Multiple sequence alignment - TraesCS4B01G193700

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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 TraesCS4B01G193700 chr4B 100.000 3473 0 0 1 3473 416626532 416623060 0.000000e+00 6414
1 TraesCS4B01G193700 chr4D 91.147 2293 98 45 360 2614 337472300 337470075 0.000000e+00 3013
2 TraesCS4B01G193700 chr4D 85.590 805 54 22 2714 3471 337467026 337466237 0.000000e+00 787
3 TraesCS4B01G193700 chr4D 88.921 343 25 5 1 331 337472636 337472295 8.970000e-111 411
4 TraesCS4B01G193700 chr4D 95.238 84 4 0 2611 2694 337467097 337467014 2.170000e-27 134
5 TraesCS4B01G193700 chr4A 88.789 1891 111 23 683 2526 134550009 134551845 0.000000e+00 2224
6 TraesCS4B01G193700 chr4A 84.937 790 70 20 2714 3471 134553064 134553836 0.000000e+00 754
7 TraesCS4B01G193700 chr4A 86.977 645 46 18 1 626 134549372 134549997 0.000000e+00 691
8 TraesCS4B01G193700 chr4A 80.905 199 13 9 2519 2694 134552880 134553076 2.170000e-27 134


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 TraesCS4B01G193700 chr4B 416623060 416626532 3472 True 6414.00 6414 100.000 1 3473 1 chr4B.!!$R1 3472
1 TraesCS4B01G193700 chr4D 337466237 337472636 6399 True 1086.25 3013 90.224 1 3471 4 chr4D.!!$R1 3470
2 TraesCS4B01G193700 chr4A 134549372 134553836 4464 False 950.75 2224 85.402 1 3471 4 chr4A.!!$F1 3470

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
228 240 0.036306 GGTTACCTGTGGACACCTGG 59.964 60.0 0.0 5.19 0.0 4.45 F
800 839 0.106116 AGTAAACCCGCACCCCAAAA 60.106 50.0 0.0 0.00 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1949 0.250209 CCTCCAGATGGCAATCGGAG 60.250 60.0 24.11 24.11 44.53 4.63 R
2487 2567 0.391793 GGGCTGCTGACCAACTAGTC 60.392 60.0 11.26 0.00 42.34 2.59 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
71 72 3.407698 GAGATCGAGCTCCAGATGAGTA 58.592 50.000 19.92 0.00 43.48 2.59
116 124 4.870363 TCTGTTTTTGTGCTGCTTTATCC 58.130 39.130 0.00 0.00 0.00 2.59
133 141 1.070445 CCATCCATCCTCTCGCCAC 59.930 63.158 0.00 0.00 0.00 5.01
156 168 0.180171 TTGGGGGCACGTCAGATATG 59.820 55.000 0.00 0.00 0.00 1.78
192 204 2.282887 GCCACACCCCGATTGGTT 60.283 61.111 0.00 0.00 36.12 3.67
207 219 0.960364 TGGTTTCTTGGATGCGAGCC 60.960 55.000 0.00 0.00 0.00 4.70
209 221 0.449388 GTTTCTTGGATGCGAGCCTG 59.551 55.000 0.00 0.00 0.00 4.85
215 227 1.523938 GGATGCGAGCCTGGTTACC 60.524 63.158 0.00 0.00 0.00 2.85
228 240 0.036306 GGTTACCTGTGGACACCTGG 59.964 60.000 0.00 5.19 0.00 4.45
239 251 2.871096 GACACCTGGGTCCAATACAA 57.129 50.000 0.00 0.00 0.00 2.41
289 301 2.047061 ACTGTACCAGTGCTCAAGGAA 58.953 47.619 0.00 0.00 43.63 3.36
292 304 4.286032 ACTGTACCAGTGCTCAAGGAAATA 59.714 41.667 0.00 0.00 43.63 1.40
303 315 6.587608 GTGCTCAAGGAAATACCAAGATTTTG 59.412 38.462 0.00 0.00 42.04 2.44
335 351 8.411318 ACTAGATCAAAAACTTTGCTTTTGTG 57.589 30.769 0.00 0.00 42.07 3.33
336 352 6.110543 AGATCAAAAACTTTGCTTTTGTGC 57.889 33.333 7.68 2.99 42.07 4.57
337 353 4.676849 TCAAAAACTTTGCTTTTGTGCC 57.323 36.364 7.68 0.00 42.07 5.01
338 354 4.067896 TCAAAAACTTTGCTTTTGTGCCA 58.932 34.783 7.68 0.00 42.07 4.92
339 355 4.083590 TCAAAAACTTTGCTTTTGTGCCAC 60.084 37.500 7.68 0.00 42.07 5.01
340 356 3.333029 AAACTTTGCTTTTGTGCCACT 57.667 38.095 0.00 0.00 0.00 4.00
341 357 3.333029 AACTTTGCTTTTGTGCCACTT 57.667 38.095 0.00 0.00 0.00 3.16
