Multiple sequence alignment - TraesCS7D01G311300

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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 TraesCS7D01G311300 chr7D 100.000 2609 0 0 1 2609 394830081 394832689 0.000000e+00 4819.0
1 TraesCS7D01G311300 chr7D 89.189 481 51 1 2130 2609 166514227 166513747 1.340000e-167 599.0
2 TraesCS7D01G311300 chr7B 94.299 1491 58 18 506 1983 394401994 394403470 0.000000e+00 2257.0
3 TraesCS7D01G311300 chr7B 93.976 415 25 0 1 415 394401445 394401859 1.700000e-176 628.0
4 TraesCS7D01G311300 chr7B 92.969 128 9 0 1476 1603 394402733 394402860 1.230000e-43 187.0
5 TraesCS7D01G311300 chr7A 96.114 1364 40 9 535 1887 448099596 448100957 0.000000e+00 2213.0
6 TraesCS7D01G311300 chr7A 86.837 509 65 2 2093 2600 448101431 448101938 3.770000e-158 568.0
7 TraesCS7D01G311300 chr7A 94.172 326 14 2 1 322 448097799 448098123 2.330000e-135 492.0
8 TraesCS7D01G311300 chr7A 92.969 128 9 0 1476 1603 448100314 448100441 1.230000e-43 187.0
9 TraesCS7D01G311300 chr7A 91.304 138 10 2 1236 1372 448100536 448100672 1.230000e-43 187.0
10 TraesCS7D01G311300 chr6A 90.000 70 7 0 2130 2199 608403387 608403456 9.940000e-15 91.6
11 TraesCS7D01G311300 chr2B 85.484 62 9 0 1971 2032 636708846 636708785 6.030000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G311300 chr7D 394830081 394832689 2608 False 4819.0 4819 100.0000 1 2609 1 chr7D.!!$F1 2608
1 TraesCS7D01G311300 chr7B 394401445 394403470 2025 False 1024.0 2257 93.7480 1 1983 3 chr7B.!!$F1 1982
2 TraesCS7D01G311300 chr7A 448097799 448101938 4139 False 729.4 2213 92.2792 1 2600 5 chr7A.!!$F1 2599

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
116 117 0.03759 CCCCGTGGAGATGTGGAAAA 59.962 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 3731 0.116342 TGGCTCTAGAGTGACCCCAA 59.884 55.0 20.75 2.37 0.0 4.12 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
111 112 1.681793 CTACTACCCCGTGGAGATGTG 59.318 57.143 0.00 0.00 34.81 3.21
116 117 0.037590 CCCCGTGGAGATGTGGAAAA 59.962 55.000 0.00 0.00 0.00 2.29
131 132 4.220382 TGTGGAAAATTGTAATCAGCCTGG 59.780 41.667 0.00 0.00 0.00 4.45
161 162 1.098712 GTTTTGGCTCCGTGGTGACA 61.099 55.000 0.00 0.00 38.70 3.58
191 192 1.562008 TGGAAACGCAGGATATTCCCA 59.438 47.619 0.00 0.00 40.49 4.37
270 271 4.286032 TGCTGTATCTAGTTTGGTGGTTCT 59.714 41.667 0.00 0.00 0.00 3.01
334 339 4.856115 AACTTTTGAATTGTTGCCAACG 57.144 36.364 2.68 0.00 32.26 4.10
377 382 0.108424 CTGCTTCCTTCGTCTCAGGG 60.108 60.000 0.00 0.00 31.50 4.45
386 391 1.847328 TCGTCTCAGGGACATAAGCA 58.153 50.000 0.15 0.00 44.70 3.91
390 395 3.617531 CGTCTCAGGGACATAAGCACTTT 60.618 47.826 0.15 0.00 44.70 2.66
421 426 3.382048 GAGTTTACCTCGTCAACCTGT 57.618 47.619 0.00 0.00 0.00 4.00
422 427 3.725490 GAGTTTACCTCGTCAACCTGTT 58.275 45.455 0.00 0.00 0.00 3.16
427 432 3.832615 ACCTCGTCAACCTGTTTTAGT 57.167 42.857 0.00 0.00 0.00 2.24
428 433 4.146745 ACCTCGTCAACCTGTTTTAGTT 57.853 40.909 0.00 0.00 0.00 2.24
430 435 4.141779 ACCTCGTCAACCTGTTTTAGTTCT 60.142 41.667 0.00 0.00 0.00 3.01
433 438 3.311322 CGTCAACCTGTTTTAGTTCTGCA 59.689 43.478 0.00 0.00 0.00 4.41
434 439 4.201871 CGTCAACCTGTTTTAGTTCTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
435 440 5.646606 GTCAACCTGTTTTAGTTCTGCAAA 58.353 37.500 0.00 0.00 0.00 3.68
436 441 6.273071 GTCAACCTGTTTTAGTTCTGCAAAT 58.727 36.000 0.00 0.00 0.00 2.32
