Multiple sequence alignment - TraesCS5D01G502100

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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 TraesCS5D01G502100 chr5D 100.000 2558 0 0 1 2558 529800065 529802622 0.000000e+00 4724.0
1 TraesCS5D01G502100 chr5D 93.152 847 44 6 1718 2558 391318706 391319544 0.000000e+00 1230.0
2 TraesCS5D01G502100 chr5D 91.608 429 36 0 1201 1629 529750791 529751219 6.090000e-166 593.0
3 TraesCS5D01G502100 chr5D 89.311 421 21 12 789 1201 529749362 529749766 8.170000e-140 507.0
4 TraesCS5D01G502100 chr5D 88.288 111 9 3 1002 1109 529815946 529816055 2.070000e-26 130.0
5 TraesCS5D01G502100 chr5D 86.585 82 8 2 1007 1085 529845331 529845412 1.260000e-13 87.9
6 TraesCS5D01G502100 chr1D 95.374 843 30 3 1719 2558 470209448 470208612 0.000000e+00 1332.0
7 TraesCS5D01G502100 chr1A 93.034 847 46 6 1718 2558 150882848 150883687 0.000000e+00 1225.0
8 TraesCS5D01G502100 chr2D 91.234 867 39 7 1722 2558 30185275 30186134 0.000000e+00 1146.0
9 TraesCS5D01G502100 chr2D 93.277 714 37 5 1721 2430 572790118 572790824 0.000000e+00 1042.0
10 TraesCS5D01G502100 chr2D 92.556 712 42 5 1719 2426 73206692 73205988 0.000000e+00 1011.0
11 TraesCS5D01G502100 chr2D 88.317 796 67 15 1 775 649601016 649601806 0.000000e+00 931.0
12 TraesCS5D01G502100 chr2D 88.148 135 13 3 641 773 638636647 638636514 9.470000e-35 158.0
13 TraesCS5D01G502100 chr7A 90.300 866 50 13 1721 2558 733524680 733523821 0.000000e+00 1103.0
14 TraesCS5D01G502100 chr7A 91.304 207 16 1 1716 1920 660142445 660142651 5.390000e-72 281.0
15 TraesCS5D01G502100 chr3A 93.986 715 34 4 1719 2430 725342533 725341825 0.000000e+00 1074.0
16 TraesCS5D01G502100 chr3A 86.808 849 78 20 1719 2558 509547649 509546826 0.000000e+00 917.0
17 TraesCS5D01G502100 chr3A 90.350 715 28 7 1870 2558 461855055 461854356 0.000000e+00 900.0
18 TraesCS5D01G502100 chr3A 93.780 209 13 0 2350 2558 661839600 661839392 5.310000e-82 315.0
19 TraesCS5D01G502100 chr3A 93.642 173 11 0 2384 2556 535010054 535010226 2.520000e-65 259.0
20 TraesCS5D01G502100 chr3A 93.529 170 11 0 2384 2553 82895105 82894936 1.170000e-63 254.0
21 TraesCS5D01G502100 chr3A 90.441 136 11 2 641 775 710843582 710843716 7.270000e-41 178.0
22 TraesCS5D01G502100 chr3A 88.971 136 14 1 641 775 57723671 57723536 1.570000e-37 167.0
23 TraesCS5D01G502100 chr3A 89.231 130 12 2 641 770 10966123 10966250 7.320000e-36 161.0
24 TraesCS5D01G502100 chr3A 87.313 134 14 3 641 773 8801267 8801398 1.590000e-32 150.0
25 TraesCS5D01G502100 chr5A 89.243 846 49 16 1721 2556 356444188 356445001 0.000000e+00 1020.0
26 TraesCS5D01G502100 chr5A 91.454 667 43 6 1 653 445151106 445150440 0.000000e+00 904.0
27 TraesCS5D01G502100 chr5A 94.872 429 22 0 1201 1629 657725553 657725981 0.000000e+00 671.0
28 TraesCS5D01G502100 chr5A 95.753 259 4 5 854 1105 657725193 657725451 6.590000e-111 411.0
29 TraesCS5D01G502100 chr5A 88.571 105 9 2 1002 1103 657757135 657757239 9.610000e-25 124.0
30 TraesCS5D01G502100 chr5A 84.810 79 9 1 1007 1082 657760481 657760559 2.730000e-10 76.8
31 TraesCS5D01G502100 chr7D 93.797 661 33 7 1 653 573372761 573372101 0.000000e+00 987.0
32 TraesCS5D01G502100 chr6A 91.641 658 48 7 1 653 22027990 22027335 0.000000e+00 904.0
33 TraesCS5D01G502100 chr2A 91.020 657 47 9 1 648 25476393 25475740 0.000000e+00 876.0
34 TraesCS5D01G502100 chr3B 89.530 659 57 10 1 653 779379127 779378475 0.000000e+00 824.0
35 TraesCS5D01G502100 chr3B 89.313 131 13 1 644 773 793373202 793373072 2.040000e-36 163.0
36 TraesCS5D01G502100 chr3B 76.207 290 40 20 853 1127 573403727 573404002 2.670000e-25 126.0
37 TraesCS5D01G502100 chr6B 88.923 659 61 8 1 653 1125236 1125888 0.000000e+00 802.0