342 358 4.464069 AACTTTGCTTTTGTGCCACTTA 57.536 36.364 0.00 0.00 0.00 2.24
343 359 3.780902 ACTTTGCTTTTGTGCCACTTAC 58.219 40.909 0.00 0.00 0.00 2.34
369 389 3.061006 CGTCACAATTGTTTGCTTCAAGC 60.061 43.478 8.77 1.04 42.82 4.01
382 402 5.818136 TGCTTCAAGCCATGATAACTTAC 57.182 39.130 7.01 0.00 41.51 2.34
383 403 5.500234 TGCTTCAAGCCATGATAACTTACT 58.500 37.500 7.01 0.00 41.51 2.24
384 404 5.945784 TGCTTCAAGCCATGATAACTTACTT 59.054 36.000 7.01 0.00 41.51 2.24
385 405 7.109501 TGCTTCAAGCCATGATAACTTACTTA 58.890 34.615 7.01 0.00 41.51 2.24
392 415 7.048512 AGCCATGATAACTTACTTAACAGGAC 58.951 38.462 0.00 0.00 0.00 3.85
434 457 2.270257 GCAATGCAGTGCACCCTCA 61.270 57.895 32.30 9.49 43.04 3.86
451 474 2.797156 CCTCAACTATTCCTGATTCGCG 59.203 50.000 0.00 0.00 0.00 5.87
462 485 3.689161 TCCTGATTCGCGATGTTCAAATT 59.311 39.130 10.88 0.00 0.00 1.82
502 525 4.238669 TGACACCCATCCATCCATACATA 58.761 43.478 0.00 0.00 0.00 2.29
503 526 4.851540 TGACACCCATCCATCCATACATAT 59.148 41.667 0.00 0.00 0.00 1.78
504 527 5.045651 TGACACCCATCCATCCATACATATC 60.046 44.000 0.00 0.00 0.00 1.63
506 529 5.190528 ACACCCATCCATCCATACATATCTC 59.809 44.000 0.00 0.00 0.00 2.75
507 530 4.406972 ACCCATCCATCCATACATATCTCG 59.593 45.833 0.00 0.00 0.00 4.04
668 695 2.106857 GGAGAGAGGCCTACTGCTACTA 59.893 54.545 18.88 0.00 40.92 1.82
669 696 3.408634 GAGAGAGGCCTACTGCTACTAG 58.591 54.545 4.42 0.00 40.92 2.57
671 698 3.203487 AGAGAGGCCTACTGCTACTAGTT 59.797 47.826 4.42 0.00 40.92 2.24
673 700 3.053544 AGAGGCCTACTGCTACTAGTTGA 60.054 47.826 4.42 0.00 40.92 3.18
674 701 3.892588 GAGGCCTACTGCTACTAGTTGAT 59.107 47.826 4.42 0.00 40.92 2.57
675 702 4.290942 AGGCCTACTGCTACTAGTTGATT 58.709 43.478 1.29 0.00 40.92 2.57
676 703 4.342665 AGGCCTACTGCTACTAGTTGATTC 59.657 45.833 1.29 0.00 40.92 2.52
677 704 4.501743 GGCCTACTGCTACTAGTTGATTCC 60.502 50.000 8.60 0.00 40.92 3.01
679 706 4.896482 CCTACTGCTACTAGTTGATTCCCT 59.104 45.833 8.60 0.00 32.19 4.20
680 707 5.364157 CCTACTGCTACTAGTTGATTCCCTT 59.636 44.000 8.60 0.00 32.19 3.95
719 749 9.462606 GATATTATATGGAACCCGGAAAGAAAT 57.537 33.333 0.73 0.00 0.00 2.17
722 752 9.822727 ATTATATGGAACCCGGAAAGAAATATT 57.177 29.630 0.73 0.00 0.00 1.28
723 753 7.761038 ATATGGAACCCGGAAAGAAATATTC 57.239 36.000 0.73 0.00 0.00 1.75
792 831 0.671251 CTGCCAAAAGTAAACCCGCA 59.329 50.000 0.00 0.00 0.00 5.69
794 833 0.319211 GCCAAAAGTAAACCCGCACC 60.319 55.000 0.00 0.00 0.00 5.01
795 834 0.315886 CCAAAAGTAAACCCGCACCC 59.684 55.000 0.00 0.00 0.00 4.61
796 835 0.315886 CAAAAGTAAACCCGCACCCC 59.684 55.000 0.00 0.00 0.00 4.95
800 839 0.106116 AGTAAACCCGCACCCCAAAA 60.106 50.000 0.00 0.00 0.00 2.44
801 840 0.751452 GTAAACCCGCACCCCAAAAA 59.249 50.000 0.00 0.00 0.00 1.94
852 891 3.428452 CCACACCTATATATACGCCACCG 60.428 52.174 0.00 0.00 41.14 4.94
886 925 1.876156 CTTCTTGCAACTCCTCACACC 59.124 52.381 0.00 0.00 0.00 4.16
887 926 0.836606 TCTTGCAACTCCTCACACCA 59.163 50.000 0.00 0.00 0.00 4.17
888 927 1.421268 TCTTGCAACTCCTCACACCAT 59.579 47.619 0.00 0.00 0.00 3.55
889 928 1.808945 CTTGCAACTCCTCACACCATC 59.191 52.381 0.00 0.00 0.00 3.51
890 929 1.059098 TGCAACTCCTCACACCATCT 58.941 50.000 0.00 0.00 0.00 2.90
891 930 1.271001 TGCAACTCCTCACACCATCTG 60.271 52.381 0.00 0.00 0.00 2.90
