Multiple sequence alignment - TraesCS5D01G316600

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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 TraesCS5D01G316600 chr5D 100.000 3113 0 0 1 3113 410380904 410384016 0.000000e+00 5749.0
1 TraesCS5D01G316600 chr5D 78.163 664 117 15 1020 1672 410249971 410250617 6.260000e-107 398.0
2 TraesCS5D01G316600 chr5D 78.130 631 114 18 1345 1958 410303035 410303658 2.270000e-101 379.0
3 TraesCS5D01G316600 chr5D 78.571 518 93 12 1444 1952 410347111 410347619 2.990000e-85 326.0
4 TraesCS5D01G316600 chr5B 93.990 1431 71 8 792 2212 492402815 492404240 0.000000e+00 2152.0
5 TraesCS5D01G316600 chr5B 78.435 524 98 13 1446 1958 492257182 492257701 8.320000e-86 327.0
6 TraesCS5D01G316600 chr5A 93.211 1414 78 9 811 2212 521859515 521860922 0.000000e+00 2063.0
7 TraesCS5D01G316600 chr5A 75.206 851 170 26 1056 1881 521757560 521756726 6.340000e-97 364.0
8 TraesCS5D01G316600 chr7D 98.037 764 14 1 2 765 511334000 511334762 0.000000e+00 1327.0
9 TraesCS5D01G316600 chr7D 74.272 206 47 3 1455 1657 90246172 90246374 7.160000e-12 82.4
10 TraesCS5D01G316600 chr3D 97.798 772 12 4 1 772 46523127 46522361 0.000000e+00 1327.0
11 TraesCS5D01G316600 chr3D 95.138 617 10 6 159 774 579364372 579363775 0.000000e+00 955.0
12 TraesCS5D01G316600 chr4D 97.781 766 15 2 2 766 20460729 20461493 0.000000e+00 1319.0
13 TraesCS5D01G316600 chr2A 93.233 798 30 3 1 774 10989423 10988626 0.000000e+00 1153.0
14 TraesCS5D01G316600 chr2A 87.406 802 87 9 2210 3003 605245723 605246518 0.000000e+00 909.0
15 TraesCS5D01G316600 chr2A 75.000 668 132 29 1019 1661 744905458 744904801 3.060000e-70 276.0
16 TraesCS5D01G316600 chr2A 74.924 662 122 35 1019 1660 744994667 744995304 2.380000e-66 263.0
17 TraesCS5D01G316600 chr2A 96.992 133 4 0 633 765 601328214 601328082 1.120000e-54 224.0
18 TraesCS5D01G316600 chr2A 72.905 716 149 24 1020 1725 744802001 744801321 4.070000e-49 206.0
19 TraesCS5D01G316600 chr2A 91.463 82 7 0 1078 1159 744981892 744981973 2.540000e-21 113.0
20 TraesCS5D01G316600 chr1A 92.481 798 28 17 1 773 104828656 104827866 0.000000e+00 1112.0
21 TraesCS5D01G316600 chr1A 87.578 805 87 10 2206 3003 427949583 427950381 0.000000e+00 920.0
22 TraesCS5D01G316600 chr1A 87.908 612 65 9 12 619 492619391 492618785 0.000000e+00 712.0
23 TraesCS5D01G316600 chr1A 87.092 612 70 9 12 619 492429567 492428961 0.000000e+00 684.0
24 TraesCS5D01G316600 chr1A 86.799 606 68 9 17 619 75803083 75802487 0.000000e+00 665.0
25 TraesCS5D01G316600 chr1A 92.424 132 10 0 635 766 75802349 75802218 4.100000e-44 189.0
26 TraesCS5D01G316600 chr1A 90.840 131 12 0 635 765 492618649 492618519 3.190000e-40 176.0
27 TraesCS5D01G316600 chr1D 88.346 798 76 8 2213 3003 142909912 142910699 0.000000e+00 942.0
28 TraesCS5D01G316600 chr1D 87.594 798 84 9 2213 3003 2431511 2430722 0.000000e+00 911.0
29 TraesCS5D01G316600 chr1D 87.578 797 85 7 2213 3003 327724979 327725767 0.000000e+00 911.0
30 TraesCS5D01G316600 chr1D 98.148 108 2 0 3006 3113 32691108 32691215 4.100000e-44 189.0
31 TraesCS5D01G316600 chr1D 98.148 108 2 0 3006 3113 66721583 66721690 4.100000e-44 189.0
32 TraesCS5D01G316600 chr1D 98.148 108 2 0 3006 3113 149904875 149904768 4.100000e-44 189.0
33 TraesCS5D01G316600 chr1D 98.148 108 2 0 3006 3113 330512569 330512462 4.100000e-44 189.0
34 TraesCS5D01G316600 chr6B 87.909 794 85 8 2213 3000 488894132 488894920 0.000000e+00 924.0