437 442 7.422399 GTCAACCTGTTTTAGTTCTGCAAATA 58.578 34.615 0.00 0.00 0.00 1.40
441 446 8.177119 ACCTGTTTTAGTTCTGCAAATAATCA 57.823 30.769 0.00 0.00 0.00 2.57
442 447 8.806146 ACCTGTTTTAGTTCTGCAAATAATCAT 58.194 29.630 0.00 0.00 0.00 2.45
443 448 9.079833 CCTGTTTTAGTTCTGCAAATAATCATG 57.920 33.333 0.00 0.00 0.00 3.07
444 449 8.984891 TGTTTTAGTTCTGCAAATAATCATGG 57.015 30.769 0.00 0.00 0.00 3.66
445 450 8.034215 TGTTTTAGTTCTGCAAATAATCATGGG 58.966 33.333 0.00 0.00 0.00 4.00
446 451 7.716799 TTTAGTTCTGCAAATAATCATGGGT 57.283 32.000 0.00 0.00 0.00 4.51
448 453 5.513233 AGTTCTGCAAATAATCATGGGTCT 58.487 37.500 0.00 0.00 0.00 3.85
449 454 5.954150 AGTTCTGCAAATAATCATGGGTCTT 59.046 36.000 0.00 0.00 0.00 3.01
450 455 6.096001 AGTTCTGCAAATAATCATGGGTCTTC 59.904 38.462 0.00 0.00 0.00 2.87
451 456 5.759059 TCTGCAAATAATCATGGGTCTTCT 58.241 37.500 0.00 0.00 0.00 2.85
452 457 5.824624 TCTGCAAATAATCATGGGTCTTCTC 59.175 40.000 0.00 0.00 0.00 2.87
454 459 5.136105 GCAAATAATCATGGGTCTTCTCCT 58.864 41.667 0.00 0.00 0.00 3.69
455 460 5.240403 GCAAATAATCATGGGTCTTCTCCTC 59.760 44.000 0.00 0.00 0.00 3.71
456 461 5.574970 AATAATCATGGGTCTTCTCCTCC 57.425 43.478 0.00 0.00 0.00 4.30
457 462 2.575921 ATCATGGGTCTTCTCCTCCA 57.424 50.000 0.00 0.00 0.00 3.86
458 463 2.575921 TCATGGGTCTTCTCCTCCAT 57.424 50.000 0.00 0.00 40.30 3.41
460 465 1.069823 CATGGGTCTTCTCCTCCATCG 59.930 57.143 0.00 0.00 37.86 3.84
461 466 1.330655 TGGGTCTTCTCCTCCATCGC 61.331 60.000 0.00 0.00 0.00 4.58
463 1736 0.387565 GGTCTTCTCCTCCATCGCTC 59.612 60.000 0.00 0.00 0.00 5.03
466 1739 2.081425 CTTCTCCTCCATCGCTCGGG 62.081 65.000 0.00 0.00 0.00 5.14
470 1743 2.587194 CTCCATCGCTCGGGCTTG 60.587 66.667 5.36 2.42 36.09 4.01
474 1747 3.127533 ATCGCTCGGGCTTGTTGC 61.128 61.111 5.36 0.00 41.94 4.17
515 1800 2.688507 ACAGTCGAATGCACGAAGATT 58.311 42.857 13.64 0.00 43.75 2.40
602 1898 5.655488 TGATCTCCGATCTTGTCTTTTCTC 58.345 41.667 5.55 0.00 0.00 2.87
666 1962 7.824704 TCTAGAGTACGCTTATATTCCTACG 57.175 40.000 3.89 0.00 0.00 3.51
684 1981 5.010719 TCCTACGGCGAGATATCTCAATTTT 59.989 40.000 27.97 12.91 43.00 1.82
830 2132 2.101185 CTCGATCGCACACTCGCT 59.899 61.111 11.09 0.00 34.94 4.93
872 2174 2.669364 TCGTTCCTTCTAGAAACGCAC 58.331 47.619 18.88 7.38 0.00 5.34
873 2175 2.295349 TCGTTCCTTCTAGAAACGCACT 59.705 45.455 18.88 0.00 0.00 4.40
883 2186 1.648467 GAAACGCACTGGAGGGCATC 61.648 60.000 1.07 0.00 0.00 3.91
913 2216 2.737180 CTCGCACCTCACACCACT 59.263 61.111 0.00 0.00 0.00 4.00
1599 2905 1.317613 ACCAGCTCAACAAAATGCGA 58.682 45.000 0.00 0.00 0.00 5.10
1614 2920 3.918220 CGATCCAACTGAGCGCGC 61.918 66.667 26.66 26.66 46.85 6.86
1615 2921 3.918220 GATCCAACTGAGCGCGCG 61.918 66.667 28.44 28.44 0.00 6.86
1616 2922 4.742201 ATCCAACTGAGCGCGCGT 62.742 61.111 32.35 18.26 0.00 6.01
1617 2923 3.350909 ATCCAACTGAGCGCGCGTA 62.351 57.895 32.35 17.73 0.00 4.42
1921 3575 5.682943 TTTTACTTCAGATTTGACCGGTG 57.317 39.130 14.63 0.00 31.71 4.94
1969 3627 8.655970 ACGAGTAAAGTTACTTTTTGTTTACGT 58.344 29.630 15.83 13.70 43.64 3.57
1998 3656 2.584791 GAACATTTGTCATGCGTGTCC 58.415 47.619 5.68 0.00 0.00 4.02
1999 3657 0.516877 ACATTTGTCATGCGTGTCCG 59.483 50.000 5.68 0.00 37.07 4.79
2014 3672 2.186644 CCGCGATGATGGTGACCA 59.813 61.111 6.84 6.84 38.19 4.02
2015 3673 2.173669 CCGCGATGATGGTGACCAC 61.174 63.158 6.40 1.42 35.80 4.16
2016 3674 1.447663 CGCGATGATGGTGACCACA 60.448 57.895 6.40 7.96 35.80 4.17