892 931 1.446907 CAACTCCTCACACCATCTGC 58.553 55.000 0.00 0.00 0.00 4.26
893 932 1.002888 CAACTCCTCACACCATCTGCT 59.997 52.381 0.00 0.00 0.00 4.24
894 933 1.356124 ACTCCTCACACCATCTGCTT 58.644 50.000 0.00 0.00 0.00 3.91
895 934 1.277557 ACTCCTCACACCATCTGCTTC 59.722 52.381 0.00 0.00 0.00 3.86
896 935 1.554160 CTCCTCACACCATCTGCTTCT 59.446 52.381 0.00 0.00 0.00 2.85
897 936 1.277273 TCCTCACACCATCTGCTTCTG 59.723 52.381 0.00 0.00 0.00 3.02
910 949 0.744057 GCTTCTGCTTCTGCTCCTCC 60.744 60.000 0.00 0.00 40.48 4.30
937 976 0.904865 TTCACTCCTCACCTCCGCAT 60.905 55.000 0.00 0.00 0.00 4.73
978 1017 4.924625 AGCTCCTCTACTCTGTTTCACTA 58.075 43.478 0.00 0.00 0.00 2.74
985 1024 3.753294 ACTCTGTTTCACTACCCACTG 57.247 47.619 0.00 0.00 0.00 3.66
987 1026 2.632996 CTCTGTTTCACTACCCACTGGA 59.367 50.000 0.00 0.00 34.81 3.86
990 1029 0.682852 TTTCACTACCCACTGGACGG 59.317 55.000 0.00 0.00 34.81 4.79
1154 1204 2.202987 GATGGCGTGCCTGGAGAG 60.203 66.667 12.84 0.00 36.94 3.20
1168 1218 2.491693 CTGGAGAGCGAGATAAGGATCC 59.508 54.545 2.48 2.48 31.81 3.36
1175 1225 2.242926 CGAGATAAGGATCCTGAGGCA 58.757 52.381 17.02 0.00 31.81 4.75
1176 1226 2.830923 CGAGATAAGGATCCTGAGGCAT 59.169 50.000 17.02 0.00 31.81 4.40
1578 1628 4.034258 GCGTCCGACGTCTGGTCA 62.034 66.667 21.37 5.39 46.42 4.02
1581 1631 1.293963 CGTCCGACGTCTGGTCACTA 61.294 60.000 20.62 4.21 46.42 2.74
1613 1663 2.187163 GGAGCTGCTAACCGGGAC 59.813 66.667 6.32 0.00 0.00 4.46
1674 1724 3.200593 CTGCTGCTCCACATCGGC 61.201 66.667 0.00 0.00 35.26 5.54
1813 1863 2.721167 CCATTCCTCTCCGCGGACA 61.721 63.158 27.28 14.66 0.00 4.02
1899 1955 2.518587 TCCGATGCGTCCTCCGAT 60.519 61.111 0.00 0.00 39.56 4.18
1907 1963 1.443407 CGTCCTCCGATTGCCATCT 59.557 57.895 0.00 0.00 39.56 2.90
1910 1966 0.690744 TCCTCCGATTGCCATCTGGA 60.691 55.000 0.00 9.75 37.39 3.86
2064 2120 2.122167 ACCGCCCAGTCTCGAGATC 61.122 63.158 19.90 12.25 0.00 2.75
2085 2141 7.733969 AGATCTCAACCGATGTAGTAGTACTA 58.266 38.462 5.90 5.90 0.00 1.82
2284 2340 0.619255 TGGGTTTGATCGGCCTCCTA 60.619 55.000 0.00 0.00 0.00 2.94
2446 2507 5.745294 CACAGTTTCTGGTTCATGTTTCTTG 59.255 40.000 0.00 0.00 35.51 3.02
2449 2510 3.874383 TCTGGTTCATGTTTCTTGGGA 57.126 42.857 0.00 0.00 0.00 4.37
2450 2511 4.387026 TCTGGTTCATGTTTCTTGGGAT 57.613 40.909 0.00 0.00 0.00 3.85
2452 2513 3.164268 TGGTTCATGTTTCTTGGGATGG 58.836 45.455 0.00 0.00 0.00 3.51
2482 2562 2.599281 TTGGGTGAGCGAGTCGGA 60.599 61.111 15.52 0.00 0.00 4.55
2487 2567 1.135731 GTGAGCGAGTCGGACAGAG 59.864 63.158 15.52 2.22 0.00 3.35
2505 2585 0.610687 AGACTAGTTGGTCAGCAGCC 59.389 55.000 0.00 0.00 38.57 4.85
2527 3649 2.197324 TGGTGTGTTTGCTCCCCC 59.803 61.111 0.00 0.00 0.00 5.40
2529 3651 1.152546 GGTGTGTTTGCTCCCCCTT 60.153 57.895 0.00 0.00 0.00 3.95
2530 3652 1.179174 GGTGTGTTTGCTCCCCCTTC 61.179 60.000 0.00 0.00 0.00 3.46
2532 3654 0.555769 TGTGTTTGCTCCCCCTTCTT 59.444 50.000 0.00 0.00 0.00 2.52
2533 3655 1.248486 GTGTTTGCTCCCCCTTCTTC 58.752 55.000 0.00 0.00 0.00 2.87
2534 3656 1.149101 TGTTTGCTCCCCCTTCTTCT 58.851 50.000 0.00 0.00 0.00 2.85
2549 3671 2.318908 TCTTCTTTTGCCAATGCCAGT 58.681 42.857 0.00 0.00 36.33 4.00
2561 3683 3.741476 GCCAGTCTTGCCTTGCCG 61.741 66.667 0.00 0.00 0.00 5.69
2562 3684 3.741476 CCAGTCTTGCCTTGCCGC 61.741 66.667 0.00 0.00 0.00 6.53
2564 3686 4.314440 AGTCTTGCCTTGCCGCGA 62.314 61.111 8.23 0.00 0.00 5.87