35 TraesCS5D01G316600 chr3A 87.688 796 90 7 2213 3003 742224319 742225111 0.000000e+00 920.0
36 TraesCS5D01G316600 chr2B 88.123 783 68 17 2212 2989 82302435 82303197 0.000000e+00 907.0
37 TraesCS5D01G316600 chr2B 73.653 668 137 26 1019 1659 748588879 748588224 4.040000e-54 222.0
38 TraesCS5D01G316600 chr4A 86.709 790 98 6 2213 2998 75950426 75951212 0.000000e+00 870.0
39 TraesCS5D01G316600 chr2D 72.970 862 180 40 1019 1849 613324759 613325598 5.150000e-63 252.0
40 TraesCS5D01G316600 chr2D 73.653 668 138 30 1019 1661 613235099 613234445 1.120000e-54 224.0
41 TraesCS5D01G316600 chr2D 80.357 112 21 1 1037 1147 24546425 24546536 1.990000e-12 84.2
42 TraesCS5D01G316600 chr6D 98.148 108 2 0 3006 3113 36964491 36964598 4.100000e-44 189.0
43 TraesCS5D01G316600 chr6D 98.148 108 2 0 3006 3113 77456715 77456822 4.100000e-44 189.0
44 TraesCS5D01G316600 chr6D 98.148 108 2 0 3006 3113 132020192 132020299 4.100000e-44 189.0
45 TraesCS5D01G316600 chr6D 98.148 108 2 0 3006 3113 193743975 193744082 4.100000e-44 189.0
46 TraesCS5D01G316600 chr6D 98.148 108 2 0 3006 3113 318254232 318254125 4.100000e-44 189.0


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 TraesCS5D01G316600 chr5D 410380904 410384016 3112 False 5749 5749 100.0000 1 3113 1 chr5D.!!$F4 3112
1 TraesCS5D01G316600 chr5D 410249971 410250617 646 False 398 398 78.1630 1020 1672 1 chr5D.!!$F1 652
2 TraesCS5D01G316600 chr5D 410303035 410303658 623 False 379 379 78.1300 1345 1958 1 chr5D.!!$F2 613
3 TraesCS5D01G316600 chr5D 410347111 410347619 508 False 326 326 78.5710 1444 1952 1 chr5D.!!$F3 508
4 TraesCS5D01G316600 chr5B 492402815 492404240 1425 False 2152 2152 93.9900 792 2212 1 chr5B.!!$F2 1420
5 TraesCS5D01G316600 chr5B 492257182 492257701 519 False 327 327 78.4350 1446 1958 1 chr5B.!!$F1 512
6 TraesCS5D01G316600 chr5A 521859515 521860922 1407 False 2063 2063 93.2110 811 2212 1 chr5A.!!$F1 1401
7 TraesCS5D01G316600 chr5A 521756726 521757560 834 True 364 364 75.2060 1056 1881 1 chr5A.!!$R1 825
8 TraesCS5D01G316600 chr7D 511334000 511334762 762 False 1327 1327 98.0370 2 765 1 chr7D.!!$F2 763
9 TraesCS5D01G316600 chr3D 46522361 46523127 766 True 1327 1327 97.7980 1 772 1 chr3D.!!$R1 771
10 TraesCS5D01G316600 chr3D 579363775 579364372 597 True 955 955 95.1380 159 774 1 chr3D.!!$R2 615
11 TraesCS5D01G316600 chr4D 20460729 20461493 764 False 1319 1319 97.7810 2 766 1 chr4D.!!$F1 764
12 TraesCS5D01G316600 chr2A 10988626 10989423 797 True 1153 1153 93.2330 1 774 1 chr2A.!!$R1 773
13 TraesCS5D01G316600 chr2A 605245723 605246518 795 False 909 909 87.4060 2210 3003 1 chr2A.!!$F1 793
14 TraesCS5D01G316600 chr2A 744904801 744905458 657 True 276 276 75.0000 1019 1661 1 chr2A.!!$R4 642
15 TraesCS5D01G316600 chr2A 744994667 744995304 637 False 263 263 74.9240 1019 1660 1 chr2A.!!$F3 641
16 TraesCS5D01G316600 chr2A 744801321 744802001 680 True 206 206 72.9050 1020 1725 1 chr2A.!!$R3 705
17 TraesCS5D01G316600 chr1A 104827866 104828656 790 True 1112 1112 92.4810 1 773 1 chr1A.!!$R1 772
18 TraesCS5D01G316600 chr1A 427949583 427950381 798 False 920 920 87.5780 2206 3003 1 chr1A.!!$F1 797
19 TraesCS5D01G316600 chr1A 492428961 492429567 606 True 684 684 87.0920 12 619 1 chr1A.!!$R2 607
20 TraesCS5D01G316600 chr1A 492618519 492619391 872 True 444 712 89.3740 12 765 2 chr1A.!!$R4 753
21 TraesCS5D01G316600 chr1A 75802218 75803083 865 True 427 665 89.6115 17 766 2 chr1A.!!$R3 749