2017 3675 0.811219 CGCGATGATGGTGACCACAT 60.811 55.000 6.40 12.79 35.80 3.21
2018 3676 0.940126 GCGATGATGGTGACCACATC 59.060 55.000 24.63 24.63 43.82 3.06
2019 3677 1.211743 CGATGATGGTGACCACATCG 58.788 55.000 33.18 33.18 46.78 3.84
2020 3678 2.602257 GATGATGGTGACCACATCGA 57.398 50.000 22.20 5.90 45.90 3.59
2021 3679 2.905075 GATGATGGTGACCACATCGAA 58.095 47.619 22.20 0.99 45.90 3.71
2022 3680 2.849294 TGATGGTGACCACATCGAAA 57.151 45.000 6.40 0.00 45.90 3.46
2023 3681 3.133141 TGATGGTGACCACATCGAAAA 57.867 42.857 6.40 0.00 45.90 2.29
2024 3682 2.811431 TGATGGTGACCACATCGAAAAC 59.189 45.455 6.40 0.00 45.90 2.43
2025 3683 1.222300 TGGTGACCACATCGAAAACG 58.778 50.000 0.00 0.00 0.00 3.60
2026 3684 0.110373 GGTGACCACATCGAAAACGC 60.110 55.000 0.00 0.00 0.00 4.84
2027 3685 0.865769 GTGACCACATCGAAAACGCT 59.134 50.000 0.00 0.00 0.00 5.07
2028 3686 0.865111 TGACCACATCGAAAACGCTG 59.135 50.000 0.00 0.00 0.00 5.18
2029 3687 0.165944 GACCACATCGAAAACGCTGG 59.834 55.000 0.00 0.00 0.00 4.85
2030 3688 1.154225 CCACATCGAAAACGCTGGC 60.154 57.895 0.00 0.00 0.00 4.85
2031 3689 1.509787 CACATCGAAAACGCTGGCG 60.510 57.895 13.56 13.56 46.03 5.69
2046 3704 3.330853 GCGTCCGCCATCGTGATC 61.331 66.667 0.00 0.00 34.56 2.92
2047 3705 3.024609 CGTCCGCCATCGTGATCG 61.025 66.667 0.00 0.00 38.55 3.69
2048 3706 2.104331 GTCCGCCATCGTGATCGT 59.896 61.111 0.00 0.00 38.33 3.73
2049 3707 2.104132 TCCGCCATCGTGATCGTG 59.896 61.111 0.00 0.00 38.33 4.35
2050 3708 3.630148 CCGCCATCGTGATCGTGC 61.630 66.667 0.00 0.00 38.33 5.34
2051 3709 2.583319 CGCCATCGTGATCGTGCT 60.583 61.111 0.00 0.00 38.33 4.40
2052 3710 2.580470 CGCCATCGTGATCGTGCTC 61.580 63.158 0.00 0.00 38.33 4.26
2053 3711 2.580470 GCCATCGTGATCGTGCTCG 61.580 63.158 0.81 0.81 38.33 5.03
2054 3712 1.946156 CCATCGTGATCGTGCTCGG 60.946 63.158 8.49 0.00 38.33 4.63
2055 3713 2.278857 ATCGTGATCGTGCTCGGC 60.279 61.111 8.49 1.89 38.33 5.54
2056 3714 4.829518 TCGTGATCGTGCTCGGCG 62.830 66.667 8.49 0.00 38.33 6.46
2057 3715 4.829518 CGTGATCGTGCTCGGCGA 62.830 66.667 10.14 10.14 42.75 5.54
2058 3716 2.951745 GTGATCGTGCTCGGCGAG 60.952 66.667 31.40 31.40 41.83 5.03
2059 3717 4.193334 TGATCGTGCTCGGCGAGG 62.193 66.667 35.03 20.44 41.83 4.63
2060 3718 3.889044 GATCGTGCTCGGCGAGGA 61.889 66.667 35.03 31.54 41.83 3.71
2061 3719 3.200887 GATCGTGCTCGGCGAGGAT 62.201 63.158 35.03 27.80 41.83 3.24
2062 3720 3.490793 ATCGTGCTCGGCGAGGATG 62.491 63.158 35.51 35.51 41.83 3.51
2064 3722 3.838271 GTGCTCGGCGAGGATGGA 61.838 66.667 35.03 11.58 31.72 3.41
2065 3723 3.074369 TGCTCGGCGAGGATGGAA 61.074 61.111 35.03 4.13 0.00 3.53
2066 3724 2.279784 GCTCGGCGAGGATGGAAG 60.280 66.667 35.03 11.46 0.00 3.46
2067 3725 2.419198 CTCGGCGAGGATGGAAGG 59.581 66.667 28.52 0.25 0.00 3.46
2068 3726 3.798954 CTCGGCGAGGATGGAAGGC 62.799 68.421 28.52 0.00 0.00 4.35
2070 3728 4.918201 GGCGAGGATGGAAGGCGG 62.918 72.222 0.00 0.00 0.00 6.13
2073 3731 4.162690 GAGGATGGAAGGCGGCGT 62.163 66.667 9.37 0.00 0.00 5.68
2074 3732 3.682292 GAGGATGGAAGGCGGCGTT 62.682 63.158 9.37 7.76 0.00 4.84
2075 3733 3.508840 GGATGGAAGGCGGCGTTG 61.509 66.667 13.20 0.00 0.00 4.10
2076 3734 3.508840 GATGGAAGGCGGCGTTGG 61.509 66.667 13.20 0.00 0.00 3.77
2085 3743 4.003788 CGGCGTTGGGGTCACTCT 62.004 66.667 0.00 0.00 0.00 3.24
2086 3744 2.642254 CGGCGTTGGGGTCACTCTA 61.642 63.158 0.00 0.00 0.00 2.43
2087 3745 1.218316 GGCGTTGGGGTCACTCTAG 59.782 63.158 0.00 0.00 0.00 2.43