38 TraesCS5D01G502100 chr6B 88.235 136 15 1 641 775 681238829 681238694 7.320000e-36 161.0
39 TraesCS5D01G502100 chr1B 88.788 660 64 7 1 653 231358968 231359624 0.000000e+00 800.0
40 TraesCS5D01G502100 chr1B 88.576 639 63 7 21 653 231356268 231356902 0.000000e+00 767.0
41 TraesCS5D01G502100 chr1B 87.500 136 16 1 641 775 231356918 231357053 3.410000e-34 156.0
42 TraesCS5D01G502100 chr2B 87.897 661 66 13 1 653 656627242 656626588 0.000000e+00 765.0
43 TraesCS5D01G502100 chr2B 88.550 131 14 1 645 775 733717144 733717015 9.470000e-35 158.0
44 TraesCS5D01G502100 chr3D 77.186 263 34 17 853 1103 437966559 437966807 2.070000e-26 130.0


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 TraesCS5D01G502100 chr5D 529800065 529802622 2557 False 4724.000000 4724 100.0000 1 2558 1 chr5D.!!$F2 2557
1 TraesCS5D01G502100 chr5D 391318706 391319544 838 False 1230.000000 1230 93.1520 1718 2558 1 chr5D.!!$F1 840
2 TraesCS5D01G502100 chr5D 529749362 529751219 1857 False 550.000000 593 90.4595 789 1629 2 chr5D.!!$F5 840
3 TraesCS5D01G502100 chr1D 470208612 470209448 836 True 1332.000000 1332 95.3740 1719 2558 1 chr1D.!!$R1 839
4 TraesCS5D01G502100 chr1A 150882848 150883687 839 False 1225.000000 1225 93.0340 1718 2558 1 chr1A.!!$F1 840
5 TraesCS5D01G502100 chr2D 30185275 30186134 859 False 1146.000000 1146 91.2340 1722 2558 1 chr2D.!!$F1 836
6 TraesCS5D01G502100 chr2D 572790118 572790824 706 False 1042.000000 1042 93.2770 1721 2430 1 chr2D.!!$F2 709
7 TraesCS5D01G502100 chr2D 73205988 73206692 704 True 1011.000000 1011 92.5560 1719 2426 1 chr2D.!!$R1 707
8 TraesCS5D01G502100 chr2D 649601016 649601806 790 False 931.000000 931 88.3170 1 775 1 chr2D.!!$F3 774
9 TraesCS5D01G502100 chr7A 733523821 733524680 859 True 1103.000000 1103 90.3000 1721 2558 1 chr7A.!!$R1 837
10 TraesCS5D01G502100 chr3A 725341825 725342533 708 True 1074.000000 1074 93.9860 1719 2430 1 chr3A.!!$R6 711
11 TraesCS5D01G502100 chr3A 509546826 509547649 823 True 917.000000 917 86.8080 1719 2558 1 chr3A.!!$R4 839
12 TraesCS5D01G502100 chr3A 461854356 461855055 699 True 900.000000 900 90.3500 1870 2558 1 chr3A.!!$R3 688
13 TraesCS5D01G502100 chr5A 356444188 356445001 813 False 1020.000000 1020 89.2430 1721 2556 1 chr5A.!!$F1 835
14 TraesCS5D01G502100 chr5A 445150440 445151106 666 True 904.000000 904 91.4540 1 653 1 chr5A.!!$R1 652
15 TraesCS5D01G502100 chr5A 657725193 657725981 788 False 541.000000 671 95.3125 854 1629 2 chr5A.!!$F2 775
16 TraesCS5D01G502100 chr7D 573372101 573372761 660 True 987.000000 987 93.7970 1 653 1 chr7D.!!$R1 652
17 TraesCS5D01G502100 chr6A 22027335 22027990 655 True 904.000000 904 91.6410 1 653 1 chr6A.!!$R1 652
18 TraesCS5D01G502100 chr2A 25475740 25476393 653 True 876.000000 876 91.0200 1 648 1 chr2A.!!$R1 647
19 TraesCS5D01G502100 chr3B 779378475 779379127 652 True 824.000000 824 89.5300 1 653 1 chr3B.!!$R1 652
20 TraesCS5D01G502100 chr6B 1125236 1125888 652 False 802.000000 802 88.9230 1 653 1 chr6B.!!$F1 652
21 TraesCS5D01G502100 chr1B 231356268 231359624 3356 False 574.333333 800 88.2880 1 775 3 chr1B.!!$F1 774
22 TraesCS5D01G502100 chr2B 656626588 656627242 654 True 765.000000 765 87.8970 1 653 1 chr2B.!!$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
786 3542 0.036732 TTTTCGGCTGGAGATGCTGT 59.963 50.0 0.0 0.0 37.96 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 5734 0.457035 CCATATATGCAATGCCCCGC 59.543 55.0 7.24 0.0 0.0 6.13 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
53 2755 3.531283 GAGGCGATCTGCTCCTCA 58.469 61.111 12.43 0.00 45.85 3.86
80 2782 2.333926 CGCTGAAAGTACATCGTCCAA 58.666 47.619 0.00 0.00 35.30 3.53
157 2861 3.928779 GGATGCGGGCGATCTCCA 61.929 66.667 3.71 0.00 0.00 3.86