22 TraesCS5D01G316600 chr1D 142909912 142910699 787 False 942 942 88.3460 2213 3003 1 chr1D.!!$F3 790
23 TraesCS5D01G316600 chr1D 2430722 2431511 789 True 911 911 87.5940 2213 3003 1 chr1D.!!$R1 790
24 TraesCS5D01G316600 chr1D 327724979 327725767 788 False 911 911 87.5780 2213 3003 1 chr1D.!!$F4 790
25 TraesCS5D01G316600 chr6B 488894132 488894920 788 False 924 924 87.9090 2213 3000 1 chr6B.!!$F1 787
26 TraesCS5D01G316600 chr3A 742224319 742225111 792 False 920 920 87.6880 2213 3003 1 chr3A.!!$F1 790
27 TraesCS5D01G316600 chr2B 82302435 82303197 762 False 907 907 88.1230 2212 2989 1 chr2B.!!$F1 777
28 TraesCS5D01G316600 chr2B 748588224 748588879 655 True 222 222 73.6530 1019 1659 1 chr2B.!!$R1 640
29 TraesCS5D01G316600 chr4A 75950426 75951212 786 False 870 870 86.7090 2213 2998 1 chr4A.!!$F1 785
30 TraesCS5D01G316600 chr2D 613324759 613325598 839 False 252 252 72.9700 1019 1849 1 chr2D.!!$F2 830
31 TraesCS5D01G316600 chr2D 613234445 613235099 654 True 224 224 73.6530 1019 1661 1 chr2D.!!$R1 642

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
584 600 1.002087 CGAAGGTCTGGTAGCAGGTTT 59.998 52.381 21.22 12.86 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2618 0.419459 AGGGAGAGAGGGATTGGTGT 59.581 55.0 0.0 0.0 0.0 4.16 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
334 342 1.343142 ACTCTGTGTGCACACCGATAA 59.657 47.619 39.34 23.66 45.88 1.75
552 566 1.429930 TGTTGGTTCTGGTGGCTAGA 58.570 50.000 0.00 0.00 0.00 2.43
584 600 1.002087 CGAAGGTCTGGTAGCAGGTTT 59.998 52.381 21.22 12.86 0.00 3.27
713 852 9.063615 AGTTCGATGTATTTTTCAAGTTTAGGT 57.936 29.630 0.00 0.00 0.00 3.08
768 907 7.016661 AGCACCACTGGTATATTTAGCTCTAAT 59.983 37.037 0.00 0.00 32.11 1.73
814 953 2.183811 CAGAGAGCTGGCCGAGTG 59.816 66.667 0.00 0.00 38.51 3.51
823 962 1.813513 CTGGCCGAGTGATTCAGTTT 58.186 50.000 0.00 0.00 0.00 2.66
945 1086 1.283736 CGTCCCGTTAAAAGGATCGG 58.716 55.000 0.00 0.00 42.22 4.18
950 1091 3.942748 TCCCGTTAAAAGGATCGGAAATG 59.057 43.478 4.00 0.00 44.86 2.32
989 1130 5.414360 TGGAAGATCGAGAACAAATCAGAG 58.586 41.667 0.00 0.00 0.00 3.35
991 1132 6.127225 TGGAAGATCGAGAACAAATCAGAGAT 60.127 38.462 0.00 0.00 0.00 2.75
992 1133 6.420604 GGAAGATCGAGAACAAATCAGAGATC 59.579 42.308 0.00 0.00 36.03 2.75
993 1134 6.462552 AGATCGAGAACAAATCAGAGATCA 57.537 37.500 0.00 0.00 37.15 2.92
1047 1199 1.145819 GCTGGTGGAGATCCTGCTC 59.854 63.158 0.00 0.00 43.37 4.26
1100 1254 2.357881 CGTCTGCAAGCTCTGGCA 60.358 61.111 7.35 7.35 41.70 4.92
1206 1363 1.820481 CGACGACCTCTCCTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
1293 1495 1.748122 GGATGAGGTGCAGCTGGTG 60.748 63.158 25.60 1.76 32.29 4.17
1393 1595 3.003173 CCGGGGAGAAGCTGTCCA 61.003 66.667 15.59 0.00 35.57 4.02
1768 2023 1.687123 ACAAGCCTGACGACTACAACT 59.313 47.619 0.00 0.00 0.00 3.16
1801 2056 3.462678 GGAGGCTGGGAGTCGTCC 61.463 72.222 0.00 0.00 43.05 4.79
1944 2208 1.434188 TCCTGAAGTTTGAGGGCAGA 58.566 50.000 0.00 0.00 31.92 4.26
1945 2209 1.988107 TCCTGAAGTTTGAGGGCAGAT 59.012 47.619 0.00 0.00 31.92 2.90
1946 2210 2.376518 TCCTGAAGTTTGAGGGCAGATT 59.623 45.455 0.00 0.00 31.92 2.40
1958 2222 3.758554 GAGGGCAGATTGTTGTTGTATGT 59.241 43.478 0.00 0.00 0.00 2.29
2032 2299 2.426024 CTGGTGGCCAAGATGAAAGATG 59.574 50.000 7.24 0.00 30.80 2.90
2036 2303 4.518211 GGTGGCCAAGATGAAAGATGATAG 59.482 45.833 7.24 0.00 0.00 2.08