2088 3746 1.255667 GGCGTTGGGGTCACTCTAGA 61.256 60.000 0.00 0.00 0.00 2.43
2089 3747 0.173708 GCGTTGGGGTCACTCTAGAG 59.826 60.000 18.49 18.49 0.00 2.43
2090 3748 0.173708 CGTTGGGGTCACTCTAGAGC 59.826 60.000 19.97 3.47 35.36 4.09
2095 3753 2.203806 GGTCACTCTAGAGCCACCC 58.796 63.158 22.48 13.55 30.80 4.61
2096 3754 1.668101 GGTCACTCTAGAGCCACCCG 61.668 65.000 22.48 6.52 30.80 5.28
2097 3755 0.966370 GTCACTCTAGAGCCACCCGT 60.966 60.000 19.97 0.00 0.00 5.28
2098 3756 0.965866 TCACTCTAGAGCCACCCGTG 60.966 60.000 19.97 9.45 0.00 4.94
2128 3786 2.835431 CGTCTCCCTCGGCCATCT 60.835 66.667 2.24 0.00 0.00 2.90
2143 3801 1.078759 CATCTCCCGTGCACGTCTTC 61.079 60.000 34.81 0.00 37.74 2.87
2150 3808 3.555324 TGCACGTCTTCCTGGCCA 61.555 61.111 4.71 4.71 0.00 5.36
2158 3816 1.376037 CTTCCTGGCCACGTTCCTC 60.376 63.158 0.00 0.00 0.00 3.71
2187 3845 1.515954 CGGCCGTTCTGTACCTCAT 59.484 57.895 19.50 0.00 0.00 2.90
2198 3856 2.431454 TACCTCATGATGCGGCCGT 61.431 57.895 28.70 7.71 0.00 5.68
2202 3860 3.945434 CATGATGCGGCCGTGCTC 61.945 66.667 28.70 20.26 35.36 4.26
2203 3861 4.166888 ATGATGCGGCCGTGCTCT 62.167 61.111 28.70 6.90 35.36 4.09
2212 3870 1.446272 GCCGTGCTCTGTGTACCTC 60.446 63.158 0.00 0.00 0.00 3.85
2216 3874 0.596577 GTGCTCTGTGTACCTCGTCA 59.403 55.000 0.00 0.00 0.00 4.35
2222 3880 3.748083 TCTGTGTACCTCGTCAACTACT 58.252 45.455 0.00 0.00 0.00 2.57
2232 3890 1.272490 CGTCAACTACTCCTGCTTCCA 59.728 52.381 0.00 0.00 0.00 3.53
2239 3897 0.179018 ACTCCTGCTTCCACACCAAC 60.179 55.000 0.00 0.00 0.00 3.77
2273 3931 0.101399 CTCCCTCGACACATTCCTCG 59.899 60.000 0.00 0.00 0.00 4.63
2292 3950 3.121030 GCACGCCAAGCTCGTCAT 61.121 61.111 0.00 0.00 38.19 3.06
2299 3957 1.596727 GCCAAGCTCGTCATCTTCATC 59.403 52.381 0.00 0.00 0.00 2.92
2310 3968 0.695803 ATCTTCATCGAGGGGGCCTT 60.696 55.000 0.84 0.00 31.76 4.35
2311 3969 1.147153 CTTCATCGAGGGGGCCTTC 59.853 63.158 0.84 0.46 31.76 3.46
2318 3976 1.452108 GAGGGGGCCTTCATTGACG 60.452 63.158 0.84 0.00 31.76 4.35
2325 3983 1.911293 GCCTTCATTGACGAGCGCAA 61.911 55.000 11.47 0.00 0.00 4.85
2327 3985 0.517132 CTTCATTGACGAGCGCAACG 60.517 55.000 21.44 21.44 0.00 4.10
2381 4039 3.685214 CTCGGGAAGGAGACGTGCG 62.685 68.421 0.00 0.00 36.08 5.34
2384 4042 3.112709 GGAAGGAGACGTGCGTGC 61.113 66.667 0.67 0.00 0.00 5.34
2410 4068 2.738521 CACCACTTCGTCCTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
2415 4073 2.202570 CTTCGTCCTGCCGTACCG 60.203 66.667 0.00 0.00 0.00 4.02
2431 4089 2.592993 CCGGAACTTGGAGGCCTCA 61.593 63.158 33.29 17.15 0.00 3.86
2432 4090 1.078848 CGGAACTTGGAGGCCTCAG 60.079 63.158 33.29 24.52 0.00 3.35
2433 4091 1.831652 CGGAACTTGGAGGCCTCAGT 61.832 60.000 33.29 25.19 0.00 3.41
2446 4105 3.372557 CTCAGTGAGGAGGTGGAGT 57.627 57.895 12.67 0.00 0.00 3.85
2449 4108 1.133167 TCAGTGAGGAGGTGGAGTTCA 60.133 52.381 0.00 0.00 0.00 3.18
2455 4114 2.103941 GAGGAGGTGGAGTTCATCATCC 59.896 54.545 0.00 0.00 36.05 3.51
2457 4116 2.507471 GGAGGTGGAGTTCATCATCCTT 59.493 50.000 0.00 0.00 36.50 3.36
2460 4119 3.054065 AGGTGGAGTTCATCATCCTTTCC 60.054 47.826 0.00 0.00 36.50 3.13
2472 4131 0.251916 TCCTTTCCGCCATTGACGAT 59.748 50.000 0.00 0.00 0.00 3.73
2475 4134 2.009774 CTTTCCGCCATTGACGATCTT 58.990 47.619 0.00 0.00 0.00 2.40
2482 4141 2.358957 CCATTGACGATCTTCTTGCCA 58.641 47.619 0.48 0.00 0.00 4.92
2488 4147 1.002366 CGATCTTCTTGCCAAGACGG 58.998 55.000 6.65 3.56 37.23 4.79
2563 4222 1.065491 CCATCCCATTCTTCACCGACA 60.065 52.381 0.00 0.00 0.00 4.35