422 3135 2.180432 AAGGCTTTCGTTGGAGGTAC 57.820 50.000 0.00 0.00 0.00 3.34
634 3362 1.945354 GAACCGAGGCGATGAGGTCA 61.945 60.000 0.00 0.00 35.68 4.02
648 3376 2.251642 GGTCAACGAAGCGGCTGTT 61.252 57.895 1.81 0.89 0.00 3.16
659 3415 2.026879 GGCTGTTTCGCGCCAAAA 59.973 55.556 0.56 0.00 45.59 2.44
668 3424 4.700365 GCGCCAAAACACTCGCCC 62.700 66.667 0.00 0.00 41.53 6.13
669 3425 4.038080 CGCCAAAACACTCGCCCC 62.038 66.667 0.00 0.00 0.00 5.80
670 3426 4.038080 GCCAAAACACTCGCCCCG 62.038 66.667 0.00 0.00 0.00 5.73
671 3427 2.281208 CCAAAACACTCGCCCCGA 60.281 61.111 0.00 0.00 0.00 5.14
672 3428 2.613506 CCAAAACACTCGCCCCGAC 61.614 63.158 0.00 0.00 0.00 4.79
673 3429 2.663852 AAAACACTCGCCCCGACG 60.664 61.111 0.00 0.00 0.00 5.12
707 3463 4.754667 GTTCGACCTGGGTCCGCC 62.755 72.222 13.41 0.00 41.76 6.13
739 3495 1.807226 GCCTAAGCCGGCGAAAAAT 59.193 52.632 23.20 6.96 40.79 1.82
742 3498 1.091537 CTAAGCCGGCGAAAAATGGA 58.908 50.000 23.20 0.00 0.00 3.41
743 3499 0.806241 TAAGCCGGCGAAAAATGGAC 59.194 50.000 23.20 0.00 0.00 4.02
744 3500 0.893727 AAGCCGGCGAAAAATGGACT 60.894 50.000 23.20 0.00 0.00 3.85
746 3502 1.800681 CCGGCGAAAAATGGACTCC 59.199 57.895 9.30 0.00 0.00 3.85
747 3503 0.676782 CCGGCGAAAAATGGACTCCT 60.677 55.000 9.30 0.00 0.00 3.69
748 3504 1.406341 CCGGCGAAAAATGGACTCCTA 60.406 52.381 9.30 0.00 0.00 2.94
749 3505 2.352388 CGGCGAAAAATGGACTCCTAA 58.648 47.619 0.00 0.00 0.00 2.69
750 3506 2.745281 CGGCGAAAAATGGACTCCTAAA 59.255 45.455 0.00 0.00 0.00 1.85
751 3507 3.189702 CGGCGAAAAATGGACTCCTAAAA 59.810 43.478 0.00 0.00 0.00 1.52
752 3508 4.482386 GGCGAAAAATGGACTCCTAAAAC 58.518 43.478 0.00 0.00 0.00 2.43
753 3509 4.022676 GGCGAAAAATGGACTCCTAAAACA 60.023 41.667 0.00 0.00 0.00 2.83
754 3510 5.336451 GGCGAAAAATGGACTCCTAAAACAT 60.336 40.000 0.00 0.00 0.00 2.71
759 3515 6.824305 AAATGGACTCCTAAAACATGACTG 57.176 37.500 0.00 0.00 0.00 3.51
784 3540 3.650647 TTTTTCGGCTGGAGATGCT 57.349 47.368 0.00 0.00 0.00 3.79
785 3541 1.167851 TTTTTCGGCTGGAGATGCTG 58.832 50.000 0.00 0.00 38.10 4.41
786 3542 0.036732 TTTTCGGCTGGAGATGCTGT 59.963 50.000 0.00 0.00 37.96 4.40
787 3543 0.036732 TTTCGGCTGGAGATGCTGTT 59.963 50.000 0.00 0.00 37.96 3.16
788 3544 0.901827 TTCGGCTGGAGATGCTGTTA 59.098 50.000 0.00 0.00 37.96 2.41
789 3545 0.901827 TCGGCTGGAGATGCTGTTAA 59.098 50.000 0.00 0.00 37.96 2.01
790 3546 1.486310 TCGGCTGGAGATGCTGTTAAT 59.514 47.619 0.00 0.00 37.96 1.40
791 3547 2.698274 TCGGCTGGAGATGCTGTTAATA 59.302 45.455 0.00 0.00 37.96 0.98
792 3548 2.802816 CGGCTGGAGATGCTGTTAATAC 59.197 50.000 0.00 0.00 32.57 1.89
793 3549 2.802816 GGCTGGAGATGCTGTTAATACG 59.197 50.000 0.00 0.00 0.00 3.06
794 3550 3.458189 GCTGGAGATGCTGTTAATACGT 58.542 45.455 0.00 0.00 0.00 3.57
795 3551 4.500887 GGCTGGAGATGCTGTTAATACGTA 60.501 45.833 0.00 0.00 0.00 3.57
796 3552 4.444720 GCTGGAGATGCTGTTAATACGTAC 59.555 45.833 0.00 0.00 0.00 3.67
797 3553 5.736492 GCTGGAGATGCTGTTAATACGTACT 60.736 44.000 0.00 0.00 0.00 2.73
798 3554 5.828747 TGGAGATGCTGTTAATACGTACTC 58.171 41.667 0.00 0.00 0.00 2.59
799 3555 5.221130 GGAGATGCTGTTAATACGTACTCC 58.779 45.833 0.00 1.46 34.51 3.85
800 3556 5.197682 AGATGCTGTTAATACGTACTCCC 57.802 43.478 0.00 0.00 0.00 4.30
801 3557 4.647853 AGATGCTGTTAATACGTACTCCCA 59.352 41.667 0.00 0.00 0.00 4.37
802 3558 5.304614 AGATGCTGTTAATACGTACTCCCAT 59.695 40.000 0.00 0.00 0.00 4.00
803 3559 6.492429 AGATGCTGTTAATACGTACTCCCATA 59.508 38.462 0.00 0.00 0.00 2.74
804 3560 6.468333 TGCTGTTAATACGTACTCCCATAA 57.532 37.500 0.00 0.00 0.00 1.90
805 3561 6.876155 TGCTGTTAATACGTACTCCCATAAA 58.124 36.000 0.00 0.00 0.00 1.40
806 3562 6.982141 TGCTGTTAATACGTACTCCCATAAAG 59.018 38.462 0.00 0.00 0.00 1.85