2102 2369 3.541632 AGCCATTAGGTGTTTACGATGG 58.458 45.455 0.00 0.00 36.40 3.51
2117 2384 2.764572 ACGATGGAACCAAGTAGGGTAG 59.235 50.000 0.00 0.00 37.53 3.18
2143 2410 2.972713 AGTGCTTACTCCCTCTTTCACA 59.027 45.455 0.00 0.00 0.00 3.58
2171 2438 0.623723 TTCCCCTAGCCATGAACACC 59.376 55.000 0.00 0.00 0.00 4.16
2184 2451 6.014327 AGCCATGAACACCTTGTTTCATTATT 60.014 34.615 0.00 0.00 41.28 1.40
2340 2618 8.995027 AGGCTCAACCAATACAATGAATATTA 57.005 30.769 0.00 0.00 43.14 0.98
2495 2782 4.867599 CTAGGGTTCGTCCGCCGC 62.868 72.222 0.00 0.00 37.00 6.53
2509 2796 4.657824 CCGCTCGTGTTGACCGGT 62.658 66.667 6.92 6.92 40.31 5.28
2528 2817 3.557264 CGGTTGCCCTAGAGTCTTTTTCT 60.557 47.826 0.00 0.00 0.00 2.52
2538 2827 3.071747 AGAGTCTTTTTCTCGAGCCCTTT 59.928 43.478 7.81 0.00 37.07 3.11
2539 2828 3.142174 AGTCTTTTTCTCGAGCCCTTTG 58.858 45.455 7.81 0.00 0.00 2.77
2540 2829 1.880027 TCTTTTTCTCGAGCCCTTTGC 59.120 47.619 7.81 0.00 41.71 3.68
2590 2885 3.363724 GGTCGTTTTGATCGGCATTTTTC 59.636 43.478 0.00 0.00 34.45 2.29
2598 2893 5.207110 TGATCGGCATTTTTCCTTTTTGA 57.793 34.783 0.00 0.00 0.00 2.69
2603 2898 7.326968 TCGGCATTTTTCCTTTTTGATTTTT 57.673 28.000 0.00 0.00 0.00 1.94
2665 2960 4.063967 CCACCGTGCGCCTCTACA 62.064 66.667 4.18 0.00 0.00 2.74
2675 2970 2.338015 GCCTCTACACCGACACCGA 61.338 63.158 0.00 0.00 38.22 4.69
2974 3271 4.203076 GGCTACACCGATCCGCGT 62.203 66.667 4.92 0.00 38.67 6.01
3019 3316 3.967332 CGTAAGGTTGGGGTAAGAAGA 57.033 47.619 0.00 0.00 0.00 2.87
3020 3317 4.482952 CGTAAGGTTGGGGTAAGAAGAT 57.517 45.455 0.00 0.00 0.00 2.40
3021 3318 4.840271 CGTAAGGTTGGGGTAAGAAGATT 58.160 43.478 0.00 0.00 0.00 2.40
3022 3319 4.634443 CGTAAGGTTGGGGTAAGAAGATTG 59.366 45.833 0.00 0.00 0.00 2.67
3023 3320 4.741928 AAGGTTGGGGTAAGAAGATTGT 57.258 40.909 0.00 0.00 0.00 2.71
3024 3321 4.034285 AGGTTGGGGTAAGAAGATTGTG 57.966 45.455 0.00 0.00 0.00 3.33
3025 3322 3.655777 AGGTTGGGGTAAGAAGATTGTGA 59.344 43.478 0.00 0.00 0.00 3.58
3026 3323 4.292306 AGGTTGGGGTAAGAAGATTGTGAT 59.708 41.667 0.00 0.00 0.00 3.06
3027 3324 4.640647 GGTTGGGGTAAGAAGATTGTGATC 59.359 45.833 0.00 0.00 0.00 2.92
3028 3325 5.253330 GTTGGGGTAAGAAGATTGTGATCA 58.747 41.667 0.00 0.00 34.60 2.92
3029 3326 5.512942 TGGGGTAAGAAGATTGTGATCAA 57.487 39.130 0.00 0.00 37.98 2.57
3030 3327 5.500234 TGGGGTAAGAAGATTGTGATCAAG 58.500 41.667 0.00 0.00 36.97 3.02
3031 3328 5.014123 TGGGGTAAGAAGATTGTGATCAAGT 59.986 40.000 0.00 0.00 36.97 3.16
3032 3329 5.946377 GGGGTAAGAAGATTGTGATCAAGTT 59.054 40.000 0.00 0.00 36.97 2.66
3033 3330 6.127897 GGGGTAAGAAGATTGTGATCAAGTTG 60.128 42.308 0.00 0.00 36.97 3.16
3034 3331 6.655003 GGGTAAGAAGATTGTGATCAAGTTGA 59.345 38.462 8.27 8.27 36.97 3.18
3035 3332 7.174946 GGGTAAGAAGATTGTGATCAAGTTGAA 59.825 37.037 10.14 0.00 36.97 2.69
3036 3333 8.233190 GGTAAGAAGATTGTGATCAAGTTGAAG 58.767 37.037 10.14 0.00 36.97 3.02
3037 3334 6.814506 AGAAGATTGTGATCAAGTTGAAGG 57.185 37.500 10.14 0.00 36.97 3.46
3038 3335 6.537355 AGAAGATTGTGATCAAGTTGAAGGA 58.463 36.000 10.14 0.00 36.97 3.36
3039 3336 7.173722 AGAAGATTGTGATCAAGTTGAAGGAT 58.826 34.615 10.14 0.41 36.97 3.24
3040 3337 6.754702 AGATTGTGATCAAGTTGAAGGATG 57.245 37.500 10.14 0.00 36.97 3.51
3041 3338 6.243900 AGATTGTGATCAAGTTGAAGGATGT 58.756 36.000 10.14 0.00 36.97 3.06
3042 3339 5.947228 TTGTGATCAAGTTGAAGGATGTC 57.053 39.130 10.14 2.31 0.00 3.06
3043 3340 5.233083 TGTGATCAAGTTGAAGGATGTCT 57.767 39.130 10.14 0.00 0.00 3.41
