCAGGGTT 59.996 52.381 0.00 0.00 40.45 4.11
730 758 4.770362 TCATCCGTCAGGGCCCGA 62.770 66.667 18.44 14.51 38.33 5.14
742 770 2.123982 CCCTGGCTTGGCTCATCC 60.124 66.667 0.00 0.00 0.00 3.51
779 817 4.016706 CGCCGTCTTTCCAGGGGT 62.017 66.667 0.00 0.00 33.88 4.95
909 947 2.799540 GCGATCGGAGTTCGTTGGC 61.800 63.158 18.30 0.00 38.81 4.52
944 982 2.592993 TTCAAGGTGAGGAGGGGCG 61.593 63.158 0.00 0.00 0.00 6.13
945 983 1.002011 GTTCAAGGTGAGGAGGGGC 60.002 63.158 0.00 0.00 0.00 5.80
946 984 1.296715 CGTTCAAGGTGAGGAGGGG 59.703 63.158 0.00 0.00 0.00 4.79
947 985 0.037232 GACGTTCAAGGTGAGGAGGG 60.037 60.000 0.00 0.00 0.00 4.30
959 1001 0.884704 GCTGCTTCCTTGGACGTTCA 60.885 55.000 0.00 0.00 0.00 3.18
966 1008 0.313043 CTTGTGTGCTGCTTCCTTGG 59.687 55.000 0.00 0.00 0.00 3.61
968 1010 1.312815 GACTTGTGTGCTGCTTCCTT 58.687 50.000 0.00 0.00 0.00 3.36
969 1011 0.536006 GGACTTGTGTGCTGCTTCCT 60.536 55.000 0.00 0.00 0.00 3.36
980 1022 4.641645 TGGCTGGCCGGACTTGTG 62.642 66.667 20.97 0.00 39.42 3.33
983 1025 2.606587 ATCTTGGCTGGCCGGACTT 61.607 57.895 20.97 0.00 39.42 3.01
984 1026 3.011517 ATCTTGGCTGGCCGGACT 61.012 61.111 20.97 0.00 39.42 3.85
986 1028 3.329542 GACATCTTGGCTGGCCGGA 62.330 63.158 18.31 8.12 39.42 5.14
987 1029 2.825836 GACATCTTGGCTGGCCGG 60.826 66.667 7.41 7.41 39.42 6.13
988 1030 3.197790 CGACATCTTGGCTGGCCG 61.198 66.667 7.14 0.00 39.42 6.13
1014 1056 1.208358 CAGGTGCTCGTCGACGTAA 59.792 57.895 34.40 19.66 40.80 3.18
1141 1183 0.984230 ACAGGAAATCTGAAGGCGGA 59.016 50.000 0.00 0.00 46.18 5.54
1171 1217 5.517054 GTGAGACATGGAGAAACGAATCTAC 59.483 44.000 0.00 0.00 0.00 2.59
1173 1219 4.499183 GTGAGACATGGAGAAACGAATCT 58.501 43.478 0.00 0.00 0.00 2.40
1175 1221 3.254060 CGTGAGACATGGAGAAACGAAT 58.746 45.455 0.00 0.00 0.00 3.34
1176 1222 2.609491 CCGTGAGACATGGAGAAACGAA 60.609 50.000 4.18 0.00 42.73 3.85
1177 1223 1.067846 CCGTGAGACATGGAGAAACGA 60.068 52.381 4.18 0.00 42.73 3.85
1178 1224 1.336887 ACCGTGAGACATGGAGAAACG 60.337 52.381 15.60 0.45 42.73 3.60
1179 1225 2.069273 CACCGTGAGACATGGAGAAAC 58.931 52.381 15.60 0.00 42.73 2.78
1184 1234 1.293179 CAGCACCGTGAGACATGGA 59.707 57.895 15.60 0.00 42.73 3.41
1189 1239 1.961277 CCAACCAGCACCGTGAGAC 60.961 63.158 1.65 0.00 0.00 3.36
1432 1506 0.103026 CGAAGCACAGGGATCGATCA 59.897 55.000 25.93 0.00 37.48 2.92
1437 1511 1.137872 AGATGACGAAGCACAGGGATC 59.862 52.381 0.00 0.00 0.00 3.36
1438 1512 1.198713 AGATGACGAAGCACAGGGAT 58.801 50.000 0.00 0.00 0.00 3.85
1439 1513 0.976641 AAGATGACGAAGCACAGGGA 59.023 50.000 0.00 0.00 0.00 4.20
1440 1514 2.093973 AGTAAGATGACGAAGCACAGGG 60.094 50.000 0.00 0.00 0.00 4.45
1468 1542 4.559063 CCCTGCAGGCCGGATGAG 62.559 72.222 28.39 7.14 0.00 2.90
1653 1727 9.286946 GAATCTTGAAAATTGTGTGATCTGATC 57.713 33.333 10.72 10.72 0.00 2.92
1654 1728 9.021807 AGAATCTTGAAAATTGTGTGATCTGAT 57.978 29.630 0.00 0.00 0.00 2.90