807 3563 6.073927 GCTGTTAATACGTACTCCCATAAAGC 60.074 42.308 0.00 0.00 0.00 3.51
832 3588 3.805267 GCGTCCCAGCTGAATCTG 58.195 61.111 17.39 1.76 0.00 2.90
923 3685 0.824759 GCTACTCACCCTCGTCCAAT 59.175 55.000 0.00 0.00 0.00 3.16
1110 3926 1.110518 CCGTAAGCCCTCTCCTCTCC 61.111 65.000 0.00 0.00 0.00 3.71
1111 3927 0.106419 CGTAAGCCCTCTCCTCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
1112 3928 1.699730 GTAAGCCCTCTCCTCTCCTC 58.300 60.000 0.00 0.00 0.00 3.71
1113 3929 1.216930 GTAAGCCCTCTCCTCTCCTCT 59.783 57.143 0.00 0.00 0.00 3.69
1114 3930 0.261696 AAGCCCTCTCCTCTCCTCTC 59.738 60.000 0.00 0.00 0.00 3.20
1115 3931 1.152546 GCCCTCTCCTCTCCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
1116 3932 1.655114 GCCCTCTCCTCTCCTCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
1117 3933 0.478507 CCCTCTCCTCTCCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
1118 3934 1.522900 CCTCTCCTCTCCTCTCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
1119 3935 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1120 3936 1.421646 CTCTCCTCTCCTCTCCTCTCC 59.578 61.905 0.00 0.00 0.00 3.71
1121 3937 0.478507 CTCCTCTCCTCTCCTCTCCC 59.521 65.000 0.00 0.00 0.00 4.30
1122 3938 0.047176 TCCTCTCCTCTCCTCTCCCT 59.953 60.000 0.00 0.00 0.00 4.20
1123 3939 0.478507 CCTCTCCTCTCCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
1124 3940 1.522900 CTCTCCTCTCCTCTCCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
1135 3951 0.034960 TCTCCCTCTCTCGTGTCCTG 60.035 60.000 0.00 0.00 0.00 3.86
1140 3956 0.172352 CTCTCTCGTGTCCTGCTTCC 59.828 60.000 0.00 0.00 0.00 3.46
1186 4002 0.962356 CTGTGTCATCAACCAGCCCC 60.962 60.000 0.00 0.00 0.00 5.80
1248 5089 1.100510 CTGGGCATGAGTGACAATGG 58.899 55.000 0.00 0.00 33.89 3.16
1249 5090 0.697658 TGGGCATGAGTGACAATGGA 59.302 50.000 0.00 0.00 33.89 3.41
1250 5091 1.340308 TGGGCATGAGTGACAATGGAG 60.340 52.381 0.00 0.00 33.89 3.86
1251 5092 1.386533 GGCATGAGTGACAATGGAGG 58.613 55.000 0.00 0.00 31.88 4.30
1263 5104 4.586841 TGACAATGGAGGTTTTTAGTTGGG 59.413 41.667 0.00 0.00 0.00 4.12
1265 5106 4.966168 ACAATGGAGGTTTTTAGTTGGGTT 59.034 37.500 0.00 0.00 0.00 4.11
1313 5154 0.694771 AATGCTCTGCTGGAGTTCCA 59.305 50.000 0.18 0.18 45.30 3.53
1543 5384 0.110056 GTTGAATCGTGCAGGCTGTG 60.110 55.000 17.16 6.78 0.00 3.66
1563 5404 9.612620 GGCTGTGTTGAATATAAATAACTATGC 57.387 33.333 0.00 0.00 0.00 3.14
1629 5470 4.441913 CCAAAAAGGCTTGTGATGTTGTCT 60.442 41.667 0.00 0.00 0.00 3.41
1630 5471 5.111293 CAAAAAGGCTTGTGATGTTGTCTT 58.889 37.500 0.00 0.00 0.00 3.01
1631 5472 5.343307 AAAAGGCTTGTGATGTTGTCTTT 57.657 34.783 0.00 0.00 0.00 2.52
1632 5473 5.343307 AAAGGCTTGTGATGTTGTCTTTT 57.657 34.783 0.00 0.00 0.00 2.27
1633 5474 5.343307 AAGGCTTGTGATGTTGTCTTTTT 57.657 34.783 0.00 0.00 0.00 1.94
1659 5500 5.659440 TTTTGCTGAAGTCTTTCCTTTGT 57.341 34.783 0.00 0.00 32.09 2.83
1660 5501 4.637483 TTGCTGAAGTCTTTCCTTTGTG 57.363 40.909 0.00 0.00 32.09 3.33
1661 5502 3.884895 TGCTGAAGTCTTTCCTTTGTGA 58.115 40.909 0.00 0.00 32.09 3.58
1662 5503 4.464008 TGCTGAAGTCTTTCCTTTGTGAT 58.536 39.130 0.00 0.00 32.09 3.06
1663 5504 4.276678 TGCTGAAGTCTTTCCTTTGTGATG 59.723 41.667 0.00 0.00 32.09 3.07
1664 5505 4.276926 GCTGAAGTCTTTCCTTTGTGATGT 59.723 41.667 0.00 0.00 32.09 3.06
1665 5506 5.221126 GCTGAAGTCTTTCCTTTGTGATGTT 60.221 40.000 0.00 0.00 32.09 2.71
1666 5507 6.135290 TGAAGTCTTTCCTTTGTGATGTTG 57.865 37.500 0.00 0.00 32.09 3.33
1667 5508 5.652014 TGAAGTCTTTCCTTTGTGATGTTGT 59.348 36.000 0.00 0.00 32.09 3.32
1668 5509 5.757850 AGTCTTTCCTTTGTGATGTTGTC 57.242 39.130 0.00 0.00 0.00 3.18
1669 5510 5.192927 AGTCTTTCCTTTGTGATGTTGTCA 58.807 37.500 0.00 0.00 0.00 3.58