3044 3341 5.624159 TGTGATCAAGTTGAAGGATGTCTT 58.376 37.500 10.14 0.00 38.65 3.01
3045 3342 7.094463 ATTGTGATCAAGTTGAAGGATGTCTTC 60.094 37.037 10.14 0.08 42.84 2.87
3053 3350 1.734465 GAAGGATGTCTTCTGTTGCCG 59.266 52.381 0.00 0.00 46.30 5.69
3054 3351 0.036010 AGGATGTCTTCTGTTGCCGG 60.036 55.000 0.00 0.00 0.00 6.13
3055 3352 0.036388 GGATGTCTTCTGTTGCCGGA 60.036 55.000 5.05 0.00 0.00 5.14
3056 3353 1.610624 GGATGTCTTCTGTTGCCGGAA 60.611 52.381 5.05 0.00 34.76 4.30
3057 3354 1.464997 GATGTCTTCTGTTGCCGGAAC 59.535 52.381 5.05 7.79 32.51 3.62
3058 3355 0.468226 TGTCTTCTGTTGCCGGAACT 59.532 50.000 5.05 0.00 35.37 3.01
3059 3356 1.134220 TGTCTTCTGTTGCCGGAACTT 60.134 47.619 5.05 0.00 35.37 2.66
3060 3357 1.264288 GTCTTCTGTTGCCGGAACTTG 59.736 52.381 5.05 5.03 35.37 3.16
3061 3358 0.593128 CTTCTGTTGCCGGAACTTGG 59.407 55.000 5.05 2.72 35.37 3.61
3062 3359 0.106918 TTCTGTTGCCGGAACTTGGT 60.107 50.000 5.05 0.00 35.37 3.67
3063 3360 0.534203 TCTGTTGCCGGAACTTGGTC 60.534 55.000 5.05 0.00 35.37 4.02
3064 3361 1.515521 CTGTTGCCGGAACTTGGTCC 61.516 60.000 5.05 0.00 35.37 4.46
3065 3362 1.228154 GTTGCCGGAACTTGGTCCT 60.228 57.895 5.05 0.00 35.31 3.85
3066 3363 1.072505 TTGCCGGAACTTGGTCCTC 59.927 57.895 5.05 0.00 35.31 3.71
3067 3364 2.046217 GCCGGAACTTGGTCCTCC 60.046 66.667 5.05 0.00 35.31 4.30
3069 3366 3.057337 CGGAACTTGGTCCTCCGT 58.943 61.111 8.75 0.00 45.62 4.69
3070 3367 1.374252 CGGAACTTGGTCCTCCGTG 60.374 63.158 8.75 0.00 45.62 4.94
3071 3368 1.003718 GGAACTTGGTCCTCCGTGG 60.004 63.158 0.00 0.00 34.56 4.94
3072 3369 1.671379 GAACTTGGTCCTCCGTGGC 60.671 63.158 0.00 0.00 36.30 5.01
3073 3370 3.192103 AACTTGGTCCTCCGTGGCC 62.192 63.158 0.00 0.00 36.30 5.36
3074 3371 3.322466 CTTGGTCCTCCGTGGCCT 61.322 66.667 3.32 0.00 36.30 5.19
3075 3372 2.852075 TTGGTCCTCCGTGGCCTT 60.852 61.111 3.32 0.00 36.30 4.35
3076 3373 2.804828 CTTGGTCCTCCGTGGCCTTC 62.805 65.000 3.32 0.00 36.30 3.46
3077 3374 3.003763 GGTCCTCCGTGGCCTTCT 61.004 66.667 3.32 0.00 35.26 2.85
3078 3375 2.593956 GGTCCTCCGTGGCCTTCTT 61.594 63.158 3.32 0.00 35.26 2.52
3079 3376 1.376037 GTCCTCCGTGGCCTTCTTG 60.376 63.158 3.32 0.00 35.26 3.02
3080 3377 1.535444 TCCTCCGTGGCCTTCTTGA 60.535 57.895 3.32 0.00 35.26 3.02
3081 3378 0.909610 TCCTCCGTGGCCTTCTTGAT 60.910 55.000 3.32 0.00 35.26 2.57
3082 3379 0.462759 CCTCCGTGGCCTTCTTGATC 60.463 60.000 3.32 0.00 0.00 2.92
3083 3380 0.462759 CTCCGTGGCCTTCTTGATCC 60.463 60.000 3.32 0.00 0.00 3.36
3084 3381 1.452108 CCGTGGCCTTCTTGATCCC 60.452 63.158 3.32 0.00 0.00 3.85
3085 3382 1.604378 CGTGGCCTTCTTGATCCCT 59.396 57.895 3.32 0.00 0.00 4.20
3086 3383 0.462759 CGTGGCCTTCTTGATCCCTC 60.463 60.000 3.32 0.00 0.00 4.30
3087 3384 0.106967 GTGGCCTTCTTGATCCCTCC 60.107 60.000 3.32 0.00 0.00 4.30
3088 3385 0.549902 TGGCCTTCTTGATCCCTCCA 60.550 55.000 3.32 0.00 0.00 3.86
3089 3386 0.849417 GGCCTTCTTGATCCCTCCAT 59.151 55.000 0.00 0.00 0.00 3.41
3090 3387 1.202867 GGCCTTCTTGATCCCTCCATC 60.203 57.143 0.00 0.00 0.00 3.51
3091 3388 1.202867 GCCTTCTTGATCCCTCCATCC 60.203 57.143 0.00 0.00 0.00 3.51
3092 3389 2.416638 CCTTCTTGATCCCTCCATCCT 58.583 52.381 0.00 0.00 0.00 3.24
3093 3390 2.782341 CCTTCTTGATCCCTCCATCCTT 59.218 50.000 0.00 0.00 0.00 3.36
3094 3391 3.434739 CCTTCTTGATCCCTCCATCCTTG 60.435 52.174 0.00 0.00 0.00 3.61
3095 3392 2.850833 TCTTGATCCCTCCATCCTTGT 58.149 47.619 0.00 0.00 0.00 3.16
3096 3393 3.192944 TCTTGATCCCTCCATCCTTGTT 58.807 45.455 0.00 0.00 0.00 2.83
