Multiple sequence alignment - TraesCS5D01G043400

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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 TraesCS5D01G043400 chr5D 100.000 4549 0 0 1 4549 42929461 42924913 0.000000e+00 8401.0
1 TraesCS5D01G043400 chr5D 84.231 520 59 10 2628 3134 42948267 42947758 6.840000e-133 484.0
2 TraesCS5D01G043400 chr5A 95.793 3684 105 20 3 3644 32709531 32705856 0.000000e+00 5899.0
3 TraesCS5D01G043400 chr5A 98.588 425 5 1 3801 4225 32705873 32705450 0.000000e+00 750.0
4 TraesCS5D01G043400 chr5A 81.462 766 118 15 2816 3568 33176875 33176121 1.400000e-169 606.0
5 TraesCS5D01G043400 chr5A 96.296 297 8 1 4256 4549 32705454 32705158 6.840000e-133 484.0
6 TraesCS5D01G043400 chr5B 94.670 3677 159 7 3 3644 38161156 38164830 0.000000e+00 5670.0
7 TraesCS5D01G043400 chr5B 83.452 846 124 14 2715 3553 41255830 41254994 0.000000e+00 773.0
8 TraesCS5D01G043400 chr5B 87.389 563 57 5 3992 4544 38165108 38165666 6.420000e-178 634.0
9 TraesCS5D01G043400 chr5B 72.930 1389 299 45 1385 2731 41260202 41258849 1.180000e-110 411.0
10 TraesCS5D01G043400 chr5B 77.376 663 137 8 2536 3188 38050598 38049939 9.230000e-102 381.0
11 TraesCS5D01G043400 chr5B 99.398 166 1 0 3645 3810 544855717 544855882 7.400000e-78 302.0
12 TraesCS5D01G043400 chr5B 93.814 194 11 1 3801 3994 38164813 38165005 1.600000e-74 291.0
13 TraesCS5D01G043400 chr6D 97.737 486 11 0 1382 1867 269966351 269966836 0.000000e+00 837.0
14 TraesCS5D01G043400 chr6D 97.101 483 14 0 1385 1867 269965684 269965202 0.000000e+00 815.0
15 TraesCS5D01G043400 chr4A 96.660 479 16 0 1389 1867 360414414 360413936 0.000000e+00 797.0
16 TraesCS5D01G043400 chr4A 99.401 167 1 0 3643 3809 710743529 710743695 2.060000e-78 303.0
17 TraesCS5D01G043400 chr4A 99.398 166 1 0 3644 3809 317089804 317089639 7.400000e-78 302.0
18 TraesCS5D01G043400 chr3D 97.285 221 6 0 1647 1867 608502017 608501797 4.300000e-100 375.0
19 TraesCS5D01G043400 chr3A 98.266 173 3 0 3637 3809 646739253 646739081 2.060000e-78 303.0
20 TraesCS5D01G043400 chr3A 98.256 172 3 0 3638 3809 136568437 136568608 7.400000e-78 302.0
21 TraesCS5D01G043400 chr3A 99.398 166 1 0 3644 3809 224366443 224366278 7.400000e-78 302.0
22 TraesCS5D01G043400 chr1B 99.401 167 1 0 3643 3809 397427466 397427300 2.060000e-78 303.0
23 TraesCS5D01G043400 chr1B 99.398 166 1 0 3644 3809 330208713 330208548 7.400000e-78 302.0
24 TraesCS5D01G043400 chr7B 99.398 166 1 0 3644 3809 716963108 716962943 7.400000e-78 302.0
25 TraesCS5D01G043400 chr1D 91.667 48 2 2 3112 3158 7444717 7444763 1.060000e-06 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 TraesCS5D01G043400 chr5D 42924913 42929461 4548 True 8401.000000 8401 100.000000 1 4549 1 chr5D.!!$R1 4548
1 TraesCS5D01G043400 chr5D 42947758 42948267 509 True 484.000000 484 84.231000 2628 3134 1 chr5D.!!$R2 506
2 TraesCS5D01G043400 chr5A 32705158 32709531 4373 True 2377.666667 5899 96.892333 3 4549 3 chr5A.!!$R2 4546
3 TraesCS5D01G043400 chr5A 33176121 33176875 754 True 606.000000 606 81.462000 2816 3568 1 chr5A.!!$R1 752
4 TraesCS5D01G043400 chr5B 38161156 38165666 4510 False 2198.333333 5670 91.957667 3 4544 3 chr5B.!!$F2 4541
5 TraesCS5D01G043400 chr5B 41254994 41260202 5208 True 592.000000 773 78.191000 1385 3553 2 chr5B.!!$R2 2168
6 TraesCS5D01G043400 chr5B 38049939 38050598 659 True 381.000000 381 77.376000 2536 3188 1 chr5B.!!$R1 652

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
893 926 0.257039 GCACCAACCTGAGGATCCAT 59.743 55.000 15.82 0.00 0.00 3.41 F
1392 1438 0.530650 CATTCATCCCCTCGACCACG 60.531 60.000 0.00 0.00 41.26 4.94 F
1641 1688 0.739462 TCAACCCATGCTTCTACGCG 60.739 55.000 3.53 3.53 0.00 6.01 F
1711 1758 2.170166 GGCATCTTGGGTTCATCAACA 58.830 47.619 0.00 0.00 33.70 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1788 1.361204 TTTCTGATGGCCCAGTCAGA 58.639 50.000 21.85 21.85 46.60 3.27 R
2282 2381 1.567504 CTCGGGTATGTTGCTTACCG 58.432 55.000 0.00 0.00 40.08 4.02 R
3527 6700 2.093553 TCATCTTGCACGATCCACATCA 60.094 45.455 2.10 0.00 0.00 3.07 R
3708 6881 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51 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
57 58 0.668706 GCTCACACTCGTCAGCATGT 60.669 55.000 0.00 0.00 37.40 3.21
128 131 3.614092 CAGGGTATCACTTCAGTGCATT 58.386 45.455 1.74 0.00 45.25 3.56
268 271 3.485394 TGCACTTCAAACTATTGCTGGA 58.515 40.909 0.00 0.00 36.45 3.86
