Multiple sequence alignment - TraesCS1B01G260000

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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 TraesCS1B01G260000 chr1B 100.000 2825 0 0 1 2825 457380636 457377812 0.000000e+00 5217.0
1 TraesCS1B01G260000 chr1B 83.817 482 56 9 1232 1712 457322698 457322238 3.340000e-119 438.0
2 TraesCS1B01G260000 chr1A 88.641 1435 98 33 549 1951 441185167 441183766 0.000000e+00 1687.0
3 TraesCS1B01G260000 chr1A 91.571 700 45 6 1007 1693 589867237 589866539 0.000000e+00 953.0
4 TraesCS1B01G260000 chr1A 87.657 478 31 14 73 534 441185617 441185152 5.360000e-147 531.0
5 TraesCS1B01G260000 chr1A 89.378 386 26 8 2450 2825 441183333 441182953 3.290000e-129 472.0
6 TraesCS1B01G260000 chr1A 85.965 285 28 3 2130 2414 441183606 441183334 7.650000e-76 294.0
7 TraesCS1B01G260000 chr1A 91.667 132 10 1 2016 2147 441183757 441183627 6.220000e-42 182.0
8 TraesCS1B01G260000 chr1A 82.400 125 13 6 2144 2264 441112207 441112088 1.790000e-17 100.0
9 TraesCS1B01G260000 chr1A 86.667 75 5 3 1959 2028 399497137 399497063 8.390000e-11 78.7
10 TraesCS1B01G260000 chr1D 92.386 985 50 11 977 1961 341494959 341494000 0.000000e+00 1380.0
11 TraesCS1B01G260000 chr1D 89.026 811 62 10 2017 2825 341494000 341493215 0.000000e+00 979.0
12 TraesCS1B01G260000 chr1D 87.638 542 35 13 1 527 341496057 341495533 4.030000e-168 601.0
13 TraesCS1B01G260000 chr1D 82.716 567 53 25 1224 1782 341478285 341477756 1.980000e-126 462.0
14 TraesCS1B01G260000 chr3A 92.363 419 22 5 1326 1741 31808744 31808333 3.130000e-164 588.0
15 TraesCS1B01G260000 chr3A 92.164 268 21 0 1007 1274 31809343 31809076 2.050000e-101 379.0
16 TraesCS1B01G260000 chr3A 100.000 29 0 0 2695 2723 61433214 61433186 1.000000e-03 54.7
17 TraesCS1B01G260000 chr4D 92.063 63 3 2 1969 2031 497465972 497465912 1.390000e-13 87.9
18 TraesCS1B01G260000 chr6B 88.889 72 4 2 1957 2025 504603095 504603165 5.010000e-13 86.1
19 TraesCS1B01G260000 chr6D 96.154 52 0 2 1969 2019 140086894 140086944 1.800000e-12 84.2
20 TraesCS1B01G260000 chr4B 92.982 57 3 1 1969 2025 670388349 670388294 6.490000e-12 82.4
21 TraesCS1B01G260000 chr3D 91.667 60 4 1 1958 2017 25393896 25393838 6.490000e-12 82.4
22 TraesCS1B01G260000 chr3D 92.982 57 3 1 1958 2014 384662878 384662823 6.490000e-12 82.4
23 TraesCS1B01G260000 chr2B 94.444 54 1 2 1969 2022 18809656 18809605 6.490000e-12 82.4
24 TraesCS1B01G260000 chr6A 87.500 72 5 2 1957 2025 456599257 456599187 2.330000e-11 80.5


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 TraesCS1B01G260000 chr1B 457377812 457380636 2824 True 5217.000000 5217 100.000000 1 2825 1 chr1B.!!$R2 2824
1 TraesCS1B01G260000 chr1A 589866539 589867237 698 True 953.000000 953 91.571000 1007 1693 1 chr1A.!!$R3 686
2 TraesCS1B01G260000 chr1A 441182953 441185617 2664 True 633.200000 1687 88.661600 73 2825 5 chr1A.!!$R4 2752
3 TraesCS1B01G260000 chr1D 341493215 341496057 2842 True 986.666667 1380 89.683333 1 2825 3 chr1D.!!$R2 2824
4 TraesCS1B01G260000 chr1D 341477756 341478285 529 True 462.000000 462 82.716000 1224 1782 1 chr1D.!!$R1 558
5 TraesCS1B01G260000 chr3A 31808333 31809343 1010 True 483.500000 588 92.263500 1007 1741 2 chr3A.!!$R2 734