2582 4241 4.869861 CGACATGATCATCCACAAGTACAA 59.130 41.667 4.86 0.00 0.00 2.41
2586 4245 6.765036 ACATGATCATCCACAAGTACAAGATC 59.235 38.462 4.86 0.00 33.19 2.75
2591 4250 2.037902 TCCACAAGTACAAGATCCGCAA 59.962 45.455 0.00 0.00 0.00 4.85
2600 4259 1.325640 CAAGATCCGCAACGACATCTG 59.674 52.381 0.00 0.00 30.63 2.90
2601 4260 0.807667 AGATCCGCAACGACATCTGC 60.808 55.000 0.00 0.00 35.14 4.26
2602 4261 0.807667 GATCCGCAACGACATCTGCT 60.808 55.000 0.00 0.00 36.38 4.24
2603 4262 0.459899 ATCCGCAACGACATCTGCTA 59.540 50.000 0.00 0.00 36.38 3.49
2604 4263 0.459899 TCCGCAACGACATCTGCTAT 59.540 50.000 0.00 0.00 36.38 2.97
2605 4264 0.578683 CCGCAACGACATCTGCTATG 59.421 55.000 0.00 0.00 36.38 2.23
2606 4265 1.280982 CGCAACGACATCTGCTATGT 58.719 50.000 5.13 5.13 36.38 2.29
2607 4266 1.005662 CGCAACGACATCTGCTATGTG 60.006 52.381 9.58 5.67 36.38 3.21
2608 4267 1.267732 GCAACGACATCTGCTATGTGC 60.268 52.381 9.58 4.23 43.25 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.125106 ATCTGCTTCGCCGGGTTC 60.125 61.111 2.18 0.00 0.00 3.62
111 112 3.195396 TGCCAGGCTGATTACAATTTTCC 59.805 43.478 17.94 0.00 0.00 3.13
116 117 3.133362 CCAAATGCCAGGCTGATTACAAT 59.867 43.478 17.94 0.00 0.00 2.71
131 132 2.290367 GGAGCCAAAACAAACCAAATGC 59.710 45.455 0.00 0.00 0.00 3.56
161 162 2.495669 CCTGCGTTTCCACCCATTATTT 59.504 45.455 0.00 0.00 0.00 1.40
211 212 7.624360 AAATCTGGTAGCAATTATTCACGAA 57.376 32.000 0.00 0.00 0.00 3.85
212 213 7.624360 AAAATCTGGTAGCAATTATTCACGA 57.376 32.000 0.00 0.00 0.00 4.35
270 271 4.635765 GGACATCAAAAGATGATCAACGGA 59.364 41.667 12.02 0.00 45.91 4.69
334 339 5.229423 ACAACACATATGCAACATCCAAAC 58.771 37.500 1.58 0.00 0.00 2.93
386 391 6.957911 GAGGTAAACTCGGTAACACTGAAAGT 60.958 42.308 0.00 0.00 42.54 2.66
390 395 4.510038 GAGGTAAACTCGGTAACACTGA 57.490 45.455 0.00 0.00 36.29 3.41
415 420 8.637986 TGATTATTTGCAGAACTAAAACAGGTT 58.362 29.630 0.00 0.00 0.00 3.50
416 421 8.177119 TGATTATTTGCAGAACTAAAACAGGT 57.823 30.769 0.00 0.00 0.00 4.00
418 423 9.079833 CCATGATTATTTGCAGAACTAAAACAG 57.920 33.333 0.00 0.00 0.00 3.16
419 424 8.034215 CCCATGATTATTTGCAGAACTAAAACA 58.966 33.333 0.00 0.00 0.00 2.83
420 425 8.034804 ACCCATGATTATTTGCAGAACTAAAAC 58.965 33.333 0.00 0.00 0.00 2.43
421 426 8.133024 ACCCATGATTATTTGCAGAACTAAAA 57.867 30.769 0.00 0.00 0.00 1.52
422 427 7.615365 AGACCCATGATTATTTGCAGAACTAAA 59.385 33.333 0.00 0.00 0.00 1.85
427 432 6.189859 AGAAGACCCATGATTATTTGCAGAA 58.810 36.000 0.00 0.00 0.00 3.02
428 433 5.759059 AGAAGACCCATGATTATTTGCAGA 58.241 37.500 0.00 0.00 0.00 4.26
430 435 4.889409 GGAGAAGACCCATGATTATTTGCA 59.111 41.667 0.00 0.00 0.00 4.08
433 438 5.433051 TGGAGGAGAAGACCCATGATTATTT 59.567 40.000 0.00 0.00 0.00 1.40
434 439 4.977739 TGGAGGAGAAGACCCATGATTATT 59.022 41.667 0.00 0.00 0.00 1.40
435 440 4.570926 TGGAGGAGAAGACCCATGATTAT 58.429 43.478 0.00 0.00 0.00 1.28
436 441 4.007581 TGGAGGAGAAGACCCATGATTA 57.992 45.455 0.00 0.00 0.00 1.75
437 442 2.850833 TGGAGGAGAAGACCCATGATT 58.149 47.619 0.00 0.00 0.00 2.57
441 446 1.418334 CGATGGAGGAGAAGACCCAT 58.582 55.000 0.00 0.00 41.70 4.00
442 447 1.330655 GCGATGGAGGAGAAGACCCA 61.331 60.000 0.00 0.00 0.00 4.51
443 448 1.045911 AGCGATGGAGGAGAAGACCC 61.046 60.000 0.00 0.00 0.00 4.46
444 449 0.387565 GAGCGATGGAGGAGAAGACC 59.612 60.000 0.00 0.00 0.00 3.85
445 450 0.030101 CGAGCGATGGAGGAGAAGAC 59.970 60.000 0.00 0.00 0.00 3.01