391 398 1.536940 TGCATTCACATGTGGGACAG 58.463 50.000 25.16 12.07 41.80 3.51
407 414 6.043411 GTGGGACAGTAAACTAAGAGCTATG 58.957 44.000 0.00 0.00 41.80 2.23
435 445 7.956420 TGACTGGCATAATAACCTATAAACG 57.044 36.000 0.00 0.00 0.00 3.60
516 546 5.209818 ACCTTCAATAGAAACGTGTGAGA 57.790 39.130 0.00 0.00 32.35 3.27
524 554 8.139350 TCAATAGAAACGTGTGAGAGAACTAAA 58.861 33.333 0.00 0.00 0.00 1.85
641 674 5.812642 TCACTTTCTTTCACTCAGACACTTC 59.187 40.000 0.00 0.00 0.00 3.01
645 678 4.938080 TCTTTCACTCAGACACTTCTCAC 58.062 43.478 0.00 0.00 0.00 3.51
652 685 5.460419 CACTCAGACACTTCTCACTACAAAC 59.540 44.000 0.00 0.00 0.00 2.93
702 735 2.226437 AGTATGCACTGCGTTTTCCAAG 59.774 45.455 0.00 0.00 32.25 3.61
713 746 3.546271 GCGTTTTCCAAGTTTGAACACTC 59.454 43.478 4.92 0.00 0.00 3.51
735 768 9.743057 CACTCAAACAATACAAAATTCAGGTAA 57.257 29.630 0.00 0.00 0.00 2.85
808 841 2.738521 CAGCTAAGTGTGCGCCGT 60.739 61.111 4.18 0.00 35.28 5.68
881 914 9.712305 AATAGTATCTCATACATAAGCACCAAC 57.288 33.333 0.00 0.00 38.21 3.77
892 925 0.842030 AGCACCAACCTGAGGATCCA 60.842 55.000 15.82 0.00 0.00 3.41
893 926 0.257039 GCACCAACCTGAGGATCCAT 59.743 55.000 15.82 0.00 0.00 3.41
920 953 4.038162 GTCTATCAAGCCTAGGGTACACAG 59.962 50.000 15.26 9.74 0.00 3.66
933 971 3.385111 GGGTACACAGTGAGATAGAAGGG 59.615 52.174 7.81 0.00 0.00 3.95
941 979 5.130145 ACAGTGAGATAGAAGGGAAATGAGG 59.870 44.000 0.00 0.00 0.00 3.86
983 1029 1.679032 GGCAGTTCTGCGGGAAGTAAT 60.679 52.381 16.84 0.00 35.98 1.89
1131 1177 1.269703 ACGTGTCAATCCCCTACCCC 61.270 60.000 0.00 0.00 0.00 4.95
1272 1318 2.107953 GACATCTCCCTGGAGCGC 59.892 66.667 8.39 0.00 41.71 5.92
1315 1361 1.605457 CCGTCAGCTACAACTGCTTCA 60.605 52.381 0.00 0.00 38.92 3.02
1317 1363 2.483876 GTCAGCTACAACTGCTTCACA 58.516 47.619 0.00 0.00 38.92 3.58
1330 1376 1.195448 GCTTCACATCGAACACCACAG 59.805 52.381 0.00 0.00 0.00 3.66
1392 1438 0.530650 CATTCATCCCCTCGACCACG 60.531 60.000 0.00 0.00 41.26 4.94
1641 1688 0.739462 TCAACCCATGCTTCTACGCG 60.739 55.000 3.53 3.53 0.00 6.01
1711 1758 2.170166 GGCATCTTGGGTTCATCAACA 58.830 47.619 0.00 0.00 33.70 3.33
1741 1788 4.263506 CCAAGAGAGGTGTCCCTGTTATTT 60.264 45.833 0.00 0.00 42.86 1.40
2282 2381 2.749621 CCAAGCTGAACAGGTGGTTATC 59.250 50.000 7.28 0.00 40.63 1.75
3188 6359 8.897752 ACAAGAAAGAAGGCTATATTCATTGAC 58.102 33.333 15.97 0.00 0.00 3.18
3261 6433 3.238441 CAGAAGAAGCTCCGCGATATAC 58.762 50.000 8.23 0.00 0.00 1.47
3527 6700 2.086610 ACACAGCCAAATTGGTCCTT 57.913 45.000 14.17 0.00 40.46 3.36
3533 6706 2.564062 AGCCAAATTGGTCCTTGATGTG 59.436 45.455 14.17 0.00 40.46 3.21
3649 6822 9.613428 TCATTATCACTGTATCTGTTTAAAGGG 57.387 33.333 0.00 0.00 0.00 3.95
3650 6823 7.859325 TTATCACTGTATCTGTTTAAAGGGC 57.141 36.000 0.00 0.00 0.00 5.19
3651 6824 5.235850 TCACTGTATCTGTTTAAAGGGCA 57.764 39.130 0.00 0.00 0.00 5.36
3652 6825 5.245531 TCACTGTATCTGTTTAAAGGGCAG 58.754 41.667 0.00 0.00 0.00 4.85
3653 6826 4.010349 ACTGTATCTGTTTAAAGGGCAGC 58.990 43.478 0.00 0.00 0.00 5.25
3654 6827 3.352648 TGTATCTGTTTAAAGGGCAGCC 58.647 45.455 1.26 1.26 0.00 4.85
3655 6828 1.852633 ATCTGTTTAAAGGGCAGCCC 58.147 50.000 24.90 24.90 45.90 5.19
3666 6839 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3667 6840 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3668 6841 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3669 6842 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
3670 6843 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
3671 6844 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
3672 6845 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
3673 6846 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
3674 6847 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
3676 6849 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3677 6850 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3678 6851 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3679 6852 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3682 6855 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3694 6867 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
3695 6868 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
3696 6869 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