2565 3687 3.793144 GTCTTGCCTTGCCGCGAG 61.793 66.667 8.23 0.00 41.03 5.03
2622 6734 2.286950 GCTTCAGATGTTGTCAAACGCA 60.287 45.455 0.00 0.00 39.30 5.24
2650 6762 0.179062 CCAGATGGGAAGCGGAGAAG 60.179 60.000 0.00 0.00 40.01 2.85
2694 6806 3.756434 CCAACAGGATTACGGTGTTCATT 59.244 43.478 0.00 0.00 32.01 2.57
2695 6807 4.142687 CCAACAGGATTACGGTGTTCATTC 60.143 45.833 0.00 0.00 32.01 2.67
2696 6808 4.553330 ACAGGATTACGGTGTTCATTCT 57.447 40.909 0.00 0.00 0.00 2.40
2697 6809 4.906618 ACAGGATTACGGTGTTCATTCTT 58.093 39.130 0.00 0.00 0.00 2.52
2698 6810 4.695455 ACAGGATTACGGTGTTCATTCTTG 59.305 41.667 0.00 0.00 0.00 3.02
2699 6811 4.695455 CAGGATTACGGTGTTCATTCTTGT 59.305 41.667 0.00 0.00 0.00 3.16
2700 6812 5.181245 CAGGATTACGGTGTTCATTCTTGTT 59.819 40.000 0.00 0.00 0.00 2.83
2701 6813 5.768164 AGGATTACGGTGTTCATTCTTGTTT 59.232 36.000 0.00 0.00 0.00 2.83
2702 6814 6.072673 AGGATTACGGTGTTCATTCTTGTTTC 60.073 38.462 0.00 0.00 0.00 2.78
2703 6815 6.293735 GGATTACGGTGTTCATTCTTGTTTCA 60.294 38.462 0.00 0.00 0.00 2.69
2704 6816 4.974368 ACGGTGTTCATTCTTGTTTCAA 57.026 36.364 0.00 0.00 0.00 2.69
2705 6817 5.317733 ACGGTGTTCATTCTTGTTTCAAA 57.682 34.783 0.00 0.00 0.00 2.69
2706 6818 5.715070 ACGGTGTTCATTCTTGTTTCAAAA 58.285 33.333 0.00 0.00 0.00 2.44
2707 6819 6.159988 ACGGTGTTCATTCTTGTTTCAAAAA 58.840 32.000 0.00 0.00 0.00 1.94
2708 6820 6.816140 ACGGTGTTCATTCTTGTTTCAAAAAT 59.184 30.769 0.00 0.00 0.00 1.82
2709 6821 7.333174 ACGGTGTTCATTCTTGTTTCAAAAATT 59.667 29.630 0.00 0.00 0.00 1.82
2710 6822 8.174422 CGGTGTTCATTCTTGTTTCAAAAATTT 58.826 29.630 0.00 0.00 0.00 1.82
2711 6823 9.838975 GGTGTTCATTCTTGTTTCAAAAATTTT 57.161 25.926 0.00 0.00 0.00 1.82
2763 6875 2.438868 AAGAAAACCAAGCATTCGGC 57.561 45.000 0.00 0.00 45.30 5.54
2785 6897 6.037610 CGGCAAGAAATTTTGATAGAGTAGCT 59.962 38.462 0.00 0.00 0.00 3.32
2805 6917 4.885907 AGCTGCATTCTATTGCTGTTACAT 59.114 37.500 1.02 0.00 43.18 2.29
2864 6976 3.700198 GGATCCCGCTACCGAATTT 57.300 52.632 0.00 0.00 36.29 1.82
2865 6977 1.226746 GGATCCCGCTACCGAATTTG 58.773 55.000 0.00 0.00 36.29 2.32
2867 6979 2.224113 GGATCCCGCTACCGAATTTGTA 60.224 50.000 0.00 0.00 36.29 2.41
2868 6980 2.589798 TCCCGCTACCGAATTTGTAG 57.410 50.000 10.28 10.28 38.95 2.74
2873 6985 0.043310 CTACCGAATTTGTAGCGCGC 60.043 55.000 26.66 26.66 30.23 6.86
2874 6986 0.736672 TACCGAATTTGTAGCGCGCA 60.737 50.000 35.10 16.82 0.00 6.09
2875 6987 1.351707 CCGAATTTGTAGCGCGCAT 59.648 52.632 35.10 20.44 0.00 4.73
2876 6988 0.654472 CCGAATTTGTAGCGCGCATC 60.654 55.000 35.10 24.61 0.00 3.91
2877 6989 0.026156 CGAATTTGTAGCGCGCATCA 59.974 50.000 35.10 26.94 0.00 3.07
2878 6990 1.528807 CGAATTTGTAGCGCGCATCAA 60.529 47.619 35.10 30.61 0.00 2.57
2879 6991 1.840141 GAATTTGTAGCGCGCATCAAC 59.160 47.619 35.10 23.94 0.00 3.18
2880 6992 0.098728 ATTTGTAGCGCGCATCAACC 59.901 50.000 35.10 13.82 0.00 3.77
2881 6993 2.234271 TTTGTAGCGCGCATCAACCG 62.234 55.000 35.10 0.00 0.00 4.44
2980 7095 4.080751 ACGGCCATCATCATCATCATCATA 60.081 41.667 2.24 0.00 0.00 2.15
2981 7096 4.272748 CGGCCATCATCATCATCATCATAC 59.727 45.833 2.24 0.00 0.00 2.39
3057 7189 3.656045 GTCCCGGCAACCACAACG 61.656 66.667 0.00 0.00 0.00 4.10
3073 7205 0.457853 AACGAGCACGCATGATACGT 60.458 50.000 2.62 0.00 46.42 3.57