446 451 1.103987 CCGAGCGATGGAGGAGAAGA 61.104 60.000 0.00 0.00 0.00 2.87
448 453 2.127869 CCCGAGCGATGGAGGAGAA 61.128 63.158 0.00 0.00 0.00 2.87
449 454 2.519541 CCCGAGCGATGGAGGAGA 60.520 66.667 0.00 0.00 0.00 3.71
450 455 4.292178 GCCCGAGCGATGGAGGAG 62.292 72.222 0.00 0.00 0.00 3.69
451 456 4.841617 AGCCCGAGCGATGGAGGA 62.842 66.667 0.00 0.00 46.67 3.71
452 457 3.854669 AAGCCCGAGCGATGGAGG 61.855 66.667 0.00 0.00 46.67 4.30
454 459 2.954684 AACAAGCCCGAGCGATGGA 61.955 57.895 3.17 0.00 46.67 3.41
455 460 2.436646 AACAAGCCCGAGCGATGG 60.437 61.111 3.17 0.00 46.67 3.51
456 461 2.787249 CAACAAGCCCGAGCGATG 59.213 61.111 0.00 0.00 46.67 3.84
457 462 3.127533 GCAACAAGCCCGAGCGAT 61.128 61.111 0.00 0.00 46.67 4.58
466 1739 1.779683 GTCTACGTCGGCAACAAGC 59.220 57.895 0.00 0.00 44.65 4.01
470 1743 0.110056 TCTTCGTCTACGTCGGCAAC 60.110 55.000 0.00 0.00 40.80 4.17
474 1747 1.081892 TTCCTCTTCGTCTACGTCGG 58.918 55.000 0.00 0.11 40.80 4.79
475 1748 2.888513 TTTCCTCTTCGTCTACGTCG 57.111 50.000 0.00 0.00 40.80 5.12
477 1750 3.317430 ACTGTTTTCCTCTTCGTCTACGT 59.683 43.478 2.02 0.00 40.80 3.57
495 1768 2.370281 ATCTTCGTGCATTCGACTGT 57.630 45.000 4.58 0.00 39.58 3.55
547 1843 2.017049 ACGTCGCTAGGTATTTACGGT 58.983 47.619 0.00 0.00 34.81 4.83
602 1898 2.958986 CGACAAGATCGTATTCGTCTCG 59.041 50.000 4.36 0.00 46.25 4.04
666 1962 4.985409 AGTCGAAAATTGAGATATCTCGCC 59.015 41.667 24.27 5.69 45.72 5.54
684 1981 3.192844 GGTAGAGTGGTGAAATGAGTCGA 59.807 47.826 0.00 0.00 0.00 4.20
830 2132 2.027285 TGTGGCTAGCTTATCTTGTGCA 60.027 45.455 15.72 0.00 0.00 4.57
872 2174 0.179048 TGTAATGCGATGCCCTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
873 2175 0.463654 GTGTAATGCGATGCCCTCCA 60.464 55.000 0.00 0.00 0.00 3.86
883 2186 1.739929 TGCGAGGGTGTGTAATGCG 60.740 57.895 0.00 0.00 0.00 4.73
913 2216 1.549950 GGCAAAAAGGTGGATGGAGGA 60.550 52.381 0.00 0.00 0.00 3.71
1284 2590 2.743928 GCCACCACGAAGAGCAGG 60.744 66.667 0.00 0.00 0.00 4.85
1545 2851 1.556911 AGGATGTTGTAGAGCACCCAG 59.443 52.381 0.00 0.00 0.00 4.45
1599 2905 3.350909 TACGCGCGCTCAGTTGGAT 62.351 57.895 32.58 8.80 0.00 3.41
1882 3190 8.020819 TGAAGTAAAAACATTTGCTAAGGATCG 58.979 33.333 0.00 0.00 0.00 3.69
1893 3430 7.651704 CCGGTCAAATCTGAAGTAAAAACATTT 59.348 33.333 0.00 0.00 31.88 2.32
1896 3433 5.591067 ACCGGTCAAATCTGAAGTAAAAACA 59.409 36.000 0.00 0.00 31.88 2.83
1897 3434 5.912955 CACCGGTCAAATCTGAAGTAAAAAC 59.087 40.000 2.59 0.00 31.88 2.43
1921 3575 5.459107 CGTTATATATTGTGGATCGGCTAGC 59.541 44.000 6.04 6.04 0.00 3.42
1969 3627 5.320723 GCATGACAAATGTTCGACGAAATA 58.679 37.500 12.67 5.05 0.00 1.40
1998 3656 0.811219 ATGTGGTCACCATCATCGCG 60.811 55.000 0.00 0.00 35.28 5.87
1999 3657 0.940126 GATGTGGTCACCATCATCGC 59.060 55.000 18.09 0.00 34.81 4.58
2000 3658 1.211743 CGATGTGGTCACCATCATCG 58.788 55.000 30.33 30.33 46.78 3.84
2003 3661 2.811431 GTTTTCGATGTGGTCACCATCA 59.189 45.455 0.00 0.00 35.28 3.07
2029 3687 3.330853 GATCACGATGGCGGACGC 61.331 66.667 8.39 8.39 43.17 5.19
2030 3688 3.024609 CGATCACGATGGCGGACG 61.025 66.667 0.00 0.00 43.17 4.79
2031 3689 2.104331 ACGATCACGATGGCGGAC 59.896 61.111 0.00 0.00 43.17 4.79
2032 3690 2.104132 CACGATCACGATGGCGGA 59.896 61.111 0.00 0.00 43.17 5.54
2033 3691 3.630148 GCACGATCACGATGGCGG 61.630 66.667 0.00 0.00 43.17 6.13
2034 3692 2.580470 GAGCACGATCACGATGGCG 61.580 63.158 0.00 0.00 42.66 5.69
2035 3693 2.580470 CGAGCACGATCACGATGGC 61.580 63.158 0.00 0.00 42.66 4.40