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
615 641 0.036875 GGAGCAACACCCAGCTACTT 59.963 55.0 0.0 0.0 42.04 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2906 0.654683 GTCGAATGTGCATCTGAGGC 59.345 55.0 7.45 7.45 0.0 4.7 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
131 132 3.252974 GCCTAGAGCAAAGCTGTAAGA 57.747 47.619 0.00 0.00 39.88 2.10
176 177 2.255172 CCGTGCGGTTTGTTGGCTA 61.255 57.895 1.93 0.00 0.00 3.93
227 230 6.608002 GCATAATGCTATCCTACCTACTACCT 59.392 42.308 0.00 0.00 40.96 3.08
228 231 7.416890 GCATAATGCTATCCTACCTACTACCTG 60.417 44.444 0.00 0.00 40.96 4.00
229 232 3.764218 TGCTATCCTACCTACTACCTGC 58.236 50.000 0.00 0.00 0.00 4.85
230 233 2.748532 GCTATCCTACCTACTACCTGCG 59.251 54.545 0.00 0.00 0.00 5.18
231 234 1.618487 ATCCTACCTACTACCTGCGC 58.382 55.000 0.00 0.00 0.00 6.09
255 259 2.568090 GTGCGGCATTTGGGTCTG 59.432 61.111 5.72 0.00 0.00 3.51
296 303 1.596934 CCGTGCCCTTCTTGCTCTA 59.403 57.895 0.00 0.00 0.00 2.43
297 304 0.179000 CCGTGCCCTTCTTGCTCTAT 59.821 55.000 0.00 0.00 0.00 1.98
418 442 0.835971 ACTTTGGGGTGGATTTGGGC 60.836 55.000 0.00 0.00 0.00 5.36
477 502 2.729028 ATGGTTGTTTATCCCCTCCG 57.271 50.000 0.00 0.00 0.00 4.63
525 550 9.444600 TCCCTTTATAAATGAGGCGAAATATAC 57.555 33.333 0.00 0.00 0.00 1.47
527 552 9.226606 CCTTTATAAATGAGGCGAAATATACCA 57.773 33.333 0.00 0.00 0.00 3.25
534 559 9.744468 AAATGAGGCGAAATATACCAAAAATAC 57.256 29.630 0.00 0.00 0.00 1.89
535 560 8.691661 ATGAGGCGAAATATACCAAAAATACT 57.308 30.769 0.00 0.00 0.00 2.12
536 561 8.514330 TGAGGCGAAATATACCAAAAATACTT 57.486 30.769 0.00 0.00 0.00 2.24
537 562 8.402472 TGAGGCGAAATATACCAAAAATACTTG 58.598 33.333 0.00 0.00 0.00 3.16
538 563 8.288689 AGGCGAAATATACCAAAAATACTTGT 57.711 30.769 0.00 0.00 0.00 3.16
539 564 8.745590 AGGCGAAATATACCAAAAATACTTGTT 58.254 29.630 0.00 0.00 0.00 2.83
540 565 9.361315 GGCGAAATATACCAAAAATACTTGTTT 57.639 29.630 0.00 0.00 0.00 2.83
584 609 3.709587 AGAAGACGAATAACCCTCTGGA 58.290 45.455 0.00 0.00 34.81 3.86
587 612 2.103263 AGACGAATAACCCTCTGGATGC 59.897 50.000 0.00 0.00 34.81 3.91
615 641 0.036875 GGAGCAACACCCAGCTACTT 59.963 55.000 0.00 0.00 42.04 2.24
616 642 1.545651 GGAGCAACACCCAGCTACTTT 60.546 52.381 0.00 0.00 42.04 2.66
617 643 1.537202 GAGCAACACCCAGCTACTTTG 59.463 52.381 0.00 0.00 42.04 2.77
619 645 1.001378 GCAACACCCAGCTACTTTGTG 60.001 52.381 0.00 0.00 0.00 3.33
620 646 2.297701 CAACACCCAGCTACTTTGTGT 58.702 47.619 0.00 0.00 41.61 3.72
621 647 2.256117 ACACCCAGCTACTTTGTGTC 57.744 50.000 0.00 0.00 35.36 3.67
626 656 1.195448 CCAGCTACTTTGTGTCTTGCG 59.805 52.381 0.00 0.00 0.00 4.85
638 692 4.820897 TGTGTCTTGCGTATCTTCTGAAT 58.179 39.130 0.00 0.00 0.00 2.57
653 707 3.778265 TCTGAATGGGAAAAGGGAAAGG 58.222 45.455 0.00 0.00 0.00 3.11
655 709 4.045846 TCTGAATGGGAAAAGGGAAAGGAT 59.954 41.667 0.00 0.00 0.00 3.24
680 792 6.710597 AGATTCATGCTGATGCTTGTTAAT 57.289 33.333 0.00 0.00 42.66 1.40
734 855 5.292101 CCAAGACTGAAACTGTATTCCGATC 59.708 44.000 0.00 0.00 0.00 3.69
761 882 3.999001 TGTTGTGCAATGAGAGAGCTAAG 59.001 43.478 0.00 0.00 0.00 2.18
762 883 2.625737 TGTGCAATGAGAGAGCTAAGC 58.374 47.619 0.00 0.00 0.00 3.09
763 884 2.027837 TGTGCAATGAGAGAGCTAAGCA 60.028 45.455 0.00 0.00 0.00 3.91
765 886 3.002451 GTGCAATGAGAGAGCTAAGCATG 59.998 47.826 0.00 0.00 32.98 4.06