3097 3394 3.054139 TCTTGATCCCTCCATCCTTGTTG 60.054 47.826 0.00 0.00 0.00 3.33
3098 3395 2.561187 TGATCCCTCCATCCTTGTTGA 58.439 47.619 0.00 0.00 0.00 3.18
3099 3396 3.125656 TGATCCCTCCATCCTTGTTGAT 58.874 45.455 0.00 0.00 0.00 2.57
3100 3397 3.528905 TGATCCCTCCATCCTTGTTGATT 59.471 43.478 0.00 0.00 0.00 2.57
3101 3398 4.017222 TGATCCCTCCATCCTTGTTGATTT 60.017 41.667 0.00 0.00 0.00 2.17
3102 3399 3.968265 TCCCTCCATCCTTGTTGATTTC 58.032 45.455 0.00 0.00 0.00 2.17
3103 3400 3.026694 CCCTCCATCCTTGTTGATTTCC 58.973 50.000 0.00 0.00 0.00 3.13
3104 3401 3.564133 CCCTCCATCCTTGTTGATTTCCA 60.564 47.826 0.00 0.00 0.00 3.53
3105 3402 4.284178 CCTCCATCCTTGTTGATTTCCAT 58.716 43.478 0.00 0.00 0.00 3.41
3106 3403 4.098960 CCTCCATCCTTGTTGATTTCCATG 59.901 45.833 0.00 0.00 0.00 3.66
3107 3404 4.025360 TCCATCCTTGTTGATTTCCATGG 58.975 43.478 4.97 4.97 0.00 3.66
3108 3405 3.133362 CCATCCTTGTTGATTTCCATGGG 59.867 47.826 13.02 0.00 0.00 4.00
3109 3406 3.541242 TCCTTGTTGATTTCCATGGGT 57.459 42.857 13.02 0.00 0.00 4.51
3110 3407 3.855668 TCCTTGTTGATTTCCATGGGTT 58.144 40.909 13.02 0.00 0.00 4.11
3111 3408 3.831911 TCCTTGTTGATTTCCATGGGTTC 59.168 43.478 13.02 7.20 0.00 3.62
3112 3409 3.834231 CCTTGTTGATTTCCATGGGTTCT 59.166 43.478 13.02 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
552 566 1.229853 ACCTTCGGGGATCCCTGTT 60.230 57.895 34.37 17.36 42.67 3.16
713 852 4.979335 TGTCATGGATGTTCACTTTGGTA 58.021 39.130 0.00 0.00 0.00 3.25
780 919 9.791801 CAGCTCTCTGCCTAATCTATATCTATA 57.208 37.037 0.00 0.00 44.23 1.31
781 920 7.725397 CCAGCTCTCTGCCTAATCTATATCTAT 59.275 40.741 0.00 0.00 44.23 1.98
782 921 7.059788 CCAGCTCTCTGCCTAATCTATATCTA 58.940 42.308 0.00 0.00 44.23 1.98
783 922 5.893255 CCAGCTCTCTGCCTAATCTATATCT 59.107 44.000 0.00 0.00 44.23 1.98
784 923 5.451798 GCCAGCTCTCTGCCTAATCTATATC 60.452 48.000 0.00 0.00 44.23 1.63
785 924 4.405358 GCCAGCTCTCTGCCTAATCTATAT 59.595 45.833 0.00 0.00 44.23 0.86
786 925 3.766591 GCCAGCTCTCTGCCTAATCTATA 59.233 47.826 0.00 0.00 44.23 1.31
787 926 2.566724 GCCAGCTCTCTGCCTAATCTAT 59.433 50.000 0.00 0.00 44.23 1.98
788 927 1.967066 GCCAGCTCTCTGCCTAATCTA 59.033 52.381 0.00 0.00 44.23 1.98
789 928 0.758123 GCCAGCTCTCTGCCTAATCT 59.242 55.000 0.00 0.00 44.23 2.40
790 929 0.250252 GGCCAGCTCTCTGCCTAATC 60.250 60.000 0.00 0.00 44.23 1.75
809 948 6.017933 GTCAATGCTTAAACTGAATCACTCG 58.982 40.000 0.00 0.00 0.00 4.18
814 953 5.545658 TCCGTCAATGCTTAAACTGAATC 57.454 39.130 0.00 0.00 0.00 2.52
823 962 4.096231 CCACAATGAATCCGTCAATGCTTA 59.904 41.667 0.00 0.00 40.32 3.09
945 1086 7.288810 TCCAGTTTATATTGCCCATCATTTC 57.711 36.000 0.00 0.00 0.00 2.17
950 1091 6.128172 CGATCTTCCAGTTTATATTGCCCATC 60.128 42.308 0.00 0.00 0.00 3.51
989 1130 2.033801 CACGCCTCCATTGGATTTGATC 59.966 50.000 5.70 0.00 0.00 2.92
991 1132 1.462616 CACGCCTCCATTGGATTTGA 58.537 50.000 5.70 0.00 0.00 2.69
992 1133 0.179129 GCACGCCTCCATTGGATTTG 60.179 55.000 5.70 1.44 0.00 2.32
993 1134 0.323725 AGCACGCCTCCATTGGATTT 60.324 50.000 5.70 0.00 0.00 2.17
1592 1809 1.760192 GCATCTCTTGCCATTGGAGT 58.240 50.000 6.95 0.00 46.15 3.85
1768 2023 3.307906 CCCGTCCACCTCGGTCAA 61.308 66.667 3.78 0.00 45.63 3.18
1927 2191 3.152341 ACAATCTGCCCTCAAACTTCAG 58.848 45.455 0.00 0.00 0.00 3.02
1944 2208 5.178623 CCGTGAGTACACATACAACAACAAT 59.821 40.000 0.00 0.00 46.20 2.71
1945 2209 4.508492 CCGTGAGTACACATACAACAACAA 59.492 41.667 0.00 0.00 46.20 2.83