2036 3694 1.946156 CCGAGCACGATCACGATGG 60.946 63.158 4.70 0.00 42.66 3.51
2037 3695 2.580470 GCCGAGCACGATCACGATG 61.580 63.158 4.70 0.00 42.66 3.84
2038 3696 2.278857 GCCGAGCACGATCACGAT 60.279 61.111 4.70 0.00 42.66 3.73
2039 3697 4.829518 CGCCGAGCACGATCACGA 62.830 66.667 4.70 0.00 42.66 4.35
2040 3698 4.829518 TCGCCGAGCACGATCACG 62.830 66.667 4.70 3.61 42.66 4.35
2041 3699 2.951745 CTCGCCGAGCACGATCAC 60.952 66.667 4.70 0.00 42.66 3.06
2042 3700 4.193334 CCTCGCCGAGCACGATCA 62.193 66.667 9.01 0.00 42.66 2.92
2043 3701 3.200887 ATCCTCGCCGAGCACGATC 62.201 63.158 9.01 0.00 42.66 3.69
2044 3702 3.219928 ATCCTCGCCGAGCACGAT 61.220 61.111 9.01 3.48 42.66 3.73
2045 3703 4.193334 CATCCTCGCCGAGCACGA 62.193 66.667 9.01 0.83 42.66 4.35
2047 3705 3.371097 TTCCATCCTCGCCGAGCAC 62.371 63.158 9.01 0.00 0.00 4.40
2048 3706 3.074369 TTCCATCCTCGCCGAGCA 61.074 61.111 9.01 0.00 0.00 4.26
2049 3707 2.279784 CTTCCATCCTCGCCGAGC 60.280 66.667 9.01 0.00 0.00 5.03
2050 3708 2.419198 CCTTCCATCCTCGCCGAG 59.581 66.667 7.25 7.25 0.00 4.63
2051 3709 3.849951 GCCTTCCATCCTCGCCGA 61.850 66.667 0.00 0.00 0.00 5.54
2053 3711 4.918201 CCGCCTTCCATCCTCGCC 62.918 72.222 0.00 0.00 0.00 5.54
2056 3714 3.682292 AACGCCGCCTTCCATCCTC 62.682 63.158 0.00 0.00 0.00 3.71
2057 3715 3.717294 AACGCCGCCTTCCATCCT 61.717 61.111 0.00 0.00 0.00 3.24
2058 3716 3.508840 CAACGCCGCCTTCCATCC 61.509 66.667 0.00 0.00 0.00 3.51
2059 3717 3.508840 CCAACGCCGCCTTCCATC 61.509 66.667 0.00 0.00 0.00 3.51
2068 3726 2.558554 CTAGAGTGACCCCAACGCCG 62.559 65.000 0.00 0.00 0.00 6.46
2069 3727 1.218316 CTAGAGTGACCCCAACGCC 59.782 63.158 0.00 0.00 0.00 5.68
2070 3728 0.173708 CTCTAGAGTGACCCCAACGC 59.826 60.000 11.89 0.00 0.00 4.84
2071 3729 0.173708 GCTCTAGAGTGACCCCAACG 59.826 60.000 20.75 0.00 0.00 4.10
2072 3730 0.537653 GGCTCTAGAGTGACCCCAAC 59.462 60.000 20.75 0.94 0.00 3.77
2073 3731 0.116342 TGGCTCTAGAGTGACCCCAA 59.884 55.000 20.75 2.37 0.00 4.12
2074 3732 0.614979 GTGGCTCTAGAGTGACCCCA 60.615 60.000 20.75 15.45 0.00 4.96
2075 3733 1.331399 GGTGGCTCTAGAGTGACCCC 61.331 65.000 22.62 15.44 0.00 4.95
2076 3734 1.331399 GGGTGGCTCTAGAGTGACCC 61.331 65.000 30.41 30.41 41.52 4.46
2077 3735 1.668101 CGGGTGGCTCTAGAGTGACC 61.668 65.000 24.06 24.06 33.62 4.02
2078 3736 0.966370 ACGGGTGGCTCTAGAGTGAC 60.966 60.000 20.75 16.08 0.00 3.67
2079 3737 0.965866 CACGGGTGGCTCTAGAGTGA 60.966 60.000 20.75 5.25 0.00 3.41
2080 3738 1.513158 CACGGGTGGCTCTAGAGTG 59.487 63.158 20.75 6.63 0.00 3.51
2081 3739 1.682684 CCACGGGTGGCTCTAGAGT 60.683 63.158 20.75 0.00 44.73 3.24
2082 3740 3.211288 CCACGGGTGGCTCTAGAG 58.789 66.667 15.85 15.85 44.73 2.43
2091 3749 4.760047 CGAGGGCTTCCACGGGTG 62.760 72.222 0.00 0.00 40.22 4.61
2093 3751 4.452733 GTCGAGGGCTTCCACGGG 62.453 72.222 2.80 0.00 43.30 5.28
2094 3752 4.452733 GGTCGAGGGCTTCCACGG 62.453 72.222 2.80 0.00 43.30 4.94
2095 3753 4.796231 CGGTCGAGGGCTTCCACG 62.796 72.222 0.00 0.00 44.23 4.94
2096 3754 3.644399 GACGGTCGAGGGCTTCCAC 62.644 68.421 0.00 0.00 0.00 4.02
2097 3755 3.379445 GACGGTCGAGGGCTTCCA 61.379 66.667 0.00 0.00 0.00 3.53
2098 3756 3.066233 GAGACGGTCGAGGGCTTCC 62.066 68.421 1.89 0.00 0.00 3.46
2112 3770 2.503382 GGAGATGGCCGAGGGAGAC 61.503 68.421 0.00 0.00 0.00 3.36
2123 3781 2.507110 AAGACGTGCACGGGAGATGG 62.507 60.000 39.21 13.10 44.95 3.51
2128 3786 2.915659 AGGAAGACGTGCACGGGA 60.916 61.111 39.21 0.00 44.95 5.14