767 888 3.806380 CAATGAGAGAGCTAAGCATGGT 58.194 45.455 0.00 0.00 0.00 3.55
769 890 1.483827 TGAGAGAGCTAAGCATGGTGG 59.516 52.381 0.00 0.00 0.00 4.61
772 893 2.697751 AGAGAGCTAAGCATGGTGGTAG 59.302 50.000 0.00 0.00 0.00 3.18
773 894 2.432510 GAGAGCTAAGCATGGTGGTAGT 59.567 50.000 0.00 0.00 0.00 2.73
774 895 3.637229 GAGAGCTAAGCATGGTGGTAGTA 59.363 47.826 0.00 0.00 0.00 1.82
775 896 3.385111 AGAGCTAAGCATGGTGGTAGTAC 59.615 47.826 0.00 0.00 0.00 2.73
776 897 3.104512 AGCTAAGCATGGTGGTAGTACA 58.895 45.455 0.00 0.00 0.00 2.90
777 898 3.118738 AGCTAAGCATGGTGGTAGTACAC 60.119 47.826 0.00 0.00 40.60 2.90
815 946 2.464459 GGTTCGGCTCCGCATCTTG 61.464 63.158 2.96 0.00 39.59 3.02
819 950 1.153647 CGGCTCCGCATCTTGTACA 60.154 57.895 0.00 0.00 0.00 2.90
831 962 2.390938 TCTTGTACAAGAACAGACGCG 58.609 47.619 31.26 3.53 43.79 6.01
835 966 0.666274 TACAAGAACAGACGCGGCTG 60.666 55.000 39.33 39.33 41.63 4.85
836 967 3.044305 AAGAACAGACGCGGCTGC 61.044 61.111 40.72 25.79 39.51 5.25
846 977 2.427410 GCGGCTGCGAGTTTTGTG 60.427 61.111 0.00 0.00 0.00 3.33
847 978 2.427410 CGGCTGCGAGTTTTGTGC 60.427 61.111 0.00 0.00 0.00 4.57
848 979 2.721231 GGCTGCGAGTTTTGTGCA 59.279 55.556 0.00 0.00 37.07 4.57
851 982 3.507290 TGCGAGTTTTGTGCAGCA 58.493 50.000 0.00 0.00 34.03 4.41
852 983 1.805910 TGCGAGTTTTGTGCAGCAA 59.194 47.368 0.00 0.00 34.03 3.91
855 986 1.746760 CGAGTTTTGTGCAGCAACTC 58.253 50.000 17.22 17.22 42.02 3.01
859 990 4.531332 GAGTTTTGTGCAGCAACTCTAAG 58.469 43.478 18.89 0.00 42.13 2.18
866 998 0.615331 CAGCAACTCTAAGCCTGGGA 59.385 55.000 0.00 0.00 0.00 4.37
885 1017 3.309193 GGGAAAAATACCTCCAGCCTTCT 60.309 47.826 0.00 0.00 32.95 2.85
887 1019 4.158579 GGAAAAATACCTCCAGCCTTCTTG 59.841 45.833 0.00 0.00 0.00 3.02
888 1020 2.426842 AATACCTCCAGCCTTCTTGC 57.573 50.000 0.00 0.00 0.00 4.01
912 1090 7.025963 GCATTGAACTAGGATCAACTTTCTTG 58.974 38.462 13.48 9.16 39.43 3.02
979 1163 5.811399 TTACCAACAACTGTTCTGTCTTG 57.189 39.130 0.00 0.00 35.83 3.02
998 1182 6.015772 TGTCTTGTACAGTACTTATGTCTGCA 60.016 38.462 12.07 0.00 33.01 4.41
1015 1199 3.131755 TCTGCACATGGAGTCATCTACAG 59.868 47.826 0.00 0.00 38.00 2.74
1040 1224 1.746615 CCGGTGACAAGCATCTGGG 60.747 63.158 0.00 0.00 0.00 4.45
1092 1276 3.619979 CGCAGTCAAAGAAAGGGGATACT 60.620 47.826 0.00 0.00 0.00 2.12
1478 1963 4.141287 CAAACATGTACAGGTTTCCCAGA 58.859 43.478 29.97 0.00 42.49 3.86
1487 1972 4.207955 ACAGGTTTCCCAGAAACTTTCTC 58.792 43.478 17.14 3.55 38.11 2.87
1488 1973 4.207165 CAGGTTTCCCAGAAACTTTCTCA 58.793 43.478 17.14 0.00 38.11 3.27
1489 1974 4.644685 CAGGTTTCCCAGAAACTTTCTCAA 59.355 41.667 17.14 0.00 38.11 3.02
1490 1975 5.127031 CAGGTTTCCCAGAAACTTTCTCAAA 59.873 40.000 17.14 0.00 38.11 2.69
1491 1976 5.719563 AGGTTTCCCAGAAACTTTCTCAAAA 59.280 36.000 17.14 0.97 38.11 2.44
1492 1977 6.384015 AGGTTTCCCAGAAACTTTCTCAAAAT 59.616 34.615 17.14 0.00 38.11 1.82
1493 1978 6.701841 GGTTTCCCAGAAACTTTCTCAAAATC 59.298 38.462 17.14 0.63 38.11 2.17
1494 1979 7.417911 GGTTTCCCAGAAACTTTCTCAAAATCT 60.418 37.037 17.14 0.00 38.11 2.40
1560 2056 2.450476 GTGGGAGGAATCAGCACAATT 58.550 47.619 0.00 0.00 0.00 2.32
1611 2107 4.985538 TGTTTAATCTGGACTTCAGGCTT 58.014 39.130 0.00 0.00 43.53 4.35
1668 2166 0.403271 AGCTGGAGAAACATGCACCT 59.597 50.000 0.00 0.00 0.00 4.00