3074 7206 0.379316 ACGAGCACGCATGATACGTA 59.621 50.000 2.62 0.00 42.96 3.57
3075 7207 0.770590 CGAGCACGCATGATACGTAC 59.229 55.000 0.00 0.00 42.96 3.67
3076 7208 0.770590 GAGCACGCATGATACGTACG 59.229 55.000 15.01 15.01 42.96 3.67
3092 7224 2.414559 CGTACGCGAGTTAAAGGAGGAA 60.415 50.000 15.93 0.00 46.40 3.36
3097 7229 3.117046 GCGAGTTAAAGGAGGAAGATCG 58.883 50.000 0.00 0.00 0.00 3.69
3098 7230 3.429135 GCGAGTTAAAGGAGGAAGATCGT 60.429 47.826 0.00 0.00 0.00 3.73
3099 7231 4.201990 GCGAGTTAAAGGAGGAAGATCGTA 60.202 45.833 0.00 0.00 0.00 3.43
3100 7232 5.512473 CGAGTTAAAGGAGGAAGATCGTAG 58.488 45.833 0.00 0.00 0.00 3.51
3114 7259 2.620251 TCGTAGAGCAAATCATGGGG 57.380 50.000 0.00 0.00 0.00 4.96
3118 7263 1.410004 AGAGCAAATCATGGGGCATG 58.590 50.000 0.00 0.00 42.60 4.06
3144 7296 0.464916 TGCCTGCCTGCTGTATGATG 60.465 55.000 0.00 0.00 0.00 3.07
3156 7308 4.152223 TGCTGTATGATGATAAATTCGCGG 59.848 41.667 6.13 0.00 0.00 6.46
3219 7375 1.588404 CAGATCCGTGTGTACAATCGC 59.412 52.381 13.24 1.96 0.00 4.58
3283 7452 2.556534 AGTACGTACTTCACATCGCC 57.443 50.000 22.45 0.00 31.13 5.54
3314 7483 2.351157 GGCTGATCAAACAGAACAGTGC 60.351 50.000 0.00 0.00 45.86 4.40
3319 7488 3.552132 TCAAACAGAACAGTGCTGGTA 57.448 42.857 13.61 0.00 37.69 3.25
3321 7490 3.118408 TCAAACAGAACAGTGCTGGTACT 60.118 43.478 13.61 0.00 37.69 2.73
3348 7518 0.742281 CCCGTCTGTGCCATGAGAAG 60.742 60.000 0.00 0.00 0.00 2.85
3350 7520 0.036952 CGTCTGTGCCATGAGAAGGT 60.037 55.000 0.00 0.00 0.00 3.50
3378 7548 3.798380 CGATCATTCGCTGTGCCA 58.202 55.556 0.00 0.00 38.75 4.92
3459 7633 2.934570 GCCCTGTGCACCAACCATG 61.935 63.158 15.69 0.00 40.77 3.66
3471 7645 3.623060 CACCAACCATGCTGTCATACTAC 59.377 47.826 0.00 0.00 0.00 2.73
3472 7646 3.206150 CCAACCATGCTGTCATACTACC 58.794 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.075482 AAGGCTGTGGTGACATGGG 59.925 57.895 0.00 0.00 46.14 4.00
17 18 3.357079 CACCGGAGCACACAAGGC 61.357 66.667 9.46 0.00 0.00 4.35
71 72 2.683933 CCACACTCCCGCTACCCT 60.684 66.667 0.00 0.00 0.00 4.34
116 124 1.332195 TAGTGGCGAGAGGATGGATG 58.668 55.000 0.00 0.00 0.00 3.51
133 141 0.251916 TCTGACGTGCCCCCAAATAG 59.748 55.000 0.00 0.00 0.00 1.73
156 168 2.361119 GGCCCCCAAAATATTTCTCGTC 59.639 50.000 0.10 0.00 0.00 4.20
192 204 1.078214 CCAGGCTCGCATCCAAGAA 60.078 57.895 0.00 0.00 0.00 2.52
207 219 1.056660 AGGTGTCCACAGGTAACCAG 58.943 55.000 10.85 0.00 33.76 4.00
209 221 0.036306 CCAGGTGTCCACAGGTAACC 59.964 60.000 0.00 0.00 32.31 2.85
228 240 5.294356 TCACGCTATATGTTGTATTGGACC 58.706 41.667 0.00 0.00 0.00 4.46
239 251 9.614792 TCTATCTATACACATCACGCTATATGT 57.385 33.333 0.00 0.00 36.78 2.29
277 289 4.640771 TCTTGGTATTTCCTTGAGCACT 57.359 40.909 0.00 0.00 37.07 4.40
312 328 6.257630 GGCACAAAAGCAAAGTTTTTGATCTA 59.742 34.615 20.61 0.00 44.37 1.98
325 341 1.066303 CGGTAAGTGGCACAAAAGCAA 59.934 47.619 21.41 0.00 44.16 3.91
326 342 0.665835 CGGTAAGTGGCACAAAAGCA 59.334 50.000 21.41 0.00 44.16 3.91
327 343 0.039527 CCGGTAAGTGGCACAAAAGC 60.040 55.000 21.41 12.53 44.16 3.51
336 352 0.672401 ATTGTGACGCCGGTAAGTGG 60.672 55.000 1.90 0.00 0.00 4.00
337 353 1.136085 CAATTGTGACGCCGGTAAGTG 60.136 52.381 1.90 0.00 0.00 3.16
338 354 1.153353 CAATTGTGACGCCGGTAAGT 58.847 50.000 1.90 0.27 0.00 2.24
339 355 1.153353 ACAATTGTGACGCCGGTAAG 58.847 50.000 11.07 0.00 0.00 2.34