1670 5511 5.652014 AGTCTTTCCTTTGTGATGTTGTCAA 59.348 36.000 0.00 0.00 38.90 3.18
1671 5512 6.322201 AGTCTTTCCTTTGTGATGTTGTCAAT 59.678 34.615 0.00 0.00 38.90 2.57
1672 5513 7.502226 AGTCTTTCCTTTGTGATGTTGTCAATA 59.498 33.333 0.00 0.00 38.90 1.90
1673 5514 8.299570 GTCTTTCCTTTGTGATGTTGTCAATAT 58.700 33.333 0.00 0.00 38.90 1.28
1674 5515 8.298854 TCTTTCCTTTGTGATGTTGTCAATATG 58.701 33.333 0.00 0.00 38.90 1.78
1675 5516 7.757941 TTCCTTTGTGATGTTGTCAATATGA 57.242 32.000 0.00 0.00 38.90 2.15
1676 5517 7.381766 TCCTTTGTGATGTTGTCAATATGAG 57.618 36.000 0.00 0.00 38.90 2.90
1677 5518 7.167535 TCCTTTGTGATGTTGTCAATATGAGA 58.832 34.615 0.00 0.00 38.90 3.27
1678 5519 7.665145 TCCTTTGTGATGTTGTCAATATGAGAA 59.335 33.333 0.00 0.00 38.90 2.87
1679 5520 8.464404 CCTTTGTGATGTTGTCAATATGAGAAT 58.536 33.333 0.00 0.00 38.90 2.40
1680 5521 9.499585 CTTTGTGATGTTGTCAATATGAGAATC 57.500 33.333 0.00 0.00 38.90 2.52
1681 5522 8.564509 TTGTGATGTTGTCAATATGAGAATCA 57.435 30.769 0.00 0.00 44.88 2.57
1684 5525 8.967664 TGATGTTGTCAATATGAGAATCATGA 57.032 30.769 0.00 0.00 45.00 3.07
1685 5526 9.569122 TGATGTTGTCAATATGAGAATCATGAT 57.431 29.630 1.18 1.18 45.00 2.45
1697 5538 7.907214 TGAGAATCATGATGCATCATTAGAG 57.093 36.000 34.39 24.19 44.70 2.43
1698 5539 7.676947 TGAGAATCATGATGCATCATTAGAGA 58.323 34.615 34.39 27.82 44.70 3.10
1699 5540 8.322091 TGAGAATCATGATGCATCATTAGAGAT 58.678 33.333 34.39 28.58 44.70 2.75
1700 5541 9.168451 GAGAATCATGATGCATCATTAGAGATT 57.832 33.333 32.40 32.40 44.70 2.40
1705 5546 9.433153 TCATGATGCATCATTAGAGATTAAGAC 57.567 33.333 34.39 1.39 44.70 3.01
1706 5547 9.216117 CATGATGCATCATTAGAGATTAAGACA 57.784 33.333 34.39 7.30 44.70 3.41
1707 5548 8.599055 TGATGCATCATTAGAGATTAAGACAC 57.401 34.615 25.42 0.00 0.00 3.67
1708 5549 7.383300 TGATGCATCATTAGAGATTAAGACACG 59.617 37.037 25.42 0.00 0.00 4.49
1709 5550 6.573434 TGCATCATTAGAGATTAAGACACGT 58.427 36.000 0.00 0.00 0.00 4.49
1710 5551 6.697455 TGCATCATTAGAGATTAAGACACGTC 59.303 38.462 0.00 0.00 0.00 4.34
1711 5552 6.697455 GCATCATTAGAGATTAAGACACGTCA 59.303 38.462 0.00 0.00 0.00 4.35
1712 5553 7.383572 GCATCATTAGAGATTAAGACACGTCAT 59.616 37.037 0.00 0.00 0.00 3.06
1713 5554 8.697960 CATCATTAGAGATTAAGACACGTCATG 58.302 37.037 0.00 0.00 0.00 3.07
1766 5608 1.689352 GCCGCGCGCTAAAAACTAGA 61.689 55.000 30.48 0.00 0.00 2.43
1782 5624 4.398598 GATTGCCGTGCGCCGTTT 62.399 61.111 4.18 0.00 36.24 3.60
1836 5678 1.584483 CAGCCGCGCTAAAATGCAG 60.584 57.895 5.56 0.00 36.40 4.41
1837 5679 2.951227 GCCGCGCTAAAATGCAGC 60.951 61.111 5.56 0.00 35.61 5.25
2085 5988 1.424635 CTCGTCCTCGTCTTCGTCC 59.575 63.158 0.00 0.00 38.33 4.79
2086 5989 1.004080 TCGTCCTCGTCTTCGTCCT 60.004 57.895 0.00 0.00 38.33 3.85
2087 5990 1.018226 TCGTCCTCGTCTTCGTCCTC 61.018 60.000 0.00 0.00 38.33 3.71
2088 5991 1.424635 GTCCTCGTCTTCGTCCTCG 59.575 63.158 0.00 0.00 38.33 4.63
2089 5992 1.004080 TCCTCGTCTTCGTCCTCGT 60.004 57.895 0.00 0.00 38.33 4.18
2090 5993 1.018226 TCCTCGTCTTCGTCCTCGTC 61.018 60.000 0.00 0.00 38.33 4.20
2149 6052 2.470057 ATCTTCCTCCCTCTCCTCAC 57.530 55.000 0.00 0.00 0.00 3.51
2218 6121 2.172505 ACGGCATCTTCATGGGAATGTA 59.827 45.455 0.00 0.00 31.34 2.29
2532 6466 6.262273 GGTTAGATGTGTCCAAGAAGAACAAA 59.738 38.462 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 2755 4.367023 TACTTTCAGCGCCGCCGT 62.367 61.111 4.98 0.00 36.67 5.68
65 2767 2.762745 ACGCTTTGGACGATGTACTTT 58.237 42.857 0.00 0.00 0.00 2.66
206 2914 2.340078 GCACGTGGAGACTGAGCA 59.660 61.111 18.88 0.00 0.00 4.26
634 3362 2.935955 CGAAACAGCCGCTTCGTT 59.064 55.556 5.03 0.00 39.60 3.85
648 3376 2.629210 CGAGTGTTTTGGCGCGAA 59.371 55.556 12.10 0.00 0.00 4.70
724 3480 0.806241 GTCCATTTTTCGCCGGCTTA 59.194 50.000 26.68 9.93 0.00 3.09