2132 3790 3.050275 GGCCAGGAAGACGTGCAC 61.050 66.667 6.82 6.82 0.00 4.57
2138 3796 1.671379 GGAACGTGGCCAGGAAGAC 60.671 63.158 31.22 17.10 0.00 3.01
2143 3801 4.410400 GGGAGGAACGTGGCCAGG 62.410 72.222 23.61 23.61 0.00 4.45
2166 3824 4.424566 GGTACAGAACGGCCGCGA 62.425 66.667 28.58 0.29 0.00 5.87
2169 3827 0.806102 CATGAGGTACAGAACGGCCG 60.806 60.000 26.86 26.86 0.00 6.13
2170 3828 0.535335 TCATGAGGTACAGAACGGCC 59.465 55.000 0.00 0.00 0.00 6.13
2172 3830 2.205074 GCATCATGAGGTACAGAACGG 58.795 52.381 9.42 0.00 0.00 4.44
2173 3831 1.854743 CGCATCATGAGGTACAGAACG 59.145 52.381 9.42 0.00 0.00 3.95
2179 3837 1.956170 CGGCCGCATCATGAGGTAC 60.956 63.158 14.67 1.97 39.68 3.34
2198 3856 1.000607 GTTGACGAGGTACACAGAGCA 60.001 52.381 0.00 0.00 0.00 4.26
2202 3860 3.119919 GGAGTAGTTGACGAGGTACACAG 60.120 52.174 0.00 0.00 0.00 3.66
2203 3861 2.816087 GGAGTAGTTGACGAGGTACACA 59.184 50.000 0.00 0.00 0.00 3.72
2212 3870 1.272490 TGGAAGCAGGAGTAGTTGACG 59.728 52.381 0.00 0.00 0.00 4.35
2216 3874 1.348036 GGTGTGGAAGCAGGAGTAGTT 59.652 52.381 0.00 0.00 0.00 2.24
2222 3880 1.150536 GGTTGGTGTGGAAGCAGGA 59.849 57.895 0.00 0.00 37.63 3.86
2232 3890 4.218686 GGTGGCTGGGGTTGGTGT 62.219 66.667 0.00 0.00 0.00 4.16
2255 3913 0.323087 TCGAGGAATGTGTCGAGGGA 60.323 55.000 0.00 0.00 40.19 4.20
2262 3920 1.738099 GCGTGCTCGAGGAATGTGT 60.738 57.895 15.58 0.00 39.71 3.72
2287 3945 0.032678 CCCCCTCGATGAAGATGACG 59.967 60.000 0.00 0.00 0.00 4.35
2292 3950 1.306997 AAGGCCCCCTCGATGAAGA 60.307 57.895 0.00 0.00 30.89 2.87
2299 3957 1.452108 GTCAATGAAGGCCCCCTCG 60.452 63.158 0.00 0.00 30.89 4.63
2310 3968 1.663388 ACGTTGCGCTCGTCAATGA 60.663 52.632 21.00 0.00 36.85 2.57
2311 3969 2.853210 ACGTTGCGCTCGTCAATG 59.147 55.556 21.00 9.68 36.85 2.82
2318 3976 3.173240 GAGACGGACGTTGCGCTC 61.173 66.667 9.73 0.00 33.30 5.03
2333 3991 3.561213 CAGCAGCCGCGTCATGAG 61.561 66.667 4.92 0.00 45.49 2.90
2356 4014 3.372554 CTCCTTCCCGAGCCCGAAC 62.373 68.421 0.00 0.00 38.22 3.95
2358 4016 4.056584 TCTCCTTCCCGAGCCCGA 62.057 66.667 0.00 0.00 38.22 5.14
2365 4023 4.052229 ACGCACGTCTCCTTCCCG 62.052 66.667 0.00 0.00 0.00 5.14
2410 4068 1.078637 GGCCTCCAAGTTCCGGTAC 60.079 63.158 2.44 2.44 0.00 3.34
2415 4073 0.322008 CACTGAGGCCTCCAAGTTCC 60.322 60.000 29.95 3.30 0.00 3.62
2416 4074 0.687354 TCACTGAGGCCTCCAAGTTC 59.313 55.000 29.95 4.45 0.00 3.01
2431 4089 2.183679 GATGAACTCCACCTCCTCACT 58.816 52.381 0.00 0.00 0.00 3.41
2432 4090 1.902508 TGATGAACTCCACCTCCTCAC 59.097 52.381 0.00 0.00 0.00 3.51
2433 4091 2.325661 TGATGAACTCCACCTCCTCA 57.674 50.000 0.00 0.00 0.00 3.86
2439 4098 3.282885 GGAAAGGATGATGAACTCCACC 58.717 50.000 0.00 0.00 33.75 4.61
2446 4105 2.689471 CAATGGCGGAAAGGATGATGAA 59.311 45.455 0.00 0.00 0.00 2.57
2449 4108 2.301346 GTCAATGGCGGAAAGGATGAT 58.699 47.619 0.00 0.00 0.00 2.45
2455 4114 1.656652 AGATCGTCAATGGCGGAAAG 58.343 50.000 7.59 0.00 0.00 2.62
2457 4116 1.207089 AGAAGATCGTCAATGGCGGAA 59.793 47.619 7.59 0.00 0.00 4.30
2460 4119 1.267732 GCAAGAAGATCGTCAATGGCG 60.268 52.381 11.35 0.00 0.00 5.69
2563 4222 6.294473 GGATCTTGTACTTGTGGATGATCAT 58.706 40.000 8.25 8.25 33.04 2.45
2582 4241 0.807667 GCAGATGTCGTTGCGGATCT 60.808 55.000 0.00 0.00 30.66 2.75
2586 4245 0.578683 CATAGCAGATGTCGTTGCGG 59.421 55.000 0.00 0.00 44.80 5.69


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

AutoCloner maintained by Alex Coulton.