3697 6870 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3698 6871 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3699 6872 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3700 6873 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3701 6874 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3702 6875 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3703 6876 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3704 6877 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
3705 6878 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3706 6879 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3707 6880 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3708 6881 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3709 6882 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3710 6883 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3711 6884 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3712 6885 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3722 6895 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
3723 6896 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
3724 6897 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
3725 6898 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
3726 6899 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
3727 6900 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
3728 6901 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
3729 6902 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
3730 6903 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
3731 6904 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
3732 6905 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
3733 6906 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
3734 6907 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
3735 6908 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
3736 6909 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
3737 6910 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3738 6911 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3739 6912 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3740 6913 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3741 6914 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3742 6915 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3743 6916 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3744 6917 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
3745 6918 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
3746 6919 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
3747 6920 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
3748 6921 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
3758 6931 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
3759 6932 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
3760 6933 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
3761 6934 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
3762 6935 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
3763 6936 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
3764 6937 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
3765 6938 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3766 6939 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3767 6940 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3768 6941 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3769 6942 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3770 6943 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3771 6944 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3772 6945 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
3773 6946 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
3774 6947 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
3775 6948 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
3776 6949 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
3777 6950 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
3778 6951 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
3779 6952 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
3780 6953 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
3781 6954 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
3782 6955 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
3793 6966 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