1859 2357 2.543848 GGCCTAAAGTTTTGCAAAGCAC 59.456 45.455 25.16 15.89 38.71 4.40
1948 2446 2.651455 GGGGTGTTTGATTAGTAGGGC 58.349 52.381 0.00 0.00 0.00 5.19
1951 2449 4.341487 GGGTGTTTGATTAGTAGGGCTTT 58.659 43.478 0.00 0.00 0.00 3.51
1958 2456 8.325787 TGTTTGATTAGTAGGGCTTTGATTCTA 58.674 33.333 0.00 0.00 0.00 2.10
1959 2457 8.613482 GTTTGATTAGTAGGGCTTTGATTCTAC 58.387 37.037 0.00 0.00 34.08 2.59
1960 2458 7.676683 TGATTAGTAGGGCTTTGATTCTACT 57.323 36.000 0.00 0.00 43.13 2.57
1961 2459 7.727181 TGATTAGTAGGGCTTTGATTCTACTC 58.273 38.462 5.30 0.00 41.54 2.59
1962 2460 6.481434 TTAGTAGGGCTTTGATTCTACTCC 57.519 41.667 5.30 0.00 41.54 3.85
1963 2461 3.712218 AGTAGGGCTTTGATTCTACTCCC 59.288 47.826 0.00 0.00 38.28 4.30
1964 2462 2.852130 AGGGCTTTGATTCTACTCCCT 58.148 47.619 0.00 0.00 37.77 4.20
1965 2463 2.774809 AGGGCTTTGATTCTACTCCCTC 59.225 50.000 0.00 0.00 38.13 4.30
1966 2464 2.774809 GGGCTTTGATTCTACTCCCTCT 59.225 50.000 0.00 0.00 0.00 3.69
1967 2465 3.432890 GGGCTTTGATTCTACTCCCTCTG 60.433 52.174 0.00 0.00 0.00 3.35
1968 2466 3.198853 GGCTTTGATTCTACTCCCTCTGT 59.801 47.826 0.00 0.00 0.00 3.41
1969 2467 4.406003 GGCTTTGATTCTACTCCCTCTGTA 59.594 45.833 0.00 0.00 0.00 2.74
1970 2468 5.104900 GGCTTTGATTCTACTCCCTCTGTAA 60.105 44.000 0.00 0.00 0.00 2.41
1971 2469 6.407202 GCTTTGATTCTACTCCCTCTGTAAA 58.593 40.000 0.00 0.00 0.00 2.01
1972 2470 6.536941 GCTTTGATTCTACTCCCTCTGTAAAG 59.463 42.308 0.00 0.00 0.00 1.85
1973 2471 7.554959 TTTGATTCTACTCCCTCTGTAAAGT 57.445 36.000 0.00 0.00 0.00 2.66
1974 2472 8.660295 TTTGATTCTACTCCCTCTGTAAAGTA 57.340 34.615 0.00 0.00 0.00 2.24
1975 2473 7.883391 TGATTCTACTCCCTCTGTAAAGTAG 57.117 40.000 0.00 0.00 41.56 2.57
1976 2474 7.640313 TGATTCTACTCCCTCTGTAAAGTAGA 58.360 38.462 6.93 6.93 45.12 2.59
1977 2475 8.282982 TGATTCTACTCCCTCTGTAAAGTAGAT 58.717 37.037 10.83 3.62 45.71 1.98
1978 2476 7.883391 TTCTACTCCCTCTGTAAAGTAGATG 57.117 40.000 10.83 0.00 45.71 2.90
1979 2477 7.209340 TCTACTCCCTCTGTAAAGTAGATGA 57.791 40.000 6.93 0.00 43.12 2.92
1980 2478 7.817440 TCTACTCCCTCTGTAAAGTAGATGAT 58.183 38.462 6.93 0.00 43.12 2.45
1981 2479 6.969993 ACTCCCTCTGTAAAGTAGATGATC 57.030 41.667 0.00 0.00 0.00 2.92
1982 2480 6.678547 ACTCCCTCTGTAAAGTAGATGATCT 58.321 40.000 0.00 0.00 0.00 2.75
1983 2481 7.817440 ACTCCCTCTGTAAAGTAGATGATCTA 58.183 38.462 0.00 0.00 0.00 1.98
1984 2482 8.282982 ACTCCCTCTGTAAAGTAGATGATCTAA 58.717 37.037 3.31 0.00 29.58 2.10
1985 2483 9.137459 CTCCCTCTGTAAAGTAGATGATCTAAA 57.863 37.037 3.31 0.00 29.58 1.85
1986 2484 8.915036 TCCCTCTGTAAAGTAGATGATCTAAAC 58.085 37.037 3.31 0.00 29.58 2.01
1987 2485 7.863375 CCCTCTGTAAAGTAGATGATCTAAACG 59.137 40.741 3.31 0.00 29.58 3.60
1988 2486 8.622157 CCTCTGTAAAGTAGATGATCTAAACGA 58.378 37.037 3.31 3.16 29.58 3.85
2010 2508 9.765795 AACGATCTTATATTTCTTTACAGAGGG 57.234 33.333 0.00 0.00 0.00 4.30
2011 2509 9.144298 ACGATCTTATATTTCTTTACAGAGGGA 57.856 33.333 0.00 0.00 0.00 4.20
2012 2510 9.632807 CGATCTTATATTTCTTTACAGAGGGAG 57.367 37.037 0.00 0.00 0.00 4.30
2073 2571 8.055402 CCACTTTGTTTAAAATGTTCACAATCG 58.945 33.333 0.00 0.00 0.00 3.34
2101 2599 4.499696 GGGAAACAACAGGTCTGAACATTG 60.500 45.833 4.84 7.84 0.00 2.82