1655 1729 8.400184 AGAATCTTGAAAATTGTGTGATCTGA 57.600 30.769 0.00 0.00 0.00 3.27
1656 1730 8.670804 GAGAATCTTGAAAATTGTGTGATCTG 57.329 34.615 0.00 0.00 0.00 2.90
1717 1791 0.606673 AGCCGCTTGAAGAGGGAAAC 60.607 55.000 16.69 0.00 40.59 2.78
1749 1823 0.737219 GGCAACTGGTCATCATGAGC 59.263 55.000 10.07 10.07 44.54 4.26
1768 1842 7.378181 AGGCATTACAAATGAAACTTGTTAGG 58.622 34.615 3.86 0.00 0.00 2.69
1962 2052 1.195448 CGCGACAATAGATGGGATTGC 59.805 52.381 0.00 0.00 37.74 3.56
1963 2053 1.800586 CCGCGACAATAGATGGGATTG 59.199 52.381 8.23 0.00 39.68 2.67
1964 2054 1.878102 GCCGCGACAATAGATGGGATT 60.878 52.381 8.23 0.00 0.00 3.01
1965 2055 0.320771 GCCGCGACAATAGATGGGAT 60.321 55.000 8.23 0.00 0.00 3.85
1966 2056 1.069090 GCCGCGACAATAGATGGGA 59.931 57.895 8.23 0.00 0.00 4.37
1967 2057 2.310233 CGCCGCGACAATAGATGGG 61.310 63.158 8.23 0.00 0.00 4.00
1968 2058 2.943345 GCGCCGCGACAATAGATGG 61.943 63.158 18.91 0.00 0.00 3.51
1969 2059 2.546321 GCGCCGCGACAATAGATG 59.454 61.111 18.91 0.00 0.00 2.90
1970 2060 2.661866 GGCGCCGCGACAATAGAT 60.662 61.111 18.91 0.00 33.63 1.98
1971 2061 4.884257 GGGCGCCGCGACAATAGA 62.884 66.667 22.39 0.00 36.10 1.98
2369 2459 6.717289 AGACCCAATTGTAAGCAACTATGTA 58.283 36.000 4.43 0.00 37.44 2.29
2371 2461 6.515272 AAGACCCAATTGTAAGCAACTATG 57.485 37.500 4.43 0.00 37.44 2.23
2374 2464 4.023193 CGAAAGACCCAATTGTAAGCAACT 60.023 41.667 4.43 0.00 37.44 3.16
2383 2473 4.749099 TCATTTTTGCGAAAGACCCAATTG 59.251 37.500 0.00 0.00 0.00 2.32
2384 2474 4.954875 TCATTTTTGCGAAAGACCCAATT 58.045 34.783 0.00 0.00 0.00 2.32
2387 2477 3.004315 GTCTCATTTTTGCGAAAGACCCA 59.996 43.478 5.30 0.00 0.00 4.51
2389 2479 3.226347 CGTCTCATTTTTGCGAAAGACC 58.774 45.455 9.64 0.00 0.00 3.85
2392 2482 3.536158 TCCGTCTCATTTTTGCGAAAG 57.464 42.857 0.00 0.00 0.00 2.62
2396 2486 2.969443 AGTTCCGTCTCATTTTTGCG 57.031 45.000 0.00 0.00 0.00 4.85
2397 2487 3.182372 GCAAAGTTCCGTCTCATTTTTGC 59.818 43.478 3.68 3.68 41.10 3.68
2425 2515 4.647399 TGGTAGCAAGTTGTTTTTAAGGCT 59.353 37.500 4.48 0.00 0.00 4.58
2462 2552 5.067674 AGCAACATGAGTACAAAATGTGTGT 59.932 36.000 0.00 0.00 41.89 3.72
2476 2566 1.432514 ACGTAGTGCAGCAACATGAG 58.567 50.000 0.00 0.00 42.51 2.90
2511 2610 6.819146 TGTATTTCTTAATGTGGCACGACATA 59.181 34.615 13.77 3.97 35.43 2.29
2517 2616 9.893305 GGTAATATGTATTTCTTAATGTGGCAC 57.107 33.333 11.55 11.55 0.00 5.01
2525 2624 9.005318 TCCCCACTGGTAATATGTATTTCTTAA 57.995 33.333 0.00 0.00 34.77 1.85
2529 2628 8.706322 ATTTCCCCACTGGTAATATGTATTTC 57.294 34.615 0.00 0.00 32.78 2.17
2531 2630 8.057246 AGATTTCCCCACTGGTAATATGTATT 57.943 34.615 0.00 0.00 34.53 1.89
2574 2674 7.485913 CACATGATGCTTCAATACTTGGTTAAC 59.514 37.037 6.36 0.00 34.96 2.01
2577 2677 5.711506 TCACATGATGCTTCAATACTTGGTT 59.288 36.000 6.36 0.00 34.96 3.67


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

AutoCloner maintained by Alex Coulton.