3794 6967 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3795 6968 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3796 6969 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3797 6970 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3798 6971 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
3799 6972 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3800 6973 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3801 6974 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3802 6975 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3803 6976 1.815003 GTCACAAGGCAGCAGCTTTAT 59.185 47.619 0.00 0.00 38.07 1.40
3804 6977 2.086869 TCACAAGGCAGCAGCTTTATC 58.913 47.619 0.00 0.00 38.07 1.75
3805 6978 1.814394 CACAAGGCAGCAGCTTTATCA 59.186 47.619 0.00 0.00 38.07 2.15
3806 6979 1.815003 ACAAGGCAGCAGCTTTATCAC 59.185 47.619 0.00 0.00 38.07 3.06
3807 6980 2.089980 CAAGGCAGCAGCTTTATCACT 58.910 47.619 0.00 0.00 38.07 3.41
3808 6981 1.747709 AGGCAGCAGCTTTATCACTG 58.252 50.000 0.00 0.00 41.70 3.66
3809 6982 1.004044 AGGCAGCAGCTTTATCACTGT 59.996 47.619 0.00 0.00 41.70 3.55
3810 6983 2.237143 AGGCAGCAGCTTTATCACTGTA 59.763 45.455 0.00 0.00 41.70 2.74
3811 6984 3.118112 AGGCAGCAGCTTTATCACTGTAT 60.118 43.478 0.00 0.00 41.70 2.29
3812 6985 3.249559 GGCAGCAGCTTTATCACTGTATC 59.750 47.826 0.00 0.00 41.70 2.24
3813 6986 4.125703 GCAGCAGCTTTATCACTGTATCT 58.874 43.478 0.00 0.00 36.26 1.98
3814 6987 4.025061 GCAGCAGCTTTATCACTGTATCTG 60.025 45.833 0.00 0.00 36.26 2.90
3815 6988 5.114780 CAGCAGCTTTATCACTGTATCTGT 58.885 41.667 0.00 0.00 36.26 3.41
3816 6989 5.583854 CAGCAGCTTTATCACTGTATCTGTT 59.416 40.000 0.00 0.00 36.26 3.16
3817 6990 6.093219 CAGCAGCTTTATCACTGTATCTGTTT 59.907 38.462 0.00 0.00 36.26 2.83
4223 7501 3.456277 AGGAAAAGTACATAGGCTGGAGG 59.544 47.826 0.00 0.00 0.00 4.30
4228 7506 4.750833 AGTACATAGGCTGGAGGTCTAT 57.249 45.455 0.00 0.00 42.93 1.98
4288 7566 1.636988 GCTTTGCTCATTGGTGATGC 58.363 50.000 0.00 0.00 35.64 3.91
4331 7614 4.947388 GCAGAACCCAGGAAATGTATTGTA 59.053 41.667 0.00 0.00 0.00 2.41
4370 7653 0.825010 ACTGAGCCCAAGGTGCTTTG 60.825 55.000 4.05 3.64 39.69 2.77
4384 7667 0.240145 GCTTTGAACCACCCGTAAGC 59.760 55.000 0.00 0.00 0.00 3.09
4459 7747 5.106515 GGGCTGAAGAAGATAACAACTGAAC 60.107 44.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.475213 GGGACTTGGAAGCCGAATAGG 60.475 57.143 0.00 0.00 44.97 2.57
1 2 1.209504 TGGGACTTGGAAGCCGAATAG 59.790 52.381 0.00 0.00 0.00 1.73
90 93 1.815003 CCTGGAGCTTGAATGGTGAAC 59.185 52.381 0.00 0.00 0.00 3.18
103 106 1.834263 ACTGAAGTGATACCCTGGAGC 59.166 52.381 0.00 0.00 0.00 4.70
128 131 1.093972 AAATGATGATCCGTGCGCAA 58.906 45.000 14.00 0.00 0.00 4.85
332 339 5.930569 GTCAGATACCGTAGTTTGGAACTTT 59.069 40.000 0.00 0.00 42.81 2.66
333 340 5.476614 GTCAGATACCGTAGTTTGGAACTT 58.523 41.667 0.00 0.00 42.81 2.66
334 341 4.081807 GGTCAGATACCGTAGTTTGGAACT 60.082 45.833 0.00 0.00 41.14 3.01
335 342 4.179298 GGTCAGATACCGTAGTTTGGAAC 58.821 47.826 0.00 0.00 38.88 3.62
391 398 7.201565 CCAGTCAAAGCATAGCTCTTAGTTTAC 60.202 40.741 0.00 0.00 38.25 2.01
407 414 6.884280 ATAGGTTATTATGCCAGTCAAAGC 57.116 37.500 0.00 0.00 0.00 3.51
435 445 8.803235 ACTTATAATTTGGAAAAGTCTTCACCC 58.197 33.333 5.81 0.05 0.00 4.61
557 587 8.158132 TCACCCATTGTACTGTTTAGTATTCAA 58.842 33.333 0.00 0.00 41.22 2.69
571 601 6.601613 TGGATAAATCTTGTCACCCATTGTAC 59.398 38.462 0.00 0.00 0.00 2.90
605 636 6.260050 GTGAAAGAAAGTGATACCACAGTTGA 59.740 38.462 0.00 0.00 45.54 3.18
641 674 7.230466 AGTTTGTTTAGTCGTTTGTAGTGAG 57.770 36.000 0.00 0.00 0.00 3.51
682 715 2.031157 ACTTGGAAAACGCAGTGCATAC 60.031 45.455 16.83 0.00 45.00 2.39
685 718 0.814457 AACTTGGAAAACGCAGTGCA 59.186 45.000 16.83 0.00 45.00 4.57
735 768 3.950397 TCAGCGTTGAATGGGATACTTT 58.050 40.909 0.00 0.00 0.00 2.66
793 826 2.173382 CAACGGCGCACACTTAGC 59.827 61.111 10.83 0.00 0.00 3.09
808 841 8.519526 GTTGATTAACTATTTCATGGGTGACAA 58.480 33.333 0.00 0.00 32.18 3.18
880 913 3.645053 AGACCATATGGATCCTCAGGT 57.355 47.619 28.77 14.99 38.94 4.00
881 914 5.275630 TGATAGACCATATGGATCCTCAGG 58.724 45.833 28.77 11.88 38.94 3.86
892 925 5.029973 ACCCTAGGCTTGATAGACCATAT 57.970 43.478 2.05 0.00 0.00 1.78
893 926 4.487282 ACCCTAGGCTTGATAGACCATA 57.513 45.455 2.05 0.00 0.00 2.74
920 953 5.622346 ACCTCATTTCCCTTCTATCTCAC 57.378 43.478 0.00 0.00 0.00 3.51
983 1029 1.496857 TCATGGTTGGGAACTTGGTGA 59.503 47.619 0.00 0.00 0.00 4.02