1946 2210 4.052608 CCGTGAGTACACATACAACAACA 58.947 43.478 0.00 0.00 46.20 3.33
2032 2299 6.382869 TTGGTAGTTAGAACCGTAGCTATC 57.617 41.667 0.00 0.00 40.08 2.08
2036 2303 3.928992 GGTTTGGTAGTTAGAACCGTAGC 59.071 47.826 0.00 0.00 40.08 3.58
2102 2369 5.624052 GCACTAACTCTACCCTACTTGGTTC 60.624 48.000 0.00 0.00 39.91 3.62
2117 2384 5.047235 TGAAAGAGGGAGTAAGCACTAACTC 60.047 44.000 0.00 0.00 41.16 3.01
2143 2410 2.487775 TGGCTAGGGGAACACATACAT 58.512 47.619 0.00 0.00 0.00 2.29
2154 2421 0.625849 AAGGTGTTCATGGCTAGGGG 59.374 55.000 0.00 0.00 0.00 4.79
2171 2438 8.557864 TGCAATGGACAAAAATAATGAAACAAG 58.442 29.630 0.00 0.00 0.00 3.16
2323 2591 9.912634 GGATTGGTGTAATATTCATTGTATTGG 57.087 33.333 0.00 0.00 0.00 3.16
2340 2618 0.419459 AGGGAGAGAGGGATTGGTGT 59.581 55.000 0.00 0.00 0.00 4.16
2434 2721 3.399181 GGTCATGGAGGCCGACCA 61.399 66.667 22.94 22.94 46.98 4.02
2495 2782 2.604174 GGCAACCGGTCAACACGAG 61.604 63.158 8.04 0.00 0.00 4.18
2509 2796 3.576982 TCGAGAAAAAGACTCTAGGGCAA 59.423 43.478 0.00 0.00 32.87 4.52
2564 2859 1.573829 GCCGATCAAAACGACCTGCA 61.574 55.000 0.00 0.00 0.00 4.41
2567 2862 1.821216 AATGCCGATCAAAACGACCT 58.179 45.000 0.00 0.00 0.00 3.85
2590 2885 8.589629 CAAGCATAGATCGAAAAATCAAAAAGG 58.410 33.333 0.00 0.00 0.00 3.11
2954 3251 2.889617 CGGATCGGTGTAGCCACA 59.110 61.111 0.00 0.00 43.71 4.17
2991 3288 1.078001 CCAACCTTACGGCCCGAAT 60.078 57.895 11.71 0.00 0.00 3.34
3003 3300 3.655777 TCACAATCTTCTTACCCCAACCT 59.344 43.478 0.00 0.00 0.00 3.50
3004 3301 4.028993 TCACAATCTTCTTACCCCAACC 57.971 45.455 0.00 0.00 0.00 3.77
3005 3302 5.253330 TGATCACAATCTTCTTACCCCAAC 58.747 41.667 0.00 0.00 32.75 3.77
3006 3303 5.512942 TGATCACAATCTTCTTACCCCAA 57.487 39.130 0.00 0.00 32.75 4.12
3007 3304 5.014123 ACTTGATCACAATCTTCTTACCCCA 59.986 40.000 0.00 0.00 35.37 4.96
3008 3305 5.501156 ACTTGATCACAATCTTCTTACCCC 58.499 41.667 0.00 0.00 35.37 4.95
3009 3306 6.655003 TCAACTTGATCACAATCTTCTTACCC 59.345 38.462 0.00 0.00 35.37 3.69
3010 3307 7.672983 TCAACTTGATCACAATCTTCTTACC 57.327 36.000 0.00 0.00 35.37 2.85
3011 3308 8.233190 CCTTCAACTTGATCACAATCTTCTTAC 58.767 37.037 0.00 0.00 35.37 2.34
3012 3309 8.156820 TCCTTCAACTTGATCACAATCTTCTTA 58.843 33.333 0.00 0.00 35.37 2.10
3013 3310 7.000472 TCCTTCAACTTGATCACAATCTTCTT 59.000 34.615 0.00 0.00 35.37 2.52
3014 3311 6.537355 TCCTTCAACTTGATCACAATCTTCT 58.463 36.000 0.00 0.00 35.37 2.85
3015 3312 6.808008 TCCTTCAACTTGATCACAATCTTC 57.192 37.500 0.00 0.00 35.37 2.87
3016 3313 6.718454 ACATCCTTCAACTTGATCACAATCTT 59.282 34.615 0.00 0.00 35.37 2.40
3017 3314 6.243900 ACATCCTTCAACTTGATCACAATCT 58.756 36.000 0.00 0.00 35.37 2.40
3018 3315 6.373774 AGACATCCTTCAACTTGATCACAATC 59.626 38.462 0.00 0.00 35.37 2.67
3019 3316 6.243900 AGACATCCTTCAACTTGATCACAAT 58.756 36.000 0.00 0.00 35.37 2.71
3020 3317 5.624159 AGACATCCTTCAACTTGATCACAA 58.376 37.500 0.00 0.00 34.65 3.33
3021 3318 5.233083 AGACATCCTTCAACTTGATCACA 57.767 39.130 0.00 0.00 0.00 3.58
3034 3331 1.611673 CCGGCAACAGAAGACATCCTT 60.612 52.381 0.00 0.00 37.93 3.36
3035 3332 0.036010 CCGGCAACAGAAGACATCCT 60.036 55.000 0.00 0.00 0.00 3.24
3036 3333 0.036388 TCCGGCAACAGAAGACATCC 60.036 55.000 0.00 0.00 0.00 3.51
3037 3334 1.464997 GTTCCGGCAACAGAAGACATC 59.535 52.381 0.00 0.00 32.52 3.06
3038 3335 1.072331 AGTTCCGGCAACAGAAGACAT 59.928 47.619 15.94 0.00 37.48 3.06
3039 3336 0.468226 AGTTCCGGCAACAGAAGACA 59.532 50.000 15.94 0.00 37.48 3.41