2106 2604 4.889409 ACAACAGGTCTGAACATTGTTCAT 59.111 37.500 27.55 13.66 34.46 2.57
2155 2691 1.156736 CCGGTTCTGTTGCCAAGTAG 58.843 55.000 0.00 0.00 0.00 2.57
2176 2712 2.358957 CCTGTCGGCAAAGATGAATCA 58.641 47.619 0.00 0.00 0.00 2.57
2177 2713 2.749076 CCTGTCGGCAAAGATGAATCAA 59.251 45.455 0.00 0.00 0.00 2.57
2179 2715 2.749076 TGTCGGCAAAGATGAATCAAGG 59.251 45.455 0.00 0.00 0.00 3.61
2201 2737 4.766891 GGTTTTCCAAGATCTGTGAATGGA 59.233 41.667 8.71 8.71 38.36 3.41
2208 2746 4.897509 AGATCTGTGAATGGACTGTTCA 57.102 40.909 0.00 0.00 33.46 3.18
2214 2752 4.326826 TGTGAATGGACTGTTCATTCTCC 58.673 43.478 31.45 24.19 46.26 3.71
2215 2753 4.202451 TGTGAATGGACTGTTCATTCTCCA 60.202 41.667 31.45 25.81 46.26 3.86
2319 2857 6.687081 AAACGAATTACTTTCCTGAACACA 57.313 33.333 0.00 0.00 0.00 3.72
2324 2862 6.565999 CGAATTACTTTCCTGAACACAAGACC 60.566 42.308 0.00 0.00 0.00 3.85
2336 2874 3.154710 ACACAAGACCATGACTACGAGA 58.845 45.455 0.00 0.00 0.00 4.04
2342 2880 4.274147 AGACCATGACTACGAGAGACATT 58.726 43.478 0.00 0.00 38.32 2.71
2368 2906 1.267806 AGCATGAAAACAGAGCCAACG 59.732 47.619 0.00 0.00 0.00 4.10
2387 2925 0.654683 GCCTCAGATGCACATTCGAC 59.345 55.000 0.00 0.00 0.00 4.20
2415 2953 7.173735 CAGAATATTTGAGTGGTGCAGCATATA 59.826 37.037 23.18 14.09 0.00 0.86
2440 2978 5.801350 TCGAAACAGATGCTATGAAAAGG 57.199 39.130 0.00 0.00 0.00 3.11
2446 2984 3.314635 CAGATGCTATGAAAAGGCTGGAC 59.685 47.826 0.00 0.00 0.00 4.02
2508 3054 8.840833 TTTGTTATCTGTAAGTAACATGAGCA 57.159 30.769 0.00 0.00 38.89 4.26
2527 3073 6.489603 TGAGCAAATTAGTTTTATGAGGGGA 58.510 36.000 0.00 0.00 0.00 4.81
2531 3078 7.340487 AGCAAATTAGTTTTATGAGGGGAAGAG 59.660 37.037 0.00 0.00 0.00 2.85
2540 3087 1.127343 GAGGGGAAGAGACCATCCAG 58.873 60.000 0.00 0.00 37.46 3.86
2547 3094 3.366396 GAAGAGACCATCCAGACTGGTA 58.634 50.000 21.06 8.59 46.95 3.25
2556 3103 5.222130 ACCATCCAGACTGGTATTTTTCTGT 60.222 40.000 21.06 4.55 45.17 3.41
2557 3104 5.355350 CCATCCAGACTGGTATTTTTCTGTC 59.645 44.000 21.06 0.00 39.03 3.51
2558 3105 5.825593 TCCAGACTGGTATTTTTCTGTCT 57.174 39.130 21.06 0.00 40.94 3.41
2589 3144 7.349711 TCAGCTTTAAATTTCTGTACGTGTTC 58.650 34.615 0.00 0.00 0.00 3.18
2629 3184 9.813446 CAAACGTTATCCCTTAATTAGACTAGT 57.187 33.333 0.00 0.00 0.00 2.57
2660 3215 3.695830 TCTGGGCAGTCGTAAAGAAAT 57.304 42.857 0.00 0.00 0.00 2.17
2676 3231 8.883731 CGTAAAGAAATCCACAATTCTAGTCAT 58.116 33.333 0.00 0.00 34.90 3.06
2680 3235 6.541641 AGAAATCCACAATTCTAGTCATGAGC 59.458 38.462 0.00 0.00 34.24 4.26
2726 3281 5.590663 CCTCCGATCCATATTAATCGAGAGA 59.409 44.000 21.35 11.36 45.83 3.10
2729 3284 5.221145 CCGATCCATATTAATCGAGAGAGGG 60.221 48.000 14.96 0.00 45.83 4.30
2730 3285 5.221145 CGATCCATATTAATCGAGAGAGGGG 60.221 48.000 9.80 0.00 45.83 4.79
2731 3286 7.359436 CGATCCATATTAATCGAGAGAGGGGA 61.359 46.154 9.80 0.00 45.83 4.81
2732 3287 8.608255 CGATCCATATTAATCGAGAGAGGGGAT 61.608 44.444 9.80 0.00 45.83 3.85
2762 3317 4.524328 ACAATTTAGGTGCAAGGAAAGGAG 59.476 41.667 0.00 0.00 0.00 3.69
2793 3349 6.840780 ATTCCTATGTTTTTCCTCCACTTG 57.159 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.007398 TCTTCTTCTTCAGGGTTGAGCTC 59.993 47.826 6.82 6.82 34.15 4.09
92 93 3.556038 TTGAGCTCGGGGGAAGGGA 62.556 63.158 9.64 0.00 0.00 4.20
131 132 5.083821 GGAGAGGCTTGGTAGATAGAGATT 58.916 45.833 0.00 0.00 0.00 2.40