1050 1096 1.482593 CCGGAAGAGGTTGCAGATAGT 59.517 52.381 0.00 0.00 0.00 2.12
1131 1177 1.519898 GCCATTGCCGATGCCAAAG 60.520 57.895 0.00 0.00 36.33 2.77
1239 1285 7.458488 AGGGAGATGTCAATGATCTCTGATAAT 59.542 37.037 12.09 0.00 43.70 1.28
1315 1361 2.416747 CATGACTGTGGTGTTCGATGT 58.583 47.619 0.00 0.00 0.00 3.06
1317 1363 1.623311 TCCATGACTGTGGTGTTCGAT 59.377 47.619 0.00 0.00 40.27 3.59
1330 1376 2.076863 GCTGGTGTAGTTGTCCATGAC 58.923 52.381 0.00 0.00 0.00 3.06
1374 1420 1.823295 CGTGGTCGAGGGGATGAAT 59.177 57.895 0.00 0.00 39.71 2.57
1641 1688 1.404391 CATCCAACCTCTGCAAGCATC 59.596 52.381 0.00 0.00 0.00 3.91
1711 1758 1.899142 GACACCTCTCTTGGCTCTCTT 59.101 52.381 0.00 0.00 0.00 2.85
1741 1788 1.361204 TTTCTGATGGCCCAGTCAGA 58.639 50.000 21.85 21.85 46.60 3.27
2282 2381 1.567504 CTCGGGTATGTTGCTTACCG 58.432 55.000 0.00 0.00 40.08 4.02
3188 6359 5.634896 AGCGCTTTCTGTTCATTAAGATTG 58.365 37.500 2.64 0.00 0.00 2.67
3527 6700 2.093553 TCATCTTGCACGATCCACATCA 60.094 45.455 2.10 0.00 0.00 3.07
3533 6706 3.119291 CAGTAGTCATCTTGCACGATCC 58.881 50.000 2.10 0.00 0.00 3.36
3648 6821 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3649 6822 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3650 6823 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3651 6824 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
3652 6825 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
3653 6826 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
3654 6827 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
3655 6828 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
3656 6829 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
3677 6850 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3678 6851 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3679 6852 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3680 6853 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3681 6854 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3682 6855 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3683 6856 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
3684 6857 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
3685 6858 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
3686 6859 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
3687 6860 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
3688 6861 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3689 6862 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3690 6863 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3691 6864 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3692 6865 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3693 6866 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3694 6867 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3695 6868 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3696 6869 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3701 6874 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
3702 6875 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
3703 6876 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
3704 6877 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
3705 6878 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
3706 6879 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
3707 6880 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
3708 6881 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
3709 6882 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
3710 6883 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
3711 6884 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
3712 6885 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
3713 6886 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
3714 6887 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
3715 6888 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
3716 6889 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
3717 6890 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
3718 6891 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3719 6892 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3720 6893 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3721 6894 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3722 6895 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3723 6896 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