732 3488 6.801862 GTCATGTTTTAGGAGTCCATTTTTCG 59.198 38.462 12.86 0.00 0.00 3.46
739 3495 3.009033 CCCAGTCATGTTTTAGGAGTCCA 59.991 47.826 12.86 0.00 0.00 4.02
742 3498 2.290960 GGCCCAGTCATGTTTTAGGAGT 60.291 50.000 0.00 0.00 0.00 3.85
743 3499 2.369394 GGCCCAGTCATGTTTTAGGAG 58.631 52.381 0.00 0.00 0.00 3.69
744 3500 1.339631 CGGCCCAGTCATGTTTTAGGA 60.340 52.381 0.00 0.00 0.00 2.94
746 3502 1.821216 ACGGCCCAGTCATGTTTTAG 58.179 50.000 0.00 0.00 0.00 1.85
747 3503 2.279935 AACGGCCCAGTCATGTTTTA 57.720 45.000 0.00 0.00 0.00 1.52
748 3504 1.408969 AAACGGCCCAGTCATGTTTT 58.591 45.000 0.00 0.00 29.01 2.43
749 3505 1.408969 AAAACGGCCCAGTCATGTTT 58.591 45.000 0.00 0.00 34.46 2.83
750 3506 1.408969 AAAAACGGCCCAGTCATGTT 58.591 45.000 0.00 0.00 0.00 2.71
751 3507 3.125520 AAAAACGGCCCAGTCATGT 57.874 47.368 0.00 0.00 0.00 3.21
775 3531 5.221185 GGAGTACGTATTAACAGCATCTCCA 60.221 44.000 13.63 0.00 38.00 3.86
776 3532 5.221130 GGAGTACGTATTAACAGCATCTCC 58.779 45.833 0.00 2.15 0.00 3.71
777 3533 5.221130 GGGAGTACGTATTAACAGCATCTC 58.779 45.833 0.00 0.00 0.00 2.75
778 3534 4.647853 TGGGAGTACGTATTAACAGCATCT 59.352 41.667 0.00 0.00 0.00 2.90
779 3535 4.940463 TGGGAGTACGTATTAACAGCATC 58.060 43.478 0.00 0.00 0.00 3.91
780 3536 5.546621 ATGGGAGTACGTATTAACAGCAT 57.453 39.130 0.00 0.00 0.00 3.79
781 3537 6.468333 TTATGGGAGTACGTATTAACAGCA 57.532 37.500 0.00 0.00 0.00 4.41
782 3538 6.073927 GCTTTATGGGAGTACGTATTAACAGC 60.074 42.308 0.00 0.00 0.00 4.40
783 3539 6.982141 TGCTTTATGGGAGTACGTATTAACAG 59.018 38.462 0.00 0.00 0.00 3.16
784 3540 6.876155 TGCTTTATGGGAGTACGTATTAACA 58.124 36.000 0.00 0.00 0.00 2.41
785 3541 7.654520 TGATGCTTTATGGGAGTACGTATTAAC 59.345 37.037 0.00 0.00 0.00 2.01
786 3542 7.728148 TGATGCTTTATGGGAGTACGTATTAA 58.272 34.615 0.00 0.00 0.00 1.40
787 3543 7.292713 TGATGCTTTATGGGAGTACGTATTA 57.707 36.000 0.00 0.00 0.00 0.98
788 3544 6.169557 TGATGCTTTATGGGAGTACGTATT 57.830 37.500 0.00 0.00 0.00 1.89
789 3545 5.784177 CTGATGCTTTATGGGAGTACGTAT 58.216 41.667 0.00 0.00 0.00 3.06
790 3546 4.500887 GCTGATGCTTTATGGGAGTACGTA 60.501 45.833 0.00 0.00 36.03 3.57
791 3547 3.741388 GCTGATGCTTTATGGGAGTACGT 60.741 47.826 0.00 0.00 36.03 3.57
792 3548 2.802816 GCTGATGCTTTATGGGAGTACG 59.197 50.000 0.00 0.00 36.03 3.67
793 3549 3.808728 TGCTGATGCTTTATGGGAGTAC 58.191 45.455 0.00 0.00 40.48 2.73
794 3550 3.745480 GCTGCTGATGCTTTATGGGAGTA 60.745 47.826 0.00 0.00 40.48 2.59
795 3551 2.928334 CTGCTGATGCTTTATGGGAGT 58.072 47.619 0.00 0.00 40.48 3.85
796 3552 1.607628 GCTGCTGATGCTTTATGGGAG 59.392 52.381 0.00 0.00 40.48 4.30
797 3553 1.683943 GCTGCTGATGCTTTATGGGA 58.316 50.000 0.00 0.00 40.48 4.37
798 3554 0.309922 CGCTGCTGATGCTTTATGGG 59.690 55.000 0.00 0.00 40.48 4.00
799 3555 1.003116 GACGCTGCTGATGCTTTATGG 60.003 52.381 0.00 0.00 40.48 2.74
800 3556 1.003116 GGACGCTGCTGATGCTTTATG 60.003 52.381 0.00 0.00 40.48 1.90
801 3557 1.303309 GGACGCTGCTGATGCTTTAT 58.697 50.000 0.00 0.00 40.48 1.40
802 3558 0.744414 GGGACGCTGCTGATGCTTTA 60.744 55.000 0.00 0.00 40.48 1.85
803 3559 2.042831 GGGACGCTGCTGATGCTTT 61.043 57.895 0.00 0.00 40.48 3.51
804 3560 2.437359 GGGACGCTGCTGATGCTT 60.437 61.111 0.00 0.00 40.48 3.91
805 3561 3.677284 CTGGGACGCTGCTGATGCT 62.677 63.158 0.00 0.00 40.48 3.79
806 3562 3.200593 CTGGGACGCTGCTGATGC 61.201 66.667 0.00 0.00 40.20 3.91
807 3563 3.200593 GCTGGGACGCTGCTGATG 61.201 66.667 13.18 0.00 0.00 3.07
848 3604 1.005804 CACATCTCCATCGATCCGCG 61.006 60.000 0.00 0.00 42.69 6.46
923 3685 3.672511 GCGATCTGGTTCAGAGTAAACGA 60.673 47.826 3.94 0.00 44.08 3.85
1000 3763 0.467474 TCCTCGATGCCTCCGTACAT 60.467 55.000 0.00 0.00 0.00 2.29
1110 3926 0.837272 ACGAGAGAGGGAGAGGAGAG 59.163 60.000 0.00 0.00 0.00 3.20