340 356 1.595466 AACAATTGTGACGCCGGTAA 58.405 45.000 12.82 0.00 0.00 2.85
341 357 1.264557 CAAACAATTGTGACGCCGGTA 59.735 47.619 12.82 0.00 0.00 4.02
342 358 0.030101 CAAACAATTGTGACGCCGGT 59.970 50.000 12.82 0.00 0.00 5.28
343 359 1.274798 GCAAACAATTGTGACGCCGG 61.275 55.000 12.82 0.00 38.85 6.13
369 389 7.262772 TCGTCCTGTTAAGTAAGTTATCATGG 58.737 38.462 0.00 0.00 0.00 3.66
401 424 3.633525 TGCATTGCCATATGTTTCCTCTC 59.366 43.478 6.12 0.00 0.00 3.20
402 425 3.634504 TGCATTGCCATATGTTTCCTCT 58.365 40.909 6.12 0.00 0.00 3.69
403 426 3.382546 ACTGCATTGCCATATGTTTCCTC 59.617 43.478 6.12 0.00 0.00 3.71
404 427 3.131577 CACTGCATTGCCATATGTTTCCT 59.868 43.478 6.12 0.00 0.00 3.36
434 457 4.060038 ACATCGCGAATCAGGAATAGTT 57.940 40.909 15.24 0.00 0.00 2.24
451 474 4.089923 GCACGCACCTTTAATTTGAACATC 59.910 41.667 0.00 0.00 0.00 3.06
462 485 0.515127 CATCAACGCACGCACCTTTA 59.485 50.000 0.00 0.00 0.00 1.85
498 521 2.165030 ACGGTTCCGTTTCGAGATATGT 59.835 45.455 11.27 0.00 39.88 2.29
502 525 0.599558 TCACGGTTCCGTTTCGAGAT 59.400 50.000 14.42 0.00 40.97 2.75
503 526 0.599558 ATCACGGTTCCGTTTCGAGA 59.400 50.000 14.42 8.75 40.97 4.04
504 527 0.989890 GATCACGGTTCCGTTTCGAG 59.010 55.000 14.42 3.42 40.97 4.04
506 529 0.668096 TGGATCACGGTTCCGTTTCG 60.668 55.000 14.42 4.14 40.97 3.46
507 530 1.664151 GATGGATCACGGTTCCGTTTC 59.336 52.381 14.42 13.38 40.97 2.78
668 695 6.095440 CACGGAATAAATCAAGGGAATCAACT 59.905 38.462 0.00 0.00 0.00 3.16
669 696 6.094881 TCACGGAATAAATCAAGGGAATCAAC 59.905 38.462 0.00 0.00 0.00 3.18
671 698 5.750524 TCACGGAATAAATCAAGGGAATCA 58.249 37.500 0.00 0.00 0.00 2.57
673 700 8.940397 AATATCACGGAATAAATCAAGGGAAT 57.060 30.769 0.00 0.00 0.00 3.01
719 749 6.605594 GGATGGGATATTAAATTGCCCGAATA 59.394 38.462 0.00 0.00 41.79 1.75
721 751 4.770010 GGATGGGATATTAAATTGCCCGAA 59.230 41.667 0.00 0.00 41.79 4.30
722 752 4.340617 GGATGGGATATTAAATTGCCCGA 58.659 43.478 0.00 0.00 41.79 5.14
723 753 3.128589 CGGATGGGATATTAAATTGCCCG 59.871 47.826 0.00 0.00 41.79 6.13
800 839 0.033366 GCTGCATCGGGTTGGTTTTT 59.967 50.000 0.00 0.00 0.00 1.94
801 840 1.665442 GCTGCATCGGGTTGGTTTT 59.335 52.632 0.00 0.00 0.00 2.43
802 841 2.625823 CGCTGCATCGGGTTGGTTT 61.626 57.895 1.09 0.00 0.00 3.27
803 842 3.055719 CGCTGCATCGGGTTGGTT 61.056 61.111 1.09 0.00 0.00 3.67
852 891 0.603975 AAGAAGAGGGCAAGCGTGAC 60.604 55.000 2.99 0.00 0.00 3.67
886 925 1.666700 GAGCAGAAGCAGAAGCAGATG 59.333 52.381 0.00 0.00 45.49 2.90
887 926 1.407162 GGAGCAGAAGCAGAAGCAGAT 60.407 52.381 0.00 0.00 45.49 2.90
888 927 0.036577 GGAGCAGAAGCAGAAGCAGA 60.037 55.000 0.00 0.00 45.49 4.26
889 928 0.036199 AGGAGCAGAAGCAGAAGCAG 60.036 55.000 0.00 0.00 45.49 4.24
890 929 0.036577 GAGGAGCAGAAGCAGAAGCA 60.037 55.000 0.00 0.00 45.49 3.91
891 930 0.744057 GGAGGAGCAGAAGCAGAAGC 60.744 60.000 0.00 0.00 45.49 3.86
892 931 0.107752 GGGAGGAGCAGAAGCAGAAG 60.108 60.000 0.00 0.00 45.49 2.85
893 932 1.557269 GGGGAGGAGCAGAAGCAGAA 61.557 60.000 0.00 0.00 45.49 3.02
894 933 1.992277 GGGGAGGAGCAGAAGCAGA 60.992 63.158 0.00 0.00 45.49 4.26
895 934 2.588989 GGGGAGGAGCAGAAGCAG 59.411 66.667 0.00 0.00 45.49 4.24
896 935 3.011517 GGGGGAGGAGCAGAAGCA 61.012 66.667 0.00 0.00 45.49 3.91
897 936 1.857638 AAAGGGGGAGGAGCAGAAGC 61.858 60.000 0.00 0.00 42.56 3.86
910 949 2.846827 AGGTGAGGAGTGAATAAAGGGG 59.153 50.000 0.00 0.00 0.00 4.79