3724 6897 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
3725 6898 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
3726 6899 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
3727 6900 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
3728 6901 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
3729 6902 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
3730 6903 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
3731 6904 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
3732 6905 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
3733 6906 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
3734 6907 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
3735 6908 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
3736 6909 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
3737 6910 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
3738 6911 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
3739 6912 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
3740 6913 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
3741 6914 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
3752 6925 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
3753 6926 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
3754 6927 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
3755 6928 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
3756 6929 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
3757 6930 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
3758 6931 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
3759 6932 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
3760 6933 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
3761 6934 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
3762 6935 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
3763 6936 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
3764 6937 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
3765 6938 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
3766 6939 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
3776 6949 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3777 6950 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3778 6951 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
3779 6952 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
3780 6953 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
3781 6954 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3782 6955 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3783 6956 1.238439 TAAAGCTGCTGCCTTGTGAC 58.762 50.000 12.44 0.00 40.80 3.67
3784 6957 2.086869 GATAAAGCTGCTGCCTTGTGA 58.913 47.619 12.44 0.00 40.80 3.58
3785 6958 1.814394 TGATAAAGCTGCTGCCTTGTG 59.186 47.619 12.44 0.00 40.80 3.33
3786 6959 1.815003 GTGATAAAGCTGCTGCCTTGT 59.185 47.619 12.44 3.77 40.80 3.16
3787 6960 2.089980 AGTGATAAAGCTGCTGCCTTG 58.910 47.619 12.44 0.00 40.80 3.61
3788 6961 2.089980 CAGTGATAAAGCTGCTGCCTT 58.910 47.619 12.44 8.34 40.80 4.35
3789 6962 1.004044 ACAGTGATAAAGCTGCTGCCT 59.996 47.619 12.44 2.45 40.80 4.75
3790 6963 1.457346 ACAGTGATAAAGCTGCTGCC 58.543 50.000 12.44 0.00 40.80 4.85
3791 6964 4.025061 CAGATACAGTGATAAAGCTGCTGC 60.025 45.833 1.35 7.62 36.26 5.25
3792 6965 5.114780 ACAGATACAGTGATAAAGCTGCTG 58.885 41.667 1.35 0.00 36.26 4.41
3793 6966 5.350504 ACAGATACAGTGATAAAGCTGCT 57.649 39.130 0.00 0.00 36.26 4.24
3794 6967 6.314896 AGAAACAGATACAGTGATAAAGCTGC 59.685 38.462 0.00 0.00 36.26 5.25
3795 6968 7.840342 AGAAACAGATACAGTGATAAAGCTG 57.160 36.000 0.00 0.32 38.58 4.24
3796 6969 8.854614 AAAGAAACAGATACAGTGATAAAGCT 57.145 30.769 0.00 0.00 0.00 3.74
3988 7161 4.457603 TGCCTTAAAACGTATGCACTCAAT 59.542 37.500 0.00 0.00 0.00 2.57
4251 7529 1.452108 CGGGGCTTCATCCTTGGAC 60.452 63.158 0.00 0.00 0.00 4.02
4288 7566 2.630158 CAGATCCAACCTTCAGCTCAG 58.370 52.381 0.00 0.00 0.00 3.35
4331 7614 5.129980 TCAGTGATATCATGCTTTCTGGACT 59.870 40.000 9.02 0.00 0.00 3.85
4384 7667 3.081133 CCGCATCAACGAAGTCCG 58.919 61.111 0.00 0.00 45.00 4.79
4391 7674 2.222574 CGTGATATATGCCGCATCAACG 60.223 50.000 9.71 9.92 30.85 4.10
4459 7747 2.746362 GAGCTCCCTGTGAAGATTTGTG 59.254 50.000 0.87 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.