1111 3927 0.544223 CACGAGAGAGGGAGAGGAGA 59.456 60.000 0.00 0.00 0.00 3.71
1112 3928 0.254747 ACACGAGAGAGGGAGAGGAG 59.745 60.000 0.00 0.00 0.00 3.69
1113 3929 0.253610 GACACGAGAGAGGGAGAGGA 59.746 60.000 0.00 0.00 0.00 3.71
1114 3930 0.750182 GGACACGAGAGAGGGAGAGG 60.750 65.000 0.00 0.00 0.00 3.69
1115 3931 0.254747 AGGACACGAGAGAGGGAGAG 59.745 60.000 0.00 0.00 0.00 3.20
1116 3932 0.034960 CAGGACACGAGAGAGGGAGA 60.035 60.000 0.00 0.00 0.00 3.71
1117 3933 1.662438 GCAGGACACGAGAGAGGGAG 61.662 65.000 0.00 0.00 0.00 4.30
1118 3934 1.679305 GCAGGACACGAGAGAGGGA 60.679 63.158 0.00 0.00 0.00 4.20
1119 3935 1.254284 AAGCAGGACACGAGAGAGGG 61.254 60.000 0.00 0.00 0.00 4.30
1120 3936 0.172352 GAAGCAGGACACGAGAGAGG 59.828 60.000 0.00 0.00 0.00 3.69
1121 3937 0.172352 GGAAGCAGGACACGAGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
1122 3938 0.251386 AGGAAGCAGGACACGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
1123 3939 0.108898 CAGGAAGCAGGACACGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
1124 3940 0.539669 TCAGGAAGCAGGACACGAGA 60.540 55.000 0.00 0.00 0.00 4.04
1140 3956 2.618709 GTTTTGGTTGGACCTGACTCAG 59.381 50.000 0.00 0.00 39.58 3.35
1186 4002 2.842208 TTTCAACTGAAGCAACCGTG 57.158 45.000 0.00 0.00 35.21 4.94
1227 5068 2.651455 CATTGTCACTCATGCCCAGAT 58.349 47.619 0.00 0.00 0.00 2.90
1229 5070 1.100510 CCATTGTCACTCATGCCCAG 58.899 55.000 0.00 0.00 0.00 4.45
1248 5089 8.349568 AGATCATTAACCCAACTAAAAACCTC 57.650 34.615 0.00 0.00 0.00 3.85
1249 5090 8.585018 CAAGATCATTAACCCAACTAAAAACCT 58.415 33.333 0.00 0.00 0.00 3.50
1250 5091 7.817478 CCAAGATCATTAACCCAACTAAAAACC 59.183 37.037 0.00 0.00 0.00 3.27
1251 5092 7.330946 GCCAAGATCATTAACCCAACTAAAAAC 59.669 37.037 0.00 0.00 0.00 2.43
1263 5104 2.111041 GCAGCGCCAAGATCATTAAC 57.889 50.000 2.29 0.00 0.00 2.01
1313 5154 2.092429 TGCTTCACCTTCACCACTTTCT 60.092 45.455 0.00 0.00 0.00 2.52
1636 5477 5.868801 CACAAAGGAAAGACTTCAGCAAAAA 59.131 36.000 0.00 0.00 32.75 1.94
1637 5478 5.184864 TCACAAAGGAAAGACTTCAGCAAAA 59.815 36.000 0.00 0.00 32.75 2.44
1638 5479 4.704540 TCACAAAGGAAAGACTTCAGCAAA 59.295 37.500 0.00 0.00 32.75 3.68
1639 5480 4.269183 TCACAAAGGAAAGACTTCAGCAA 58.731 39.130 0.00 0.00 32.75 3.91
1640 5481 3.884895 TCACAAAGGAAAGACTTCAGCA 58.115 40.909 0.00 0.00 32.75 4.41
1641 5482 4.276926 ACATCACAAAGGAAAGACTTCAGC 59.723 41.667 0.00 0.00 32.75 4.26
1642 5483 6.183360 ACAACATCACAAAGGAAAGACTTCAG 60.183 38.462 0.00 0.00 32.75 3.02
1643 5484 5.652014 ACAACATCACAAAGGAAAGACTTCA 59.348 36.000 0.00 0.00 32.75 3.02
1644 5485 6.136541 ACAACATCACAAAGGAAAGACTTC 57.863 37.500 0.00 0.00 0.00 3.01
1645 5486 5.652014 TGACAACATCACAAAGGAAAGACTT 59.348 36.000 0.00 0.00 29.99 3.01
1646 5487 5.192927 TGACAACATCACAAAGGAAAGACT 58.807 37.500 0.00 0.00 29.99 3.24
1647 5488 5.499139 TGACAACATCACAAAGGAAAGAC 57.501 39.130 0.00 0.00 29.99 3.01
1648 5489 6.713762 ATTGACAACATCACAAAGGAAAGA 57.286 33.333 0.00 0.00 36.92 2.52
1649 5490 8.298854 TCATATTGACAACATCACAAAGGAAAG 58.701 33.333 0.00 0.00 36.92 2.62
1650 5491 8.175925 TCATATTGACAACATCACAAAGGAAA 57.824 30.769 0.00 0.00 36.92 3.13
1651 5492 7.665145 TCTCATATTGACAACATCACAAAGGAA 59.335 33.333 0.00 0.00 36.92 3.36
1652 5493 7.167535 TCTCATATTGACAACATCACAAAGGA 58.832 34.615 0.00 0.00 36.92 3.36
1653 5494 7.381766 TCTCATATTGACAACATCACAAAGG 57.618 36.000 0.00 0.00 36.92 3.11
1654 5495 9.499585 GATTCTCATATTGACAACATCACAAAG 57.500 33.333 0.00 0.00 36.92 2.77
1655 5496 9.012161 TGATTCTCATATTGACAACATCACAAA 57.988 29.630 0.00 0.00 36.92 2.83
1656 5497 8.564509 TGATTCTCATATTGACAACATCACAA 57.435 30.769 0.00 0.00 36.92 3.33
1657 5498 8.617809 CATGATTCTCATATTGACAACATCACA 58.382 33.333 0.00 0.00 34.28 3.58