176 177 5.126384 GTGCAACTTGAGATCTAGGAGTACT 59.874 44.000 0.00 0.00 0.00 2.73
223 226 2.892640 CACCTAGCTGCGCAGGTA 59.107 61.111 38.19 38.19 37.74 3.08
224 227 4.767255 GCACCTAGCTGCGCAGGT 62.767 66.667 39.99 39.99 39.37 4.00
231 234 1.430632 CAAATGCCGCACCTAGCTG 59.569 57.895 0.00 0.00 42.61 4.24
270 277 1.377202 GAAGGGCACGGCAGATTGA 60.377 57.895 0.00 0.00 0.00 2.57
342 358 0.673644 AGATTTGTGCTTCCCCGACG 60.674 55.000 0.00 0.00 0.00 5.12
355 371 2.202518 CGCGGGCAAGCAGATTTG 60.203 61.111 0.00 0.00 36.85 2.32
375 391 2.124983 CACACCGCCCCATCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
427 451 2.550180 GCAAGAAACACTCCTTCCTGAC 59.450 50.000 0.00 0.00 0.00 3.51
477 502 5.279306 GGAAATCCTAAACCCTCAACCAAAC 60.279 44.000 0.00 0.00 0.00 2.93
552 577 9.117183 GGGTTATTCGTCTTCTATTTTTGGTAT 57.883 33.333 0.00 0.00 0.00 2.73
569 594 1.543429 GGGCATCCAGAGGGTTATTCG 60.543 57.143 0.00 0.00 34.93 3.34
615 641 4.251543 TCAGAAGATACGCAAGACACAA 57.748 40.909 0.00 0.00 43.62 3.33
616 642 3.934457 TCAGAAGATACGCAAGACACA 57.066 42.857 0.00 0.00 43.62 3.72
617 643 4.033358 CCATTCAGAAGATACGCAAGACAC 59.967 45.833 0.00 0.00 43.62 3.67
619 645 3.557595 CCCATTCAGAAGATACGCAAGAC 59.442 47.826 0.00 0.00 43.62 3.01
620 646 3.450817 TCCCATTCAGAAGATACGCAAGA 59.549 43.478 0.00 0.00 43.62 3.02
626 656 5.755849 TCCCTTTTCCCATTCAGAAGATAC 58.244 41.667 0.00 0.00 0.00 2.24
638 692 5.813965 ATCTAATCCTTTCCCTTTTCCCA 57.186 39.130 0.00 0.00 0.00 4.37
680 792 3.243873 TGCACCAAAACACACACAAGAAA 60.244 39.130 0.00 0.00 0.00 2.52
717 837 6.873997 ACATACTGATCGGAATACAGTTTCA 58.126 36.000 9.00 4.80 43.27 2.69
734 855 4.201792 GCTCTCTCATTGCACAACATACTG 60.202 45.833 0.00 0.00 0.00 2.74
769 890 1.402456 CGTGAGGCAGTGGTGTACTAC 60.402 57.143 0.00 0.00 37.60 2.73
772 893 4.261888 CGTGAGGCAGTGGTGTAC 57.738 61.111 0.00 0.00 0.00 2.90
785 906 0.672401 GCCGAACCAAGATTCCGTGA 60.672 55.000 0.00 0.00 0.00 4.35
786 907 0.673644 AGCCGAACCAAGATTCCGTG 60.674 55.000 0.00 0.00 0.00 4.94
815 946 0.666577 AGCCGCGTCTGTTCTTGTAC 60.667 55.000 4.92 0.00 0.00 2.90
819 950 3.044305 GCAGCCGCGTCTGTTCTT 61.044 61.111 19.32 0.00 36.49 2.52
831 962 1.370900 CTGCACAAAACTCGCAGCC 60.371 57.895 0.00 0.00 45.85 4.85
835 966 0.248621 AGTTGCTGCACAAAACTCGC 60.249 50.000 0.00 0.00 40.82 5.03
836 967 1.746760 GAGTTGCTGCACAAAACTCG 58.253 50.000 14.34 0.00 40.13 4.18
845 976 0.321919 CCAGGCTTAGAGTTGCTGCA 60.322 55.000 0.00 0.00 0.00 4.41
846 977 1.028868 CCCAGGCTTAGAGTTGCTGC 61.029 60.000 0.00 0.00 0.00 5.25
847 978 0.615331 TCCCAGGCTTAGAGTTGCTG 59.385 55.000 0.00 0.00 0.00 4.41
848 979 1.362224 TTCCCAGGCTTAGAGTTGCT 58.638 50.000 0.00 0.00 0.00 3.91
849 980 2.200373 TTTCCCAGGCTTAGAGTTGC 57.800 50.000 0.00 0.00 0.00 4.17
850 981 5.125578 GGTATTTTTCCCAGGCTTAGAGTTG 59.874 44.000 0.00 0.00 0.00 3.16
851 982 5.015284 AGGTATTTTTCCCAGGCTTAGAGTT 59.985 40.000 0.00 0.00 0.00 3.01
852 983 4.540502 AGGTATTTTTCCCAGGCTTAGAGT 59.459 41.667 0.00 0.00 0.00 3.24
855 986 4.207955 GGAGGTATTTTTCCCAGGCTTAG 58.792 47.826 0.00 0.00 0.00 2.18
859 990 2.379005 CTGGAGGTATTTTTCCCAGGC 58.621 52.381 0.00 0.00 40.39 4.85
866 998 3.511540 GCAAGAAGGCTGGAGGTATTTTT 59.488 43.478 0.00 0.00 0.00 1.94