937 976 4.402829 AGCTCAGAGAGAAACAGAGTGTA 58.597 43.478 0.00 0.00 0.00 2.90
1154 1204 1.067213 GCCTCAGGATCCTTATCTCGC 60.067 57.143 13.00 4.41 32.29 5.03
1175 1225 2.102357 CGTACGGCGAGCACAGAT 59.898 61.111 16.62 0.00 44.77 2.90
1176 1226 3.318539 GACGTACGGCGAGCACAGA 62.319 63.158 21.06 0.00 44.77 3.41
1222 1272 4.003788 CAGGTTCCTGGACGCGGT 62.004 66.667 12.47 0.00 0.00 5.68
1674 1724 4.867599 GGTCGCTTCCCGCCGTAG 62.868 72.222 0.00 0.00 36.73 3.51
1893 1949 0.250209 CCTCCAGATGGCAATCGGAG 60.250 60.000 24.11 24.11 44.53 4.63
1907 1963 3.147595 CCTCGATGTCGGCCTCCA 61.148 66.667 0.00 0.00 40.29 3.86
1910 1966 3.518998 CGTCCTCGATGTCGGCCT 61.519 66.667 0.00 0.00 40.29 5.19
1999 2055 2.690510 GCCTTCCTCCAGCTCCCT 60.691 66.667 0.00 0.00 0.00 4.20
2001 2057 3.803162 GGGCCTTCCTCCAGCTCC 61.803 72.222 0.84 0.00 0.00 4.70
2085 2141 1.271840 ATGGCGATGGTACCAGTGGT 61.272 55.000 21.41 20.91 39.88 4.16
2359 2415 1.311859 TCACTGGTTGCTTGCTGAAG 58.688 50.000 0.00 0.00 0.00 3.02
2446 2507 1.839424 ACTAGCAGCAAAACCATCCC 58.161 50.000 0.00 0.00 0.00 3.85
2449 2510 1.895131 CCCAACTAGCAGCAAAACCAT 59.105 47.619 0.00 0.00 0.00 3.55
2450 2511 1.327303 CCCAACTAGCAGCAAAACCA 58.673 50.000 0.00 0.00 0.00 3.67
2452 2513 1.953686 TCACCCAACTAGCAGCAAAAC 59.046 47.619 0.00 0.00 0.00 2.43
2482 2562 2.560542 CTGCTGACCAACTAGTCTCTGT 59.439 50.000 0.00 0.00 37.66 3.41
2487 2567 0.391793 GGGCTGCTGACCAACTAGTC 60.392 60.000 11.26 0.00 42.34 2.59
2505 2585 1.355210 GAGCAAACACACCACACGG 59.645 57.895 0.00 0.00 38.77 4.94
2527 3649 3.243975 ACTGGCATTGGCAAAAGAAGAAG 60.244 43.478 14.35 1.91 43.71 2.85
2529 3651 2.297033 GACTGGCATTGGCAAAAGAAGA 59.703 45.455 14.35 0.00 43.71 2.87
2530 3652 2.298163 AGACTGGCATTGGCAAAAGAAG 59.702 45.455 14.35 2.93 43.71 2.85
2532 3654 1.999648 AGACTGGCATTGGCAAAAGA 58.000 45.000 14.35 0.00 43.71 2.52
2533 3655 2.409975 CAAGACTGGCATTGGCAAAAG 58.590 47.619 14.35 5.45 43.71 2.27
2534 3656 1.540797 GCAAGACTGGCATTGGCAAAA 60.541 47.619 14.35 0.00 43.71 2.44
2587 3718 2.203294 AAGCCAAGCGACGGGTTT 60.203 55.556 0.00 0.00 41.37 3.27
2622 6734 2.237392 GCTTCCCATCTGGAGTAGTTGT 59.763 50.000 0.00 0.00 46.24 3.32
2642 6754 6.367422 CAGGAAATGTTATATCTCTTCTCCGC 59.633 42.308 0.00 0.00 0.00 5.54
2650 6762 5.822519 TGGTGTGCAGGAAATGTTATATCTC 59.177 40.000 0.00 0.00 0.00 2.75
2710 6822 7.094975 CCTCTGACATTATGAACACCGTAAAAA 60.095 37.037 0.00 0.00 30.69 1.94
2711 6823 6.370442 CCTCTGACATTATGAACACCGTAAAA 59.630 38.462 0.00 0.00 30.69 1.52
2712 6824 5.872617 CCTCTGACATTATGAACACCGTAAA 59.127 40.000 0.00 0.00 30.69 2.01
2713 6825 5.186215 TCCTCTGACATTATGAACACCGTAA 59.814 40.000 0.00 0.00 0.00 3.18
2714 6826 4.707934 TCCTCTGACATTATGAACACCGTA 59.292 41.667 0.00 0.00 0.00 4.02
2715 6827 3.513912 TCCTCTGACATTATGAACACCGT 59.486 43.478 0.00 0.00 0.00 4.83
2716 6828 4.123497 TCCTCTGACATTATGAACACCG 57.877 45.455 0.00 0.00 0.00 4.94
2717 6829 6.115446 TGAATCCTCTGACATTATGAACACC 58.885 40.000 0.00 0.00 0.00 4.16
2718 6830 6.820656 ACTGAATCCTCTGACATTATGAACAC 59.179 38.462 0.00 0.00 0.00 3.32
2719 6831 6.950842 ACTGAATCCTCTGACATTATGAACA 58.049 36.000 0.00 0.00 0.00 3.18
2720 6832 8.948631 TTACTGAATCCTCTGACATTATGAAC 57.051 34.615 0.00 0.00 0.00 3.18
2721 6833 8.981659 TCTTACTGAATCCTCTGACATTATGAA 58.018 33.333 0.00 0.00 0.00 2.57