1658 5499 8.833493 TCATGATTCTCATATTGACAACATCAC 58.167 33.333 0.00 0.00 34.28 3.06
1659 5500 8.967664 TCATGATTCTCATATTGACAACATCA 57.032 30.769 0.00 0.00 34.28 3.07
1660 5501 9.827411 CATCATGATTCTCATATTGACAACATC 57.173 33.333 5.16 0.00 34.28 3.06
1661 5502 8.297426 GCATCATGATTCTCATATTGACAACAT 58.703 33.333 5.16 0.00 34.28 2.71
1662 5503 7.283580 TGCATCATGATTCTCATATTGACAACA 59.716 33.333 5.16 0.00 34.28 3.33
1663 5504 7.645402 TGCATCATGATTCTCATATTGACAAC 58.355 34.615 5.16 0.00 34.28 3.32
1664 5505 7.811117 TGCATCATGATTCTCATATTGACAA 57.189 32.000 5.16 0.00 34.28 3.18
1665 5506 7.663905 TGATGCATCATGATTCTCATATTGACA 59.336 33.333 25.42 0.00 34.28 3.58
1666 5507 8.040716 TGATGCATCATGATTCTCATATTGAC 57.959 34.615 25.42 0.00 34.28 3.18
1667 5508 8.807948 ATGATGCATCATGATTCTCATATTGA 57.192 30.769 35.54 7.56 45.27 2.57
1671 5512 9.601217 CTCTAATGATGCATCATGATTCTCATA 57.399 33.333 36.37 22.63 46.22 2.15
1672 5513 8.322091 TCTCTAATGATGCATCATGATTCTCAT 58.678 33.333 36.37 22.72 46.22 2.90
1673 5514 7.676947 TCTCTAATGATGCATCATGATTCTCA 58.323 34.615 36.37 17.93 46.22 3.27
1674 5515 8.725405 ATCTCTAATGATGCATCATGATTCTC 57.275 34.615 36.37 7.08 46.22 2.87
1679 5520 9.433153 GTCTTAATCTCTAATGATGCATCATGA 57.567 33.333 36.37 29.68 46.22 3.07
1680 5521 9.216117 TGTCTTAATCTCTAATGATGCATCATG 57.784 33.333 36.37 26.22 46.22 3.07
1682 5523 7.383300 CGTGTCTTAATCTCTAATGATGCATCA 59.617 37.037 30.47 30.47 41.70 3.07
1683 5524 7.383572 ACGTGTCTTAATCTCTAATGATGCATC 59.616 37.037 20.14 20.14 0.00 3.91
1684 5525 7.212976 ACGTGTCTTAATCTCTAATGATGCAT 58.787 34.615 0.00 0.00 0.00 3.96
1685 5526 6.573434 ACGTGTCTTAATCTCTAATGATGCA 58.427 36.000 0.00 0.00 0.00 3.96
1686 5527 6.697455 TGACGTGTCTTAATCTCTAATGATGC 59.303 38.462 0.00 0.00 0.00 3.91
1687 5528 8.697960 CATGACGTGTCTTAATCTCTAATGATG 58.302 37.037 0.00 0.00 0.00 3.07
1688 5529 8.417106 ACATGACGTGTCTTAATCTCTAATGAT 58.583 33.333 0.00 0.00 35.77 2.45
1689 5530 7.702348 CACATGACGTGTCTTAATCTCTAATGA 59.298 37.037 0.00 0.00 39.62 2.57
1690 5531 7.835520 CACATGACGTGTCTTAATCTCTAATG 58.164 38.462 0.00 0.00 39.62 1.90
1691 5532 7.993821 CACATGACGTGTCTTAATCTCTAAT 57.006 36.000 0.00 0.00 39.62 1.73
1706 5547 5.508153 GGAGATGCTCTTATACACATGACGT 60.508 44.000 0.00 0.00 0.00 4.34
1707 5548 4.920340 GGAGATGCTCTTATACACATGACG 59.080 45.833 0.00 0.00 0.00 4.35
1708 5549 5.847304 TGGAGATGCTCTTATACACATGAC 58.153 41.667 0.00 0.00 0.00 3.06
1709 5550 6.127083 TGTTGGAGATGCTCTTATACACATGA 60.127 38.462 0.00 0.00 0.00 3.07
1710 5551 6.051074 TGTTGGAGATGCTCTTATACACATG 58.949 40.000 0.00 0.00 0.00 3.21
1711 5552 6.239217 TGTTGGAGATGCTCTTATACACAT 57.761 37.500 0.00 0.00 0.00 3.21
1712 5553 5.664457 CTGTTGGAGATGCTCTTATACACA 58.336 41.667 0.00 0.00 0.00 3.72
1713 5554 4.509600 GCTGTTGGAGATGCTCTTATACAC 59.490 45.833 0.00 0.00 0.00 2.90
1714 5555 4.443457 GGCTGTTGGAGATGCTCTTATACA 60.443 45.833 0.00 0.00 0.00 2.29
1715 5556 4.061596 GGCTGTTGGAGATGCTCTTATAC 58.938 47.826 0.00 0.00 0.00 1.47
1716 5557 3.243873 CGGCTGTTGGAGATGCTCTTATA 60.244 47.826 0.00 0.00 0.00 0.98
1782 5624 3.358707 GCCGCGTAAAACCAGGCA 61.359 61.111 4.92 0.00 46.48 4.75
1886 5734 0.457035 CCATATATGCAATGCCCCGC 59.543 55.000 7.24 0.00 0.00 6.13
2085 5988 2.017782 TCTTCCGAAGATGAGGACGAG 58.982 52.381 6.75 0.00 36.06 4.18
2086 5989 1.743958 GTCTTCCGAAGATGAGGACGA 59.256 52.381 13.92 0.00 40.18 4.20
2087 5990 2.196295 GTCTTCCGAAGATGAGGACG 57.804 55.000 13.92 0.00 40.18 4.79
2088 5991 1.743958 TCGTCTTCCGAAGATGAGGAC 59.256 52.381 23.58 7.26 45.93 3.85
2089 5992 2.124277 TCGTCTTCCGAAGATGAGGA 57.876 50.000 23.58 12.34 45.93 3.71
2532 6466 2.905415 TGTTGGAATGGGAGAAGCAT 57.095 45.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.