885 1017 6.716628 AGAAAGTTGATCCTAGTTCAATGCAA 59.283 34.615 8.19 0.00 35.68 4.08
887 1019 6.749923 AGAAAGTTGATCCTAGTTCAATGC 57.250 37.500 8.19 0.00 35.68 3.56
888 1020 8.019669 CACAAGAAAGTTGATCCTAGTTCAATG 58.980 37.037 8.19 5.06 35.68 2.82
912 1090 5.705905 AGTAGATACTTTGAAGGTTTGGCAC 59.294 40.000 0.00 0.00 31.13 5.01
961 1141 5.794687 TGTACAAGACAGAACAGTTGTTG 57.205 39.130 1.62 0.00 33.61 3.33
974 1154 6.308282 GTGCAGACATAAGTACTGTACAAGAC 59.692 42.308 19.27 0.00 43.15 3.01
979 1163 5.520288 CCATGTGCAGACATAAGTACTGTAC 59.480 44.000 9.93 9.93 41.12 2.90
998 1182 3.369175 TCAGCTGTAGATGACTCCATGT 58.631 45.455 14.67 0.00 35.30 3.21
1015 1199 3.044059 GCTTGTCACCGGCATCAGC 62.044 63.158 0.00 0.00 41.10 4.26
1040 1224 0.912486 ACCCAATGTCAGGTAGCTCC 59.088 55.000 0.00 0.00 33.52 4.70
1092 1276 3.735591 CGACAGGACCTTTGGAAACTTA 58.264 45.455 0.00 0.00 0.00 2.24
1478 1963 8.365647 AGATGCATTGAGATTTTGAGAAAGTTT 58.634 29.630 0.00 0.00 0.00 2.66
1560 2056 2.032675 CAGCTCGAGACGATTCATCTCA 59.967 50.000 18.75 0.00 42.39 3.27
1611 2107 5.105473 CCCGAATGTCTCTAGGTTCACTTTA 60.105 44.000 0.00 0.00 0.00 1.85
1668 2166 0.676184 GCAGTCTCTCTGGTGACACA 59.324 55.000 8.08 0.00 43.78 3.72
1748 2246 1.702299 CAAAACTCGTCGGCGCTAG 59.298 57.895 3.52 0.00 38.14 3.42
1859 2357 8.425577 AAAGAATTATCAGTAATCAGGTCACG 57.574 34.615 0.00 0.00 30.28 4.35
1902 2400 7.487189 CCAGAACAACTTAATGCAATCTGAATC 59.513 37.037 0.00 0.00 33.85 2.52
1948 2446 7.616313 ACTTTACAGAGGGAGTAGAATCAAAG 58.384 38.462 0.00 0.00 0.00 2.77
1951 2449 7.640313 TCTACTTTACAGAGGGAGTAGAATCA 58.360 38.462 9.04 0.00 44.40 2.57
1958 2456 6.678547 AGATCATCTACTTTACAGAGGGAGT 58.321 40.000 0.00 0.00 0.00 3.85
1959 2457 8.698973 TTAGATCATCTACTTTACAGAGGGAG 57.301 38.462 0.00 0.00 0.00 4.30
1960 2458 8.915036 GTTTAGATCATCTACTTTACAGAGGGA 58.085 37.037 0.00 0.00 0.00 4.20
1961 2459 7.863375 CGTTTAGATCATCTACTTTACAGAGGG 59.137 40.741 0.00 0.00 0.00 4.30
1962 2460 8.622157 TCGTTTAGATCATCTACTTTACAGAGG 58.378 37.037 0.00 0.00 0.00 3.69
1984 2482 9.765795 CCCTCTGTAAAGAAATATAAGATCGTT 57.234 33.333 0.00 0.00 0.00 3.85
1985 2483 9.144298 TCCCTCTGTAAAGAAATATAAGATCGT 57.856 33.333 0.00 0.00 0.00 3.73
1986 2484 9.632807 CTCCCTCTGTAAAGAAATATAAGATCG 57.367 37.037 0.00 0.00 0.00 3.69
1997 2495 9.939802 GAAGTAAAATACTCCCTCTGTAAAGAA 57.060 33.333 0.00 0.00 38.26 2.52
1998 2496 9.322769 AGAAGTAAAATACTCCCTCTGTAAAGA 57.677 33.333 0.00 0.00 38.26 2.52
1999 2497 9.372369 CAGAAGTAAAATACTCCCTCTGTAAAG 57.628 37.037 8.53 0.00 36.84 1.85
2000 2498 8.877195 ACAGAAGTAAAATACTCCCTCTGTAAA 58.123 33.333 16.17 0.00 45.44 2.01
2001 2499 8.431910 ACAGAAGTAAAATACTCCCTCTGTAA 57.568 34.615 16.17 0.00 45.44 2.41
2002 2500 9.537852 TTACAGAAGTAAAATACTCCCTCTGTA 57.462 33.333 18.00 18.00 45.44 2.74
2003 2501 6.936968 ACAGAAGTAAAATACTCCCTCTGT 57.063 37.500 13.62 13.62 43.89 3.41
2004 2502 8.311836 TGTTACAGAAGTAAAATACTCCCTCTG 58.688 37.037 12.71 12.71 42.59 3.35
2005 2503 8.312564 GTGTTACAGAAGTAAAATACTCCCTCT 58.687 37.037 0.00 0.00 41.58 3.69
2006 2504 8.312564 AGTGTTACAGAAGTAAAATACTCCCTC 58.687 37.037 0.00 0.00 41.58 4.30
2007 2505 8.095169 CAGTGTTACAGAAGTAAAATACTCCCT 58.905 37.037 0.00 0.00 41.58 4.20
2008 2506 7.876582 ACAGTGTTACAGAAGTAAAATACTCCC 59.123 37.037 0.00 0.00 41.58 4.30