2722 6834 8.539117 TCTTACTGAATCCTCTGACATTATGA 57.461 34.615 0.00 0.00 0.00 2.15
2723 6835 9.605275 TTTCTTACTGAATCCTCTGACATTATG 57.395 33.333 0.00 0.00 34.24 1.90
2725 6837 9.436957 GTTTTCTTACTGAATCCTCTGACATTA 57.563 33.333 0.00 0.00 34.24 1.90
2731 6843 6.348868 GCTTGGTTTTCTTACTGAATCCTCTG 60.349 42.308 0.00 0.00 34.24 3.35
2763 6875 7.755591 TGCAGCTACTCTATCAAAATTTCTTG 58.244 34.615 0.00 0.00 0.00 3.02
2785 6897 8.049655 TGTTTATGTAACAGCAATAGAATGCA 57.950 30.769 1.82 0.00 42.50 3.96
2805 6917 1.393196 CACGCGATGCACATCTGTTTA 59.607 47.619 15.93 0.00 35.72 2.01
2856 6968 1.366111 ATGCGCGCTACAAATTCGGT 61.366 50.000 33.29 0.54 0.00 4.69
2857 6969 0.654472 GATGCGCGCTACAAATTCGG 60.654 55.000 33.29 0.00 0.00 4.30
2858 6970 0.026156 TGATGCGCGCTACAAATTCG 59.974 50.000 33.29 0.00 0.00 3.34
2859 6971 1.840141 GTTGATGCGCGCTACAAATTC 59.160 47.619 31.59 21.30 0.00 2.17
2860 6972 1.467374 GGTTGATGCGCGCTACAAATT 60.467 47.619 31.59 12.35 0.00 1.82
2861 6973 0.098728 GGTTGATGCGCGCTACAAAT 59.901 50.000 31.59 19.89 0.00 2.32
2862 6974 1.499949 GGTTGATGCGCGCTACAAA 59.500 52.632 31.59 20.06 0.00 2.83
2864 6976 3.185365 CGGTTGATGCGCGCTACA 61.185 61.111 33.29 26.79 0.00 2.74
2865 6977 3.925238 CCGGTTGATGCGCGCTAC 61.925 66.667 33.29 24.54 0.00 3.58
2872 6984 3.499737 CCTGACGCCGGTTGATGC 61.500 66.667 1.90 0.00 0.00 3.91
2873 6985 1.153369 ATCCTGACGCCGGTTGATG 60.153 57.895 1.90 0.00 0.00 3.07
2874 6986 1.144057 GATCCTGACGCCGGTTGAT 59.856 57.895 1.90 0.00 0.00 2.57
2875 6987 2.577059 GATCCTGACGCCGGTTGA 59.423 61.111 1.90 0.00 0.00 3.18
2876 6988 2.511600 GGATCCTGACGCCGGTTG 60.512 66.667 3.84 0.00 0.00 3.77
2877 6989 3.782443 GGGATCCTGACGCCGGTT 61.782 66.667 12.58 0.00 0.00 4.44
2981 7096 4.528920 AGTAGAGTACTGCTCCCAAGTAG 58.471 47.826 0.00 0.00 45.21 2.57
3057 7189 0.770590 CGTACGTATCATGCGTGCTC 59.229 55.000 11.44 0.97 42.87 4.26
3073 7205 3.084039 TCTTCCTCCTTTAACTCGCGTA 58.916 45.455 5.77 0.00 0.00 4.42
3074 7206 1.891150 TCTTCCTCCTTTAACTCGCGT 59.109 47.619 5.77 0.00 0.00 6.01
3075 7207 2.649331 TCTTCCTCCTTTAACTCGCG 57.351 50.000 0.00 0.00 0.00 5.87
3076 7208 3.117046 CGATCTTCCTCCTTTAACTCGC 58.883 50.000 0.00 0.00 0.00 5.03
3092 7224 3.244353 CCCCATGATTTGCTCTACGATCT 60.244 47.826 0.00 0.00 0.00 2.75
3097 7229 2.057137 TGCCCCATGATTTGCTCTAC 57.943 50.000 0.00 0.00 0.00 2.59
3098 7230 2.175284 TCATGCCCCATGATTTGCTCTA 59.825 45.455 3.91 0.00 44.60 2.43
3099 7231 1.063492 TCATGCCCCATGATTTGCTCT 60.063 47.619 3.91 0.00 44.60 4.09
3100 7232 1.405872 TCATGCCCCATGATTTGCTC 58.594 50.000 3.91 0.00 44.60 4.26
3144 7296 1.278637 CACCGCCCGCGAATTTATC 59.721 57.895 8.23 0.00 42.83 1.75
3170 7322 3.485633 CTGTCTGCACATTGATTGTTCG 58.514 45.455 0.00 0.00 36.00 3.95
3219 7375 0.670546 CAACACCAGCAGGAGTACCG 60.671 60.000 0.35 0.00 37.78 4.02
3283 7452 1.725641 TTGATCAGCCGCAGTAACAG 58.274 50.000 0.00 0.00 0.00 3.16
3314 7483 0.901580 ACGGGGTGTACCAGTACCAG 60.902 60.000 5.53 0.00 46.38 4.00
3321 7490 2.874664 GCACAGACGGGGTGTACCA 61.875 63.158 3.11 0.00 42.91 3.25
3322 7491 2.047560 GCACAGACGGGGTGTACC 60.048 66.667 5.48 0.00 38.51 3.34
3430 7600 2.360350 ACAGGGCATGGCAACTCG 60.360 61.111 22.06 6.36 37.61 4.18


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

AutoCloner maintained by Alex Coulton.