3040 3337 1.264288 CAAGTTCCGGCAACAGAAGAC 59.736 52.381 15.94 0.00 37.48 3.01
3041 3338 1.593196 CAAGTTCCGGCAACAGAAGA 58.407 50.000 15.94 0.00 37.48 2.87
3042 3339 0.593128 CCAAGTTCCGGCAACAGAAG 59.407 55.000 15.94 5.64 37.48 2.85
3043 3340 0.106918 ACCAAGTTCCGGCAACAGAA 60.107 50.000 15.94 0.00 37.48 3.02
3044 3341 0.534203 GACCAAGTTCCGGCAACAGA 60.534 55.000 15.94 0.00 37.48 3.41
3045 3342 1.515521 GGACCAAGTTCCGGCAACAG 61.516 60.000 15.94 9.53 37.48 3.16
3046 3343 1.527380 GGACCAAGTTCCGGCAACA 60.527 57.895 15.94 0.00 37.48 3.33
3047 3344 1.228154 AGGACCAAGTTCCGGCAAC 60.228 57.895 0.00 2.25 41.04 4.17
3048 3345 1.072505 GAGGACCAAGTTCCGGCAA 59.927 57.895 0.00 0.00 41.04 4.52
3049 3346 2.747686 GAGGACCAAGTTCCGGCA 59.252 61.111 0.00 0.00 41.04 5.69
3050 3347 2.046217 GGAGGACCAAGTTCCGGC 60.046 66.667 0.00 0.00 41.04 6.13
3053 3350 1.003718 CCACGGAGGACCAAGTTCC 60.004 63.158 0.00 0.00 41.22 3.62
3054 3351 1.671379 GCCACGGAGGACCAAGTTC 60.671 63.158 0.00 0.00 41.22 3.01
3055 3352 2.430367 GCCACGGAGGACCAAGTT 59.570 61.111 0.00 0.00 41.22 2.66
3056 3353 3.637273 GGCCACGGAGGACCAAGT 61.637 66.667 0.00 0.00 40.85 3.16
3062 3359 0.909610 ATCAAGAAGGCCACGGAGGA 60.910 55.000 5.01 0.00 41.22 3.71
3063 3360 0.462759 GATCAAGAAGGCCACGGAGG 60.463 60.000 5.01 0.00 41.84 4.30
3064 3361 0.462759 GGATCAAGAAGGCCACGGAG 60.463 60.000 5.01 0.00 0.00 4.63
3065 3362 1.602237 GGATCAAGAAGGCCACGGA 59.398 57.895 5.01 2.74 0.00 4.69
3066 3363 1.452108 GGGATCAAGAAGGCCACGG 60.452 63.158 5.01 0.00 0.00 4.94
3067 3364 0.462759 GAGGGATCAAGAAGGCCACG 60.463 60.000 5.01 0.00 0.00 4.94
3068 3365 0.106967 GGAGGGATCAAGAAGGCCAC 60.107 60.000 5.01 0.00 0.00 5.01
3069 3366 0.549902 TGGAGGGATCAAGAAGGCCA 60.550 55.000 5.01 0.00 0.00 5.36
3070 3367 0.849417 ATGGAGGGATCAAGAAGGCC 59.151 55.000 0.00 0.00 0.00 5.19
3071 3368 1.202867 GGATGGAGGGATCAAGAAGGC 60.203 57.143 0.00 0.00 0.00 4.35
3072 3369 2.416638 AGGATGGAGGGATCAAGAAGG 58.583 52.381 0.00 0.00 0.00 3.46
3073 3370 3.201708 ACAAGGATGGAGGGATCAAGAAG 59.798 47.826 0.00 0.00 0.00 2.85
3074 3371 3.192944 ACAAGGATGGAGGGATCAAGAA 58.807 45.455 0.00 0.00 0.00 2.52
3075 3372 2.850833 ACAAGGATGGAGGGATCAAGA 58.149 47.619 0.00 0.00 0.00 3.02
3076 3373 3.054139 TCAACAAGGATGGAGGGATCAAG 60.054 47.826 0.00 0.00 0.00 3.02
3077 3374 2.918934 TCAACAAGGATGGAGGGATCAA 59.081 45.455 0.00 0.00 0.00 2.57
3078 3375 2.561187 TCAACAAGGATGGAGGGATCA 58.439 47.619 0.00 0.00 0.00 2.92
3079 3376 3.872459 ATCAACAAGGATGGAGGGATC 57.128 47.619 0.00 0.00 0.00 3.36
3080 3377 4.540715 GAAATCAACAAGGATGGAGGGAT 58.459 43.478 0.00 0.00 0.00 3.85
3081 3378 3.309121 GGAAATCAACAAGGATGGAGGGA 60.309 47.826 0.00 0.00 0.00 4.20
3082 3379 3.026694 GGAAATCAACAAGGATGGAGGG 58.973 50.000 0.00 0.00 0.00 4.30
3083 3380 3.700538 TGGAAATCAACAAGGATGGAGG 58.299 45.455 0.00 0.00 0.00 4.30
3084 3381 4.098960 CCATGGAAATCAACAAGGATGGAG 59.901 45.833 5.56 0.00 32.40 3.86
3085 3382 4.025360 CCATGGAAATCAACAAGGATGGA 58.975 43.478 5.56 0.00 32.40 3.41
3086 3383 3.133362 CCCATGGAAATCAACAAGGATGG 59.867 47.826 15.22 0.00 0.00 3.51
3087 3384 3.770933 ACCCATGGAAATCAACAAGGATG 59.229 43.478 15.22 0.00 0.00 3.51
3088 3385 4.065214 ACCCATGGAAATCAACAAGGAT 57.935 40.909 15.22 0.00 0.00 3.24
3089 3386 3.541242 ACCCATGGAAATCAACAAGGA 57.459 42.857 15.22 0.00 0.00 3.36
3090 3387 3.834231 AGAACCCATGGAAATCAACAAGG 59.166 43.478 15.22 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.