2009 2507 8.828688 ACAGTGTTACAGAAGTAAAATACTCC 57.171 34.615 0.00 0.00 41.58 3.85
2101 2599 5.278169 GCATTGGATATCACAGGACATGAAC 60.278 44.000 4.83 0.00 0.00 3.18
2106 2604 2.485302 CGGCATTGGATATCACAGGACA 60.485 50.000 4.83 0.00 0.00 4.02
2165 2701 7.601705 TCTTGGAAAACCTTGATTCATCTTT 57.398 32.000 0.00 0.00 0.00 2.52
2176 2712 5.244626 CCATTCACAGATCTTGGAAAACCTT 59.755 40.000 4.60 0.00 0.00 3.50
2177 2713 4.768968 CCATTCACAGATCTTGGAAAACCT 59.231 41.667 4.60 0.00 0.00 3.50
2179 2715 5.474876 AGTCCATTCACAGATCTTGGAAAAC 59.525 40.000 13.50 10.03 38.16 2.43
2201 2737 4.232188 AGATGCATGGAGAATGAACAGT 57.768 40.909 2.46 0.00 38.72 3.55
2208 2746 5.765677 CAGAATCAGAAGATGCATGGAGAAT 59.234 40.000 2.46 0.00 31.60 2.40
2214 2752 6.127980 ACTCAAACAGAATCAGAAGATGCATG 60.128 38.462 2.46 0.00 31.60 4.06
2215 2753 5.944599 ACTCAAACAGAATCAGAAGATGCAT 59.055 36.000 0.00 0.00 31.60 3.96
2319 2857 3.687125 TGTCTCTCGTAGTCATGGTCTT 58.313 45.455 0.00 0.00 0.00 3.01
2324 2862 3.119291 GGCAATGTCTCTCGTAGTCATG 58.881 50.000 0.00 0.00 34.69 3.07
2368 2906 0.654683 GTCGAATGTGCATCTGAGGC 59.345 55.000 7.45 7.45 0.00 4.70
2387 2925 4.201891 GCTGCACCACTCAAATATTCTGAG 60.202 45.833 18.31 18.31 44.90 3.35
2404 2942 6.048073 TCTGTTTCGAATTATATGCTGCAC 57.952 37.500 3.57 0.00 0.00 4.57
2407 2945 6.895898 AGCATCTGTTTCGAATTATATGCTG 58.104 36.000 25.24 9.19 45.11 4.41
2415 2953 7.253422 CCTTTTCATAGCATCTGTTTCGAATT 58.747 34.615 0.00 0.00 0.00 2.17
2446 2984 1.529010 TGTTGAAGCTGCAGGTGGG 60.529 57.895 20.97 0.00 0.00 4.61
2504 3050 7.339466 TCTTCCCCTCATAAAACTAATTTGCTC 59.661 37.037 0.00 0.00 32.27 4.26
2508 3054 7.834681 GGTCTCTTCCCCTCATAAAACTAATTT 59.165 37.037 0.00 0.00 34.92 1.82
2540 3087 8.035394 TGAGTATCAGACAGAAAAATACCAGTC 58.965 37.037 0.00 0.00 42.56 3.51
2559 3106 8.870879 ACGTACAGAAATTTAAAGCTGAGTATC 58.129 33.333 17.34 6.43 32.86 2.24
2560 3107 8.656849 CACGTACAGAAATTTAAAGCTGAGTAT 58.343 33.333 17.34 3.50 32.86 2.12
2561 3108 7.654520 ACACGTACAGAAATTTAAAGCTGAGTA 59.345 33.333 17.34 5.80 32.86 2.59
2562 3109 6.482308 ACACGTACAGAAATTTAAAGCTGAGT 59.518 34.615 17.34 12.41 32.86 3.41
2563 3110 6.888430 ACACGTACAGAAATTTAAAGCTGAG 58.112 36.000 17.34 11.99 32.86 3.35
2583 3138 1.374758 GGACTGCCCAGAGAACACG 60.375 63.158 1.69 0.00 34.14 4.49
2589 3144 0.671781 CGTTTGAGGACTGCCCAGAG 60.672 60.000 1.69 0.00 37.41 3.35
2628 3183 4.393680 CGACTGCCCAGATATCTACTCTAC 59.606 50.000 4.54 0.00 0.00 2.59
2629 3184 4.041815 ACGACTGCCCAGATATCTACTCTA 59.958 45.833 4.54 0.00 0.00 2.43
2635 3190 4.215908 TCTTTACGACTGCCCAGATATCT 58.784 43.478 0.00 0.00 0.00 1.98
2660 3215 3.430790 CCGCTCATGACTAGAATTGTGGA 60.431 47.826 0.00 0.00 0.00 4.02
2676 3231 7.279313 GGAGTAGTTAATTTTACAATCCGCTCA 59.721 37.037 0.00 0.00 0.00 4.26
2680 3235 7.226128 GGAGGGAGTAGTTAATTTTACAATCCG 59.774 40.741 0.00 0.00 0.00 4.18
2732 3287 6.535540 TCCTTGCACCTAAATTGTAGTACAA 58.464 36.000 17.74 17.74 42.95 2.41
2746 3301 3.181429 TGAATTCTCCTTTCCTTGCACCT 60.181 43.478 7.05 0.00 0.00 4.00
2747 3302 3.157087 TGAATTCTCCTTTCCTTGCACC 58.843 45.455 7.05 0.00 0.00 5.01
2793 3349 7.875971 ACAAGTTGTTCTTTGATTCATAGGAC 58.124 34.615 1.64 8.22 33.63 3.85


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

AutoCloner maintained by Alex Coulton.